The Case for Intelligent Design, in Laypeople's Language

• In this post, I'm going to explain why Intelligent Design is a scientific theory and neo-Darwinism is not. In a nutshell: it all boils down to numbers. Any scientific theory has to be capable of quantifying its statements. As Lord Kelvin once put it, "When you can measure what you are speaking about and express it in numbers, you know something about it" (Lecture to the Institution of Civil Engineers, 3 May 1883).

• The key point at issue between Intelligent Design proponents and Darwinian evolutionists is not common descent (which many ID proponents believe in), or even evolution by natural selection. The key point is whether natural selection alone can amplify, over the course of time, the probability of a system which is capable of performing a specific function (i.e. doing a useful task) arising as a result of "blind" processes (chance plus necessity). Intelligent Design proponents claim that natural selection can't amplify the antecedent probability of such a system arising. The only way to amplify this probability is to narrow down your choice of starting points or your choice of possible pathways, thereby biasing the likelihood of obtaining a system that can do the job in question. In other words, you have to either rig the initial set-up or rig the rules, or manipulate the system from outside. And it takes an intelligent being to either rig a system, or manipulate that system, so as to obtain a specified result. What Intelligent Design proponents are saying is that the universe was somehow either rigged or manipulated to produce life. However, at the present time, they don't claim to know how it was rigged, let alone when or how many times. Future research will shed light on these questions.

• I'm assuming at the outset that if Darwinian evolution requires us to postulate a multiverse in order to explain how life evolved in this universe, then it is useless as a scientific theory. If you posit a multiverse, then all you are really saying that anything can happen if you give it enough time. But if that's the case, then appealing to natural selection is redundant.

• Intelligent Design is capable of quantifying its key assertions about how unlikely the emergence of a system performing a particular function has to be, before we can reliably infer that this system was produced by an intelligent agent. By contrast, Neo-Darwinism is totally incapable of quantifying the amount of time needed for evolution by natural selection to work. We may therefore conclude that while Intelligent Design might be a valid scientific theory, Neo-Darwinism doesn't even get to first base.

• Intelligent Design makes two kinds of quantifiable assertions.
  First, it asserts that if we find a system performing a specific function, where the probability of the system arising as a result of unguided processes falls below a certain threshold (1 in 10 to the power of 150), we can be certain beyond reasonable doubt that this system is the work of an intelligent agent. Intelligent Design would therefore be falsified as a method of identifying artifacts produced by intelligent agents if someone came up with a system performing a specific function, whose probability of arising through blind processes fell below the 1 in 10 to the power of 150 threshold, but which could nevertheless be shown to be the result of blind processes (chance, necessity, or some combination of both).
  Second, Intelligent Design theory asserts that living things contain lots of biological components that perform very specific functions, whose probability of arising through blind processes falls below the critical threshold of 1 in 10 to the power of 150. Indeed, ID proponents claim that even a single protein often fall below this threshold. The theory of Intelligent Design would therefore be falsified if it could be empirically demonstrated that the biological components of living things aren't that improbable after all.

• The Intelligent Design argument I'll be putting forward here is a very simple one. I won't be using jargon like "complex specified information," and I won't be talking about digital codes or genetic programs here, since I want to keep my argument as non-technical as possible. In a nutshell, my argument is all about proteins. In a nutshell, proteins perform very specific functions within the cell. What's more, living things need lots of proteins: the simplest living cell needs at least 250 proteins; the molecular machines within the cell require dozens of proteins each; the first eukaryotic cell (i.e. a cell having a nucleus, as cells in animals, plants, fungi and protists do) requires hundreds more proteins than a simple bacterial cell; and the new cell types which appeared in the bodies of complex animals required layers upon layers of protein regulation, in a hierarchical system of control. However, as far as we can tell, the odds of even a single protein forming by blind processes (chance plus necessity) are astronomically low: well below 1 in 10 to the power of 150. That's so rare that you wouldn't expect it to happen even once, in the lifetime of the observable universe. Short of positing a supernatural act, the only way to narrow those odds is to suppose that either the starting conditions of the universe were rigged, or the laws of Nature are somehow rigged in ways unknown to us, so as to favor the evolution of proteins. But it takes an intelligent being to rig things like that, so we're back with a Designer.

• My Intelligent Design argument can be formulated on five levels, as there are at least five kinds of functional specificity in living things that point to their having been intelligently designed:

  (1) Proteins. Every living thing on this planet contains proteins, which are made up of amino acids. Proteins are fundamental components of all living cells and include many substances, such as enzymes, hormones, and antibodies, that are necessary for the proper functioning of an organism. They're involved in practically all biological processes. To fulfil their tasks, proteins need to be folded into a complicated three-dimensional structure. Proteins can tolerate slight changes in their amino acid sequences, but a single change of the wrong kind can render them incapable of folding up, and hence, totally incapable of doing any kind of useful work within the cell. That's why not every amino-acid sequence represents a protein: only one that can fold up properly and perform a useful function within the cell can be called a protein. Now let's consider a protein made up of 150 amino acids - which is a fairly modest length. If we compare the number of 150-amino-acid sequences that correspond to some sort of functional protein to the total number of possible 150-amino-acid sequences, we find that only a tiny proportion of possible amino acid sequences are capable of performing a function of any kind. The vast majority of amino-acid sequences are good for nothing. So, what proportion are we talking about here? An astronomically low proportion: 1 in 10 to the power of 74, according to work done by Dr. Douglas Axe. When we add the requirement that a protein has to be made up of amino acids that are either all left-handed or all right-handed, and when we finally add the requirement that the amino acids have to be held together by peptide bonds, we find that only 1 in 10 to the power of 164 amino-acid sequences of that length are suitable proteins. 1 in 10 to the power of 164 is 1 in 1 followed by 164 zeroes. The Earth has been around for 4,500,000,000 years, but it should be obvious to the reader that that's nowhere near enough time for a protein to form as a result of unguided natural processes. To get round this difficulty, scientists have hypothesized that maybe Nature has a hidden bias that makes proteins more likely to form, but all the evidence suggests there isn't any such bias - and even if there were one, that would need explaining too. Finally, scientists have suggested that maybe another molecule - RNA - formed first, and proteins came later, but the same problem arises for RNA: the vast majority of possible sequences are non-functional, and only an astronomically tiny proportion work.

