In this, my final post on panda evolution, I’d like to conclude with some clinching evidence for panda evolution and respond to Professor Dilley’s arguments in the last two posts of his five-part series.

The red panda and the giant panda: a case of convergent evolution

(a) The evidence from the false “thumb” of the red panda and the giant panda

I’d like to begin by referring readers to a news article in AsianScientist magazine by Sim Shuzhen, titled, How Two Pandas Got Their Thumbs (Feb. 2, 2017). The article provides some fascinating evidence for the evolution of the giant panda. Interestingly, this evidence comes from the red panda, which isn’t even a bear:

Giant pandas and red pandas look nothing alike. Evolutionarily speaking, they are different as well, having diverged more than 40 million years ago. Giant pandas are grouped along with other bears into the family Ursidae; red pandas, on the other hand, are more closely related to raccoons and ferrets, and have been placed in their own family, the Ailuridae.

Despite these differences, the pandas do share certain unique characteristics. They both evolved from meat-eating ancestors, but are now specialized herbivores that eat an almost exclusively bamboo diet. Both pandas have also evolved false or pseudothumbs — enlarged bone protrusions on their paws, all the better to grasp sticks of bamboo with.

Both giant pandas and red pandas eat bamboo and possess false “thumbs.” This sounds like a clear-cut case of convergent evolution. What makes it especially convincing, however, is that the same genes appear to be responsible for the development of these false “thumbs” in both pandas, according to a 2017 research paper titled, Comparative genomics reveals convergent evolution between the bamboo-eating giant and red pandas (PNAS 114 (5) 1081-1086, January 17, 2017, https://doi.org/10.1073/pnas.1613870114), authored by a team led by conservation geneticist Professor Wei Fuwen, at the Chinese Academy of Sciences’ Institute of Zoology. Although the team already had access to the genome assembly of the giant panda, they managed to include more genetic sequencing data in their analysis. They also sequenced the genome of the red panda, for the first time ever. What they found after comparing the genomes of the red panda and the giant panda was electrifying:

[They] found 70 genes that showed evidence of convergent adaptation in both pandas.

Two such genes — DYNC2H1 and PCNT — play roles in limb development. In mice and humans, mutations in these genes have been found to cause polydactyly (extra digits) and abnormal skeletal development. These genes also encode amino acid changes in both pandas that are not found in other related mammalian species…

Professor Wei Fuwen and his team of researchers believe that it is these two genes that contribute to the development of false “thumbs” in both the red panda and the giant panda:

Among the 70 adaptively convergent genes, DYNC2H1 and PCNT are involved in limb development and their missense or null mutations result in a polydactyly phenotype and abnormal skeletogenesis in both mice and humans (25–28). These findings suggest that convergent amino acid substitutions in these genes may introduce subtle changes in the functional spectrum of focal proteins and consequently contribute to pseudothumb development in both pandas… We propose that convergent amino acid substitutions in the two genes may work synergistically for pseudothumb development in both pandas, although their effects on other aspects of skeletal development remain elusive.

In his acclaimed essay on the panda’s “thumb,” paleontologist Stephen Jay Gould (1941-2002) cited the work of the late vertebrate curator D. Dwight Davis, who had suggested in his monograph, The Giant Panda: A Morphological Study of Evolutionary Mechanisms (Chicago Natural History Museum, Chicago, 1964), that the increase in the size of the giant panda’s radial sesamoid bone (or false “thumb”), as well as the increase in size of its tibial sesamoid bone, “probably reflects a simple kind of genetic change” (Gould’s paraphrase). In Davis’s own words, “most of the differences between Ailuropoda [giant pandas] and the bears can be attributed to a few simple morphogenetic mechanisms.” Viewed in the light of the recent discoveries made by Professor Wei Fuwen and his team of researchers, Davis’ remarks appear startlingly prescient. It now seems that as few as two genes may have been involved in the evolution of the panda’s “thumb.” Indeed, the paper by Professor Wei Fuwen and his team explicitly cites the work of D. Dwight Davis and commends it:

In the present study, comparative genomics has revealed the signatures of adaptive protein convergence associated with digestive physiology and limb development, taking the first step toward confirming D. Dwight Davis’s genetic hypothesis for the pseudothumb (13).

