Right of Reply: Our Response to Jerry Coyne

Right of Reply: Our Response to Jerry Coyne

Günter Bechly, Brian Miller and David Berlinski
Günter Bechly, Brian Miller and David Berlinski
13 min read

Jerry Coyne has offered a response in the pages of Quillette to David Gelernter’s provocative article, “Giving Up Darwin.” Gelernter rejected the standard model of neo-Darwinian evolution for a simple reason: he looked at three pieces of scientific evidence that appeared to be incompatible with that model:

  • The sudden appearance of new body plans in the fossil record.
  • The extreme rarity of protein folds.
  • The absence of early-acting beneficial mutations, the kind that would be needed to generate new animal body plans.

In knowing where to look, Gelernter had help from Stephen Meyer’s Darwin’s Doubt, and David Berlinski’s The Deniable Darwin. These books both contain many references to the literature. Gelernter also highlighted the book Debating Darwin’s Doubt, which responded in detail to all notable critiques of the arguments that swayed him. For all that, Coyne faulted Gelernter for not examining counter-arguments to his own position. “One simply can’t do good science,” Coyne wrote, “by spouting only one side of an argument and ignoring the claims of the other.” A certain measure of irony is conveyed by this unjustified remark. Had Coyne followed it more faithfully, he would have spared himself some embarrassment.

The Cambrian Explosion, Coyne argues, “is an explosion only in geological terms, and allows for a lot of biological evolution to take place, (after all, modern whales evolved from small terrestrial deerlike organisms in just 12 million years).”

This is wrong in its first assertion, it is wrong in its second assertion; and it is wrong all around. The Cambrian Explosion is an abrupt event in geological and biological terms. The average longevity of marine invertebrate species is 5-10 million years. This is standard evolutionary biology. Thus, the transition from an assumed worm-like ancestor to all of the Cambrian animal phyla took place during the lifespan of, at most, a few successive species. (The phyla represent the largest division of animal classification exemplifying the most significant differences in biological form, whereas species which represent the smallest divisions and exemplify much more minor differences). Yet neo-Darwinists envision the new body plans that characterize the animal phyla arising as the result of an accumulation of many, many species-level changes and transitions over long periods of time—indeed, far more time than the Cambrian paleontological record allows. Consequently, the Cambrian Explosion is called the Cambrian explosion for a very good reason: something dramatic happened in a very short period of time.

The whales? And in twelve million years? Not likely. The available window of time for the transition from the terrestrial pakicetids to fully marine basilosaurids (Pelagiceti) is only 4.5 million years. This corresponds to the lifespan of a single larger mammal species, as Donald Prothero correctly notes. Prothero is Coyne’s ideological ally. They should be better friends. Short time spans give rise to a generic waiting time problem—a much-discussed issue in mainstream population genetics. It is easy to see why. The time required for even a single pair of coordinated mutations to originate and spread in a population is, at least, an order of magnitude longer than the window of time established by the fossil record. Either the fossil record must go, or the waiting time must go, but they cannot go on together. The whales are the least of it. The emergence of a single pair of coordinated mutations in the human lineage required a waiting time of 216 million years. The separation of the chimpanzee and human lineages took place only six or seven million years ago. These figures are clearly in conflict. This is the standard view, the one held by mainstream evolutionary biologists.

If the Cambrian Explosion cannot be contained by a play on words, perhaps it may be constrained by a sleight of hand? The very concept of an explosion, Coyne argues, “is disappearing, with paleontologists increasingly speaking of a ‘Cambrian diversification’.” Are they? Are they really? A search on Google Scholar for academic publications between 2000 and 2019 yields 13,400 matches for the term ‘Cambrian Explosion’ but only 392 matches for ‘Cambrian Diversification.’ The Cambrian Explosion continues to explode: “Evidence is converging,” paleontologists have written recently, “towards picturing the Cambrian explosion as even swifter than what we thought.” This does not look like a disappearing concept at all. Some scholars should leave sleights of hand alone.

David Gelernter accepted the conclusion that there were no putative ancestors of the Cambrian phyla in the preceding Ediacaran strata. He is in good company. So do most paleontologists who specialize in this field. This conclusion is not controversial, and it is obviously at odds with Darwin’s theory. Coyne is unpersuaded, maintaining that, yes, we have found Ediacaran “animals that appear to be arthropods, muscle-clad cnidarians (the group that includes modern jellyfish and anemones), echinoderms, mollusks, and probable sponges.”