  (2) The simplest living cell. Even a minimally complex cell needs at least 250 proteins, for it to work. If the odds of generating even one protein by blind processes during the 4.5-billion-year history of the Earth are astronomically low, then the odds of generating a living cell are much, much worse. To get round this difficulty, some scientists have hypothesized that the first living things didn't contain proteins: they used RNA instead. But as we saw above, the same problem arises for RNA: only an astronomically tiny proportion of possible sequences can do any useful work, so the chances of a useful RNA molecule forming are very, very low. To get round these astronomical odds, other scientists have proposed that the first living things were made up of something shorter: polypeptides, or TNA. But polypeptides and TNA aren't alive: even if they could replicate, they can't evolve. What's more, all the living things we know of contain very long digital code sequences. For instance, the DNA letters of the genome of the simplest free-living organism - Mycoplasma genitalium - would span 147 pages, if they were printed in 10 point font. So the hypothesis that the first living things were much shorter than they were today is unsupported by any evidence. Finally, some scientists have proposed that the first living things were made of something more exotic than DNA or RNA - maybe clay crystals. But once again, that's pure supposition, which isn't backed up by any hard evidence.

  (3) Molecular machines. Most cellular functions are executed by complexes containing multiple proteins. These proteins work together in sync, acting like molecular machines. A molecular machine is an assemblage of parts that transmit energy from one to another in a predetermined manner. In living things - even the simplest ones - these machines are each composed of dozens or even hundreds of protein components. If the odds of generating even one functional protein by blind processes are astronomically low, the odds of making a molecular machine are unimaginably low. Some scientists have argued that these molecular machines may have once been simpler, on the grounds that some of the proteins in these machines appear to have been derived from other ones. That's true, but even when you take out the derived proteins that came along later, you're still stuck with machines that have dozens or even hundreds of components. So the problem remains.

  (4) Eukaryotic cells. Plants, animals, fungi, slime moulds, protozoa and algae are all made up of eukaryotic cells. A eukaryotic cell is like a miniature factory. The cell nucleus contains a multitude of robot-like machines working in synchrony, which shuttle a huge range of products and raw materials along conduits leading to and from the various assembly plants in the outer parts of the cell. Everything is precisely choreographed. A eukaryotic cell exhibits features such as quality control, feedback systems and automated parcel processing ("zip codes"). What's more, each cell has to be capable of replicating its entire structure within just a few hours. To do all these things, a eukaryotic cell requires thousands of different kinds of proteins. Some scientists have proposed that eukaryotic cells formed gradually in a step-by-step process called endosymbiosis, where one smaller organism came to live inside another, and it's true that some parts of the eukaryotic cell, such as mitochondria and chloroplasts, seem to have arisen that way. But that doesn't explain the origin of the nucleus of the cell, which is where most of the DNA resides. A nucleus requires hundreds of different kinds of proteins for it to do its work: an evolutionist's nightmare.

  (5) Animals with complex body plans (e.g. arthropods, annelid worms, molluscs, echinoderms and chordates, as opposed to simple animals like sponges and coelenterates). Complex animals need more cell types in order to perform their diverse functions. New cell types require many new and specialized proteins. But these new proteins also have to be organized into new, hierarchically ordered systems within the cell. That's because in complex animals, new cell types need to be organized into new tissues, organs, and body parts, which in turn have to be organized to form body plans. In other words, complex animals embody hierarchically organized systems of lower-level parts within a functional whole. So we're not only talking about lots of proteins, we're talking about proteins organized into hierarchical levels of control. Once again, no evolutionist has put forward a quantifiable model of how these levels of control might have arisen.

• Neo-Darwinian evolution refuses to make quantifiable predictions regarding the amount of time needed for evolution to work. If you ask a Darwinist, "How much time should it take for natural processes to produce life from simple organic chemicals? How much time should it take for Darwinian natural selection to produce a complex eukaryotic cell from a relatively simple prokaryotic cell, or to produce complex animals from sponge-like creatures, or to produce a whale from a land animal?" you will be met with silence. Darwinists have no method of coming up with even approximate estimates for the answers to these questions. That's their dirty little secret. They can't quantify the time needed for their mechanism to work.

• Darwinists know that their theory is incapable of coming up with the hard numbers. To cover up their embarrassment on this score, they often put forward proposals for the origin of proteins, the origin of life and the origin of complex animals which are highly speculative. But a good mathematical argument should only appeal to processes that are already known to generate results. As they say in Missouri, "Show me."

The Argument in a Nutshell:

Every living thing on this planet contains proteins, which are made up of amino acids. Proteins are fundamental components of all living cells and include many substances, such as enzymes, hormones, and antibodies, that are necessary for the proper functioning of an organism. They're involved in practically all biological processes. To fulfil their tasks, proteins need to be folded into a complicated three-dimensional structure. Proteins can tolerate slight changes in their amino acid sequences, but a single change of the wrong kind can render them incapable of folding up, and hence, totally incapable of doing any kind of useful work within the cell. That's why not every amino-acid sequence represents a protein: only one that can fold up properly and perform a useful function within the cell can be called a protein.

Now let's consider a protein made up of 150 amino acids - which is a fairly modest length. If we compare the number of 150-amino-acid sequences that correspond to some sort of functional protein to the total number of possible 150-amino-acid sequences, we find that only a tiny proportion of possible amino acid sequences are capable of performing a function of any kind. The vast majority of amino-acid sequences are good for nothing. So, what proportion of amino acid sequences are capable of doing something useful? An astronomically low proportion: 1 in 10 to the power of 74, according to work done by Dr. Douglas Axe. When we add the requirement that a protein has to be made up of amino acids that are either all left-handed or all right-handed, and when we finally add the requirement that the amino acids have to be held together by peptide bonds, we find that only 1 in 10 to the power of 164 amino-acid sequences of that length are suitable proteins. 1 in 10 to the power of 164 is 1 in 1 followed by 164 zeroes. The Earth has been around for 4,500,000,000 years, but it should be obvious to the reader that that's nowhere near enough time for a protein to form as a result of unguided natural processes.

The Argument in More Detail:

The following passage is taken from Dr. Stephen Meyer's book, Signature in the Cell (HarperOne, 2009). On pages 210-213, Myer discusses the "pure chance" hypothesis for the origin of life. He begins by calculating the odds of obtaining even a single functional protein, of any kind, over the time period that the Earth has existed.

[B]y taking what he knew about protein folding into acocunt, Axe estimated the ratio of (a) the number of 150-amino-acid sequences that produce any functional protein whatsoever to (b) the whole set of possible amino-acide sequences of that length. Axe's estimated ratio of 1 in 10^74 implied that the probability of producing any properly sequenced 150-amino-acid protein at random is also about 1 in 10^74. In other words, a random process producing amino-acid chains of this length would stumble onto a functional protein only about once in every 10^74 attempts...

