A Kairosfocus Briefing Note:
GEM 06:03:17; this adj. 06:12:16 - 17 to 08:09:28 further adj.to 09:01:04 - 12:06:01, &12: 09:29 Ver 1.7.2c
https://www.angelfire.com/pro/kairosfocus/resources/Info_design_and_science.htm

On Information, Design, Science, Creation & Evolutionary Materialism:

Engaging the Current controversies over the role of information and design in understanding the origins of the Cosmos, Life, Biodiversity, Mind, Man and Morality

Is it possible for any man to behold these things, and yet imagine that certain solid and individual bodies move by their natural force and gravitation, and that a world so beautifully adorned was made by their fortuitous concourse? He who believes this may as well believe that if a great quantity of the one-and-twenty letters, composed either of gold or any other matter, were thrown upon the ground, they would fall into such order as legibly to form the Annals of Ennius. I doubt whether fortune could make a single verse of them. How, therefore, can these people assert that the world was made by the fortuitous concourse of atoms, which have no color, no quality—which the Greeks call [poiotes], no sense? [Cicero, THE NATURE OF THE GODS BK II Ch XXXVII, C1 BC, as trans Yonge (Harper & Bros., 1877), pp. 289 - 90.]

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SYNOPSIS: The raging controversy over inference to design too often puts out more heat and smoke than light. However, as Cicero pointed out in the cite just above, the underlying issues are of such great importance, that all educated people need to think about them carefully. Accordingly, in the below we shall examine a cluster of key cases, starting with the often overlooked but crucial point that in communication systems, we first start with an apparent message, then ask how much information is in it. This directly leads to the question first posed by Cicero, as to what is the probability that the received apparent message was actually sent, or is it "noise that got lucky"? The solution to this challenge is in fact an implicit inference to design, and it is resolved by essentially addressing the functionality and complexity of what was received, relative to what it is credible -- as opposed to logically possible -- that noise could do. That is, the design inference has long since been deeply embedded in scientific thought, once we have had to address the issue: what is information? Then, we look at several key cases: informational macromolecules such as DNA, the related origins of observed biodiversity, and cosmological finetuning. Thereafter, the issue is broadened to look at the God of the gaps challenge. Finally, a technical note on thermodynamics and several other technical or detail appendices are presented: (p) a critical look at the Dover/ Kitzmiller case (including a note on Plato on chance, necessity and agency in The Laws, Bk X), (q) the roots of the complex specified information concept, (r) more details on chance, necessity and agency, (s) Newton in Principia as a key scientific founding father and design thinker, (t) Fisherian vs Bayesian statistical inference in light of the Caputo case, and (u) the issue of the origin and nature of mind. Cf. Notice below. (NB: For FAQs and primers go here. This Y-zine also seems to be worth a browse.) 

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Reason & Belief | Evolutionary Materialism | The Secularist challenge | Home Page | Links and References | Forum

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CONTENTS:

INTRODUCTION

--> ID in a nutshell
--> ID FAQs and Primers
--> A basic survey of the ID issue and its significance
--> On research-level ID topics

A] The Core Question: Information, Messages and Intelligence

--> Defining "Intelligent Design"
--> Three causal factors: chance, necessity, agency
--> The design inference explanatory filter
--> Defining "Intelligence"
--> On "Lucky Noise" 
--> Defining "Information"
--> Shannon Info (AKA Informational Entropy) and the link to thermodynamic entropy
--> Defining "Functionally Specific, Complex Information" [FSCI]
--> Metrics for FSCI (and  CSI)

--> A Simple, brute-force X-metric for FSCI
--> Dembski's Chi-metric for CSI
--> Durston et al and a modified Shannon H-metric for Functional Sequence Complexity [FSC], in FITS, i.e functional bits
--> FSCI/CSI metrics as effectively measuring  "number of bits beyond a plausible threshold  of sufficient complexity (bit depth) to practically rule out non- foresighted causes"

--> Orgel vs Shapiro on getting to origin of life

B] Case I: DNA as an Informational Macromolecule

--> Dembski's Universal Probability Bound
--> "Definitionitis" vs. the case by case recognition of FSCI
--> Of monkeys and keyboards, updated
--> Implications of the scale of the configuration space of the genome
--> Optimality and structured codon assignments in the DNA code
--> Objections and responses

C] Case II: Macroevolution and the Diversity of Life

--> the observed fossil record pattern: sudden appearance, stasis, disappearance
--> Defining "Irreducible Complexity"
--> The Bacterial Flagellum
--> Macro- vs. Micro- Evolution
--> Natural selection as a probabilistic culler vs. an innovator (& the gambler's ruin challenge)

D] Case III: The evidently Fine-tuned Cosmos

--> Leslie on convergent fine-tuning
--> On "multiverses"
--> Objections and responses

E] Broadening the Issue: Persistent "Gaps," Man, Nature, Science and Worldviews

--> On "Defining" Science
--> The US NSTA's attempted naturalistic redefinition of the nature of science, July 2000
--> Lewontin's materialism agenda in  the name of "Science"
--> The NAS-NSTA intervention on science education in Kansas
--> On marking the key distinction between origins and operations sciences

CONCLUSION

APPENDIX I: On Thermodynamics, Information and Design

--> On the consequences of injecting raw energy into an open system
--> On energy conversion devices and their origin, in light of having FSCI
--> Brillouin's Negentropy view of the link between Information and Entropy
--> A Thought Experiment using "nanobots" building "a flyable micro-jet" to illustrate the issues involved in Origin of Life (OOL) and neo-Darwinian-style Macroevolution in light of thermodynamics

APPENDIX 2:  On Censorship and Manipulative Indoctrination in science education and in the court-room: the Kitzmiller/Dover Case

--> Plato on chance, necessity and agency in The Laws, Book X

APPENDIX 3: On the source, coherence and significance of the concept, Complex, Specified Information (CSI)

--> Thaxton, Bradley and Olsen on the source of CSI
--> Orgel -- the first known documented use of the term; in 1973
--> Wicken's "wiring diagram" functional organisation and the roots of the term Functionally Specific, Complex Information [FSCI]
--> Trevors and Abel on sequence complexity: OSC, RSC, FSC
--> Yockey and Wickens and the source of the term used in this note,  Functionally Specified, Complex Information [FSCI]
--> Of the creation of tropical cyclones and the origin of snowflakes
--> Dembski's work and the identification of the edge of chance

APPENDIX 4: Of chance, necessity, agency, the natural vs. the supernatural vs. the artificial, Kant and Fisher vs Bayes:

--> Kant's "little error at the beginning" and its fruit
--> On natural/supernatural vs. natural/artificial analyses of causal factors
--> On worldview level Logos Theology vs. the scientific inference to design
--> On self-evident truth
--> De Moivre's inference to chance vs design (1718)
--> Mind vs matter and evolutionary materialism
--> Contingency, dice, DNA, digital information system and the edge of chance

APPENDIX 5: Newton's thoughts on the designer of  "[t]his most beautiful system of the sun, planets, and comets . . . " in his General Scholium to the Principia

APPENDIX 6: Fisher, Bayes, Caputo and Dembski

APPENDIX 7:  Of the Weasel "cumulative selection" program and begging the question of FSCI, c. 1986

--> On the Law of Large Numbers

APPENDIX 8: Of the inference to design and the origin and nature of mind [and thence, of morals]

--> The (modified) Welcome to Wales thought experiment
-->  Key cites: Liebnitz's mill, Taylor on Wales, Reppert on Lewis' AFR,  Shapiro's blind forces golf game, Plantinga on natural selection vs the accuracy of beliefs, Crick's astonishing hypothesis & Philip Johnson's rejoinder, Hofstadter on Godel, Atmanspacher on Quantum theory, randomness and free will, Calef's corrective on mind's influence, the Penrose- Hameroff  graviton suggestion, the Derek Smith two-tier controller cybernetic loop model
--> Evolutionary materialism and self-referential incoherence 
--> Evolutionary materialism and the is-ought gap
--> Implications of the reality of evil etc
--> On the hard problem of consciousness

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INTRODUCTION: The raging controversy over inference to design, sadly, too often puts out more heat and blinding, noxious smoke than light. (Worse, some of the attacks to the man and to strawman misrepresentations of the actual technical case for design [and even of the basic definition of design theory] that have now become a routine distracting rhetorical resort and public relations spin tactic of too many of the defenders of the evolutionary materialist paradigm, show that this resort to poisoning the atmosphere of the discussion is in some quarters quite deliberately intended to rhetorically blunt the otherwise plainly telling force of the mounting pile of evidence and issues that make the inference to design a very live contender indeed.) 

Be that as it may, thanks to the transforming impacts of the ongoing Information Technology revolution, information has now increasingly joined matter, energy, space and time as another recognised fundamental constituent of the cosmos as we experience it. For, it has become increasingly clear over the past sixty years or so, that information is deeply embedded in key dimensions of existence. This holds from the evidently fine-tuned complex organisation of the physics of the cosmos as we observe it, to the intricate nanotechnology of the molecular machinery of life [cf. also J Shapiro here! (NB on AI here, and on Strong vs Weak AI here and here . . . ! )],  through the informational requisites of body-plan level biodiversity, on to the origin of mannishness as we experience it, including mind and reasoning, as well as conscience and morals. So, we plainly must frankly and fairly address the question of design as a proposed best current explanation -- and as a paradigm framework for transforming the praxis of science and thought in general, not just technology -- as, it has profound implications for how we see ourselves in our world, indeed (as the intensity of the rhetorical reaction noted just now indicates) it powerfully challenges the dominant evolutionary materialism that still prevails among the West's secularised educated elites. 

In a nutshell:

The scientific study of origins helps us probe the roots of our existence. Unfortunately, some have recently undercut this search by trying to re-define science as a search for “natural causes,” which imposes materialistic conclusions before the facts can speak. However, through objectively studying signs of intelligence -- the intelligent design approach -- we can allow the evidence to speak for itself. For, reliably, functionally specified complex information comes from intelligence. Thus, ID helps us restore balance to science and to many other aspects of our culture that are shaped by our views on our origins. [HT: StephenB, a long-standing commenter at UD. (NB: For basic FAQs and primers on ID-related topics and issues, kindly go to the IDEA Center, here. For a layman's level introduction to the basic design issue go here, and for a similar layman's level discussion of why it is an important challenge to the assumptions, assertions and agendas of our secularised intellectual culture, go here. For a discussion of ID-related research and associated topics, go to the Research-ID Wiki  here.)]

However, it is obviously also necessary for us to now pause and survey in more details on the key facts, concepts and issues, drawing out implications as we seek to infer the best explanation for the information-rich world in which we live. That is the task of this briefing.

A] The Core Question: Information, Messages and Intelligence

Since the end of the 1930's, five key trends have emerged, converged and become critical in the worlds of science and technology:

1. Information Technology and computers, starting with the Atanasoff-Berry Computer [ABC], and other pioneering computers in the early 1940's;
   
   
2. Communication technology and its underpinnings in information theory, starting with Shannon's breakthrough analysis in 1948;
   
   
3. The partial elucidation of the DNA code as the information basis of life at molecular level, since the 1950s, as, say Thaxton reports by citing Sir Francis Crick's March 19, 1953 remarks to his son: "Now we believe that the DNA is a code. That is, the order of bases (the letters) makes one gene different from another gene (just as one page of print is different from another)";
   
   
4. The "triumph" of the Miller-Urey spark-in-gas experiment, also in 1953, which produced several amino acids, the basic building blocks of proteins; but, also, we have seen a persistent failure thereafter to credibly and robustly account for the origin of life through so-called chemical evolution across subsequent decades ; and,
   
   
5. The discovery of the intricate finetuning of the parameters in the observed cosmos for life as we know and experience it -- strange as it may seem: again, starting in 1953.

The common issue in all of these lies in the implications of the concepts, communication and information -- i.e. the substance that is communicated. Thus, we should now focus on the basic communication system model, as that sets the context for further discussion:

Fig. A.1: A Model of the "Typical" Communication System

In this model, information-bearing messages flow from a source to a sink, by being: (1) encoded, (2) transmitted through a channel as a signal, (3) received, and (4) decoded. At each corresponding stage: source/sink encoding/decoding, transmitting/receiving, there is in effect a mutually agreed standard, a so-called protocol. [For instance, HTTP -- hypertext transfer protocol -- is a major protocol for the Internet. This is why many web page addresses begin: "http://www . . ."]

However, as the diagram hints at, at each stage noise affects the process, so that under certain conditions, detecting and distinguishing the signal from the noise becomes a challenge. Indeed, since noise is due to a random fluctuating value of various physical quantities [due in turn to the random behaviour of particles at molecular levels], the detection of a message and accepting it as a legitimate message rather than noise that got lucky, is a question of inference to design. In short, inescapably, the design inference issue is foundational to communication science and information theory.

Let us note, too, that similar empirically testable inferences to intelligent agency are a commonplace in forensic science, archaeology, pharmacology and a great many fields of pure and applied science. Climatology is an interesting case: the debate over anthropogenic climate change is about unintended consequences of the actions of intelligent agents.

Thus, Dembski's definition of design theory as a scientific project through pointed question and answer is apt:

intelligent design begins with a seemingly innocuous question: Can objects, even if nothing is known about how they arose, exhibit features that reliably signal the action of an intelligent cause? . . . Proponents of intelligent design, known as design theorists, purport to study such signs formally, rigorously, and scientifically. Intelligent design may therefore be defined as the science that studies signs of intelligence. [BTW, it is sad but necessary to highlight what should be obvious: namely, that it is only common academic courtesy (cf. here, here, here, here, here and here!) to use the historically justified definition of a discipline that is generally accepted by its principal proponents.]

So, having now highlighted what is at stake, we next clarify two key underlying questions. Namely, what is "information"? Then, why is it seen as a characteristic sign of intelligence at work?

First, let us identify what intelligence is. This is fairly easy: for, we are familiar with it from the characteristic behaviour exhibited by certain known intelligent agents -- ourselves. 

Specifically, as we know from experience and reflection, such agents take actions and devise and implement strategies that creatively address and solve problems they encounter; a functional pattern that does not depend at all on the identity of the particular agents. In short, intelligence is as intelligence does. So, if we see evident active, intentional, creative, innovative and adaptive [as opposed to merely fixed instinctual] problem-solving behaviour similar to that of known intelligent agents, we are justified in attaching the label: intelligence. [Note how this definition by functional description is not artificially confined to HUMAN intelligent agents: it would apply to computers, robots, the alleged alien residents of Area 51, Vulcans, Klingons or Kzinti, or demons or gods, or God.] But also, in so solving their problems, intelligent agents may leave behind empirically evident signs of their activity; and -- as say archaeologists and detectives know -- functionally specific, complex information [FSCI] that would otherwise be utterly improbable, is one of these signs.

Such preliminary points should also immediately lay to rest the assertion in some quarters that inference to design is somehow necessarily "unscientific" -- as, such is said to always and inevitably be about improperly injecting "the supernatural" into scientific discourse. (We hardly need to detain ourselves here with the associated claim that intelligence is a "natural" phenomenon, one that spontaneously emerges from the biophysical world; for that is plainly one of the issues to be settled by investigation and analysis in light of empirical data, conceptual issues and comparative difficulties, not dismissed by making question-begging evolutionary materialist assertions. Cf App 6 below. [Also, HT StephenB, a longstanding commenter at the Uncommon Descent [UD] blog, for deeply underscoring the significance of the natural/supernatural issue and for providing incisive comments, which have materially helped shape the below.])

Now, Dembski's definition just above draws on the common-sense point that: [a] we may quite properly make a significantly different contrast from "natural vs. supernatural": i.e. "natural" vs. "artificial." [Where "natural" = "spontaneous" and/or "tracing to chance + necessity as the decisive causal factors" -- what we may term material causes; and, "artificial" = "intelligent."] He and other major design thinkers therefore propose that: [b] we may then set out to identify key empirical/ scientific factors (= "signs of intelligence") to reliably mark the distinction.

One of these, is that when we see regularities of nature, we are seeing low contingency, reliably observable, spontaneous patterns and therefore scientifically explain such by law-like mechanical necessity: e.g. an unsupported heavy object, reliably, falls by "force of gravity."  But, where we see instead high contingency -- e.g., which side of a die will be uppermost when it falls -- this is chance ["accident"] or intent ["design"]. Then, if we further notice that the observed highly contingent pattern is otherwise very highly improbable [i.e. "complex"] and is independently functionally specified, it is most credible that it is so by design, not accident. (Think of a tray of several hundreds of dice, all with "six" uppermost: what is its best explanation -- mechanical necessity, chance, or intent? [Cf further details below.]) Consequently, we can easily see that [c] the attempt to infer or assert that intelligent design thought invariably constitutes "a 'smuggling-in' of  'the supernatural' " (as opposed to explanation by reference to the "artificial" or "intelligent") as the contrast to "natural," is a gross error; one that not only begs the question but also misunderstands, neglects or ignores (or even sometimes, sadly, calculatedly distorts) the explicit definition of ID and its methods of investigation as has been repeatedly published and patiently explained by its leading proponents. (Cf. here for a detailed case study on how just this -- too often, sadly, less than innocent -- mischaracterisation of Design Theory is used by secularist advocates such as the ACLU.)

Further, given the significance of what routinely happens when we see an apparent message, we know or should know that [d] we routinely and confidently infer from signs of intelligence to the existence and action of intelligence. On this, we should therefore again observe that Sir Francis Crick noted to his son, Michael, in 1953, in the already quoted letter: "Now we believe that the DNA is a code. That is, the order of bases (the letters) makes one gene different from another gene (just as one page of print is different from another)."  

For, complex, functional messages, per reliable observation, credibly trace to intelligent senders.

This holds, even where in certain particular cases one may then wish to raise the subsequent question: what is the identity (or even, nature) of the particular intelligence inferred to be the author of certain specific messages? In turn, this may lead to broader, philosophical -- that is, worldview level -- questions. Observe carefully, though: [e] such questions go beyond the "belt" of science theories, proper, into the worldview-tinged issues that -- as Imre Lakatos reminded us -- are embedded in the inner core of scientific research programmes, and are in the main addressed through philosophical rather than specifically scientific methods. [It helps to remember that for a long time, what we call "science" today was termed "natural philosophy."] Also, I think it is wiser to acknowledge that we have no satisfactory explanation of a matter, rather than insist that one will only surrender one's position (which has manifestly failed after reasonable trials) if a "better" one emerges -- all the while judging "better" by selectively hyperskeptical criteria.

In short, those who would make such a rhetorical dismissal, would do well to ponder anew the cite at the head of this web page. For, the key insight of Cicero [C1 BC!] is that, in particular, a sense-making (thus, functional), sufficiently complex string of digital characters is a signature of a true message produced by an intelligent actor, not a likely product of a random process. He then [logically speaking] goes on to ask concerning the evident FSCI in nature, and challenges those who would explain it by reference to chance collocations of atoms. 

That is a good challenge, and it is one that should not be ducked by worldview-level begging of serious definitional questions or -- worse -- shabby rhetorical misrepresentations and manipulations.

Therefore, let us now consider in a little more detail a situation where an apparent message is received. What does that mean? What does it imply about the origin of the message . . . or, is it just noise that "got lucky"?

• If an apparent message is received, it means that something is working as an intelligible -- i.e. functional -- signal for the receiver. In effect, there is a standard way to make and send and recognise and use messages in some observable entity [e.g. a radio, a computer network, etc.], and there is now also some observed event, some variation in a physical parameter, that corresponds to it. [For instance, on this web page as displayed on your monitor, we have a pattern of dots of light and dark and colours on a computer screen, which correspond, more or less, to those of text in English.]
  
  
• Information theory, as Fig A.1 illustrates, then observes that if we have a receiver, we credibly have first had a transmitter, and a channel through which the apparent message has come; a meaningful message that corresponds to certain codes or standard patterns of communication and/or intelligent action. [Here, for instance, through HTTP and TCP/IP, the original text for this web page has been passed from the server on which it is stored, across the Internet, to your machine, as a pattern of binary digits in packets. Your computer then received the bits through its modem, decoded the digits, and proceeded to display the resulting text on your screen as a complex, functional coded pattern of dots of light and colour. At each stage, integrated, goal-directed intelligent action is deeply involved, deriving from intelligent agents -- engineers and computer programmers. We here consider of course digital signals, but in principle anything can be reduced to such signals, so this does not affect the generality of our thoughts.]
  
  
• Now, it is of course entirely possible, that the apparent message is "nothing but" a lucky burst of noise that somehow got through the Internet and reached your machine. That is, it is logically and physically possible [i.e. neither logic nor physics forbids it!] that every apparent message you have ever got across the Internet -- including not just web pages but also even emails you have received -- is nothing but chance and luck: there is no intelligent source that actually sent such a message as you have received; all is just lucky noise:

"LUCKY NOISE" SCENARIO: Imagine a world in which somehow all the "real" messages sent "actually" vanish into cyberspace and "lucky noise" rooted in the random behaviour of molecules etc, somehow substitutes just the messages that were intended -- of course, including whenever engineers or technicians use test equipment to debug telecommunication and computer systems! Can you find a law of logic or physics that: [a] strictly forbids such a state of affairs from possibly existing; and, [b] allows you to strictly distinguish that from the "observed world" in which we think we live? That is, we are back to a Russell "five- minute- old- universe"-type paradox. Namely, we cannot empirically distinguish the world we think we live in from one that was instantly created five minutes ago with all the artifacts, food in our tummies, memories etc. that we experience.  We solve such paradoxes by worldview level inference to best explanation, i.e. by insisting that unless there is overwhelming, direct evidence that leads us to that conclusion, we do not live in Plato's Cave of deceptive shadows that we only imagine is reality, or that we are "really" just brains in vats stimulated by some mad scientist, or we live in a The Matrix world, or the like. (In turn, we can therefore see just how deeply embedded key faith-commitments are in our very rationality, thus all worldviews and reason-based enterprises, including science. Or, rephrasing for clarity: "faith" and "reason" are not opposites; rather, they are inextricably intertwined in the faith-points that lie at the core of all worldviews. Thus, resorting to selective hyperskepticism and objectionism to dismiss another's faith-point [as noted above!], is at best self-referentially inconsistent; sometimes, even hypocritical and/or -- worse yet -- willfully deceitful. Instead, we should carefully work through the comparative difficulties across live options at worldview level, especially in discussing matters of fact. And it is in that context of humble self consistency and critically aware, charitable open-mindedness that we can now reasonably proceed with this discussion.) 

• In short, none of us actually lives or can consistently live as though s/he seriously believes that: absent absolute proof to the contrary, we must believe that all is noise. [To see the force of this, consider an example posed by Richard Taylor. You are sitting in a railway carriage and seeing stones you believe to have been randomly arranged, spelling out: "WELCOME TO WALES." Would you believe the apparent message? Why or why not?]
  
  

Q: Why then do we believe in intelligent sources behind the web pages and email messages that we receive, etc., since we cannot ultimately absolutely prove that such is the case?

ANS: Because we believe the odds of such "lucky noise" happening by chance are so small, that we intuitively simply ignore it. That is, we all recognise that if an apparent message is contingent [it did not have to be as it is, or even to be at all], is functional within the context of communication, and is sufficiently complex that it is highly unlikely to have happened by chance, then it is much better to accept the explanation that it is what it appears to be -- a message originating in an intelligent [though perhaps not wise!] source -- than to revert to "chance" as the default assumption. Technically, we compare how close the received signal is to legitimate messages, and then decide that it is likely to be the "closest" such message. (All of this can be quantified, but this intuitive level discussion is enough for our purposes.)

In short, we all intuitively and even routinely accept that: Functionally Specified, Complex Information, FSCI, is a signature of messages originating in intelligent sources.

Thus, if we then try to dismiss the study of such inferences to design as "unscientific," when they may cut across our worldview preferences, we are plainly being grossly inconsistent. 

Further to this, the common attempt to pre-empt the issue through the attempted secularist redefinition of science as in effect "what can be explained on the premise of evolutionary materialism - i.e. primordial matter-energy joined to cosmological- + chemical- + biological macro- + sociocultural- evolution, AKA 'methodological naturalism' " [ISCID def'n: here]  is itself yet another begging of the linked worldview level questions. 

For in fact, the issue in the communication situation once an apparent message is in hand is: inference to (a) intelligent -- as opposed to supernatural -- agency [signal] vs. (b) chance-process [noise]. Moreover, at least since Cicero, we have recognised that the presence of functionally specified complexity in such an apparent message helps us make that decision. (Cf. also Meyer's closely related discussion of the demarcation problem here.)

More broadly the decision faced once we see an apparent message, is first to decide its source across a trichotomy: (1) chance; (2) natural regularity rooted in mechanical necessity (or as Monod put it in his famous 1970 book, echoing Plato, simply: "necessity"); (3) intelligent agency. These are the three commonly observed causal forces/factors in our world of experience and observation.  [Cf. abstract of a recent technical, peer-reviewed, scientific discussion here. Also, cf. Plato's remark in his The Laws, Bk X, excerpted below.]

Each of these forces stands at the same basic level as an explanation or cause, and so the proper question is to rule in/out relevant factors at work, not to decide before the fact that one or the other is not admissible as a "real" explanation. 

This often confusing issue is best initially approached/understood through a concrete example . . . 

A CASE STUDY ON CAUSAL FORCES/FACTORS -- A Tumbling Die: Heavy objects tend to fall under the law-like natural regularity we call gravity. If the object is a die, the face that ends up on the top from the set {1, 2, 3, 4, 5, 6} is for practical purposes a matter of chance. 

But, if the die is cast as part of a game, the results are as much a product of agency as of natural regularity and chance. Indeed, the agents in question are taking advantage of natural regularities and chance to achieve their purposes! 

This concrete, familiar illustration should suffice to show that the three causal factors approach is not at all arbitrary or dubious -- as some are tempted to imagine or assert.  [More details . . .]

Then also, in certain highly important communication situations, the next issue after detecting agency as best causal explanation, is whether the detected signal comes from (4) a trusted source, or (5) a malicious interloper, or is a matter of (6) unintentional cross-talk. (Consequently, intelligence agencies have a significant and very practical interest in the underlying scientific questions of inference to agency then identification of the agent -- a potential (and arguably, probably actual) major application of the theory of the inference to design.)

Next, to identify which of the three is most important/ the best explanation in a given case, it is useful to extend the principles of statistical hypothesis testing through Fisherian elimination to create the Explanatory Filter:

Fig A.2:  The explanatory filter allows for an evidence-based investigation of causal factors. By setting a quite strict threshold between chance and intelligence, i.e. the UPB, a reliable inference to design may be made when we see especially functionally specific, complex information [FSCI] -rich patterns, but at the cost of potentially ruling "chance" incorrectly. UNDERLYING LOGIC: Once the aspect of a process, object or phenomenon under investigation is significantly contingent, natural regularities rooted in mechanical necessity can plainly be ruled out as the dominant factor for that facet. So, the key issue is whether the observed high contingency is unambiguously evidently purposefully directed; relative to the type and body of experiences or observations that would warrant a reliable inductive inference. For this, the UPB sets a reasonable, conservative and reliable threshold: Unless (i) the search resources of the observed cosmos would generally be fruitlessly exhausted in an attempt to arrive at the observed result (or materially similar results) by random searches, AND (ii) the outcome is [especially functionally] specified, observed high contingency is by default assigned to "chance." Thus, FSCI and the associated wider concept, complex, specified information [CSI] are identified as reliable (but not exclusive) signs of intelligence. [In fact, even though -- strictly -- "lucky noise" could account for the existence of apparent messages such as this web page, we routinely identify that if an apparent message has functionality, complexity and specification, it is better explained by intent than by accident and confidently infer to intelligent rather than mechanical cause. This is proof enough -- on pain of self-referentially incoherent selective hyperskepticism -- of just how reasonable the explanatory filter is.] ________________

The second major step is to refine our thoughts, through discussing the communication theory definition of and its approach to measuring information. A good place to begin this is with British Communication theory expert F. R Connor, who gives us an excellent "definition by discussion" of what information is:

From a human point of view the word 'communication' conveys the idea of one person talking or writing to another in words or messages . . . through the use of words derived from an alphabet [NB: he here means, a "vocabulary" of possible signals]. Not all words are used all the time and this implies that there is a minimum number which could enable communication to be possible. In order to communicate, it is necessary to transfer information to another person, or more objectively, between men or machines.

This naturally leads to the definition of the word 'information', and from a communication point of view it does not have its usual everyday meaning. Information is not what is actually in a message but what could constitute a message. The word could implies a statistical definition in that it involves some selection of the various possible messages. The important quantity is not the actual information content of the message but rather its possible information content.

This is the quantitative definition of information and so it is measured in terms of the number of selections that could be made. Hartley was the first to suggest a logarithmic unit . . . and this is given in terms of a message probability. [p. 79, Signals, Edward Arnold. 1972. Bold emphasis added. Apart from the justly classical status of Connor's series, his classic work dating from before the ID controversy arose is deliberately cited, to give us an indisputably objective benchmark.]

To quantify the above definition of what is perhaps best descriptively termed information-carrying capacity, but has long been simply termed information (in the "Shannon sense" - never mind his disclaimers . . .), let us consider a source that emits symbols from a vocabulary: s₁,s₂, s₃, . . . s_n, with probabilities p₁, p₂, p₃, . . . p_n. That is, in a "typical" long string of symbols, of size M [say this web page], the average number that are some s_j, J, will be such that the ratio J/M --> p_j, and in the limit attains equality. We term p_j the a priori -- before the fact -- probability of symbol s_j. Then, when a receiver detects s_j, the question arises as to whether this was sent. [That is, the mixing in of noise means that received messages are prone to misidentification.] If on average, s_j will be detected correctly a fraction, d_j of the time, the a posteriori -- after the fact -- probability of s_j is by a similar calculation, d_j. So, we now define the information content of symbol s_j as, in effect how much it surprises us on average when it shows up in our receiver:

I = log [d_j/p_j], in bits [if the log is base 2, log₂] . . . Eqn 1

This immediately means that the question of receiving information arises AFTER an apparent symbol s_j has been detected and decoded. That is, the issue of information inherently implies an inference to having received an intentional signal in the face of the possibility that noise could be present. Second, logs are used in the definition of I, as they give an additive property: for, the amount of information in independent signals, s_i + s_j, using the above definition, is such that:

I total = I_i + I_j . . . Eqn 2

For example, assume that d_j for the moment is 1, i.e. we have a noiseless channel so what is transmitted is just what is received. Then, the information in s_j is:

I = log [1/p_j] = - log p_j . . . Eqn 3

This case illustrates the additive property as well, assuming that symbols s_i and s_j are independent. That means that the probability of receiving both messages is the product of the probability of the individual messages (p_i *p_j); so:

I_tot = log1/(p_i *p_j) = [-log p_i] + [-log p_j] = I_i + I_j . . . Eqn 4

So if there are two symbols, say 1 and 0, and each has probability 0.5, then for each, I is - log [1/2], on a base of 2, which is 1 bit. (If the symbols were not equiprobable, the less probable binary digit-state would convey more than, and the more probable, less than, one bit of information. Moving over to English text, we can easily see that E is as a rule far more probable than X, and that Q is most often followed by U. So, X conveys more information than E, and U conveys very little, though it is useful as redundancy, which gives us a chance to catch errors and fix them: if we see "wueen" it is most likely to have been "queen.")

Further to this, we may average the information per symbol in the communication system thusly (giving in termns of -H to make the additive relationships clearer):

- H = p₁ log p₁ + p₂ log p₂ + . . . + p_n log p_n 

or,  H = -  SUM [p_i log p_i]  . . . Eqn 5

H, the average information per symbol transmitted [usually, measured as: bits/symbol], is often termed the Entropy; first, historically, because it resembles one of the expressions for entropy in statistical thermodynamics. As Connor notes: "it is often referred to as the entropy of the source." [p.81, emphasis added.] Also, while this is a somewhat controversial view in Physics, as is briefly discussed in Appendix 1below, there is in fact an informational interpretation of thermodynamics that shows that informational and thermodynamic entropy can be linked conceptually as well as in mere mathematical form. Though somewhat controversial even in quite recent years, this is becoming more broadly accepted in physics and information theory, as Wikipedia now discusses [as at April 2011]  in its article on Informational Entropy (aka Shannon Information, cf also here):

At an everyday practical level the links between information entropy and thermodynamic entropy are not close. Physicists and chemists are apt to be more interested in changes in entropy as a system spontaneously evolves away from its initial conditions, in accordance with the second law of thermodynamics, rather than an unchanging probability distribution. And, as the numerical smallness of Boltzmann's constant k_B indicates, the changes in S / k_B for even minute amounts of substances in chemical and physical processes represent amounts of entropy which are so large as to be right off the scale compared to anything seen in data compression or signal processing.

But, at a multidisciplinary level, connections can be made between thermodynamic and informational entropy, although it took many years in the development of the theories of statistical mechanics and information theory to make the relationship fully apparent. In fact, in the view of Jaynes (1957), thermodynamics should be seen as an application of Shannon's information theory: the thermodynamic entropy is interpreted as being an estimate of the amount of further Shannon information needed to define the detailed microscopic state of the system, that remains uncommunicated by a description solely in terms of the macroscopic variables of classical thermodynamics. For example, adding heat to a system increases its thermodynamic entropy because it increases the number of possible microscopic states that it could be in, thus making any complete state description longer. (See article: maximum entropy thermodynamics.[Also,another article remarks:  >>in the words of G. N. Lewis writing about chemical entropy in 1930, "Gain in entropy always means loss of information, and nothing more" . . .   in the discrete case using base two logarithms, the reduced Gibbs entropy is equal to the minimum number of yes/no questions that need to be answered in order to fully specify the microstate, given that we know the macrostate.>>]) Maxwell's demon can (hypothetically) reduce the thermodynamic entropy of a system by using information about the states of individual molecules; but, as Landauer (from 1961) and co-workers have shown, to function the demon himself must increase thermodynamic entropy in the process, by at least the amount of Shannon information he proposes to first acquire and store; and so the total entropy does not decrease (which resolves the paradox).

Summarising Harry Robertson's Statistical Thermophysics (Prentice-Hall International, 1993) -- excerpting desperately and adding emphases and explanatory comments, we can see, perhaps, that this should not be so surprising after all. (In effect, since we do not possess detailed knowledge of the states of the vary large number of microscopic particles of thermal systems [typically ~ 10^20 to 10^26; a mole of substance containing ~ 6.023*10^23 particles; i.e. the Avogadro Number], we can only view them in terms of those gross averages we term thermodynamic variables [pressure, temperature, etc], and so we cannot take advantage of knowledge of such individual particle states that would give us a richer harvest of work, etc.)

For, as he astutely observes on pp. vii - viii:

. . . the standard assertion that molecular chaos exists is nothing more than a poorly disguised admission of ignorance, or lack of detailed information about the dynamic state of a system . . . . If I am able to perceive order, I may be able to use it to extract work from the system, but if  I am unaware of internal correlations, I cannot use them for macroscopic dynamical purposes. On this basis, I shall distinguish heat from work, and thermal energy from other forms . . .

And, in more details, (pp. 3 - 6, 7, 36, cf Appendix 1 below for a more detailed development of thermodynamics issues and their tie-in with the inference to design; also see recent ArXiv papers by Duncan and Samura here and here):

. . . It has long been recognized that the assignment of probabilities to a set represents information, and that some probability sets represent more information than others . . . if one of the probabilities say p₂ is unity and therefore the others are zero, then we know that the outcome of the experiment . . . will give [event]  y₂. Thus we have complete information . . . if we have no basis . . . for believing that event y_i is more or less likely than any other [we] have the least possible information about the outcome of the experiment . . . . A remarkably simple and clear analysis by Shannon [1948] has provided us with a quantitative measure of the uncertainty, or missing pertinent information, inherent in a set of probabilities [NB: i.e. a probability different from 1 or 0 should be seen as, in part, an index of ignorance] . . . . 

[deriving informational entropy, cf. discussions here, here, here, here and here; also Sarfati's discussion of debates and the issue of open systems here . . . ]

H({p_i}) = - C [SUM over i] p_i*ln p_i, [. . . "my" Eqn 6]

[where [SUM over i] p_i = 1, and we can define also parameters alpha and beta such that: (1) p_i = e^-[alpha + beta*y_i]; (2) exp [alpha] = [SUM over i](exp - beta*y_i) = Z [Z being in effect the partition function across microstates, the "Holy Grail" of statistical thermodynamics]. . . .

[H], called the information entropy, . . . correspond[s] to the thermodynamic entropy [i.e. s, where also it was shown by Boltzmann that s = k ln w], with C = k, the Boltzmann constant, and y_i an energy level, usually e_i, while [BETA] becomes 1/kT, with T the thermodynamic temperature . . . A thermodynamic system is characterized by a microscopic structure that is not observed in detail . . . We attempt to develop a theoretical description of the macroscopic properties in terms of its underlying microscopic properties, which are not precisely known. We attempt to assign probabilities to the various microscopic states . . . based on a few . . . macroscopic observations that can be related to averages of microscopic parameters. Evidently the problem that we attempt to solve in statistical thermophysics is exactly the one just treated in terms of information theory. It should not be surprising, then, that the uncertainty of information theory becomes a thermodynamic variable when used in proper context . . . . 

Jayne's [summary rebuttal to a typical objection] is ". . . The entropy of a thermodynamic system is a measure of the degree of ignorance of a person whose sole knowledge about its microstate consists of the values of the macroscopic quantities . . . which define its thermodynamic state. This is a perfectly 'objective' quantity . . . it is a function of [those variables] and does not depend on anybody's personality. There is no reason why it cannot be measured in the laboratory." . . . .   [pp. 3 - 6, 7, 36; replacing Robertson's use of S for Informational Entropy with the more standard H.] 

As is discussed briefly in Appendix 1, Thaxton, Bradley and Olsen [TBO], following Brillouin et al, in the 1984 foundational work for the modern Design Theory, The Mystery of Life's Origins [TMLO], exploit this information-entropy link, through the idea of moving from a random to a known microscopic configuration in the creation of the bio-functional polymers of life, and then -- again following Brillouin -- identify a quantitative information metric for the information of polymer molecules. For, in moving from a random to a functional molecule, we have in effect an objective, observable increment in information about the molecule. This leads to energy constraints, thence to a calculable concentration of such molecules in suggested, generously "plausible" primordial "soups." In effect, so unfavourable is the resulting thermodynamic balance, that the concentrations of the individual functional molecules in such a prebiotic soup are arguably so small as to be negligibly different from zero on a planet-wide scale.

By many orders of magnitude, we don't get to even one molecule each of the required polymers per planet, much less bringing them together in the required proximity for them to work together as the molecular machinery of life. The linked chapter gives the details. More modern analyses [e.g. Trevors and Abel, here and here], however, tend to speak directly in terms of information and probabilities rather than the more arcane world of classical and statistical thermodynamics, so let us now return to that focus; in particular addressing information in its functional sense, as the third step in this preliminary analysis.

As the third major step, we now turn to information technology, communication systems and computers, which provides a vital clarifying side-light from another view on how complex, specified information functions in information processing systems:

[In the context of computers] information is data -- i.e. digital representations of raw events, facts, numbers and letters, values of variables, etc. -- that have been put together in ways suitable for storing in special data structures [strings of characters, lists, tables, "trees" etc], and for processing and output in ways that are useful [i.e. functional]. . . . Information is distinguished from [a] data: raw events, signals, states etc represented digitally, and [b] knowledge: information that has been so verified that we can reasonably be warranted, in believing it to be true. [GEM, UWI FD12A Sci Med and Tech in Society Tutorial Note 7a, Nov 2005.]

That is, we have now made a step beyond mere capacity to carry or convey information, to the function fulfilled by meaningful -- intelligible, difference making -- strings of symbols. In effect, we here introduce into the concept, "information," the meaningfulness, functionality (and indeed, perhaps even purposefulness) of messages -- the fact that they make a difference to the operation and/or structure of systems using such messages, thus to outcomes; thence, to relative or absolute success or failure of information-using systems in given environments. 

And, such outcome-affecting functionality is of course the underlying reason/explanation for the use of information in systems. [Cf. the recent peer-reviewed, scientific discussions here, and here by Abel and Trevors,  in the context of the molecular nanotechnology of life.] Let us note as well that since in general analogue signals can be digitised [i.e. by some form of analogue-digital conversion], the discussion thus far is quite general in force.

So, taking these three main points together, we can now see how information is conceptually and  quantitatively defined, how it can be measured in bits, and how it is used in information processing systems; i.e., how it becomes functional. In short, we can now understand that:

Functionally Specific, Complex Information [FSCI] is a characteristic of complicated messages that function in systems to help them practically solve problems faced by the systems in their environments. Also, in cases where we directly and independently know the source of such FSCI (and its accompanying functional organisation) it is, as a general rule, created by purposeful, organising intelligent agents. So, on empirical observation based induction, FSCI is a reliable sign of such design, e.g. the text of this web page, and billions of others all across the Internet. (Those who object to this, therefore face the burden of showing empirically that such FSCI  does in fact -- on observation --  arise from blind chance and/or mechanical necessity without intelligent direction, selection, intervention or purpose.)

Indeed, this FSCI perspective lies at the foundation of information theory:

(i) recognising signals as intentionally constructed messages transmitted in the face of the possibility of noise,
(ii) where also, intelligently constructed signals have characteristics of purposeful specificity, controlled complexity and system- relevant functionality based on meaningful rules that  distinguish them from meaningless noise;
(iii)  further noticing that signals  exist in functioning generation- transfer and/or storage- destination systems that
(iv)  embrace co-ordinated transmitters, channels, receivers, sources and sinks.

That this is broadly recognised as true, can be seen from a surprising source, Dawkins, who is reported to have said in his The Blind Watchmaker (1987), p. 8:

Hitting upon the lucky number that opens the bank's safe [NB: cf. here the case in Brown's The Da Vinci Code] is the equivalent, in our analogy, of hurling scrap metal around at random and happening to assemble a Boeing 747. [NB: originally, this imagery is due to Sir Fred Hoyle, who used it to argue that life on earth bears characteristics that strongly suggest design. His suggestion: panspermia -- i.e. life drifted here, or else was planted here.] Of all the millions of unique and, with hindsight equally improbable, positions of the combination lock, only one opens the lock. Similarly, of all the millions of unique and, with hindsight equally improbable, arrangements of a heap of junk, only one (or very few) will fly. The uniqueness of the arrangement that flies, or that opens the safe, has nothing to do with hindsight. It is specified in advance. [Emphases and parenthetical note added, in tribute to the late Sir Fred Hoyle. (NB: This case also shows that we need not see boxes labelled "encoders/decoders" or "transmitters/receivers" and "channels" etc. for the model in Fig. 1 above to be applicable; i.e. the model is abstract rather than concrete: the critical issue is functional, complex information, not electronics.)]

Here, we see how the significance of FSCI naturally appears in the context of considering the physically and logically possible but vastly improbable creation of a jumbo jet by chance. Instantly, we see that mere random chance acting in a context of blind natural forces is a most unlikely explanation, even though the statistical behaviour of matter under random forces cannot rule it strictly out. But it is so plainly vastly improbable, that, having seen the message -- a flyable jumbo jet -- we then make a fairly easy and highly confident inference to its most likely origin: i.e. it is an intelligently designed artifact. For, the a posteriori probability of its having originated by chance is obviously minimal -- which we can intuitively recognise, and can in principle quantify. 

FSCI is also an observable, measurable quantity; contrary to what is imagined, implied or asserted by many objectors. This may be most easily seen by using a quantity we are familiar with: functionally specific bits [FS bits], such as those that define the  information on the screen you are most likely using to read this note: 

1 --> These bits are functional, i.e. presenting a sceenful of (more or less) readable and coherent text. 

2 --> They are specific, i.e. the screen conforms to a page of coherent text in English in a web browser window; defining a relatively small target/island of function by comparison with the number of arbitrarily possible bit configurations of the screen.

3 --> They are contingent, i.e your screen can show diverse patterns, some of which are functional, some of which -- e.g. a screen broken up into "snow" -- would not (usually) be.

4 --> They are quantitative: a screen of such text at 800 * 600 pixels resolution, each of bit depth 24 [8 each for R, G, B] has in its image 480,000 pixels, with 11,520,000 hard-working, functionally specific bits. 

5 --> This is of course well beyond a "glorified common-sense" 500 - 1,000 bit rule of thumb complexity threshold at which contextually and functionally specific information is sufficiently complex that the explanatory filter would confidently rule such a screenful of text "designed," given that -- since there are at most that many quantum states of the atoms in it -- no search on the gamut of our observed cosmos can exceed 10^150 steps:

Fig A.3: The needle- in-the haystack search challenge: the credibly accessible search window for our observed cosmos (< 10^150 states) is a tiny fraction of the configuration space specified by 1,000 or more bits of information storage capacity.

EXPLANATION: This empirically anchored rule of thumb limit credibly works because the set of locally accessible states [at ~ 10^43 states/second] for our observed cosmos as a whole [~ 10^80 atoms] across its usually estimated lifespan [~ 10^25 seconds]  is ~ 10^150 states. These states are in large part dynamically (and thus more or less "smoothly") connected to earlier, neighbouring ones; all the way back to the big bang and its initial conditions and constraints. 

So, [a] search in the space of possible states of an abstractly possible universe is constrained relative to the credible starting conditions of the observed cosmos; indeed, the observed cosmos will not be able to search out 10^150 states. For instance, MIT Mechanical Engineering professor Seth Lloy'd calculation is that "[t]he amount of information that the Universe can register and the number of elementary operations that it can have performed over its history are calculated. The Universe can have performed 10^120  ops on 10^90  bits ( 10^120  bits including gravitational degrees of freedom)." [Cf. discussions here and here. It takes a significant number of such operations to carry out any process (such as running the general dynamics of the universe), much less to do one step in a search process. So, by far and away, most of the operations would not be available for a search process.]

Now, too, it is known that [b] observed functionality of systems and elements in systems is vulnerable to often quite slight perturbation, i.e. we deal with islands of function in a sea of non-function, and also that [c] the functions delimited by 500 - 1,000+ bits of information-storing capacity are complex. This leads to: [d] deep isolation of the islands of function, or at least of the archipelagos in which they may sit. [This is why for instance, even ardent Darwinists typically fear exposure to mutation inducing trauma, e.g. chemicals or radiation -- we all know from observation that dysfunctions such as cancer are the overwhelmingly likely result from significant random changes to genes or other functional molecules in the cells of our bodies. Similarly, it fits well with the fossil record's observed pattern of sudden emergence, structural-functional stasis and disappearance. Likewise, contrary to the urban legend on monkeys and typewriters, Mr Gates does not write new versions of his operating system by putting Bonobos to bang away at keyboards, thus modifying the existing OS at random! (This family of PC operating systems also shows that effective design is not necessarily "perfect" or even "optimal" relative to any one purpose or aspect: trade-offs and constraints are key challenges of real-world design, especially if it has to be robust against the vagaries of a highly uncertain environment.)]  

