EVOLUTION  &  GENETICS

 

To most people through history it has always seemed obvious that the teeming diversity of life, the uncanny perfection with which living organisms are equipped to survive and multiply, and the bewildering complexity of living machinery, can only have come about through divine creation. Yet repeatedly it has occurred to isolated thinkers that there might be an alternative to supernatural creation. The notion of species changing into other species was contemplated, like so many other good ideas, in ancient Greece. It went into eclipse until the 18^th century, when it resurfaced in the minds of such advanced thinkers as Pierre de Maupertuis, Erasmus Darwin, and the man who styled himself the Chevalier de Lamarck. In the first half of the 19^th century the idea became not uncommon in intellectual circles, especially geological ones, but always in a rather vague form and without any clear picture of the mechanism by which change might come about. It was Charles Darwin (Erasmus's grandson), spurred into print by the independent discovery by Alfred Russel Wallace of his principle of natural selection, who finally established the theory of evolution. In 1859 he published his On the Origin of Species by Means of Natural Selection or the Preservation of Favoured Races in the Struggle for Life, usually abbreviated to The Origin of Species. After 1859 it was difficult for reasonable people to doubt that all living species, ourselves included, had evolved from other species. Modern molecular biology makes it hard to doubt that all species can be traced back ultimately to a single common ancestor, for all known life forms share the same genetic code and it is wildly improbable that they could have tumbled upon it independently.

 

Evolutionary History

Between 5,000 million and 4,000 million years ago the earth was formed. By 3,000 million years ago life had arisen and we have fossils of microscopic bacteria-like creatures to prove it. Some time between these two dates—independent molecular evidence suggests about 4,000 million years ago—that mysterious event, the origin of life, must have occurred. Nobody knows what happened, but theorists agree that the key was the spontaneous arising of self-replicating entities, i.e. something equivalent to “genes” in the general sense. There is less agreement over how this happened.

 

The atmosphere of the early earth probably contained methane, ammonia, carbon dioxide, and other gases still abundant today on other planets in the solar system. Chemists have experimentally reconstructed these primeval conditions in the laboratory. If plausible gases are mixed in a flask with water, and energy is added by an electric discharge (simulated primordial lightning), organic substances are spontaneously synthesized. These include, most significantly, amino acids (the building blocks of proteins, including the all-important enzymes that control the chemical processes of life), and purines and pyrimidines (the building blocks of RNA and DNA). It seems probable that something like this happened on the early earth. Consequently, the sea would have become a “soup” of prebiological organic compounds.

 

It is not enough, of course, that organic molecules appeared in the primeval soup. The crucial step, as noted above, was the origin of self-replicating molecules, molecules capable of assembling copies of themselves. Today the most famous self-replicating molecule is DNA (deoxyribonucleic acid, See Genetics and Nucleic Acids), but it is widely thought that DNA itself could not have been present at the origin of life because its replication is too dependent on support from specialized machinery, which could not have been available before evolution itself began. DNA has been described as a “high-tech” molecule which probably arose some time after the origin of life itself. Perhaps the related molecule RNA, which still plays various vital roles in living cells, was the original self-replicating molecule. Or perhaps the primordial replicator was a different kind of molecule altogether. Once self-replicating molecules had been formed by chance, something like Darwinian natural selection could have begun: variation would have come into the population because of random errors in copying. Variants that were particularly good at replication would automatically have come to predominate in the primeval soup. Varieties that did not replicate, or that did so inaccurately, would have become relatively less numerous. A kind of molecular natural selection led to ever-increasing efficiency among replicating molecules.

 

As the competition between replicating molecules warmed up, success must have gone to the ones that happened to hit upon special tricks or devices for their own self-preservation and their own rapid replication. Such devices probably were constructed by the manipulation of other molecules, proteins perhaps. Other manipulated devices were the forerunners of membranes which provided circumscribed volumes for the enclosure of chemical reactions. It may have been soon after this stage that simple bacteria-like creatures gave rise to the first fossils, between 3,000 million and 4,000 million years ago. The rest of evolution may be regarded as a continuation of the natural selection of replicator molecules, now called genes, by virtue of their capacity to build for themselves efficient devices (cells and multicellular bodies) for their own preservation and reproduction. Three thousand million years is a long time, and it seems to have been long enough to have produced such astonishingly complex contrivances as the vertebrate body and the insect body. Genes are often referred to as the means by which bodies reproduce themselves. This is superficially undeniable, but it is a more profound truth that bodies are the means by which genes reproduce themselves.