In June 2007, Axe had a chance to present his findings at a symposium commemorating the publication of the proceedings from the original Wistar symposium forty years earlier. In attendance at this symposium was MIT engineering professor Murray Eden…

Axe's improved estimate of how rare functional proteins are within "sequence space" has now made it possible to calculate the probability that a 150 amino-acid compound assembled by a random interaction in a prebiotic soup would be a functional protein. This calculation can be made by multiplying the three independent probabilities by one another: the probability of incorporating only peptide bonds (1 in 10^45) , the probability of incorporating only left-handed amino acids (1 in 10^45), and the probability of achieving correct amino acid sequencing (using Axe's 1 in 10^74 estimate). Making that calculation (multiplying the separate probabilities by adding their exponents: 10^45+45+74) gives a dramatic answer. The odds of getting even one functional protein of modest length (150 amino acids) by chance from a prebiotic soup is no better than 1 chance in 10^164...[T]he probability of finding a functional protein by chance alone is a trillion, trillion, trillion, trillion, trillion, trillion, trillion times smaller than the odds of finding a single specified particle among all the particles in the [observable - VJT] universe.

And the probability is even worse than this for at least two reasons. First, Axe's experiments calculated the odds of finding a relatively short protein by chance alone. More typical proteins have hundreds of amino acids, and in many cases their function requires close association with other protein chains...

Second, as discussed, a minimally complex cell would require many more proteins than just one.

Objection: You mentioned Dr. Douglas Axe. Who is he? Is he a qualified scientist?

Reply: Yes, he is. Dr. Douglas Axe is the director of the Biologic Institute. His research uses both experiments and computer simulations to examine the functional and structural constraints on the evolution of proteins and protein systems. After obtaining a Caltech Ph.D., he held postdoctoral and research scientist positions at the University of Cambridge, the Cambridge Medical Research Council Centre, and the Babraham Institute in Cambridge. He has also written two articles for the Journal of Molecular Biology (see here and here for abstracts). He has also co-authored an article published in the Proceedings of the National Academy of Sciences, an article in Biochemistry and an article published in PLoS ONE. His work has been reviewed in Nature and featured in a number of books, magazines and newspaper articles, including Life's Solution by Simon Conway Morris, The Edge of Evolution by Michael Behe, and Signature in the Cell by Stephen Meyer.

Objection: Plant biologist Art Hunt has claimed that Douglas Axe's 2004 paper in the Journal of Molecular Biology doesn't claim to support Intelligent Design or challenge Darwinism, so it's a mistake to use it for those purposes.

Reply: Dr. Douglas Axe himself has rebutted this claim in his article, Correcting Four Misconceptions about my 2004 Article in JMB (May 4, 2011).

Objection: Your argument against the possibility of proteins forming appeals to chance processes alone: it assumes that all amino acid sequences are equally likely. But why couldn't a combination of chance plus necessity improve the likelihood of proteins forming? Maybe there are hidden laws of chemical affinity, which would have favored the evolution of proteins on the primordial Earth. Given enough time and a suitable planet like ours, it could have happened.

Reply:
(1) You're talking about the hypothesis of biochemical predestination. Conceptually, the key problem with this view is that if bonding affinities in biological molecules determined their sequencing, they would be unable to perform the specific tasks that they have to do. These molecules would be characterized by regular, repeating sequences with lots of redundancy - e.g. "ABABABABAB" - rather than specified sequences like: "DO THIS JOB."

(2) In any case, there is very strong experimental evidence that for complex molecules such as DNA, RNA and proteins, there are no stringent chemical constraints on chaining that would be sufficient to account for the information contained in these chains. This was already investigated by Bradley et al. in the mid 1980s, and it's a major reason why Professor Dean Kenyon (who is Professor Emeritus of biology at San Francisco State University, and the author of a text called Biochemical Predestination) chose to take the opportunity of publicly recanting from biochemical predestination in the preface he wrote for the first technical work on Intelligent Design: a book titled, The Mystery of Life's Origin by Charles B. Thaxton, Walter L. Bradley and Roger L. Olson.

(3) Even if biochemical predestination were true, it would only boost the argument for a Designer. Here's why. We already know that if the constants of Nature were a little different, carbon-based life would be impossible. If biochemical predestination were true, it would mean that the universe is even more life-friendly than we imagined. If biochemistry and life-functional DNA and/or protein chains are written into the underlying physics that drives the creation, abundance and environments of H, He, C, O and N — the main atoms involved — then that would be the ultimate proof that the laws of physics are a program designed to create life.

Objection: What about the RNA world scenario? Your argument assumes that proteins formed as a direct result of amino acids linking together into longer and longer sequences. Most scientists now believe that it didn't happen that way. They believe that another molecule - RNA - formed first, and that proteins were formed from that molecule.

Reply: The same problem arises for RNA: the vast majority of possible sequences are non-functional, and only an astronomically tiny proportion work. Robert Shapiro (1935-2011) was professor emeritus of chemistry at New York University. In a discussion hosted by Edge in 2008, entitled, Life! What a Concept, with scientists Freeman Dyson, Craig Venter, George Church, Dimitar Sasselov and Seth Lloyd, Professor Shapiro explained why he found the RNA world hypothesis incredible:

... I looked at the papers published on the origin of life and decided that it was absurd that the thought of nature of its own volition putting together a DNA or an RNA molecule was unbelievable.

I'm always running out of metaphors to try and explain what the difficulty is. But suppose you took Scrabble sets, or any word game sets, blocks with letters, containing every language on Earth, and you heap them together and you then took a scoop and you scooped into that heap, and you flung it out on the lawn there, and the letters fell into a line which contained the words "To be or not to be, that is the question," that is roughly the odds of an RNA molecule, given no feedback — and there would be no feedback, because it wouldn't be functional until it attained a certain length and could copy itself — appearing on the Earth.

The Argument in a Nutshell:

Even a minimally complex cell needs at least 250 proteins, for it to work. If the odds of generating even one protein by blind processes during the 4.5-billion-year history of the Earth are astronomically low, then the odds of generating a living cell are much, much worse. Finally, some scientists have proposed that the first living things were made of something more exotic than DNA or RNA - maybe clay crystals. But once again, that's pure supposition, which isn't backed up by any hard evidence.

