This is the third, and final, part of a three-part essay in which I defend Evolution: A Theory in Crisis (Evolution), in the light of scientific advances and discoveries of the past thirty years.1 In Evolution, I argued that the major, taxa-defining innovations in the history of life were not derived from ancestral forms by functional intermediates.
In Part One of this essay, I considered in detail the origin of the enucleate red cell; in Part Two, the tetrapod limb, the feather, and flowering plants. In Part Three, I continue an argument that proceeds by the accretion of examples.
The Wings of the Bat
Appearing in the fossil record fifty million years ago, the first bats had modern wings and were as completely adapted to flight as any modern bat.2 It is by no means clear how this took place. The issue is an old one: of what use is a partially developed wing? Witness Glenn Jepson:
It has long been debated whether the processes and mechanisms responsible for phenotypic variation within a population or between closely related populations can be extrapolated to explain … the generation of novel structures.3
Push and pull, the staples of political science, are of little use in biology. Jepson again:
No one has successfully proposed any kind of selection pressure that would be effective in the change from one niche to the other; whether the bridging group would be pulled by advantages in the new milieu or pushed by disadvantages in the old.4
Whether by pull or push, the evolution of the bat “required many molecular changes to dramatically alter morphology from a limb to a wing.”5
Rewiring the gene circuits required for bat flight, recent studies show, is immensely complex:
Overall, comparisons of gene expression profiles between digit morphologies and limbs identified hundreds of differentially expressed genes. Several interesting patterns have emerged from this data. Specifically, we highlight 21 genes likely related to wing formation or to morphological and functional similarities between thumb and hindlimb digits … First, we found 14 genes that are likely associated with digit elongation in bats—two Tbx genes (Tbx3 and Tbx15), five genes from the BMP pathway (Bmp3, Rgmb, Smad1, Smad4 and Nog), four Homeobox genes (Hoxd8, Hoxd9, Satb1 and Hoxa1) and three other genes (Twist1, Tmeff2 and Enpp2) related to either digit malformation or cell proliferation. Next, we identified seven genes (Tbx4, Pitx2, Acta1, Tnnc2, Atp2a1, Hrc and Myoz1) that are likely associated with the morphological and functional similarities between the thumb and hindlimb digits.6
Karen Sears has argued that “a simple change in a single developmental pathway” might lead to dramatically different morphologies in the bat.7 Other researchers have also speculated that major morphological transitions may be achieved by minor genetic changes.8
In light of the facts, this is a view best described as primitive. Morphological change requires extensive genetic rewriting.
The Origin of the Endometrial Cell
The differentiation of endometrial stromal cells in the inner lining of the uterus offers a good example of the complexity involved in major morphological change. The placenta is unique to placental mammals, along with their specific dental formulae and mammary glands.9 It is the endometrial stromal cell (ESC) that makes implantation and placentation possible.10 An essential step in the establishment of pregnancy is the differentiation of the endometrial stromal cells into decidual cells, a process driven by hormonal changes associated with the menstrual cycle. This cell differentiation requires the extensive reprogramming of many cellular functions, including the simultaneous silencing of cellular proliferation pathways and the activation of progesterone and cAMP signaling pathways. If implantation does not occur, the functional endometrial lining is shed, causing menstrual bleeding, another defining characteristic of the placental clade.
Günter Wagner has studied the changes in gene expression associated with the evolution of the ESC. He found that no fewer than 1,532 genes were recruited into endometrial expression in placental mammals; the evolution of pregnancy, he concluded, “was associated with a large-scale rewiring of the gene regulatory network.”11 The study showed that about 13 percent of the new genes were recruited from a unique transposon, MER 20. This transposon binds transcription factors essential for pregnancy and regulates endometrial stromal cell gene expression throughout the genome.
It is questionable whether the origin of complex novelties—such as the origin of new cell types, which involves the recruitment of hundreds of genes—can be achieved by these small-scale changes.12
If not small-scale changes, then what? “[G]enetic mechanisms,” Vincent Lynch has argued, “that are distinct from those involved in the modification of existing characters.”13
The Blurst of Times
Human language is restricted to the human species; it is, as Noam Chomsky has observed, without any homologue in any other species.14 In the early 1960s, in one of the landmark advances of twentieth-century science, Chomsky showed that all human languages share the same set of syntactic rules and principles—what has come to be called universal grammar.15 Universal grammar is innate. It is for this reason that children learn language easily.16 Because universal grammar underlies every human language, we can speak the language of a San Bushman or an Australian aborigine, and they in turn can speak English. “So far as anyone knows,” Chomsky has argued, “there is virtually no detectable genetic difference across the species that is language-related.”17 This suggests that universal grammar must have remained unchanged since modern human beings diverged from their last common African ancestor 100,000 years ago.
If universal grammar has remained invariant, so too have our musical, artistic, and mathematical abilities, as well as our general capacity for abstract thought. These too must have been present in our common ancestor, and they must have remained unchanged ever since.
Chomsky assigned the origin of language to the sudden reorganization of the brain’s circuits.18 How quickly language was acquired is, of course, controversial; most researchers argue that it came about gradually by natural selection.19 Not so, Chomsky argued. The assumption that language evolved incrementally
doesn’t seem at all consistent with even the most basic facts. If you look at the literature on the evolution of language, it’s all about how language could have evolved from gesture, or from throwing, or something like chewing, or whatever. None of which makes any sense.20
In this, Chomsky was almost certainly right.