In the interests of scientific accuracy, I would like to point out here that the pseudothumb in red pandas actually serves a dual function, assisting with both arboreal locomotion and bamboo eating. Indeed, Professor Wei Fuwen and his team readily acknowledge in their paper that in the red panda, “the pseudothumb also facilitates arboreal locomotion,” citing a 2006 paper by M.J. Salesa et al. (Evidence of a false thumb in a fossil carnivore clarifies the evolution of pandas, PNAS 103 (2) 379-382, December 30, 2005, https://doi.org/10.1073/pnas.050489910) describing the fossil of a newly discovered semi-arboreal red panda from the late Miocene epoch, Simocyon batalleri, which was carnivorous but which also possessed a false “thumb” and concluding:

Thus, it seems that, whereas the false thumb of the giant panda probably evolved for manipulating bamboo, the false thumbs of the red panda and of S. batalleri more likely evolved as an aid for arboreal locomotion, with the red panda secondarily developing its ability for item manipulation and thus producing one of the most dramatic cases of convergence among vertebrates.

Recent research involving a modular, biomimetic red panda paw conducted by Braden Barnett et al. (Mechanical Evidence for the Phylogenetic Origin of the Red Panda’s False Thumb as an Adaptation to Arboreal Locomotion, arXiv:2305.05086 [q-bio.PE], 8 May 2023) bears out this claim, as the authors contend in the conclusion of their paper:

The current length of the red panda’s thumbs allows them to grasp a wider range of diameters, in particular, those diameters that are representative of the branches they climb along. This result supports the theory that the red panda’s thumb is primarily adapted for arboreal locomotion, and only secondarily applied to food manipulation.

Barnett et al. are well aware of the evolutionary implications of their research. As they put it: “if the false thumbs of the two pandas are not related, then the red panda and giant panda represent a remarkable example of convergent evolution.”

(b) Further compelling evidence of convergent evolution: shared genes for digesting bamboo, and shared pseudogenes that were once used for tasting meat

The evidence I’ve presented will probably be enough to persuade most of my readers that the anatomical and genetic similarities between the giant panda and the red panda are the result of convergent evolution. But wait, there’s more! As the above-cited news article in AsianScientist points out, the red panda and giant panda also share genes that help them digest bamboo, and because they’re descended from carnivores, they both possess genes for tasting meat which are now no longer functional (i.e. pseudogenes):

Several other genes which show evidence of convergent adaptation are involved in protein digestion and vitamin uptake and metabolism; these may help pandas extract the maximum amount of sustenance from bamboo, which is nutrient-poor and difficult to digest.

The two pandas also share ten pseudogenes — genes that have been rendered non-functional over evolutionary time and that no longer encode working proteins. Notably, this included TAS1R1, which encodes a receptor that allows animals to taste the umami flavor in meat and other protein-rich foods. Both pandas evolved from meat-eating ancestors; this loss of function, say the authors, could be due to evolutionary constraints on the gene being relaxed as the animals shifted from carnivory to herbivory.