So, if [e] we suggest a provisional upper limit for the universal probability bound based on in aggregate as many functional states as there are accessible quantum states for our observed comsos, i.e. 10^150, and [f] isolate the islands and archipelagos at least to the degree that a search window of that many states are at most 1 in 10^150 of the states in the configuration space set by the 1,000+ bits [cf. Fig. A.4], then [g] it becomes maximally unlikely to initially get to the islands of function, or to hop beyond very local archipelagos, through random search processes culling by degree of functional success. That sets up 10^300 states as a plausible upper bound; where also 1,000 bits corresponds to 2^1,000 ~ 1.071 * 10^301 accessible states.  

To see what that means for bio-functionality, consider now a hypothetical enzyme of 232 amino acid residues [20^232 ~ 2^1,000], where each AA is of general form H2N-CHR-COOH; proline being the main exception, as its R-group bonds back to the N-atom, making it technically an imino acid. 

The "hypothesine" protein would be functional in a specific reaction, and in a particular cluster of processes in the cell; being useless (or worse than merely useless) in the wrong cell-process contexts. (For, function is contextually specific.) Now, consider for a simple initial argument that -- bearing in mind that the different R-groups are considerably divergent in shape, size, reactivity, H-atom locations, tendency to mix with aqueous media, etc. -- on average 150 of the R-groups could take up any of 10 AA values each in any combination; the remainder being fixed by, say, the requisites of key-lock fittting and/or chemical functionality. This would give us a variability of 10^150 configurations that preserve the required specific functionality. 

(AT A MORE COMPLEX LEVEL: If, instead, we model the the individual AA's as varying at random among 4 - 5 "similar" R-group AA's on average without causing dys-functional change, the full 232-length string would vary across 10^150 states. As a cross-check, Cytochrome-C, a commonly studied protein of about 100 AA's that is used for taxonomic research, typically varies across 1 - 5 AA's in each position, with a few AA positions showing more variability than that. About a third of the AA positions are invariant across a range from humans to rice to yeast. That is, the observed variability, if scaled up to 232 AA's, would be well within the 10^150 limit suggested; as, e.g. 5^155 ~ 2.19 * 10^108. [Cf also this summary of a study of the same protein among 388 fish species.]

Moreover, from Voegel's summary of Hurst, Haig and Freeland, the real-world DNA code evidently exhibits a near-optimal degree of built-in redundancy such that typical random single-point changes in three-letter codons will replace the R-group with one of a few chemically and/or structurally very similar ones; reducing the likelihood of functional deranging of folded [secondary] and/or agglomerated [tertiary] structures. [Variablity at random across all 20 AA's is not reasonable; as that would make proline typically ~ 5% of the changes, and proline's structural rigidity due to the R-group's bonding back to the N-atom would most likely destroy desired folding and onward structures, thus deranging functionality. It is noteworthy, for instance, that sickle-cell anaemia is typically caused by a single point change in a haemoglobin AA sequence.] 

Given the key-lock fitting requisites of working proteins in the cell, this sort of "close replacement" is credibly responsible for most of the variability across AA configurations as is studied for say the Cytosine-C taxonomic trees for life-forms.)

Similarly, a 143-element ASCII text string (about eighteen typical English words, with provision for spaces and punctuation) has a contingency space of ~ 2^1,000. Starting from such a string that is correctly spelled, has correct grammar and is contextually relevant, it would be quite hard to get 10^150 random variations of characters that would also be of correct spelling and grammar, and just as much contextually relevant. It would be even harder to get to the first such sentence by random chance. 

In short, the rule of thumb is plausible and has a reasonable fit to a key context, the biological world.

Ultimately, though, the warrant for such a rule of thumb is provisional (as are all significant scientific findings and models)  and based on empirical tests. In effect: can you identify a well established case of independently known origin where a functionally specified entity with at least 1,000 bits of storage capacity has been generated by chance + necessity without the intelligent intervention of an agent (e.g through an "oracle" in a genetic algorithm that broadcasts information on and so rewards closeness to islands of function)? [A routine example of such a test would be contextually relevant ASCII text in English embracing 143 or more characters, as 128^143 ~ 2^1,000. That is, the test is very widely carried out and the rule is strongly empirically supported.]

6 --> So we can construct a rule of thumb functionally specific bit metric for FSCI:

a] Let complex contingency [C] be defined as 1/0 by comparison with a suitable exemplar, e.g. a tossed die that on similar tosses may come up in any one of six states: 1/ 2/ 3/ 4/ 5/ 6; joined to having at least 1,000 bits of information storage capacity. That is, diverse configurations of the component parts or of outcomes under similar initial circumstances must be credibly possible, and there must be at least 2^1,000 possible configurations.

b] Let specificity [S] be identified as 1/0 through specific functionality [FS] or by compressibility of description of the specific information [KS] or similar means that identify specific target zones in the wider configuration space. [Often we speak of this as "islands of function" in "a sea of non-function." (That is, if moderate application of random noise altering the bit patterns will beyond a certain point destroy function [notoriously common for engineered systems that require working parts mutually co-adapted at an operating point, and also for software and even text in a recognisable language] or move it out of the target zone, then the topology is similar to that of islands in a sea.)]

c] Let  degree of complexity [B] be defined by the quantity of bits to store the relevant information, where from [a] we already see how 500 -  1,000 bits serves as the threshold for "probably" to "morally certainly" sufficiently complex to meet the FSCI/CSI threshold by which a random walk from an arbitrary initial configuration backed up by trial and error is utterly unlikely to ever encounter an island of function, on the gamut of our observed cosmos. (Such a random walk plus trial and error is a reasonable model for the various naturalistic mechanisms proposed for chemical and body plan level biological evolution. It is worth noting that "infinite monkeys" type tests have shown that  a search space of the order of 10^50 or so is searchable so that functional texts can be identified and accepted on trial and error. But searching 2^1,000 = 1.07 * 10^301 possibilities for islands of function is a totally different matter.)

d] Define the vector {C, S, B} based on the above [as we would take distance travelled and time required, D and t: {D, t}], and take the element product  C*S*B [as we would take the element ratio D/t to get speed].

e] Now we identify the simple FSCI metric, X: 

C*S*B = X,

. . . the required FSCI/CSI-metric in [functionally] specified bits.

f] Once we are beyond 500 - 1,000 functionally specific bits, we are comfortably beyond a threshold of sufficient complex and specific functionality that the search resources of the observed universe would by far and away most likely be fruitlessly exhausted on the sea of non-functional states if a random walk based search (or generally equivalent process) were used to try to get to shores of function on islands of such complex, specific function. 

[WHY: For, at 1,000 bits, the 10^150 states scanned by the observed universe acting as search engine would be comparable to: marking one of the 10^80 atoms of the universe for just 10^-43 seconds out of 10^25 seconds of available time, then taking a spacecraft capable of time travel and at random going anywhere and "any-when" in the observed universe, reaching out, grabbing just one atom and voila that atom is the marked atom at just the instant it is marked. In short, the "search" resources are so vastly inadequate relative to the available configuration space for just 1,000 bits of information storage capacity that debates on "uniform probability distributions" etc are moot: the whole observed universe acting as a search engine could not put up a credible search of such a configuration space. And, observed life credibly starts with DNA storage in the 100's of kilo bits of information storage. (100 k bits of information storage specifies a config space of order ~ 9.99 *10^30,102; which vastly dwarfs the ~ 1.07 * 10^301 states specified by 1,000 bits.)]

7 --> For instance, for the 800 * 600 pixel PC screen, C = 1, S = 1, B = 11.52 * 10^6, so C*S*B = 11.52 * 10^6, FS bits. This is well beyond the threshold. [Notice that if the bits were not contingent or were not specific, then X = 0 automatically. Similarly, if B < 500, the metric would indicate the bits as functionally or compressibly etc specified, but without enough bits to be comfortably beyond the UPB threshold. Of course, the DNA strands of observed life forms start at about 200,000 FS bits, and that for forms that depend on others for crucial nutrients. 600,000 - 10^6 FS bits is a reported reasonable estimate for a minimally complex independent life form.]

8 --> A more sophisticated (though sometimes controversial) metric has of course been given by Dembski, in a 2005 paper, as follows:

define ϕS as . . . the number of patterns for which [agent] S’s semiotic description of them is at least as simple as S’s semiotic description of [a pattern or target zone] T. [26] . . . . where M is the number of semiotic agents [S's] that within a context of inquiry might also be witnessing events and N is the number of opportunities for such events to happen . . . . [where also] computer scientist Seth Lloyd has shown that 10^120 constitutes the maximal number of bit operations that the known, observable universe could have performed throughout its entire multi-billion year history.[31] . . . [Then] for any context of inquiry in which S might be endeavoring to determine whether an event that conforms to a pattern T happened by chance, M·N will be bounded above by 10^120. We thus define the specified complexity [χ] of T given [chance hypothesis] H [in bits] . . . as  [the negative base-2 log of the conditional probability P(T|H) multiplied by the number of similar cases ϕS(t) and also by the maximum number of binary search-events in our observed universe 10^120]

χ = – log₂[10^120 ·ϕS(T)·P(T|H)].

9 --> When 1 >/= χ, the probability of the observed event in the target zone or a similar event is at least 1/2, so the available search resources of the observed cosmos across its estimated lifespan are in principle adequate for an observed event [E] in the target zone to credibly occur by chance. But if χ significantly exceeds 1 bit [i.e. it is past a threshold that as shown below, ranges from about 400 bits to 500 bits -- i.e. configuration spaces of order 10^120 to 10^150], that becomes increasingly implausible. The only credibly known and reliably observed cause for events of this last class is intelligently directed contingency, i.e. design. Given the scope of the Abel plausibility bound for our solar system, where available probabilistic resources

 ^qΩ_s = 10^43 Planck-time quantum [not chemical -- much, much slower] events per second x 

10^17 s since the big bang  x 
10^57 atom-level particles in the solar system

Or,  ^qΩ_s = 10^117 possible atomic-level events [--> and perhaps 10^87 "ionic reaction chemical time" events, of 10^-14 or so s],

  . . . that is unsurprising.

10 --> Thus, we have a rule of thumb informational X-metric and a more sophisticated informational Chi-metric for CSI/FSCI, both providing reasonable grounds for confidently inferring to design. As will be shown below, both rely on finding a reasonable measure for the information in an item on a target or hot zone -- aka island of function where the zone is set off observed function -- and then comparing this to a reasonable threshold for sufficently complex that non-foresighted mechanisms (such as blind watchmaker random walks from an initial start point and leading to trial and error), will be maximally unlikely to reach such a zone on the gamut of resources set by our observable cosmos. the Durston et al metric helps us see how that works.

11 --> Durston, Chiu, Abel and Trevors provide a third metric, the Functional H-metric in functional bits or fits, a functional bit extension of Shannon's H-metric of average information per symbol, here. The way the Durston et al metric works by extending Shannon's H-metric of the average info per symbol to study null, ground and functional states of a protein's AA linear sequence -- illustrating and providing a metric for the difference between order, randomness and functional sequences discussed by Abel and Trevors -- can be seen from an excerpt of the just linked paper. Pardon length and highlights, for clarity in an instructional context:

Abel and Trevors have delineated three qualitative aspects of linear digital sequence complexity [2,3], Random Sequence Complexity (RSC), Ordered Sequence Complexity (OSC) and Functional Sequence Complexity (FSC). RSC corresponds to stochastic ensembles with minimal physicochemical bias and little or no tendency toward functional free-energy binding. OSC is usually patterned either by the natural regularities described by physical laws or by statistically weighted means. For example, a physico-chemical self-ordering tendency creates redundant patterns such as highly-patterned polysaccharides and the polyadenosines adsorbed onto montmorillonite [4]. Repeating motifs, with or without biofunction, result in observed OSC in nucleic acid sequences. The redundancy in OSC can, in principle, be compressed by an algorithm shorter than the sequence itself. As Abel and Trevors have pointed out, neither RSC nor OSC, or any combination of the two, is sufficient to describe the functional complexity observed in living organisms, for neither includes the additional dimension of functionality, which is essential for life [5]. FSC includes the dimension of functionality [2,3]. Szostak [6] argued that neither Shannon's original measure of uncertainty [7] nor the measure of algorithmic complexity [8] are sufficient. Shannon's classical information theory does not consider the meaning, or function, of a message. Algorithmic complexity fails to account for the observation that 'different molecular structures may be functionally equivalent'. For this reason, Szostak suggested that a new measure of information–functional information–is required [6] . . . .

Shannon uncertainty, however, can be extended to measure the joint variable (X, F), where X represents the variability of data, and F functionality. This explicitly incorporates empirical knowledge of metabolic function into the measure that is usually important for evaluating sequence complexity. This measure of both the observed data and a conceptual variable of function jointly can be called Functional Uncertainty (H_f) [17], and is defined by the equation:

H(X_f(t)) = -∑P(X_f(t)) logP(X_f(t)) . . . (1)

where X_f denotes the conditional variable of the given sequence data (X) on the described biological function f which is an outcome of the variable (F). For example, a set of 2,442 aligned sequences of proteins belonging to the ubiquitin protein family (used in the experiment later) can be assumed to satisfy the same specified function f, where f might represent the known 3-D structure of the ubiquitin protein family, or some other function common to ubiquitin. The entire set of aligned sequences that satisfies that function, therefore, constitutes the outcomes of X_f. Here, functionality relates to the whole protein family which can be inputted from a database . . . .

In our approach, we leave the specific defined meaning of functionality as an input to the application, in reference to the whole sequence family. It may represent a particular domain, or the whole protein structure, or any specified function with respect to the cell. Mathematically, it is defined precisely as an outcome of a discrete-valued variable, denoted as F={f}. The set of outcomes can be thought of as specified biological states. They are presumed non-overlapping, but can be extended to be fuzzy elements . . . Biological function is mostly, though not entirely determined by the organism's genetic instructions [24-26]. The function could theoretically arise stochastically through mutational changes coupled with selection pressure, or through human experimenter involvement [13-15] . . . .

The ground state g (an outcome of F) of a system is the state of presumed highest uncertainty (not necessarily equally probable) permitted by the constraints of the physical system, when no specified biological function is required or present. Certain physical systems may constrain the number of options in the ground state so that not all possible sequences are equally probable [27]. An example of a highly constrained ground state resulting in a highly ordered sequence occurs when the phosphorimidazolide of adenosine is added daily to a decameric primer bound to montmorillonite clay, producing a perfectly ordered, 50-mer sequence of polyadenosine [3]. In this case, the ground state permits only one single possible sequence . . . .

The null state, a possible outcome of F denoted as ø, is defined here as a special case of the ground state of highest uncertainly when the physical system imposes no constraints at all, resulting in the equi-probability of all possible sequences or options. Such sequencing has been called "dynamically inert, dynamically decoupled, or dynamically incoherent" [28,29]. For example, the ground state of a 300 amino acid protein family can be represented by a completely random 300 amino acid sequence where functional constraints have been loosened such that any of the 20 amino acids will suffice at any of the 300 sites. From Eqn. (1) the functional uncertainty of the null state is represented as

H(X_ø(t_i))= - ∑P(X_ø(t_i)) log P(X_ø(t_i)) . . . (3)

where (X_ø(t_i)) is the conditional variable for all possible equiprobable sequences. Consider the number of all possible sequences is denoted by W. Letting the length of each sequence be denoted by N and the number of possible options at each site in the sequence be denoted by m, W = m^N. For example, for a protein of length N = 257 and assuming that the number of possible options at each site is m = 20, W = 20²⁵⁷. Since, for the null state, we are requiring that there are no constraints and all possible sequences are equally probable, P(X_ø(t_i)) = 1/W and

H(X_ø(t_i))= - ∑(1/W) log (1/W) = log W . . . (4)

The change in functional uncertainty from the null state is, therefore,

ΔH(X_ø(t_i), X_f(t_j)) = log (W) - H(X_f(t_i)). (5)

. . . . The measure of Functional Sequence Complexity, denoted as ζ, is defined as the change in functional uncertainty from the ground state H(X_g(t_i)) to the functional state H(X_f(t_i)), or

ζ = ΔH (X_g(t_i), X_f(t_j)) . . . (6)

The resulting unit of measure is defined on the joint data and functionality variable, which we call Fits (or Functional bits). The unit Fit thus defined is related to the intuitive concept of functional information, including genetic instruction and, thus, provides an important distinction between functional information and Shannon information [6,32].

Eqn. (6) describes a measure to calculate the functional information of the whole molecule, that is, with respect to the functionality of the protein considered. The functionality of the protein can be known and is consistent with the whole protein family, given as inputs from the database. However, the functionality of a sub-sequence or particular sites of a molecule can be substantially different [12]. The functionality of a sub-molecule, though clearly extremely important, has to be identified and discovered . . . .

To avoid the complication of considering functionality at the sub-molecular level, we crudely assume that each site in a molecule, when calculated to have a high measure of FSC, correlates with the functionality of the whole molecule. The measure of FSC of the whole molecule, is then the total sum of the measured FSC for each site in the aligned sequences. Consider that there are usually only 20 different amino acids possible per site for proteins, Eqn. (6) can be used to calculate a maximum Fit value/protein amino acid site of 4.32 Fits/site [NB: Log₂ (20) = 4.32]. We use the formula log (20) - H(X_f) to calculate the functional information at a site specified by the variable X_f such that X_f corresponds to the aligned amino acids of each sequence with the same molecular function f. The measured FSC for the whole protein is then calculated as the summation of that for all aligned sites. The number of Fits quantifies the degree of algorithmic challenge, in terms of probability, in achieving needed metabolic function. For example, if we find that the Ribosomal S12 protein family has a Fit value of 379, we can use the equations presented thus far to predict that there are about 10⁴⁹ different 121-residue sequences that could fall into the Ribsomal S12 family of proteins, resulting in an evolutionary search target of approximately 10^-106 percent of 121-residue sequence space. In general, the higher the Fit value, the more functional information is required to encode the particular function in order to find it in sequence space. A high Fit value for individual sites within a protein indicates sites that require a high degree of functional information. High Fit values may also point to the key structural or binding sites within the overall 3-D structure.

11 --> Thus, we here see an elaboration, in the peer reviewed literature, of the concepts of Functionally Specific, Complex Information [FSCI] (and related, broader specified complexity) that were first introduced by Orgel and Wicken in the 1970's. This metric gives us a way to compare the fraction of residue space that is used by identified islands of function, and so validates the islands of function in a wider configuration space concept. So, we can profitably go on to address the issue of how plausible it is for a stochastic search mechanism to find such islands of funciton on essentially random walks and trial and error without foresight of location or functional possibilities. We already know that intelligent agents routinely create entities on islands of function based on foresight, purpose, imagination, skill, knowledge and design.

12 --> Such entities typically exhibit FSCI, as Wicken describes:

‘Organized’ systems are to be carefully distinguished from ‘ordered’ systems.  Neither kind of system is ‘random,’ but whereas ordered systems are generated according to simple algorithms[i.e. “simple” force laws acting on objects starting from arbitrary and common- place initial conditions] and therefore lack complexity, organized systems must be assembled element by element according to an [originally . . . ] external ‘wiring diagram’ with a high information content . . . Organization, then, is functional complexity and carries information. It is non-random by design or by selection, rather than by the a priori necessity of crystallographic ‘order.’ [“The Generation of Complexity in Evolution: A Thermodynamic and Information-Theoretical Discussion,” Journal of Theoretical Biology, 77 (April 1979): p. 353, of pp. 349-65. (Emphases and notes added. Nb: “originally” is added to highlight that for self-replicating systems, the blue print can be built-in.)]

13 --> The Wicken wiring diagram is actually a very useful general concept. Strings of elements -- e.g. S-T-R-I-N-G -- are of course a linear form of the nodes, arcs and interfaces pattern that is common in complex structures.  Indeed, even the specification of controlled points and a "wire mesh" that joins them then is faceted over in digital three-dimensional image modelling and drawing, is an application of this principle. Likewise, the flow network or the flowchart or blocks and arrows diagrams common in instrumentation, control, chemical engineering and software design are another application. So is the classic exploded view used to guide assembly of complex machinery. All such can be reduced to combinations of strings thsat specify nodes, interfaces and interconnecting relationships. From this set of strings, we can get a quantitiative estimate of the functionally specific complex information embedded in such a network, and can thus estimate the impact of random changes to the components on functionality. This allows clear identification and even estimating the scope of  Islands of Function in wider configuration spaces, through a Monte Carlo type sampling of the impacts of random variation on known functional configurations.

(NB: If we add in a hill climbing subroutine, this is now a case of a genetic algorithm. Of course the scope of resources available limits the scope of such a search, and so we know that such an approach cannot credibly initially find such islands of function from arbitrary initial points once the space is large enough. 1,000 bits of space is about 1.07 * 10^301 possibilities, and that is ten times the square of the number of Planck-time states for the 10^80 or so atoms in our obsereved cosmos. That is why genetic type algorithms can model micro-evolution but not body-plan origination level macro-evolution, which credibly requires of the order of 100,000+ bits for first life and 10,000,000+ for the origin of trhe dozens of main body plans. So far, also, the range of novel functional informaiton "found"  by such algorithms navigating fitness landscapes within islands of funciton -- intelligently specified, BTW --  seems (from the case of ev) to have peaked at less than 300 bits. HT, PAV.)

14 --> Indeed, the use of the observed variability of AA sequences in biological systems by Durston et al, is precisely an example of thisan entity thst is naturally based on strings that then fold to the actual functional protein shapes.

15 --> Going beyond this, and building on some recent open notebook science work by Torley and Giem at the blog Uncommon Descent, we may do some integration of the various metrics of CSI and FSCI, showing how they are based on the idea of bits beyond a reasonable threshold of complexity to eliminate blind watchmaker searches as a plausible cause. That is . . .

[VJT in his original post makes]  the following remark, after various [corrective and simplifying] mods to Dembski’s Chi-metric for CSI; I insert Eqn numbers:

CSI-lite=-log2(1-(1-p)^(10^150)) . . . Eqn 1,

where p is the probability of the locally observed probability distribution having the anomalous value or range of values. Where p is very small, we can approximate this by:

CSI-lite=-log2[(10^150).p] . . . Eqn 2

Following up . . . Dr Giem observed that:

Your math equation for large numbers can be simplified by noting that

(1 + 1/t) ^ t

approaches e as t approaches infinity . . . .

(1 – 1/t) ^ at ~ 1/e^(-a)
Thus if we define D as 10^150, your formula

CSI-lite=-log2((1-(1-p))^(10^150)) . . . Eqn 1

can be very closely approximated by

CSI-lite=-log2(1-(1-p)^D)
=-log2(1-(1-p)^(D*p/p))
=-log2(1-e^(-D*p)) . . . Eqn 3

for D*p much smaller than 1 (but above zero), we have as a very close approximation (because the slope of e^x is 1 at x=0) [NB: the slope of e^x at x = 0.01 is 1.01, at x = 0.1 it is 1.105, at 1 it is 2.72], e^(-D*p) = 1-D*p,and so we have, approximately

CSI-lite = -log2(D*p), . . . Eqn 4

which is of course the approximation you gave.

Now, let us look a bit more closely at that rough (~order of magnitude) then increasingly good approximation as p falls further and further below 1/D; in light of the Hartley-Shannon view of information as a negative log metric:

C = – log2(D*p) = -log2(D) -log2(p)

That is, C = I – K, . . . Eqn 5

where I is the [Hartley] info metric for p, in bits.

What we are doing above is specifying a threshold K, beyond which we are confident in inferring to the relevant info-set being a product of art not chance and/or necessity . . . .

Define a metric Q, for K-C compressibility [and being functional in a specific -- reducible to algorithmic or data structure -- way will fit in such] and st it to 0/1 — or even a sliding scale where 1 is a peak value, and multiply the above by it, i.e if the constraint is not met the metric is forced to a zero, and if we use the sliding scale version it forces a higher and higher complexity threshold as specificity falls:

C’ = [Q] * [-log2(D*p)] . . . Eqn 6

Now, let us revert to the case where D = 10^150, or more helpfully, D = 2^500:

Where C = I – K, . . . Eqn 5

and K = 500 bits

C’ = I – 500 bits . . . Eqn 7

THAT IS, THE C’ METRIC IS BASED ON IDENTIFYING A THRESHOLD BEYOND WHICH THE SPECIFIC OUTCOME OF LOW PROBABILITY ON A CHANCE HYP, IS INFERRED AS MAXIMALLY UNLIKELY TO BE THE RESULT OF BLIND WATCHMAKER TYPE PROCESSES OF CHANCE AND/OR NECESSITY.

16 --> Taking this as a rough but reasonable enough approximation [which will work even though the Dembski result is not based on the analytically exact forms], we may now analyse what is going on in the Dembski metric given under point 8 above:

χ = – log₂[10^120 ·ϕS(T)·P(T|H)].

This can be broken up:

χ = – log₂[2^398 ·D₂·P(T|H)].

Or, as - log2(P(T|H)) = I(T):

χ = I(T) - 398 - K₂

Where, K₂ has a natural upper limit of about 100 further bits.

That is the Dembski metric boils down to analysing the informaiton in T as compared tothe space of possibilites, in terms of how far it is beyond a variable threhold of about 400 - 500 bits.

17 --> This allows us to tie the various metrics together. For, what is being done is to assess an information estimate for a functional or otherwise specified target zone in a config space then estimate how hard it is to find on a random walk leading to trial and error, from an arbitrary initial point, as an estimate of the informaiton in it. By comparing that quantum of informaiton to a threshold that measures a size beyond which it is credible that such a search would be maxmally unlikely to succeed, we can then get an estimate of whether or not the best explanation of the FSCI or CSI being seen is intelligence. (For, intelligence can clearly make arbitrarily large cases of functionally specific complex information.)

18 --> In that context, the Durston metric gives us a way to estimate sizes of islands of function, and information content in a more sophisticated way than using the Laplace-Bernouilli indifference approximation, useful as that is. It also provides a conceptual-analytical apparatus for validating the islands of function approach.

19 --> And, the simple brute force X-metric identified in 6(a) - (f) just above, X = C*S*B, is seen as simply imposing a threshold so large that the specifics of probability models are irrelvant as the search resources of the cosmos are swamped by the scope of the config space; which comes at a surprisingly small level: 1,000 bits or 125 bytes or 143 ASCII characters worth of information.

(Those experienced with programming system controllers will readily acknowledge that 1,000 bits or 125 bytes is a surprisingly small quantum for such a program to have to fit in to be reachable by random walk searches leading to trial and error. So, since the evidence is that first life requires about 100 k bits or more, and that novel body plans require 10+ M bitrs, these are not credibly reachable by such blind watchmaker mechanisms. That leaves intelligence as the best -- and as a known -- cause of that sort of level of FSCI.)

20 --> And so, we have now opened the way to the scientific investigation of: 

(i) natural regularities tracing to mechanical forces of lawlike necessity [law], 

(ii) naturally variable outcomes tracing to undirected contingency [chance], and 

(iii) artificially variable outcomes tracing to directed contingency [design].  

So, let us now take a preview of the case in the main for this note. 

For instance, as Robert Shapiro, a well-known "metabolism first" origin of life [OOL] theorist, in a recent Scientific American article, notes of the currently popular RNA world OOL model:

RNA's building blocks, nucleotides, are complex substances as organic molecules go. They each contain a sugar, a phosphate and one of four nitrogen-containing bases as sub-subunits. Thus, each RNA nucleotide contains 9 or 10 carbon atoms, numerous nitrogen and oxygen atoms and the phosphate group, all connected in a precise three-dimensional pattern. Many alternative ways exist for making those connections, yielding thousands of plausible nucleotides that could readily join in place of the standard ones but that are not represented in RNA. That number is itself dwarfed by the hundreds of thousands to millions of stable organic molecules of similar size that are not nucleotides . . . . 

The RNA nucleotides are familiar to chemists because of their abundance in life and their resulting commercial availability. In a form of molecular vitalism, some scientists have presumed that nature has an innate tendency to produce life's building blocks preferentially, rather than the hordes of other molecules that can also be derived from the rules of organic chemistry. This idea drew inspiration from . . . Stanley Miller. He applied a spark discharge to a mixture of simple gases that were then thought to represent the atmosphere of the early Earth. ["My" NB: Subsequent research has sharply undercut this idea, a point that is unfortunately not accurately reflected in Sci Am's caption on a picture of the Miller-Urey apparatus, which in part misleadingly reads, over six years after Jonathan Wells' Icons of Evolution was published: The famous Miller-Urey experiment showed how inanimate nature could have produced amino acids in Earth's primordial atmosphere . . .] Two amino acids of the set of 20 used to construct proteins were formed in significant quantities, with others from that set present in small amounts . . .  more than 80 different amino acids . . . have been identified as components of the Murchison meteorite, which fell in Australia in 1969 . . . By extrapolation of these results, some writers have presumed that all of life's building could be formed with ease in Miller-type experiments and were present in meteorites and other extraterrestrial bodies. This is not the case.

A careful examination of the results of the analysis of several meteorites led the scientists who conducted the work to a different conclusion: inanimate nature has a bias toward the formation of molecules made of fewer rather than greater numbers of carbon atoms, and thus shows no partiality in favor of creating the building blocks of our kind of life . . . I have observed a similar pattern in the results of many spark discharge experiments . . . . no nucleotides of any kind have been reported as products of spark discharge experiments or in studies of meteorites, nor have the smaller units (nucleosides) that contain a sugar and base but lack the phosphate.

To rescue the RNA-first concept from this otherwise lethal defect, its advocates have created a discipline called prebiotic synthesis. They have attempted to show that RNA and its components can be prepared in their laboratories in a sequence of carefully controlled reactions, normally carried out in water at temperatures observed on Earth . . . . Unfortunately, neither chemists nor laboratories were present on the early Earth to produce RNA . . . .

Shapiro then acidly observes -- in a remark that inadvertently also applies to his preferred metabolism first scenario -- that:

The analogy that comes to mind is that of a golfer, who having played a golf ball through an 18-hole course, then assumed that the ball could also play itself around the course in his absence. He had demonstrated the possibility of the event; it was only necessary to presume that some combination of natural forces (earthquakes, winds, tornadoes and floods, for example) could produce the same result, given enough time. No physical law need be broken for spontaneous RNA formation to happen, but the chances against it are so immense, that the suggestion implies that the non-living world had an innate desire to generate RNA. The majority of origin-of-life scientists who still support the RNA-first theory either accept this concept (implicitly, if not explicitly) or feel that the immensely unfavorable odds were simply overcome by good luck.

The equally famous OOL researcher [and, again, not an ID supporter] Orgel wrote a January 2008 posthumous rejoinder to Shapiro that is just as telling. Thus, each of these two distinguished researchers exposes the holes in the other's favoured model, underscoring that neither evolutionary materialist school of thought on origin of life has a credible, robust chance + necessity only model for the origin of the FSCI in life:

If complex cycles analogous to metabolic cycles could have operated on the primitive Earth, before the appearance of enzymes or other informational polymers, many of the obstacles to the construction of a plausible scenario for the origin of life would disappear . . . Could a nonenzymatic “metabolic cycle” have made such compounds available in sufficient purity to facilitate the appearance of a replicating informational polymer?

It must be recognized that assessment of the feasibility of any particular proposed prebiotic cycle must depend on arguments about chemical plausibility, rather than on a decision about logical possibility . . . few would believe that any assembly of minerals on the primitive Earth is likely to have promoted these syntheses in significant yield. Each proposed metabolic cycle, therefore, must be evaluated in terms of the efficiencies and specificities that would be required of its hypothetical catalysts in order for the cycle to persist. Then arguments based on experimental evidence or chemical plausibility can be used to assess the likelihood that a family of catalysts that is adequate for maintaining the cycle could have existed on the primitive Earth . . . . 

Why should one believe that an ensemble of minerals that are capable of catalyzing each of the many steps of [for instance] the reverse citric acid cycle was present anywhere on the primitive Earth [8], or that the cycle mysteriously organized itself topographically on a metal sulfide surface [6]? The lack of a supporting background in chemistry is even more evident in proposals that metabolic cycles can evolve to “life-like” complexity. The most serious challenge to proponents of metabolic cycle theories—the problems presented by the lack of specificity of most nonenzymatic catalysts—has, in general, not been appreciated. If it has, it has been ignored. Theories of the origin of life based on metabolic cycles cannot be justified by the inadequacy of competing theories: they must stand on their own . . . . 

The prebiotic syntheses that have been investigated experimentally almost always lead to the formation of complex mixtures. Proposed polymer replication schemes are unlikely to succeed except with reasonably pure input monomers. No solution of the origin-of-life problem will be possible until the gap between the two kinds of chemistry is closed. Simplification of product mixtures through the self-organization of organic reaction sequences, whether cyclic or not, would help enormously, as would the discovery of very simple replicating polymers. However, solutions offered by supporters of geneticist or metabolist scenarios that are dependent on “if pigs could fly” hypothetical chemistry are unlikely to help. 

In short, there is a distinct difference and resulting massive, probability-based credibility gap between having components of a complex, information-rich functional system with available energy but no intelligence to direct the energy to construct the system, and getting by the happenstance of "lucky noise," to that system. Physical and logical possibility is not at all to be equated with probabilistic credibility -- especially when there are competing explanations on offer -- here, intelligent agency -- that routinely generate the sort of phenomenon being observed.

Howbeit, this point -- while it does underscore the significance and inherent credibility of intelligent intervention in the creation of tightly functionally integrated, complex, information-rich systems -- is getting a little ahead of the main argument. But, through multiplying the many similar familiar cases, we can plainly make a serious argument that FSCI is highly likely to be a "signature" or reliable sign that points to intelligent -- purposeful -- action. [Indeed, there are no known cases where, with independent knowledge of the causal story of the origin of a system, we see that chance forces plus natural regularities without  intelligent action has produced systems that exhibit FSCI. On the contrary, in every such known case of the origin of FSCI, we see the common factor of intelligent agency at work.]

Consequently, we freely infer on a best and most likely explanation basis [to be further developed below], that:

Absent compelling reason to conclude otherwise, when we see FSCI we should infer to the work of an intelligence as its best, most credible and most likely explanation. (And, worldview level question-begging does not constitute such a "compelling reason.")

But, then, what do we make of -- say -- the case of DNA? Of the origin of the diversity of life? Or, that of the evidently fine-tuned cosmos? Does the known absence of human intelligent agents at the origin of such cases materially alter the balance of our inference? Why or why not?

B] Case I: DNA as an informational macromolecule

Now, this is perhaps the most hotly debated case where we do not directly know the causal story of origin of a complex information-using system, especially as it makes an empirically anchored observation that goes to the heart of the dominant secularist, evolutionary materialist, modernist and/or post-/hyper- modernist worldview held by a critical mass among the elites of the West (including many theologians!). However, the force of the inference to design here can be seen from the title of a textbook I vividly recall often seeing in my old University's Natural Sciences Library, over 20 years ago now: Functional Design in Fishes. Accordingly, we see two contrasting stances:

Dembski: intelligent design is . . . a scientific investigation into how patterns exhibited by finite arrangements of matter can signify intelligence.

Dawkins: biology is the study of complicated things that give the appearance of having been designed for a purpose. [Elsewhere, he defines that systems which only appear to be designed should be viewed as designoid.]

We can of course immediately observe that -- however many Darwinists may wish to disown him, Dawkins is here reflecting a pattern that is obvious. Plainly, if something seems to exhibit FSCI as above, and thus gives the strong appearances of being designed, we need a very good cluster of evidence and argument to reject the obvious conclusion that such things appear designed for the excellent reason that they are. Equally plainly, an implicit reference to a worldview's claims (and usually, without a careful comparative difficulties assessment across live options) just will not do.

So, to address this vexed issue, let us begin with a summary of the challenge from a recent review article:

There is an enormous leap from pre-biotic chemistry to the complexity of DNA replication, protein manufacture and biochemical pathways existing at the time of the primary divergence of life. Although progress is being made on the evolution of some structural components and biochemical pathways, there remain numerous unsolved ‘chicken and egg’ problems. Margulis (1996a ) said, ‘To go from a bacterium to people is less of a step than to go from a mixture of amino acids to that bacterium’, yet accumulated evidence from the physical and biological sciences indicates that advanced life existed at a very early stage of Earth’s development . . . . Hence the enigma: an origin of life on Earth appears highly improbable, an origin elsewhere is highly conjectural. While this conundrum has been identified in various forms for several decades, its magnitude has dramatically increased over the last five years as new constraints are placed on the timing of the primary divergence of the domains of life. (Shen et al., 2001. Emphases added.)

This article then goes on to speculate on possible evolution at hydrothermal vents on some other planet (which dodges the twin bullets of UV radiation and oxygen poisoning of pre-life chemistry that have put atmospheric and surface pond scenarios to rest for now at least), then the drifting of life to earth -- "panspermia." That openly confessed resort to the highly conjectural, unobserved and improbable is telling.

For a further illustration, we may also observe, in a recent PLoS summary article by a science writer:

Give biologists a cell, and they'll give you the world. [cf Case II below] But beyond assuming the first cell must have somehow come into existence, how do biologists explain its emergence from the prebiotic world four billion years ago? The short answer is that they can't, yet . . . . While the past half century has seen an explosion of knowledge about the evolution of life after it began, there has been relatively little progress in the past half century on how it began—the so-called origin question . . . . finding the answer to the origin question will require not only money but also progress in understanding how the most basic of biological molecules were put together before life began, how they became organized and self-sustaining, and how they developed into the membrane-bound cells that are our ancestors. Scientists have come a long way from the early days of supposing that all this would inevitably arise in the “prebiotic soup” of the ancient oceans; indeed, evidence eventually argued against such a soup, and the concept was largely discarded as the field progressed. But significant problems persist with each of the two competing models that have arisen—usually called “genes first” and “metabolism first”—and neither has emerged as a robust and obvious favorite. [Robinson, 2005. Emphases and remarks in parentheses added.]

What is the underlying, unresolved issue? We can perhaps best get at it by presenting some remarks by Dr Gary Parker of ICR, as excerpted by Royal Trueman:

A cell needs over 75 "helper molecules", all working together in harmony, to make one protein (R-group series) as instructed by one DNA base series. A few of these molecules are RNA (messenger, transfer, and ribosomal RNA); most are highly specific proteins. ‘When it comes to "translating" DNA’s instructions for making proteins, the real "heroes" are the activating enzymes. Enzymes are proteins with special slots for selecting and holding other molecules for speedy reaction. Each activating enzyme has five slots: two for chemical coupling, one for energy (ATP), and most importantly, two to establish a non-chemical three-base "code name" for each different amino acid R-group. You may find that awe-inspiring, and so do my cell-biology students! [Even more awe-inspiring, since the more recent discovery that some of the activating enzymes have editing machinery to remove errant products, including an ingenious "double sieve" system.[2],[3]] ‘And that’s not the end of the story. The living cell requires at least 20 of these activating enzymes I call "translases," one for each of the specific R-group/code name (amino acid/tRNA) pairs. Even so, the whole set of translases (100 specific active sites) would be (1) worthless without ribosomes (50 proteins plus rRNA) to break the base-coded message of heredity into three-letter code names; (2) destructive without a continuously renewed supply of ATP energy [as recently shown, this is produced by ATP synthase, an enzyme containing a miniature motor, F1-ATPase.[4],[5],[6],[7]] to keep the translases from tearing up the pairs they are supposed to form; and (3) vanishing if it weren’t for having translases and other specific proteins to re-make the translase proteins that are continuously and rapidly wearing out because of the destructive effects of time and chance on protein structure! [8] [Cf also, Abel and Trevors, here.]

The proteins involved in this work of the cell are similarly highly complex and quite specific as to both monomer sequence and folded, three-dimensional "key- and- lock- fit" structure. That is, as we consider the nanotechnology of the cell, we are looking at evident, sequence- perturbation- sensitive functional finetuning resting on complex information. As Meyer recently noted:

By the mid-1950s, biochemists recognized that . . .  [i]n addition to their complexity, proteins also exhibit specificity, both as one-dimensional arrays and three-dimensional structures. Whereas proteins are built from chemically rather simple amino acid “building blocks,” their function (whether as enzymes, signal transducers, or structural components in the cell) depends crucially on a complex but specific arrangement of those building blocks.13 In particular, the specific sequence of amino acids in a chain and the resultant chemical interactions between amino acids largely determine the specific three-dimensional structure that the chain as a whole will adopt. Those structures or shapes in turn determine what function, if any, the amino acid chain can perform in the cell.

For a functioning protein, its three-dimensional shape gives it a hand-in-glove fit with other molecules, enabling it to catalyze specific chemical reactions or to build specific structures within the cell. Because of its three dimensional specificity, one protein can usually no more substitute for another than one tool can substitute for another. A topoisomerase can no more perform the job of a polymerase than a hatchet can perform the function of a soldering iron. Instead, proteins perform functions only by virtue of their three-dimensional specificity of fit, either with other equally specified and complex molecules or with simpler substrates within the cell. Moreover, the three-dimensional specificity derives in large part from the one-dimensional sequence specificity in the arrangement of the amino acids that form proteins. Even slight alterations in sequence often result in the loss of protein function . . . . 

Whereas the function of the protein molecule derives from the specific arrangement of twenty different types of amino acids, the function of DNA depends on the arrangement of just four kinds of bases. This lack of a one-to-one correspondence means that a group of three DNA nucleotides (a triplet) is needed to specify a single amino acid. [NB: observe that  4 x 4 x 4 = 64, but 4 x 4 = 16  where 16 < 20, so we need at least and not more than the triplet, usually termed a codon.] In any case, the sequential arrangement of the nucleotide bases determines (in large part) the one-dimensional sequential arrangement of amino acids during protein synthesis.26 Since protein function depends critically on amino acid sequence and amino acid sequence depends critically on DNA base sequence, the sequences in the coding regions of DNA themselves possess a high degree of specificity relative to the requirements of protein (and cellular) function . . . . 

The essentially digital character of the nucleotide bases in DNA and of the amino acid residues in proteins enabled molecular biologists to calculate the information-carrying capacity (or syntactic information) of those molecules using the new formalism of Shannon’s theory. Because at every site in a growing amino acid chain, for example, the chain may receive any one of twenty amino acids, placement of a single amino acid in the chain eliminates a quantifiable amount of uncertainty and increases the Shannon or syntactic information of a polypeptide by a corresponding amount. Similarly, since at any given site along the DNA backbone any one of four nucleotide bases may occur with equal probability, the p value for the occurrence of a specific nucleotide at that site equals 1/4, or .25.[30] The information- carrying capacity of a sequence of a specific length n can then be calculated using Shannon’s familiar expression (I =–log₂p) once one computes a p value for the occurrence of a particular sequence n nucleotides long where p = (1/4)^n. The p value thus yields a corresponding measure of information-carrying capacity or syntactic information for a sequence of n nucleotide bases.[31] . . . .

Biological organisms also exhibit specifications, though not necessarily semantic or subjectively “meaningful” ones. The nucleotide base sequences in the coding regions of DNA are highly specific relative to the independent functional requirements of protein function, protein synthesis, and cellular life. To maintain viability, the cell must regulate its metabolism, pass materials back and forth across its membranes, destroy waste materials, and do many other specific tasks. Each of these functional requirements in turn necessitates specific molecular constituents, machines, or systems (usually made of proteins) to accomplish these tasks. Building these proteins with their specific three-dimensional shapes requires specific arrangements of nucleotide bases on the DNA molecule. [Bold emphasis and parenthesis on codon triplets added.]

In short, the functioning cell is an enormously sophisticated, specific and complex, fine-tuned information-carrying and information- processing system -- vastly beyond anything we have as yet been able to design and develop. For, it is inter alia a self-regulating, self-repairing, self-replicating automaton -- a class of system we have yet to design and implement with human technologies; even though John Von Neumann long ago specified the required subsystems to achieve this high degree of functionality, indeed, reportedly predicting that the cell would exhibit this sort of systemic structure, even before the microbiological revolution of fifty-odd years ago now. 

The cell is also controlled by the information stored in the DNA, using a computer language based on three-letter codons that (1) give procedures, such as: start/stop, and (2) specify amino acid chains for proteins, the workhorse molecules of the cell. Other portions (3) provide regulatory functions. Yet others are often called (4) "junk DNA," as for these no function has as yet been identified (though in some parts, that is changing as we speak). Now, of course, DNA is error-prone and has to be replicated. These critical tasks are achieved by the cell's molecular machinery; which in turn is manufactured based on DNA's stored information -- a classic "chicken-and-egg" dilemma, as Shen et al. remark on. So, the big (and growing) problem faced by evolutionary materialists is to account for this evident FSCI and associated molecular processing machinery on the basis of spontaneous chemistry in plausible prebiotic environments, given the decisive issue of the adverse thermodynamics of such environments.

The magnitude of that challenge to make the evident FSCI in DNA (and thus cells) out of in effect chemical and thermal noise in hydrothermal vents or some new version of Darwin's prebiotic soup in a small warm pond, can best be appreciated in light of observations made at popular level by Dan Peterson in a recent American Spectator article:

. . . . suppose my computer keyboard had only one key, and all I could type was:

AAAAAAAAAAAAAAAAAAAAAA

My computer would be incapable of producing contingency. This is rather like the operation of many physical laws in nature . . . . The sequence of 22 letters:

KAZDNHF OPZSJHQL ZXFNV

is complex in a certain sense, because that exact pattern is highly unlikely to be produced by chance . . . The total number of unique sequences of [27] characters that could be produced would be 27 multiplied by itself 22 times, or 27 to the 22nd power . . . If we . . . generate random strings 22 characters long . . . [with] a trillion tries every second, the odds would still be against producing this exact sequence by chance in 20 billion years . . . .

The third criterion is specification. Here's another 22-character sequence:

THE AMERICAN SPECTATOR

. . . . [which] is complex . . . It is also specified in relation to a pre-existing standard or function; in this case, the rules, spelling, and vocabulary of the English language . . . . In every case in which we know the "causal story" underlying complex specified information (writing a sonnet, creating a computer program, or sculpting Mount Rushmore) we know that it has been produced by an intelligence. [Source: "The Little Engine That Could...Undo Darwinism," Published 8/5/2005. Bold emphases added.] 