No one has shown, even in outline, how the rules of universal grammar might have come about over thousands of generations. Recursion is a case in point. In the sentence, “The man who was wearing a blue hat which he bought from the girl who sat on the wall was six feet tall,” the words in italics are embedded sentences. Human beings, but not chimpanzees, are able to handle and understand such sentences. The rules that govern recursion are complex and specific. How did they evolve? David Premack expressed an understandable sense of skepticism with respect to prevailing accounts:
I challenge the reader to reconstruct the scenario that would confer selective fitness on recursiveness. Language evolved, it is conjectured, at a time when humans or protohumans were hunting mastodons … Would it be a great advantage for one of our ancestors squatting alongside the embers of a fire to be able to remark: “Beware of the short beast whose front hoof Bob cracked when, having forgotten his own spear back at camp, he got in a glancing blow with the dull spear he borrowed from Jack”? Human language is an embarrassment for evolutionary theory because it is vastly more powerful than one can account for in terms of selective fitness. A semantic language with simple mapping rules, of a kind one might suppose that the chimpanzee would have appears to confer all the advantages one normally associates with discussions of mastodon hunting or the like. For discussions of that kind, syntactical classes, structure-dependent rules, recursion and the rest, are overly powerful devices, absurdly so.21
It is not language alone that seems absurdly powerful. Human beings all share the potential for higher intellectual functioning. The mind of an Albert Einstein, an Isaac Newton, or a Wolfgang Amadeus Mozart must have been latent in our last common ancestor. Just as it is hard to envisage the utility of recursion on those brutal unforgiving plains, the same is true of our abilities in the fields of art, mathematics, and music. How could they have arisen by a series of cumulative steps governed by natural selection millennia before their utility was manifest?
More than a century ago, Alfred Russel Wallace noted correctly that brain size is today more or less uniform across the human species. Assuming that brain size is a marker of intellectual ability, Wallace reasoned that prehistoric man did not use his brain to its capacity. The human brain was, for prehistoric man, “an instrument beyond the needs of its possessor,” and “of a kind and degree far beyond what he ever requires to do.”22
Why should this be so? This is Wallace’s Enigma.
Mathematics is a case in point. As Chomsky observed, paraphrasing Wallace, mathematical capabilities:
could not have evolved by natural selection; it’s impossible because everybody’s got them, and nobody’s ever used them, except for a very tiny fringe of people in very recent times. Plainly it developed in some other way.23
Ancient African hunters were equipped with all the basic linguistic and cognitive potential that modern human beings share. These they never used. The great frescos of Lascaux and Les Combarelles were painted only thirty thousand years ago. Written languages are only five thousand years old. Only during the past five hundred years have human beings undertaken a scientific revolution.
It is curious that these human powers were acquired over only a few million years. Not only was the interval short, but the miracle occurred in small populations with limited reproduction rates and long generational times. Selection may be a powerful force, but it works effectively only when given a large number of mutations. The size of DNA sequence space searched during primate evolution is a trivial fraction of that searched by bacteria in the human gut in a single day.
The argument goes further. There is only a small genetic difference between humans and chimpanzees—about one percent, which is less than that between mouse and rat (three percent), or dog and fox (two percent). The genome of the chimpanzee provides no support for the thesis that our unique abilities came about as the result of natural selection.24 Only a few genes turned out to be under positive selection, and these had no apparent relationship to language or neural development. Subsequent genomic comparisons have confirmed that selection played no major role in shaping the differences between humans and chimpanzees.25
If the differences are not in the genes, selection has nothing to select.
The Origin of the Cell
Consider now the origins of the cell. The design of the cell has not changed in four billion years. The cell membrane, the basic metabolic paths, the ribosome, and the genetic code are invariant. In Evolution I wrote: “Between a living cell and the most highly ordered non-biological system … there is a chasm as vast and absolute as it is possible to conceive.”26 Thirty years later, the situation is unchanged.
“At the heart of the problem,” Eugene Koonin and Artem Novozhilov (along with everyone else) observed, “is a dreary vicious circle.”27 In every modern organism, DNA and the proteins that it generates are co-dependent.
Property was thus appall'd
That the self was not the same;
Single nature’s double name
Neither two nor one was call'd.28
DNA gives rise to the theater of the proteins by means of an immensely complicated translational system. The translation system is itself powered by a suite of enzymes, and enzymes are themselves proteins. If this is so,
[W]hat would be the selective force behind the evolution of the extremely complex translation system before there were functional proteins? And, of course, there could be no proteins without a sufficiently effective translation system.29
Crudely made proteins would have been of no help. It is gratifying in this regard to quote myself.
The trouble with “crudely made proteins” is that everything we have learned about protein structure and function … implies that the function of a protein depends on it … possessing exact highly specific configurations.30
If the modern cell did not arise fully formed, as surely it did not, then perhaps it arose from simpler antecedents, worlds in which DNA and the proteins that it generates were not bound indissolubly together? RNA is, like DNA, a nucleic acid, a link in the great chain from DNA to the proteins. The discovery in 1982 of autocatalytic forms of RNA, or ribozymes, indicated that the nucleic acids, so long thought to be inert without enzymes, could under certain circumstances exhibit enzymatic activity on their own. Imaginative biochemists at once envisaged a world in which the chicken (DNA) and egg (the proteins) of the modern cell were resolved into a single catalytic system.
This profoundly suggestive hypothesis is not free from difficulties. In collapsing the functions of DNA and the proteins into a single dynamic molecule, autocatalytic RNA achieves a stunning reduction in complexity. But if the sophisticated apparatus of the modern cell had its origins in autocatalytic RNA, then what goes down analytically, in the chemist’s laboratory, must have come up biologically, in some step-by-step progression. The gap between the modern cell and nothing is unfathomable; but the gap between autocatalytic RNA and the modern cell is no trifle either.
