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Response to John Wise

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[Note: This response was co-authored by Stephen Meyer, Paul Nelson, Rick Sternberg and Jonathan Wells, who each presented at the “4 Nails in Darwin’s Coffin” event at SMU. Doug Axe, who also presented, responded here.]
On Thursday, September 23, 2010, following a showing of the film Darwin’s Dilemma, we presented a program of short talks in the Hughes-Trigg Theatre at Southern Methodist University (SMU). We argued that the neo-Darwinian theory of evolution has not solved these related problems:

  • The origin of novel protein folds (talk by Axe)
  • The origin of anatomical novelties (talk by Sternberg)
  • The origin of animal body plans (talks by Nelson and Wells)

SMU biology lecturer John Wise attended the event – or so it appears, because he wrote a long “reply” to both the movie and our presentations, and cites our handout distributed at the information table. Wise did not ask any questions during the Q & A, however, or interact with any of us during our visit. Over the weekend (September 25-26), he then posted his comments at his webpage.
We put “reply” within quotation marks because Wise’s page comprises such a rambling pastiche of assertions – some mutually contradictory, others irrelevant, or simply non-sequiturs – that it is difficult to sort out what he is actually arguing. Wise and 7 other SMU faculty members also published a somewhat more coherent letter in the SMU Daily Campus, objecting to the event. We have replied to that letter separately, and Doug Axe has written his own reply to Wise’s critique.

In what follows, we’ll respond to Wise’s webpage criticisms of Darwin’s Dilemma and our talks, at least insofar as we can make sense of those criticisms. Responses to the copious extraneous material on Wise’s webpage can be found elsewhere.
1. Does the Neo-Darwinian Theory of Evolution Explain the Cambrian Explosion?
We argued that if the theory of evolution is understood according to its textbook definition, namely, “the descent with modification of organisms from a common ancestor, via natural selection and other undirected processes acting on randomly-arising genetic variation” – a definition Wise appears to accept – then that theory does not explain the Cambrian Explosion, the geologically sudden appearance of most animal body plans 540-530 million years ago. We presented multiple lines of evidence in support of our position, some of which can be seen in the handout.
Wise disagrees, vehemently – but sorting out why is a bit of a mystery. Take, for instance, his treatment of the fossil evidence. Wise asserts that neo-Darwinian theory predicts we should not expect to find transitional forms between the major animal groups. He writes:

We have strong evidence that evolution happens most quickly in small populations. Migrations from these source areas to an area conducive to fossilization then make it appear as if a new form arrived suddenly in the fossil record….We know that evolution can act quite quickly on small populations that are isolated. It’s quite likely that the new Cambrian phyla would have originally evolved in an isolated system like this, and then populated the whole ocean. If so, then it’s actually fairly improbable that we’ll stumble upon fossil evidence of these ancestors: we’ll have to find the inland sea, and hope that part of it somehow got buried in mud well enough to preserve some fossils, and hope that those fossils didn’t erode away in the half-billion years since then — i.e., don’t hold your breath.

Okay – let’s label this neo-Darwinian prediction ~F, for “Fossil ancestors or transitions for the Cambrian phyla have not been discovered, because of how evolution works.”
But hang on: fossil transitional forms between phyla have been found, says Wise, borrowing a list from Oxford paleontologist Martin Brasier. Over 100 million years elapsed, he adds, from the first fossil evidence of sponges to the Cambrian Explosion itself, plenty of time to capture transitional forms. (We’ll return to Brasier’s list of putative ancestors in a moment.)
Let’s label this second prediction F, for “Fossils ancestors for the Cambrian phyla have been discovered, because of how evolution works.”
And the consequence? Neo-Darwinian theory predicts F and ~F. So if we haven’t found the transitional or ancestral fossils, the theory predicts such fossils won’t be discovered. Wait, we found some? Well, the theory predicts that, too.
In short, when conjoined, the predictions F and ~F cover every conceivable paleontological outcome. Obviously this does not bode well for the ordinary empirical testing of neo-Darwinian theory. A theory consistent with every possible paleontological observation is in very serious trouble.
About those putative ancestral groups: we looked at Brasier’s list, borrowed by Wise. The first candidate mentioned was Halkieria, proposed to be the ancestor (stem group) of molluscs.
But the taxonomic position of Halkieria, like other coeloscleritophorans – an enigmatic extinct taxon “of uncertain rank and affinities” (Valentine 2004, 333), sometimes jokingly referred to as “balloons covered with scales” – is hardly as straightforward as Brasier claims. This is a problem endemic to the interpretation of extinct fossil groups. Paleontologist James Valentine, looking at the same fossils, argues for skepticism about molluscan affinities: “The purported homologies…are quite speculative. There is no special reason to believe that chiton valves or conchiferan shells evolved from fused spicules, and even if chiton plates were originally spicular, homology with halkierid shells is to say the least uncertain” (2004, 335).
From long experience, we know that Brasier’s other candidate ancestral groups will yield the same uncertainty, and encourage the reader (if he has a day to spend) to pursue them into the literature. We do not think the exercise worth the time.
2. Wise Picked Up Our Cambrian Explosion Handout At the Event…
…but he seems not to have read it.
For instance, we say on page 1 of the handout, “Precambrian fossils exist; this has been known for many decades, from fossil localities around the world.” The movie makes the same point, illustrating (with animations) the Precambrian Ediacaran fauna, as an example of such early groups.
Thus, when Wise asserts that the discovery of 635 mya sponge chemical trace fossils “completely demolishes” our argument, he does not grasp that (1) the Precambrian occurrence of Porifera (sponges) is something we acknowledge, but more importantly, (2) the body plan of Porifera does not provide the stem-group (ancestor) to the disparate Cambrian explosion phyla. As the handout explains, those ancestral groups are missing from the fossil record, a fact widely accepted among paleontologists – and even by Wise’s other often-cited authority, developmental biologist Sean Carroll.
As Carroll notes, one can only infer (as contrasted with observe) that the Cambrian phyla shared common ancestors, because the requisite fossils are missing from the record:

The first appearance of clearly recognizable members of many protostome and deuterostome groups is in the Cambrian period. Because those branches of the animal tree are clearly distinguishable at this time, we deduce that the common ancestors of various groups must predate the Cambrian by some chunk of time. This is an inference because the fossil record of protostomes and deuterostomes before the Cambrian is very scanty. In fact, only one body fossil from the Precambrian, an animal called Kimberella, dated at 555 million years, has been suggested to represent a protostome.
So, where then are those ancestors? Fossil preservation conditions were adequate to preserve animals such as jellyfish, corals, and sponges, as well as the Ediacaran fauna. It does not appear that scarcity is a fault of the fossil record. (2005, 141-2; emphasis added)

Wise criticizes Darwin’s Dilemma for featuring the fossils of the Burgess Shale because they do not represent the earliest Cambrian fauna. But Sean Carroll, the authority upon whom he relies, also opens his chapter on the Cambrian Explosion by praising the beauty, and emphasizing the scientific relevance, of the Burgess Shale fossils (2005, 137-9). In any case, while Darwin’s Dilemma described the Burgess Shale fossils, both the movie and Stephen Meyer’s talk at SMU emphasized the importance of the even earlier Chengjiang fauna. As the movie explained, the fossils in Chenjiang predate the Burgess formation by millions of years, and render the unsolved problem of the origin of animal body plans even more acute.
3. Has Sean Carroll (or Evo Devo generally) explained the Cambrian Explosion?
And this brings us to the main problem with Wise’s critique. In fact, Wise missed the point of the entire evening, which was not a discussion of whether alleged ancestral or transitional fossils exist for the Cambrian phyla (in the overwhelming majority of cases they do not), or the timing of the Cambrian Explosion. Instead, our presentations focused on whether the neo-Darwinian mechanism is capable of producing either (a) the novel genes and proteins or (b) the novel body plans that arise in events such as the Cambrian explosion. We argued, based upon four independent lines of evidence, that the mechanism lacks these powers.
Concerning the first issue (the origin of novel genes and proteins), Wise offered no rebuttal whatsoever to Doug Axe’s careful empirical and mathematical analysis of the problem of generating novel genes and protein folds as the result of an undirected mutational search. Wise’s silence on this point is conspicuous, since it’s the one area where his own expertise intersected the topics presented.
Concerning the second issue (the origin of novel body plans), Wise again relied solely on, in this case, the unproven assertions, of another authority. In particular, he cites Sean Carroll’s (2005) popular science book Endless Forms Most Beautiful and argues that this “modern evolutionary view,” usually abbreviated as “evo devo,” explains the origin of the phyla. Here is Wise’s summary of the evo-devo hypothesis; we’ve numbered its sub-parts for ease of reference:

  1. Carroll and others show that new genetic switches used by “toolkit master proteins” can lead to many different variations in body plans….
  2. This new advance in body building mechanisms would lead to many different body forms (read Carroll’s book) and different evolutionary trajectories….
  3. These mechanisms could clearly have resulted in different body plans that would be (and have been) classified as different phyla.
  4. These different phyla could arise simultaneously or close in time in a manner that could be called “from the bottom up”, i.e. from early common ancestors…