Then also, in TMLO, Ch 8, Thaxton et al (the first technical authors in the modern Design framework) show -- cf. Appendix 3 below -- that the concept, complex, functionally specified information, emerged organically from the natural development of OOL studies, through the work of Polanyi, Orgel, Yockey and Wickens in particular. CSI, or, as I have expressed its relevant subset, FSCI, is therefore NOT an alien imposition on OOL studies by "Creationists," whether hiding in "cheap tuxedos" or otherwise. Indeed, in this context, Mr Dembski's work is best understood as a serious and arguably at least partly successful attempt to give mathematical formalism and definition through a probabilistic-statistical model tied to information theory, to an existing concept. Indeed, as the cite a the head of this page shows, that concept was first seriously broached in Western culture, as early as ~ 50 BC, by Cicero.

Irreducible Complexity, Behe's concept [which builds on Darwin's suggestion for an empirical test of his scheme, cf. the next section below], is in turn a subset of FSCI, relating to systems made up from components, containing a core fraction that is such that removal of any of these critical components disrupts its proper function. (This is very familiar from say, the experience of anyone who has experienced breakdown of a car, or a PC or a television set due to failure of just one key component. in biology, genetic knockout studies work by knocking out one genetic component at a time and seeing what breaks down. E.g., by such studies Scott Minnich -- as he testified to at Dover -- reports that he has empirically shown that the bacterial flagellum is irreducibly complex. [NB: observe remarks here as well on informational redundancy in the genome and its potential impact on such studies.)

The relevance of this lies in the observation, ever since Polanyi and Yockey et al that DNA is in fact a functional, complex, digitally encoded, data string based on chains of nucleic acids. This observation was followed up by Thaxton, Bradley and Olsen [TBO] in the early 1980's; then thereafter by the Design Theory movement that emerged from their breakthrough 1984 technical level book, The Mystery of Life's Origin [TMLO]. For, as just noted, highly complex informational macromolecules control the core functions of life; constituting a communication system with digitally coded messages that are functional, specified and complex. As Peterson therefore goes on to note:

The DNA in genes and chromosomes . . . makes up the blueprint for life . . . There are four potential bases for any "slot" in the sequence, often abbreviated by the letters A, C, G, and T . . . . Like computer code or language, the sequencing of those four bases is contingent -- the nucleotides don't bond with the nucleotides next to them in a necessary, repeating sequence. DNA sequences are also complex. In the human genome (that is, in the DNA present in each of our cells) there are about three billion such slots. The amount of information in the DNA of every human cell is greater than the information in all of the volumes of the Encyclopedia Britannica. Most importantly, DNA sequences in living things are specified in relation to a function: building a human, animal, or plant that can, at minimum, survive and reproduce.

In short, on the face of it, there is an excellent case that DNA [and other molecules of life] bear the characteristics of complex, functionally specific messages beyond the credible reach of undirected chance forces and blind natural regularities, and indeed vastly compound the point by having these function together in an integrated entity, the cell. That immediately raises what is in several quarters a very unwelcome inference: DNA is probably the product of a purposeful, intelligent agent, i.e. it is the product of design.

It is also worth pausing to further cite Peterson's remarks on a way to set a "reasonable" yardstick for rejecting chance explanation through improbability, as has been proposed by William Dembski; especially as this is often a focus for misunderstanding. For, we can move beyond simply hypothesising a supercomputer that can make a trillion tries a second and lasts for the lifetime of the cosmos, to create a more natural bound for "improbability":

Dembski has formulated what he calls the "universal probability bound." This is a number beyond which, under any circumstances, the probability of an event occurring is so small that we can say it was not the result of chance, but of design. He calculates this number by multiplying the number of elementary particles in the known universe (10^80) by the maximum number of alterations in the quantum states of matter per second (10^45) by the number of seconds between creation and when the universe undergoes heat death or collapses back on itself (10^25). The universal probability bound thus equals 10^150, and represents all of the possible events that can ever occur in the history of the universe. If an event is less likely than 1 in 10^150, therefore, we are quite justified in saying it did not result from chance but from design. Invoking billions of years of evolution to explain improbable occurrences does not help Darwinism if the odds exceed the universal probability bound. [Link added. Cf. Dembski's more technical discussions that are available online here and here. The related philosophical challenge due to Hume and his current followers, including especially Elliott Sober, is discussed here.]

For instance, if I type out a paragraph of 120 characters, all in upper case English Alphabet letters, without spaces or punctuation [so-called scriptua continua, as the oldest manuscripts of the New Testament often use], then the set of all possible strings is: 26^120, which is about 6.26 * 10^169. If I were to factor in the usual set of 128 ASCII characters, there would be about 7.33 * 10^252 possible random strings of 120 characters. In short, once we specify it, it would be most improbable to reproduce any given 120-character string of characters merely by chance. So, when we see, not an arbitrary nonsense string -- i.e. any random set of keys would do: jnfvjwqyue2bfhaewfh . . . . , or: l,fchjfvcyodyflxpd87r0ejkf . . . . , or: bfytfdiidtclsp;strfhid . . . . etc. -- but rather specific text in English, we have good reason to infer that such is an intentional message, not a matter of the famous million monkeys hitting keyboards at random for a million years, or the like. 

CASE STUDY -- of Monkeys and keyboards (updated): Updating this tired C19 rhetorical counter-example used by Darwinists, take a million PC's, with floppy drives modified to spew magnetic noise across the inserted initially unformatted disks, perhaps using zener diode noise circuits or the like source of guaranteed random noise. Then once every 30 seconds for a year, run the noise circuit, and then test for a formatted disk with 500 or more bits of data in any standard PC format. We get thereby 10^12 tests per year. Continue for the lifetime of the observed cosmos, i.e. 10^25 seconds or so, giving 10^37 tests. Is it credible that we will ever get a properly formatted disk, or thence a message at this reasonable threshold of complexity by chance? 

[NB: The 500-bit threshold is chosen as 2^500 ~ 10^150, and because it is credible that the molecular nanotechnology of life has in it orders of magnitude more information than that, judging by the 300 - 500,000 4-state elements (equivalent to 600,000 to 1 million 2-state elements) in the DNA code of the simplest existing unicellular life forms. Also, observe that we are here putting a far more realistic threshold of accidentally generated functional complexity than we see in the often met with cases of designed genetic algorithms that carry out targetted searches, step by step promoting increments towards the target. Random walk-type searches, or searched reducible to that, in short, only "work" when the searched space is sufficiently richly -- and implausibly [Cf here Denton's telling discussion in his classic 1985 Evolution, a Theory in Crisis, ch 13] -- populated by islands of functional complexity.]

Of course, in some cases, code-makers deliberately produce nonsense-like strings, but that can be recognised once an appropriate receiver (and its decoder) can decode them. We can rule out this situation, without loss of force on the main point: first, receive and decode your message, then discuss whether it comes from noise or intelligence. In short, we do not need to have a "super-definition" of functionally specified complex information and/or an associated super-algorithm in hand that can instantly recognise and decode any and all such ciphers, to act on a case by case basis once we have already identified a code. 

This is of course another common dismissive rhetorical tactic. Those who use it should consider whether we cannot properly study cases of life under the label "Biology," just because there is no such generally accepted definition of "life." In any case, precise definitions that identify all and only cases of a given entity X, depend for their credibility on the prior fact that we recognise that there are cases of X, and cases of NOT-X, which the definition reliably separates. That is, intuitive, conceptual recognition on a case by case basis is prior to precising definition. 

DNA, in any case, is already long since [partially] decoded, so we can turn back from this rabbit trail to the material issue: how do we account for what we do know about this case?

Now, too, DNA strings take on four values in any position, G/C/A/T [and in odd cases, U], with certain constraints. Thus, there is an apparent coded message, where three letters in sequence correspond to certain amino acids in protein chains. We also see in real cells DNA strands with 500,000 or so for the simplest functional cells; up to 3,000,000,000 or more base pairs, for species such as man -- plainly a functional and complex coded message.

But, log manipulations on a pocket calculator will soon show that just 500,000 four-state elements have 9.9 * 10^301,029 possible combinations, and the constraints on on sequences do not bring an exponent of over 300,000 down below the threshold, 10^150. 

For instance, let us assume that only 10% of the code in the bacteria with DNA strands at the lower end of the range is functional, and that at each minimally contingent functional point, there is a pair of nucleic acids, thus, that we have a binary sequence with 25,000 positions. [That is, in effect at each point, we assume minimal contingency: two choices not four.] The number of possible states for such a digital DNA string of data would then be: 2^25,000; or, ~ 5.62 * 10^7,525. Now, too, it is credible that here have been less than 10^500 DNA-based life forms in our cosmos, so the functional states (which would cluster species by species) would be impossibly sparse in the resulting "DNA-space." (To give an idea, we observe perhaps 10^80 atoms in the cosmos, and if every atom were to become another whole universe of similar scale, we would then have 10^80 universes of 10^80 atoms each, giving 10^160 atoms overall. We would then have to multiply the number of atoms similarly four times over again to get to 10^5120 atoms, which is still vastly below the number just given.) Finally, on this, we note that knockout studies reportedly lead to disintegration of life function when the remaining active DNA in such "simple" bacteria is ~ 360,000. NB: For a more elaborate discussion [which in particular addresses "chance-plus" scenarios and shows in summary why they are unsatisfactory], cf. here, esp. from p. 239  on.

This point may be extended by recognising that the observed genome reportedly currently ranges from about 160 - 500,000 four-state elements up to about 130 - 670 *10^9 such elements.  We may therefore look at an illustrative case study:

CASE STUDY: on getting to "islands" of bio-functionality in the "digital genome ocean": In effect, since genomes commonly range from about half a million to three to four billion elements, we may consider the genome as constituting a configuration space based on five-state digital elements [G, C, A, T or 0, this last meaning (a) the relevant genome has no digit at the place in question [the real genome has truncated], or (b) while it may have a physical digit, it is non-functional, i.e. so-called "junk"]. Every genome thus would be of nominal length  700*10^9 elements, per the more or less upper limit of observed genomes. That way, we may display all actual and possible genomes in a common digital configuration space.(Conceptually, for the purposes of visualising the configuration space, we can view the DNA string as if it formed a "loop," so that there is no one preferred location or direction of reading it, even though we may [again in our imaginations] tag some digit as the first for each string so that we have a reference point for uniquely identifying each possible loop. Similarly, for convenience, we may imagine that the resulting space fans out from the "zero-length genome" in an arc, with the radius from the origin at any given cell being proportional to the string-length of the physical genome. Similar genomes are, of course, clustered together.)

Using this model, we may now view each configuration as occupying one cell [pixel], so that the genomic space is imagined as a vast digital "Pacific Ocean," with an overall configuration space of 5^[700*10^9] ~ 1.63 *10^489,279,003,035 states or cells.  (NB: There are a "mere" 10^80 or so atoms in the observed universe, which as Dembski calculates, would take up ~ 10^150 quantum states across its typically estimated lifetime.)

Within that vast, fan-shaped imaginary mathematical ocean, every possible genome from 0 elements up to 700 * 10^9 elements can be mapped as sitting in the sea of non-function, or on an island of functionality. Each of these islands can be imagined as having a shoreline of minimally functional configurations, ranging up to an inland range of hills of increasingly effective then ultimately locally optimal bio-functionality at its peaks. (In short, each island corresponds to a functional body plan, with room for enough variation to take in every possible individual functional expression of that plan.)

Within that digital Pacific, we will expect to observe islands and perhaps archipelagos or even continents of bio-function, corresponding to observed and possible bio-forms. Indeed, they correspond to every past, existing and even possible individual cell-based lifeform. [Of course, if we observe yet longer genomes, we can easily enough extend the space beyond 700 billions, but that would simply further underscore the force of the point.] 

The first challenge of abiogenesis is to start from the 0 square [genome length zero], and in a plausible chemical environment, (i) get to a viable and sustainable prebiotic soup with the requisite monomers in it, then (ii) move to the first islands of function. (For the moment, we will simply assume for the sake of our argument that once a proto-genome reaches the shores of a viable island, it may then proceed through hill-climbing processes such as "random variation" and "natural selection" [i.e. culling based on differential average reproductive success], to move to the mountains of peak performance in that bio-functional niche.)

The immediate problem is that the first such observed islands are of order 100,000 - 1,000,000 base pairs; and in a context where the organisms at the lower end are in effect typically dependent on more complex life forms to make life components they cannot. The relevant 1 million chain-length sub-space has about 1.010 * 10^698,970 configurations, which is again a very large number, which will easily swamp the search resources of the observed cosmos. Even if we take 100,000 elements as a working lower limit, that puts us at 1.001 * 10^69,897; still well beyond the available search resources of the observed cosmos. In effect, if an inflatable but slowly leaking raft [i.e. there are finite, exhaust-able search resources . . . ] were to drift from the zero-length cell in the digital Pacific at random until it grounds on an island of function or sinks due to a loss of air, it would be maximally improbable for it to reach a shore before sinking.

Why is that so?

First, biofunction is observed to be code based and specific, i.e. it is vulnerable to perturbation. For instance, three of the 64 possible three-letter codons code for STOP. So, immediately, if we form a substring of three DNA letters at random,  the odds are just under 5% that they will be a stop codon. This alone means that in a prebiotic scenario -- even ignoring the basic thermodynamics challenge of climbing up the energy and complexity hill to spontaneously synthesise the monomers in adequate concentration (itself a major challenge, cf. Appendix 1) -- randomly formed codon sub-strings will tend to be too short to be functional in coding for a protein. That means that functional genomes must be quite rare in the configuration space, even in the initial short-genome corner. For instance: 

. . . consider a hypothetical genome that requires 100 "necessary" proteins, each with just 100 residues, using altogether 10,000 codons, or 30,000 DNA base pairs. This will require 10,000 codons without an accidental stop in the wrong place, to get the required complement of proteins. The fraction of such 30,000-length genomes that would not be truncated by wrongly placed stop codons is (61/64)^10,000 ~ 1 in [3 * 10^208]. This in itself would make it maximally unlikely that we would get by chance concatenation of DNA elements to a single such minimally functional genome; on the gamut of our observed universe across its typically estimated lifetime. (Nor will autocatalysis of RNA molecules in a hypothetical RNA world, get us to bio-functional, protein-making DNA codes.)

Next, to get to actual bio-function is itself a challenge. 

For, the DNA molecule is a code storing component in cell-based life. It must inter alia code for proteins that must fold to specific shapes and have various appropriate functional groups dependent on the overall structures of the protein chains. To express that code, DNA requires a large number of associated molecules to put it to work. That is, as we observe in the cell, we require a rather carefully organised cluster of complex molecular scale machines, that work together in close coordination to produce biofunction. Without the molecules in the correct proximity, arrangement and order of operation, the step by step -- i.e algorithmic -- processes of life will not work. To assemble and preserve such molecules in the correct proximity is also a further major challenge; again, easily beyond the available search resources of our observed cosmos. In short, to get to just having the molecules for observed life function, we are already iterating the search space problem, vastly compounding its impact.

Worse, life function is observed to be based on algorithms and codes; which constitute functional, specific, complex information. Such algorithms and codes are observed to have but one empirically observed source: intelligent agents. (And, this is apparently for the excellent reason that chance processes run into the same isolated islands of function in a sea of non-functional configurations challenge.) Genetic algorithms and the like are not counter-examples, as they are in effect rather constrained hill-climbing searches, within a wider program that is already intelligently designed and functional. Often, the target is pre-specified and closeness of approach to the desired target is rewarded; i.e. they are premised on exactly the sort of foresighted purposiveness that Darwinian evolutionary processes, on pain of transformation into intelligently designed processes, cannot have.

After the origin of life hurdle, we may then briefly look at the challenge of breaking out into the wider genome space. 

For that, starting from the low-length genome corner above, we have to generate the required considerably larger genomes required to sustain novel major body plans at, e.g., the kingdom and phylum level.  This arguably initially requires moving from maybe 1 million to ~ 100 million base pairs. The 100 million base pair sub-space has in it about 2.714 * 10^69,897,000 configurations; that is, the search space problem has further exploded.

Thus, it is reasonable to at least consider whether the natural, chance + necessity causal factors that are often held to drive the origin and body plan level diversification of life are inadequate to explain the origin of such functionally specified complexity. Especially, given the routinely observed source of functionally specified, complex information: intelligent agents.

To further see what such "beyond imaginable" numbers mean, let us for the moment turn to the related point that most molecules of life show a certain "handedness," similar to the mirror-image shapes of left and right hands, and also we know that the resulting geometry is a critical issue in bio-functionality. So, as we may see in a recent Royal Society paper by Martin and Russell on the subject, "On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells," Section 6:

none of the [current abiogenesis] models have proposed a solution to one of the more vexing origin problems: chirality. Three-dimensional molecules such as sugars and amino acids can exist in two mirror-image forms, like left and right hands (chiros is Greek for hand). Any nonbiological synthesis of such molecules, as would have occurred before life arose, produces equal amounts of each type. Nonetheless, modern cells use exclusively left-handed amino acids and right-handed ribose sugars, and interference from the wrong kind shuts down biological reactions. How could chiral life arise in the presence of so much interference?

It's a serious problem, Orgel admits, but not an overwhelmingly serious one. Orgel suggests that one of several possible solutions may be chance, a frozen accident that brought together, and kept together, molecules of the right chirality. Such an accident is perhaps not so unlikely, says Martin, who calculates that a mixture of every possible left- and right-handed combination of a 25 amino acid peptide (amino acid chain) would weigh 25 kilograms. Any smaller sample is imperfect, he says. [Emphases added.]

COMMENT: Here, the attempt is made to exhaust the possible combinations of 25-acid-length peptides [protein components], to credibly arrive at the required bioactive components relative to life as we know it. This is of course essentially the project of shuffling though the available possible states to get to those that "work" at random, as Dembski in effect discusses as the threshold for complexity. Now, also, since Glycine is achiral, we have 39 possible monomers at each stage, and also from empirical studies of bond frequency for such amino acids only half of the bonds might be the "right" kind. Taking in the first only we are looking at 39^25 ~ 5.99*10^39 possible molecules, ~ 9.94*10^15 moles. (If we factor in bonding, that takes us to something like 78^25 possible molecular configuration states for our "25 kg ball.")

But, something is evidently and tellingly wrong with the "25 kg" estimate made by Martin. For, if we use a simplistic estimate of 100 AMU per amino acid monomer [4*C = 48, N = 14, 2*O = 32, just for starters, ignoring H], we see that a 25-acid molecule should have molecular mass ~ 2,500 AMU, thus molar mass 2,500 g [similar to the estimates used by TBO in TMLO]. But then, 9.94*10^15 mol would weigh in at ~ 2.49*10^16 kg. 1,000 kg is a tonne, so we are looking at ~2.5*10^13 tonnes, a rather large quantity and not one credible for a spongy mass of FeS at an undersea hydrothermal vent in a primordial ocean -- the suggested context for abiogenesis through chemical evolution being discussed. And, the issue compounds itself rapidly when we go to the other molecules needed to get life going, all of which have to be right geometrically and sequentially -- and in the right proximity, for biochemical activities to work. So, there are serious issues on the possibility of chemical evolution, which is antecedent to biological evolution. ( In turn, biological macroevolution meets similar difficulties of information generation other than by intelligent processes, as is ably discussed by Meyer and Lönnig, in two recent peer-reviewed papers.)

In short, DNA as observed in life forms, is plainly comfortably complex beyond the Dembski-type bound of sets of states reachable by random search strategies in the scope of matter and time that cosmologists often give for the observed universe. Plainly, then, DNA is a credible candidate for an observed bio-functionally specified, complex message from an intelligent agent. The same holds therefore, for the rest of the core machinery of the cell.

Observe, also, that we have not proposed an identity for such an agent, only inferred that it is credible that DNA be viewed as a message-entity; which is best explained through the logic of explanation as a signature of intelligent agency. Such an explanation is not a science-stopper either: e.g. it invites the onward project of reverse-engineering life, and forward engineering systems that take advantage of what we so discover in the information systems of life. For that matter, as with all scientific reasoning, it is defeatable, thus provisional: i.e., subject to correction in light of further empirical findings and logical/mathematical analysis.

Perhaps even more interesting is the observation by Hurst, Haig and Freeland, that the actual protein-forming code used by DNA is [near-] optimal. As Vogel reports (HT: Mike Gene) in the 1998 Science article "Tracking the History of the Genetic Code," Science [281: 329]:

. . . in 1991, evolutionary biologists Laurence Hurst of the University of Bath in England and David Haig of Harvard University showed that of all the possible codes made from the four bases and the 20 amino acids, the natural code is among the best at minimizing the effect of mutations. They found that single-base changes in a codon are likely to substitute a chemically similar amino acid and therefore make only minimal changes to the final protein.

Now [circa 1998] Hurst's graduate student Stephen Freeland at Cambridge University in England has taken the analysis a step farther by taking into account the kinds of mistakes that are most likely to occur. First, the bases fall into two size classes, and mutations that swap bases of similar size are more common than mutations that switch base sizes. Second, during protein synthesis the first and third members of a codon are much more likely to be misread than the second one. When those mistake frequencies are factored in, the natural code looks even better: Only one of a million randomly generated codes was more error-proof. [3] [Emphases added]

Fig B.1 The actual standard DNA code is in the top one-millionth or so of a random sample of codes, in capacity to buffer against deleterious mutations. (Adapted, Freeland et al, 2000. TIBS 25: 44 - 45. [HT: MG.])

As the pseudonymous Mike Gene then summarises, when various biosynthetic pathway restrictions [the codes seem to come from families sharing an initial letter] and better metrics of amino acid similarity are factored in, it is arguable that the code becomes essentially optimal. So, he poses the obvious logical question:

. . . the take home message from these studies, and several others, is that nature's code is very good at buffering against deleterious mutations. This theme nicely fits with many other findings that continue to underscore how cells have layers and layers of safeguards and proof-reading mechanisms to ensure minimal error rates. Thus, contrary to Miller's assertion, the "universal code" is easily explained from an ID perspective - if you have designed a code that is very good at buffering against deleterious mutations, why not reuse it again and again?

In short, not only is the DNA code a code that functions in an algorithmic context, but of the range of possible code assignments, the actual one we see seems very close to optimal against the impacts of random changes. Further, the codons themselves fall into a highly structured pattern, as "amino acids from the same biosynthetic pathway are generally assigned to codons sharing the same first base." [Taylor and Coates 1989, cited, Freeland SJ, Knight RD, Landweber LF, Hurst LD. 2000 in "Early fixation of an optimal genetic code." Mol Biol Evol 17(4):511-8. (HT: MG.)] That is, the DNA code itself is significantly non-random in how it assigns base pairs to amino acids. 

(But also, I must note that such suggests an inference: (a) the coding assignments are not driven by the mechanical necessity of the underlying chemistry of chaining either nucleic acids or proteins, and (b) they are not a matter of random chance. An observation of (c) a structured coding pattern tied to the one-stage-removed chemistry of synthesis of the amino acids that are components to be subsequently chained to form proteins therefore strongly supports that (d) the code is an intelligent act of an orderly-minded, purposeful designer. For, of the three key causal factors, if neither chance nor necessity is credibly decisive, that lends itself to the conclusion that intentional  choice (here, tied to a prior component assembly stage!) is at work. In short, intelligent design.)

Gene tellingly concludes: 

. . . there are two very good (and obvious) reasons for a designer to have employed the same code in bacteria and eukaryotes: 1) The code is extremely good at preventing deleterious amino acid substitutions and; 2) the shared code allows for the lateral transfer of genetic material and facilitates symbiotic unions. That Miller thought ID incapable of explaining the code, and Pace thought the shared code proved the common descent of bacteria and eukaryotes, only shows how an a priori commitment to non-teleological explanations creates a large intellectual blind spot.

Once these and other reasons why DNA is a credible candidate for a real message from an intelligent agent are on the table, we may then briefly address the usual objections:

1. Denying the validity of the sort of probability calculation used, e.g., by proposing that a fairly high fraction of random short RNA strands show catalytic effects. Often, this is joined to the idea that primitive life was so much less complex that it could have started by chance, e.g. in a so-called RNA world; which then builds up on itself until, we see life as we know it. (However, this has of course not as yet been observed. Second, the implied highly improbable spontaneous origin of the DNA's language and codes for proteins by random processes is simply passed over in silence. Also, this does not address the core issue: the creation of the OBSERVED complex, functional information system. For, DNA is based on a code stored in a class of molecules that are not just chemically catalytic, but drive a step-by-step controlled processing system that carries out the observed biochemical pathways of life using a large cluster of molecules that are themselves coded for in the DNA. (Cf. a special issue of the Journal Cell, on the observed cellular machines, linked here.) In short, this first objection is a resort to faith in unobserved, speculative pathways to life that dodges the twin thermodynamics and origin of information challenges. Besides, the islands of function in genomic space issue above is NOT a direct probability calculation, but a search-space and search resources exhaustion challenge.)
   
   
2. Inference to design is inherently "unscientific," as this inference violates the rules of science. In short, science is here being redefined as so-called "methodological naturalism." More or less, this boils down to claiming that science is the best evolutionary materialist account of the cosmos from hydrogen to humans. That is, it makes conformity to the theories/models of cosmological, then chemical, then biological then socio-cultural evolution the test of whether or not an idea is scientific. (This obviously and massively begs the question, and it is inaccurate to the history of modern science, which originated in C16 - 17 Europe through men who had been shaped by the Judaeo-Christian thought world, and therefore sought to understand the orderliness of the universe as God's handiwork: "thinking God's thoughts after him." Science, is better understood as an open-ended, provisional approach to knowledge through observation, theorising, experiment and debate among the community of the informed. As such, it has no proper basis for ruling out ahead of time any of the three generally known sources of cause: chance, regularities of nature, agency. [Also cf. AiG's remarks on the rules of science.])
   
   
3. Inference to design is unjustified because it is untestable, unless one has independent knowledge of the designer and what such an agent is likely to do. (This objection would carry greater force if it were not now so obviously a case of special pleading in the teeth of the implications of detecting FSCI as is discussed above. But also, thanks to Elliott Sober's confession, in a footnote in his 1999 Presidential lecture to the American Philosophical Association, "Testability," we see that this objection is more rhetorical than substantial: “To infer watchmaker from watch, you needn’t know exactly what the watchmaker had in mind; indeed, you don’t even have to know that the watch is a device for measuring time. Archaeologists sometimes unearth tools of unknown function, but still reasonably draw the inference that these things are, in fact, tools.” In short, we CAN properly infer to design from its objective traces in the entities being observed, without having to refer to independent knowledge of the designers, their intent and characteristics. So as long as, say, the search for extraterrestrial intelligence, SETI, is held to be scientific, the objectors are guilty of selective hyperskepticism. At a more serious level, this objection is based on arguing for Bayesian rather than Fisherian reasoning about using probability to eliminate chance hypotheses. But in fact, as Dembski summarises, the former predominates in real-world praxis: we set up a chance hypothesis as the null, then eliminate it if the observed cases fall into the rejection regions at some reasonable threshold. And for excellent reason: the latter raises a string of issues that in the end reveal its frequent impracticability and dependence on the former. Dembski's universal probability bound, of course, is a case in point of a "reasonable" yardstick for a rejection region -- one with greater warrant than the usual 0.05 or 0.01 thresholds used in the social sciences.)
   
   
4. Expanding the assumed scope of the universe beyond what we observe. In effect, it is claimed that (1) the currently observed universe is an arbitrarily restrictive scope, and (2) probably there is an in effect [or even actual] infinite wider universe as a whole, and (3) we are in that sub-universe that happened to be such that life emerged. In short, the speculated scope of the universe as a whole -- which has not been observed, let us emphasise -- is so large that it swamps out the odds above. (Notice the resort to faith in unseen proposed realities. More to the point, the Dembski-type bound is a measure of improbability that asserts that beyond a certain reasonable point, it is more credible to infer to intent than to spontaneous origin to explain functionally specific information, i.e. the threshold of "complexity." It is a matter of inconsistency and selective hyperskepticism to on the one hand routinely infer to design on encountering FSCI in a great many communicative contexts where the probabilities are similar [cf. above], but then insist that on the issue of DNA origin, the best answer "must be" that the universe as a whole is wider than we thought. Underneath, lurks the issue of worldviews, and the inference to a speculative, wider universe to keep evolutionary materialist views going. But, on such a metaphysical question, the proper approach is to use comparative difficulties across ALL live options. In short, the Dembski bound is an excellent filter of the point where the discussion crosses over -- often unacknowledged -- from observationally controlled science to metaphysical speculation!)
   
   
5. There are underlying, as yet undiscovered, laws of nature that force the emergence of life, i.e. life is not a random chance-driven event. That is, life is not contingent, so probability is irrelevant. (Notice the resort to faith in unobserved, yet to be discovered laws of nature. In effect, this concedes the point, and it raises interesting implications: where did such a strange law of nature come from? That leads to the issue under Case III below.)

Summarising, the first of these of course simply fails to address the issue, by substituting a simpler and arguably irrelevant, fundamentally unobserved model for empirically anchored science. The second and third attempt to rule design out of court by unjustifiably changing the rules of science, taking it out of the context of being an open-ended, open-minded, empirically controlled search for truth. At a more serious level, the third would also substitute a more difficult approach that is dependent on the one it objects to, as a basis for eliminating chance hypotheses. The fourth is an outright resort to speculative metaphysics on the nature of the cosmos as a whole, not science as such; for science must plainly be accountable to observations -- and the proposed infinite array of subuniverses model is plainly not so constrained. But, if we are constructing philosophical worldviews, the proper method is comparative difficulties: putting all the major live options on the table and seeing which is more factually adequate, coherent and powerful as an explanation. Once that is done, it is an obvious point that design is at least as credible as the unobserved quasi-infinite universe: we observe what intelligence does all the time, and we here have a case of a highly complex, biofunctionally specified molecule and associated molecular information processing system. The fifth, is simply a promissory note, as yet unredeemed after 50 years of active, heavily funded research in this and linked fields. It also has perhaps surprising implications, i.e. it immediately raises the question: why would the laws of nature force the origin of life on planets with the appropriate chemical and physical conditions?

These last two objections therefore also bleed over into Case III below, but first let us pause and address an extension of Case I:

C] Case II: Macroevolution and the Diversity of Life

Here, we move from the origin of life to its diversity as observed in the current world and as is generally inferred from the fossil record and geological dating schemes. (It is not my purpose here to challenge the generally accepted dating systems and their "standard" chronology. [Cf. ICR's summary remarks here for a start if you are interested in that secondary issue. Also cf. Wiens' remarks here from the Old Earth Creationist view, as well as J P Moreland, here, on the related Bible interpretation issues. The YEC view is summarised here, in a report on a debate: Ross/Lisle.] Nor is it my purpose to attempt to refute that at some significant level macroevolution may have happened across time. Only, let us take time to rethink the credibility of the claims made by the predominant school of thought on the origin of life.)

The underlying issue to be addressed, then, is that there is reason to infer that the observed and inferred diversity cannot credibly be accounted for on the basis of a fundamentally random process of genetic mutation and a selection filter. For, there is a need to generate FUNCTIONAL and highly complex genetic information that works in an integrated organism by chance processes in the context of blind natural forces. The reason for that, is the observation that this requires FSCI, and the claim that such can be generated through essentially random processes, is not credible. So, it is useful to first cite from Lönnig's recent [2004] paper on "Dynamic genomes, morphological stasis, and the origin of irreducible complexity."

Speaking of the horseshoe crab as an organism that seems to have been morphologically static across 250 million years of fossil record and on into the contemporary world, he notes:

examples like the horseshoe crab are by no means rare exceptions from the rule of gradually evolving life forms . . . In fact, we are literally surrounded by 'living fossils' in the present world of organisms when applying the term more inclusively as "an existing species whose similarity to ancient ancestral species indicates that very few morphological changes have occurred over a long period of geological time" [85] . . . . Now, since all these "old features", morphologically as well as molecularly, are still with us, the basic genetical questions should be addressed in the face of all the dynamic features of ever reshuffling and rearranging, shifting genomes, (a) why are these characters stable at all and (b) how is it possible to derive stable features from any given plant or animal species by mutations in their genomes? . . . .

A first hint for answering the questions . . . is perhaps also provided by Charles Darwin himself when he suggested the following sufficiency test for his theory [16]: "If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down." . . . Biochemist Michael J. Behe [5] has refined Darwin's statement by introducing and defining his concept of "irreducibly complex systems", specifying: "By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning" . . . [for example] (1) the cilium, (2) the bacterial flagellum with filament, hook and motor embedded in the membranes and cell wall and (3) the biochemistry of blood clotting in humans . . . .

One point is clear: granted that there are indeed many systems and/or correlated subsystems in biology, which have to be classified as irreducibly complex and that such systems are essentially involved in the formation of morphological characters of organisms, this would explain both, the regular abrupt appearance of new forms in the fossil record as well as their constancy over enormous periods of time. For, if "several well-matched, interacting parts that contribute to the basic function" are necessary for biochemical and/or anatomical systems to exist as functioning systems at all (because "the removal of any one of the parts causes the system to effectively cease functioning") such systems have to (1) originate in a non-gradual manner and (2) must remain constant as long as they are reproduced and exist. And this could mean no less than the enormous time periods mentioned for all the living fossils hinted at above. Moreover, an additional phenomenon would also be explained: (3) the equally abrupt disappearance of so many life forms in earth history . . . The reason why irreducibly complex systems would also behave in accord with point (3) is also nearly self-evident: if environmental conditions deteriorate so much for certain life forms (defined and specified by systems and/or subsystems of irreducible complexity), so that their very existence be in question, they could only adapt by integrating further correspondingly specified and useful parts into their overall organization, which prima facie could be an improbable process -- or perish . . . .

According to Behe and several other authors [5-7, 21-23, 53-60, 68, 86] the only adequate hypothesis so far known for the origin of irreducibly complex systems is intelligent design (ID) . . . in connection with Dembski's criterion of specified complexity . . . . "For something to exhibit specified complexity therefore means that it matches a conditionally independent pattern (i.e., specification) of low specificational complexity, but where the event corresponding to that pattern has a probability less than the universal probability bound and therefore high probabilistic complexity" [23]. For instance, regarding the origin of the bacterial flagellum, Dembski calculated a probability of 10^{^-234}[22].

Now, first, we must observe that Darwin's proposed test, on at least one major interpretation, is less generous than it first appears: "If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down." For, as Shapiro acidly but aptly noted, on the defects in such an appeal to bare possibility in defense of the RNA world hypothesis -- making a remark that, we observe, inadvertently also applies to his preferred metabolism first scenario -- that:

The analogy that comes to mind is that of a golfer, who having played a golf ball through an 18-hole course, then assumed that the ball could also play itself around the course in his absence. He had demonstrated the possibility of the event; it was only necessary to presume that some combination of natural forces (earthquakes, winds, tornadoes and floods, for example) could produce the same result, given enough time. No physical law need be broken for spontaneous RNA formation to happen, but the chances against it are so immense, that the suggestion implies that the non-living world had an innate desire to generate RNA. The majority of origin-of-life scientists who still support the RNA-first theory either accept this concept (implicitly, if not explicitly) or feel that the immensely unfavorable odds were simply overcome by good luck.

In short, there is a distinct difference and resulting massive, probability-based credibility gap between having components of an irreducibly complex,tightly integrated, information-rich functional system with available energy but no intelligence to direct the energy to construct the system, and getting by the happenstance of "lucky noise," to that system. That is, physical and logical possibility are not at all to be equated with probabilistic credibility -- especially when there are competing explanations on offer -- here, intelligent agency -- that routinely generate the sort of phenomenon being observed.

So, having duly noted this caveat, through reasoning within the generally accepted framework of the geological record, and using a classic abductive approach (If X, then otherwise puzzling facts F1, F2, . . . follow at once; so the facts support but do not prove explanation X; this is the core agenda of science, and its core epistemological characteristic) we can see that irreducible complexity and FSCI, working together, can explain major and otherwise unexplained [for 150 - 200 years] features of the fossil record of life. Of course, this sort of claim has not remained unchallenged, and in particular the case of the bacterial flagellum -- a cellular outboard motor that has an ion-driven rotor tied to a hooked filament, that drives the bacterium as it spins at up to upwards of 10,000 rpm -- has been a focus for debate.

On this, we can sum up the current score by again citing Peterson:

Behe's most famous example is the bacterial flagellum described above. If you take away the driveshaft from the flagellar motor, you do not end up with a motor that functions less well. You have a motor that does not function at all. All of the essential parts must be there, all at once, for the motor to perform its function of propelling the bacterium through liquid . . . . that is precisely what Darwinian evolution cannot accomplish. Darwinian evolution is by definition "blind." It cannot plan ahead and create parts that might be useful to assemble a biological machine in the future. For the machine to be assembled, all or nearly all the parts must already be there and be performing a function. Why must they already be performing a function? Because if a part does not confer a real, present advantage for the organism's survival or reproduction, Darwinian natural selection will not preserve the gene responsible for that part. In fact, according to Darwinian theory, that gene will actually be selected against. An organism that expends resources on building a part that is useless handicaps itself compared to other organisms that are not wasting resources, and will tend to get outcompeted . . . .

Behe the biochemist . . . search[ed] the relevant scientific journals, books, and proceedings of meetings to find out what the Darwinists had really proven about the origin of complex biochemical systems . . . . "There has never been a meeting, or a book, or a paper on details of the evolution of complex biochemical systems" . . . Behe, recalling the "fierce resistance" he encountered after the publication of Darwin's Black Box, remarks that much of it came from "Internet fans of Darwinism who claimed that, why, there were hundreds or thousands of research papers describing Darwinian evolution of irreducibly complex biochemical systems." Except that there aren't.

Well, this sent the Darwinians scrambling. Kenneth Miller, a biologist at Brown University who argues in favor of Darwinian evolution, made a splash when he announced (and he bolded the language in his article) that "the bacterial flagellum is not irreducibly complex." Miller cited a cellular structure known as the type III secretory system (TTSS) that allows certain bacteria to inject toxins through the cell walls of their hosts . . . .

But . . . the bubonic plague bacterium already has the full set of genes necessary to make a flagellum. Rather than making a flagellum, Y. pestis uses only part of the genes that are present to manufacture that . . . injector instead. As pointed out in a recent article by design theorist Stephen Meyer and microbiologist Scott Minnich (an expert on the flagellar system), the gene sequences suggest that "flagellar proteins arose first and those of the pump came later." If evolution was involved, the pump came from the motor, not the motor from the pump. Also, "the other thirty proteins in the flagellar motor (that are not present in the [pump]), are unique to the motor and are not found in any other living system." . . . In short, the proteins in the TTSS do not provide a "gradualist" Darwinian pathway to explain the step-by-step evolution of the irreducibly complex flagellar motor.

Further to this, Meyer's discussion of the Cambrian life revolution (which -- despite much rhetoric to the contrary -- evidently passed proper peer review by renowned scientists) in the same record shows that the underlying pattern of sudden diversification is particularly present and challenging for the Neo-Darwinian Theory [NDT] at the point where the record first shows a dramatic widening of the range of animal life at the highest level, the phylum, with dozens of basic body plans appearing within a fairly narrow temporal window in the record:

The Cambrian explosion represents a remarkable jump in the specified complexity or "complex specified information" (CSI) of the biological world. For over three billions years, the biological realm included little more than bacteria and algae (Brocks et al. 1999). Then, beginning about 570-565 million years ago (mya), the first complex multicellular organisms appeared in the rock strata, including sponges, cnidarians, and the peculiar Ediacaran biota (Grotzinger et al. 1995). Forty million years later, the Cambrian explosion occurred (Bowring et al. 1993) . . . One way to estimate the amount of new CSI that appeared with the Cambrian animals is to count the number of new cell types that emerged with them (Valentine 1995:91-93) . . . the more complex animals that appeared in the Cambrian (e.g., arthropods) would have required fifty or more cell types . . . New cell types require many new and specialized proteins. New proteins, in turn, require new genetic information. Thus an increase in the number of cell types implies (at a minimum) a considerable increase in the amount of specified genetic information. Molecular biologists have recently estimated that a minimally complex single-celled organism would require between 318 and 562 kilobase pairs of DNA to produce the proteins necessary to maintain life (Koonin 2000). More complex single cells might require upward of a million base pairs. Yet to build the proteins necessary to sustain a complex arthropod such as a trilobite would require orders of magnitude more coding instructions. The genome size of a modern arthropod, the fruitfly Drosophila melanogaster, is approximately 180 million base pairs (Gerhart & Kirschner 1997:121, Adams et al. 2000). Transitions from a single cell to colonies of cells to complex animals represent significant (and, in principle, measurable) increases in CSI . . . .

In order to explain the origin of the Cambrian animals, one must account not only for new proteins and cell types, but also for the origin of new body plans . . . Mutations in genes that are expressed late in the development of an organism will not affect the body plan. Mutations expressed early in development, however, could conceivably produce significant morphological change (Arthur 1997:21) . . . [but] processes of development are tightly integrated spatially and temporally such that changes early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream. For this reason, mutations will be much more likely to be deadly if they disrupt a functionally deeply-embedded structure such as a spinal column than if they affect more isolated anatomical features such as fingers (Kauffman 1995:200) . . . McDonald notes that genes that are observed to vary within natural populations do not lead to major adaptive changes, while genes that could cause major changes--the very stuff of macroevolution--apparently do not vary. In other words, mutations of the kind that macroevolution doesn't need (namely, viable genetic mutations in DNA expressed late in development) do occur, but those that it does need (namely, beneficial body plan mutations expressed early in development) apparently don't occur.6 [Emphases added. Cf a more easily readable (and also peer-reviewed) but longer discussion, with illustrations, here.]

Now, this analysis highlights a significant distinction we need to make: micro-evolutionary changes are late-developing, and do not affect the core body plan and its associated functions. Such mutations are indeed possible and are observed. But, when the mutations get to the fundamental level of changing body plans -- i.e. macro-evolution -- they face the implication that we are now disturbing the core of a tightly integrated system, and so the potential for destructive change is much higher. Consequently, the genes that control such core features are stabilised by a highly effective negative feedback effect: random changes strongly tend to eliminate themselves through loss of integrity of vital body functions.

In response, it is often claimed that sufficient microevolution accumulates across time to constitute macroevolution. But, what we "see" in the fossil record of the Cambrian rocks is just that innovation at the core levels coming first, and coming massively -- just the opposite of what the NDT model would lead us to expect. For, as Dan Peterson summarises in his recent article:

To take just one example, a well-known (and unsolved) problem for Darwinism is the Cambrian Explosion. As noted by Stephen Meyer in the book Debating Design, this event might be better called the Cambrian Information Explosion. For the first three billion years of life on Earth, only single-celled organisms such as bacteria and bluegreen algae existed. Then, approximately 570 million years ago, the first multi-cellular organisms, such as sponges, began to appear in the fossil record. About 40 million years later, an astonishing explosion of life took place. Within a narrow window of about 5 million years, "at least nineteen and perhaps as many as 35 phyla (of 40 total phyla) made their first appearance on Earth...." Meyer reminds us that "phyla constitute the highest categories in the animal kingdom, with each phylum exhibiting unique architecture, blueprint, or structural body plan." These high order, basic body plans include "mollusks (squids and shellfish), arthropods (crustaceans, insects, and trilobites), and chordates, the phylum to which all vertebrates belong."

These new, fundamental body plans appeared all at once, and without the expected Darwinian intermediate forms.

In addition, we should observe in passing that there is also an underlying problem with the commonly encountered natural selection model, in which small variations confer significant cumulative advantages in populations,and cumulate to give the large changes that would constitute body-plan level macroevolution. To see this, let us excerpt a typical definition of natural selection:

Natural selection is the process by which favorable heritable traits become more common in successive generations of a population of reproducing organisms, and unfavorable heritable traits become less common. Natural selection acts on the phenotype, or the observable characteristics of an organism, such that individuals with favorable phenotypes are more likely to survive and reproduce than those with less favorable phenotypes. The phenotype's genetic basis . . . will increase in frequency over the following generations. Over time, this process can result in adaptations that specialize organisms for particular ecological niches and may eventually result in the emergence of new species. In other words, natural selection is the mechanism by which evolution may take place in a population of a specific organism. [Emphases added.]

From this, we may immediately observe that natural selection is envisioned as a probabilistic culler of competing sub-populations with varying adaptations coming from another source [usually some form of chance-based variation]. That is, it does not cause the actual variation, it is only a term that summarises differences in likelihood of survival and reproduction and possibly resulting cumulative effects on populations across time. So, when innovations in life-forms require the origin of functionally specific, information-rich organised complexity, we are back to some form of chance variation to explain it, and soon run right back into the FSCI-origination barrier.

Moreover, there are linked issues with the related gambler's ruin challenge (as is discussed here). 

For, if a given selection advantage is small and the absolute numbers of the sub-population with the innovation are also relatively low, most of the time, such an innovation will simply be lost due to the overwhelming effects of mere chance on odds of survival and reproduction. In other words, one has to have enough population resources to "spend" for long enough to get to the long-run point where modest differential effects will pay off to one's advantage. And, if we take isolation to a niche without competition as a typical example by which such innovations will have a good chance to grow into a viable sub-population that can then migrate back and compete with then dominate over the original population, we still have not accounted for the rise of information-rich organically coherent innovations, especially at that core body-plan level which expresses itself in the vulnerable early phases of the embryological development process. 

Pulling the strands of analysis together, we may see that, in light of the evident FSCI embedded in life-forms at cellular level, and its implications, the NDT has a major challenge accounting precisely for the macro-evolution that it sets out to explain. But, by sharp contrast, the concepts of irreducible complexity and FSCI/CSI leading to design as a new paradigm are in fact able to relatively easily account for these phenomena, within the generally accepted geochronological and fossil frameworks. 

Thus, it is fair comment to observe that the design inference seems to better explain the generally accepted framework than the dominant paradigm, NDT. 

This is in addition to the basic fact that, strictly, the NDT does not address the origin of life -- a situation where the dominant school in biology (as seen above), after 50 years of various models, still struggles to find a robust, empirically adequate model. So, whatever objections may be made -- and are often made, sadly, to the point of evident workplace harassment in some cases [cf. US Congress Committee staff investigation summary here and main report here with appendix here; also the earlier OSC Letter here as well as the Klinghoffer reports that publicly broke and now follow up the story] -- this basic contrast of explanatory failure/success should be soberly reckoned with.