Thus Koonin and Novozhilov again:
On the experimental front, findings on the catalytic capabilities of selected ribozymes are impressive. In particular, highly efficient self-aminoacylating ribozymes and ribozymes that catalyze the peptidyltransferase reaction have been obtained. Moreover, ribozymes whose catalytic activity is stimulated by peptides have been selected, hinting at the possible origins of the RNA-protein connection.31
Those hints notwithstanding, Koonin and Novozhilov remained skeptical.
It seems that the two-pronged fundamental question: “why is the genetic code the way it is and how did it come to be?”, that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology.32
The Origin of ORFan Genes
New functional genes may be homologues to genes in other species, or they may be orphans (ORFan genes), without homologues in other genomes. ORFan genes are species specific, and so isolated on the great manifold of genetic possibilities. New functional genes have been created throughout the evolution of life as genomes have expanded, from a few hundred genes in viruses, to a few thousand in bacteria, to twenty thousand in vertebrates. For many decades, it was assumed that new genes evolved in Darwinian fashion. A gene duplicates. The descendent is then able to undergo evolution until a new function is established. Genes come from other genes.33
This was the standard story until a few years ago, when it was predicted that:
With [the] explosive increase in genomic data and rapid advances in molecular genetic technology, the manifold and fundamental roles of gene duplication will become even more evident and the once imaginative idea of evolution by gene duplication will be established as one of the cornerstones of evolutionary biology.34
If gene duplication today retains its vitality as a guiding idea, it is because the contrary idea that genes originate spontaneously by mutation, recombination and random genetic drift—and what else is there?—is liable to the objection that it is absurd. The probability that a functional gene sequence might emerge from a random sequence of nucleic letters is miniscule. Adam Siepel listed some of the features likely to be necessary to transform an (otherwise non-coding) nucleotide string into a gene specifying a functional product:
While a single gene is not as complex as a complete organ, such as an eye or even a feather, it still has a series of nontrivial requirements for functionality, for instance, an ORF, an encoded protein that serves some useful purpose, a promoter capable of initiating transcription, and presence in a region of open chromatin structure that permits transcription to occur. How could all of these pieces fall into place through the random processes of mutation, recombination, and neutral drift—or at least enough of these pieces to produce a protogene that was sufficiently useful for selection to take hold?35
The emergence of protein-coding genes, Siepel concluded glumly, from random sequences of DNA “would seem highly improbable, almost like the elusive transmutation of lead into gold that was sought by medieval alchemists.”36
Against every Darwinian expectation, there is now a “growing appreciation of the oft-dismissed possibility of evolution of new genes from scratch…”37 As genomic comparisons become ever more sophisticated, it is increasingly apparent that evolution from scratch may have been the route to new genes throughout the history of life.38 It appears that some 30 percent of all genomes are made of ORFan genes.39
A very significant proportion of all functional genes did not emerge in the course of evolution.
In the century after Darwin, the majority of paleontologists subscribed to, or otherwise endorsed, some version of orthogenesis: the doctrine that evolutionary change is directed by internal factors having no connection with adaptive fitness—Edward Cope and Henry Osborn among them. Leo Berg listed Theodor Eimer, Hans Przibram, and Charles Whitman in his own manifesto, Nomogenesis.40 Even Thomas Huxley, otherwise fond of barking on behalf of Darwin, was not averse to the idea that long-term evolution might be directed by non-adaptive constraints.
[This variation] is not indefinite, nor does it take place in all directions, because it is limited by the general characters of the type to which the organism exhibiting the variation belongs. A whale does not tend to vary in the direction of producing feathers, nor a bird in the direction of a developing whalebone.41
The reduction of gametophyte generations in land plants is an example of a long-term trend with no obvious Darwinian explanation. The temporal succession of land plants begins in the Middle Ordovician period some 470 million years ago. The simple non-vascular plants were first to appear. These were without either lignified internal transport mechanisms or roots, stems or true leaves. After these appeared mosses and the liverworts, followed by club mosses, horsetails and ferns. These were still lacking seeds and woody trunks. Still later came the seed-bearing conifers, and finally the flowering plants or angiosperms.
Successive forms show increased development of the water transport mechanism, the development of woody trunks, increasingly complex leaves, and advances in reproduction involving the evolution of the seed, and, in the case of the flowering plants, the fruit. Each new plant has become more successful than its predecessors.42
While many of the new features which emerged during this succession can be viewed as adaptive, a mysterious trend was occurring at the heart of the reproductive cycle. To understand the enigmatic nature of this trend—the reduction of the gametophyte generation—recall that in all land plants, the reproductive cycle is divided into two multicellular phases. There is first the sporophyte phase, in which the diploid generation has the full complement of chromosomes, and there is second the gametophyte phase, in which the haploid generation has half the full complement of chromosomes. In mammals and most other animals, the gametes are always unicellular and never undergo cell division to generate a multicellular gametophyte. In flowering plants, the sporophyte is the main body of the plant, while in mosses, the gametophyte phase forms the main and more conspicuous part of the plant. The sporophyte in all plants from mosses to angiosperms produces the sex cells or gametes. And in all plants, the gametes undergo ordinary cell divisions, producing a multicellular gametophyte that eventually gives rise to the final generation of gametes. These fuse to form a fertilized egg cell that grows into the sporophyte.
In the earliest plants the haploid phase or gametophyte is the main body of the plant and the sporophyte is a reproductive appendage. But in the case of the angiosperms, the stems, leaves, and flowers make up the sporophyte. As we move from mosses to horsetails to ferns to conifers to flowering plants, the gametophyte becomes reduced from a small independent plant in the ferns to only handful of the cells in the angiosperms.43
We may … trace the entire process of the reduction of the gametophyte, commencing with its flourishing condition in mosses, and proceeding with its gradual decline in the Pteridophyta, until we come to its complete disappearance in gymnosperms and its final replacement by the sporophyte in angiosperms. A definite course of evolution is here strikingly exemplified.44
Berg is surely right.