Further details regarding these ten shared pseudogenes can be found in the 2017 PNAS research paper by Professor Wei Fuwen and his team:

The selective relaxation of functional constraint on protein-coding genes may occur during the dietary shift and specialization of both pandas. Thus, we identified the signatures of pseudogenization in both pandas based on genome-wide comparison of these eight species. We identified 129 and 140 pseudogenes in giant and red pandas, respectively, among which 10 pseudogenes were shared (SI Appendix, Table S29). Interestingly, the umami taste receptor gene TAS1R1 has been pseudogenized in both pandas (Fig. 3), representing a remarkable scenario of genetic convergence. Umami is a critical taste sense for meat-eating animals that can perceive components of meat and other protein-rich foods through the umami taste receptor TAS1R1/TAS1R3 heterodimer (37). In the red panda, TAS1R1 has become a pseudogene because of one nucleotide deletion in the sixth exon, as confirmed by Sanger sequencing of three additional individuals (Fig. 3 and SI Appendix, Table S24), whereas the loss of function of TAS1R1 in the giant panda is due to three insertion/deletion mutations in the third and sixth exons, as reported (18, 38).

Summarizing their results, the authors discuss the evolutionary implications of their research:

These findings demonstrate that genetic convergence occurred at multiple levels spanning metabolic pathways, amino acid convergence, and pseudogenization, providing a fascinating example for genome-scale convergent evolution analysis of dietary shift and specialization.

At this stage, readers may be wondering, “What more proof do we need?” And they would be right. Vertebrate curator D. Dwight Davis, in his acclaimed monograph on the giant panda, made a bold prediction (cited by paleontologist Stephen Jay Gould in his essay on the panda’s “thumb”) which has been strikingly borne out, and to cap it all, it appears that the same genes that gave rise to the false “thumb” in the giant panda also gave rise to a false “thumb” in the red panda. Not only that, but the two animals, which are both bamboo eaters, share genes that help them digest bamboo, and have switched off ten genes that would have helped them taste meat – genes which their carnivorous ancestors would have needed, but which they no longer need. It is these ten pseudogenes that provide the most convincing refutation of the hypothesis that red pandas and giant pandas are products of an engineering process. Even if we grant that an engineer might use the same genes to produce a shared adaptation to bamboo eating in two very different animals, there is no good reason why an engineer would endow these animals with switched-off genes for meat-eating. On the other hand, if these animals were both (separately) descended from carnivores, then we have a ready explanation for why their genomes are littered with pseudogenes that were once used for meat-eating. Under this weighty mountain of evidence, who could resist drawing the conclusion that both animals evolved from carnivorous ancestors, developing adaptations that enables them to survive on bamboo?

How Professor Dilley’s position contrasts with that of a leading Intelligent Design theorist, Professor Michael Behe

Professor Michael Behe, a leading Intelligent Design proponent, readily acknowledges the strength of the evidence for the common ancestry of living organisms in his book, The Edge of Evolution (Free Press: New York, 2007). Commenting on the fact that humans and chimps share broken genes (pseudogenes) containing the same mistakes at the same positions in their DNA, Behe writes:

If a common ancestor first sustained the mutational mistakes and subsequently gave rise to those two modern species, that would very readily account for why both species have them now. It’s hard to imagine how there could be stronger evidence for common ancestry of both chimps and humans. (2007, pp. 71-72)

Behe, who is a leading Intelligent Design theorist, considers shared pseudogenes in identical locations in two species to be decisive evidence for their having evolved from a common ancestor. The red panda and the giant panda are not closely related, but they nonetheless share ten pseudogenes. Unlike the human and chimp pseudogenes discussed by Behe, which contain exactly the same mistakes, the pseudogenes shared by red pandas and giant pandas are broken in different ways in the two species. For instance, TAS1R1 became a pseudogene because of one nucleotide deletion in the red panda, as opposed to three insertion/deletion mutations in the giant panda. In their 2017 paper, Professor Wei Fuwen and his team conclude that convergent evolution is the best explanation for these changes: “Convergent pseudogenization of TAS1R1 in both pandas may be an evolutionary response to the dietary shift from carnivory and omnivory to herbivory.” And I don’t think Behe would dispute this conclusion, given his generous acknowledgement that “there’s no reason to doubt that Darwin had this point right, that all creatures on earth are biological relatives” (2007, p. 72). Moreover, in the frontispiece of his book, Behe appears to identify the family (rather than the species) as “the tentative edge of random evolution.” Given that the giant panda (unlike the red panda) belongs in the same family as other bears (Ursidae), I presume he would have no problem with affirming that the giant panda evolved naturally, and that no intelligent design was needed to account for its origin. (Red pandas belong in a family of their own.)