 

Fossils were not laid down on more than a small scale until the Cambrian era, nearly 600 million years ago. By then most of the major animal phyla (the large groups into which the animal kingdom is classified) had appeared. Obviously creatures with hard skeletal parts, including teeth, are more likely to fossilize, and they dominate the fossil record. The first vertebrates appear abundantly in fossil beds between 300 and 400 million years ago: fish-like creatures, completely covered with heavy armour-plating, perhaps adapted to escape from Eurypterids, giant undersea scorpion-like predators which infested the seas at that time. Among vertebrates, the land was first colonized by lobe-finned and lung-bearing fish about 250 million years ago, then by amphibians and, in more thoroughgoing fashion, by various kinds of animals that we loosely lump together as “reptiles”. Mammals and, later, birds, arose from two different branches of reptiles. The rapid divergence of mammals into the rich variety of types that we see today, from opossums to elephants, from anteaters to monkeys, seems to have been unleashed into the vacuum left by the catastrophic extinction of the dinosaurs, 65 million years ago.

 

Although we naturally emphasize the evolution of our own kind—the vertebrates, the mammals, and the primates—these constitute only a small branch of the great tree of life. Some dozens of animal phyla are recognized, of one of which the vertebrates are only a subphylum. In addition to the animal kingdom, other evolved groupings that are conventionally granted kingdom status are the plants, the fungi, and the single-celled protista (now protoctista), all within the single, major grouping, the Eukaryotes. Creatures that are not Eukaryotes are called Prokaryotes and they include various kinds of bacteria (the status of viruses as living things is a matter for argument: many of them are probably relatively recently “escaped” fragments of parasitic genetic material). It is now widely accepted that the eukaryotic cell originated as a symbiotic union of several prokaryotic cells. Organelles such as mitochondria and chloroplasts, within eukaryotic cells, contain their own DNA and are almost certainly the lineal descendants of ancestral prokaryotes.

 

Human Evolution

Our own species evolved within the group of African apes by a rapid evolutionary spurt during the last few million years. Molecular evidence suggests that our last common ancestor with chimpanzees and gorillas lived not much more than five million years ago. The fossil record of our immediate ancestors is now richer than it is often said to be in older textbooks. It shows various archaic forms of Homo sapiens with heavy brow ridges (including the famous Neanderthalers of Europe), preceded by Homo erectus which extends back to nearly two million years ago. Homo erectus lived in Asia as well as Africa but it is controversial whether the Asian members of this species leave any surviving descendants. Several anthropologists favor the view that there was a second “out of Africa” migration of Homo sapiens within the past couple of hundred thousand years, and they trace all modern humans back to a Homo sapiens ancestor who lived in Africa less than a quarter of a million years ago (the quaintly named “African Eve”). Homo erectus had a smaller brain than Homo sapiens and our still earlier ancestors had even smaller brains. With the possible interpolation of species of Homo such as Homo habilis, our immediately previous ancestors seem to have been members of the genus Australopithecus. These have been described as bipedal apes and certainly their brains were not noticeably larger than those of modern chimpanzees. Before them, our ancestry merges with that of the other African apes, the chimpanzees and gorillas, and for some tens of millions of years back becomes dominated by adaptations for living in trees, for example forward-pointing eyes and grasping hands and feet. Before that, our ancestors seem to have been small, shrew-like, insectivorous creatures who lived nocturnally in a world dominated by dinosaurs. These small mammals were descended from the large group of “mammal-like reptiles” which enjoyed their great flowering before the rise of the dinosaurs.

 

Charles Robert Darwin 1809 – 1882

British scientist, who laid the foundation of modern evolutionary theory with his concept of the development of all forms of life through the slow-working process of natural selection. His work was of major influence on the life and earth sciences and on modern thought in general.