The Reduction of the Aortic Arch
Another evolutionary enigma lies in the aortic arches. The aortic arches are a series of paired blood vessels that in primitive vertebrates and fish lead from the ventral aorta via the gills to the dorsal aorta, which then carries the aerated blood to the rest of the body. In fish and in the embryos of higher vertebrates, there are six arches. The primitive chordate amphioxus, a simple fish-like organism, has over fifty pairs of arches. The next most advanced chordates are the jawless fish, such as hagfish and lampreys, which have up to fifteen. In jawed fishes, the number of aortic arches never exceeds six. In adult sharks the number is five. In lungfish it is also five, and in most familiar bony fishes, four. In terrestrial vertebrates it is never more than four. In newts and salamanders, it is four, while in frogs, three. In lizards it is also three. In adult birds and mammals it is, in effect, two and a half. This is because in mammals and birds only one branch of the fourth arch is conserved in the adult. In mammals the left branch of the fourth arch forms the aorta, which curves to the left from the heart, and in birds, the right branch of the fourth arch forms the aorta, which curves to the right from the heart.45
We can trace the reduction in the aortic arches as a gradual and persistent phenomenon throughout five hundred million years of chordate phylogeny. Moreover, the reduction appears to have occurred in parallel in different lineages. In the lineage leading from primitive bony fish to the modern teleosts, and in the lineage leading from primitive bony fish to newts and salamanders, the second arch has been lost in parallel; both groups have the same aortic formula. In the lineage leading from stem reptiles to birds, and in the lineage leading from stem reptiles to mammals, the fifth arch has been lost in parallel. In a quite different lineage leading to frogs from stem amphibian, the fifth arch has also been lost. So in three tetrapod lineages, adapted to very different lifestyles and subject to very different environmental pressures, the same arch has been lost.
Why is that?
Or consider the gradual reduction of forelimbs throughout the evolution of theropod dinosaurs.46 It is a reduction that over one hundred million years led eventually to the bizarre limbs of huge predatory dinosaurs. Never mind the dinosaurs. Did the whales lose their hind limbs for adaptive reasons? One aspect of the transition is hard to account for in adaptive terms: the reduction from tiny, but almost complete, hind limbs in proto-whales to mere vestigial remnants in most modern whales. “[W]hat conceivable pressure of natural selection,” Stephen Jay Gould asked, “could account for gradual stages in the disappearance of a functionless organ?”47
It is a good question.
Many large marine vertebrates, after all, have retained their hind limbs: ichthyosaurs, plesiosaurs, and, of course, modern seals. If seals have retained their hind limbs for adaptive reasons, why have the whales lost theirs?
Additional questions arise when various morphological changes are considered in detail. The teeth of the basilosaurids are typical of primitive mammals; there are forty-four in all, and they are very seal-like; while the teeth of dolphins and killer whales comprise nothing more than simple pegs. Was the change adaptive? Seals are able to catch fish efficiently with standard mammalian teeth and presumably so did the basilosaurids.
Why the difference?
The reduction of the post-dentary bones in synapsids is another example of the same phenomenon. Reptiles have four main bones in the lower jaw, while mammals have only one.48 In successive groups of synapsids, the articular and angular bones were successively reduced until they became tiny post-dentary bones, while the surangular bone was gradually absorbed into the dentary. As the reduction occurred, a second joint appeared between the squamosal and the dentary in several synapsid lines.49
It is no wonder that so many paleontologists interpreted these trends in orthogenetic terms. Osborn was impressed by the peculiar occurrence in diverse mammalian lines of recurrent patterns of dental cusps, the small tubercles on the upper surface of the molars and premolars in mammals. Osborn’s studies convinced him that there were very striking non-adaptive trends in the evolution of cusp patterns.50
My study of teeth in a great many phyla of Mammalia in past times has convinced me that there are fundamental predispositions to vary in certain directions; that the evolution of teeth is marked out beforehand by hereditary influences which extend back hundreds of thousands of years.51
Osborn was sensitive to the risks he was running:
Philosophically, predeterminate variation and evolution brings us upon dangerous ground. If all that is involved in the Tertiary molar tooth is included in a latent or potential form in the Cretaceous molar tooth, we are nearing the emboitement hypothesis of Bonnet or the archetype of Oken and Owen.52
In 1909, Osborn affirmed that no discoveries since he first wrote had materially changed his view:
In all the research since 1869 on the transformations observed in successive phyletic series no evidence whatever, to my knowledge, has been brought forward by any palaeontologist, either of the vertebrated or invertebrated animals, that the fit originates by selection from the fortuitous.53
I would suggest that some of the basic forms of life on earth are intrinsic elements of the world. The very icon of modern biology, the double helix itself, is a natural form determined in all its exquisite geometry by the laws of chemistry and physics. Its basic structure arises from the self-organizing properties of matter.54 No entity in biology exemplifies so beautifully Richard Owen’s two types of order: the helix as the primal pattern, and the base sequence as the adaptive mask.55
Protein folds are the basic building blocks of all proteins.56 The rules that generate the one thousand or so possible protein folds have now been largely elucidated; and remarkably they amount to laws of precisely the kind sought by early nineteenth-century biologists. These rules arise from higher-order packing constraints of alpha helices and beta sheets.57 The protein forms are analogous to a set of crystals.58 And while all proteins exhibit adaptive modifications, these are again in perfect conformity with pre-Darwinian structuralism. The globin fold has thus been adapted in hemoglobin to carry oxygen, but the underlying form is an abstract pattern, one of the permissible protein forms constructed out of alpha helices. Moreover, as Daniel Weinreich has shown, even the adaptations built upon the folds are greatly constrained by the biophysical properties and structures of the folds themselves.