D] Case III: The evidently fine-tuned cosmos

In this section, we focus on the underlying point Cicero was making in his remarks cited above, at the head of this web page: the complex arrangement of the cosmos as a whole is credibly a signature of agency as the force that brought it into being. 

To address this, we will turn to cosmological finetuning: how the life-facilitating underlying physics of our observed cosmos seems to exhibit fine-tuned organised complexity. In effect, if we were to give an outline description of the physical laws, constants and ratios for the observed cosmos, we would find a fairly complex, quite mathematically elegant set of delicately balanced information. For, if we were to start from the values we observe then perturb them slightly [just how much depends on the particular relationship or parameter], for many, many cases, the resulting changed cosmos would be radically unfriendly to life as we observe it. 

To get an idea of the degree of functionally specified complex information involved in that organised complexity, we can consider just four fine-tuned parameters of the observed cosmos and their precision and estimate the number of bits required to define the numbers, using the relationship that lg[a]/lg [b] = log_b[a]:

Fine Tuning of the Physical Constants of the Universe

Parameter	Max. Deviation*	Estimated number of "required" bits
Ratio of Electrons:Protons	1:1037	123
Ratio of Electromagnetic Force:Gravity	1:1040	133
Expansion Rate of Universe	1:1055	183
Mass of Universe1	1:1059	196
Cosmological Constant	1:10120	399
*These numbers represent the maximum deviation from the accepted values, that would either prevent the universe from existing now, not having matter, or be unsuitable for any atom-based form of life.  (Cf. below for details.)		TOTAL: 1,034

Table D.1:  Degree of Fine-tuning of four key parameters of the observed cosmos. [Adapted: Deem, R, of RTB. Ref 1 links onward to Prof Ed White of UCLA. The Cosmological constant is in effect the requisite energy density of free space to compensate for the "missing" matter density, consistent with the observed accelerating expansion of the universe.]

Thus, just these four initial fine-tuned parameters would require 1,034 bits of information capacity to store them, whilst there are dozens of other parameters and an entire framework of physics for them to fit in. Now, too, 500 to 1,000 bits express a configuration space with ~ 3.27*10^150 to *10^301 cells. That is, we are looking at a clear instance of functionally specified, complex information[FSCI]; as, to get just these four parameters right at the same time, we would need to be in just the right one of ~1.84*10^311 cells. 

But, we have got a bit ahead of ourselves and we need to pause to discuss what "fine tuning" means.

So, since, by common consent, it is he who first identified a major cosmological finetuning issue, it is appropriate to give pride of place to a cite from the late, great Sir Fred Hoyle:

From 1953 onward, Willy Fowler and I have always been intrigued by the remarkable relation of the 7.65 MeV energy level in the nucleus of 12 C to the 7.12 MeV level in 16 O. If you wanted to produce carbon and oxygen in roughly equal quantities by stellar nucleosynthesis, these are the two levels you would have to fix, and your fixing would have to be just where these levels are actually found to be. Another put-up job? Following the above argument, I am inclined to think so. A common sense interpretation of the facts suggests that a super intellect has "monkeyed" with the physics as well as the chemistry and biology, and there are no blind forces worth speaking about in nature. [F. Hoyle, Annual Review of Astronomy and Astrophysics, 20 (1982): 16.Cited, Bradley, in "Is There Scientific Evidence for the Existence of God? How the Recent Discoveries Support a Designed Universe". Emphasis added.]

Why is this particular balance so important?

Astrophysicist Hugh Ross, in his The Creator and the Cosmos (Colorado Springs: NavPress, 1993), explains -- based on the conditions and consequences for nuclear fusion reactions in stars -- that: "In the late 1970's and early 1980's, Fred Hoyle discovered that an incredible fine tuning of the nuclear ground state energies for helium, beryllium, carbon and oxygen was necessary for any kind of life to exist. The ground state energies for these elements cannot be higher or lower with respect to each other by more than 4% without yielding a universe with insufficient oxygen or carbon for life." [p. 107.]

Later, Ross notes that "[b]oron and silicon are the only other elements on which complex molecules can be based, but boron is extremely rare, and silicon can hold together no more than about a hundred amino acids. Given the constraints of physics and chemistry, we can reasonably assume that life must be carbon-based." [p.125.] He also notes that:

there is one life-essential heavy element that is not made by supernovae, fluorine. It is made only on . . . the surfaces of white dwarf stars bound into stellar systems with larger stellar companions. The larger companion must orbit closely enough . . . that it loses sufficient material to the white dwarf . . . [on whose surface] some of the material is converted into fluorine. Then the white dwarf must lose this fluoridated material into interstallar space . . . . The location, types, rates and timings of both supernova events and white dwarf binaries severely constrains the possibility of finding a life support site. [p.125.]

In short, within the generally accepted, Big Bang theory-derived framework for the origin of the cosmos [here, string landscapes, brane cosmologies and the like are viewed as so far more or less empirically untested extensions -- and indeed, one of the latest "hot ideas," colliding branes that yield expanding universes, according to Linde et al, 2001, would require that "the branes [are]  to be parallel to each other with an accuracy better than 10^{-60} on a scale 10^{30} times greater than the distance between the branes"], the conditions for creating the elements foundational to biological life as we know it are quite constrained. Similarly, the underlying forces in the cosmos are delicately balanced indeed. For, as William Lane Craig summarised in brief:

Changes in the gravitational or electromagnetic forces, for example, by only one part in 10^40 would preclude the existence of stars like our sun, making life impossible. Changes in the speed of the expansion by only one part in a million million when the temperature of the universe was 10^10 degrees would have either resulted in the universe's recollapse long ago, or precluded galaxies' condensing, in both cases making life impossible. The present temperature of the universe is so isotropic [uniform] that Roger Penrose of Oxford calculates that "the accuracy of the Creator's aim," when he selected this world from the set of physically possible ones, must have been on the order of one part in 10^10(^124). [That is, 1 followed by 10^124 zeros, far more than there are atoms in the observed universe.]

Altogether, there are dozens of such in aggregate finely balanced parameters, perhaps the most finely balanced being the so-called cosmological constant, which seems to be accurate to better than one part in 10^100. Similarly, as Ross also reports, "[u]nless the number of electrons is equivalent to the number of protons to an accuracy of one part in 10^37, or better, electromagnetic forces in the universe would have so overcome gravitational forces that galaxies, stars, and planets never would have formed." [p. 109.] But, perhaps the most significant overall observation is due to John Leslie:

One striking thing about the fine tuning is that a force strength or a particle mass often appears to require accurate tuning for several reasons at once. Look at electromagnetism. Electromagnetism seems to require tuning for there to be any clear-cut distinction between matter and radiation; for stars to burn neither too fast nor too slowly for life’s requirements; for protons to be stable; for complex chemistry to be possible; for chemical changes not to be extremely sluggish; and for carbon synthesis inside stars (carbon being quite probably crucial to life). Universes all obeying the same fundamental laws could still differ in the strengths of their physical forces, as was explained earlier, and random variations in electromagnetism from universe to universe might then ensure that it took on any particular strength sooner or later. Yet how could they possibly account for the fact that the same one strength satisfied many potentially conflicting requirements, each of them a requirement for impressively accurate tuning? [Our Place in the Cosmos, 1998 (courtesy Wayback Machine) Emphases added.]

So robust is this pattern of convergent, integrated, finely balanced parameters, that the majority of scientific cosmologists currently accept that the finetuning is real; the question is to account for it. Nor, plainly, does this ultimately rely on there being just one cosmos, i.e. the currently observed one. For, as he also notes, through the metaphor of the fly on the wall:

. . . the need for such explanations does not depend on any estimate of how many universes would be observer-permitting, out of the entire field of possible universes. Claiming that our universe is ‘fine tuned for observers’, we base our claim on how life’s evolution would apparently have been rendered utterly impossible by comparatively minor alterations in physical force strengths, elementary particle masses and so forth. There is no need for us to ask whether very great alterations in these affairs would have rendered it fully possible once more, let alone whether physical worlds conforming to very different laws could have been observer-permitting without being in any way fine tuned. Here it can be useful to think of a fly on a wall, surrounded by an empty region. A bullet hits the fly Two explanations suggest themselves. Perhaps many bullets are hitting the wall or perhaps a marksman fired the bullet. There is no need to ask whether distant areas of the wall, or other quite different walls, are covered with flies so that more or less any bullet striking there would have hit one. The important point is that the local area contains just the one fly. [Emphasis his.]

Walter Bradley gives the wider context, by laying out some general "engineering requisites" for a life-habitable universe; design specifications, so to speak:

• Order to provide the stable environment that is conducive to the development of life, but with just enough chaotic behavior to provide a driving force for change.
  
• Sufficient chemical stability and elemental diversity to build the complex molecules necessary for essential life functions: processing energy, storing information, and replicating. A universe of just hydrogen and helium will not "work."
  
• Predictability in chemical reactions, allowing compounds to form from the various elements.
  
• A "universal connector," an element that is essential for the molecules of life. It must have the chemical property that permits it to react readily with almost all other elements, forming bonds that are stable, but not too stable, so disassembly is also possible. Carbon is the only element in our periodic chart that satisfies this requirement.
  
• A "universal solvent" in which the chemistry of life can unfold. Since chemical reactions are too slow in the solid state, and complex life would not likely be sustained as a gas, there is a need for a liquid element or compound that readily dissolves both the reactants and the reaction products essential to living systems: namely, a liquid with the properties of water. [Added note: Water requires both hydrogen and oxygen.]
  
• A stable source of energy to sustain living systems in which there must be photons from the sun with sufficient energy to drive organic, chemical reactions, but not so energetic as to destroy organic molecules (as in the case of highly energetic ultraviolet radiation).
  
• A means of transporting the energy from the source (like our sun) to the place where chemical reactions occur in the solvent (like water on Earth) must be available. In the process, there must be minimal losses in transmission if the energy is to be utilized efficiently. [Emphases added.]

Robert C. Koons, in discussing "Post-Agnostic Science," therefore draws out the logical skeleton of the associated design inference. So, he argues, first to an intelligence, and that could include a system of nature that is in itself intelligent, then onward to the required nature of such an agent, one capable of and actually creating a cosmos. (But note that, while it is compatible with such a worldview, this inference to explanation of the finetuning of the cosmos argument is not at all the same as an inference to a specifically theistic -- much less, the Judaeo-Christian -- Creator. That broader question goes into broader philosophical, historical, biblical and theological rather than strictly scientific issues, and so most design thinkers hold these to be strictly beyond the remit of science proper. Of course, though, in a science-dominated age it is important to be able to see and show that the actual scientific data are compatible with such a theistic view. [Cf. Ross's critique of the general design theory view on these points, here.])

Specifically, Koons argues:

1] The physical constants of the cosmos take anthropic values [that is, those conducive to C-based, intelligent life].

2] This coincidence must have a causal explanation (we set aside for the moment the possibility of a chance explanation through the many-worlds hypothesis [cf. on this, the points raised by Leslie as cited above; noting too that such a wider "multiverse" is speculative rather than observationally anchored]). 

________________________________________________

3] Therefore, the constants take the values that they do because these values are anthropic (i.e., because they cause the conditions needed for life).

4] Therefore, the purpose of the values of these constants is to permit the development of life (using the aetiological definition of purpose).

5] Therefore, the values of these constants are the purposive effects of an intelligent agent (using the minimalist conception of agency).

6] Therefore, the cosmos has been created.

Now, of course, objections and alternatives have been put forth. These are of course fairly easy to find on the Internet, as the compatibility of the above line of reasoning with theistic worldviews rubs a raw nerve in many secularist quarters. (Counters to these objections can also be found, and so forth.)

Here, we can briefly summarise several typical objections and associated questions, and note briefly on them:

1. Multiple sub-universes: It is asserted that there is an at least quasi-infinite array of sub-universes that have popped up out of the underlying eternal universe as a whole, with randomly scattered parameters. So, we are in the one that just happened to get lucky: somebody will as a rule win a lottery! We should therefore not be surprised, and there is nothing more to "explain." (Of course, this first resorts to suggesting that there is/must be a vast, unobserved wider universe as a whole. So, right from the start it moves into the province of a worldview claim; it is not at all properly a scientific theory. It therefore cannot fairly exclude other worldview claims from the table of comparative difficulties analysis, nor can it stand apart from the other claims of the underlying worldview it attempts to save: that morally indefensible and factually inadequate and logically self-defeating naturalistic philosophical system that can be best described as evolutionary materialism. Moreover, following Koons, we may paraphrase Leslie tellingly: let us think of a miles-long wall, some of whose sections are actually carpeted with flies; but there is a 100-yard or so stretch with just one fly. Then, suddenly, a bullet hits it. Is it more credible to think that the fly is just monstrously unlucky, or do we celebrate the marksmanship of the hidden shooter? That is, in the end, a locally rare and finetuned possibility is just as wondrous as a globally finetuned one.)
   
   
2. But, Science cannot think in terms of the supernatural: That is, "science" is here redefined in terms of so-called methodological naturalism, which in effect implies that a claim can only be deemed scientific if it explains in terms compatible with the materialist's sequence of postulated evolutions: cosmological, chemical, biological, socio-cultural. (That is not only demonstrably historically inaccurate, but it also reduces to: imposition of philosophical materialism by implication. In short, it reduces to philosophical materialism disguised as science. Nor is it fair: in fact the distinction the inference to design makes, strictly is to selecting intelligent agency from the three-way split: chance, regularity of nature [aka necessity], agency. If FSCI is a signature of intelligence, then its detection points us to intelligence, and so we should not resort to intellectual gerrymandering to rule out such possibilities.)
   
   
3. "Chance" is good enough, we just plain got lucky: In effect, odds mean nothing as SOMEONE has to win a lottery, and there is probably much more universe out there than we happen to see just now. (First, not all lotteries are winnable, and cosmologically evolving a life-habitable universe that then forms life is not set up to deliver a winner, on pain of reducing to yet another design inference -- cf. Leslie's argument above on the point that the cosmos is designed to get to life, even through a random array of sub-cosmi. But, of course, the point of the fly on the wall analogy is that, a locally rare and finetuned possibility is just as wondrous as a globally rare one. More to the point, the argument self-refutes through its underlying inconsistency: routinely, in the face of the logical possibility that all apparent messages we have ever decoded are simply lucky noise, we infer to intent as the explanation of many things, once they exhibit FSCI: in effect, we take the "welcome to Wales sign" made out of arranged stones seriously, and do not dismiss it as a quirk of geology. In short, the selective resort to "chance" to explain some of the most complex and functionally specific entities we observe is driven by a worldview commitment, not a consistent pattern of reasoning. So, the objector first needs to stop being selectively hyperskeptical, and should fairly address the comparative difficulties problems of his/her own worldview.)
   
   
4. The "probabilities"/"Sensitivities" are not credible: usually, this is said by, say challenging the fineness of the balance, perhaps by asserting that some of the parameters may be linked, or that they are driven by an underlying regularity, one that is not as yet discovered. It may even be asserted that the scope of the universe as a whole is such that the size swamps the probabilities in the "little" sub-cosmos we can see. (The first two of these face the problem that while say the Carbon-Oxygen balance is of the order of several percent, the ratio of electrons to protons is unity to within 10^-37, and other parameters that simply do not depend on the accident of how many electrons and protons exist, are even finer. An underlying regularity that drives cosmic values and parameters to such fine balances of course itself raises the issue of design. And, not only is the proposed wider universe concept not empirically controlled, thus strictly a philosophical issue; but also it is manifestly an after the fact ad hoc assertion driven by the discovery of the finetuning.)
   
   
5. You can't objectively assign "probabilities": First, the argument strictly speaking turns on sensitivities, not probabilities-- we have dozens of parameters, which are locally quite sensitive in aggregate, i.e. slight [or modest in some cases] changes relative to the current values will trigger radical shifts away from the sort of life-habitable cosmos we observe. Further, as Leslie has noted, in some cases the Goldilocks zone values are such as meet converging constraints. That gives rise to the intuitions that we are looking at complex, co-adapted components of a harmonious, functional, information-rich whole. So we see Robin Collins observing, in the just linked:"Suppose we went on a mission to Mars, and found a domed structure in which everything was set up just right for life to exist . . . Would we draw the conclusion that it just happened to form by chance? Certainly not . . . .  The universe is analogous to such a "biosphere," according to recent findings in physics. Almost everything about the basic structure of the universe--for example, the fundamental laws and parameters of physics and the initial distribution of matter and energy--is balanced on a razor's edge for life to occur. As the eminent Princeton physicist Freeman Dyson notes, "There are many . . . lucky accidents in physics. Without such accidents, water could not exist as liquid, chains of carbon atoms could not form complex organic molecules, and hydrogen atoms could not form breakable bridges between molecules" (p. 251)--in short, life as we know it would be impossible." So, independent of whether or not we accept the probability estimates that are often made, the fine-tuning argument in the main has telling force.
   
   
6. Can one assign reasonable Probabilities? Yes. Where the value of a variable is not otherwise constrained across a relevant range, one may use the Laplace criterion of indifference to assign probabilities. In effect, since a die may take any one of six values, in absence of other constraints, the credible probability of each outcome is 1/6. Similarly, where we have no reason to assume otherwise, the fact that relevant cosmological parameters may for all we know vary across a given range may be converted into a reasonable (though of course provisional -- as with many things in science!) probability estimate. So, for instance,  the Cosmological Constant [considered to be a metric of the energy density of empty space, which triggers corresponding rates of expansion of space itself], there are good physical science reasons [i.e. inter alia Einsteinian General Relativity as applied to cosmology] to estimate that the credible possible range is 10^53 times the range that is life-accommodating, and there is no known constraint otherwise on the value. Thus, it is reasonable to apply indifference to the provisionally known possible range to infer a probability of being in the Goldilocks zone of 1 in 10^53. Relative to basic principles of probability reasoning and to the general provisionality of science, it is therefore reasonable to infer that this is an identifiable, reasonably definable value. (Cf Collins' discussion, for more details.)
   
   
7. There are/may be underlying forcing laws or circumstances: It is possible that as yet undiscovered physics may lead us to see that the values in question are more or less as they "have" to be. (However, such a "theory of everything" would itself imply exquisitely balanced functionally specific complexity in the cosmos as a whole, i.e. it is itself a prospect that would lead straight to the issue of design as its explanation.)
   
   
8. What about radically different forms of life: We do not know for certain that life must be based on carbon chemistry, so perhaps there is some strange configuration of matter and/or energy (or perhaps, borrowing from the Avida experiments, information) that can be called "life" without being based on the chemistry of carbon and related atoms. (Indeed, theists would immediately agree: spirit is a way that life can exist without being tied down to atoms and molecules! They would also immediately agree that information and -- more fundamentally -- mind are key components of intelligent life. So, this point may lead in surprising directions. But more on the direct point, the proposal is again highly speculative and ad hoc, once it was seen that the cosmos seems designed for life as we know it.)
   
   
9. Naturalistic Anthropic Principles: Perhaps, the most important version, the Weak form [WAP] asserts that intelligent life can only exist in a cosmos that has properties permitting their origin and existence. Then, it is inferred, if we are here, we should not be surprised that the parameters are so tight: if they were not met, we would not be here to wonder about it. (Now, of course, if the universe did not permit life like ours, we would not be here to see that we do not exist. But that still leaves open the implications of the point that the cosmos in which we do exist is exquisitely finely tuned for that existence, at least on a local basis. That is, we are simply back to the fly on the wall gets swatted by a bullet example; it is still wondrous and raises the question of marksmanship and intent as the best explanation.)

While of course the above is (relatively speaking!) brief and basic, it brings into focus the key point that the evident finetuning of the cosmos for intelligent life puts the issue of design squarely on the table. And, once that is on the table, since we are dealing with the origins of the universe as we know it, with remarkable finetuning and at a defined time in the past, some 13.7 BYA by current estimates.

The alternative to a Creator as the explanation, it soon turns out, is a speculative wider cosmos as a whole that is eternal and necessary. Once that has been suggested -- often under the label "science" though it is properly speculative metaphysics -- we then hear the classic challenge: God of the gaps fallacy! [Cf. here on the arguments to/against God.]

To that, let us now turn:

E] Broadening the Issue: Persistent "Gaps," Man, Nature, Science and Worldviews

"God of the Gaps!"

At the mere mention of the term -- one dripping with memories of now-filled-in "gaps" in scientific explanations that were once used as ill-advised "proofs" or "evidences" of God's existence, many thinkers (especially some theistic ones) wish to look no further. Thus, under this banner, the issue of inference to design as discussed so far is then brushed aside as "obviously not proper science." That is, in large part through the rhetorical power of the phrase, God of the gaps, the attempted redefinition of science as methodological naturalism -- in effect "the best evolutionary materialist account of the cosmos, from hydrogen to humans" -- has far too often been allowed to prevail without facing squarely (much less, having to satisfactorily work out in detail) the many thorny challenges that lurk in the underlying demarcation problem.

But, in fact, not only across the past 350 years but currently, it is simply not accurate nor justifiable to reduce science to such terms. For, it is abundantly warranted by the history of the rise of modern science, and by contemporary praxis, to accept the more traditional -- and less philosophically loaded -- definition of science, such as we may easily read in high-quality dictionaries:

science: a branch of knowledge conducted on objective principles involving the systematized observation of and experiment with phenomena, esp. concerned with the material and functions of the physical universe. [Concise Oxford, 1990 -- and yes, they used the "z" Virginia!]

scientific method: principles and procedures for the systematic pursuit of knowledge [”the body of truth, information and principles acquired by mankind”] involving the recognition and formulation of a problem, the collection of data through observation and experiment, and the formulation and testing of hypotheses. [Webster's 7th Collegiate, 1965]

Further to this, not only in science but also in wider worldview analysis, we are not dealing with that mythical holy grail: proof beyond rational dispute. Instead, we must grapple with the messy world of creative abductive inferences to explanations and provisional warrant in light of the challenge of comparative difficulties. That is, serious explanations must face the three-headed issue of explanatory adequacy directly and as compared with live option alternatives:

(1) adequacy relative to the material facts -- those that make a difference to the conclusion;

(2) coherence: logical consistency without undue circularity; and,

(3) power: elegant simplicity as opposed to being either simplistic or an ad hoc patchwork.

Also, in the end we think as humans, beings who inevitably wonder about how we came to be here; beings who have to use and rely on our minds to think about such problems; beings who find ourselves sensing a duty to be honest and fair-minded in how we think about these things.

That this is not just an academic exercise is aptly illustrated by the sad course of events surrounding the evolution of Kansas Board of Education state science standards (and in particular the definition of science), from about 1999 to the present. For instance, we may contrast two alternative definitions of science, the first a radical evolutionary materialist agenda-driven redefinition attempt from 2001, the second, a now unfortunately defeated attempted corrective from 2005; which was based on a more traditional, historically and philosophically well-warranted understanding similar to those cited just above:

2001 Definition: “Science is the human activity of seeking natural explanations of the world around us.”

2005 Definition: “Science is a systematic method of continuing investigation, that uses observation, hypothesis testing, measurement, experimentation, logical argument and theory building, to lead to more adequate explanations of natural phenomena.” [Emphases added.]

Sadly, the 2001 radical redefinition (NB: more or less reimposed, circa 2007: "Science is a human activity of systematically seeking natural explanations for what we observe in the world around us" [cf p. xii here]) is an implicit and improper imposition of materialism in the name of science. For, it was immemorial in the days of Plato's The Laws Book X, that what in our day Monod termed "chance and necessity" do not exhaust the list of credible fundamental causal factors. As, what Plato termed "art" -- i.e. intelligent action --  is just as much an empirically observed  and possible causal factor; including specifically on origins. So, we must not a priori rule out possible causal factors simply because certain possible candidates for the actual cause of what we see may not fit comfortably with our worldview and associated ideological agendas. At least, if science is to retain the fundamental mission and vision that it is an empirically anchored, unfettered, open-ended and open-minded search for the truth about our universe based on observation, hypothesis, predictions, experimental/observational testing and objective reasoned argument.

But, sadly, in the 2001 redefinition "natural" is held to contrast with "supernatural," with the highly relevant, longstanding alternative contrast: nature/art being passed over in a rhetorically convenient, strawman-shaped silence. So, by making a tendentious contrast (often under the guise that science "must" apply the rule of so-called "methodological naturalism"), the idea is smuggled in that inference to design is inescapably or at least invariably about bringing in an improper, empirically unsupported inference to the supernatural. [Cf. typical rationales for the methodological naturalism rule here and here, a corrective rebuttal to such views here and here, a related discussion of its metaphysical connexions here, and also Plantinga's somewhat tangential but enriching discussion here and here. This discussion on a proposed successor, methodological neutralism, is also well worth a read.] 

A further illustration of what is going on can be seen from the current US National Academy of Sciences update to/version of their booklet, Science, Evolution and Creationism, p. 10, where they provide a contextualised definition of science. 

Standing by itself, the 2008 NAS definition is generally reasonable (insofar as any "simple" definition of so diverse a phenomenon as science is at all possible):

Definition of Science

The use of evidence to construct testable explanations and predictions of natural phenomena, as well as the knowledge generated through this process. [US NAS, 2008]

This is fine, insofar as it goes [on what is probably better termed Natural Science]. It closely parallels the high quality dictionaries cited above; and, for that  matter, the 2005 Kansas definition. What is not so fine, however, is what happens in its immediate context; which is meant to control how the definition is understood and used. Specifically, in the paragraph leading up to the just cited definition, we may read:

In science, explanations must be based on naturally occurring phenomena. Natural causes are, in principle, reproducible and therefore can be checked independently by others. If explanations are based on purported forces that are outside of nature, scientists have no way of either confirming or disproving those explanations. Any scientific explanation has to be testable — there must be possible observational consequences that could support the idea but also ones that could refute it. Unless a proposed explanation is framed in a way that some observational evidence could potentially count against it, that explanation cannot be subjected to scientific testing. [Emphases added.]

But of course, the very NAS scientists themselves provide instances of an alternative to forces tracing to chance and/or mechanical necessity: they are intelligent, creative agents who act into the empirical world in ways that leave empirically detectable and testable traces. (Indeed, when such scientists set up an experiment then test for the results of their interventions, they are not only studying natural causes and phenomena, but also what intelligent investigators have artificially induced; confident that there are underlying natural regularities that will come out, even in artificially selected and set up circumstances. Such regularities would include for instance, the probability distributions of chance forces at work: flat, reverse-J, U, "bell-shaped," Gaussian, binomial, Poisson, Weibull, etc. And, the open assertion or implicit assumption that all such intelligences "must" trace ultimately to chance and/or necessity acting within a materialistic cosmos, is a debatable philosophical position on  the remote and unobserved past history of our cosmos; not at all an established scientific "fact" on the level of direct and repeatable observations that have led to the conclusion that the planets orbit the sun. [Cf. here for a current instance of this unwarranted assertion, and below for the crucially important distinction between operational and origins studies in science.] )

In short, we see here yet another saddening illustration of the subtly fallacious, censoring insertion of the dichotomy: natural/ supernatural, in the teeth of the obvious alternative: natural/ artificial. And, that, in a general situation where this precise alternative is on the table and is much discussed; courtesy the efforts of the design thinkers. So, the failure to frankly face and objectively engage that alternative is a telling, prejudicial suppression of materially relevant evidence and views. Such is inexcusable on the part of scientists and educators who are presumably dedicated to discovering and communicating the truth about the world, based on empirical observation and/or experiment, resulting collected evidence and inferred provisional best explanations of those credible empirical facts.

The US National Science Teachers Association [NSTA] as of July 2000, and over the signature of its Board of Directors, makes the same question-begging imposition of naturalism in its definition of the nature of science for educational purposes:

All those involved with science teaching and learning should have a common, accurate view of the nature of science. Science is characterized by the systematic gathering of information through various forms of direct and indirect observations and the testing of this information by methods including, but not limited to, experimentation. The principal product of science is knowledge in the form of naturalistic concepts and the laws and theories related to those concepts . . . . science, along with its methods, explanations and generalizations, must be the sole focus of instruction in science classes to the exclusion of all non-scientific or pseudoscientific methods, explanations, generalizations and products . . . .

Although no single universal step-by-step scientific method captures the complexity of doing science, a number of shared values and perspectives characterize a scientific approach to understanding nature. Among these are a demand for naturalistic explanations supported by empirical evidence that are, at least in principle, testable against the natural world. Other shared elements include observations, rational argument, inference, skepticism, peer review and replicability of work . . . .

Science, by definition, is limited to naturalistic methods and explanations and, as such, is precluded from using supernatural elements in the production of scientific knowledge. [Emphases added.]

By strongest contrast with the above attempted dismissals by the NAS and NSTA et al, the design inference is an induction made based on a well supported empirical observation: intelligent agents act into our world, and when they do so they often leave characteristic signs of art-ificial -- or, intelligent -- action; such as functionally specified, complex information.

Notice again, as we are swimming against the tide here: on empirical evidence and empirically reliable well-tested signs, we may properly and reasonably  contrast natural causes traceable to chance and/or mechanical necessity from intelligent or artificial -- as opposed to "supernatural" [that, is an intentionally polarising and denigratory strawman caricature] -- causes. On the strength of this very well-supported observation, and the common-sense principle that "like causes like," it is plainly an empirically well justified and properly scientific induction to infer from such observed signs to the action of such agents; regardless of possible onward worldview level implications and debates -- which it is no business of science to censor itself over. 

Arguably, the impact of such "methodological naturalism" as we have just seen is to subtly establish evolutionary materialistic Secular Humanism as a de facto, functional equivalent to a religion backed by state power on law, education, institutionalised science and many other aspects of the public square. ("Subtly?" Yes: in Western cultures, we do not usually think of non-theistic worldviews and associated ideologies and institutions they influence in the terms of being potentially the functional equivalent of established and potentially domineering institutionalised religions.  Especially, if such non-theistic ideologies come to us wearing the highly respected lab coat of the scientist . . . )

On this last, Richard Lewontin's notorious hidden agenda admission, in its actual context (a review of Sagan's The Demon-Haunted World), should give us serious pause:

. . . to put a correct view of the universe into people's heads we must first get an incorrect view out . . .   the problem is to get them to reject irrational and supernatural explanations of the world, the demons that exist only in their imaginations, and to accept a social and intellectual apparatus, Science, as the only begetter of truth . . . . Sagan's argument is straightforward. We exist as material beings in a material world, all of whose phenomena are the consequences of physical relations among material entities. The vast majority of us do not have control of the intellectual apparatus needed to explain manifest reality in material terms, so in place of scientific (i.e., correct material) explanations, we substitute demons . . . . Most of the chapters of The Demon-Haunted World are taken up with exhortations to the reader to cease whoring after false gods and to accept the scientific method as the unique pathway to a correct understanding of the natural world. To Sagan, as to all but a few other scientists, it is self-evident that the practices of science provide the surest method of putting us in contact with physical reality, and that, in contrast, the demon-haunted world rests on a set of beliefs and behaviors that fail every reasonable test . . . . 

Our willingness to accept scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door. The eminent Kant scholar Lewis Beck used to say that anyone who could believe in God could believe in anything. To appeal to an omnipotent deity is to allow that at any moment the regularities of nature may be ruptured, that miracles may happen.

This, sirs, is worldview warfare, raw and naked and reeking of the outright subversion of science in service to a wider agenda. 

All, driven by the view that "Science" -- by that term, Lewontin plainly means evolutionary materialism (which, ironically, is inherently self-refuting and so inescapably irrational) -- is "the only begetter of truth," which gives us "correct material" that constitutes "the surest method of putting us in contact with physical reality." A "reality" that, with disgust, dismisses the possibility of God from the outset, thus tilting the playing field so that the committed "take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because [they] have a prior commitment, a commitment to materialism." [Link and final emphasis added.] 

Science, in the end -- whatever its many contributions to progress --  in such hands and minds primarily becomes a stalking horse for evolutionary materialism and for the imposition of associated socio-cultural, policy and political agendas that would otherwise be unacceptable. 

Minds that are blinded to what the founding era scientists of three hundred years ago instinctively understood from the basic principles and teachings of their Judaeo-Christian worldview: a world created by the God who is "the author of order, not confusion" would be set up, sustained and run according to intelligible ordering principles manifesting themselves in reliable cause-effect chains -- i.e. actual "laws" by an actual Legislator -- that would therefore obtain in general. But at the same time, such a world would be open to the intervention of minds and Mind. Thus, too, the classic motto of the early modern scientists: thinking God's thoughts after him. 

But, consistent with the classic "divide and rule" political and propaganda stratagem, the evolutionary materialist ideologues have now set up a strawman opponent, which they have turned into a demonic bogeyman. Even, as they push a ruthlessly pursued agenda that looks more and more convincingly like the creation of an ideological establishment with themselves as de facto Magisterium.

What that sort of agenda means on the ground can be clearly seen from the intervention made in 2005 by the US National Academy of Sciences [NAS] and the National Science Teachers Association [NSTA], through their joint statement on the 2005 science education standards for Kansas. 

The crucial paragraph of that statement reads, in its key part:

. . . the members of the Kansas State Board of Education who produced Draft 2-d of the KSES have deleted text defining science as a search for natural explanations of observable phenomena, blurring the line between scientific and other ways of   understanding.  Emphasizing controversy in the theory of evolution -- when in fact all modern theories of science are continually tested and verified -- and distorting the definition of science are inconsistent with our Standards and a disservice to the students of Kansas. Regretfully, many of the statements made in the KSES related to the nature of science and evolution also violate the document’s mission and vision.  Kansas students will not be well-prepared for the rigors of higher education or the demands of an increasingly complex and technologically-driven world if their science education is based on these standards.  Instead, they will put the students of Kansas at a competitive disadvantage as they take their place in the world.  

 This statement is deeply flawed and inadvertently highly revealing:

1 --> Immediately, there is no one "the definition of science" that may be owned or authoritatively imposed by any institution or group of institutions. Nor can such bodies, however august, properly demand that we must take their presented definitions at face value; without critical assessment or drawing our own conclusions for ourselves in light of our own investigation and analysis. For, science is a vital part of our common heritage as a civilisation, and what it is, and how it works are matters of historically grounded fact and philosophical discussion on comparative difficulties relative to those facts, not rulings by any officially established or de facto "Magisterium." [Moreover, scientists and teachers are as a rule not at all expert on the detailed ins and outs and resulting balances on the merits of developments and arguments in the various schools of thought on philosophy of science over recent decades.]

2 --> As a matter of fairly easily checked fact, the Kansas definition of 2005, as cited above, reflects longstanding praxis, and the resulting historic general consensus on what science is and should do; without imposing question-begging agendas. This can easily be seen from a look at the sorts of summaries we may read in high quality dictionaries from before the recent attempted imposition of methodological naturalism as an alleged criterion of science vs. non-science or pseudo-science.

3 --> Further to this, I happen to be a reasonably philosophically literate, scientifically trained person who has worked in science and technology education at secondary and tertiary level. Pardon my ignorance if that is what is reflected in my own thoughts on the subject of defining and teaching science, but I must confess that I fail to see which part of good and historically well-warranted scientific praxis over the past three or so centuries is not properly reflected in the 2005 statement: “Science is a systematic method of continuing investigation, that uses observation, hypothesis testing, measurement, experimentation, logical argument and theory building, to lead to more adequate explanations of natural phenomena.”

4 --> The phrase on "blurring the line between scientific and other ways of  understanding . . ." reflects, at best, a deep and disqualifying ignorance by the representatives of the NAS and NSTA of the overall result after decades of intense philosophical debate over the demarcation lines between science and non-science. For, there is no set of distinctive approaches to acquiring knowledge and understanding or inferring to best explanation that are universal across the conventionally accepted list of sciences, and/or that are so necessary to, sufficient for and unique to scientific investigation and argument that we may use them to mark a defining line between science and non-science. (For that matter, the real epistemological challenge is not over attaching the prestigious label "science," but over [1] whether we are using sound, effective, reliable and fair methods of inquiry, and [2] the actual degree of warrant that attaches to what we accept as knowledge, however labelled.)

5 --> Yet further, when coupled with the non-disclosure by the two bodies of the effect of imposing the rule that science may only seek "natural causes," such agenda-serving questionable demarcation criteria mislead and can even manipulate the general public on the true status of the relevant theories and factual claims being made on origins science. For, the public at large still believes that science is an unfettered search for the truth about the world in light of evidence, instead of being what the rule enforces: the best evolutionary materialist -- note the censoring constraint -- explanation of the cosmos from hydrogen to humans. Non-disclosure of the effects of such an imposition on the part of responsible parties who know or should know better ["ignorance of the law is no excuse"], on even the most charitable interpretation, must raise questions of deception by gross and culpable negligence. (Such should therefore pause and reflect soberly on "the definition" of this F-word.)

6 --> Next, it is simply and manifestly false that the [Neo-] Darwinian Theory of Evolution is in the same well-tested, abundantly empirically supported category as, say, Newtonian gravitation and mechanics circa 1680 - 1880. (And, let us observe: after about 200 years of being the best supported and most successful scientific theory, the Newtonian synthesis collapsed into being a limiting case at best, in light of unexpected findings in the world of the very small and the very fast; provoking a scientific revolution from about 1900 to 1930 that resulted in Modern Physics. Science is open-ended, provisional and hopefully progressive. A pattern of progress in which theory replacement is at least as prominent as theory refinement.) 

7 --> For, Newtonian dynamics was and is about currently and directly observable phenomena, i.e. so-called operational science: what are the evident patterns and underlying ordering principles of the currently operating, observable natural world? 

8 --> By contrast, the material part of the Theory of Evolution -- we are not talking about what has been termed microevolution --  is about trying to make a "plausible" reconstruction of an unobservable, projected remote past of life based on traces in the present and on extrapolation of currently observed or "reasonable" processes and principles. That is, it is an origins science, a fundamentally historical investigation based on principles of inference to best explanation. Its findings and explanations on the reconstructed, extrapolated and projected natural history of life are thus inherently less well tested than those of theories that deal with present accessible and directly observable reality.  Further to this, once we observe that in developing or studying any reasonably complex scientific theory, one is forced to rely on the credibility of records, testimony, memories and other traces of an unrepeatable past, one can see -- per point 4 just above -- that, on pain of Simon Greenleaf's selective hyperskepticism, no wedge can properly be pushed between the methods of what are conventionally labelled sciences and historical-forensic or other serious objective investigations carried out by finite, fallible, sometimes mistaken (or even ill-willed, or biased and/or outright deceptive) human beings.]

9 --> So also, the too often seen tendency to over-claim the degree of warrant for evolutionary reconstructions of the remote past naturally provokes controversies, especially where rhetorical resort is made (often, in the name of "education") to misleading icons. Therefore, broad-brush dismissive claims such as "all modern theories of science are continually tested and verified" -- i.e. in effect confirmed as credibly true for practical purposes -- constitute a highly misleading over-reach.  Especially, when these claims are coupled with the imposition of methodological naturalism and non-disclosure of its censoring, worldview-level question-begging effects as pointed out at point 5 just above. [NB: Cf. here for remarks by AiG's Dr Jonathan Sarfati on what the much despised Creationists actually teach on this general issue.]

10 --> Worse yet, given the primary reference in context of "these standards," all of this is backed up by a subtle -- and on the evidence of events since 2005, successful -- unjustifiable intimidatory threat. For, it is simply not true that students exposed to the traditional, historically well-warranted understanding of what good science is (and/or should strive to be) "will not be well-prepared for the rigors of higher education or the demands of an increasingly complex and technologically-driven world."

11 --> Instead, we can note that NAS and NSTA hold significant prestige, and are viewed by a great many people and institutions as responsible, reasonable and authoritative. So, if they refuse their imprimatur to the Kansas Board's work, then it could materially damage the prospects for Kansan students to get into so-called "good" Colleges, jobs, etc. In short, the children of the state were being held hostage by ideologised institutions and associated individuals holding positions of great trust and responsibility, but abjectly failing in their duties of care to truth, disclosure and justice. 

12 --> Moreover, all of this was in a situation where a public relations person for an oppositional "grassroots" group, Kansas Citizens For Science [KCFS] in 2005, outlined the following public relations strategy on a KCFS online forum. That forum was moderated by a NCSE member- cum- KCFS leader- cum- state education administrator and Statistics teacher who sat on the experts committee consulted by the Board in 2004 - 5. In October 2004 this committee evidently suppressed the input of the minority. It is that suppressive action that evidently provoked the whistleblowing minority report that is a highly relevant context for the "breakers of rules" accusation in the just below:

My strategy at this point is the same as it was in 1999: notify the national and local media about what's going on and portray them in the harshest light possible, as political opportunists, evangelical activists, ignoramuses, breakers of rules, unprincipled bullies, etc. There may no way to head off another science standards debacle, but we can sure make them look like asses as they do what they do. Our target is the moderates who are not that well educated about the issues, most of whom probably are theistic evolutionists. There is no way to convert the creationists. The solution is really political. [Emphases added. Note the significance of "[o]ur"; this is not just a personal observation, but a longstanding strategy of an ideological movement in dealing with its perceived opponents and the general public, presented by one of those responsible for its public relations, and who worked closely with its leadership.]

In short, in our post-/ultra- modern time -- one in which a certain politician, trying to justify himself in the public mind, notoriously said "It depends on what the definition of 'is,' is . . ." --  the apparently simple question of what science is, is quite prone to ideological manipulation in service to radical evolutionary materialistic agendas. 

So, we should be forewarned and forearmed.

Now, of course, we plainly do not have the space or time to now go into a full-orbed tangential essay on the full range of worldview analysis issues and topics that the above points to, but if we are to responsibly address the design issue, it is necessary to at least highlight a few core points and issues relevant to the above. So, it is perhaps best to start with the intuitively obvious: we think, make decisions, argue as if it matters, and expect others to respect moral principles such as fairness. However, if we resort to evolutionary materialist accounts, we soon see that characteristically, they reduce mentality to little more than an illusion riding on top of "real" brain chemistry and neuronal activity, and that there is an unbridgeable gap between the is and the ought: what we do and what we thing we (or others!) should do.

As a result, there are serious gaps issues to be faced by advocates of such a view, and to be pondered by the rest of us, too:

1] Origin and credibility of a reliable mind that you need to think through these matters. (Here one must consider both the issues of determinism and/or random noise and chance boundary conditions as the root of "thinking" and the question of getting the link between a world of the conscious, deciding mind as we experience it and the naturalistic proposed world of physical objects where mind reduces to one form or another of an illusion that can have no effect on the physical world. Consider especially the issue that our direct intuitive knowledge that we think, decide and act may well be more certain than the theories that imply that such an experience is in effect an illusion, for thoughts and decisions are driven by deterministic and/or random forces. If that is so, how can you trust the chains of thought and reasoning that may have led you to decide to accept naturalism as true?)

2] Origin of a cosmos that is so exquisitely and finely balanced as a locus for life that it naturally raises the issue of intentional design by an agent powerful and wise enough to pull it off successfully. If this is logically on the table, can we properly use demarcation arguments to rule it out of consideration? Should we not instead point out to students and the general public that science exists within a wider grand discourse of the ages, i.e. philosophy?

3] Origin and diversification of life within the ambit of the observed cosmos, given the complexity and integrated functionality of the molecular machinery involved, as well as associated issues of getting to such complexity through chance initial conditions and processes, plus associated known natural laws such as those of thermodynamics. (Cf Voie's analysis here.)

4] The validity of morals, again relative to evolutionary materialist premises. [Note that quite often, advocates of evolutionary materialism are expecting us to believe in and act according to binding moral principles. Okay, on such premises, where do these principles come from? And, why should they be regarded as binding -- apart from something that in the end sounds suspiciously like: "might makes right"?]

This cluster of challenges brings back into focus a line of philosophical thought that is often unwelcome in current discourse among many who consider themselves educated. As William Lane Craig put the cosmological challenge:

We can summarize our argument as follows:

1. Whatever exists has a reason for its existence, either in the necessity of its own nature or in an external ground.

2. Whatever begins to exist is not necessary in its existence. [Here, we advert to both the evident beginning of the observed universe and its fine-tuning as just discussed.]

3. If the [observed] universe [which is generally viewed by cosmologists as originating in a "big bang" some 13.7 BYA] has an external ground of its existence, then there exists a Personal Creator of the universe, who, sans the universe, is timeless, spaceless, beginningless, changeless, necessary, uncaused, and enormously powerful.

[NOTE: For, impersonal but deterministic causes will produce a result as soon as they are present, e.g. as soon as heat, fuel and oxidiser are jointly present, a fire bursts into being. That is, it takes an agent cause to act in a structured fashion at a particular beginning-point. See (4) below on the idea of sub-universes popping up at random in an underlying infinite, eternal universe as a whole.]

4. The [observed] universe began to exist.

[NOTE: To deny this, one in effect must propose a speculative, eternally existing wider universe as a whole; in which sub-universes (such as our own) pop up more or less at random. This, of course is not at all what we have actually observed. Such a resort thus brings out the underlying speculative -- and after-the-fact -- metaphysics embedded in such "multiverse" proposals. In light of (3) just above, it also requires that points in the wider universe throw up expanding sub-universes at random. But, when this is wedded to the infinite proposed age, as Craig points out, it leads to the issue that every point in that wider universe as a whole should have birthed a sub-universe in infinite time. Thus, we should see multiple expansions in our zone of space, not just the observed number: one. Similarly,the idea of sub-universes randomly budding off from earlier expansions still implies a beginning, and the resort to imaginary time is a mathematical device, one that collapses back into requiring a beginning as soon as we get back to real time and space. In turn, there is an even more specific speculation: multiple, independent, non-interacting (and presumably undetectable) space-time domains -- but, how could we know of such, relative to empirical tests? It also leads to the issue Leslie raised: this local, observed domain exhibits the characteristics of the lone fly on the wall suddenly hit by a bullet. And so on, as an ad hoc patchwork slowly but surely emerges out of the evolutionary materialist system. In short, the better approach to explanation is to take the one observed, finely tuned universe and its evident beginning seriously.]

From (2) and (4) it follows that

5. Therefore, the universe is not necessary in its existence.

From (1) and (5) it follows further that

6. Therefore, the universe has an external ground of its existence.

From (3) and (6) it we can conclude that

7. Therefore, there exists a Personal Creator of the universe, who, sans the universe, is timeless, spaceless, beginningless, changeless, necessary, uncaused, and enormously powerful.