But if one opens Carroll’s book looking for the experimental evidence to support these claims, it isn’t there. One chapter deals with variations in butterfly wing spots; another cites data on melanism (pigment differences) in peppered moths, jaguars, and birds. The closest relevant evidence Carroll offers comes from David Kingsley’s work on the reduction or loss of pelvic spines in stickleback fish – but even here, the variations occur within a single genus, and involve the loss of a structure, not its origin.
The evidence isn’t there, frankly, because it doesn’t exist.
Mutations to “genetic switches” involved in body plan formation – as we argued at SMU, explained in our handout, and supported with evidence – disrupt the normal development of animals. With the possible exception of the loss of structures (not a promising avenue for novelty-building evolution, in any case), these mutations either destroy the embryo in which they occur or render it gravely unfit as an adult. What the mutations do not provide are “many different variations in body plans.”
Wise accepts Carroll’s authority on this question, but what he should be asking for is evidence. Here is some that we urge him to consider.
According to Wise, Jonathan Wells’s argument that new body plans can’t evolve simply by changing the DNA “is fallacious for precisely the same reason that it would be fallacious to argue that, since factors other than your recipe play a role in baking your cake (e.g., gravity plays a role), switching recipes can’t give you a different type of dessert. Furthermore, even if you thought that evolving a new body plan would require changing the structure of the egg (e.g., perhaps adding new markers to attract the growth of new limbs), no reason was given for thinking that changes in DNA couldn’t lead mothers to produce these differently structured eggs.”
But there are solid empirical grounds for arguing that changes in DNA alone cannot produce new organs or body plans. A technique called “saturation mutagenesis”1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12
None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans–because none of the observed developmental mutations benefit the organism.
Indeed, the evidence justifies only one conclusion, which Wells summarized in his last slide at SMU:

We can modify the DNA of a fruit fly embryo in any way we want, and there are only three possible outcomes:

A normal fruit fly;
A defective fruit fly; or
A dead fruit fly.

This same pattern of normal, defective, or dead exists for the other model systems of evo-devo. This is what nature has told us, and it’s based on evidence, not speculation.
4. Stray irrelevancies and non-sequiturs

We don’t mind being criticized for what we do say. That comes with the territory when one challenges a prevailing theory.
We do mind, however, having to respond to outright fabrications or total non-sequiturs. For instance, according to Wise, Wells argued that “intervention from an intelligent designer would be necessary to plan out the developmental process for new species, and perhaps even within the developmental process of each embryo.” Yet about half of human embryos are spontaneously aborted, and “many feel it is quite implausible that an intelligent designer would set up developmental processes so prone to failure.”
Of course, Wells never argued that an intelligent designer must intervene “within the developmental process of each embryo.” Instead of criticizing what Wells did say, Wise fabricates something, attributes it to Wells, and criticizes that instead.
Wise also claims that that “there is confusion in the Discovery Institute itself on Wells’ stance” on Archaeopteryx in Icons of Evolution.13 But Archaeopteryx was not discussed at the SMU event. Wise might as well be criticizing Wells’s restaurant preferences.
Wise also criticized Sternberg for the latter’s citation of a 2008 paper by Durrett and Schmidt. But Sternberg correctly drew on Durrett and Schmidt’s paper to argue that the numerous specific changes that would be needed for the origin of whales cannot plausibly have appeared in the available time frame. Their paper shows that particular adaptations requiring two changes are not expected to be fixed in this time.
Instead of dealing with the implications of this, however, Wise quotes a reply these authors made to Michael Behe, where they say that a small fraction of double mutations will successfully be fixed, though most will not. Wise may think this undermines Sternberg’s argument, but it doesn’t. When a large number of specific changes need to be made in a coordinated way, partial success isn’t good enough.
In conclusion, we wish to thank the many people at SMU who attended our event, asked questions, and spoke with us (at length, in some cases) afterwards. Science thrives on informed discussion and dissent.
It doesn’t do so well, however, with unwise (pun intended) sniping.
Carroll, Sean. 2005. Endless Forms Most Beautiful: The New Science of Evo-Devo. New York: W. W. Norton.
Durrett, R. and Schmidt, D. 2008. Waiting for two mutations: with applications to regulatory sequence evolution and the limits of Darwinian evolution. Genetics 180:1501-1509.
Valentine, James. 2004. On the Origin of Phyla. Chicago: University of Chicago Press.
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2T. S. Wong, et al., “Sequence saturation mutagenesis (SeSaM): a novel method for directed evolution,” Nucleic Acids Research 32 (2004): e26. Available online (2010) at http://nar.oxfordjournals.org/content/32/3/e26.full.pdf+html
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8M. C. Mullins, et al., “Large-scale mutagenesis in the zebrafish: in search of genes controlling development in a vertebrate,” Current Biology 4 (1994): 189-202.
9P. Haffter, et al., “The identification of genes with unique and essential functions in the development of the zebrafish, Danio rerio,” Development 123 (1996): 1-36. Available online (2010) at http://dev.biologists.org/content/123/1/1.long
10W. Dreiver, et al., “A genetic screen for mutations affecting embryogenesis in zebrafish,” Development 123 (1996): 37-46. Available online (2010) at http://dev.biologists.org/content/123/1/37.long
11K. E. Hentges, et al., “Regional variation in the density of essential genes in mice,” PLoS Genetics 3 (2007): e72. Available online (2010) at http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.0030072
12J. A. Hagarman & T. P. O’Brien, “An essential gene mutagenesis screen across the highly conserved piebald deletion region of mouse chromosome 14,” Genesis 47 (2009): 392-403.
13J. Wells, Icons of Evolution (Washington, DC: Regnery Publishing, 2000). For more information go to http://www.iconsofevolution.com/

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