It now appears that intramolecular interactions render many mutational trajectories selectively inaccessible, which implies that replaying the protein tape of life might be surprisingly repetitive.59
During the 1960s, molecular biologists succeeded in elucidating the structure of the bilayer lipid membrane that forms the outer boundary of living cells.60 The same basic structure makes up the endoplasmic reticulum, and encloses the nucleus, the mitochondrion, and the chloroplast. Lipid membranes form a vast variety of tubes, vesicles and various types of sheets, but a simple organizing principle is at work in all this vastness, a point nicely described by Conrad Waddington. They are all, he argued, “variants on three basic types; the vesicle, the disc, and the tube.”61
Biolipid forms arise by energy minimization from the self-organization of the membranes themselves. There is no direction from anything like a genetic blueprint. Many analogous forms can be generated in vitro in solutions of amphiphilic compounds. Philip Ball offers several dramatic examples of their self-organizing capabilities.62 As the concentration of amphiphiles in an aqueous medium increases, eventually micelles form, and as more surfactant is added, plane lamellae. Eventually, as the concentration of the lipid is increased even more, a bi-continuous phase is formed consisting of a vast labyrinth of interconnected tubes.
In living systems, these basic lipid forms are modified to serve specific adaptive ends, but the forms themselves owe nothing to adaptation—and thus nothing to natural selection.
The Robustness of Type
In Evolution, I argued that homologues were not reducible to common embryological development or genetic similarities. My opinion is unchanged. Consider regeneration. That regenerated organs are, as Ronald Amundson pointed out, “clearly homologous to those originally developed in embryos, but ... constructed in a different manner ... from different tissue sources” has always been seen as evidence of their robustness.63 Hans Driesch cites many examples in The Science and Philosophy of the Organism.64 Some are remarkable. In the case of the newt, for example, virtually every organ in the body can be regenerated after surgical excision in the adult organism.
The most robust homologies arise when the same homologous structures are generated in different species by means of different genes and genetic pathways.65 The early embryos of all vertebrates are similar at the post-gastrula stage, when the vertebrate body plan is first apparent, but the developmental processes and pathways that lead to this homologous stage differ markedly by class. There are several diverse routes to the angiosperm embryo, or to the vertebrate zootype in reptiles, amphibians, birds, and mammals.66
In regard to insect segmentation, one might have imagined that the genetic mechanisms that conserve so stringently their body plan would themselves have been stringently conserved. But, in fact, three different mechanisms are utilized to generate segments even among closely related species within one insect order, among beetles for example. Paul Liu and Thomas Kaufman observe that:
The insect body consists of a head of six or seven segments, a thorax of three, and an abdomen of eight to 11 segments, and is essentially invariant across species. Although it makes intuitive sense that differing developmental mechanisms should lead to differing final morphologies, the converse seems counter-intuitive; that differing developmental trajectories should arrive at the same endpoint. Yet this is the case with insect segmentation.67
That homologies are stable through different generative processes in different species suggests that homologies are robust natural kinds. Like strange attractors, the homologies appear to be exerting a mysterious influence on the bio-matter in which they form.
Laws of Nature, Life on Earth
In his great classic, The Fitness of the Environment, Lawrence Henderson argued that carbon-based life depends on a unique alignment of the properties of carbon, water, carbon dioxide, and oxygen. If the various fundamental forces and constants, which determine the structure of the cosmos and the properties of its constituents, did not have precisely the values they do, there would be no stars, no supernovae, no planets, no atoms, and, thus, no life. This fine-tuning gives the striking impression that the basic laws of physics have been designed to generate a cosmos adapted for life as it exists on earth.68 Witness Paul Davies:
The numerical values that nature has assigned to the fundamental constants, such as the charge on the electron, the mass of the proton, and the Newtonian gravitational constant, may be mysterious, but they are crucially relevant to the structure of the universe that we perceive. As more and more physical systems, from nuclei to galaxies, have become better understood, scientists have begun to realize that many characteristics of these systems are remarkably sensitive to the precise values of the fundamental constants. Had nature opted for a slightly different set of numbers, the world would be a very different place. Probably we would not be here to see it.69
Commenting on the fine-tuning necessary to generate carbon, Fred Hoyle remarked that:
A commonsense interpretation of the facts suggests that a superintellect has monkeyed with physics, as well as chemistry and biology, and that there are no blind forces worth speaking about in nature.70
Might Hoyle be right in thinking that the fine-tuning extends to the laws of chemistry and biology? If the laws of nature are, for whatever reason, fine-tuned to generate environmental conditions ideally suited to life on earth, it is surely not so outrageous to envisage that they might be also biologically fine-tuned to generate the grand hierarchy of the forms themselves. The extrapolation is intriguing and very hard to resist. It is particularly hard to resist considering that the fitness of the cosmic, chemical, and physiological environment for life as it exists on earth does not stop at the microbial level.
It extends to the higher organisms. It extends to us.71
One of the most curious aspects of the almost universal acknowledgement that the cosmos is fine-tuned for life is the failure to take the next logical step and infer that nature is fine-tuned, as well, for the origin and evolution of life. This failure is one of the most striking in recent scientific history, an episode made all the more extraordinary when it is also widely conceded that the origin of life remains utterly enigmatic.
If typology is correct, profound questions nonetheless remain. Of this, there is no doubt. If life is a natural phenomenon, how might its forms have been actualized? How can one type lead to another? Since there is, by definition, nothing between types, how did jumps occur? It is by no means clear that comparable questions have been answered in the case of inorganic chemistry.
How much deeper and more subtle the problem at hand!