The argument in more detail: The astronomical improbability of the cell, or: why Fred Hoyle was right!

Above, I quoted a passage taken from pages 210-213 of Dr. Stephen Meyer's best-selling book, Signature in the Cell (Harper One, 2009), where he calculated the odds of getting even a single functional protein, of any kind, over the time period that the Earth has existed: about 1 in 10 to the power of 164. In the passage below, Dr. Meyer explains how the astronomical odds against even one protein forming as a result of unguided processes puts the origin of life from non-living matter (abiogenesis) out of the question:

The probability of finding a functional protein by chance alone is a trillion, trillion, trillion, trillion, trillion, trillion, trillion times smaller than the odds of finding a single specified particle among all the particles in the universe.

And the probability is even worse than this for at least two reasons. First, Axe's experiments calculated the odds of finding a relatively short protein by chance alone. More typical proteins have hundreds of amino acids, and in many cases their function requires close association with other protein chains...

Second, as discussed, a minimally complex cell would require many more proteins than just one. Taking this into account only causes the improbability of generating the necessary proteins by chance – or the genetic information needed to produce them – to balloon beyond comprehension. In 1983 distinguished British cosmologist Sir Fred Hoyle calculated the odds of producing the proteins necessary to service a simple one-celled organism by chance at 1 in 10^40,000. At that time scientists could have questioned his figure...

Axe's experimental findings suggest that Hoyle's guesses were pretty good. If we assume that a minimally complex cell needs at least 250 proteins of, on average, 150 amino acids and that the probability of producing just one such protein is 1 in 10^164 as calculated above, then the probability of producing all the necessary proteins needed to service a minimally complex cell is 1 in 10^164 multiplied by itself 250 times, or in in 10^41,000. This kind of number allows a great deal of quibbling about the accuracy of various estimates without altering the conclusion.

Meyer's last sentence should suffice to refute claims made on the Internet that the 1 in 10^164 estimate for the likelihood of a single functional protein arising by chance is far too pessimistic. Even if we revise the estimate by dozens of orders of magnitude, we are still left with an astronomically improbable event, for a cell which requires 250 functional proteins.

Why life had to have been designed: the video that tells it all

Professor John C. Walton is a Research Professor of Chemistry at St. Andrews University, and a Chartered Chemist. He is a Fellow of the Royal Society of Chemistry, and also a Fellow of the Royal Society of Edinburgh. Professor Walton made his views on the origin of life public in a recent talk for the Edinburgh Creation Group entitled, The Origin of Life, given on September 21, 2010, and available online at http://vimeo.com/415018 .

The Origin of Life from Phil Holden on Vimeo.

(VERY IMPORTANT: Before you play this video, press the PAUSE button and wait about two minutes, until the gray bar at the bottom has finished scrolling across to the right. Then press the PLAY button to start the video. Enjoy!) Or watch the video on this link.

Highlights of Professor Walton's talk

• Statistically, the chance of forming even one "useful" RNA sequence can be shown to be essentially zero in the lifetime of the earth.
• The complexity of the first self-replicating system, and the information needed to build it, imply intelligent design.
• Hope of beating the colossal odds against random formation of replicating RNA is based on ideology rather than science.
• As lab experiments on model replicators become more complex they demonstrate the need for input from intelligent mind(s).
• Acceptance of an early earth atmosphere free of oxygen atoms strains belief beyond breaking point!
• No chemically or geologically plausible routes to nucleotides or RNA strands have been developed.
• Geological field work shows no support for a "prebiotic soup." It favors little change in the atmosphere over time. Living things have been present since the first crustal rocks.
• After over 50 years of sterile origin of life research it is time to give intelligent design a fair hearing.

Objection: The origin of life is not a problem for Darwinism.

Reply: That's an often-repeated "party line," but it's false. Writing in The Scientist (20 June 2008), Gordy Slack acknowledged in an article entitled, What neo-creationists get right:

First, I have to agree with the ID crowd that there are some very big (and frankly exciting) questions that should keep evolutionists humble. While there is important work going on in the area of biogenesis, for instance, I think it's fair to say that science is still in the dark about this fundamental question. It's hard to draw conclusions about the significance of what we don't know. Still, I think it is disingenuous to argue that the origin of life is irrelevant to evolution. It is no less relevant than the Big Bang is to physics or cosmology. Evolution should be able to explain, in theory at least, all the way back to the very first organism that could replicate itself through biological or chemical processes. And to understand that organism fully, we would simply have to know what came before it. And right now we are nowhere close. I believe a material explanation will be found, but that confidence comes from my faith that science is up to the task of explaining, in purely material or naturalistic terms, the whole history of life. My faith is well founded, but it is still faith.

Objection: If the first living things didn't contain proteins, then the problem of how 250 proteins could have spontaneously originated on the primordial Earth does not arise. Many scientists now accept the RNA world hypothesis, which proposes that life based on ribonucleic acid (RNA) pre-dates the current world of life based on deoxyribonucleic acid (DNA), RNA and proteins.

Reply: If you watch the video by Professor John C. Walton above, you'll see why the RNA world hypothesis won't work. Unlike proteins, which are made up of amino acids, RNA is a long chain made up of nucleotides. Nevertheless, the same problem arises for RNA as for proteins: only an astronomically tiny proportion of possible sequences are capable of doing any biologically useful work, so the chances of a useful RNA molecule forming by blind processes are very, very low.

The late Robert Shapiro (1935-2011) was professor emeritus of chemistry at New York University. In a discussion hosted by Edge in 2008, entitled, Life! What a Concept, with scientists Freeman Dyson, Craig Venter, George Church, Dimitar Sasselov and Seth Lloyd, Professor Shapiro explained why he found the RNA world hypothesis incredible:

... I got into the question of the origin of life, and knowing the DNA chemistry that I did know — and helped write — I looked at the papers published on the origin of life and decided that it was absurd that the thought of nature of its own volition putting together a DNA or an RNA molecule was unbelievable.

I'm always running out of metaphors to try and explain what the difficulty is. But suppose you took Scrabble sets, or any word game sets, blocks with letters, containing every language on Earth, and you heap them together and you then took a scoop and you scooped into that heap, and you flung it out on the lawn there, and the letters fell into a line which contained the words "To be or not to be, that is the question," that is roughly the odds of an RNA molecule, given no feedback — and there would be no feedback, because it wouldn't be functional until it attained a certain length and could copy itself — appearing on the Earth.