Darwinism

It is important to distinguish two quite distinct parts of Darwin's contribution. He collected an overwhelming quantity of evidence for the fact that evolution has occurred, and he thought up the only known workable theory of the reason why it has occurred. In the latter achievement, Wallace joined him as independent discoverer. We remember Darwin's name above Wallace's because of Darwin's comprehensive amassing of evidence, set out with overwhelming clarity and force in The Origin of Species.

 

 

The solution to the problem that so worried Darwin lay in the theory of particular inheritance developed by Gregor Mendel, published in 1865 but unfortunately unread by Darwin, or practically anyone else, until after Darwin's death.

 

Mendel's research, rediscovered at the turn of the century, demonstrated what Darwin himself had at one time dimly glimpsed, that heredity is particulate, not blending.

 

The modern genetic theory of natural selection can be summarized as follows. The genes of a population of sexually interbreeding animals or plants constitute a gene pool. The genes compete in the gene pool in something like the same way as the early replicating molecules competed in the primeval soup. In practice genes in the gene pool spend their time either sitting in individual bodies which they helped to build, or travelling from body to body via sperm or egg in the process of sexual reproduction. Sexual reproduction keeps the genes shuffled, and it is in this sense that the long-term habitat of a gene is the gene pool. Any given gene originates in the gene pool as a result of a mutation, a random error in the gene-copying process. Once a new mutation has been formed, it can spread through the gene pool by means of sexual mixing. Mutation is the ultimate origin of genetic variation. Sexual reproduction, and genetic recombination due to crossing over, see to it that genetic variation is rapidly distributed and recombined in the gene pool.

 

The Origin of Species and the Evolution of Diversity

Evolution under the influence of natural selection leads to adaptive improvement. Evolution, whether under the influence of natural selection or not, leads to divergence and diversity. From a single ultimate ancestor, many hundreds of millions of separate species have, at one time or another, evolved. The process whereby one species splits into two is called speciation. Subsequent divergence leads to ever wider separation of taxonomic units—genera, families, orders, classes, etc. Even creatures as different as, for example, snails and monkeys, are derived from ancestors who originally diverged from a single species in a speciation event.

 

It is widely accepted that the first step in speciation is normally geographical separation. A species is accidentally divided into two geographically separated populations. Often there may be subpopulations isolated on islands, generalized to include islands of water in land (lakes), islands of vegetation in deserts (oases), etc. Even trees in a meadow may be effective islands to some of their small inhabitants. Geographical isolation means no gene flow, no sexual contamination of each gene pool by the other. Under these conditions the average gene frequencies in the two gene pools can change, either because of different selection pressures or because of random statistical changes in the two areas. After sufficient genetic divergence while in geographical isolation, the two subpopulations are no longer capable of interbreeding even if later circumstances chance to reunite them. When they can no longer interbreed, speciation is said to have occurred and a new species (or two) is said to have come into being. This “biological” definition of the species cannot be used for organisms that do not reproduce sexually. It has been controversially suggested that natural selection itself may reinforce the divergence between incipient species by penalizing any tendency to hybridize. It is also controversial whether geographical separation is always necessarily implicated in speciation (it is agreed that it usually is).

Issues and Arguments

 

Genetics is scientific study of how physical, biochemical, and behavioral traits are transmitted from parents to their offspring. The word itself was coined in 1906 by the British biologist William Bateson. Geneticists determine the mechanisms of inheritance whereby the offspring of sexually reproducing organisms do not exactly resemble their parents, and the differences and similarities between parents and offspring recur from generation to generation in repeated patterns. The investigation of these patterns has led to some of the most exciting discoveries in modern biology.

 

Gregor Johann mendel 1822 – 1884

Austrian monk, whose experimental work became the basis of modern heredity theory.

Mendel was born on July 22, 1822, to a peasant family in Heinzendorf (now Hyncice, Czech Republic). He entered the Augustinian monastery at Brünn (now Brno, Czech Republic), which was known as a centre of learning and scientific endeavor. He later became a substitute teacher at the technical school in Brünn. There Mendel became actively engaged in investigating variation, heredity, and evolution in plants at the monastery's experimental garden. Between 1856 and 1863 he cultivated and tested at least 28,000 pea plants, carefully analyzing seven pairs of seed and plant characteristics. His tedious experiments resulted in the enunciation of two generalizations that later became known as the laws of heredity. His observations also led him to coin two terms still used in present-day genetics: dominant and recessive.