A great deal of research over the next century will be necessary to illuminate how descent with modification occurred. As the creation of atoms in the stars depended on a highly fortuitous nuclear energy pathway, so it is possible to imagine analogous minimum energy pathways at all levels of the organic hierarchy, arranged so that the distances between types are massively reduced in ontogenetic space. One might suppose that gene functions are clustered in the space of all possible genes, rather than scattered widely.
The distinctness of the types, like the distinctness of atoms, does not exclude this possibility.
In this three-part essay I have reviewed the claims I made in Evolution in light of new discoveries throughout the biological sciences; and I have found them still pertinent. Nature is stubbornly discontinuous, resistant to all attempts to reduce her to a Darwinian functional continuum. The great divisions in the natural order are still profound. There is no empirical or hypothetical series of adaptive transformations among them.
Darwin’s theory is a way station in the intellectual history of biology.
- Michael Denton, Evolution: A Theory in Crisis (London: Adler & Adler, 1985). ↩
- Karen Sears et al., “Development of Bat Flight: Morphologic and Molecular Evolution of Bat Wing Digits,” Proceedings of the National Academy of Sciences of the United States of America 103, no. 17 (2006): 6,581–86; Kimberly Cooper, and Clifford Tabin, “Understanding of Bat Wing Evolution Takes Flight,” Genes & Development 22, no. 2 (2008): 121–24. ↩
- Kimberly Cooper, and Clifford Tabin, “Understanding of Bat Wing Evolution Takes Flight,” Genes & Development 22, no. 2 (2008): 121. ↩
- Glenn Jepson, “Bat Origins and Evolution,” in William Wimsett, ed., Biology of Bats, Vol. 1, (New York: Academic Press, 1970), 53. ↩
- Kimberly Cooper and Clifford Tabin, “Understanding of Bat Wing Evolution Takes Flight,” Genes & Development 22, no. 2 (2008): 123. ↩
- Zhe Wang et al., “Digital Gene Expression Tag Profiling of Bat Digits Provides Robust Candidates Contributing to Wing Formation,” BMC Genomics 11 (2010): 619. ↩
- Karen Sears et al., “Development of Bat Flight: Morphologic and Molecular Evolution of Bat Wing Digits,” Proceedings of the National Academy of Sciences of the United States of America 103, no. 17 (2006): 6,585. ↩
- Sean Carroll, “Evolution at Two Levels: On Genes and Form,” PLoS Biology 3, no. 7 (2005): e245; Benjamin Prud’homme et al., “Emerging Principles of Regulatory Evolution,” Proceedings of the National Academy of Sciences of the United States of America 104 Suppl. 1 (2007): 8,605–12; Sean Carroll, “Evolution at Two Levels: On Genes and Form,” PLoS Biology 3, no. 7 (2005): e245; Sean Carroll, Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom (New York: W. W. Norton & Co., 2006); Nicolas Gompel et al., “Chance Caught on the Wing: Cis-Regulatory Evolution and the Origin of Pigment Patterns in Drosophila,” Nature 433, no. 7025 (2005): 481–87. ↩
- Günter Wagner, and Vincent Lynch, “Evolutionary Novelties,” Current Biology 20, no. 2 (2010): R48–52. ↩
- Carolyn Dunn et al., “Decidualization of the Human Endometrial Stromal Cell: An Enigmatic Transformation,” Reproductive BioMedicine Online 7, no. 2 (2003): 151–61; Griselda Vallejo et al., “Changes in Global Gene Expression during in Vitro Decidualization of Rat Endometrial Stromal Cells,” Journal of Cellular Physiology 222, no. 1 (2010): 127–37. ↩
- Vincent Lynch et al., “Transposon-Mediated Rewiring of Gene Regulatory Networks Contributed to the Evolution of Pregnancy in Mammals,” Nature Genetics 43, no. 11 (2011):1,154–59, 1,154. ↩
- Vincent Lynch et al., “Transposon-Mediated Rewiring of Gene Regulatory Networks Contributed to the Evolution of Pregnancy in Mammals,” Nature Genetics 43, no. 11 (2011): 1,154–59, 1,158. ↩
- Vincent Lynch et al., “Transposon-Mediated Rewiring of Gene Regulatory Networks Contributed to the Evolution of Pregnancy in Mammals,” Nature Genetics 43, no. 11 (2011):1,154–59, 1,158. ↩
- Noam Chomsky, The Science of Language: Interviews with James McGilvray (Cambridge, UK: Cambridge University Press, 2012), 47. ↩
- McGill University, “Tool Module: Chomsky’s Universal Grammar”:
His approach thus remains radically opposed to that of Skinner or Piaget, for whom language is constructed solely through simple interaction with the environment. This latter, behaviourist model, in which the acquisition of language is nothing but a by-product of general cognitive development based on sensorimotor interaction with the world, would appear to have been abandoned as the result of Chomsky’s theories.↩
- Noam Chomsky, The Science of Language: Interviews with James McGilvray (Cambridge, UK: Cambridge University Press, 2012), 47. ↩
- Noam Chomsky, The Science of Language: Interviews with James McGilvray (Cambridge, UK: Cambridge University Press, 2012), 13. ↩
- Noam Chomsky, The Science of Language: Interviews with James McGilvray (Cambridge, UK: Cambridge University Press, 2012), 14. ↩
- Terrence Deacon, The Symbolic Species: The Co-Evolution of Language and the Brain (New York: W.W. Norton, 1998); Steven Pinker, The Language Instinct, 1st ed. (New York: W. Morrow and Co, 1994). ↩