Christian de Duve, the Nobel laureate, once wrote a letter to Nature which was headed, 'Did God Make RNA?' Because it's hard to think of any other manner in which RNA out of purely abiotic chemistry would assemble itself on the early Earth.

The recent publication of new research (reorted in ScienceDaily, March 12, 2012) on the origin of the ribosome (a component of cells that synthesizes protein chains) deals a further blow to the RNA world scenario, which "posits that the first stages of molecular evolution involved RNA and not proteins, and that proteins (and DNA) emerged later," because it suggests that a large number of proteins were present in living things, right from the get-go: "according to a new analysis, even before the ribosome's many working parts were recruited for protein synthesis, proteins also were on the scene and interacting with RNA." Where did all these proteins come from? (For the original paper, see Ajith Harish, Gustavo Caetano-Anolles. "Ribosomal History Reveals Origins of Modern Protein Synthesis." PLoS ONE, 2012; 7(3): e32776. DOI: 10.1371/journal.pone.0032776.)

Objection: Could DNA (or RNA) have been biologically predestined to arise naturally, by a kind of chemical necessity?

Reply: Biochemical predestination can be safely rejected for DNA, for reasons explained by Dr. Stephen Meyer in his book, Signature in the Cell (HarperOne, 2009):

In sum, two features of DNA ensure that "self-organizing" bonding affinities cannot explain the specific arrangement of nucleotides in the molecule: (1) there are no bonds between bases along the information-bearing axis of the molecule and (2) there are no differential affinities between the backbone and the specific bases that could account for variations in the sequence. (Meyer, 2009, p. 244)

The same considerations apply to RNA.

Objection: Maybe the first living things were made up of much shorter molecules: polypeptides, or TNA.

Reply:
(1) Polypeptides and TNA aren't alive: even if they could replicate, they can't evolve. The much-vaunted self-replicating Ghadiri polypeptide, created in 1996, is not a living thing, according to its co-creator, Dr. Ghadiri. In an interview with philosopher Cliff Walker, of "Positive Atheism" magazine (October 29, 1999), Dr. Ghadiri categorically denied that the Ghadiri polypeptide was alive.

I asked him if it was proper to consider these molecules "life" and he shot back a resounding "No!" Nobody has even come close to creating what we would call life, according to Dr. Ghadiri...

None of the molecules that have been made would sustain themselves (be able to continue self-replication) in an environment outside of the chemical reactions under which they are able to self-replicate, says Dr. Ghadiri. These molecules, he says, are themselves chemical reactions. They just happen to be self-replicating molecules that mimic one of the processes -- self-replication -- that is found in what we call living organisms.

Finally, the Ghadiri polypeptide is incapable of undergoing Darwinian evolution. Even the smallest changes in structure would render it incapable of working as it does.

(2) Recently, Yu et al. have suggested in a scientific article ("Darwinian evolution of an alternative genetic system provides support for TNA as an RNA progenitor", Nature Chemistry 2012, published online 10 January 2012, doi:10.1038/nchem.1241) that TNA may have acted as a precursor to RNA. First of all, this assumes that the RNA world hypothesis is true, which recent research shows is almost certainly not the case (see PLoS ONE, 2012; 7(3): e32776. DOI: 10.1371/journal.pone.0032776). Moreover, Yu's proposal leaves a lot of questions answered, as a recent critical review (February 3, 2012) in Evolution News and Views points out:

How would TNA be synthesized in an early-Earth environment? Heat vents, ice crystals, concentrated pools, magma, in an oxidizing or a reducing environment? Is TNA more stable than RNA? If so, is it stable enough not to decompose under harsh environmental conditions? How did TNA eventually convert into RNA or DNA and is this synthesis prohibitively complex for an early-Earth scenario? If the early Earth only had three bases, how did it eventually come up with a fourth? And, most importantly, how did the relationship among DNA, mRNA, tRNA, and proteins evolve and where does TNA figure in that process?

(3) All the living things we know of contain very long digital code sequences. For instance, the shortest genome found in any free-living organism today is that of the bacterium, Mycoplasma genitalium . This genome has nearly 600,000 pairs of bases, or about 6,000,000 atoms. The DNA letters of the genome of Mycoplasma genitalium would span 147 pages, if they were printed in 10 point font. So far, scientists haven't been able to make a free-living organism with a genome shorter than that. So the hypothesis that the first living things were much shorter than they were today is unsupported by any evidence.

Objection: Maybe the first life was based on a fundamentally different kind of chemistry, such as clay.

Reply: That's an interesting hypothesis. But if you want to call it a scientific hypothesis, you have to do the mathematical spadework and show that the formation of a clay molecule that was capable of performing a specific function was more probable than the formation of an RNA, DNA or protein molecule that could perform a useful function. Where are the numbers?

Objection: Anything is possible, given enough time. As Harvard biology Professor George Wald wrote about the beginning of life back in 1955:

"The time with which we have to deal is of the order of two billion years.... Given so much time the 'impossible' becomes possible, the possible probable, and the probable virtually certain. One has only to wait: time itself performs miracles." {George Wald, "The origin of Life", in The Physics and Chemistry of Life, 1955, p. 12.}

Othe scientists have echoed the same sentiment:

"The other important requirement for the origin of life is plenty of time. The events necessary for the beginnings of life were extremely unlikely." {K. Arms and P. Camp, Biology, Holt Rinehart and Winston, 1979, p. 156.}

Reply: The problem with this objection is that we don't have an infinite amount of time. We only have billions of years. Billions pale into insignificance, when compared to gazillions. 1 followed by 9 zeroes is nothing compared to 1 followed by 164 zeroes, let alone 1 followed by 41,000 zeroes.

The Argument in a Nutshell:

Most cellular functions are executed by complexes containing multiple proteins. These proteins work together in sync, acting like molecular machines. A molecular machine is an assemblage of parts that transmit energy from one to another in a predetermined manner. In living things - even the simplest ones - these machines are each composed of dozens or even hundreds of protein components. If the odds of generating even one functional protein by blind processes are astronomically low, the odds of making a molecular machine are unimaginably low.

Objection: We have indirect but very powerful evidence that these molecular machines evolved. These molecular machines must have once been simpler than they are now, because some of the proteins in a machines appear to have been derived from other ones in the same machine.

Reply: I'm not arguing that molecular machines are the same as they originally were, and I'm happy to concede that they've undergone some degree of evolution. Nor am I attempting to argue that these machines are irreducibly complex, as I'm not a scientist. I'll leave that argument to qualified biochemists, such as Professor Michael Behe. All I'm concerned to show here is that even in their original form, these machines must have contained a large number of proteins. That's all. Even when you take out the obviously derived proteins that came along later, you're still stuck with machines that have dozens of component proteins. So the problem remains. Where did all these proteins come from?