It is therefore mystifying that Professor Dilley, in his paper, “God, Gould, and the Panda’s Thumb” (Religions 2023, 14(8), 1006; https://doi.org/10.3390/rel14081006) chooses to critique Gould’s argument for evolution from the panda’s thumb, which he describes as “one of the most famous polemics for common ancestry,” on the grounds that it rests on a “theological claim.” To be clear, Dilley defines “evolution” solely in terms of common ancestry: “By ‘evolution’, I mean ‘common ancestry’, the view that all flora and fauna are the physical descendants of one (or a few) life forms that lived long ago.” In other words, for Dilley, “evolution” means not merely “common descent via unguided processes,” but rather “common descent via any process, guided or unguided.” This would include some forms of Intelligent Design. Although Dilley stresses that his intent is not to critique evolutionary theory as such, and that Gould’s argument for evolution is but one of many, he cannot resist a parting shot in his concluding paragraph: “More generally, from Darwin to Gould, atheists, agnostics, and theists have all contributed to theology-laden arguments for evolution.” In the body of his article, he even provides a list of names: “[L]ike Gould, a number of prominent biologists do offer theology-laden arguments for evolution, sometimes as their self-reported best stand-alone argument for the theory. These luminaries include Theodosius Dobzhansky, Niles Eldredge, Douglas Futuyma, Francisco Ayala, Jerry Coyne, Émile Zuckerkandl, Richard Dawkins, George Williams, Francis Collins, Kenneth Miller, and others.” One is tempted to ask: can Professor Dilley name any evolutionary thinker who, in his view, doesn’t offer a theology-laden argument for evolution?

Professor Dilley’s position here is in striking contrast with the position taken by Professor Michael Behe, for whom common descent is a trivial fact: “It says merely that commonalities were there from the start, present in a common ancestor” (2007, p. 72). What needs to be explained, however, is how these common features arose in the first place. Behe contends that any new control mechanism in organisms requiring three or more steps to set it up (for example, “two or three control proteins acting in concert”) can be reliably identified as a product of intelligent design (2007, p. 195, 198-199). His arguments have been heavily criticized, but he accepts common descent as a given.

How Professor Dilley saws off the branch he is sitting on

What is even more damaging to Professor Dilley’s case is that he undercuts his own conclusions in footnote 4 of his 2023 paper, where he writes:

There are a number of ways that the grounds for evolutionary theory extend beyond the scope of this article. For example, if it were demonstrated that complex biological systems, such as the bacterial flagellum or vertebrate eye, could be built by stepwise physical processes, then all things being equal, such data might be plausibly taken to confirm evolutionary theory over, say, intelligent design theory. Moreover, if the version of ID theory under consideration specifies a non-divine designer, rather than a supernatural designer, then theology-laden claims would not be required to argue in favor of evolution over intelligent design. Thus, in certain contexts, the grounds for evolution do not require God-talk. As such, the comprehensive case for evolution is in principle much broader than the particular theology-laden claims addressed in this essay. It is also notable that the standard definition of ‘evolutionary theory’ as ‘common descent brought about by the mutation-selection mechanism (and other natural processes)’ does not per se include theological content. The theory itself is not theology-laden (in the relevant sense) and, as just noted, in some contexts, arguments for it are likewise not theology-laden. Thus, one can speak coherently about evolutionary theory and some of its grounds in non-theological terms.

Two quick questions for Professor Dilley:

(1) Does he concede that Professor Michael Behe’s argument for the common ancestry of humans and chimps does not require making any theology-laden assumptions?