And this, as Thomas Aquinas laconically remarked,{67} is what everybody means by God.

So, we are forced in the end to address the issue of the worldview implications of what we have discovered over the past century through science: (1) the observed universe shows abundant evidence that it is finetuned for life, which (2) is itself based on a tightly integrated and complex information system, and both have (3) a beginning, so neither the universe nor life in it constitutes a necessary being. 

So, what best explains that?

---

CONCLUSION: It is clear that the issue of FSCI cannot be easily brushed aside, and should be soberly considered -- as Cicero long ago counselled -- before coming to a conclusion for oneself. Nor should one allow him-/her- self to be intimidated by those who claim "expertise," when issues as profound as God and our nature as human beings are potentially on the table. Nor, should we be impressed by question-begging attempted redefinitions of science -- even when backed by impressive-sounding arguments and major credentialled scientific institutions. For, the question of origins and associated issues over inference to design in light of the existence of FSCI are too big and serious to be left to the scientists and philosophers, the rest of us then just taking their declarations at face value. I therefore trust that the above notes (which present at hopefully a relatively simple level an overview of the side of the issue that is too often dismissed with contempt and distortion), will be helpful to you as you think about these points for oneself.

Also, it is worth citing another classical author in this context, Paulo Apostolo Mart; not least, as a caution that our thoughts on these matters may not be as objective on the matters in the above as we wish to imagine:

Rom 1:19 . . . what may be known about God is plain to them, because God has made it plain to them. 20 For since the creation of the world God's invisible qualities--his eternal power and divine nature--have been clearly seen, being understood from what has been made, so that men are without excuse.

    RO 1:21 For although they knew God, they neither glorified him as God nor gave thanks to him, but their thinking became futile and their foolish hearts were darkened. 22 Although they claimed to be wise, they became fools 23 and exchanged the glory of the immortal God for images made to look like mortal man and birds and animals and reptiles [yesteryear, in temples, today, often in museums, magazines, textbooks and on TV] . . . .

 RO 1:28 . . .  since they did not think it worthwhile to retain the knowledge of God, he gave them over to a depraved mind, to do what ought not to be done. 29 They have become filled with every kind of wickedness, evil, greed and depravity. They are full of envy, murder, strife, deceit and malice. They are gossips, 30 slanderers, God-haters, insolent, arrogant and boastful; they invent ways of doing evil; they disobey their parents; 31 they are senseless, faithless, heartless, ruthless. 32 Although they know God's righteous decree that those who do such things deserve death, they not only continue to do these very things but also approve of those who practice them.

RO 2:6 God "will give to each person according to what he has done." 7 To those who by persistence in doing good seek glory, honor and immortality, he will give eternal life. 8 But for those who are self-seeking and who reject the truth and follow evil, there will be wrath and anger. 9 There will be trouble and distress for every human being who does evil . . . 10 but glory, honor and peace for everyone who does good . . .  11 For God does not show favoritism . . . . 14 (Indeed, when [men without the Scriptures] . . .  do by nature things required by the [biblical] law, they . . . 15 . . . show that the requirements of the law are written on their hearts, their consciences also bearing witness, and their thoughts now accusing, now even defending them.) . . . . 

RO 13:8 Let no debt remain outstanding, except the continuing debt to love one another, for he who loves his fellowman has fulfilled the law. 9 The commandments, "Do not commit adultery," "Do not murder," "Do not steal," "Do not covet," and whatever other commandment there may be, are summed up in this one rule: "Love your neighbor as yourself." 10 Love does no harm to its neighbor. Therefore love is the fulfillment of the law.

Food for thought. Feel free to drop me a line, here.

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APPENDIX 1:

On Thermodynamics, Information and Design

This is the side of the issue that gets technical the fastest of all, hence relegation to an appendix.

Let us reflect on a few remarks on the link from thermodynamics to information:

1] TMLO: In 1984, this well-received work provided the breakthrough critical review on the origin of life that led to the modern design school of thought in science. The three online chapters, as just linked, should be carefully read to understand why design thinkers think that the origin of FSCI in biology is a significant and unmet challenge to neo-darwinian thought. (Cf also Klyce's relatively serious and balanced assessment, from a panspermia advocate. Sewell's remarks here are also worth reading. So is Sarfati's discussion of Dawkins' Mt Improbable.)

2] But open systems can increase their order: This is the "standard" dismissal argument on thermodynamics, but it is both fallacious and often resorted to by those who should know better. My own note on why this argument should be abandoned is:

a] Clausius is the founder of the 2nd law, and the first standard example of an isolated system -- one that allows neither energy nor matter to flow in or out -- is instructive, given the "closed" subsystems [i.e. allowing energy to pass in or out] in it. Pardon the substitute for a real diagram, for now:

Isol System:

| | (A, at Thot) --> d'Q, heat --> (B, at T cold) | |

b] Now, we introduce entropy change dS >/= d'Q/T . . .  "Eqn" A.1

c] So, dSa >/= -d'Q/Th, and dSb >/= +d'Q/Tc, where Th > Tc

d] That is, for system, dStot >/= dSa + dSb >/= 0, as Th > Tc . . . "Eqn" A.2

e] But, observe: the subsystems A and B are open to energy inflows and outflows, and the entropy of B RISES DUE TO THE IMPORTATION OF RAW ENERGY.

f] The key point is that when raw energy enters a body, it tends to make its entropy rise. This can be envisioned on a simple model of a gas-filled box with piston-ends at the left and the right:

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1: Consider a box as above, filled with tiny perfectly hard marbles [so collisions will be elastic], scattered similar to a raisin-filled Christmas pudding (pardon how the textual elements give the impression of a regular grid, think of them as scattered more or less hap-hazardly as would happen in a cake).

2: Now, let the marbles all be at rest to begin with.

3: Then, imagine that a layer of them up against the leftmost wall were given a sudden, quite, quite hard push to the right [the left and right ends are pistons].

4: Simply on Newtonian physics, the moving balls would begin to collide with the marbles to their right, and in this model perfectly elastically. So, as they hit, the other marbles would be set in motion in succession. A wave of motion would begin, rippling from left to right

5:As the glancing angles on collision will vary at random, the marbles hit and the original marbles would soon begin to bounce in all sorts of directions. Then, they would also deflect off the walls, bouncing back into the body of the box and other marbles, causing the motion to continue indefinitely.

6: Soon, the marbles will be continually moving in all sorts of directions, with varying speeds, forming what is called the Maxwell-Boltzmann distribution, a bell-shaped curve.

7: And, this pattern would emerge independent of the specific initial arrantgement or how we impart motion to it, i.e. this is an attractor in the phase space: once the marbles are set in motion somehow, and move around and interact, they will soon enough settle into the M-B pattern. E.g. the same would happen if a small charge of explosive were set off in the middle of the box, pushing our the balls there into the rest, and so on. And once the M-B pattern sets in, it will strongly tend to continue. (That is, the process is ergodic.)

8: A pressure would be exerted on the walls of the box by the average force per unit area from collisions of marbles bouncing off the walls, and this would be increased by pushing in the left or right walls (which would do work to push in against the pressure, naturally increasing the speed of the marbles just like a ball has its speed increased when it is hit by a bat going the other way, whether cricket or baseball). Pressure rises, if volume goes down due to compression. (Also, volume of a gas body is not fixed.)

9: Temperatureemerges as a measure of the average random kinetic energy of the marbles in any given direction, left, right, to us or away from us. Compressing the model gas does work on it, so the internal energy rises, as the average random kinetic energy per degree of freedom rises. Compression will tend to raise temperature. (We could actually deduce the classical — empirical — P, V, T gas laws [and variants] from this sort of model.)

10: Thus, from the implications of classical, Newtonian physics, we soon see the hard little marbles moving at random, and how that randomness gives rise to gas-like behaviour. It also shows how there is a natural tendency for systems to move from more orderly to more disorderly states, i.e. we see the outlines of the second law of thermodynamics.

11: Is the motion really random? First, we define randomness in the relevant sense: 

In probability and statistics, a random process is a repeating process whose outcomes follow no describable deterministic pattern, but follow a probability distribution, such that the relative probability of the occurrence of each outcome can be approximated or calculated. For example, the rolling of a fair six-sided die in neutral conditions may be said to produce random results, because one cannot know, before a roll, what number will show up. However, the probability of rolling any one of the six rollable numbers can be calculated.

12: This can be seen by the extension of the thought experiment of imagining a large collection of more or less identically set up boxes, each given the same push at the same time, as closely as we can make it. At first, the marbles in the boxes will behave very much alike, but soon, they will begin to diverge as to path. The same overall pattern of M-B statistics will happen, but each box will soon be going its own way. That is, the distribution pattern is the same but the specific behaviour in each case will be dramatically different.

13: Q: Why?

14: A: This is because tiny, tiny differences between the boxes, and the differences in the vibrating atoms in the walls and pistons, as well as tiny irregularites too small to notice in the walls and pistons will make small differences in initial and intervening states -- perfectly smooth boxes and pistons are an unattainable ideal. Since the system is extremely nonlinear, such small differences will be amplified, making the behaviour diverge as time unfolds. A chaotic system is not predictable in the long term. So, while we can deduce a probabilistic distribution, we cannot predict the behaviour in detail, across time. Laplace's demon who hoped to predict the future of the universe from the covering laws and the initial conditions, is out of a job.

15: To see diffusion in action, imagine that at the beginning, the balls in the right half were red, and those in the left half were black. After a little while, as they bounce and move, the balls would naturally mix up, and it would be very unlikely indeed — through logically possible — for them to spontaneously un-mix, as the number of possible combinations of position, speed and direction where the balls are mixed up is vastly more than those where they are all red to the right, all alack to the left or something similar.

(This can be calculated, by breaking the box up into tiny little cells such that they would have at most one ball in them, and we can analyse each cell on occupancy, colour, location, speed and direction of motion. thus, we have defined a phase or state space, going beyond a mere configuration space that just looks at locations.)

16: So, from the orderly arrangement of laws and patterns of initial motion, we see how randomness emerges through the sensitive dependence of the behaviour on initial and intervening conditions. There would be no specific, traceable deterministic pattern that one could follow or predict for the behaviour of the marbles, through we could work out an overall statistical distribution, and could identify overall parameters such as volume, pressure and temperature.

17: For Osmosis, let us imagine that the balls are of different size, and that we have two neighbouring boxes with a porous wall between them; but only the smaller marbles can pass through the holes. If the smaller marbles were initially on say the left side, soon, they would begin to pass through to the right, until they were evenly distributed, so that on average as many small balls would pass left as were passing right, i.e., we see dynamic equilibrium. [this extends to evaporation and the vapour pressure of a liquid, once we add in that the balls have a short-range attraction that at even shorter ranges turns into a sharp repulsion, i.e they are hard.]

18: For a solid, imagine that the balls in the original box are now connected through springs in a cubical grid. The initial push will now set the balls to vibrating back and forth, and the same pattern of distributed vibrations will emerge, as one ball pulls on its neigbours in the 3-D array. (For a liquid, allow about 3% of holes in the grid, aned let the balls slide over one another, making nes connextions, some of them distorted. The fixed volume but inability to keep a shape that defines a liquid will emerge. The push on the liquid will have much the same effect as for the solid, except that it will also lead to flows.)

19: Randomness is thus credibly real, and naturally results from work on or energy injected into a body composed of microparticles, even in a classical Newtonian world; whether it is gas, solid or liquid. Raw injection of energy into a body tends to increase its disorder, and this is typically expressed in its temperature rising.

20: Quantum theory adds to the picture, but the above is enough to model a lot of what we see as we look at bulk and transport properties of collections of micro-particles.

21: Indeed, even viscosity comes out naturally, as . . .  if there are are boxes stacked top and bottom that are sliding left or right relative to one another, and suddenly the intervening walls are removed, the gas-balls would tend to diffuse up and down from one stream tube to another, so their drift verlocities will tend to even out, The slower moving stream tubes exert a dragging effect on the faster moving ones.

22: And many other phenomena can be similarly explained and applied, based on laws and processes that we can test and validate, and their consequences in simplified but relevant models of the real world.

23: When we see such a close match, especially when quantum principles are added in, it gives us high confidence that we are looking at a map of reality. Not the reality itself, but a useful map. And, that map tells us that thanks to sensitive dependence on initial conditions, randomness will be a natural part of the micro-world, and that when energy is added to a body its randomness tends to increase, i.e we see the principle of entropy, and why simply opening up a body to receive energy is not going to answer to the emergence of funcitonal internal organisation.

24: For, organised states will be deeply isolated in the set of possible configurations. Indeed, if we put a measure of possible configurations in terms of say binary digits, bits, if we have 1,000 two-state elements there are already 1.07*10^301 possible configs. The whole observed universe searching at one state per Planck time, could not go through enough states of its 10^80 or so atoms, across its thermodynamically credible lifespan -- about 50 mn times the 13.7 BY said to have elapsed form the big bang --  to go through more than about 10^150 states. That is, the whole cosmos could not search more than a negligible fraction of the space. The hay stack could be positively riddled with needles, but at that rate we have not had any serious search at all..

25: That is, there is a dominant distribution, not a detailed plan a la Laplace’s (finite) Demon who could predict the long term path of the world on its initial conditions and sufficient calculating power and time.

26: But equally, since short term interventions that are subtle can have significant effects, there is room for the intelligent and sophisticated intervention; e.g. through a Maxwell’s Demon who can spot faster moving and slower moving molecules and open/shut a shutter to set one side hotter and the other colder in a partitioned box. Providing he has to take active steps to learn which molecules are moving faster/slower in the desired direction, Brillouin showed that he will be within the second law of thermodynamics.

. . . So, plainly, for the injection of energy to instead do predictably and consistently do something useful, it needs to be coupled to an energy conversion device.

g] When such energy conversion devices, as in the cell, exhibit FSCI, the question of their origin becomes material, and in that context, their spontaneous origin is strictly logically possible but -- from the above --  negligibly different from zero probability on the gamut of the observed cosmos. (And, kindly note: the cell is an energy importer with an internal energy converter. That is, the appropriate entity in the model is B and onward B' below. Presumably as well, the prebiotic soup would have been energy importing, and so materialistic chemical evolutionary scenarios therefore have the challenge to credibly account for the origin of the FSCI-rich energy converting mechanisms in the cell relative to Monod's "chance + necessity" [cf also Plato's remarks] only.)

h] Now, as just mentioned, certain bodies have in them energy conversion devices: they COUPLE input energy to subsystems that harvest some of the energy to do work, exhausting sufficient waste energy to a heat sink that the overall entropy of the system is increased. Illustratively, for heat engines -- and (in light of exchanges with email correspondents circa March 2008) let us note: a good slice of classical thermodynamics arose in the context of studying, idealising and generalising from steam engines [which exhibit organised, functional complexity, i.e FSCI; they are of course artifacts of intelligent design and also exhibit step-by-step problem-solving processes (even including "do-always" looping!)]:

| | (A, heat source: Th): d'Qi --> (B', heat engine, Te): -->

d'W [work done on say D] + d'Qo --> (C, sink at Tc) | |

i] A's entropy: dSa >/= - d'Qi/Th

j] C's entropy: dSc >/= + d'Qo/Tc

k] The rise in entropy in B, C and in the object on which the work is done, D, say, compensates for that lost from A. The second law -- unsurprisingly, given the studies on steam engines that lie at its roots -- holds for heat engines.

l] However for B since it now couples energy into work and exhausts waste heat, does not necessarily undergo a rise in entropy having imported d'Qi. [The problem is to explain the origin of the heat engine -- or more generally, energy converter -- that does this, if it exhibits FSCI.]

m] There is also a material difference between the sort of heat engine [an instance of the energy conversion device mentioned] that forms spontaneously as in a hurricane [directly driven by boundary conditions in a convective system on the planetary scale, i.e. an example of order], and the sort of complex, organised, algorithm-implementing energy conversion device found in living cells [the DNA-RNA-Ribosome-Enzyme system, which exhibits massive FSCI].

n] In short, the decisive problem is the [im]plausibility of the ORIGIN of such a FSCI-based energy converter through causal mechanisms traceable only to chance conditions and undirected [non-purposive] natural forces. This problem yields a conundrum for chem evo scenarios, such that inference to agency as the probable cause of such FSCI -- on the direct import of the many cases where we do directly know the causal story of FSCI -- becomes the better explanation. As TBO say, in bridging from a survey of the basic thermodynamics of living systems in CH 7,  to that more focussed discussion in ch's 8 - 9: 

While the maintenance of living systems is easily rationalized in terms of thermodynamics, the origin of such living systems is quite another matter. Though the earth is open to energy flow from the sun, the means of converting this energy into the necessary work to build up living systems from simple precursors remains at present unspecified (see equation 7-17). The "evolution" from biomonomers of to fully functioning cells is the issue. Can one make the incredible jump in energy and organization from raw material and raw energy, apart from some means of directing the energy flow through the system? In Chapters 8 and 9 we will consider this question, limiting our discussion to two small but crucial steps in the proposed evolutionary scheme namely, the formation of protein and DNA from their precursors.

It is widely agreed that both protein and DNA are essential for living systems and indispensable components of every living cell today.¹¹ Yet they are only produced by living cells. Both types of molecules are much more energy and information rich than the biomonomers from which they form. Can one reasonably predict their occurrence given the necessary biomonomers and an energy source? Has this been verified experimentally? These questions will be considered . . . [Bold emphasis added. Cf summary in the peer-reviewed journal of the American Scientific Affiliation, "Thermodynamics and the Origin of Life," in Perspectives on Science and Christian Faith 40 (June 1988): 72-83, pardon the poor quality of the scan. NB:as the journal's online issues will show, this is not necessarily a "friendly audience."]

3] So far we have worked out of a more or less classical view of the subject. But, to explore such a question further, we need to look more deeply at the microscopic level. Happily, there is a link from macroscopic thermodynamic concepts to the microscopic, molecular view of matter, as worked out by Boltzmann and others, leading to the key equation:

s = k ln W . . . Eqn.A.3

That is, entropy of a specified macrostate [in effect, macroscopic description or specification] is a constant times a log measure of the number of ways matter and energy can be distributed at the micro-level consistent with that state [i.e. the number of associated microstates; aka "the statistical weight of the macrostate," aka "thermodynamic probability"]. The point is, that there are as a rule a great many ways for energy and matter to be arranged at micro level relative to a given observable macro-state. That is, there is a "loss of information" issue here on going from specific microstate to a macro-level description, with which many microstates may be equally compatible. Thence, we can see that if we do not know the microstates specifically enough, we have to more or less treat the micro-distributions of matter and energy as random, leading to acting as though they are disordered. Or, as Leon Brillouin, one of the foundational workers in modern information theory, put it in his 1962  Science and Information Theory, Second Edition:

How is it possible to formulate a scientific theory of information? The first requirement is to start from a precise definition. . . . . We consider a problem involving a certain number of possible answers, if we have no special information on the actual situation. When we happen to be in possession of some information on the problem, the number of possible answers is reduced, and complete information may even leave us with only one possible answer. Information is a function of the ratio of the number of possible answers before and after, and we choose a logarithmic law in order to insure additivity of the information contained in independent situations [as seen above in the main body, section A] . . . . 

Physics enters the picture when we discover a remarkable likeness between information and entropy. This similarity was noticed long ago by L. Szilard, in an old paper of 1929, which was the forerunner of the present theory. In this paper, Szilard was really pioneering in the unknown territory which we are now exploring in all directions. He investigated the problem of Maxwell's demon, and this is one of the important subjects discussed in this book. The connection between information and entropy was rediscovered by C. Shannon in a different class of problems, and we devote many chapters to this comparison. We prove that information must be considered as a negative term in the entropy of a system; in short, information is negentropy. The entropy of a physical system has often been described as a measure of randomness in the structure of the system. We can now state this result in a slightly different way:

Every physical system is incompletely defined. We only know the values of some macroscopic variables, and we are unable to specify the exact positions and velocities of all the molecules contained in a system. We have only scanty, partial information on the system, and most of the information on the detailed structure is missing. Entropy measures the lack of information; it gives us the total amount of missing information on the ultramicroscopic structure of the system.

This point of view is defined as the negentropy principle of information [added links: cf. explanation here and "onward" discussion here -- noting on the brief, dismissive critique of Brillouin there, that you never get away from the need to provide information -- there is "no free lunch," as Dembski has pointed out  ; ->) ], and it leads directly to a generalization of the second principle of thermodynamics, since entropy and information must, be discussed together and cannot be treated separately. This negentropy principle of information will be justified by a variety of examples ranging from theoretical physics to everyday life. The essential point is to show that any observation or experiment made on a physical system automatically results in an increase of the entropy of the laboratory. It is then possible to compare the loss of negentropy (increase of entropy) with the amount of information obtained. The efficiency of an experiment can be defined as the ratio of information obtained to the associated increase in entropy. This efficiency is always smaller than unity, according to the generalized Carnot principle. Examples show that the efficiency can be nearly unity in some special examples, but may also be extremely low in other cases.

This line of discussion is very useful in a comparison of fundamental experiments used in science, more particularly in physics. It leads to a new investigation of the efficiency of different methods of observation, as well as their accuracy and reliability . . . . [From an online excerpt of the Dover Reprint edition, here. Emphases, links and bracketed comment added.]

4] Yavorski and Pinski, in the textbook Physics, Vol I [MIR, USSR, 1974, pp. 279 ff.], summarise the key implication of the macro-state and micro-state view well: as we consider a simple model of diffusion, let us think of ten white and ten black balls in two rows in a container. There is of course but one way in which there are ten whites in the top row; the balls of any one colour being for our purposes identical. But on shuffling, there are 63,504 ways to arrange five each of black and white balls in the two rows, and 6-4 distributions may occur in two ways, each with 44,100 alternatives. So, if we for the moment see the set of balls as circulating among the various different possible arrangements at random, and spending about the same time in each possible state on average, the time the system spends in any given state will be proportionate to the relative number of ways that state may be achieved. Immediately, we see that the system will gravitate towards the cluster of more evenly distributed states. In short, we have just seen that there is a natural trend of change at random, towards the more thermodynamically probable macrostates, i.e the ones with higher statistical weights. So "[b]y comparing the [thermodynamic] probabilities of two states of a thermodynamic system, we can establish at once the direction of the process that is [spontaneously] feasible in the given system. It will correspond to a transition from a less probable to a more probable state." [p. 284.] This is in effect the statistical form of the 2nd law of thermodynamics. Thus, too, the behaviour of the Clausius isolated system above is readily understood: importing d'Q of random molecular energy so far increases the number of ways energy can be distributed at micro-scale in B, that the resulting rise in B's entropy swamps the fall in A's entropy. Moreover, given that FSCI-rich micro-arrangements are relatively rare in the set of possible arrangements, we can also see why it is hard to account for the origin of such states by spontaneous processes in the scope of the observable universe. (Of course, since it is as a rule very inconvenient to work in terms of statistical weights of macrostates [i.e W], we instead move to entropy, through s = k ln W.  Part of how this is done can be seen by imagining a system in which there are W ways accessible, and imagining a partition into parts 1 and 2. W = W₁*W₂, as for each arrangement in 1 all accessible arrangements in 2 are possible and vice versa, but it is far more convenient to have an additive measure, i.e we need to go to logs. The constant of proportionality, k, is the famous Boltzmann constant and is in effect the universal gas constant, R, on a per molecule basis, i.e we divide R by the Avogadro Number, N_A, to get: k = R/N_A. The two approaches to entropy, by Clausius, and Boltzmann, of course, correspond. In real-world systems of any significant scale, the relative statistical weights are usually so disproportionate, that the classical observation that entropy naturally tends to increase, is readily apparent.)

5] The above sort of thinking has also led to the rise of a school of thought in Physics -- note, much spoken against in some quarters, but I think they clearly have a point -- that ties information and thermodynamics together. Robertson presents their case; in summary:

. . . It has long been recognized that the assignment of probabilities to a set represents information, and that some probability sets represent more information than others . . . if one of the probabilities say p₂ is unity and therefore the others are zero, then we know that the outcome of the experiment . . . will give [event]  y₂. Thus we have complete information . . . if we have no basis . . . for believing that event y_i is more or less likely than any other [we] have the least possible information about the outcome of the experiment . . . . A remarkably simple and clear analysis by Shannon [1948] has provided us with a quantitative measure of the uncertainty, or missing pertinent information, inherent in a set of probabilities [NB: i.e. a probability should be seen as, in part, an index of ignorance] . . . . 

[deriving informational entropy, cf. discussions here, here, here, here and here; also Sarfati's discussion of debates and open systems here; the debate here is eye-opening on rhetorical tactics used to cloud this and related issues . . . ]

S({p_i}) = - C [SUM over i] p_i*ln p_i, [. . . "my" Eqn A.4]

[where [SUM over i] p_i = 1, and we can define also parameters alpha and beta such that: (1) p_i = e^-[alpha + beta*y_i]; (2) exp [alpha] = [SUM over i](exp - beta*y_i) = Z [Z being in effect the partition function across microstates, the "Holy Grail" of statistical thermodynamics]. . . .[pp.3 - 6]

S, called the information entropy, . . . correspond[s] to the thermodynamic entropy, with C = k, the Boltzmann constant, and yi an energy level, usually ei, while [BETA] becomes 1/kT, with T the thermodynamic temperature . . . A thermodynamic system is characterized by a microscopic structure that is not observed in detail . . . We attempt to develop a theoretical description of the macroscopic properties in terms of its underlying microscopic properties, which are not precisely known. We attempt to assign probabilities to the various microscopic states . . . based on a few . . . macroscopic observations that can be related to averages of microscopic parameters. Evidently the problem that we attempt to solve in statistical thermophysics is exactly the one just treated in terms of information theory. It should not be surprising, then, that the uncertainty of information theory becomes a thermodynamic variable when used in proper context [p. 7] . . . . 

Jayne's [summary rebuttal to a typical objection] is ". . . The entropy of a thermodynamic system is a measure of the degree of ignorance of a person whose sole knowledge about its microstate consists of the values of the macroscopic quantities . . . which define its thermodynamic state. This is a perfectly 'objective' quantity . . . it is a function of [those variables] and does not depend on anybody's personality. There is no reason why it cannot be measured in the laboratory." . . . .   [p. 36.] 

[Robertson, Statistical Thermophysics, Prentice Hall, 1993. (NB: Sorry for the math and the use of text for symbolism. However, it should be clear enough that Roberson first summarises how Shannon derived his informational entropy [though Robertson uses s rather than the usual H for that information theory variable, average information per symbol], then ties it to entropy in the thermodynamic sense using another relation that is tied to the Boltzmann relationship above. This context gives us a basis for looking at the issues that surface in prebiotic soup or similar models as we try to move from relatively easy to form monomers to the more energy- and information- rich, far more complex biofunctional molecules.)]

6] It is worth pausing to now introduce a thought (scenario) experiment that helps underscore the point, by scaling down to essentially molecular size the tornado- in- a- junkyard- forms- a- jet example raised by Hoyle and mentioned by Dawkins with respect in the just linked excerpt in Section A above. Then, based on (a) the known behaviour of molecules and quasi-molecules through Brownian-type motion (which, recall, was Einstein's Archimedian point for empirically demonstrating the reality of atoms), and (b) the also known requirement of quite precise configurations to get to a flyable micro-jet, we may (c) find a deeper understanding of what is at stake in the origin of life question:

NANOBOTS & MICRO-JETS THOUGHT EXPT:

i] Consider the assembly of a Jumbo Jet, which requires intelligently designed, physical work in all actual observed cases. That is, orderly motions were impressed by forces on selected, sorted parts, in accordance with a complex specification. (I have already contrasted the case of a tornado in a junkyard that it is logically and physically possible can do the same, but the functional configuration[s] are so rare relative to non-functional ones that random search strategies are maximally unlikely to create a flyable jet, i.e. we see here the logic of the 2nd Law of Thermodynamics, statistical thermodynamics form, at work. [Intuitively, since functional configurations are rather isolated in the space of possible configurations, we are maximally likely to exhaust available probabilistic resources long before arriving at such a functional configuration or "island" of such configurations (which would be required before hill-climbing through competitive functional selection, a la Darwinian natural Selection could take over . . . ); if we start from an arbitrary initial configuration and proceed by a random walk.])

ii] Now, let us shrink the Hoylean example, to a micro-jet so small [~ 1 cm or even smaller] that the parts are susceptible to Brownian motion, i.e they are of about micron scale [for convenience] and act as "large molecules." (Cf. "materialism-leaning 'prof' Wiki's" blowing-up of Brownian motion to macro-scale by thought expt, here; indeed, this sort of scaling-up thought experiment was just what the late, great Sir Fred was doing in his original discussion of 747's.) Let's say there are about a million of them, some the same, some different etc. In principle, possible: a key criterion for a successful thought experiment. Next, do the same for a car, a boat and a submarine, etc.

iii] In several vats of "a convenient fluid," each of volume about a cubic metre, decant examples of the differing mixed sets of nano-parts; so that the particles can then move about at random, diffusing through the liquids as they undergo random thermal agitation.

iv] In the control vat, we simply leave nature to its course. 

Q: Will a car, a boat a sub or a jet, etc, or some novel nanotech emerge at random? [Here, we imagine the parts can cling to each other if they get close enough, in some unspecified way, similar to molecular bonding; but that the clinging force is not strong enough at appreciable distances [say 10 microns or more] for them to immediately clump and precipitate instead of diffusing through the medium.]

ANS: Logically and physically possible (i.e. this is subtler than having an overt physical force or potential energy barrier blocking the way!) but the equilibrium state will on statistical thermodynamics grounds overwhelmingly dominate — high disorder.

Q: Why?

A: Because there are so many more accessible scattered state microstates than there are clumped-at -random state ones, or even moreso, functionally configured flyable jet ones. (To explore this concept in more details, cf the overviews here [by Prof Bertrand of U of Missouri, Rolla], and here -- a well done research term paper by a group of students at Singapore's NUS. I have extensively discussed on this case with a contributer to the ARN known as Pixie, here. Pixie: Appreciation for the time & effort expended, though of course you and I have reached very different conclusions.)

v] Now, pour in a cooperative army of nanobots into one vat, capable of recognising jet parts and clumping them together haphazardly. [This is of course, work, and it replicates bonding at random. "Work" is done when forces move their points of application along their lines of action. Thus in addition to the quantity of energy expended, there is also a specificity of resulting spatial rearrangement depending on the cluster of forces that have done the work. This of course reflects the link between "work" in the physical sense and "work" in the economic sense; thence, also the energy intensity of an economy with a given state of technology: energy per unit GDP tends to cluster tightly while a given state of technology and general level of economic activity  prevail. (Current estimate for Montserrat: 1.6 lbs CO₂ emitted per EC$ 1 of GDP, reflecting an energy intensity of 6 MJ/EC$, and the observation that burning one US Gallon of gasoline or diesel emits about 20 lbs of that gas. Thereby, too, lies suspended much of the debate over responses to feared climate trends (and the ironies shown in the 1997, Clinton era Byrd-Hagel 95-0 Senate resolution that unless certain key "developing" nations also made the sacrifice, the US would not sign to the Kyoto protocol [they refused to amend the draft to include non-Annex I countries, and the US has refused to sign; signatories then have gone on to bust the required emissions cuts . . .], but that bit of internationalist "folly-tricks" and spin-doctoring is off topic, though illuminating on the concept of work and how it brings the significance of intelligent direction to bear on energy flows once we get to the level of building complicated things that have to function . . .)] 

Q: After a time, will we be likely to get a flyable nano jet?

A: Overwhelmingly, on probability, no. (For, the vat has ~ [10^6]^3 = 10^18 one-micron locational cells, and a million parts or so can be distributed across them in vastly more ways than they could be across say 1 cm or so for an assembled jet etc or even just a clumped together cluster of micro-parts. [a 1 cm cube has in it [10^4]^3 = 10^12 cells, and to confine the nano-parts to that volume obviously sharply reduces the number of accessible cells consistent with the new clumped macrostate.] But also, since the configuration is constrained, i.e. the mass in the microjet parts is confined as to accessible volume by clumping, the number of ways the parts may be arranged has fallen sharply relative to the number of ways that the parts could be distributed among the 10^18 cells in the scattered state. (That is, we have here used the nanobots to essentially undo diffusion of the micro-jet parts.) The resulting constraint on spatial distribution of the parts has reduced their entropy of configuration. For, where W is the number of ways that the components may be arranged consistent with an observable macrostate, and since by Boltzmann, entropy, s = k ln W, we see that W has fallen so S too falls on moving from the scattered to the clumped state.

vi] For this vat, next remove the random cluster nanobots, and send in the jet assembler nanobots. These recognise the clumped parts, and rearrange them to form a jet, doing configuration work. (What this means is that within the cluster of cells for a clumped state, we now move and confine the parts to those sites consistent with a flyable jet emerging. That is, we are constraining the volume in which the relevant individual parts may be found, even further.) A flyable jet results — a macrostate with a much smaller statistical weight of microstates. We can see that of course there are vastly fewer clumped configurations that are flyable than those that are simply clumped at random, and thus we see that the number of microstates accessible due to the change, [a] scattered --> clumped and now [b] onward --> functionally configured macrostates has fallen sharply, twice in succession. Thus, by Boltzmann's result s = k ln W, we also have seen that the entropy has fallen in succession as we moved from one state to the next, involving a fall in s on clumping, and a further fall on configuring to a functional state; dS tot = dSclump + dS config. [Of course to do that work in any reasonable time or with any reasonable reliability, the nanobots will have to search and exert directed forces in accord with a program, i.e this is by no means a spontaneous change, and it is credible that it is accompanied by a compensating rise in the entropy of the vat as a whole and its surroundings. This thought experiment is by no means a challenge to the second law. But, it does illustrate the implications of the probabilistic reasoning involved in the microscopic view of that law, where we see sharply configured states emerging from much less constrained ones.]

vii] In another vat we put in an army of clumping and assembling nanobots, so we go straight to making a jet based on the algorithms that control the nanobots. Since entropy is a state function, we see here that direct assembly is equivalent to clumping and then reassembling from a random “macromolecule” to a configured functional one. That is: dS tot (direct) = dSclump + dS config.

viii] Now, let us go back to the vat. For a large collection of vats, let us now use direct microjet assembly nanobots, but in each case we let the control programs vary at random a few bits at a time -– say hit them with noise bits generated by a process tied to a zener noise source. We put the resulting products in competition with the original ones, and if there is an improvement, we allow replacement. Iterate, many, many times.

Q: Given the complexity of the relevant software, will we be likely to for instance come up with a hyperspace-capable spacecraft or some other sophisticated and un-anticipated technology? (Justify your answer on probabilistic grounds.)

My prediction: we will have to wait longer than the universe exists to get a change that requires information generation (as opposed to information and/or functionality loss) on the scale of 500 – 1000 or more bits. [See the info-generation issue over macroevolution by RM + NS?]

ix] Try again, this time to get to even the initial assembly program by chance, starting with random noise on the storage medium. See the abiogenesis/ origin of life issue?

x] The micro-jet is of course an energy converting device which exhibits FSCI, and we see from this thought expt why it is that it is utterly improbable on the same grounds as we base the statistical view of the 2nd law of thermodynamics, that it should originate spontaneously by chance and necessity only, without agency.

xi] Extending to the case of origin of life, we have cells that use sophisticated machinery to assemble the working macromolecules, direct them to where they should go, and put them to work in a self-replicating, self-maintaining automaton. Clumping work [if you prefer that to TBO’s term chemical work, fine], and configuring work can be identified and applied to the shift in entropy through the same s = k ln W equation. For, first we move from scattered at random in the proposed prebiotic soup, to chained in a macromolecule, then onwards to having particular monomers in specified locations along the chain -- constraining accessible volume again and again, and that in order to access observably bio-functional macrostates. Also, s = k ln W, through Brillouin, TBO link to information, viewed as "negentropy," citing as well Yockey-Wicken’s work and noting on their similar definition of information; i.e this is a natural outcome of the OOL work in the early 1980's, not a "suspect innovation" of the design thinkers in particular. BTW, the concept complex, specified information is also similarly a product of the work in the OOL field at that time, it is not at all a "suspect innovation" devised by Mr Dembski et al, though of course he has provided a mathematical model for it. [ I have also just above pointed to Robertson, on why this link from entropy to information makes sense — and BTW, it also shows why energy converters that use additional knowledge can couple energy in ways that go beyond the Carnot efficiency limit for heat engines.]

7] We can therefore see the cogency of Mathematician, Granville Sewell's observations, here. Excerpting:

. . . The second law is all about probability, it uses probability at the microscopic level to predict macroscopic change: the reason carbon distributes itself more and more uniformly in an insulated solid is, that is what the laws of probability predict when diffusion alone is operative. The reason natural forces may turn a spaceship, or a TV set, or a computer into a pile of rubble but not vice-versa is also probability: of all the possible arrangements atoms could take, only a very small percentage could fly to the moon and back, or receive pictures and sound from the other side of the Earth, or add, subtract, multiply and divide real numbers with high accuracy. The second law of thermodynamics is the reason that computers will degenerate into scrap metal over time, and, in the absence of intelligence, the reverse process will not occur; and it is also the reason that animals, when they die, decay into simple organic and inorganic compounds, and, in the absence of intelligence, the reverse process will not occur.

The discovery that life on Earth developed through evolutionary "steps," coupled with the observation that mutations and natural selection -- like other natural forces -- can cause (minor) change, is widely accepted in the scientific world as proof that natural selection -- alone among all natural forces -- can create order out of disorder, and even design human brains, with human consciousness. Only the layman seems to see the problem with this logic. In a recent Mathematical Intelligencer article ["A Mathematician's View of Evolution," The Mathematical Intelligencer 22, number 4, 5-7, 2000] I asserted that the idea that the four fundamental forces of physics alone could rearrange the fundamental particles of Nature into spaceships, nuclear power plants, and computers, connected to laser printers, CRTs, keyboards and the Internet, appears to violate the second law of thermodynamics in a spectacular way.1 . . . .

What happens in a[n isolated] system depends on the initial conditions; what happens in an open system depends on the boundary conditions as well. As I wrote in "Can ANYTHING Happen in an Open System?", "order can increase in an open system, not because the laws of probability are suspended when the door is open, but simply because order may walk in through the door.... If we found evidence that DNA, auto parts, computer chips, and books entered through the Earth's atmosphere at some time in the past, then perhaps the appearance of humans, cars, computers, and encyclopedias on a previously barren planet could be explained without postulating a violation of the second law here . . . But if all we see entering is radiation and meteorite fragments, it seems clear that what is entering through the boundary cannot explain the increase in order observed here." Evolution is a movie running backward, that is what makes it special.

THE EVOLUTIONIST, therefore, cannot avoid the question of probability by saying that anything can happen in an open system, he is finally forced to argue that it only seems extremely improbable, but really isn't, that atoms would rearrange themselves into spaceships and computers and TV sets . . . [NB: Emphases added. I have also substituted in isolated system terminology as GS uses a different terminology. Cf as well his other remarks here and here.]

8] What is the result of applying such considerations on the link between entropy and information to the issue of the suggested spontaneous origin of life? TBO in CH 8 set up a model prebiotic soup, on a planetary scale, with quite generous unimolar concentrations of the required amino acids [L-form only] to give rise to a hypothetical, relatively simple 100-link, 101-monomer biofunctional protein. Then, using the separability of the components of entropy, a state function, they work out that there is a configurational component, which can be estimated. 

Taking a step back to their analysis in Ch 7, which introduces the Gibbs Free Energy they will use:

By energy conservation: change in internal energy, dE is heat flow into the system, d'Q plus work done on the system, dW (a "simple" form of the 1st law of thermodynamics-- never mind mass flows etc for now):

dE = d'Q + dW . . . [Eqn A.5, cf. TBO 7.1 ]

using also: dS >/= d'Q/T, and using pressure-volume work of expansion against a pressure P, so dW = P*dV, we may blend the first and 2nd laws of thermodynamics:

dS >/= [dE + PdV]/T  . . . ["Eqn" A.6 cf. TBO 7.5]

or, multiplying through by T:  TdS >/= dE + PdV . . . ["Eqn" A.6.1]

Thus: dE + PdV - TdS </= 0  . . . ["Eqn" A.6.2]

Introducing the "simplifying" quantities Enthalpy [H] and Gibbs Free energy [G]: 

dH = dE + PdV . . . "Def'n" (with pressure, P, constant)

--> NB: if PdV = 0, then increment in enthalpy is the change in the internal energy of a system. [Thus, the common comment in Chemistry circles that enthalpy is "heat content": dW = 0, so d'Q = dE + 0 = dH, at constant pressure, and with no pressure-volume work involved.)

--> Of course, strictly, H = E + PV, so dE = dH + PdV + VdP, but if P is constant, VdP = 0. (I give this detail, as there is a common tendency among Evo Mat advocates, to suspect, assume, assert or even insist that Design-friendly thinkers are all hopelessly ignorant on these matters. An irrelevancy is then trotted out a a "proof" that the argument in the main can be dismissed. A red herring, leading out to a strawman to be pummelled.)

dG = dH - TdS . . . "Def'n" (where T is also effectively constant)

So, dH - TdS </= 0 . . . ["Eqn" A.6.3]

or, dG </= 0 . . . ["Eqn" A.6.4, cf. TBO 7.6]

Bringing in rates, through increment in time, dt, in a closed system:

dG/dt </= 0 . . .  ["Eqn" A.6.5, cf. TBO, 7.7]

Also, as a system approaches thermodynamic equilibrium under the particular circumstances obtaining:

dG/dt --> 0 . . . ["Eqn" A.7, cf. TBO, 7.8]

--> In other words, decrease in Gibbs free energy as a criterion of spontaneous process, is in effect the same as saying that entropy increases in a real world spontaneous process.

Then, also, we can back-substitute and rearrange to get:

dS/dt - [dE/dt + PdV/dt]/T >/= 0

i.e. dS/dt - [dH/dt]/T >/= 0  . . . ["Eqn" A.8]

--> That is, in spontaneous processes, rate of entropy change in the system {dS/dt} added to entropy change due to exchange of mechanical or thermal energy with surroundings {[dH/dt]/T} will be at least zero.

Going forward to the discussion in Ch 8, in light of the definition dG = dH - Tds, we may then split up the TdS term into contributing components, thusly:

First, dG = dE + PdV - TdS . . . [Eqn A.9, cf def'ns for G, H above]

But, [1] since pressure-volume work may be seen as negligible in the context we have in mind, and [2] since we may look at dE as shifts in bonding energy [which will be more or less the same in DNA or polypeptide/protein chains of the same length regardless of the sequence of the monomers], we may focus on the TdS term. This brings us back to the clumping then configuring sequence of changes in entropy in the Micro-Jets example above:

dG = dH - T[dS_"clump" +dS_config]  . . . [Eqn A.10, cf. TBO 8.5]

Of course, we have already addressed the reduction in entropy on clumping and the further reduction in entropy on configuration, through the thought expt. etc., above. In the DNA or protein formation case, more or less the same thing happens. Using Brillouin's negentropy formulation of information, we may see that the dSconfig is the negative of the information content of the molecule.

A bit of back-tracking will help:

S = k ln W . . . Eqn A.3

Now, W may be seen as a composite of the ways energy as well as mass may be arranged at micro-level. That is, we are marking a distinction between the entropy component due to ways energy [here usually, thermal energy] may be arranged, and that due to the ways mass may be configured across the relevant volume. The configurational component arises from in effect the same considerations as lead us to see a rise in entropy on having a body of gas at first confined to part of an apparatus, then allowing it to freely expand into the full volume:

Free expansion:

|| * * * * * * * * |            ||  

Then:

||  *   *   *   *  *   *  *  *  ||

Or, as Prof Gary L. Bertrand of university of Missouri-Rollo summarises:

The freedom within a part of the universe may take two major forms: the freedom of the mass and the freedom of the energy. The amount of freedom is related to the number of different ways the mass or the energy in that part of the universe may be arranged while not gaining or losing any mass or energy. We will concentrate on a specific part of the universe, perhaps within a closed container. If the mass within the container is distributed into a lot of tiny little balls (atoms) flying blindly about, running into each other and anything else (like walls) that may be in their way, there is a huge number of different ways the atoms could be arranged at any one time. Each atom could at different times occupy any place within the container that was not already occupied by another atom, but on average the atoms will be uniformly distributed throughout the container. If we can mathematically estimate the number of different ways the atoms may be arranged, we can quantify the freedom of the mass. If somehow we increase the size of the container, each atom can move around in a greater amount of space, and the number of ways the mass may be arranged will increase . . . .

The thermodynamic term for quantifying freedom is entropy, and it is given the symbol S. Like freedom, the entropy of a system increases with the temperature and with volume . . . the entropy of a system increases as the concentrations of the components decrease. The part of entropy which is determined by energetic freedom is called thermal entropy, and the part that is determined by concentration is called configurational entropy." 

In short, degree of confinement in space constrains the degree of disorder/"freedom" that masses may have. And, of course, confinement to particular portions of a linear polymer is no less a case of volumetric confinement (relative to being free to take up any location at random along the chain of monomers) than is confinement of gas molecules to one part of an apparatus. And, degree of such confinement may appropriately be termed, degree of "concentration." 

Diffusion is a similar case: infusing a drop of dye into a glass of water -- the particles spread out across the volume and we see an increase of entropy there. (The micro-jets case of course is effectively diffusion in reverse, so we see the reduction in entropy on clumping and then also the further reduction in entropy on configuring to form a flyable microjet.)

So, we are justified in reworking the Boltzmann expression to separate clumping/thermal and configurational components:

S = k ln (W_clump*W_config) = k lnW_th*W_c . . . [Eqn A.11, cf. TBO 8.2a]

or, S = k ln W_th + k ln W_c = S_th + S_c . . . [Eqn A.11.1]

We now focus on the configurational component, the clumping/thermal one being in effect the same for at-random or specifically configured DNA or polypeptide macromolecules of the same length and proportions of the relevant monomers, as it is essentially energy of the bonds in the chain, which are the same in number and type for the two cases. Also, introducing Brillouin's negentropy formulation of Information, with the configured macromolecule [m] and the random molecule [r], we see the increment in information on going from the random to the functionally specified macromolecule:

I_B = -[S_cm - S_cr]  . . . [Eqn A.12, cf. TBO 8.3a]

Or, I_B = S_cr - S_cm = k ln W_cr - k ln W_cm = k ln (W_cr/W_cm) . . . [Eqn A12.1.]