This is pure fantasy. Coyne is unacquainted with the facts. There are no Ediacaran arthropods. There are no Ediacaran echinoderms either. Akarua adami, it is true, was initially attributed to the echinoderms. But apart from pentaradial symmetry, Akarua adami lack all of the synapomorphic characteristics of the echinoderms. The Cambrian fossil record contains stem echinoderms in helicoplacoids and homalozoans (carpoids) after all; and we know from reconstructed phylogenetic trees that pentaradial symmetry does not belong to their ground plan. The mollusks to which Coyne confidently appeals as friends of the family? They belong to the Ediacaran fossil genus Kimberella. First described as a jellyfish, Kimberella was later indeed sometimes associated with early mollusks. This attribution remained controversial: several characteristics contradicted it. A comprehensive paper recently reviewed the “problem of Kimberella” and concluded that “the possibility that Kimberella is coelenterate grade should therefore not be excluded.” Although likely a metazoan, they went on to write, “its placement remains problematic; it may be on the bilaterian stem group rather than within the stem group of any particular phylum.”

That leaves sponges and cnidarians. There is not much there, and it is of no interest. These groups branched off the metazoan tree long before the origin of bilaterian animals, and thus are irrelevant to the question of the abrupt appearance of the Cambrian animal phyla.

In passing, Coyne mentions a putative bilaterian segmented worm-like animal from the terminal Ediacaran period. The body plan of this worm is unlike the body plan of all known fossil or living animals. It is not ancestral to any of them. It’s confirmation as a worm among worms would, at best, establish the presence of a single phylum in the shape of the annelids at the very end of the Ediacaran. This would marginally extend the length of the Cambrian Explosion by a few million years.

What about the other Ediacaran trace fossils? All gone. A seminal study published in 2016 experimentally demonstrated that these Ediacaran trace fossils can be easily reproduced as artifacts of stirred up bacterial mats that covered the Ediacaran sea floors.

Careless in his facts, Coyne is also careless in his references. There is, for example, the recent study by Wood et al. (2019). It is there, Coyne assures himself, that all those Cambrian antecedents may be found. In fact, this paper contains no evidence for Ediacaran bilaterian animals. There are reasonable candidates for primitive metazoan lineages, like sponges, ctenophores, and cnidarians, but not a single putative ancestor for any of the 21 Cambrian bilaterian animal phyla. If this is unequivocal, the attribution of the very Ediacaran Dickinsonia to stem metazoan animals is dubious. Had Coyne done a more thorough survey of the paleontological literature himself, he would have discovered that the absence of Ediacaran predecessors to the Cambrian is an established fact of modern paleontology.

Wood’s more general conclusion is pertinent, convincing, and correct: “The Cambrian Explosion represents a radiation of crown-group bilaterians … one phase amongst several metazoan radiations.” That there were many such abrupt radiations is undisputed. There were, at least, 18! Why Coyne thinks this a point in his favor is mysterious. Those radiating facts comprise a fatal objection to Darwin’s theory. It was Richard Dawkins who observed that “evolution not only is a gradual process as a matter of fact; it has to be gradual if it is to do any explanatory work.” If evolution must be gradual, or continuous, as a matter of fact and as a matter of theory, those 18 explosive events, which are neither gradual nor continuous, would seem to represent considerable conflicting evidence.

Some time ago, paleontologists tried to explain the absence of soft-bodied ancestors in pre-Cambrian sediments as artifacts of preservation. No longer. This hypothesis has been refuted by evidence from fossil sites of the Burgess Shale type in Mongolia and China. They yielded nothing but fossil algae.

This made the problem of the Cambrian Explosion even more acute: 550 million years ago there were no animals at all, and 537 million years ago there were already fully developed crown-group arthropods like trilobites with sophisticated compound eyes, exoskeletons, and articulated legs. Does anybody seriously believe that such an enormous transition within 13 million years is a piece of cake? Gelernter is right to be skeptical, and mainstream science supports his arguments.

The progression from micro to macro-evolution is a staple of Darwinian theory; and it is a staple to which Coyne gratefully repairs. Numerous fossil transitional series, he argues, provide “ample evidence from the fossil record for gradual but really substantial macroevolution.” There are the transitions from fish to amphibians, amphibians to reptiles, reptiles to mammals, dinosaurs to birds, terrestrial mammals to marine whales, and ape-like australopithecines to modern humans.