(2) Given that, as I demonstrated in Part One of my series “Was the panda’s ‘thumb’ designed?”, despite the brief theological references in Gould’s argument for evolution, the central point Gould is making – namely, that mere tinkering (i.e. a series of step-by-step natural changes involving the adaptation of pre-existing parts) does not warrant an inference to intelligent design, as it requires no foresight – makes no reference to a Deity of any sort, will he now acknowledge that at its core, Gould’s argument is free of theology-laden assumptions?

A Response to Professor Dilley’s final two articles at Evolution News and Views

In the light of the evidence I have presented above for the giant panda’s evolution, I can only marvel at Professor Dilley’s chutzpah in titling the fourth article in his five-part series, Does the Panda Argument Hurt the Case for Evolution? (April 10, 2024).

In a section of the article titled, “Gould and NOMA,” Professor Dilley argues that Gould’s use of the panda’s “thumb” to argue for evolution is at odds with his insistence that religion and science should not step on each other’s toes: they have non-overlapping magisteria. One tells us how to get to heaven; the other, how the heavens go. As Dilley puts it:

It is a crucial feature of Gould’s case that the “clumsy” thumb counts as evidence in favor of evolution over divine design…

But, of course, such an argument mixes science and theology. It uses a theology-laden premise in a scientific argument. Why might that be a problem? It is a problem because Gould himself claimed that such mixtures are verboten. He famously championed the doctrine of NOMA (non-overlapping magisteria)…

Gould cannot have it both ways: either theology-laden arguments are legitimate within scientific discourse or not. If he wants to retain his panda argument, he must jettison NOMA. Or, if he wants to retain NOMA, he must jettison the panda argument. The choice is binary.

I hope I have shown to the satisfaction of my readers that Gould’s argument has no need to invoke any theological premises. (See Part One of my series.) All the argument requires is an honest recognition of the fact that the panda’s “thumb” is a makeshift adaptation which is not (as far as scientists can tell) the product of engineering. That being the case, Dilley’s assertion that Gould must either jettison the panda argument or jettison NOMA is invalid.

In his final article for Evolution News and Views, titled, Gould’s Panda Argument Is a Problem for Atheistic and Agnostic Views (April 15, 2024), Professor Dilley attacks Gould for his narrow-minded theology. The following quote which is taken from his 2023 paper, conveys his point:

Gould’s theological claims are partisan. Gould does not borrow the tenets of his various creationist rivals to show on their own grounds that the facts of the natural world support evolution more than [their creationist views]. Instead, Gould imports his own positive intuitions about what a “sensible God” would do. In short, Gould’s theology is sectarian relative to a range of perspectives, including some, like young-earth creationism, that are heavily involved in origins discussions.

The response Gould could make here is that he is not concerned with the question of whether the panda’s thumb was ultimately produced by some intelligence (be it a Deity or otherwise), but rather, with the question of whether it is a product of engineering. The identity of the engineer is secondary. What his argument attempts to establish is that whatever produced the panda’s thumb, it wasn’t an engineer. If Gould’s argument succeeds, then we can rule out a Divine artificer – or an alien artificer, for that matter. This is not theological narrowness on Gould’s part; he is simply not interested in any other kind of Deity, as a Divine Artificer is the only kind of Deity about Whom one can make scientific predictions regarding its manner of designing. If people want to believe in some other sort of Deity, I presume Gould would have no quarrel with them.

The Catholic thinker (and later, Cardinal) John Henry Newman, in his letter to J. Walker of Scarborough on Darwin’s Theory of Evolution, dated May 22, 1868, wrote that he had no problems with living things having arisen via a blind, law-governed process which to us appears entirely accidental:

It does not seem to me to follow that creation is denied because the Creator, millions of years ago, gave laws to matter. He first created matter and then he created laws for it — laws which should construct it into its present wonderful beauty, and accurate adjustment and harmony of parts gradually. We do not deny or circumscribe the Creator, because we hold he has created the self acting originating human mind, which has almost a creative gift; much less then do we deny or circumscribe His power, if we hold that He gave matter such laws as by their blind instrumentality moulded and constructed through innumerable ages the world as we see it. If Mr Darwin in this or that point of his theory comes into collision with revealed truth, that is another matter — but I do not see that the principle of development, or what I have called construction, does. As to the Divine Design, is it not an instance of incomprehensibly and infinitely marvellous Wisdom and Design to have given certain laws to matter millions of ages ago, which have surely and precisely worked out, in the long course of those ages, those effects which He from the first proposed. Mr Darwin’s theory need not then to be atheistical, be it true or not; it may simply be suggesting a larger idea of Divine Prescience and Skill. Perhaps your friend has got a surer clue to guide him than I have, who have never studied the question, and I do not [see] that ‘the accidental evolution of organic beings’ is inconsistent with divine design — It is accidental to us, not to God.

If I understand Gould’s position correctly, he would have no quarrel with Newman’s God. The only God which Gould’s argument rules out is a God Who engineered living organisms, with all their complex parts, into existence. The panda’s “thumb” may (for all we know) have been foreseen and even approved (or at least, tolerated) by God, but whatever it is, it is still “a contraption, not a lovely contrivance.”

Does belief in the evolution of the human mind render theological reasoning impossible?

Elsewhere in his final article for Evolution News and Views, Professor Dilley appears to be invoking Alvin Plantinga’s Evolutionary Argument Against Naturalism, that if evolution and naturalism are both true, then human cognitive faculties must have evolved to produce beliefs that have survival value rather than beliefs that are true – which (according to Plantinga) implies that our belief in the truth of both evolution and naturalism is unwarranted, as neither belief has survival value. Here is how Professor Dilley expresses the argument, in his own words:

Are our minds able to reliably do theology? That is a very difficult question for a person who believes that our minds are the result of mindless processes aimed at survival and reproduction.

Clearly, natural selection has favored survival over truth when it comes to worldview-level beliefs. How then can atheists and agnostics trust the reliability of their brains when it comes to their own worldview-level beliefs?

…[I]f a person doesn’t believe in God, then there’s no one around to do the planning. This means that the human mind was not formed by a Being who wants to be understood and known, but rather by mindless processes that care nothing about theology. Yet it is precisely atheists and agnostics who sometimes have strong opinions about what God would or wouldn’t do in organic history!

In response: Gould was a self-professed agnostic, rather than a dogmatic atheist. (See here for a discussion of Gould’s religious views.) An agnostic does not have to trust the reliability of his brain when reasoning on theological matters. Indeed, the whole point of agnosticism is that we cannot do so. We can, however, reason reliably about engineers, and about what they would and wouldn’t do. Gould’s argument, if valid, implies that if there is a God, He is no engineer.

Gould could also point out that on an evolutionary account, we should expect that our minds are able to detect intentional agency, because that is what they evolved to do. For that reason, we might expect some false positives (mistaken identification of agents where there are none), but not false negatives. Consequently, if our top scientific minds tell us that the panda’s thumb doesn’t exhibit any of the hallmarks of intentional agency, it would be prudent of us to believe what they say.

Conclusion

My four-part series, “Was the panda7s ‘thumb’ designed?” can be summarized in three simple propositions:

1. Contrary to Professor Dilley’s claims, Gould’s argument for evolution based on the panda’s “thumb” can be formulated without reference to any theological claims; rather than being an argument about what God would or wouldn’t do, it is best understood as an argument about what an engineer would or wouldn’t do.

2. Contrary to Professor Dilley’s assertions, the case for pandas (and their “thumbs”) having evolved is an extremely powerful one.

3. The Intelligent Design community is a house divided: Professor Dilley’s position on evolution and common descent is diametrically at odds with that of leading ID thinker Professor Michael Behe. They need to get their story straight.

I shall lay down my pen here. Professor Dilley is welcome to respond, if he so chooses.