Where also, for N objects in a linear chain, n1 of one kind, n2 of another, and so on to ni, we may see that the number of ways to arrange them (we need not complicate the matter by talking of Fermi-Dirac statistics, as TBO do!) is:

W = N!/[n1!n2! . . . ni!] . . . [Eqn A13, cf TBO 8.7]

So, we may look at a 100-monomer protein, with as an average 5 each of the 20 types of amino acid  monomers along the chain , with the aid of log manipulations -- take logs to base 10, do the sums in log form, then take back out the logs --  to handle numbers over 10^100 on a calculator:

W_cr  =  100!/[(5!)^20] = 1.28*10^115

For the sake of initial argument, we consider a unique polymer chain , so that each monomer is confined to a specified location, i.e Wcm = 1, and Scm = 0. This yields -- through basic equilibrium of chemical reaction thermodynamics (follow the onward argument in TBO Ch 8) and the Brillouin information measure which contributes to estimating the relevant Gibbs free energies (and with some empirical results on energies of formation etc) -- an expected protein concentration of ~10^-338 molar, i.e. far, far less than one molecule per planet. (There may be about 10^80 atoms in the observed universe, with Carbon a rather small fraction thereof; and 1 mole of atoms is ~ 6.02*10^23 atoms. )  Recall, known life forms routinely use dozens to hundreds of such information-rich macromolecules, in close proximity in an integrated self-replicating information system on the scale of about 10^-6 m.

9] Recently, Bradley has done further work on this, using Cytochrome C, which is a 110-monomer protein. He reports, for this case (noting along the way that Shannon information is of course really a metric of information-carrying capacity and using Brillouin information as a measure of complex specified information, i.e I_B = I_CSI below), that:

Cytochrome c (protein) -- chain of 110 amino acids of 20 types

If each amino acid has pi = .05, then average information “i” per amino acid is given by log2 (20) = 4.32

The total Shannon information is given by I = N * i = 110 * 4.32 = 475, with total number of unique sequences “W0” that are possible is W0 = 2^I = 2^475 = 10^143

Amino acids in cytochrome c are not equiprobable (pi ≠ 0.05) as assumed above. 

If one takes the actual probabilities of occurrence of the amino acids in cytochrome c, one may calculate the average information per residue (or link in our 110 link polymer chain) to be 4.139 using i = - ∑ pi log2 pi [TKI NB: which is related of course to the Boltzmann expression for S]

Total Shannon information is given by I = N * i = 4.139 x 110 = 455. 

The total number of unique sequences “W0” that are possible for the set of amino acids in cytochrome c is given by W0 = 2^455 = 1.85 x 10^137

. . . . Some amino acid residues (sites along chain) allow several different amino acids to be used interchangeably in cytochrome-c without loss of function, reducing i from 4.19 to 2.82 and I (i x 110) from 475 to 310 (Yockey)

M = 2^310 = 2.1 x 10^93 = W1

Wo / W1 = 1.85 x 10^137 / 2.1 x 10^93 = 8.8 x 10^44

Recalculating for a 39 amino acid racemic prebiotic soup [as Glycine is achiral] he then deduces (appar., following Yockey):

W1 is calculated to be 4.26 x 10^62

Wo/W1 = 1.85 x 10^137 / 4.26 x 10^62 = 4.35 x 10^74

I_CSI = log2 (4.35 x 10^74) = 248 bits

He then compares results from two experimental studies:

Two recent experimental studies on other proteins have found the same incredibly low probabilities for accidental formation of a functional protein that Yockey found 

1 in 10^75 (Strait and Dewey, 1996) and 

1 in 10^65 (Bowie, Reidhaar-Olson, Lim and Sauer, 1990).

--> Of course, to make a functioning life form we need dozens of proteins and other similar information-rich molecules all in close proximity and forming an integrated system, in turn requiring a protective enclosing membrane. 

--> The probabilities of this happening by the relevant chance conditions and natural regularities alone, in aggregate are effectively negligibly different from zero in the gamut of the observed cosmos.

--> But of course, we know that agents, sometimes using chance and natural regularities as part of what they do, routinely produce FSCI-rich systems. [Indeed, that is just what the Nanobots and Micro-jets thought experiment shows by a conceivable though not yet technically feasible example.]

10] Ch 9 extends the discussion by exploring different scenarios for getting the required synthesis through spontaneous mechanisms, circa 1984: chance, prebiotic "natural selection," self-ordering tendencies, mineral catalysis, nonlinear non-equilibrium processes, experimental thermal synthesis, solar energy, energy-rich condensing agents, and energy-rich precursor molecules. The results are uniformly fruitless as soon as degree of investigator involvement is reduced to a credible one relative to the proposed prebiotic type environment.  In the twenty or so years since, as we just saw in Bradley's updated work, the manner of addressing the issue has generally shifted towards discussing information and probabilities more directly: complex, specified information, probability filters, etc., but as we also saw just above, the result is still more or less the same. (Cf. the recent peer-reviewed, scientific discussions here and here, by Abel and Trevors, in the context of the origin of the molecular nanotechnology of life.) 

11] In short summary: thermodynamics issues tied to the second law are both relevant and strongly adverse for the proposed spontaneous [chance + necessity only] origin of life in prebiotic conditions; rhetoric to the contrary notwithstanding. But, at he same time, we know that FSCI, the key factor in driving that adverse thermodynamics, is routinely produced by intelligent agents. Thus, based on what we do directly know about the source of FSCI in every case where we observe or experience its origin, the origin of the FSCI-rich nanotechnologies of life in the cell is best explained as the product of agency. (The further issue of identification of the agency/agencies directly or indirectly involved, of course, is not currently within the ambit of science, proper. A suggestive clue, however is to be found in the similarly fine-tuned observed cosmos, which is "set" so that biological life as we know it becomes possible. This is discussed supra. Related philosophical issues are addressed here.) 

---

APPENDIX 2:

On Censorship and Manipulative Indoctrination in science education 
and in the court-room: the Kitzmiller/Dover Case

The following was posted to the KairosFocus blog,  on receipt of the breaking news that Judge Jones' decision was, insofar as it addressed the scientific status of Intelligent design, essentially a near-verbatim excerpt of an ACLU post-trial submission. This not only underscores the case's status as a classic of improper judicial activism, but given the fact explained below that the Judge reproduced even the ACLU's many factual errors and misrepresentations in this part of his decision, it utterly destroys its credibility.

_____________________

Thursday, December 14, 2006

1 Chron 12:32 Report, no 9: the Dover ID case as a showcase example of manipulative secularist radicalism in the courts and media

BREAKING NEWS: A year after the Kitzmiller Decision in Dover, Pennsylvania, the Discovery Institute [DI] has just published a 34 p. article in which it shows, in devastating parallel columns, that Judge Jones' discussion of the alleged unscientific status of the empirically based inference to design, was largely copied from an ACLU submission, factual errors, misrepresentations and all.

DI summarises its findings thusly:

In December of 2005, critics of the theory of intelligent design (ID) hailed federal judge John E. Jones’ ruling in Kitzmiller v. Dover, which declared unconstitutional the reading of a statement about intelligent design in public school science classrooms in Dover, Pennsylvania. Since the decision was issued, Jones’ 139-page judicial opinion has been lavished with praise as a “masterful decision” based on careful and independent analysis of the evidence. However, a new analysis of the text of the Kitzmiller decision reveals that nearly all of Judge Jones’ lengthy examination of “whether ID is science” came not from his own efforts or analysis but from wording supplied by ACLU attorneys. In fact, 90.9% (or 5,458 words) of Judge Jones’ 6,004- word section on intelligent design as science was taken virtually verbatim from the ACLU’s proposed “Findings of Fact and Conclusions of Law” submitted to Judge Jones nearly a month before his ruling. Judge Jones even copied several clearly erroneous factual claims made by the ACLU. The finding that most of Judge Jones’ analysis of intelligent design was apparently not the product of his own original deliberative activity seriously undercuts the credibility of Judge Jones’ examination of the scientific validity of intelligent design.

Now, a year ago, Judge Jones of Pennsylvania issued his "landmark" decision on the Dover School Board case, which was indeed hailed in much of the major international media as a death-blow to the Intelligent Design movement (which has of course not gone away!). In effect, he ruled unconstitutional the reading out to students in 9th Grade [roughly, 3rd form] Biology the following statement:

The Pennsylvania Academic Standards require students to learn about Darwin’s Theory of Evolution and eventually to take a standardized test of which evolution is a part.

Because Darwin’s Theory is a theory, it continues to be tested as new evidence is discovered. The Theory is not a fact. Gaps in the Theory exist for which there is no evidence. A theory is defined as a well-tested explanation that unifies a broad range of observations.

Intelligent Design is an explanation of the origin of life that differs from Darwin’s view. The reference book, Of Pandas and People, is available for students who might be interested in gaining an understanding of what Intelligent Design actually involves.

With respect to any theory, students are encouraged to keep an open mind. The school leaves the discussion of the Origins of Life to individual students and their families. As a Standards-driven district, class instruction focuses upon preparing students to achieve proficiency on Standards-based assessments.

That such a statement -- in a time in which Darwinian Biology and the broader ideas of evolutionary materialism plainly continue to be scientifically, philosophically and culturally controversial -- would be widely seen as an attempt to impose "religion" in the name of "science," is itself a clue that something has gone very wrong indeed.

For, it is immediately obvious on examining basic, easily accessible facts, that:

a] The Neo-Darwinian Theory of Evolution [NDT] is just that: theory, not fact. This means that insofar as it is science, it is an open-ended explanatory exercise, one that is subject to correction or replacement in light of further evidence and/or analysis, and one that seeks to summarise and make sense of a vast body of empirical data -- in which effort there are indeed key, persistent explanatory gaps.

b] Design Theory, in that light, is a re-emerging challenger as a scientific explanation, one that arguably better explains certain key features of, say the fossil record. (And, let us observe here, that ID should not be confused with, say Young Earth, specifically Biblically-oriented Creationism [YEC], which seeks to scientifically explain origins in a context that often -- but not always -- makes explicit reference to the Bible, regarded as an accurate record of origins. Nor, is it merely a critique of darwinian thought, but rather a working out of addressing the full range of root-explanations for phenomena: chance, necessity and agency, in light of the only actually known, empirically observed source of FSCI: intelligent agency. For example, design thought, as a movement, does not deny that significant macro-level evolution may well have happened across geological time [NB: YEC thinkers accept that micro-evolution can and does occur], but it is raising and addressing the really central, empirically based, scientific issue: how may we best explain where the functionally specific, complex information in life and in the biodiversity in the fossil record and current came from, given what we know about the observed source of such FSCI?)

c] For instance, as Loennig points out in a recent peer-reviewed paper -- a paper submitted to Judge Jones, BTW -- on the well-known problem for the NDT that the fossil record is marked by sudden appearances and disappearances, starting from the Cambrian life explosion, and a resulting multitude of "missing links":

[On the hypothesis that] there are indeed many systems and/or correlated subsystems in biology, which have to be classified as irreducibly complex and that such systems are essentially involved in the formation of morphological characters of organisms, this would explain both, the regular abrupt appearance of new forms in the fossil record as well as their constancy over enormous periods of time . . . For, if "several well-matched, interacting parts that contribute to the basic function" are necessary for biochemical and/or anatomical systems to exist as functioning systems at all (because "the removal of any one of the parts causes the system to effectively cease functioning") such systems have to (1) originate in a non-gradual manner and (2) must remain constant as long as they are reproduced and exist [and also] (3) the equally abrupt disappearance of so many life forms in earth history . . . The reason why irreducibly complex systems would also behave in accord with point (3) is also nearly self-evident: if environmental conditions deteriorate so much for certain life forms (defined and specified by systems and/or subsystems of irreducible complexity), so that their very existence be in question, they could only adapt by integrating further correspondingly specified and useful parts into their overall organization, which prima facie could be an improbable process -- or perish . . . .

d] The call to an OPEN [but critically aware] mind in light of knowing the dominant theory and its gaps and that alternatives exist [note that ID was not to be expounded in the classroom!] is not a closing off of options but an opening of minds. (Notice how actual censorship is being praised when it serves the agenda of the secularist elites here.

e] Given the persistent absence of a credible, robust account of the origin of the functionally specific, complex information [FSCI] and associated tightly integrated information systems at the heart of the molecular technology of life, the origin of life is the first gap in the broader -- and, BTW, arguably self-refuting -- evolutionary materialist account of origins. Further to this, we must observe the force of the issue Loennig raises in his peer reviewed article on the challenge of viable macro-level spontaneous ["chance"] changes in DNA that express themselves embryologically early bring this gap issue not only to chemical evolution, but to the macro-evolution that NDT is supposed to explain, but does not. Ands such major explanatory gaps in the account of macro-evolution start with the Cambrian life explosion as Meyer noted in another peer-reviewed article. [Both of these were of course brought to Judge Jones' attention, and both were obviously ignored, even at he cost of putting out falsehoods and misrepresentations authored by the ACLU in his opinion. No prizes for guessing why.]

f] So, while -- as DI argues -- ID is too pioneering to be a part of the High School level classroom exposition (as opposed to an issue that legitimately arises incidentally in debates and discussions), the cluster of persistent issues that NDT and wider evolutionary materialism cannot account for, definitely should be; on pain of turning the science classroom into an exercise in manipulative indoctrination. The ongoing censorship of this scientific, philosophical, and cultural controversy is therefore utterly telling.

A glance at major features of the ruling itself amply confirms the problem. For instance, observe how the Judge addresses a major concern in the case, revealing that he is indulging in improper activism in his attempt to decide by judicial fiat a matter that properly belongs to the philosophy of science:

. . . the Court is confident that no other tribunal in the United States is in a better position than are we to traipse into this controversial area. Finally, we will offer our conclusion on whether ID is science not just because it is essential to our holding that an Establishment Clause violation has occurred in this case, but also in the hope that it may prevent the obvious waste of judicial and other resources which would be occasioned by a subsequent trial involving the precise question which is before us. [p. 63] (emphasis added)

It is unsurprising to see that, in the 139 page ruling, Judge Jones held -- among other things -- that the inference to design was an inherently illegitimate attempt to impose the supernatural on science, and so falls afoul of the US Constitution's First Amendment's principle of separation of Church and state. He also held, as a key plank in his decision -- even though an actual list of such papers was presented to him in a submission by the Discovery Institute [cf Appendix A4, p. 17, here] -- that there was no peer-reviewed ID supporting scientific literature.

Further to this, he refused to allow FTE, the publishers of the key book referenced in the case, Of Pandas and People, to intervene in the case to defend itself by participating in the trial, even though their work was being materially misrepresented -- which clearly affected the ruling. 

Misrepresented? Yes, this book, in the actually published version [the one that is relevant to determining what the authors and publishers intended and what the impact of the book being in school libraries would likely be] explicitly states:

This book has a single goal: to present data from six areas of science that bear on the central question of biological origins. We don't propose to give final answers, nor to unveil The Truth. Our purpose, rather, is to help readers understand origins better, and to see why the data may be viewed in more than one way. (Of Pandas and People, 2nd ed. 1993, pg. viii) . . . .

Today we recognize that appeals to intelligent design may be considered in science, as illustrated by current NASA search for extraterrestrial intelligence (SETI). Archaeology has pioneered the development of methods for distinguishing the effects of natural and intelligent causes. We should recognize, however, that if we go further, and conclude that the intelligence responsible for biological origins is outside the universe (supernatural) or within it, we do so without the help of science. (pg. 126-127, emphasis added)

In short -- and exactly as the 1984 technical level book, The Mystery of Life's Origins, the publication of which (claims to the contrary notwithstanding) is the actual historical beginning of the modern design movement [apart from in cosmology!] also argues -- we may properly and scientifically infer to intelligence as a cause from its empirically observable traces that are not credibly the product of chance or natural regularities.

But, of course, such an inference -- just as its opposite, the philosophically based premise that science "must" only infer to chance and natural regularities on questions of origins -- soon raises worldview issues. For, just as darwinian evolution is often used as a support for evolutionary materialism, a credible, empirically anchored scientific inference to design on the cases of: the origin of the molecular nanotechnology of life, that of the macro-level diversity of life and the origin of a finitely old, elegantly fine-tuned cosmos, plainly opens the philosophical and cultural doors to taking seriously what is "unacceptable" to many among the West's intensely secularised intellectual elites: God as the likely/credible intelligent designer, thence credibly the foundation of morality, law, and justice.

(So, let us pause: why is it that evolutionary materialist worldviews that go far beyond what is empirically and logically well-warranted are allowed to pass themselves off as "science," thus can freely go into the classroom, but empirically and logically/mathematically based serious challenges and alternatives to the claims of these worldviews that in fact appear in the peer-reviewed scientific and associated literature are excluded as "religion" [even when this is not at all objectively true]? Is this not blatant secularist indoctrination and censorship? Is not secular humanism, at minimum, a quasi-religion -- one that now is effectively established by court fiat under the pretence that we are "separating church and state"? Should we not instead teach key critical thinking skills and expose students to the range of live options, allowing them to draw their own, objectively defensible conclusions for themselves in the context of honest classroom dialogue based on comparative difficulties? [NB: Here are my thoughts on science education, from a science teaching primer that I was once asked to develop. Perhaps, this lays out a few ideas on a positive way forward.])

Nor, is this worldview-level dispute a new point. Indeed, as far back as Plato in his The Laws, we may read:

Ath. . . . we have . . . lighted on a strange doctrine.
Cle. What doctrine do you mean?
Ath. The wisest of all doctrines, in the opinion of many.
Cle. I wish that you would speak plainer.
Ath. The doctrine that all things do become, have become, and will become, some by nature, some by art, and some by chance.
Cle. Is not that true?
Ath. Well, philosophers are probably right; at any rate we may as well follow in their track, and examine what is the meaning of them and their disciples.
Cle. By all means.
Ath. They say that the greatest and fairest things are the work of nature and of chance, the lesser of art, which, receiving from nature the greater and primeval creations, moulds and fashions all those lesser works which are generally termed artificial . . . . . fire and water, and earth and air, all exist by nature and chance . . . The elements are severally moved by chance and some inherent force according to certain affinities among them . . . After this fashion and in this manner the whole heaven has been created, and all that is in the heaven, as well as animals and all plants, and all the seasons come from these elements, not by the action of mind, as they say, or of any God, or from art, but as I was saying, by nature and chance only . . . . Nearly all of them, my friends, seem to be ignorant of the nature and power of the soul [i.e. mind], especially in what relates to her origin: they do not know that she is among the first of things, and before all bodies, and is the chief author of their changes and transpositions. And if this is true, and if the soul is older than the body, must not the things which are of the soul's kindred be of necessity prior to those which appertain to the body? . . . . if the soul turn out to be the primeval element, and not fire or air, then in the truest sense and beyond other things the soul may be said to exist by nature; and this would be true if you proved that the soul is older than the body, but not otherwise. [Emphases added]

Plato, of course is here seeking to ground the moral basis of law [cf the introduction to Book 10 in the linked], and thus exposes what is at stake in the current debate over the scientific status of the inference to design: the moral foundation of civilisation itself - not just a matter of the nominal, vexed but technical issue of demarking science from non-science. Thus, the intensity of the debate and the too-frequent resort to dubious rhetorical and legal tactics as just outlined are all too understandable: a lot is at stake.

Dubious rhetorical and legal tactics?

Yes, sad to say:

1] First and tellingly, as a lower court Federal Judge under the US Congress, Mr Jones, strictly, has no proper jurisdiction on the matter. The First Amendment to the US Constitution, in the relevant clauses states: Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech. That is, there is to be no Church of the United States [though at the time of passage in 1789, nine of thirteen states had state churches]. In that context, dissenters were to be free to hold and freely express and publish their beliefs. So, the specific matter in question in the Dover case should have been decided democratically by a well-informed local community, (That this is manifestly not so, shows -- sadly, but tellingly -- just how much the public has been ill-served by both the media and the courts.)

2] That on the ground, this is not so, and the related commonplace idea that the US Constitution establishes a separation of church and state -- increasingly, a separation of Judaeo-Christian worldview and state such that any tracing of any policy to such a worldview at once renders the policy in question suspect and to be banned, is a mark of longstanding successful manipulative misreadings of the US Constitution, and of associated legislation from the bench by unaccountable judges, also known as judicial activism.

3] Indeed, the case in view is a showcase example of improper judicial activism and where it leads: Judge Jones took the submittal from one side, ignoring testimony and evidence in open court and in submittals from relevant parties that would have exposed the errors and misrepresentations. So, he took the ACLU's arguments, misrepresentations, obvious factual errors and all, and by and large reproduced it wholesale as his decision.

4] The root of these misrepresentations is the idea that inference to design is inherently about the injection of the supernatural into science, which is deemed improper. But in fact Judge Jones' idea that for centuries, science has been defined as exclusively naturalistic is simply false to the history of Science. For, as Dan Peterson notes: 

Far from being inimical to science, then, the Judeo-Christian worldview is the only belief system that actually produced it. Scientists who (in Boyle's words) viewed nature as "the immutable workmanship of the omniscient Architect" were the pathfinders who originated the scientific enterprise. The assertion that intelligent design is automatically "not science" because it may support the concept of a creator is a statement of materialist philosophy, not of any intrinsic requirement of science itself.

5] Nor (as we saw above) is the design inference -- ACLU et al notwithstanding, properly speaking, as a scientific inference, an inference to the supernatural [as opposed to the intelligent]. Indeed, when William Dembski (perhaps the leading design theorist) sets out to formally define, he writes:

. . . intelligent design begins with a seemingly innocuous question: Can objects, even if nothing is known about how they arose, exhibit features that reliably signal the action of an intelligent cause? . . . Proponents of intelligent design, known as design theorists, purport to study such signs formally, rigorously, and scientifically. Intelligent design may therefore be defined as the science that studies signs of intelligence.

6] In this context, the Judge's [and the ACLU's] gross factual error of insisting in the teeth of actual listed and accessible peer reviewed scientific publications that are supportive of the design inference, is utterly inexcusable -- and (since the judge may simply naively have allowed himself to be misled) it is frankly dishonest on the part of the likes of the ACLU and others who insistently assert this falsehood.

So, what a difference a year makes! Those who stood up a year ago and said -- with reasons -- from day one that this case was wrongly ruled on and unjustly decided, are now vindicated. However, given what is at stake, I will not hold my breath waiting for an apology and retraction.

For, sadly, the discourse in education, the media, courts and parliaments these days is too often more a matter of spin than of fearless straight thinking that seeks to discover and stand up for the truth, the right, the wise and the sound. As the Greeks used to say, a word to the wise . . . END

UPDATE: Minor editing, addition of a few comments and of links. Also, Dec 16, expanding on the Dover statement in light of a comment made at EO.

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APPENDIX 3:

On the origin, coherence and significance of the concept, "Complex, Specified Information."

It has often been claimed that the concept, Complex Specified Information, CSI, as has been championed by Dr William Dembski and other leading Intelligent Design theorists, is vague,  incoherent and useless, "not scientific," etc. This assertion is then often used to dismiss without serious consideration the matters gone into above.

Even though the above note focuses on a more easily identified and explained subset of the CSI concept, functionally specified complex information, FSCI, clarifying the general contentiousness over the wider term CSI is relevant to those interested in making a considered judgement on the issue of inference to design.

It is therefore appropriate to first of all point out that the core idea in the CSI concept is in fact simple, coherent and a result of the natural evolution of  Origin of Life [OOL] studies by the turn of the 1980's. 

This, we may do by citing the very first (and then quite well-received) technical level Design Theory book, The Mystery of Life's Origin [TMLO]. [This work was first published in 1984, was authored by by Thaxton, Bradley and Olson [TBO] and bears a foreword by noted OOL researcher, Dean Kenyon (who, astonishingly, publicly recanted his earlier biochemical predestination thesis in the foreword; in part, based on the arguments in TMLO). ]

Indeed, based on TBO's report in TMLO, if any one person can be said to have originated the term, it is noted OOL researcher Leslie Orgel, as the following excerpts and notes from Chapter 8 indicate:

--> In that chapter, we may first see how TBO build up to their discussion on thermodynamics and the origin of life, by first highlighting that the key issue is the origin of the cell's informational macromolecule-based metabolic motor. 

--> Prigogine's remark that his Nobel Prize-winning work on systems constrained to be far from equilibrium has not solved the problem of "the mechanisms responsible for the emergence and maintenance of coherent states" is also tellingly important. 

--> The crucial distinction between order and complexity is thus introduced by TBO: "a periodic structure has order. An aperiodic structure has complexity."  Such orderly periodic structures, as a rule, are in the main governed by natural regularities tracing to mechanical necessity and also tend to reflect boundary conditions at their time and place of origin. 

CASE STUDY -- of cyclones and snowflakes: A tropical cyclone is by and large shaped by convective and Coriolis forces acting on a planetary scale over a warm tropical ocean whose surface waters are at or above about 80 degrees F. That is, it is a matter of chance + necessity leading to order under appropriate boundary conditions, rather than to complex, functionally specified information. 

Similarly, the hexagonal, crystalline symmetry of snowflakes is driven by the implications of the electrical polarisation in the H-O-H (water) molecule -- which is linked to its kinked geometry, and resulting hexagonal close packing. Their many, varied shapes are controlled by the specific micro-conditions of the atmosphere along the path travelled by the crystal as it forms in a cloud.

As the just linked summarises [in a 1980's era, pre-design movement Creationist context] and illustrates by apt photographic examples [which is a big part of why it is linked]:

Hallet and Mason². . . found that water molecules are preferentially incorporated into the lattice structure of ice crystals as a function of temperature. Molecules from the surrounding vapor that land on a growing crystal migrate over its surface and are fixed to either the axial [tending to lead to plate- or star-shaped crystals] or basal planes [tending to lead to columnar or needle-like crystals] depending upon four temperature conditions. For example, snow crystals will grow lengthwise to form long, thin needles and columns . . . when the temperature is between about -3°C and -8°C. When the temperature is between about -8°C and -25°C, plate-like crystals will form . . . Beautiful stellar and dendritic crystals form at about -15°C. In addition, the relative humidity of the air and the presence of supercooled liquid cloud droplets will cause secondary growth phenomena known as riming and dendritic growth. [NB: this is what leads to the most elaborate shapes.] The small, dark spheres attached to the edges of the plate[-type crystal] in Figure 5 are cloud droplets that were collected and attached to the snow crystal as rime as the crystal fell through these droplets on its way to the earth's surface. The dendritic and feathery edges . . . are produced by the rapid growth of snow crystals in a high-humidity environment  . . . . The modern explanation of the hexagonal symmetry of snow crystals is that a snow crystal is a macroscopic, outward manifestation of the internal arrangement of the molecules in ice. The molecules form an internal pattern of lowest free energy, one that possesses high structural symmetry. For the water molecule this is a type of symmetry called hexagonal close pack.

["Microscopic Masterpieces: Discovering Design in Snow Crystals," Larry Vardiman, ICR, 1986. (Note, too, from the context of the above excerpts, on how "design"  and "creation" are rather hastily inferred to in this 1980's era Creationist article; a jarringly different frame of thought from the far more cautious, empirical, step by step explanatory filter process and careful distinctions developed by TBO and other design theorists. Subsequently, many Creationists have moved towards the explanatory filter approach pioneered by the design thinkers. This article -- from Answers in Genesis' Technical Journal -- on the peacock's tail is an excellent example, and a telling complement to the debates on the bacterial flagellum. Notice, in particular, how it integrates the aesthetic impact issue that is ever so compelling intuitively with the underlying issue of organised complexity to get to the aesthetics.) Cf also an AMS article here.]

A snowflake may indeed be (a) complex in external shape [reflecting random conditions along its path of formation] and (b) orderly in underlying hexagonal symmetrical structure [reflecting the close-packing molecular forces at work], but it simply does not encode functionally specific information. Its form simply results from the point-by-point particular conditions in the atmosphere along its path as it takes shape under the impact of chance [micro-atmospheric conditions] + necessity [molecular packing forces]. 

The tendency to wish to use the snowflake as a claimed counter-example alleged to undermine the coherence of the CSI concept thus plainly reflects a basic confusion between two associated but quite distinct features of this phenomenon: 

(a) external shape -- driven by random forces and yielding complexity [BTW, this is in theory possibly useful for encoding information, but it is probably impractical!]; and, 

(b) underlying hexagonal crystalline structure -- driven by mechanical forces and yielding simple, repetitive, predictable order. [This is not useful for encoding at all . . .] Of course, other kinds of naturally formed crystals reflect the same balance of forces and tend to have a simple basic structure with a potentially complex external shape, especially if we have an agglomeration of in effect "sub-crystals" in the overall observed structure.

In short, a snowflake is fundamentally a crystal, not an aperiodic and functionally specified information-bearing structure serving as an integral component of an organised, complex information-processing system, such as DNA or protein macromolecules manifestly are.

--> Such a careful distinction between order, complexity and aperiodic, functionally specified complexity is vital, as: "Nucleic acids and protein are aperiodic polymers, and this aperiodicity is what makes them able to carry much more information."  

--> Thus, we see that "only certain sequences of amino acids in polypeptides and bases along polynucleotide chains correspond to useful biological functions."

--> Moreover, as has been pointed out, if one breaks a snowflake, one still has (smaller) ice crystals. But, if one breaks a bio-functional protein, one does not have smaller, similarly bio-functional proteins. That is, the complexity of the protein molecule as a whole is an integral part of its specific functionality.

--> This leads us back to the crucial point of departure, in 1973, with Orgel's observation that defines the concept of specified complexity on observation and comparison of:

(a) the complex, specific, functional organisation of living cell-based organisms, with

(b) the simple order of crystals and

(c) the complex disorder of random polymers or lumps of granite.

Citing:

 . . . In brief, living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity. [The Origins of Life (John Wiley, 1973), p. 189.]

--> As well, in 1979, J S Wicken brought out the closely related concept of functionally specific, complex information in the context of living systems thusly:

‘Organized’ systems are to be carefully distinguished from ‘ordered’ systems.  Neither kind of system is ‘random,’ but whereas ordered systems are generated according to simple algorithms [[i.e. “simple” force laws acting on objects starting from arbitrary and common- place initial conditions] and therefore lack complexity, organized systems must be assembled element by element according to an [originally . . . ] external ‘wiring diagram’ with a high information content . . . Organization, then, is functional complexity and carries information. It is non-random by design or by selection, rather than by the a priori necessity of crystallographic ‘order.’ [“The Generation of Complexity in Evolution: A Thermodynamic and Information-Theoretical Discussion,” Journal of Theoretical Biology, 77 (April 1979): p. 353, of pp. 349-65. (Emphases and notes added. Nb: “originally” is added to highlight that for self-replicating systems, the blue print can be built-in.)]

--> The idea-roots of the term "functionally specific complex information" [FSCI] are thus plain: "Organization, then, is functional[[ly specific] complexity and carries information."

We may therefore contrast three sets of letters that show the distinction among three classes of linearly ordered digital sequences, by way of illustrative example (one paralleled by Peterson as cited above):

1. [Class 1:] An ordered (periodic) and therefore specified arrangement:

THE END THE END THE END THE END

Example: Nylon, or a crystal . . . . 

2. [Class 2:] A complex (aperiodic) unspecified arrangement:

AGDCBFE GBCAFED ACEDFBG

Example: Random polymers (polypeptides).

3. [Class 3:] A complex (aperiodic) specified arrangement:

THIS SEQUENCE OF LETTERS CONTAINS A MESSAGE!

Example: DNA, protein.

Such a linear spatial pattern makes the case in a very simple, effective and relevant way, as DNA and proteins as initially formed are precisely such linear discrete-state chains of information-bearing elements, typically 300 monomers long -- requiring 900 DNA base pairs, which can store 1,800 bits of information. And, we observe that sufficiently long class-three strings of letters are invariably the product of intelligent agents. (Thus, we see again the point that the inference to design on observing such a pattern is based on a great deal of empirically based knowledge about the sources of such phenomena.) 

But also, proteins are folded into three-dimensional, key- and- lock fitting frameworks that are precisely functional and strongly dependent on that spatial ordering. Obviously, and in light of the pattern of hydrophilic and hydrophobic elements and other bonding forces, the three-dimensional state is largely a result of the linear one. That is, the linear sequence in part encodes information that determines the functionality of the folded protein.

It is worth pausing to jump several decades ahead in time, and introduce and briefly comment on an illustrative figure by Trevors and Abel, Fig 4 from their recent [peer-reviewed] 2005 paper on "Three subsets of sequence complexity and their relevance to biopolymeric information":

Fig A3.1:  Contrasting different types of sequences and their characteristics [used under the US NIH's Open Access permission] TA's description of their Fig 4: Superimposition of Functional Sequence Complexity onto Figure 2 [i.e. from their paper]. The Y1 axis plane plots the decreasing degree of algorithmic compressibility as complexity increases from order towards randomness. The Y2 (Z) axis plane shows where along the same complexity (more ...

Here we may observe that sequences that exhibit order  are quite distinct from those that exhibit either random sequence complexity or complex functional organisation. We may observe that complexity is maximised and algorithmic compressibility [ability to be simply and briefly described, in effect] is minimised in a long random sequence [cf TBO's Class 2 supra]. By contrast, a long but orderly sequence [Class 1] is of high compressibility but low complexity. A long, functionally specified, organised, complex sequence [Class 3]  is as a rule not quite as "complex" -- per metrics of complexity -- as a long random sequence; as it would have in it the redundancies and periodicities that are part and parcel of effective communication. However, by contrast with both order and randomness, it exhibits high functionality; which is of course observable (and so can in principle be associated with a count of the number of ways that components may be configured compatible with that functionality, as opposed to the usually far higher number of possible arrangements in total; cf the microjets case supra). [NB: while of course these ideas are developed relative to linear sequences, they extend to higher dimensionalities as well, and can be generalised in thinking about order, randomness and organised, functional complexity.]

Further to this, let us observe that crystals, a paradigmatic instance of order, form due to the mechanical necessity imposed by inter-atomic [or ionic or molecular] forces, once the random energy always present at micro level has been brought sufficiently low under the prevailing local circumstances that the order may manifest itself through crystallisation; that is, natural regularities tracing to mechanical necessity prevail and there is a low contingency that results; thence, low information-storing capacity. In the case of the sort of random arrangements of say particles diffused or dissolved in a fluid, there are typically a great many -- as a rule aperiodic -- arrangements that are compatible with the conditions prevailing: high contingency, but low periodicity and low useful information, but (per that high contingency) a high potential for information storing capacity. In the case of a functionally organised, information-bearing entity, there is relatively high contingency and relatively high aperiodicity but that is associated with also, a highly specific functionality requirement such that the number of compatible configurations, as a fraction of all possible configurations, is relatively low: information is actually stored, and is in large part manifest in the specificity of the actual -- as opposed to potential -- arrangement. Functional, information-rich organisation is specific, aperiodic and complex, depending for its existence on high contingency.

From their examination of different types of linear sequences, TBO then proceed to Yockey and Wickens' powerful summary of the key issue:

Yockey⁷ and Wickens⁵ develop the same distinction, that "order" is a statistical concept referring to regularity such as could might characterize a series of digits in a number, or the ions of an inorganic crystal. On the other hand, "organization" refers to physical systems and the specific set of spatio-temporal and functional relationships among their parts. Yockey and Wickens note that informational macromolecules have a low degree of order but a high degree of specified complexity. In short, the redundant order of crystals cannot give rise to specified complexity of the kind or magnitude found in biological organization; attempts to relate the two have little future. 

[NB: Emphases and colours added for clarity. The green highlighted portions just above, of course, indicate one of the key idea-sources for my own terminology, FSCI. Observe as well the long-since given answer to the commonly encountered confusion between the order of crystals and the like, the complexity found in random polymers and the like, and the specified complexity found in the key informational macromolecules of life: "the redundant order of crystals cannot give rise to specified complexity of the kind or magnitude found in biological organization; attempts to relate the two have little future." ]

So, by 1984, the concept of complex specified information had emerged from the natural progression of OOL studies, and its implications for the source of such organised complexity had been recognised by the pioneer workers in design theory, Thaxton, Bradley and Olsen, [TBO]. 

However, perhaps due to their context of OOL studies (which has to deal with extraordinary degrees of complexity on a routine basis), and also due to their focus on thermodynamics issues, this cluster of original design theory authors did not explicitly identify the degree of complexity that would be required to mark an upper limit of what was feasibly reachable by random, stochastic processes. However, in the thermodynamics calculations TBO made in Ch 8 of TMLO, they were able to show from fundamental classical and statistical thermodynamics principles calculations, that the likely concentrations of even relatively simple proteins and DNA strands in even generous pre-biotic soups would be negligibly different from zero. (Compare, Appendix 1 above, and also the updated information theory-oriented calculations presented by Bradley, here.)

Thus, Dembski plainly did not not introduce a dubious novelty. Instead, starting in the 1990's, he refined, elaborated and mathematically modelled an existing and well-accepted concept -- quantifying in particular what we may descriptively term "the edge of chance." 

Namely:

1]  By focusing on the classic causal factors, (a) chance, (b) necessity and (c) agency, he was able to highlight that a highly contingent situation is not dominated by necessity. [NB: This is discussed in the just linked.]

2] By developing the concept of the universal probability bound, UPB, he was able to stipulate a yardstick for sufficient complexity to be of interest, namely odds of 1 in 10^150. Thus, we can see that for a uniquely specified configuration, if it has in it significantly more than 500 bits of information storage capacity, it is maximally unlikely that it is a product of chance processes. (To make this an even more generous yardstick: since we can have islands or archipelagos of function in a configuration space, we can stipulate that once the information storage capacity of an entity exceeds 500 - 1,000 bits, it is maximally unlikely to have been formed by chance, on the gamut of the observed cosmos. 1,000 bits of course corresponds to about 10^301 possible states.) 

3]  He then used the concept of specification as an independent, detachable pattern that characterises the relevant cluster of states, to create the third element of his now famous explanatory filter. (Cf. also here, on coming back from the cut and thrust of [too often dubious] debate tactics to the core scientific questions on this.)

4] In effect, if we can have [a] an independent, precise, "detachable" description of the state, and/or [b] it is functionally observable and distinct [such as biofunction as is noted on above or "flyability" as is discussed in Appendix 1 section 6], and/or [c] the precise description is compressible through a process identified by Kolmogorov [as opposed to you in effect have to list out the details of the state to precisely describe it, taking up more or less as much information storage capacity as the original state does (cf. here how we have to describe the winning number in a lottery by citing it)], we can objectively identify specification. The concept can be mathematically elaborated in great detail as a model, but this is enough for our purposes. [Cf here, here, here and especially here for a start on such elaboration.]

5] Dembski et al then tellingly and correctly observed that in all cases where we do directly know the causal story of an instance of CSI, the explanatory filter aptly rules that agents are responsible. (Given the willingness to cheerfully accept a potentially enormous number of false negatives in the interests of not having false positives, through the use of the UPB, that is no surprise.)

6]  In effect, through the explanatory filter, we have now identified what we may descriptively term, "the edge of chance." For, on the gamut of the "observed" universe, if a contingent event includes over 500 - 1,000 bits of information storage capacity, and is specified (especially functionally so) then it is maximally unlikely to have formed by chance dominated processes. At the same time, it is a member of a class of phenomena known to be routinely caused by intelligent agents. Thus, the action of such intelligent agency becomes its best, empirically anchored explanation.

Enormous consequences stem from that. 

For, as we discuss in the main body of this note, the origin of life, the body-plan level biodiversity we observe and the organised complexity of the fine-tuned, life facilitating cosmos we inhabit all are well beyond the UPB and are manifestations of functionally specified complex information [FSCI], a subset of CSI.

So, on inference to empirically anchored best explanation, OOL, body-plan level biodiversity and the physics of a life-facilitating cosmos all are credibly sourced in agent action. This of course cuts clean across the evolutionary materialist worldview and linked research programmes in science, so it is enormously controversial. 

Thus, also, the worldviews-tinged controversies surrounding Dr Dembski's work. END

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APPENDIX 4:

MORE ON CHANCE, NECESSITY AND AGENCY:

This often confusing issue is best initially approached/understood through a concrete example . . . 

A CASE STUDY ON CAUSAL FORCES/FACTORS -- A Tumbling Die: Heavy objects tend to fall under the law-like natural regularity we call gravity. If the object is a die, the face that ends up on the top from the set {1, 2, 3, 4, 5, 6} is for practical purposes a matter of chance. 

But, if the die is cast as part of a game, the results are as much a product of agency as of natural regularity and chance. Indeed, the agents in question are taking advantage of natural regularities and chance to achieve their purposes! 

This concrete, familiar illustration should suffice to show that the three causal factors approach is not at all arbitrary or dubious -- as some are tempted to imagine or assert. 

[NB: This example is simple, concrete and familiar enough to get away with saying that chance processes are significantly "like that," but the underlying concept is hard to pin down and/or highly technical once we move beyond such "family resemblance to key exemplary cases." Summarising from such simple cases: a chance process or causal factor gives or potentially gives outcomes that vary across a range of possibilities; beyond our actual control or ability to specifically and consistently accurately predict; and, often in accord with a random variable- based mathematical probability/statistical distribution such as the flat, Gaussian, Binomial or Weibull, etc. In short, it is contingent, but not evidently directed; that is why it is the default ruling for the explanatory filter when we see significant contingency but cannot unambiguously identify FSCI, which is associated with active intelligent direction. (Cf. discussions of chance, randomness and probability here, here (or here, simpler), here, and here [v. interesting book] for somewhat more technical expositions.) ] 

However, despite the familiarity of playing a game and tossing a die or two as an illustration of chance, necessity and purpose in action, some argue that in the key cases in mind for ID, there is an unjustified worldview level basic assumption at work; i.e. we are accused of improperly assuming that a designer (especially -- shudder -- a supernatural one!) exists, then inferring to such question-beggingly. This objection is apparently ultimately rooted in Kant's idea that in effect we can never know things as such [the noumenal world] but only as our senses and thought-world shapes them [the phenomenal world]: 

1 --> First, a basic corrective: we must beg to remind those who are misled by the now all-too-pervasive (and at best irresponsible and prejudicial) anti-design dismissive rhetoric about natural/supernatural causes, that intelligent design quite explicitly studies SIGNS of intelligence, not intelligence itself. That is, it is premised on the well-known or easily accessible facts that: 

[a] we routinely experience and observe the reality of intelligence in action and so can identify/recognise intelligent agents [at minimum; on a "family-resemblance" case-by-case basis], 

[b] from that base of experience we know beyond reasonable doubt that the actions by intelligent agents often issue in characteristic and empirically recognisable traces (such as functionally specified, complex information, FSCI), so

[c] we therefore may and do routinely and often reliably distinguish the natural and the artificial as causal factors; which -- as Plato pointed out, 2300+ years ago -- is a distinction long since made by serious thinkers, one that was immemorial in his day. 

[d] The "natural" category, as we view it today, includes: material or mechanical factors tracing to (1) chance and (2) necessity. (NB: Plato used phusis in a way that seems closely related to the lawlike mechanical necessity we focus so much on in scientific work, separating out chance as a separate category.) The latter category, "artificial" factors tracing to (3) intelligence.

[e] Where the natural/supernatural issue is concerned, first, ever since the first technical level design theory book, by Thaxton et al, The Mystery of Life's Origin, 1984 [Epilogue, pp. 188 - 214], it has been repeatedly noted that (for instance) (i) life on earth may arguably be traced to an intelligent cause, per signs of intelligence, but (ii) locating the provenance of such a cause as being within/beyond the cosmos is a step beyond what science proper is capable of. Indeed, the first major popular-level design theory book, Of Pandas and People explicitly notes:

This book has a single goal: to present data from six areas of science that bear on the central question of biological origins. We don't propose to give final answers, nor to unveil The Truth. Our purpose, rather, is to help readers understand origins better, and to see why the data may be viewed in more than one way. (2nd ed. 1993, pg. viii) . . . .

Today we recognize that appeals to intelligent design may be considered in science, as illustrated by current NASA search for extraterrestrial intelligence (SETI). Archaeology has pioneered the development of methods for distinguishing the effects of natural and intelligent causes. We should recognize, however, that if we go further, and conclude that the intelligence responsible for biological origins is outside the universe (supernatural) or within it, we do so without the help of science. (pg. 126-127, emphasis added)

[f] However, once we see credible signs of intelligence and infer to intelligent causes (e.g. on the best explanation for the origin of an evidently multiply fine-tuned, life facilitating cosmos), circumstantial details and wider philosophical questions, investigations and experiences may lead some to infer to an extra-cosmic intelligent and even supernatural cause (e.g. of the observed cosmos). For instance, many Christian thinkers are impressed by the Logos Theology in John 1:1 - 5 (cf. Gen 1:1 ff. & Isa. 45:18 - 24 with Phil 2:5 - 11); and, by closely related texts such as Acts 17:22 - 28, Rom. 1:20 ff., Col 1:15 - 20, and Heb 1:1 - 3, which jointly put Reason/ Intelligence/ Communication Himself at the centre of our origin and sustained existence. [NB: In reading Rom 1:20 ff., compare vv 1 - 4 in light of 1 Cor 15:1 - 11; also 2 Peter 3:3 - 13 & 1:2 - 4 (cf. Rom 8:9 - 11) and Prov. 20:27, along with Locke's remarks in the introduction to his essay on human understanding section 5, which crucially cites 2 Peter 1:2 - 4 and Prov 20:27.]  Such an extension of the scientific considerations above is plainly a worldview-level right and also a philosophical/ theological case that arguably may reasonably be made; but, strictly speaking, it is not in itself a scientific inference. (Just as, properly, the now commonly met with inference to an unobserved infinitely large multiverse which has thrown up our observed sub-cosmos at random is strictly a worldview level philosophical, not a scientific, inference. [Cf. Leslie's "fly on the wall" response to it, excerpted above.])

2 --> Now also, Kant's underlying concept is self refuting; for, as F. H. Bradley aptly showed in his gentle but stinging opening salvo in his Appearance and Reality, 2nd Edn: “The man who is ready to prove that metaphysical knowledge is impossible has . . . himself . . . perhaps unknowingly, entered the arena [of metaphysics] . . . . To say that reality is such that our knowledge cannot reach it, is to claim to know reality.”  [(Clarendon Press, 1930), p.1.] 

3 -->  The philosophers Kreeft and Tacelli provide a bit of clarifying expansion on F. H. Bradley's key but rather compressed point:

[Kant’s] “Copernican Revolution in philosophy” was the claim that our knowledge does not conform to a real object but vice versa . . . All the form, determination, specificity or knowable content comes from the mind and is projected out onto the world rather than coming from the world and being impressed upon the mind . . . .