Objection: What about the recent publication of new research (reorted in ScienceDaily, March 12, 2012), showing some of the key steps by which the ribosome (pictured above) originated? (For the original paper, see Ajith Harish, Gustavo Caetano-Anolles. "Ribosomal History Reveals Origins of Modern Protein Synthesis." PLoS ONE, 2012; 7(3): e32776. DOI: 10.1371/journal.pone.0032776.)

Reply: Intelligent Design proponents welcome the publication of such research - otherwise I wouldn't be publicizing it here. But it actually highlights the problem I've been talking about, because it suggests that a large number of proteins were present in living things, right from the get-go: "according to a new analysis, even before the ribosome's many working parts were recruited for protein synthesis, proteins also were on the scene and interacting with RNA." Where did all these proteins come from?

The new findings also pose a direct challenge to the long-dominant "RNA world" hypothesis, which "posits that the first stages of molecular evolution involved RNA and not proteins, and that proteins (and DNA) emerged later." In short: the new paper is a major boon for the Intelligent Design proponents.

The Argument in a Nutshell:

Plants, animals, fungi, slime moulds, protozoa and algae are all made up of eukaryotic cells, which contain a nucleus and a number of internal structures called organelles, as well as a cytoskeleton, made out of protein, which helps define the cell's organization and shape. A eukaryotic cell is like a miniature factory. The cell nucleus contains a multitude of robot-like machines working in synchrony, which shuttle a huge range of products and raw materials along conduits leading to and from the various assembly plants in the outer parts of the cell. Everything is precisely choreographed. A eukaryotic cell exhibits features such as quality control, feedback systems and automated parcel processing ("zip codes"). What's more, each cell has to be capable of replicating its entire structure within just a few hours. To do all these things, a eukaryotic cell requires hundreds of different kinds of proteins: an evolutionist's nightmare.

Objection: Thanks to the work of the late Dr. Lynne Margulis, we now know that eukaryotic cells formed gradually in a step-by-step process called endosymbiosis, where some of the structures within the eukaryotic cell were once free-living bacteria that were taken inside another, bigger cell. In particular, scientists now know that mitochondria and chloroplasts arose in this way.

Reply: That's true as far as it goes, but it still doesn't explain the origin of the nucleus of the eukaryotic cell, which is where most of the DNA resides. A nucleus requires hundreds of different kinds of proteins for it to do its work. That's what needs to be explained.

Objection: Hartman and Fedorov have addressed the origin of the nucleus, in their paper, The origin of the eukaryotic cell: A genomic investigation (Proceedings of the National Academy of Sciences USA, 2002 February 5; 99(3): 1420–1425. doi: 10.1073/pnas.032658599.)

Reply: Hartman and Fedorov's paper actually refutes the dominant hypothesis for the formation of the nucleus of the eukaryotic cell - that it arose from the fusion of two simple prokaryotic cells (an archaeon and a bacterium), both of which lacked a nucleus. The authors correctly point out that this hypothesis leaves a lot unexplained: "a whole set of new cellular structures (i.e., endoplasmic reticulum, spliceosome, etc.) other than the cytoskeleton had to be constructed from prokaryotes that lacked them."

Hartman and Fedorov also identified "a set of 347 proteins that are found in eukaryotic cells but have no significant homology to proteins in Archaea and Bacteria" [simpler life-forms which lack a nucleus in their cells - VJT]. No less than 254 of these proteins have an assigned function. To account for the origin of these proteins, the authors put forward a new proposal of their own: that the nucleus of the eukaryotic cell was formed when a number of archaea and bacteria (simple cells) were engulfed by a third kind of cell, which they refer to as a chronocyte. However, chronocytes do not exist in Nature today, and the authors freely acknowledge that their proposal is a "conjecture."

What's more, as Hartman and Fedorov point out, this chronocyte would itself have been quite complex:

The chronocyte had a cytoskeleton that enabled it to engulf prokaryotic cells and a complex internal membrane system where lipids and proteins were synthesized. It also had a complex internal signaling system involving calcium ions, calmodulin, inositol phosphates, ubiquitin, cyclin, and GTP-binding proteins.

Finally, the authors freely admit that the chronocyte, which they posit to account for the origin of the nucleus, would have required a large number of proteins, governing its membrane-protein-synthesizing machinery and cytoskeleton:

There was a complex inner membrane system where proteins were synthesized and broken down which eventually evolved into the ER, the GTP-binding proteins, ubiquitin, and the 11 ESP ribosomal proteins. This result is not a complete picture of the chronocyte, as we still cannot account for the functions of 93 ESPs [eukaryotic signature proteins - VJT].

In short: even if the authors' speculative proposal for the origin of the eukaryotic cell nucleus turns out to be correct, it still means that we are left with the problem of accounting for the origin of hundreds of proteins.

The Argument in a Nutshell:

Animals with complex body plans include arthropods, annelid worms, molluscs, echinoderms and chordates (the group that vertebrates belong to), as opposed to simple animals like sponges and coelenterates. Complex animals need more cell types in order to perform their diverse functions. New cell types require many new and specialized proteins. But these new proteins also have to be organized into new, hierarchically ordered systems within the cell. That's because in complex animals, new cell types need to be organized into new tissues, organs, and body parts, which in turn have to be organized to form body plans. In other words, complex animals embody hierarchically organized systems of lower-level parts within a functional whole. So we're not only talking about lots of proteins, we're talking about proteins organized into hierarchical levels of control. Once again, no evolutionist has put forward a quantifiable model of how these levels of control might have arisen.

The Argument in More Detail:

All animals belong to about 30 basic types, or phyla, each with its own distinct body plan. Over a period of about 20 million years, from 540 to 520 million years ago, nearly all of these 30 different types of animals appeared in the geological record. 20 million years is a geological eye-blink: it represents about 0.4% of the Earth's geological history. Dr. Stephen Meyer explains why the relatively sudden appearance of these 30 different types of animals poses a giant problem for Darwinian evolution, in his 2004 article, Intelligent Design: The Origin of Biological Information and the Higher Taxonomic Categories, which was originally published in the Proceedings of the Biological Society of Washington (volume 117, no. 2, pp. 213-239):

Studies of modern animals suggest that the sponges that appeared in the late Precambrian, for example, would have required five cell types, whereas the more complex animals that appeared in the Cambrian (e.g., arthropods) would have required fifty or more cell types. Functionally more complex animals require more cell types to perform their more diverse functions. 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 [complex specified information - VJT].