Mendel published his important work on heredity in 1866. Despite, or perhaps because of, its descriptions of large numbers of experimental crosses which allowed him to express his results numerically and subject them to statistical analysis, this work made virtually no impression for the next 34 years. Only in 1900 was his work recognized more or less independently by three investigators, one of whom was the Dutch botanist Hugo De Vries, and not until the late 1920s and the early 1930s was its full significance realized, particularly in relation to evolutionary theory. As a result of years of research in population genetics, investigators were able to demonstrate that Darwinian evolution can be described in terms of the change in gene frequency of Mendelian pairs of characteristics in a population over successive generations.

Mendel's later experiments with the hawkweed Hieracium proved inconclusive, and because of the pressure of other duties he had ceased his experiments on heredity by the 1870s. He died in Brünn on January 6, 1884.

 

Through recent advances of genetic engineering, scientists can isolate an individual gene or group of genes from one organism and grow it in another organism belonging to a different species. The species chosen as a recipient is usually one that can reproduce asexually, such as a bacterium or yeast. Thus it is able to produce a clone of organisms, or of cells, that all contain the same foreign gene, or genes. Because bacteria, yeasts, and other cultured cells can multiply rapidly, these methods make possible the production of many copies of a particular gene. The copies can then be isolated and used for the purposes of study (for example, to investigate the chemical nature and structure of the gene) or for the purposes of medicine and commerce (for example, with a view to making large quantities of a useful gene-product such as insulin, interferon, and growth hormone). This technique is called cloning, because it uses clones of organisms or cells. It has great economic and medical potential and is the subject of active research. Identical-twin animals may be produced by cloning as well. An embryo in the early stage of development is removed from the uterus and split, then each separate part is placed in a surrogate uterus. Mammals such as mice and sheep have been produced in this way.

 

Another development has been the discovery that a whole nucleus, containing an entire set of chromosomes, can be taken from a cell and injected into a fertilized egg whose own nucleus has been removed. The division of the egg brings about the division of the nucleus, and the descendant nuclei can, in their turn, be injected into eggs. After several such transfers, the nuclei may become capable of directing the development of the eggs into complete organisms genetically identical to the organism from which the original nucleus was taken. This cloning technique is thus, in theory, capable of producing large numbers of genetically identical individuals. Such experiments have been successfully carried out with frogs, mice, and sheep. This technique is known as the “nuclear transfer from cultured cells”.

Genetic Engineering is the method of changing the inherited characteristics of an organism in a predetermined way by altering its genetic material. This is often done to cause micro-organisms, such as bacteria or viruses, to synthesize increased yields of compounds, to form entirely new compounds, or to adapt to different environments. Other uses of this technology, which is also called recombinant DNA technology, include gene therapy, which is the supply of a functional gene to a person with a genetic disorder or with other diseases such as AIDS or cancer.

 

Genetic engineering involves the manipulation of deoxyribonucleic acid, or DNA. Important tools in this process are so-called restriction enzymes that are produced by various species of bacteria. Restriction enzymes can recognize a particular sequence of the chain of chemical units, called nucleotide bases, that make up the DNA molecule and cut the DNA at that location. Fragments of DNA generated in this way can be joined using other enzymes called ligases. Restriction enzymes and ligases therefore allow the specific cutting and reassembling of portions of DNA. Also important in the manipulation of DNA are so-called vectors, which are pieces of DNA that can self-replicate (produce copies of themselves) independently of the DNA in the host cell in which they are grown. Examples of vectors include plasmids, viruses, and yeast artificial chromosomes. These vectors permit the generation of multiple copies of a particular piece of DNA, making this a useful method for generating sufficient quantities of material with which to work. The process of engineering a DNA fragment into a vector is called “cloning”, because multiple copies of an identical molecule are produced. Another way, recently discovered, of producing many identical copies of a particular DNA fragment is the polymerase chain reaction. This method is rapid and avoids the need for cloning DNA into a vector.