- Noam Chomsky, The Science of Language: Interviews with James McGilvray (Cambridge, UK: Cambridge University Press, 2012), 49. ↩
- Steven Pinker, Language, Cognition, and Human Nature: Selected Articles, 1st ed. (Oxford, UK: Oxford University Press, 2013), 146. ↩
- Alfred Russel Wallace, Contributions to the Theory of Natural Selection (London: Macmillan and Co., 1870), 338, 343. ↩
- Noam Chomsky, The Science of Language: Interviews with James McGilvray (Cambridge, UK: Cambridge University Press, 2012), 15. ↩
- The Chimpanzee Sequencing and Analysis Consortium, “Initial Sequence of the Chimpanzee Genome and Comparison with the Human Genome,” Nature 437 (2005): 69–87. ↩
- See In the Light of Evolution IV: The Human Condition (Supplement 2), Proceedings of the National Academy of Sciences of the United States of America 107 (May 11, 2010). ↩
- Michael Denton, Evolution: A Theory in Crisis (London: Adler & Adler, 1985), 249–50. ↩
- Eugene Koonin, and Artem Novozhilov, “Origin and Evolution of the Genetic Code: The Universal Enigma,” International Union of Biochemistry and Molecular Biology Life 61, no. 2 (2009): 108. ↩
- William Shakespeare, “The Phoenix and the Turtle” (1601). ↩
- Eugene Koonin, and Artem Novozhilov, “Origin and Evolution of the Genetic Code: The Universal Enigma,” International Union of Biochemistry and Molecular Biology Life 61, no. 2 (2009): 108. ↩
- Michael Denton, Evolution: A Theory in Crisis (London: Adler & Adler, 1985), 266–67. ↩
- Eugene Koonin, and Artem Novozhilov, “Origin and Evolution of the Genetic Code: The Universal Enigma,” International Union of Biochemistry and Molecular Biology Life 61, no. 2 (2009): 110. ↩
- Eugene Koonin, and Artem Novozhilov, “Origin and Evolution of the Genetic Code: The Universal Enigma,” International Union of Biochemistry and Molecular Biology Life 61, no. 2 (2009): 111. ↩
- Daniele Guerzoni, and Aoife McLysaght, “De Novo Origins of Human Genes,” David Begun, ed., PLoS Genetics 7, no. 11 (2011): e1002381; Dong-Dong Wu et al., “De Novo Origin of Human Protein-Coding Genes,” PLoS Genetics 7, no. 11 (2011): e1002379. ↩
- Jianzhi Zhang, “Evolution by Gene Duplication: An Update,” TRENDS in Ecology and Evolution 18, no.6 (2003): 297. ↩
- Adam Siepel, “Darwinian Alchemy: Human Genes from Noncoding DNA,” Genome Research 19, no. 10 (2009): 1,694. ↩
- Adam Siepel, “Darwinian Alchemy: Human Genes from Noncoding DNA.” Genome Research 19, no. 10 (2009): 1,693; see also Benjamin Wilson and Joanna Masel, “Putatively Noncoding Transcripts Show Extensive Association with Ribosomes,” Genome Biology and Evolution 3 (2011): 1,245–52; Jean Armengaud et al., “Microbial Proteogenomics, Gaining Ground with the Avalanche of Genome Sequences,” Journal of Bacteriology & Parasitology (2011): S3-001; Susumu Ohno, Evolution by Gene Duplication (New York: Springer-Verlag, 1970); François Jacob, “Evolution and Tinkering,” Science 196, no. 4295 ( 1977): 1161–66; Douglas Axe, “Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors,” Journal of Molecular Biology 301, no. 3 (2000): 585–95; Douglas Axe, “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds,” Journal of Molecular Biology 341, no. 5 (2004): 1,295–1,315; Moisés Mallo and Claudio Alonso, “The Regulation of Hox Gene Expression during Animal Development,” Development 140, no. 19 (2013): 3,951–63. ↩
- Daniele Guerzoni and Aoife McLysaght, “De Novo Origins of Human Genes,” David Begun, ed., PLoS Genetics 7, no. 11 (2011): e1002381. ↩
- Russell Doolittle, “Biodiversity: Microbial Genomes Multiply,” Nature 416, no. 6882 (2002): 697–700; Diethard Tautz and Tomislav Domazet-Lošo, “The Evolutionary Origin of Orphan Genes,” Nature Reviews Genetics 12, no. 10 (2011): 692–702; Konstantin Khalturin et al., “More Than Just Orphans: Are Taxonomically-Restricted Genes Important in Evolution?” Trends in Genetics 25, no. 9 (2009): 404–13. ↩
- Nicola Palmieri et al., “The Life Cycle of Drosophila Orphan Genes,” eLife 3 (2014): e01311. ↩
- Leo Berg, Nomogenesis: or, Evolution Determined by Law (Cambridge, MA: M.I.T. Press, 1926), 149. ↩
- T. H. Huxley, “Mr. Darwin’s Critics ,” in Darwiniana: Essays (New York: D. Appleton and Co., 1896), 181. ↩
- Wikipedia, “Evolution of Plants.” ↩
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- Leo Berg, Nomogenesis: or, Evolution Determined by Law (Cambridge, MA: M.I.T. Press, 1926), 120. ↩
- Alfred Romer and Thomas Parsons, The Vertebrate Body, 5th ed. (Philadelphia: Saunders Co, 1977), 416–24. ↩
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- Stephen Jay Gould, The Structure of Evolutionary Theory (Cambridge, MA: Harvard University Press, 2002), 203. ↩
- Palaeos: Life Through Deep Time, “The Mandibular Series: Surangular”:
In syanapsids, a secondary jaw joint develops between the surangular and the squamosal, which becomes the unique mammalian jaw articulation. However, the surangular fuses with the dentary and becomes the unitary mammalian ‘mandible’ without a separate identity.↩
- Thomas Kemp, The Origin and Evolution of Mammals (Oxford, UK: Oxford University Press, 2005): 80–87. ↩