Building a new animal from a single-celled organism requires a vast amount of new genetic information. It also requires a way of arranging gene products--proteins--into higher levels of organization. New proteins are required to service new cell types. But new proteins must be organized into new systems within the cell; new cell types must be organized into new tissues, organs, and body parts. These, in turn, must be organized to form body plans. New animals, therefore, embody hierarchically organized systems of lower-level parts within a functional whole. Such hierarchical organization itself represents a type of information, since body plans comprise both highly improbable and functionally specified arrangements of lower-level parts. The specified complexity of new body plans requires explanation in any account of the Cambrian explosion.

Objection: The Cambrian explosion is an illusion, caused by poorly preserved fossils. There were animals before the Cambrian, but they lacked hard parts, and thus never fossilized in the first place. The Cambrian explosion merely represents the sudden appearance of shells and skeletons in animal that had evolved long before.

Reply: This is an old canard that you may have heard when you were in high school. Unfortunately for Darwinists, it's completely false. A Discovery Institute Briefing Paper, The Scientific Controversy Over the Cambrian Explosion, provides some excellent references for rebutting this hoary old myth:

The fossil evidence ... does not support this hypothesis. First, as Harvard paleontologist Stephen Jay Gould and Cambridge paleontologist Simon Conway Morris have pointed out, the majority of Cambrian explosion fossils are soft-bodied (Stephen Jay Gould, Wonderful Life [New York: Norton, 1989]; Simon Conway Morris, The Crucible of Creation [Oxford: Oxford University Press, 1998). Second, the fossil evidence points to the appearance of many new body plans in the Cambrian, not just the acquisition of hard parts by existing phyla. According to Berkeley paleontologist James Valentine, the Cambrian explosion "involved far more major animal groups than just the durably skeletonized living phyla." It was "new kinds of organisms, and not old lineages newly donning skeleton-armor, that appeared" (Excerpt C, p. 533). Valentine concluded: "the record that we have is not very supportive of models that posit a long period of the evolution of metazoan phyla" before the Cambrian (Excerpt C, p. 547).

References
(C) James W. Valentine, "The Macroevolution of Phyla," pp. 525-553 in Jere H. Lipps & Philip W. Signor (editors), Origin and Early Evolution of the Metazoa (New York: Plenum Press, 1992).

Objection: Hasn't the discovery of Precambrian animal fossils solved the problem of the Cambrian explosion?

Reply: No, for two reasons. First, most of the 30-plus major groups (phyla) of animals appeared relatively suddenly, in the Cambrian period; there are no traces of these groups in Precambrian fossils. It is generally acknowledged among scientists that most of the 30-plus major groups of animals have no precedents before the beginning of the Cambrian period, 542 million years ago, as the Darwin's Dilemma FAQ, Questions about the Cambrian Explosion, Evolution, and Intelligent Design, points out in its reply to Question 2:

That the precursors to the Cambrian groups are indeed missing from the record is widely accepted among paleontologists; thus, this is not the controversial aspect of the ID position. About the missing precursors at the base of the tree of the animal phyla, Valentine notes:

...many of the branches, large as well as small, are cryptogenetic (cannot be traced into ancestors). Some of these gaps are surely caused by the incompleteness of the fossil record..., but that cannot be the sole explanation for the cryptogenetic nature of some families, many invertebrate orders, all invertebrate classes, and all metazoan phyla. [Metazoan phyla = major groups of animals - VJT.]
(James Valentine, On the Origin of Phyla, University of Chicago Press, 2004, p. 35.)

Charles Marshall concurs:

While the fossil record of the well-skeletonized animal phyla is pretty good, we have virtually no fossils that are unambiguously assignable to the most basal stem groups [putative ancestors] of these phyla, those first branches that lie between the last common ancestor of all bilaterians and the last common ancestor of the living representatives of each of the phyla.... their absence is striking. Where are they?
(Marshall, C.R. (2006). Explaining the Cambrian "Explosion" of Animals. Annual Review of Earth and Planetary Sciences, Vol. 34: 355-384. DOI: 10.1146/annurev.earth.33.031504.103001.)

To be clear: Valentine and Marshall, leading paleontologists, oppose ID theory.

Second, Precambrian animals were much simpler than Cambrian animals. They would have lacked the hierarchical patterns of protein regulation that are found in complex animals. Dr. Stephen Meyer, P. A. Nelson, and Paul Chien provides an excellent description of the sudden increase in animal complexity during the Cambrian explosion in their 2001 paper, The Cambrian Explosion: Biology's Big Bang (later published in Darwinism, Design, and Public Education, Michigan State University Press, 2004):

One way to measure the increase in the complexity of the animals that appeared in the Cambrian is to assess the number of cell types that are required to build such animals and to compare that number with those creatures that went before.(19) Functionally more complex animals require more cell types to perform their more diverse functions. Each new cell type requires many new and specialized proteins. New proteins in turn require new genetic information encoded in DNA. Thus, an increase in the number of cell types implies (at a minimum) a considerable increase in the amount of specified genetic information. For example, molecular biologists have recently estimated that a minimally complex cell would require between 318 to 562 kilobase pairs of DNA to produce the proteins necessary to maintain life.(20) Yet to build the proteins necessary to sustain a complex arthropod such as a trilobite would require an amount of DNA greater by several orders of magnitude (e.g., the genome size of the worm Caenorhabditis elegans is approximately 97 million base pairs(21) while that of the fly Drosophila melanogaster (an arthropod), is approximately 120 million base pairs.(22) For this reason, transitions from a single cell to colonies of cells to complex animals represent significant (and in principle measurable) increases in complexity and information content. Even C. elegans, a tiny worm about one millimeter long, comprises several highly specialized cells organized into unique tissues and organs with functions as diverse as gathering, processing and digesting food, eliminating waste, external protection, internal absorption and integration, circulation of fluids, perception, locomotion and reproduction. The functions corresponding to these specialized cells in turn require many specialized proteins, genes and cellular regulatory systems, representing an enormous increase in specified biological complexity... Cambrian animals required 50 or more different cell types to function, whereas sponges required only 5 cell types.