Kant’s “Copernican Revolution” is self-contradictory, just as simple [radical or selective] skepticism is. After all, if Kant was right, how could he possibly have known he was right in terms of his system? He couldn’t. He could never know that there are “things- in- themselves,” onto which the knowing self projects all knowable content. That would be knowing the unknowable, thinking both sides of thought’s limit. 

There is a half truth in Kantianism. Some knowledge is conditioned by our forms of consciousness(e.g. Colors by the eye, measurements by artificial scales and ideological positions by personal preferences). But even here there must be some objective content first that is received and known, before it can be classified or interpreted by the knowing subject. [Handbook of Christian Apologetics, (Crowborough, England: Monarch, 1995) pp. 372 – 373. (The reader may also wish to peruse Mortimer Adler's essay on "Little Errors at the Beginning," here, on the underlying pervasive problem of such errors in modern philosophising.)]

4 --> So, we ARE discussing what may objectively be in the external world not just in our perceptions considered as pre-filtered mental data, and a preconceived infrastructure of ideas. Hence also, the Kantianism-derived notion that in effect to infer to agent cause is “necessarily” to impose within our minds the unwarranted, before the fact category of agents -- and thus (in the minds of such objectors to the design inference) to invite all sorts of rhetorical assertions on how such an assumption is a priori, ill-founded, unnecessarily limiting, etc, etc, etc -- is plainly hopelessly fallacious.

5 --> By sharpest corrective contrast, let us consider the point raised by Josiah Royce: “error exists” implies that there is knowable truth. (To see that just try to deny that little claim –- it is undeniably and self-evidently true, as, the attempted denial will only manage to exemplify its truth. Thus, once (a) we understand what the terms speak of and (b) we see how they are connected in light of our experience of reality [applying a modicum of common sense], we will see that (c) it must be true. [NB: This last is in effect a simple "description/definition" of "self-evident truth," following Adler.]) 

6 --> Consequently, we can credibly objectively experience and observe intelligent agency in action, and can identify recognisable and even reliable empirical signs of it, at least on the provisional basis that is the inevitable constraint on scientific reasoning. Then, we can note that such agents routinely leave recognisable traces of their actions: functionally specified, complex information [FSCI] in cases ranging from the digital text of Internet messages all the way to the pyramids, cave-paintings, burials in beds of flowers and flint-knappings of ancient men. This, William Dembski aptly illustrates by citing Abraham de Moivre:

7 --> Nor is it reasonable to then beg the worldviews level question ahead of examining  the evidence; by trying to insist that since the generally accepted highly intelligent code-using agents we see in action around us are embodied and human, we may only "properly" consider embodied human entities as candidates to be intelligent agents. First, we have no good reason to infer that humans exhaust the possible or actual set of such agents. Also, we have no good grounds for rejecting the possibility of agents based on pure mind -- indeed, we have no sound materialistic account of the origin of mind, or of how mind acts on our own brains and bodies. But, we know that we do act and that we act in ways that cannot be reasonably accounted for on mechanical necessity showing itself through natural regularities, or mere random chance showing itself in random walks from arbitrary initial configurations of contingent entities.  So, we should let the evidence speak for itself rather than insisting on thinking in a self-refuting materialist circle. (Cf further discussion in Appendix 8 below.)

8 --> Moreover, creative, innovative information -- a characteristic property of mind at work (as we have seen above), is not restricted to any one embodiment or code, and can be in multiple places at the same time; it works into intelligible, complex and functional configurations, which (as Cicero pointed out long ago) are neither the product of mechanical necessity nor of chance, but of the understanding, purposeful mind. 

9 --> More directly, the creative mind (the characteristic manifestation of agency as we experience and observe it), has radically different properties from those observed for either chance or necessity.  Indeed, insightful innovative, complex, active, purposeful, self-directing yet orderly and intelligible creativity is the hallmark of mind as it shows itself in language [thus also codes], imagination and action. (Cf discussion of cybernetics by Derek Smith here.) 

10 --> FSCI is a reliable hallmark of such creative action, from experience and observation. We have a right to trust it until and unless on fair (empirically well-supported, non-question-begging and non self-refuting) evidence that reliability can be overthrown.

11 --> Further to all of this, we see that the idea that the design inference unwarrantedly "assumes" the existence of a designer at the outset is simply wrong-headed. For, in fact, as our investigatory start point, we simply observe that cause-effect patterns in general trace to one or more of chance, necessity, agency; i.e. the only "assumption" is that agents (including, where relevant, purely mental ones) are POSSIBLE, not excluded before we look at the empirical data -- we merely refuse to beg the question ahead of looking at the objective facts. 

12 --> Then, as outlined above, we also see that a highly contingent situation (such as: which face of a die is uppermost) is either chance or agency, not necessity. For, the outcome can take on a range of values, and we can observe the frequency distribution in that range. After that, as Fig A.2 above illustrates, we test for whether the observed outcome is (1) sufficiently improbable -- i.e complex --  and also (2) functionally specified, to warrant inference that it is caused by agency not chance. (For instance if the die in our game keeps on coming up sixes, to the benefit of one player, that strongly suggests sleight of hand and loading.)

13 --> Next, on the technical issues of Fisherian vs Bayesian inference testing and Hume vs Reid on inference to design, Dr Dembski has presented significant, albeit controversial, arguments here and here respectively. In desperately compressed summary: when Bayesian approaches are applied to relevant "practical" situations [such as the Caputo case], we as a rule go looking for alternative hypotheses only when we already have seen that there is reason to be "suspicious" [i.e the Bayesian approach to testing in such cases, in effect implicitly uses Fisherian (or at least "law of averages") expectations that things too far from the typical result are "unlikely" to happen by chance, as its context. [Cf Appendix 6 for mathematical details. One of those details is that while a likelihood approach may allow us to infer to the most probable shift away from an "unbiased" 50:50 probability, a functionally specified and purpose-serving bias that shows itself significant at a credibly relevant confidence level is a strong sign of deisgn. Just ask anyone who has been rooked by the use of artfully loaded dice.]

14 --> Thus, we can see that the traditional “elimination" approach to inference testing rests on the well known, easily observed principle of the valid form of the layman's "law of averages." Namely, that in a "sufficiently" and "realistically" large [i.e. not so large that it is unable or very unlikely to be instantiated] sample, wide fluctuations from "typical" values characteristic of predominant clusters, are very rarely observed. [For instance, if one tosses a "fair" coin 500 times, it is most unlikely that one would by chance go far from a 50-50 split that would be in no apparent order. So if the observed pattern turns out to be ASCII code for a message or to be nearly all-heads or alternating heads and tails, or the like, then it is most likely NOT to have been by chance. The Caputo case, after all the back and forth debate on Dr Dembski's mathematics, remains as a striking and apt case in point. (Not least, we should observe that after the court case, the long-running "streak" vanished.)] 

15 --> So the material consequence follows: when we can “simply" specify a cluster of outcomes of interest in a configuration space, and such a space is sufficiently large that a reasonable random search will be maximally unlikely within available probabilistic/ search resources, to reach the targetted cluster, we have good reason to believe that if the actual outcome is in that cluster, it was by agency. [Thus, we see the telling force of Sir Fred Hoyle’s celebrated illustration of the utter improbability of  a tornado passing through a junkyard and assembling a 747 by chance. By far and away, most of the accessible configurations of the relevant parts will most emphatically be unflyable. So, if we are in a flyable configuration, that is most likely (indeed, beyond REASONABLE -- as oposed to "all" -- doubt) by intent and intelligently directed action, not chance. ]

16 --> We therefore see why the traditional, Fisherian, eliminationist approach to hypothesis testing makes good sense even though it does not so neatly line up with the algebra and calculus of probability as would a likelihood or full Bayesian type approach. Thence, we see why the Dembski-style explanatory filter 9which builds on Fisher's approach) can be so effective, too. Thus, to extend the idea of Bayesian comparisons of likelihoods of alternative hypotheses relative to evidence and insist that one may not properly walk away from a hyp unless there is an "acceptable" alt hyp, is dubious; especially if one hinges the assertion on things like: to infer to agency relative to an explanatory filter argument across chance-necessity-agency plus probabilistic filtering is to imply a before-the-fact question-begging assumption that the probability of the existence of a relevant Agent was (nearly) unity.

17 --> For, all that is actually required is to refuse to beg the real question by ruling out agency ahead of time; then to examine the evidence. Further, as this section points out, we already routinely accept, on vast experience, that functionally specified complex information is a reliable objective marker of agency; so we may infer from evidence of FSCI to agency. Third, it is better to acknowledge that one has not got a credible hyp, than to stick with what has failed after reasonable tests on the insistence that one has not got a better alternative. (Which is too often the underlying rhetorical point being made by adverting to Bayesian style likelihood testing.)

18 --> Also, the inference to design is not simply "a weak analogy." Instead, it is an inference to best explanation relative to what we know agents routinely do: generate FSCI, which in every observed case where we know the causal story directly is not the product of chance but of agency. (Natural regularities, almost by definition, do not produce highly contingent outcomes. E.g., by mechanical necessity, when we put oxidiser, fuel and enough heat together, we reliably have a fire.)

19 --> Moreover, significant information storage, as Appendix 3 discusses, requires high contingency, and code-bearing functionally specified particular states of the contingent elements to hold the information. This can be shown by doing a brief thought-experiment on using six-sided dice to encode and store information:

Sub-case study: a hypothetical, dice-based information system: If one were so inclined, s/he could define a six-state code and use a digital string of dice to store or communicate a message by setting each die in turn to the required functional value for communicating the message. In principle, we could then develop information-processing and communication systems that use dice as the data-storage and transmission elements [say, using registers made from plastic troughs loaded with strings of dice set to particular values and "read" by scanning the pips]; rather like the underlying two-state [binary] digital code-strings used for this web page. So also, since  6^193 ~ 10^150,  if a functional code-string using dice requires significantly more than 193 to 386 six-state elements [we can conveniently round this up to 200 - 400], it would be beyond the edge of chance as can be specified by the Dembski universal probability bound, UPB. [That is, the probabilistic resources of the observed universe would be most likely fruitlessly exhausted if a random-walk search starting from an arbitrary initial point in the configuration space were to be tasked to find an "island" of functionality: not all "lotteries" are winnable (and those that are, are designed to be winnable but profitable for their owners). So, if we were to then see a code-bearing, functionally meaningful string of say 500 dice, it would be most reasonable to infer that this string was arranged by an agent, rather than to assume it came about because someone tossed a box of dice and got really lucky! (Actually, this count is rather conservative, because the specification of the code, algorithms and required executing machinery are further -- rather large -- increments of organised, purposeful complexity.)] 

20 --> For more relevant instance, DNA is a complex, highly contingent and functionally specified digital data-string using four-state chemical bases (the famous nucleic acids: A, G, C, T) as information storing elements. For DNA, then, the UPB comes after some 250 - 500 elements, as 4^250 ~ 10^150. Now, too, as Meyer reports, the simplest reasonable living cells credibly require 300,000 - 500,000 4-state bases, so the odds of getting to a functioning DNA string by chance [the alternative to agency for obtaining highly contingent outcomes!], on the gamut of our observed universe, are negligibly different from zero. It is therefore reasonable to infer -- absent imposition of arbitrary selective hyperskepticism or philosophically question-begging, historically unwarranted rules such as so-called methodological naturalism -- that observed, bio-functional DNA as we see in living cells is designed.

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APPENDIX 5

 Newton's thoughts on the designer of  "[t]his most beautiful system 
of the sun, planets, and comets . . . " in his General Scholium to the Principia

Newton's Principia is perhaps the most important scientific work of all time. 

It contains a General Scholium that begins with a global inference to design and onward to the Designer, in part from the nature of the cosmos and its physics, and in part based on Newton's adherence to the biblical, Judaeo-Christian tradition:

. . . This most beautiful system of the sun, planets, and comets, could only proceed from the counsel and dominion of an intelligent and powerful Being. And if the fixed stars are the centres of other like systems, these, being formed by the like wise counsel, must be all subject to the dominion of One; especially since the light of the fixed stars is of the same nature with the light of the sun, and from every system light passes into all the other systems: and lest the systems of the fixed stars should, by their gravity, fall on each other mutually, he hath placed those systems at immense distances one from another.

This Being governs all things, not as the soul of the world, but as Lord over all; and on account of his dominion he is wont to be called Lord God pantokrator , or Universal Ruler; for God is a relative word, and has a respect to servants; and Deity is the dominion of God not over his own body, as those imagine who fancy God to be the soul of the world, but over servants. The Supreme God is a Being eternal, infinite, absolutely perfect; but a being, however perfect, without dominion, cannot be said to be Lord God; for we say, my God, your God, the God of Israel, the God of Gods, and Lord of Lords; but we do not say, my Eternal, your Eternal, the Eternal of Israel, the Eternal of Gods; we do not say, my Infinite, or my Perfect: these are titles which have no respect to servants. The word God usually signifies Lord; but every lord is not a God. It is the dominion of a spiritual being which constitutes a God: a true, supreme, or imaginary dominion makes a true, supreme, or imaginary God. And from his true dominion it follows that the true God is a living, intelligent, and powerful Being; and, from his other perfections, that he is supreme, or most perfect. He is eternal and infinite, omnipotent and omniscient; that is, his duration reaches from eternity to eternity; his presence from infinity to infinity; he governs all things, and knows all things that are or can be done. He is not eternity or infinity, but eternal and infinite; he is not duration or space, but he endures and is present. He endures for ever, and is every where present; and by existing always and every where, he constitutes duration and space. Since every particle of space is always, and every indivisible moment of duration is every where, certainly the Maker and Lord of all things cannot be never and no where. Every soul that has perception is, though in different times and in different organs of sense and motion, still the same indivisible person. There are given successive parts in duration, co-existent puts in space, but neither the one nor the other in the person of a man, or his thinking principle; and much less can they be found in the thinking substance of God. Every man, so far as he is a thing that has perception, is one and the same man during his whole life, in all and each of his organs of sense. God is the same God, always and every where. He is omnipresent not virtually only, but also substantially; for virtue cannot subsist without substance. In him are all things contained and moved [i.e. cites Ac 17, where Paul evidently cites Cleanthes]; yet neither affects the other: God suffers nothing from the motion of bodies; bodies find no resistance from the omnipresence of God. It is allowed by all that the Supreme God exists necessarily; and by the same necessity he exists always, and every where. [i.e accepts the cosmological argument to God.] Whence also he is all similar, all eye, all ear, all brain, all arm, all power to perceive, to understand, and to act; but in a manner not at all human, in a manner not at all corporeal, in a manner utterly unknown to us. As a blind man has no idea of colours, so have we no idea of the manner by which the all-wise God perceives and understands all things. He is utterly void of all body and bodily figure, and can therefore neither be seen, nor heard, or touched; nor ought he to be worshipped under the representation of any corporeal thing. [Cites Exod 20.] We have ideas of his attributes, but what the real substance of any thing is we know not. In bodies, we see only their figures and colours, we hear only the sounds, we touch only their outward surfaces, we smell only the smells, and taste the savours; but their inward substances are not to be known either by our senses, or by any reflex act of our minds: much less, then, have we any idea of the substance of God. We know him only by his most wise and excellent contrivances of things, and final cause [i.e from his designs]: we admire him for his perfections; but we reverence and adore him on account of his dominion: for we adore him as his servants; and a god without dominion, providence, and final causes, is nothing else but Fate and Nature. Blind metaphysical necessity, which is certainly the same always and every where, could produce no variety of things. [i.e necessity does not produce contingency] All that diversity of natural things which we find suited to different times and places could arise from nothing but the ideas and will of a Being necessarily existing. [That is, implicitly rejects chance, Plato's third alternative and explicitly infers to the Designer of the Cosmos.] But, by way of allegory, God is said to see, to speak, to laugh, to love, to hate, to desire, to give, to receive, to rejoice, to be angry, to fight, to frame, to work, to build; for all our notions of God are taken from. the ways of mankind by a certain similitude, which, though not perfect, has some likeness, however. And thus much concerning God; to discourse of whom from the appearances of things, does certainly belong to Natural Philosophy. [Cf also his Rules of Reasoning.]

The design-oriented context of Newton's thought could hardly be more explicit. END

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APPENDIX 6

Fisher, Bayes, Caputo and Dembski

On the technical issues of Fisherian vs Bayesian inference testing and Hume vs Reid on inference to design, Dr Dembski has presented significant arguments here and here respectively. 

In desperately compressed summary: when Bayesian approaches are applied to relevant situations [such as the Caputo case], we go looking for alternative hypotheses only when we already have seen that there is reason to be "suspicious" [i.e the Bayesian approach to testing in such cases, in effect implicitly uses Fisherian (or at least "law of averages") expectations that things too far from the typical result are "unlikely" to happen by chance, as its context; e.g. in the now notorious Caputo case], and the explanatory filter approach provides a tool for objectively deciding that "suspicious enough":  

In short, we need to ask, for instance, why the Caputo case was in court at all, as, in principle, any given specific pattern of outcomes from 41 R:0 D to 0 R:41 D -- i.e which party would come first on the ballot list (which apparently gives a small but significant advantage to that party) --  was mathematically speaking equiprobable. 

The answer is, from one perspective, "obvious." 

For, when we look at the relative number of ways we may end up with a near 50-50 outcome vs the number of ways we get at least so extreme an outcome as was observed [40 D:1 R], we soon see that outcomes very close to 50-50 form a strongly predominant group, and so we have good reason to suspect that an agenda-serving pattern [Caputo was a Democrat!] that is far indeed from the overwhelmingly expected low-fluctuation outcome was most unlikely to be by chance. (In short we see contingency, a functionally specified outcome, and one that would most likely exhaust available probabilistic resources, on a chance hypothesis. So, "design" is the most likely explanation.)

But, that sort of "obviousness" in this context is quite unwelcome in some quarters; thus, we see the rise of the Bayes vs Fisher objection that Dembski addressed.

A short mathematical excursus is now therefore in order, with thanks to prof PO for the exchanges that have shown that this is necessary:

We often wish to find evidence to support a theory, where it is usually easier to show that the theory [if it were for the moment assumed true] would make the observed evidence “likely" to be so [on whatever scale of weighting subjective/epistemological "probabilities" we may wish etc . . .].

So in effect we have to move: from p[E|T] to p[T|E], i.e from "probability of evidence given theory" to "probability of theory given evidence," which last is what we can see. (Notice also how easily the former expression p[E|T] "invites" the common objection that design thinkers are "improperly" assuming an agent at work ahead of looking at the evidence, to infer to design. Not so, but why takes a little explanation.)

Let us therefore take a quick look at the algebra of Bayesian probability revision and its inference to a measure of relative support of competing hypotheses provided by evidence:

a] First, look at p[A|B] as the ratio, (fraction of the time we would expect/observe A AND B to jointly occur)/(fraction of the the time B occurs in the POPULATION). 

--> That is, for ease of understanding in this discussion, I am simply using the easiest interpretation of probabilities to follow, the frequentist view.

b] Thus, per definition given at a] above: 

p[A|B] = p[A AND B]/p[B], 

or, p[A AND B] = p[A|B] * p[B]

c] By “symmetry," we see that also:

p[B AND A] = p[B|A] * p[A],

where the two joint probabilities (in green) are plainly the same, so:

p[A|B] * p[B] = p[B|A] * p[A],

which rearranges to . . .

d] Bayes’ Theorem, classic form: 

p[A|B] = (p[B|A] * p[A]) / p[B]

e] Substituting, E = A, T = B, E being evidence and T theory:

p[E|T] = (p[T|E] * p[E])/ p[T],

p[T|E] -- probability of theory (i.e. hypothesis or model) given evidence seen -- being here by initial simple "definition," turned into L[E|T]:

L[E|T] is (by definition) the likelihood of theory T being "responsible" for what we observe, given observed evidence E [NB: note the "reversal" of how the "|" is being read]; at least, up to some constant. (Cf. here, here, here, here and here for a helpfully clear and relatively simple intro. A key point is that likelihoods allow us to estimate the most likely value of variable parameters that create a spectrum of alternative probability distributions that could account for the evidence: i.e. to estimate the maximum likelihood values of the parameters; in effect by using the calculus to find the turning point of the resulting curve. But, that in turn implies that we have an "agreed" model and underlying context for such variable probabilities.)

Thus, we come to a deeper challenge: where do we get agreed models/values of p[E] and p[T] from? 

This is a hard problem with no objective consensus answers, in too many cases. (In short, if there is no handy commonly accepted underlying model, we may be looking at a political dust-up in the relevant institutions.)

f] This leads to the relevance of the point that we may define a certain ratio,

LAMBDA = L[E|h2]/L[E|h1],

This ratio is a measure of the degree to which the evidence supports one or the other of competing hyps h2 and h1. (That is, it is a measure of relative rather than absolute support. Onward, as just noted, under certain circumstances we may look for hyps that make the data observed "most likely" through estimating the maximum of the likelihood function -- or more likely its logarithm -- across relevant variable parameters in the relevant sets of hypotheses. But we don't need all that for this case.)

g] Now, by substitution A --> E, B --> T1 or T2 as relevant:

p[E|T1] = p[T1|E]* p[E]/p[T1], 

and 

p[E|T2] = p[T2|E]* p[E]/p[T2]; 

so also, the ratio:

p[E|T2]/ p[E|T1]

= {p[T2|E] * p[E]/p[T2]}/ {p[T1|E] * p[E]/p[T1]}

= {p[T2|E] /p[T2]}/ {p[T1|E] /p[T1]}

h] Thus, rearranging:

p[T2|E]/p[T1|E]  

= {p[E|T2]/ p[E|T1]} * {P(T1)/P(T2)}

i] So, substituting:

L[E|T2]/ L[E|T1] = LAMBDA 

= {p[E|T2]/ p[E|T1]} * {P(T2)/P(T1)}

Thus, the lambda measure of the degree to which the evidence supports one or the other of competing hyps T2 and T1, is a ratio of the conditional probabilities of the evidence given the theories (which of course invites the "assuming the theory" objection, as already noted), times the  ratio of the probabilities of the theories being so.  [In short if we have relevant information we can move from probabilities of evidence given theories to in effect relative probabilities of theories given evidence, and in light of an agreed underlying model.] 

All of this is fine as a matter of algebra (and onward, calculus) applied to probability, but it confronts us with the issue that we have to find the outright credible real world probabilities of T1, and T2 (or onward, of the underlying model that generates a range of possible parameter values). In some cases we can get that, in others, we cannot; but at least, we have eliminated p[E]. Then, too, what is credible to one may not at all be so to another.  This brings us back to the problem of selective hyperskepticism, and possible endless spinning out of -- too often specious or irrelevant but distracting -- objections [i.e closed minded objectionism].

Now, by contrast the “elimination" approach rests on the well known, easily observed principle of the valid form of the layman's "law of averages." Namely, that in a "sufficiently" and "realistically" large [i.e. not so large that it is unable or very unlikely to be instantiated] sample, wide fluctuations from "typical" values characteristic of predominant clusters, are very rarely observed. [For instance, if one tosses a "fair" coin 500 times, it is most unlikely that one would by chance go far from a 50-50 split that would be in no apparent order. So if the observed pattern turns out to be ASCII code for a message or to be nearly all-heads or alternating heads and tails, or the like, then it is most likely NOT to have been by chance. (See, also, Joe Czapski's "Law of Chance" tables, here.)] 

Elimination therefore  looks at a credible chance hyp and the reasonable distribution across possible outcomes it would give [or more broadly the "space" of possible configurations and the relative frequencies of relevant "clusters" of individual outcomes in it]; something we are often comfortable in doing. Then, we look at the actual observed evidence in hand, and in certain cases -- e.g. Caputo -- we see it is simply too extreme relative to such a chance hyp, per probabilistic resource exhaustion.

So the material consequence follows: when we can “simply" specify a cluster of outcomes of interest in a configuration space, and such a space is sufficiently large that a reasonable random search will be maximally unlikely within available probabilistic/ search resources, to reach the cluster, we have good reason to believe that if the actual outcome is in that cluster, it was by agency. [Thus the telling force of Sir Fred Hoyle’s celebrated illustration of the utter improbability of  a tornado passing through a junkyard and assembling a 747 by chance. By far and away, most of the accessible configurations of the relevant parts will most emphatically be unflyable. So, if we are in a flyable configuration, that is most likely by intent and intelligently directed action, not chance. ]

We therefore see why the Fisherian, eliminationist approach makes good sense even though it does not so neatly line up with the algebra and calculus of probability as would a likelihood or full Bayesian type approach. Thence, we see why the Dembski-style explanatory filter can be so effective, too.

---

DRAFT APPENDIX 7:  

Of the Weasel "cumulative selection" program and begging the question of FSCI, c. 1986

In December 2008, the issue of the 1986 Weasel "cumulative selection" program came up in a discussion thread at the UD blog, and I commented on it thusly:

[UD December 2008 Unpredictability thread, excerpt from comment 107:] . . . the problem with the fitness landscape [model] is that it is flooded by a vast sea of non-function, and the islands of function are far separated one from the other. So far in fact . . . that searches on the order of the quantum state capacity of our observed universe are hopelessly inadequate. Once you get to the shores of an island, you can climb away all you want using RV + NS as a hill climber or whatever model suits your fancy.

But you have to get TO the shores first. THAT is the real, and too often utterly unaddressed or brushed aside, challenge. [NB: And, in fact, that was the challenge Sir Fred Hoyle had posed. A challenge that Weasel, from its outset, has unfortunately ducked and distracted attention from. Weasel is -- and has always been -- a question-begging strawman fallacy.]

And . . .  that [unmet challenge] starts with both the metabolism first and the D/RNA first schools of thought on OOL. As indeed Shapiro and Orgel recently showed . . . .

As for Weasel . . .  it is . . .  trivially irrelevant as a plainly DIRECTED, foresighted targetted search.

It instantiates intelligent design, not the power of RV + NS. Even going up to Avida and the like, similar issues come up, as is highlighted under the issue of active information by Dembski and Marks.

[ slice from comment no 111: this was the excerpt that was used to inject the latching issue in a distractive fashion:] Weasel [i.e. c. 1986] sets a target sentence then once a letter is guessed it preserves it for future iterations of trials until the full target is met. [That is, I inferred that Weasel latches the o/p as is likely from the below.] That means it rewards partial but non-functional success, and is foresighted. Targetted search, not a proper RV + NS model. [Emphases and notes added.]

Thus, it should be clear what was the central issue, and what was a secondary note on an observed fact of evident o/p behaviour that pointed to the underlying root issue.

However, in 2009, the secondary observation was picked up by an evolutionary materialist commenter at UD, leading to a fairly lengthy exchange over several UD threads. Apart from the significant civility problems that emerged -- contemptuous and insistent privacy violations, the slanderous conflation of design thought and creationism, gleeful citation of dismissive remarks by a journalist that in fact turned out to be based on the moral equating of Christians with IslamIST terrorists in the cause of creating a confused moral climate that in effect enables public lewdness etc. (all unapologised for and plainly unregretted) -- it became very clear that (a) Weasel's fundamental flaw is just as has already been described, and (b) the issue of disputes over  "latching" was in the end a distraction from the main problem.  Namely, that: far from being an example of a claimed BLIND watchmaker's capacity to create functional information from chance variations and a crude analogue to natural selection, Weasel is targetted, intelligently designed search that uses degree of proximity -- without reference to degree of reasonable functionality -- to select the "champion" of the current generation, which is then varied and used to select the champion for the next, until the target is hit.

Notwithstanding, the issue of whether or not the o/p's in the two cases published in Mr Dawkins' The Blind Watchmaker, in 1986 "latched" the o/ps became a debate in itself, which -- despite its now venerable age -- interestingly illustrates some of the key pitfalls of such proposed computer simulations of evolution.

Analysing the case, where a random 28-letter string is changed by degrees towards the target, "Methinks if is like a weasel":

1 --> We may conveniently begin by inspecting the published o/p patterns circa 1986, thusly [being derived from Dawkins, R, The Blind Watchmaker , pp 48 ff, and New Scientist, 34, Sept. 25, 1986; p. 34  HT: Dembski, Truman]:

 1 WDL*MNLT*DTJBKWIRZREZLMQCO*P
2? WDLTMNLT*DTJBSWIRZREZLMQCO*P
10 MDLDMNLS*ITJISWHRZREZ*MECS*P
20 MELDINLS*IT*ISWPRKE*Z*WECSEL
30 METHINGS*IT*ISWLIKE*B*WECSEL
40 METHINKS*IT*IS*LIKE*I*WEASEL
43 METHINKS*IT*IS*LIKE*A*WEASEL

 1 Y*YVMQKZPFJXWVHGLAWFVCHQXYPY
10 Y*YVMQKSPFTXWSHLIKEFV*HQYSPY
20 YETHINKSPITXISHLIKEFA*WQYSEY
30 METHINKS*IT*ISSLIKE*A*WEFSEY
40 METHINKS*IT*ISBLIKE*A*WEASES
50 METHINKS*IT*ISJLIKE*A*WEASEO
60 METHINKS*IT*IS*LIKE*A*WEASEP
64 METHINKS*IT*IS*LIKE*A*WEASEL

2 --> What is happening here may best be summarised in the words of the author himself, prof Richard Dawkins, suitably highlighted:

I don't know who it was first pointed out that, given enough time, a monkey bashing away at random on a typewriter could produce all the works of Shakespeare. [NB: cf above] and this discussion on chance, necessity and intelligence.] The operative phrase is, of course, given enough time. Let us limit the task facing our monkey somewhat. Suppose that he has to produce, not the complete works of Shakespeare but just the short sentence 'Methinks it is like a weasel', and we shall make it relatively easy by giving him a typewriter with a restricted keyboard, one with just the 26 (capital) letters, and a space bar. How long will he take to write this one little sentence? . . . .

It . . . begins by choosing a random sequence of 28 letters ... it duplicates it repeatedly, but with a certain chance of random error – 'mutation' – in the copying. The computer examines the mutant nonsense phrases, the 'progeny' of the original phrase, and chooses the one which, however slightly, most resembles the target phrase, METHINKS IT IS LIKE A WEASEL . . . . What matters is the difference between the time taken by cumulative selection, and the time which the same computer, working flat out at the same rate, would take to reach the target phrase if it were forced to use the other procedure of single-step selection: about a million million million million million years. This is more than a million million million times as long as the universe has so far existed . . . .

Although the monkey/Shakespeare model is useful for explaining the distinction between single-step selection and cumulative selection, it is misleading in important ways. One of these is that, in each generation of selective 'breeding', the mutant 'progeny' phrases were judged according to the criterion of resemblance to a distant ideal target, the phrase METHINKS IT IS LIKE A WEASEL. Life isn't like that. Evolution has no long-term goal. There is no long-distance target, no final perfection to serve as a criterion for selection, although human vanity cherishes the absurd notion that our species is the final goal of evolution. In real life, the criterion for selection is always short-term, either simple survival or, more generally, reproductive success. [TBW, Ch 3, as cited by Wikipedia, various emphases and colours added.]

3 --> In short, Weasel is picking a line of descent of "champions" by cumulative selection from generational populations created by random variation of a previous champion (or, of course, the initial "nonsense phrase"). It is intended to illustrate the power of "cumulative selection" vs what is dismissed as "single step" selection. It is also acknowledged that the selection process used is not at all parallel to what is expected in the real world: natural selection and the like which respond to present functionality or want thereof, rather than foresighted targetted selection. But, it is held that Weasel aptly illustrates the advantages of "cumulative selection."

4 --> However, it is credibly the case that  the DNA for the simplest realistic life form will be about 600,000 bits of infomation storage capacity, which specifies a configuration space of rather roughly 1 in 10^180,000. Also,  innovative major body plans relative to that will require some 10's - 100's of millions of additional bits, as is discussed in the main text of this note. By contrast the space of 28, 27-state elements has 27^28 ~ 1.2 * 10^40 states. That is, the "single step" that Mr Dawkins would dismiss and avoid by resort to hill-climbing is itself vastly too small to be relevant to the complexity of first life. So, from the outset, the Weasel program fails to address the real issue posed by the need to credibly get to the functionally specific complex information required to implement a viable life form, before hill-climbing can be properly applied.

5 --> Summed up, Weasel begs the key question at stake, for (i) it substitutes an intelligently designed, cumulative, foresighted selection process for the ones that would be relevant to what is needed if natural selection and the like are to account for body plans. Worse, (ii) it does not impose a realistic degree of initial or comparative function as a criterion of initial selection, so that (iii) "nonsense phrases" are allowed to progress to the target whereas (iv) in the biological world non-functional forms would not work as living entities or would fail to reproduce adequately; in fact, would be culled out by failure to function and/or reproduce as well as their competitors. Thus, Weasel is indeed "misleading."

6 --> Next, the excerpted runs of champions for Weasel 1986 above show how, of over 300 possible cases where a correct letter may change in principle, the o/p goes correct in some 200+ of them, and never once reverts in the published sample. (The highlighted N, * and T in the first case show this with particular force. Notice, also, how the fact that by happenstance three initial letters were correct seems to have cut off 20 generations in the run, by comparison with the second case.) Relevant to all of this, on the law of large numbers [the valid form of the layman's law of averages], we may see that if  a population has a segment x of probability p [where this is really relative statistical weight in the distribution as a whole) and we take a sample of size N, the expected occurrence of x in the sample is N*p.  And, as N*p --> ~ 1, from the low side, we can reasonably deem x an observable event.

7 --> The law of large numbers -- that as sample size N frrom a large population rises, the likely number of observations of a phenomenon x of probability p will tend to N*p -- can be visualised and experimented with. So, to help us to see why it makes sense, let's imagine a typical bell-shaped statistical distribution chart or a Reverse-J distribution chart,  and draw it on say bristol board, backing it on perhaps a sheet of particle board.  

DARTS AND CHARTS EXERCISE: If we divide the chart into even-width stripes, say 5 - 9 bands or so, and then drop darts on it from a sufficient height that the darts more or less will hit the chart in an evenly scattered way, we can easily observe how a sample builds up a picture of a population. How: simply count the relative number per strip and compare to the relative area per strip; which is of course a good measure of probability. One hit will be more or less anywhere. A few will be quite scattered, but by the time we get to 2 - 3 dozens, we will usually have a fair view of the bulk of the distribution, i.e. relative number of hits per strip is beginning to correspond to the fractional area the strip represents. (Indeed, that is why 20 - 30 is a useful rule of thumb cutoff for doing small statistical samples; for if 30* p = 1, p = 0.03.)  Also, as we mount up into the low hundreds, the far tails of the distribution will as a rule begin to show up in the sample:  if 300 * p = 1, p = 0.003.  [As a consequence, key statistical parameters such as averages of large enough and reasonably random samples will tend to the average of the actual population.]

8 --> So, we have reasonably good reason to infer that the samples above are more or less representative of the published "good" runs of what have for convenience been called generational champions, circa 1986. And indeed, since Mr Dawkins was trying to illustrate the power of "cumulative selection" to achieve an otherwise utterly  improbable target, we can very reasonably conclude that the observed no-reversions excerpts of runs were reflective of and showcased what was happening at large with "good" runs. That is, beyond reasonable dispute, the good runs circa 1986 latched the o/p's in the sense that once a letter went correct it stayed that way; as the sequence of generational champions ratcheted their way ever closer to the target, hitting it in the published cases in 40+ and 60+ generations.  (And BTW: the New Scientist case is a reproduction of one of the two in TBW. Also, during the UD exchanges, a 1987 BBC Horizon video of a Weasel run was linked. The rather long and fast run showed quite frequent reversions and a strange "winking" effect where repeatedly the reverting letter often very rapidly seemed to come back to correct . . . an incorrect letter should revert to the dynamics of a fairly slow search. The 1987 plainly unlatched runs seem to exhibit considerably different behaviour than the showcased steady, cumulative progress presented and described in 1986. This is suggestive -- on preponderance of the lines of evidence -- of a material difference in the program; probably its parameters (e.g. population size, mutation rate and/or filter characteristics).)

9 --> In principle all of the described events could happen by random chance, as a chance sequence can mimic any pattern whatsoever (one of the challenges of empirically based inductive reasoning, which reveals the relevance and practical value of the explanatory filter). However, on general principles, this is so improbable that we may discount it as a serious explanation; and indeed, Mr Dawkins deprecated such as being "single step selection," which he was trying to show was not a serious challenge to the power of the BLIND watchmaker of the book's title.

10 --> Back story:  Mr Hoyle had raised the issue that the origin of a first life form -- such as, roughly, a bacterium -- is a matter of such complexity that the odds of that happening in a prebiotic soup by chance was negligible.  In a more up to date form, this is the challenge that is still raised by the design theory movement: life shows a threshold of function at about 600,000 bits of DNA storage capacity, so before one may properly apply hill climbing algorithms to scale Mt Improbable, one needs first to have a credible BLIND watchmaker mechanism to land one on the shores of Isle Improbable; e.g. drifting by reasonable random configurations of molecules in empirically justified pre biotic soups and empirically credible pre-life selection forces. (But, as we can see from Section B above, this OOL challenge is still unmet.  And similarly, Section C shows how the origin of body plan level biodiversity requiring 10's - 100's or millions of bits of functional genetic information, dozens of times over, is equally unmet.) 

11 -->  So, it looks uncommonly like Weasel distracts attention from and begs the question. That sums up the balance on the main issue. However, the latching question is clearly in need of a responsible answer.

12 --> To explain the latching more realistically, we may have an explicit latching algorithm based on letterwise search, i.e. the 28 letter Weasel sentence is split up (partitioned) into 28 targets, with each taking up states from the set {A, B, C . . . Z and * (for space)}. A random search proceeds in 28 parallel columns, and as each letter hits its target, it is preserved. (The easy way to do that is to set up a mask register. Such a register also suggests a simple measure of proximity: if a letter is correct [ C], we assign a distance value 0. If it is incorrect [I], we assign a distance value 1. So, 28 incorrect letters gives distance 28, and 28 correct ones give distance 0. Once a letter in a champion for a generation goes to 0, we mask it off from further random change -- i.e. EXPLICIT latching. Of course, the odds of a given letter going correct are of order 1 of 27. A two letter word, e.g. "it" is one of 27^2 = 729 random possibilities. A 4-letter unique word such as "like" is one of 27^4 = 531,441 configurations, an 8-letter one like "methinks" is one of 2.8 * 10^11 eight-letter clusters, and a specific 28-letter sentence is one of 1.2 * 10^40 configurations. That is, we see that even so crude an analogy to bio-function as forming a word or phrase makes for an exponentially growing search challenge as the required digital string's length increases. So, threshold of initial effective functionality is a serious constraint on the credibility of Weasel and similar exercises.)

13 --> Letterwise partitioned search is also a very natural way to understand the Weasel o/p in light of Mr Dawkins' cited remarks about cumulative selection and rewarding the slightest increment to target of mutant nonsense phrases. As such, it has long been and remains a legitimate interpretation of Weasel. However, on recently and indirectly received reports from Mr Dawkins, we are led to understand that he did not in fact explicitly latch the o/p of Weasel, but used a phrasewise search.

14 --> Q: Can that be consistent with an evidently latched o/p?

ANS: yes, for IMPLICIT latching is possible as well.  

15 --> Namely, (i) the mutation rate per letter acts with (ii) the size of population per generation and (iii) the proximity to target filter to (iv) strongly select for champions that will preserve currently correct letters and/or add new ones, with sufficient probability that we will see a latched o/p. (This effect has in fact been demonstrated through runs of the EIL's recreation of Weasel.)

16 --> in a slightly weaker manifestation, the implicit mechanism will have more or less infrequent cases of letters that will revert to incorrect status; which has been termed implicit quasi-latching. This too has been demonstrated, and it occurs because an implicit latching mechanism is a probabilistic barrier not an absolute one. So, as the parameters are sufficiently detuned to make reversions occur, we will see quasi-latched cases.  Sometimes, under the same set of parameters, we will see some runs that latch and some that quasi-latch.

17 --> In a litle more detail, we will see reversions in a case where the odds of mutation per letter are sufficientluy low that in a reasonable generation of size N, there will be a significant fraction of no-change members, and so the proximity filter will select no-change to be next champion,  or a single step increment in proximity; or, in some cases a substitution where one correct letter reverts and one incorrect letter advances.

18 --> First, the odds of no-change in a population:

A letter in the string of length L [= 28] has probability of being selected to mutate, s. Once so selected, it can equally take up any of the g [= 27] available states at random. Of these, one is identical to the original state and 26 are changed outcomes. So, we can see that, for a given letter:

chance to be NOT selected = 1 - s
chance to be selecd but not change value = s * 1/g
overall chance to remain the same = (1 - s) + s/g

chance of no-change for a string of L letters = [(1 - s) + s/g]^L

Set s = 4%, P_{no change} = [0.96 + 0.04/27]^28 = 0.9615^28 = 0.333
(That is, about 1/3 of strings on average in a generation of mutants, will be unchanged.)

For a generation of N = 50, the chance that it will have no unchanged strings, then, is:

(1 - P_{no change})^N = (1 - 0.333)^50 = 1.61*10^-9

19 --> In short, there is almost no chance that such a mutant generation population will have no unchanged members. In that context, with the proximity filter at work, no-change cases or substitutions or single step advances will dominate the run of champions. Indeed, the Weasel 1986 o/p samples show that runs to target took 40+ and 60+ generations, i.e. no-change won about half the time and single step changes dominated the rest. No substitutions were observed in the samples, suggesting strongly that there were none in the showcased runs. (Double step advances etc or substitutions plus advances will be much less probable. But in principle, per sheer  "luck,"  we could see the very first random variant going right to the target. Just, the odds are astronomically against it. As, probabilistic barriers may be stiff, but are not absolute roadblocks.)

20 --> Let us now broaden the analysis in light of these patterns of behaviour:

chance of selection per letter = s.
[NB: We are working with s = 4% for illustrations, as that is the default setting at the EIL's Weasel page.]

raw per letter chance of reversion, P_C-->I = s* (g -1)/g  [= 0.04 (27 - 1)/27 = 0.0385, for s = 4%]

similarly, per letter chance of advance, P_I-->C = s*(1/g) = s/g [ = 0.04/27 = 0.00148, for s = 4%]

21 --> CASE A: (L - c) incorrect letters in a string, one or more becoming correct:

chance of selecting none = (1 - s)^[L-c]  
so, chance to select at least one changing letter = {1 - (1 - s)^[L-c]}

Now also, single change will dominate, so for the string:

P_I-->C ~ (1/g)*{1 - (1 - s)^[L-c]}

E.g. 1: c = 1, P_I-->C ~ 1/27 * {1 - 0.96^27} = 0.0247

E.g. 2: c = 14, P_I-->C ~ 1/27 * {1 - 0.96^14} = 0.0161

E.g. 3: c = 27, P_I-->C ~ 1/27 * {1 - 0.96} = 0.00148

In a population of N such strings, the expected number of such advancing letters is N*P_I-->C  , and where N = 50:

E.g. 1: c = 1, 0.0247 * 50 = 1.24

E.g. 2: c = 14,  0.0161 * 50 = 0.81

E.g. 3: c = 27,  0.00148 * 50 = 0.074

22 --> CASE B: c correct letters in a string, one or more becoming incorrect:

chance of selecting none = (1 - s)^c
chance to select at least one = [1 - (1 - s)^c]

Since, again single change instances will dominate the string:

P_C-->I ~ [(g - 1)/g]*[1 - (1 - s)^c]

E.g. 1: c = 1, P_C-->I ~ 26/27 * [1 - 0.96] = 0.0385

E.g. 2: c = 14,  P_C-->I ~ 26/27 * [1 - 0.96^14] = 0.419

E.g. 3: c = 27,  P_C-->I ~ 26/27 * [1 - 0.96^27] = 0.643

23 --> CASE C: a substitution, i.e. a joint occurence of one letter advancing to correct while one retreats to incorrect:

P_s = P_I-->C*P_C-->I 

so, P_s ~ (1/g)*{1 - (1 - s)^[L-c]} * [(g - 1)/g]*[1 - (1 - s)^c]

E.g. 1: c = 1, P_s ~  0.0247 * 0.0385 = 0.00951

E.g. 2: c = 14, P_s ~ 0.0161 * 0.419 = 0.00675

E.g. 3: c = 27, P_s ~ 0.00148 * 0.643 = 0.000952

Thus also, for a population of such strings, of size N [= 50 in the default example], the expected number of such occurences is N* P_s:

E.g. 1: c = 1, N* P_s ~  50 * 0.00951 = 0.48

E.g. 2: c = 14, N* P_s ~ 50 * 0.00675 = 0.34

E.g. 3: c = 27, N* P_s ~ 50* 0.000952 = 0.0048

(Such numbers suggest that substitutions are reasonably observable within the population per generation.)  

24 --> In turn that means that a further key issue on champion selection per generation is the specific action of the proximity filter, in a context where -- continuing the concerete example -- the expected number of zero change cases in a generation is about 17, that for single step advances is about 1, and that for substitutions ranges from 1/2 down to 5/1000, depending on degree of proximity already acheived. That turns out to be a fairly complex issue:

a] It would be possible to measure proximity letter by letter for a string, e.g. by assigning 1 for a miss, 0 for a hit (as mentioned above); so that the proximity scale ranges from 28 to 0, the latter being the target sentence. In that case, substitutions have the same proximity as no-change cases.  

b] If the proximity filtering tie-breaker rule is established that on no letter being closer than the previous champion used to generate the N mutants in a given generation, we skip the generation, re-use the champion and go on to the next generation, no substitution cases would appear in the run of champions.

c] if the rule instead is that on every such case, a string different from the previous champion is chosen, we will probably see relatively frequent substitutions. (There would be no apparent latching.)

d] If instead, the rule is to have a lottery of the closest strings, no-change cases will dominate but occasional substitutions will break through; creating a more or less quasi-latched outcome.

e] It is also possible to measure proximity in various ways based on the bit values of the underlying ASCII codes for letters, which count up in the range [A, B, C, D . . . Z}. In that case, very complex outcomes will be possible, depending on how close the run is to target, and the specific letters that have been substituted or have reverted to what values, relative to the codes for the target.

25 --> Case [e] just above is the most likely case, and its further complexity easily explains why Weasel type programs can show considerably diverse behaviour, including implicit latching, quasi-latching and non-latching.