A thirsty man cannot be too scrupulous about what he is prepared to drink, but this argument is addressed to a position no one is challenging, least of all David Gelernter. If these transitional series provide evidence of anything, they provide evidence for common ancestry. The gravamen of Gelernter’s argument was not common ancestry but its explanation in terms of a Darwinian process. Transitional series do not, and cannot, provide evidence for such a process. Nor are these transitional series gradual in any meaningful way. They represent a succession of very distinct and different stages, often separated by many millions of years.

It is when he moves on to the details that Coyne decisively parts company with the facts. These transitional series, he argues, represent evidence for anagenetic speciation—gradual species transformation within an unbranched lineage. It is odd, and disappointing, to find such a blunder solemnly promoted by an evolutionary biologist—a specialist in speciation, no less (author of a textbook on speciation). Nearly all the fossil species in these transitional series exhibit autapomorphies, or uniquely derived characters; they thus belong to side branches of the stem line and cannot be part of an unbranched lineage. If they cannot be a part of an unbranched lineage, they cannot arise by anagenetic speciation. This is beyond dispute, and, apart from Coyne, unique in his isolation, no one considers this evidence for anagenetic speciation.

In fact, the meagre fossil evidence for anagenetic and/or gradualistic speciation has proven to be no evidence at all. The Steinheim freshwater snails?—an ecophenotypic variation; the marine foraminifers of the genus Globorotalia?an abrupt speciation. There remains the transition from Australopithecus anamensis to A. afarensis. The last has long been considered by paleontologists as “one of the strongest cases for anagenesis in the fossil record.” Unfortunately, it has just been overturned by the discovery of a new hominin skull that documents the temporal overlap of both species.

Coyne alludes briefly to evidence for the origin of new lineages within human lifetimes. The allusion is brief because the evidence is likewise scanty. The possible examples are, in any case, well-known: polyploid plants, stickleback fish, East African cichlids, Pacific salmons, Madeiran house mice, London underground mosquitoes, and the Hawaiian banana-feeding Omiodes (Hedylepta) moths. Some of these examples are just intra-specific changes (sticklebacks, salmons, underground mosquitoes), while others are highly controversial (the banana-feeding moths). Even if a new cichlid fish species can arise from another cichlid species within a relatively short time, this does nothing to explain the origin of complex new organs or new protein folds. No one doubts that different species of Darwin finches could originate by neo-Darwinian microevolution from a single founder species. The claim that microevolution can be extended to macroevolution is the very contention challenged by Darwin’s critics.

If Jerry Coyne is wrong about paleontology, he is wrong, as well, about protein evolution. David Gelernter observed that amino acid sequences that correspond to functional proteins are remarkably rare among the “space” of all possible combinations of amino acid sequences of a given length. Protein scientists call this set of all possible amino acid sequences or combinations “amino acid sequence space” or “combinatorial sequence space.” Gelernter made reference to this concept in his review of Meyer and Berlinski’s books. He also referenced the careful experimental work by Douglas Axe who used a technique known as site-directed mutagenesis to assess the rarity of protein folds in sequence space while he was working at Cambridge University from 1990-2003. Axe showed that the ratio of sequences in sequence space that will produce protein folds to sequences that won’t is prohibitively and vanishingly small. Indeed, in an authoritative paper published in the Journal of Molecular Biology Axe estimated that ratio at 1 in 1074. From that information about the rarity of protein folds in sequence space, Gelernter—like Axe, Meyer and Berlinski—has drawn the rational conclusion: finding a novel protein fold by a random search is implausible in the extreme.

Not so, Coyne argued. Proteins do not evolve from random sequences. They evolve by means of gene duplication. By starting from an established protein structure, protein evolution had a head start.

This is not an irrational position, but it is anachronistic.

Indeed, Harvard mathematical biologist Martin Nowak has shown that random searches in sequence space that start from known functional sequences are no more likely to enter regions in sequence space with new protein folds than searches that start from random sequences. The reason for this is clear: random searches are overwhelmingly more likely to go off into a non-folding, non-functional abyss than they are to find a novel protein fold. Why? Because such novel folds are so extraordinarily rare in sequence space. Moreover, as Meyer explained in Darwin’s Doubt, as mutations accumulate in functional sequences, they will inevitably destroy function long before they stumble across a new protein fold. Again, this follows from the extreme rarity (as well as the isolation) of protein folds in sequence space.