- Henry Osborn, Evolution of Mammalian Molar Teeth to and from the Triangular Type (New York: The Macmillan Company, 1907). ↩
- Henry Osborn, “Organic Selection,” Science 7, no. 146 (1897): 583–87, quoted in Stephen Jay Gould, The Structure of Evolutionary Theory (Cambridge, MA: Harvard University Press, 2002), 1,085. ↩
- Henry Osborn, “Homoplasy as a law of latent or potential homology,” The American Naturalist 36 (1902): 270, quoted in Stephen Jay Gould, The Structure of Evolutionary Theory (Cambridge, MA: Harvard University Press, 2002), 1085. For Charles Bonnet’s theory that all future generations were “encased” in the female generative organs, see Lorin Anderson, Charles Bonnet and the Order of the Known (Dordrecht: Springer, 2012); for Richard Owen’s theory of the vertebrate archetype (drawing on work by Lorenz Oken), see Nicholas Rupke, Richard Owen: Biology without Darwin (Chicago: University of Chicago Press, 2009), 90–140. ↩
- Henry Osborn, “Darwin and Paleontology,” in Fifty Years of Darwinism: Modern Aspects of Evolution (New York: Henry Holt, 1909), 223, cited by Leo Berg, Nomogenesis: or, Evolution Determined by Law (Cambridge, MA: M.I.T. Press, 1926), 127. ↩
- William Dembski and Jonathan Wells, The Design of Life: Discovering Signs of Intelligence in Biological Systems (Dallas, TX: Foundation for Thought and Ethics, 2008); Stephen Meyer, Signature in the Cell: DNA and the Evidence for Intelligent Design (New York: HarperCollins, 2009). ↩
- See Michael Denton, “The Types: A Persistent Structuralist Challenge to Darwinian Pan-Selectionism,” Biocomplexity 3 (2013): 1–18. ↩
- Michael Denton and Craig Marshall, “Laws of Form Revisited,” Nature 410 (2001): 417; George Rose et al., “A Backbone-Based Theory of Protein Folding,” Proceedings of the National Academy of Sciences of the United States of America 103(45): 16,623–33; Michael Denton et al., “The Protein Folds as Platonic Forms: New Support for the Pre-Darwinian Conception of Evolution by Natural Law,” Journal of Theoretical Biology 219 (2002): 325–42. ↩
- Cyrus Chothia et al., “Protein Folds in the All-Beta and All-Alpha Classes,” Annual Review of Biophysics and Biomolecular Structure 26 (1997): 597–627. ↩
- Michael Denton et al., “The Protein Folds as Platonic Forms: New Support for the Pre-Darwinian Conception of Evolution by Natural Law,” Journal of Theoretical Biology 219 (2002): 325–42. ↩
- Daniel Weinreich et al., “Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins,” Science 312 (2006): 111–14, 113. ↩
- Seymour Singer and Garth Nicolson, “The Fluid Mosaic Model of the Structure of Cell Membranes,” Science 175 (1972): 720–31. ↩
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- Ronald Amundson, The Changing Role of the Embryo in Evolutionary Thought: Roots of Evo-Devo (Cambridge, UK: Cambridge University Press, 2007), 241. ↩
- Hans Driesch, The Science and Philosophy of the Organism (Aberdeen, UK: University of Aberdeen, 1928). ↩
- Gregory Davis and Nipam Patel, “Short, Long, and Beyond: Molecular and Embryological Approaches to Insect Segmentation,” Annual Review of Entomology 47 (2002): 669–99; Paul Liu and Thomas Kaufman, “Short and Long Germ Segmentation: Unanswered Questions in the Evolution of a Developmental Mode,” Evolution & Development 7 (2005): 629–46. ↩
- Gregory Davis and Nipam Patel, “Short, Long, and Beyond: Molecular and Embryological Approaches to Insect Segmentation,” Annual Review of Entomology 47 (2002): 669–99; Paul Liu and Thomas Kaufman, “Short and Long Germ Segmentation: Unanswered Questions in the Evolution of a Developmental Mode,” Evolution & Development 7 (2005): 629–46; Günter Wagner, “How Wide and How Deep is the Divide between Population Genetics and Developmental Evolution?” Biology and Philosophy 22 (2005): 145–53. ↩
- Paul Liu and Thomas Kaufman, “Short and Long Germ Segmentation: Unanswered Questions in the Evolution of a Developmental Mode,” Evolution & Development 7 (2005): 629–46, 629. ↩
- Paul Davies, The Accidental Universe (Cambridge, UK: Cambridge University Press, 1982); John Barrow and Frank Tipler, The Anthropic Cosmological Principle (Oxford, UK: Oxford University Press, 1988); John Gribbin and Martin Rees, Cosmic Coincidences: Dark Matter, Mankind and Anthropic Cosmology (New York: Bantam Books, 1989); Paul Davies, The Cosmic Blueprint: New Discoveries in Nature’s Creative Ability to Order the Universe (Philadelphia: Templeton Foundation Press, 2004). ↩
- Paul Davies, The Accidental Universe (Cambridge, UK: Cambridge University Press, 1982), vii. ↩
- Fred Hoyle, “The Universe: Past and Present Reflections,” Engineering and Science (1981): 12; quoted in Paul Davies, The Accidental Universe (Cambridge, UK: Cambridge University Press, 1982), 118. ↩
- Lawrence Henderson, The Fitness of the Environment: An Inquiry into the Biological Significance of the Properties of Matter (New York: Macmillan, 1913); Michael Denton, Nature’s Destiny: How the Laws of Biology Reveal Purpose in the Universe (New York: Free Press, 1998). ↩
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