References
19 James W. Valentine, "Late Precambrian Bilaterians: Grades and Clades," in Tempo and Mode in Evolution: Genetics and Paleontology 50 Years After Simpson, eds. W.M. Fitch and F.J. Ayala (Washington, DC: National Academy Press, 1995), pp. 87-107, especially 91-93.
20 Mitsuhiro Itaya, "An estimation of the minimal genome size required for life," FEBS Letters 362 (1995): 257-60. Claire Fraser, Jeannine D. Gocayne, Owen White, et. al., "The Minimal Gene Complement of Mycoplasma genitalium," Science 270 (1995): 397-403. Arcady R. Mushegian and Eugene V. Koonin, "A minimal gene set for cellular life derived by comparison of complete bacterial genomes," Proceedings of the National Academy of Sciences USA 93 (1996): 10268-73.
21 The C. elegans Sequencing Consortium, "Genome Sequence of the Nematode C. elegans: A Platform for Investigating Biology," Science 282 (1998): 2012-18.
22 John Gerhart and Marc Kirschner, Cells, Embryos, and Evolution (London: Blackwell Science, 1997), p. 121.

Objection: The Cambrian explosion didn't happen overnight. It took 20 million years. Some explosion!

Reply: The real point at issue is not whether the Cambrian explosion was instantaneous, but whether blind processes are capable of generating complex animals in the relatively short time available (20 million years). All the available evidence indicates that they're not.

Objection: Don't mutations in the genes controlling development (such as Hox genes), explain how new bodyplans evolved?

Reply: No. Mutations in the genes controlling developing development are especially lethal, as the Darwin's Dilemma FAQ, Questions about the Cambrian Explosion, Evolution, and Intelligent Design, points out, in its reply to Question 3:

Animals do not tolerate mutations to genes involved in regulating bodyplan construction.

Because these genes act early in development, as the fertilized egg begins to divide (or even earlier, as the egg itself is built by the mother), mutations affecting the expression of regulatory genes have cascading, and devastating, consequences for the embryo. These mutants are known as “embryonic lethals,” and die before birth. With mutations expressed later in development, the animal may survive to adulthood, but it is gravely crippled, and cannot mate or establish a new lineage. The famous Antennapedia mutant in fruit flies, for instance, has legs where its antennae should be. Outside the lab, such mutants are complete nonstarters in Darwinian competition. They do not constitute novel adaptations, but dead ends.

Objection: But couldn't circumstances have been different in the past, to allow for the rapid evolution of novel bodyplans from a common ancestor?

Reply: The Darwin's Dilemma FAQ, Questions about the Cambrian Explosion, Evolution, and Intelligent Design, exposes the unsupported speculation that lies behind this objection. Here is an excerpt from the reply to Question 7:

Well, maybe. But why think this? What is the evidence? ...

If new animal bodyplans evolved rapidly from an (unknown) common ancestor, therefore, mutations that today would destroy or cripple embryos must somehow have been tolerated. Furthermore, the genetics of such mutations must have been very different from what we see today in the well-studied models systems of developmental biology. As Campbell and Marshall argue,

There seems to be no alternative but to seek some unusual feature of the primitive genome that would allow it to change in such a way that large coordinated viable morphological changes could take place over short periods of geological time.
(K. Campbell and C. Marshall, "Rates of Evolution in Paleozoic Echinoderms," in Rates of Evolution, eds. K. Campbell and M. Day (London: Allen & Unwin, 1987), p. 97.)

Now, notice that this hypothesis assumes that the disparate Cambrian bodyplans stem from a common ancestor, by unknown evolutionary pathways. In short, the hypothesis assumes what needs to be demonstrated.

Objection: If an Intelligent Designer was responsible for the Cambrian explosion, why would He have taken so long to bring it about? Why take 20 million years? Why not do it instantly?

Reply: This objection assumes that an Intelligent Designer who engineered the Cambrian explosion would have wanted it to happen overnight. That's a theological objection, not a scientific one. And in any case, it's highly doubtful. Here are two fairly obvious reasons why a Designer would not have wanted complex animals to appear overnight.

(a) Terra-forming. Complex animals have their own specialized physiological needs, to support their uniquely active way of life. Some changes in the Earth's environment may have been required before complex animals could appear. For instance, recent research suggests that volcanically active midocean ridges caused a massive and sudden surge of the calcium concentration in the oceans, making it possible for marine organisms to build skeletons and hard body parts for the first time. (See Xavier Fernandez-Busquets, Andre Kornig, Iwona Bucior, Max M. Burger, and Dario Anselmetti. Self-Recognition and Ca2+-Dependent Carbohydrate-Carbohydrate Cell Adhesion Provide Clues to the Cambrian Explosion. Molecular Biology and Evolution, 2009; 26 (11): 2551.) Geological transformations take time to attain chemical equilibrium. Lest anyone think that this calcium upsurge "explains" the Cambrian explosion: it should be borne in mind that a necessary condition is not the same as a sufficient condition. Calcium upsurges don't explain how hierarchical patterns of protein regulation suddenly arose in animals from that time.

(b) Ecological engineering. The appearance of complex animals would have added to the complexity of ecosystems. There would have been an increase in the number of needs that the first bilaterian animals had to meet, as complex ecological interactions developed. (See Marshall, C.R. (2006). Explaining the Cambrian "Explosion" of Animals. Annual Review of Earth and Planetary Sciences, Vol. 34: 355-384. DOI: 10.1146/annurev.earth.33.031504.103001. ) It takes time to set up a self-sustaining food chain. Once again: ecological explanations of the Cambrian explosion are well suited to explaining why there had to have been a rapid increase in both disparity and diversity, but by themselves, they cannot explain why the "explosion" happened when it did. Nor can they explain how hierarchical patterns of protein regulation suddenly arose in animals from that time.

Objection: These are ad hoc arguments, which perfectly illustrates why Intelligent Design isn't science. You can prove anything you want using arguments like that.

Reply: No, you can't. Intelligent Design arguments are precise where they need to be. They give us clear quantitative criteria for determining which systems in Nature must have been intelligently designed. Briefly, we can be certain beyond reasonable doubt that systems in Nature which are capable of performing a specific function, and whose likelihood of originating as a result of blind processes (chance plus necessity) is less than 1 in 10 to the power of 150, must have been designed by an Intelligent Agent. That's all we need to be precise about: which systems can be shown to have been intelligently designed, and which cannot. The other questions you might want to ask about a Designer - who, when, where, why and how - are icing on the cake. You can speculate all you like about those questions, but that doesn't affect the central, scientifically established fact that some biological systems were intelligently designed.