26 --> Even more interesting, it is possible to program an explicitly latched algorithm to show reversions, substitutions and the like. This means that only credible code can prove what is what for sure. But, in the case in view, the testimony as reported can be taken as indicating that explicit latching was not used in 1986. In that case, we have good reason to infer to implicit latching as just discussed, or at least quasi-latching.

We can now close the circle, by again citing the remarks in the December thread again as a well-substantiated conclusion:

[UD December 2008 Unpredictability thread, excerpt from comment 107:] . . . the problem with the fitness landscape [model] is that it is flooded by a vast sea of non-function, and the islands of function are far separated one from the other. So far in fact . . . that searches on the order of the quantum state capacity of our observed universe are hopelessly inadequate. Once you get to the shores of an island, you can climb away all you want using RV + NS as a hill climber or whatever model suits your fancy.

But you have to get TO the shores first. THAT is the real, and too often utterly unaddressed or brushed aside, challenge. [NB: And, in fact, that was the challenge Sir Fred Hoyle had posed. A challenge that Weasel, from its outset, has ducked and distracted attention from. Weasel is -- and has always been -- a question-begging strawman fallacy.]

And . . .  that [unmet challenge] starts with both the metabolism first and the D/RNA first schools of thought on OOL. As indeed Shapiro and Orgel recently showed . . . .

[ slice from comment no 111: ] Weasel [i.e. c. 1986] sets a target sentence then once a letter is guessed it preserves it for future iterations of trials until the full target is met. [that is, I inferred that Weasel latches the o/p as is likely from the below.] That means it rewards partial but non-functional success, and is foresighted. Targetted search, not a proper RV + NS model. [Emphases and notes added.]

---

APPENDIX 8: 

Of the inference to design and the origin and nature of mind [and thence, of morals]

by GEM of TKI [responsible for content],
with significant stimulating suggestions, critiques and other  inputs from FROSTY at UD

As at April 2008, a thread at UD has drawn out an interesting link between the inference to design and the origin and nature of mind [and thence, of morality]. The heart of that connexion may be seen from an adapted form of an example by Richard Taylor:

. . . suppose you were in a train and saw [outside the window] rocks you believe were pushed there by chance + necessity only, spelling out: WELCOME TO WALES. Would you believe the apparent message, why?

Now, it is obviously highly improbable [per the principles of statistical thermodynamics applied to, say, a pile of rocks falling down a hill and scattering to form randomly distributed patterns]. But, it is plainly logically and physically possible for this to happen.  

So, what would follow from -- per thought experiment -- actually having "good reason" to believe that this is so?

1 --> We know, immediately, that chance + necessity, acting on a pile of rocks on a hillside, can make them roll down the hillside and take up an arbitrary conformation. There thus is no in-principle reason to reject them taking up the shape: "WELCOME TO WALES" any more than any other configuration. Especially if, say, by extremely good luck we have seen the rocks fall and take up this shape for ourselves. [If that ever happens to you, though, change your travel plans and head straight for Las Vegas before your "hot streak" runs out! (But also, first check that the rocks are not made of magnetite, and that there is not a magnetic apparatus buried under the hill's apparently innocent turf! "Trust, but verify.")] 

2 --> Now, while you are packing for Vegas [having verified that the event is not a parlour trick writ large . . . ], let's think a bit: [a] the result of the for- the- sake- of- argument stroke of good luck is an apparent message, which was [b] formed by chance + necessity only acting on matter and energy across space and time. That is, [c] it would be lucky noise at work. Let us observe, also: [d] the shape taken on by the cluster of rocks as they fall and settle is arbitrary, but [e] the meaning assigned to the apparent message is as a result of the imposition of symbolic meaning on certain glyphs that take up particular alphanumerical shapes under certain conventions. That is, it is a mental (and even social) act. One pregnant with the points that [f] language at its best refers accurately to reality, so that [g] we often trust its deliverances once we hold the source credible. [Indeed, in the original form of the example, if one believes that s/he is entering Wales on the strength of seeing such a rock arrangement, s/he would be grossly irrational to also believe the intelligible and aptly functional arrangement of rocks to have been accidental.]

3 --> But, this brings up the key issue of credibility: should we believe the substantial contents of such an apparent message sourced in lucky noise rather than a purposeful arrangement? That is, would it be well-warranted to accept it as -- here, echoing Aristotle in Metaphysics, 1011b -- "saying of what is, that it is, and of what is not, that it is not"? (That is, (i) is such an apparent message credibly a true message? Or (ii) is any observed truth in it merest coincidence?)

4 --> The answers are obvious: (i) no, and (ii) yes.  For, the adjusted example aptly illustrates how cause-effect chains tracing to mechanical necessity and chance circumstances acting on matter and energy are utterly unconnected to the issue of making logically and empirically well-warranted assertions about states of affairs in the world. For a crude but illuminating further instance, neuronal impulses are in volts and are in specific locations in the body; but the peculiarly mental aspects -- meaningfulness, codes, algorithms, truth and falsehood, propositions and their entailments, etc -- simply are not like that. That is, mental concepts and constructs are radically different from physical entities, interactions and signals. 

5 --> So, it is highly questionable (thus needs to be shown not merely assumed or asserted) that such radical differences could or do credibly arise from mere interaction of physical components under only the forces of chance and blind mechanical necessity. For this demonstration, however, we seek in vain: the matter is routinely assumed or asserted away, often by claiming (contrary to the relevant history and philosophical considerations) that science can only properly explain by reference in the end to such ultimately physical-material forces. Anything less is "science-stopping." 

6 --> But in fact, in say a typical real-world cybernetic system, the physical cause-effect chains around a control loop are set up by intelligent, highly skilled designers who take advantage of and manipulate a wide range of natural regularities. As a result, the sensors, feedback, comparator, and forward path signals, codes and linkages between elements in the system are intelligently organised to cause the desired interactions and outcomes of moving observed plant behaviour closer to the targetted path in the teeth of disturbances, drift in component parameters, and noise. And, that intelligent input is not simply reducible to the happenstance of accidental collocations and interactions of physical forces, bodies and materials.

7 --> Further, as UD commenter Frosty pointed out in the linked UD thread, Leibnitz long ago highlighted one of the key challenges to an emergentist, property- and/or emanation- of- matter view of perception [and thence consciousness etc.], in The Monadology, 16 - 17. So, giving a little context to see what Leibnitz means by monads etc, and without endorsing, let us simply reflect on what is now probably a very unfamiliar way to look at things; noting his astonishing remarks on the analogy of the mill in no 17:

1. The monad, of which we will speak here, is nothing else than a simple substance, which goes to make up compounds; by simple, we mean without parts.

2. There must be simple substances because there are compound substances; for the compound is nothing else than a collection or aggregatum of simple substances.

3. Now, where there are no constituent parts there is possible neither extension, nor form, nor divisibility. These monads are the true atoms [i.e. "indivisibles," the original meaning of a-tomos] of nature, and, in a word, the elements of things . . . .

6. We may say then, that the existence of monads can begin or end only all at once, that is to say, the monad can begin only through creation and end only through annihilation. Compounds, however, begin or end by parts . . . .

14. The passing condition which involves and represents a multiplicity in the unity, or in the simple substance, is nothing else than what is called perception. This should be carefully distinguished from apperception or consciousness . . . .

16. We, ourselves, experience a multiplicity in a simple substance, when we find that the most trifling thought of which we are conscious involves a variety in the object. Therefore all those who acknowledge that the soul is a simple substance ought to grant this multiplicity in the monad . . . .

17. It must be confessed, however, that perception, and that which depends upon it, are inexplicable by mechanical causes, that is to say, by figures and motions. Supposing that there were a machine whose structure produced thought, sensation, and perception, we could conceive of it as increased in size with the same proportions until one was able to enter into its interior, as he would into a mill. Now, on going into it he would find only pieces working upon one another, but never would he find anything to explain perception. It is accordingly in the simple substance, and not in the compound nor in a machine that the perception is to be sought. Furthermore, there is nothing besides perceptions and their changes to be found in the simple substance. And it is in these alone that all the internal activities of the simple substance can consist.

8 --> We may bring this up to date by making reference to more modern views of elements and atoms, through an example from chemistry. For instance, once we understand that ions may form and can pack themselves into a crystal, we can see how salts with their distinct physical and chemical properties emerge from atoms like Na and Cl, etc. per natural regularities (and, of course, how the compounds so formed may be destroyed by breaking apart their constituents!). However, the real issue evolutionary materialists face is how to get to mental properties that accurately and intelligibly address and bridge the external world and the inner world of ideas. This, relative to a worldview that accepts only physical components and must therefore arrive at other things by composition of elementary material components and their interactions per the natural regularities and chance processes of our observed cosmos. Now, obviously, if the view is true, it will be possible; but if it is false, then it may overlook other possible elementary constituents of reality and their inner properties. Which is precisely what Liebnitz was getting at. 

9 --> Indeed, Richard Taylor speaks to this too:

Just as it is possible for a collection of stones to present a novel and interesting arrangement on the side of a hill . . . so it is possible for our such things as our own organs of sense [and faculties of cognition etc.] to be the accidental and unintended results, over ages of time, of perfectly impersonal, non-purposeful forces. In fact, ever so many biologists believe that this is precisely what has happened . . . . [But] [w]e suppose, without even thinking about it, that they [our sense organs etc] reveal to us things that have nothing to do with themselves, their structures or their origins . . . . [However] [i]t would be irrational for one to say both that his sensory and cognitive faculties had a natural, non-purposeful origin and also that they reveal some truth with respect to something other than themselves . . . [For, if] we do assume that they are guides to some truths having nothing to do with themselves, then it is difficult to see how we can, consistently with that supposition [and, e.g. by comparison with the case of the stones on a hillside], believe them to have arisen by accident, or by the ordinary workings of purposeless forces, even over ages of time. [Metaphysics, 2nd Edn, (Prentice-Hall, 1974), pp 115 - 119.]

10 --> A more elaborate example, from cybernetics, will help reinforce the point. For, we can understand -- perhaps after a bit of study (cf. the biomedical applications-oriented discussion here too) -- how feedback control loop elements interact. But as already mentioned, the intelligence of the system that gives rise to its performance lies in the design and the resulting built-in active information, not mere physicality, accidental proximity and chance co-adaptation of physical components and their parts. Moreover, it is evident that the probability of spontaneous assembly of such a system by undirected chance + necessity, on the gamut of our observed cosmos, is vanishingly different from zero. This extends to case after case, once we see functionally specified, complex information at work and directly know the origin of the system. 

11 --> Moreover, as C S Lewis aptly put it (cf. Reppert's discussion here), we can see that the physical relationship between cause and effect is utterly distinct from the conceptual and logical one between ground and consequent, and thus we have no good reason to trust the deliverances of the first to have anything credible to say about the second. Or, as Reppert aptly brings out:

. . . let us suppose that brain state A, which is token identical to the thought that all men are mortal, and brain state B, which is token identical to the thought that Socrates is a man, together cause the belief that Socrates is mortal. It isn’t enough for rational inference that these events be those beliefs, it is also necessary that the causal transaction be in virtue of the content of those thoughts . . . [But] if naturalism is true, then the propositional content is irrelevant to the causal transaction that produces the conclusion, and [so] we do not have a case of rational inference. In rational inference, as Lewis puts it, one thought causes another thought not by being, but by being seen to be, the ground for it. But causal transactions in the brain occur in virtue of the brain’s being in a particular type of state that is relevant to physical causal transactions. [Emphases added. Also cf. Reppert's summary of Barefoot's argument here.]

12 -->  Indeed, so obvious and strong are the implications of the Wales example, that in the relevant UD discussion thread, objectors repeatedly insisted on trying to turn the discussed case of lucky noise "credibly" making an apparent message into the very different one of creation of an intentional message by presumably human agents. The next step was to triumphantly announce that there is "no evidence" of other intelligent, verbalising, writing agents out there. One even went on to suggest that a pure mind could not interact with matter to form such messages; indeed, that an immaterial mind could not interact with the material realm, and so could not have "experiences." [Shades of Kant!] Later on, another objector tried to turn this into a discussion on origin of life (while pointedly not reckoning with the force of Sections A, B and C above). S/he also suggested that natural selection was a naturally occurring filter that would tip the odds substantially towards chance + necessity producing intelligent information and systems capable of handling it with reliability and accuracy. In short, sadly, we saw the insistent substitution of a convenient strawman or two for the actual case to be considered on the merits.

13 --> However, as it is further revealing, it is worth pausing a moment, to deal with such objections:

a] The resort to the above strawman arguments first inadvertently shows that many objectors to the inference to design are fully aware that the basic structure of the design inference is an empirically and epistemologically well-warranted induction. For, [a] when we see natural regularities, we see low contingency and explain in terms of mechanical necessity (e.g. how a die falls to, tumbles across and then eventually sits on a table); [b] when we see high contingency, it is by chance or design (e.g. which face of the die is uppermost); [c] when an outcome is sufficiently improbable/complex and functionally specific that available probabilistic/search resources could not credibly have arrived at the relevant configurations by chance, it is much more likely to be agency than chance (e.g. a sufficiently long string of dice that, together, spell out a message in a recognisable code). 

b] So, per inference to best causal explanation across necessity, chance and agency, when we see functionally specified complex information [FSCI], intelligent action is generally to be preferred, at least on that provisional basis that attends to all scientific inferences.

c] What is done next is to try to use the Elliot Sober argument: restricting such inference to cases of "independently" observed agents only. But, the first problem is that we have no good grounds for assuming or asserting that humans exhaust either (i) the set of actual or (ii) that of possible intelligent agents.  Secondly, the immediate implication of our own existence is that intelligent agents are possible in our cosmos. Thirdly, once we see -- per repeated empirical observation -- that signs such as FSCI reliably point to intelligent action, then when we see such signs, that is in itself empirical evidence pointing to such an agent at work. Fourthly, and as just highlighted, the reasoning used is not specific to human-ness, but instead to intelligent agency: as the Wales example shows, chance and necessity -- per the vast improbabilities involved -- simply cannot credibly do what intelligent agents reliably and routinely can; on the gamut of our observed cosmos. 

d] So, the Sober-style objection is question-begging. For, in fact, even among ourselves, we recognise agency from the works of such agents -- the signs of intelligence they leave behind; of which FSCI is a most obvious and routine example. (Q: How do you know to moral certainty that this web page is not lucky noise mimicking a signal? A: By inference to agency from FSCI as a reliable sign thereof. So: As long as agency is logically possible in a situation, we should be open to recognising it from its signs and associated circumstances.)
 
e] Next, we have reason to note that the observed cosmos' underlying physics reflects multi-dimensional, convergent, fine-tuned, highly complex, functional order that facilitates cell-based life, and similar reason to note that the said observed cosmos credibly began at a specific time in the past. Thus, we have good reason to infer (per inference to best, empirically anchored explanation) that the origin of the cosmos itself is marked by the signs of purposeful  intelligent design. And, pace the remarks of objectors, as the just linked section discusses, that IS evidence of non-human intelligent agent(s). [For, "mere objection on your part does not constitute "absence of evidence" on my part"!]

f] Moreover, since we are speaking of the beginnings of our observed matter-energy and space-time domain, said inferred intelligence was credibly able to create -- thus, interact with -- matter while not being material; this last referring to the "stuff" of the physical cosmos. For, matter is here an effect, not a cause, and -- per self-evident proposition -- an entity cannot cause its own origin. (Classically: "that which begins has a cause, but that which has no beginning needs have no cause"; i.e we are here raising the issue of the difference between contingent and necessary beings; duly modified by the observation that we credibly live in an observed, contingent cosmos. And, the most credible "alternative," in effect a quasi-infinite array of sub cosmi, is just as much a metaphysical proposition -- and one that runs into much more serious difficulties on a comparative basis. )

g] Consequently, it is not at all an obvious given that a "pure mind" entity would be unable to observe, interact with, speak into and act upon -- thus, experience -- the physical world. 

h] Indeed, considering our own minds and brains, the brain is a bodily, material entity; subject therefore to chance and necessity under the electrochemical etc. forces and interactions acting on and in it. Thus (given the Wales example) it is not credible as the ultimate source of messages and actions that point -- beyond the credible reach of such forces -- to intelligent, purposeful, creative [as opposed to mere random], functionally successful action. (NB: The Derek Smith cybernetic model of a two-tier controller for a biologically relevant system, with the upper level strategic, imaginative and creative controller guiding and overseeing a lower level one acting as a supervised input-output controller, may be a fruitful discussion model for a mind-brain system. For instance, one -- for the sake of argument -- may look at a mind as using quantum gaps to "feed" signals into the brain-body system.)

i] When we come to the natural selection argument, we first need to address the problem of origin of life models that was aptly posed by Robert Shapiro in challenging the popular RNA world model. Adverting to the gap between what presumably purposeful and intelligent chemists can do by design in labs and what was credible in plausible prebiotic environments, he noted -- in words that inadvertently are equally applicable to his own preferred metabolism first model:

The analogy that comes to mind is that of a golfer, who having played a golf ball through an 18-hole course, then assumed that the ball could also play itself around the course in his absence. He had demonstrated the possibility of the event; it was only necessary to presume that some combination of natural forces (earthquakes, winds, tornadoes and floods, for example) could produce the same result, given enough time. No physical law need be broken for spontaneous RNA formation to happen, but the chances against it are so immense, that the suggestion implies that the non-living world had an innate desire to generate RNA. The majority of origin-of-life scientists who still support the RNA-first theory either accept this concept (implicitly, if not explicitly) or feel that the immensely unfavorable odds were simply overcome by good luck. [Emphasis added.]

j] When it comes to the proposal that "natural selection" credibly accounts for the mind, Plantinga highlights that [a] natural selection is said to reward successful adaptations, but also that [b] the inner thought world is not directly connected to the success of survival-enhancing behaviour. Consequently [c] such mind-blind, behaviour-oriented selection cannot ground the reliability or accuracy of perceptions, inferences or motivations for action. In Plantinga's words:

. . . evolution is interested (so to speak) only in adaptive behavior, not in true belief. Natural selection doesn’t care what you believe; it is interested only in how you behave. It selects for certain kinds of behavior, those that enhance fitness, which is a measure of the chances that one’s genes are widely represented in the next and subsequent generations . . . But then the fact that we have evolved guarantees at most that we behave in certain ways–ways that contribute to our (or our ancestors’) surviving and reproducing in the environment in which we have developed . . . . there are many belief-desire combinations that will lead to the adaptive action; in many of these combinations, the beliefs are false. (Link. Emphases added. [Note: even major and well-supported scientific beliefs/models -- such as Newton's laws of motion, circa 1680 - 1880 -- were/are not necessarily true to actual reality but rather were/are empirically reliable under the tested circumstances.] Cf. blog exchange contributions here, here, here, and here.) 

k] That is why something is very wrong with Sir Francis Crick's remark in his 1994 The Astonishing Hypothesis, to the effect that:

"You," your joys and your sorrows, your memories and your ambitions, your sense of personal identity and free will, are in fact no more than the behaviour of a vast assembly of nerve cells and their associated molecules . . .

l] Philip Johnson duly corrected him by asking whether he would be willing to preface his own writings thusly:

"I, Francis Crick, my opinions and my science, and even the thoughts expressed in this book, consist of nothing more than the behavior of a vast assembly of nerve cells and their associated molecules." [Reason in the Balance, 1995.]

m] In short, as Prof Johnson then went on to say:

“[t]he plausibility of materialistic determinism requires that an implicit exception be made for the theorist.”

n] Thus, unless evident "fact no 1" -- that we are conscious, mental creatures who at least some of the time have freedom to think, intend, decide, speak, act and even write based on the logic and evidence of the situation  -- is true, the project of rationality itself is at an end. That is, self-referential absurdity is the dagger pointing to the heart of any such evolutionary materialistic determinism as seeks to explain "all" -- including mind -- by "nothing but" natural forces acting on matter and energy, in light of chance boundary conditions. (This is as opposed to restricted, truly scientific, explanations that explain [i] natural regularities by reference to [a] underlying mechanical necessity, and explain [ii] highly contingent situations by reference to [b] chance and/or [c] intelligent action. We then distinguish the two by identifying and applying reliable signs of intelligence; similar to what obtains in statistical hypothesis testing and in control-treatment experiment designs and related factor analysis.)

14 --> So, as the Wales example and the debates it sparked at UD have brought out, the inference to design highlights the radical difference between [1] what chance + necessity acting on matter + energy on the gamut of our observed universe can credibly do (up to an apparent message by lucky noise) and [2] what mind routinely does (i.e. routinely creating real messages). But [3] it thus also has in it an aspect that points to the nature and origin of mind (and, thence, of morals as a particularly important function of mind). Indeed, [4] in the cosmological form, the inference to design also points to the serious possibility that mind is the source of matter, not the converse.  Inter alia, this would make it utterly unsurprising that -- as we experience it every time we decide to speak or type on a keyboard, or click a mouse button or the like --  mind can interact causally with matter, even though we may not currently know how to explain just how that happens. We know that mind, even though as yet we do not really know how mind.

Howbeit, it is also worth pausing to briefly speak to some possibilities, plausibilities and constraints on that "how":

15 --> Classically, the exact, mechanistic form of Newtonian physics [e.g. F = m.a, F_grav = G. m₁.m₂/r²] as discovered in the C17 and associated differential equations suggested to many C18 - 19 scientists and mathematicians (often the same people) that once the universe's initial conditions were specified, everything thereafter would have unfolded according to precise trajectories set by the laws in light of those conditions. (In praxis of course, even so simple a case as a three-body gravitational system has proved astonishingly and humblingly resistant to general solution.) But, never mind such embarrassing little quibbles: the Newtonian vision lent great plausibility to the idea that the universe forms a closed, mechanistic, naturalistic system, and to associated determinism.  (Of course -- equally embarrassingly -- we now also know that in many systems that exhibit sensitive dependence to initial conditions and so have nonlinear amplification of minute differences in initial conditions, the long-run behaviour is, practically speaking, unpredictable.) In the end, though, even when solution difficulty, chance conditions, random elements, unpredictability and random, stochastic processes have had to be recognised, there has still been a trend to evolutionary materialistic determinism. On such a view, there is little or no room for immaterial entities or influences, whether mental or spiritual. And, of course, miracles were then also often viewed as literally incredible; i.e. they were dismissed by many speaking in the name of "science" as credulous, superstitious nonsense.

16 --> Immediately, though, something is wrong. Very, very wrong.

17 --> For, first, Newtonian dynamics is arrived at by a process of incremental scientific induction and testing of explanatory hypotheses, which may be very persuasive but which simply is not a demonstrative proof. Indeed, strictly, the inference IF theory, THEN observations and predictions; observations and predictions, so theory, is the fallacy known as affirming the consequent. In short, scientific knowledge is inherently provisional and we should be critically aware, humble and open-minded in approaching matters and claims of science. Indeed, in  the period from the 1880's to 1930's, the then unexpected limitations of Newtonian physics were starkly revealed, as various quantum, statistical and relativistic phenomena came to the fore. (Oddly, the much derided and even despised pope Urban VIII had warned Galileo about precisely those sorts of limitations. [Cf also here.]) The early C20 jump from classical to modern physics through a scientific revolution therefore underscored that observed patterns and even highly reliable well-tested explanations of such patterns are not to be confused with a globally accurate view of reality; i.e. the truth. Further, as statistics warns us, an observed, described, explained/modelled and tested pattern may be a part of a wider more complex -- and not yet fully observed -- pattern. So, it is plainly also wise for us to be open to the possibility of "exceptions"; including such that are so unusual and contextually significant that we would not be amiss to call them "miracles."

18 --> Moreover, scientific induction is a process of thinking. But, if all that is, is "nothing but" matter and energy acted upon by purposeless mechanical necessity and chance conditions, then allegedly reasoned thought is in the end caused and controlled by circumstances and forces that are utterly irrelevant to purpose, truth, validity, cogency or soundness. There would thus be no room for truly logical inference, which -- as the Wales example above shows -- fatally undermines our confidence in the perceptions, consciousness, thoughts and reasoning that we need. Even, to set up a deterministic, materialistic system of thought. 

19 --> Further to this, we must reflect on implications and applications of Kurt Gödel's justly famous incompleteness theorems. For, KG showed in the early 1930's that [a] no axiomatic mathematical system sufficiently rich to cover say ordinary arithmetic, can be both internally consistent and complete, and [b] there is no constructive process for devising a system of axioms for such a system that will be known to be self-consistent. In effect, Mathematico-logical reasoning [including computing and computation] are irreducibly complex, non-mechanical ventures in which we may and often do confidently know or believe more -- often, far more -- than we can individually or even collectively deductively prove relative to any sufficiently rich sets of axiomatic premises we may decide to use and trust.  

20 --> More generally, mind and knowing cannot be reduced to input -> mechanical processing -> output based algorithms that deterministically grind out complete sets of "known truths" premised on sufficiently rich, but elegantly sparse sets of axioms acceptable to all sufficiently informed rational agents. (Often, the relevant processing is not based on meanings, but on mechanical manipulation of well-chosen symbols; based on axioms, theorems and physical realisations of mathematical operations and variables.) 

21 --> Thus, deductive proof and associated mechanical computing algorithms are now no longer credible as escape-hatches from the inextricable intertwining of reasoning and believing in the core of our worldviews, mathematics, science, real-world thinking and real-world information technology. This, in short, is the end of mechanical necessity as an engine to generate the field of knowledge and associated effective, algorithm-based function. Creativity, imagination, intuition and provisionality -- do I daresay, "faith" -- have won the day, even in mathematics. (Indeed, in recent days, Hawking is inclining to the view that this is also the end of the decades-long project in physics to construct a global "theory of everything.")

22 --> So, we see Douglas Hofstadter -- a critic, BTW, of such extensions of Gödel --conceding in his Gödel, Escher, Bach: an Eternal Golden Braid:

. . . Godel's proof suggests -- though by no means does it prove! -- that there could be some high-level way of viewing the mind/brain, involving concepts which do not appear on lower levels, and that this level might have explanatory power that does not exist -- not even in principle -- on lower levels. It would mean that some facts could be explained on the high level quite easily, but not on lower levels at all. No matter how long and cumbersome a low-level statement were made, it would not explain the phenomena in question. It is analogous to the fact that, if you make derivation after derivation in [Peano arithmetic], no matter how long and cumbersome you make them, you will never come up with one for G -- despite the fact that on a higher level, you can see that [the Godel sentence] is true. What might such high-level concepts be? It has been proposed for eons, by various holistically or "soulistically" inclined scientists and humanists that consciousness is a phenomenon that escapes explanation in terms of brain components; so here is a candidate at least. There is also the ever-puzzling notion of free will. So perhaps these qualities could be "emergent" in the sense of requiring explanations which cannot be furnished by the physiology alone [p. 708; emphases added.]

23 --> Pulling the various threads together, we may now find a way for conscious reason to be credible [even if provisional], thus for the conscious reasoning mind that is sufficiently independent of -- though obviously strongly interacting with -- the brain-body system, that we can be confident in our thought. Otherwise, science itself falls into self-referential incoherence, absurdity and confusion. A first step to that, would be to examine some implications of quantum uncertainty and related phenomena for the brain and the mind. For instance,  Harald Atmanspacher, writing in the Stanford Encyclopedia of Philosophy observes:

It is widely accepted that consciousness or, more generally, mental activity is in some way correlated to the behavior of the material brain. Since quantum theory is the most fundamental theory of matter that is currently available, it is a legitimate question to ask whether quantum theory can help us to understand consciousness . . . .

The original motivation in the early 20th century for relating quantum theory to consciousness was essentially philosophical. It is fairly plausible that conscious free decisions (“free will”) are problematic in a perfectly deterministic world,^[1] so quantum randomness might indeed open up novel possibilities for free will. (On the other hand, randomness is problematic for volition!)

Quantum theory introduced an element of randomness standing out against the previous deterministic worldview, in which randomness, if it occurred at all, simply indicated our ignorance of a more detailed description (as in statistical physics). In sharp contrast to such epistemic randomness, quantum randomness in processes such as spontaneous emission of light, radioactive decay, or other examples of state reduction was considered a fundamental feature of nature, independent of our ignorance or knowledge. To be precise, this feature refers to individual quantum events, whereas the behavior of ensembles of such events is statistically determined. The indeterminism of individual quantum events is constrained by statistical laws.

24 --> This brings in a new level of considerations, but is itself not unproblematic. For, mere randomness is not enough; we need a viable mechanism of orderly, intelligent interaction. 

25 --> To get to that, we may not only use the above noted indeterminacy of particle behaviour as is found in Quantum theory; but also, we apply Einstein's energy-time form of the Heisenberg uncertainty principle. For, at microscopic level force-based interactions between bodies can be viewed in terms of exchanges of so-called "virtual particles." That is, once the product of the energy and time involved in a particle being exchanged between two interacting bodies falls below the value of Planck's constant h (suitably multiplied or divided by a small constant), bodies may interact through exchanging undetected -- so, "virtual" -- particles. We can in effect have a situation crudely similar to two people tugging or pushing on opposite ends of a stick: they interact through the means of the intervening stick; which we then see as attractions or repulsions between the bodies. Thus, as the just linked explains in more details, the quantum theory of forces and interactions between bodies is now strongly based on Heisenberg's principle of uncertainty; yet another case where the deterministic view has been undermined, and one that opens the doorway to a model of the workings of the brain-mind interface. 

26 --> As Scott Calef therefore observes:

Keith Campbell writes, “The indeterminacy of quantum laws means that any one of a range of outcomes of atomic events in the brain is equally compatible with known physical laws. And differences on the quantum scale can accumulate into very great differences in overall brain condition. So there is some room for spiritual activity even within the limits set by physical law. There could be, without violation of physical law, a general spiritual constraint upon what occurs inside the head.” (p.54). Mind could act upon physical processes by “affecting their course but not breaking in upon them.” (p.54). If this is true, the dualist could maintain the conservation principle but deny a fluctuation in energy because the mind serves to “guide” or control neural events by choosing one set of quantum outcomes rather than another. Further, it should be remembered that the conservation of energy is designed around material interaction; it is mute on how mind might interact with matter. After all, a Cartesian rationalist might insist, if God exists we surely wouldn’t say that He couldn’t do miracles just because that would violate the first law of thermodynamics, would we? [Article, "Dualism and Mind," Internet Encyclopedia of Philosophy.]

27 --> Within this broad framework, there have been several interesting suggestions. Of these, the Penrose- Hameroff proposal is quite original:

It is argued that elementary acts of consciousness are non-algorithmic, i.e., non-computable, and they are neurophysiologically realized as gravitation-induced reductions of coherent superposition states in microtubuli . . . . Penrose's rationale for invoking state reduction is not that the corresponding randomness offers room for mental causation to become efficacious (although this is not excluded). His conceptual starting point, at length developed in two books (Penrose 1989, 1994), is that elementary conscious acts must be non-algorithmic. Phrased differently, the emergence of a conscious act is a process which cannot be described algorithmically, hence cannot be computed. His background in this respect has a lot to do with the nature of creativity, mathematical insight, Gödel's incompleteness theorem, and the idea of a Platonic reality beyond mind and matter . . . . With his background as an anaesthesiologist, Hameroff suggested to consider microtubules as an option for where reductions of quantum states can take place in an effective way, see e.g., Hameroff and Penrose (1996). The respective quantum states are assumed to be coherent superpositions of tubulin states, ultimately extending over many neurons. Their simultaneous gravitation-induced collapse is interpreted as an individual elementary act of consciousness. The proposed mechanism by which such superpositions are established includes a number of involved details that remain to be confirmed or disproven.

28 --> In short, there is much room for both potentially fruitful speculation and future empirical research to test the ideas. (Yet another instance where the design-oriented view is anything but a science-stopper.)

29 --> The Derek Smith model for cybernetics offers a further fruitful line of thought for understanding the mind-brain interface and also for developing an architecture for artificially intelligent robotic systems. Take a multiple input-multiple output control loop, with many effectors, sensors and feedback loops. A lower order controller acts to co-ordinate the processes, based on a projected path and a moment by moment comparison between actual and projected. Corrective action is taken to adjust performance to desired. A higher order controller provides a supervisory level, with the creative, imaginative insight and projections that lay out the path for action for the lower order motion etc. controller. Thus, the brain here can be viewed as the mind's front-end input-output controller, with informational interfaces going both ways: brain-body and mind-brain:



Fig. A8.1: A simplified view of Derek Smith's two-tier controller cybernetic system model, illustrating how mind and brain could interact informationally without "locking" mind down to brain wiring. Memory can be of course [in part?] provided through the brain. (Cf Smith's detailed discussion here.)

In sum, we have no shortage of more or less plausible (or at least interesting!) models of how a mind-brain interface may work, in a context where the concept that our minds are in effect produced and controlled by forces based on chance and mechanical necessity cannot credibly ground the reliability of our minds.  This brings up an excerpt from another page in this site, which helps us further elaborate on and apply Taylor's point on the implications of the evolutionary materialist worldview, on what happens so soon as it tries to completely account for the origin of reliable mind and senses within the cosmos through the impacts of chance + necessity on matter and energy configured as biological entities:

. . . [evolutionary] materialism [a worldview that often likes to wear the mantle of "science"] . . . argues that the cosmos is the product of chance interactions of matter and energy, within the constraint of the laws of nature.  Therefore, all phenomena in the universe, without residue, are determined by the working of purposeless laws acting on material objects, under the direct or indirect control of chance.

But human thought, clearly a phenomenon in the universe, must now fit into this picture.  Thus, what we subjectively experience as "thoughts" and "conclusions" can only be understood materialistically as unintended by-products of the natural forces which cause and control the electro-chemical events going on in neural networks in our brains.  (These forces are viewed as ultimately physical, but are taken to be partly mediated through a complex pattern of genetic inheritance ["nature"] and psycho-social conditioning ["nurture"], within the framework of human culture [i.e. socio-cultural conditioning and resulting/associated relativism].)

Therefore, if materialism is true, the "thoughts" we have and the "conclusions" we reach, without residue, are produced and controlled by forces that are irrelevant to purpose, truth, or validity.  Of course, the conclusions of such arguments may still happen to be true, by lucky coincidence — but we have no rational grounds for relying on the “reasoning” that has led us to feel that we have “proved” them.   And, if our materialist friends then say: “But, we can always apply scientific tests, through observation, experiment and measurement,” then we must note that to demonstrate that such tests provide empirical support to their theories requires the use of the very process of reasoning which they have discredited!

Thus, evolutionary materialism reduces reason itself to the status of illusion.  But, immediately, that includes “Materialism.”  For instance, Marxists commonly deride opponents for their “bourgeois class conditioning” — but what of the effect of their own class origins? Freudians frequently dismiss qualms about their loosening of moral restraints by alluding to the impact of strict potty training on their “up-tight” critics — but doesn’t this cut both ways?  And, should we not simply ask a Behaviourist whether s/he is simply another operantly conditioned rat trapped in the cosmic maze?

In the end, materialism is based on self-defeating logic . . . . 

In sum, we again see a pattern of self-referential inconsistencies on the origin and credibility of the mind, and a reduction of morality to "might makes 'right.' " Neither of these can stand on their own feet. But, to clench over the nails in the coffin of evolutionary materialism, it is also worth excerpting a well expressed point from Will Hawthorne at the blog, Atheism is Dead, on the [a-]moral implications of evolutionary materialism: 

Assume (per impossibile) that atheistic naturalism [= evolutionary materialism] is true. Assume, furthermore, that one can't infer an 'ought' from an 'is' [the 'is' being in this context physicalist: matter-energy, space- time, chance and mechanical forces].  (Richard Dawkins and many other atheists should grant both of these assumptions.) Given our second assumption, there is no description of anything in the natural world from which we can infer an 'ought'. And given our first assumption, there is nothing that exists over and above the natural world; the natural world is all that there is. It follows logically that, for any action you care to pick, there's no description of anything in the natural world from which we can infer that one ought to refrain from performing that action. Add a further uncontroversial assumption: an action is permissible if and only if it's not the case that one ought to refrain from performing that action. (This is just the standard inferential scheme for formal deontic logic.) We've conformed to standard principles and inference rules of logic and we've started out with assumptions that atheists have conceded in print. And yet we reach the absurd conclusion: therefore, for any action you care to pick, it's permissible to perform that action. If you'd like, you can take this as the meat behind the slogan 'if atheism is true, all things are permitted'. For example if atheism is true, every action Hitler performed was permissible. Many atheists don't like this consequence of their worldview. But they cannot escape it and insist that they are being logical at the same time.

Now, we all know that at least some actions are really not permissible (for example, racist actions). Since the conclusion of the argument denies this, there must be a problem somewhere in the argument. Could the argument be invalid? No. The argument has not violated a single rule of logic and all inferences were made explicit. Thus we are forced to deny the truth of one of the assumptions we started out with. That means we either deny atheistic naturalism or (the more intuitively appealing) principle that one can't infer 'ought' from 'is'. [Emphases added.]

Of course, if an evolutionary materialist wishes to now assert instead that s/he can in fact infer the ought from the mere PHYSICAL is, that has to be shown, not merely assumed. Good luck. (On the other hand, if the "is" of our observed contingent cosmos is premised on the necessary reality of the beginningless and endless  Creator-Sustainer God, then that most relevant "is" of all  -- I AM THAT I AM -- grounds at once the soundness of morality in the holy, just and loving nature of the very source of creation. [And the claimed Eutryphro dilemma also at once evaporates: reality itself is grounded in the nature of him who is inescapably moral so that which is commanded is grounded inescapably in the root nature of reality itself, without that reality being independent of God the Law-giver.])

If one now wishes to bring forth the hot button (thus, often highly distracting) issue of the problem of evil, please cf. some discussions on Plantinga's Free Will defense, and Koukl's summary of the argument FROM evil. This last raises some very interesting and highly relevant observations for our current purposes: 

Evil is real . . .  That's why people object to it.  Therefore, objective moral standards must exist as well [i.e. as that which evil offends and violates]  . . . .  The first thing we observe about [such] moral rules is that, though they exist, they are not physical because they don't seem to have physical properties. We won't bump into them in the dark.  They don't extend into space.  They have no weight.  They have no chemical characteristics.  Instead, they are immaterial things we discover through the process of thought, introspection, and reflection without the aid of our five senses  . . . .

We have, with a high degree of certainty, stumbled upon something real.  Yet it's something that can't be proven empirically or described in terms of natural laws.  This teaches us there's more to the world than just the physical universe.  If non-physical things--like moral rules--truly exist, then materialism as a world view is false.

There seem to be many other things that populate the world, things like propositions, numbers, and the laws of logic.  Values like happiness, friendship, and faithfulness are there, too, along with meanings and language.  There may even be persons--souls, angels, and other divine beings.

Our discovery also tells us some things really exist that science has no access to, even in principle.  Some things are not governed by natural laws.  Science, therefore, is not the only discipline giving us true information about the world.  It follows, then, that naturalism as a world view is also false.

 Our discovery of moral rules forces us to expand our understanding of the nature of reality and open our minds to the possibility of a host of new things that populate the world in the invisible realm.

Going back to the more direct implications of the Wales example, the detection of functionally specified, complex information is a profound indicator that there is more to the world of our experiences than merely chance + necessity blindly acting on matter and energy. In short, signs of intelligence in the world around us -- in light of our own experience as (at least sometimes rational) intelligent agents -- point strongly to the reality of active mind that transcends the credible reach of chance + necessity acting on matter + energy. Bringing in the organised complexity of the observed cosmos and its credible origin at a specific point in the past, we see good reason to infer to -- i.e. this is a destination arrived at after examining and seeking to explain observed evidence, not a question-begging assumption -- the origin of the cosmos itself at the hands of Mind beyond the reach of matter.  Indeed, it is fair comment to note that: the evidence of signs of intelligence strongly speaks to matter being the product of mind, and not the reverse.

In turn, that means that the so-called "hard problem of consciousness" is very often ill-conceived, and typically worse stated. For, as Ned Block observes in an article for The Encyclopedia of Cognitive Science:

The Hard Problem of consciousness is how to explain a state of consciousness in terms of its neurological basis . . . . There are many perspectives on the Hard Problem but I will mention only the four that comport with a naturalistic framework . . . . Eliminativism . . . . Philosophical Reductionism or Deflationism . . . . Phenomenal Realism, or Inflationism . . . . Dualistic Naturalism. 

[NB: In fairness, we must now contrast the better balanced summary here, at the -- often, for very good reason -- much lambasted Wikipedia: "The term hard problem of consciousness, coined by David Chalmers^[1], refers to the "hard problem" of explaining why we have qualitative phenomenal experiences." (But note how in the onward linked discussion of experiences, we see the reversion to naturalism: "Phenomenal consciousness (P-consciousness) is simply experience; it is moving, coloured forms, sounds, sensations, emotions and feelings with our bodies and responses at the center. These experiences, considered independently of any impact on behavior, are called qualia. The hard problem of consciousness was formulated by Chalmers in 1996, dealing with the issue of "how to explain a state of phenomenal consciousness in terms of its neurological basis" (Block 2004).") ] 

Let us therefore note how, in Block's -- clearly influential -- formulation, the materialistic-naturalistic perspective is imposed, right from the outset, via the presented definition of the problem (and the underlying assumed definition of "Science"): explain[ing] a state of consciousness in terms of its neurological basis. So, any explanation that does not set out to in effect account for consciousness on the basis of neurons and their electrochemistry or the like is excluded from the outset. AKA, begging the question.

Block then sets out to look at four “naturalistic” alternatives: [1] the view that “consciousness as understood above simply does not exist,” [2] allowing that “consciousness exists, but they ‘deflate’ this commitment—again on philosophical grounds—taking it to amount to less than meets the eye,” [3] the view that in effect consciousness emerges from but is not reducible to neurological activity [a comparison is made to how heat as a concept may be explained as tracing physically to thermal agitation of molecules, but is conceptually different], [4] views that “standard materialism is false but that there are naturalistic alternatives to Cartesian dualism such as pan-psychism."  [This last is explained here.]

But, what is never seriously on the table is the key issue that the design inference points to: we know, immemorial, that there are three major causal factors, chance, necessity, intelligence. Necessity is associated with mechanical regularities [e.g. how heavy objects fall and come to rest on a table], so is not associated with highly contingent outcomes. Contingency [e.g. which face of a die, having fallen to and settled on a table is uppermost] traces to chance or agency. When we have functionally specified, complex information, we have a situation that in observation and on grounds of inadequacy of required search resources, reliably traces to intelligence, not chance.

It is thus -- vast erudition of many discussions by scholars of the highest calibre notwithstanding -- utterly unsurprising to see that the whole evolutionary materialistic project to "explain" consciousness grinds to a halt in the face of self referential incoherence and failure to adequately reckon with the radical differences between the properties of mind and matter. So, options 1 and 2 fall apart directly, and 3 and 4 boil down to defiantly flying the materialistic flag and passing out promissory notes in the teeth of consistent explanatory failure. But persistent explanatory failure is not just a matter to be fobbed off with a promissory note or two on future deliverances of “Science” and/or alternative materialistic explanations, it is inherent in the materialistic imposed -- historically and philosophically suspect -- redefinition of what science is and tries to do. For, the exclusion of intelligence from explanation when it is inconvenient to the evolutionary materialist view, ends up in question-begging, and is in violation of basic facts on the history of science. It is also philosophically ill-founded, and is self referentially incoherent; as has been shown above. 

That is -- as the case of Sir Francis Crick vividly illustrates -- such evolutionary materialist "explanations" cannot even coherently explain the intellectual works of the researchers themselves. For, we know that complex, functionally organised information such as apparent messages, reliably trace to mind, and that mind has capabilities that do not credibly trace to chance + necessity acting on matter + energy. In short, we have strong, empirically based reason to see that once mind is viewed through the characteristics of its traces, we are dealing with something that strongly points beyond the world of matter + energy acted on by forces tracing to chance + necessity only.

So, pardon a bit of an altar call: let us now call on the denizens of the evolutionary materialist cave of manipulative shadow shows -- “step into the sunshine, and step out of the shade . . .”

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NOTICES: This briefing note was originally created by GEM of TKI, in March 2006, for use in briefing Christian leaders and others interested in the ongoing controversy on Intelligent Design and related concerns. [NB: Because of abuse of my given name in blog commentary threads, I have deleted my given name from this page, and invite serious and responsible interlocutors to use my email contact below to communicate with me.] This page has been subsequently revised and developed, to date; so far, to clean up the clarity and flow of the argument, which is admittedly a difficult one, and add to the substance especially as key references are discovered one by one such as the recent Shapiro article in Sci Am. Thanks are due to the ad hoc group of regular commenters at The Evangelical Outpost Blog over the period since April 2005, for many useful comments, on both sides of the question. (DISCLAIMER: While reasonable attempts have been made to provide accurate, fair and informative materials for use in training, no claim is made for absolute truth, and corrections based on factual errors and/or gaps or inconsistencies in reasoning, etc., or typos, are welcome.) FAIR USE: The contents of this note are in part intended for use as a support for learning about responding to the typical intellectual challenges to the Christian Faith and gospel that are commonly encountered in the Caribbean, especially in tertiary education, or on the Internet, or in commentary in the regional and international media: here, (i) as the evolutionary materialists have abused science over the past century and more in promotion of materialistic philosophies -- requiring a serious response on the merits; presented (ii) at a semi-popular, introductory technical level suitable to College level students and graduates with some background in the sciences and mathematics used. In turn, that is intended to support the ongoing work of reformation of Western and global cultures through the positive, corrective impacts of the Gospel - observe here, how Plato grounds his Laws in the implications of the inference to design, as cited, in context. In this case, as just noted, the contents are also intended to provide an accurate briefing on the actual merits of the case on the inference to design, as a basis for restoring balance to science, science education and linked public perceptions and policy. (It is also hoped that the presentation will stimulate students to dig deeper into the relevant sciences, as well, thus enriching their educational experience through developing their own perspectives and building deeper familiarity with key technical points, techniques and issues.) Permission is therefore granted to link to this page for fair use under intellectual property law, and for reasonable fair use citation of the linked content on this site for church- or parachurch- group related training and/or for personal or specifically institutional academic use. [But kindly have mercy on the available bandwidth at a freebie site . . . ask me to use the page whole or make significant excerpts on your own site as appropriate . . .] This permission specifically excludes reproduction, linking or citation for commercial, controversial or media purposes without the Author's written permission -- especially where matters relating to the validity and value of Faith/Religious/Atheological Commitments and Truth-Claims are being debated or disputed. COPYRIGHT: GEM 2006. All rights are reserved, save as specifically noted just above.

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