Recent work by Weizmann Institute protein scientist Dan Tawfik has reinforced this conclusion. Tawfik’s work shows that as mutations to functional protein sequences accumulate, the folds of those proteins become progressively more thermodynamically and structurally unstable. Typically, 15 or fewer mutations will completely destroy the stability of known protein folds of average size. Yet, generating (or finding) a new protein fold requires far more amino acid sequence changes than that. Finally, calculations based on Tawfik’s work confirm and extend the applicability of Axe’s original measure of the rarity of protein folds. These calculations confirm that the measure of rarity that Axe determined for the protein he studied is actually representative of the rarity for large classes of other globular proteins. Not surprisingly, Dan Tawfik has described the origination of a truly novel protein or fold as “something like close to a miracle.” Tawfik is on Coyne’s side: He is mainstream.

The archipelago of functional proteins remains what it has always been: an isolated series of island-like points in a vast sea of possibilities.

Can the genes that direct an organism’s early development and establish its basic architecture undergo selectable mutations? If on this point, Gelernter is skeptical, Coyne, for his part, is credulous. Some mutations do occur in some genes, he argues, and they occur early in development. All is well. This claim is true but trivial. These mutations do not drive any large-scale transformation. They are rarely noticeable. They are there for the ride. The mutations that substantially alter early development are usually fatal. The genetic networks that control an organism’s early development cannot be changed without catastrophic results. It is precisely for this reason that developmental biologists working with paleontologists have appealed to the idea that ancestral species possessed far more flexible genetic networks than species today. There is no evidence in favor of this ad hoc claim, and beyond the fact that it is untestable, no reason to entertain it.

Prof. Gerd Müller at the Royal Society in London 2016 (image courtesy of Bechly)

Throughout his essay Coyne suggests that David Gelernter came to his doubts by failing to recognize what he did not know. Did he? If so, he is in remarkably good company. Many distinguished theoretical biologists seem to have overlooked their own intellectual deficiencies. This became obvious during the conference ‘New Trends in Evolutionary Biology’ hosted by the Royal Society of London in November of 2016. In his keynote lecture, Gerd Müller listed several explanatory deficits of neo-Darwinism, among which he included phenotypic novelty, phenotypic complexity, and non-gradual forms of transition.

If Darwin’s theory is encumbered with these explanatory deficits, what good is it, and if it is not, where are the explanations it affords?

Müller voice is hardly alone. It is part of a choir. Consider the conference announcement from a meeting held in 2018 and entitled ‘Evolution—Genetic Novelty/Genomic Variations by RNA Networks and Viruses.’ “For more than half a century it has been accepted that new genetic information is mostly derived from random‚ error-based events. Now it is recognized that errors cannot explain genetic novelty and complexity.”

If random mutations cannot explain genetic novelty and complexity, just what can it explain? Not much, David Gelernter argues.

If not old-fashioned Darwinism, then, perhaps, new-fashioned Darwinism—the Extended Evolutionary Synthesis, or the Third Way of Evolution? Anything is better than nothing, but Coyne, at least, is on record as a supporter of neo-Darwinism. He is skeptical of the need for an Extended Synthesis and so remains committed to the view that nothing is better than anything.

For a very good reason. No part of the Extended Synthesis—niche construction, phenotypic plasticity, evolvability, epigenetics, hybridogenesis, natural genetic engineering—addresses the explanatory deficits of neo-Darwinism. In accommodating phenotypic plasticity or evolvability, it is neo-Darwinism that presumptively did the original construction work. These views thus embody the better aspects of nothing and anything.

The Darwinian mechanism of random mutation and natural selection is the only suggestion ever forged by human ingenuity to explain things from the bottom-up. Daniel Dennett called Darwin‘s Dangerous Idea a universal acid, and Richard Dawkins admitted that only “Darwin made it possible to be an intellectually fulfilled atheist.” How a universal acid might promote intellectual fulfillment without eating into all that fulfillment, he did not say. If the theory fails the acid test of explaining what it was designed to explain, the need for a change in biology cannot be dismissed in such a nonchalant manner as Coyne does.

A straightforward reading of the data from paleontology, protein studies, research on developmental mutations, and many other fields, uniformly support Gelernter’s thesis that Darwinism’s time has now passed. Gelernter, who is a top-ranked intellectual, carefully studied the arguments from both sides and was not afraid to follow the evidence wherever it led, even if it meant giving up on a beautiful theory. The atheist philosopher Thomas Nagel came to the same conclusion that “the materialist Neo-Darwinian conception of nature is almost certainly false.” The first author of this article has been a staunch Darwinian evolutionary biologist and paleontologist for decades. No longer staunch, he changed his mind, based on the evidence and arguments presented by Darwin’s critics. Still strong in his staunchness, Coyne might eventually change his mind, too.

Anything is possible.

DarwinismFossil RecordIntelligent DesignrecentRight of Reply