Note: This is Part 5 in a series reviewing Jerry Coyne’s Why Evolution Is True. Read Part 1 here, Part 2 here, Part 3 here, and Part 4 here.

Darwin argued in The Origin of Species that the widespread occurrence of vestigial organs — organs that may have once had a function but are now useless — is evidence against creation. “On the view of each organism with all its separate parts having been specially created, how utterly inexplicable is it that organs bearing the plain stamp of inutility … should so frequently occur.” But such organs, he argued, are readily explained by his theory: “On the view of descent with modification, we may conclude that the existence of organs in a rudimentary, imperfect, and useless condition, or quite aborted, far from presenting a strange difficulty, as they assuredly do on the old doctrine of creation, might even have been anticipated in accordance with the views here explained.”²⁵

In The Descent of Man, Darwin cited the human appendix as an example of a vestigial organ. But Darwin was mistaken: The appendix is now known to be an important source of antibody-producing blood cells and thus an integral part of the human immune system. It may also serve as a compartment for beneficial bacteria that are needed for normal digestion. So the appendix is not useless at all.²⁶

In 1981, Canadian biologist Steven Scadding argued that although he had no objection to Darwinism, “vestigial organs provide no evidence for evolutionary theory.” The primarily reason is that “it is difficult, if not impossible, to unambiguously identify organs totally lacking in function.” Scadding cited the human appendix as an organ previously thought to be vestigial but now known to have a function. Another Canadian biologist, Bruce Naylor, countered that an organ with some function can still be considered vestigial. Furthermore, Naylor argued, “perfectly designed organisms necessitated the existence of a creator,” but “organisms are often something less than perfectly designed” and thus better explained by evolution. Scadding replied: “The entire argument of Darwin and others regarding vestigial organs hinges on their uselessness and inutility.” Otherwise, the argument from vestigiality is nothing more than an argument from homology, and “Darwin treated these arguments separately recognizing that they were in fact independent.” Scadding also objected that Naylor’s “less than perfectly designed” argument was “based on a theological assumption about the nature of God, i.e. that he would not create useless structures. Whatever the validity of this theological claim, it certainly cannot be defended as a scientific statement, and thus should be given no place in a scientific discussion of evolution.”²⁷

In Why Evolution Is True, Coyne (like Darwin) cites the human appendix as an example of a vestigial organ. Unlike Darwin, however, Coyne concedes that “it may be of some small use. The appendix contains patches of tissue that may function as part of the immune system. It has also been suggested that it provides a refuge for useful gut bacteria. But these minor benefits are surely outweighed by the severe problems that come with the human appendix.” In any case, Coyne argues, “the appendix is still vestigial, for it no longer performs the function for which it evolved.”²⁸

As Scadding had pointed out nearly thirty years ago, however, Darwin’s argument rested on lack of function, not change of function. Furthermore, if vestigiality were redefined as Coyne proposes, it would include many features never before thought to be vestigial. For example, if the human arm evolved from the leg of a four-footed mammal (as Darwinists claim), then the human arm is vestigial. And if (as Coyne argues) the wings of flying birds evolved from feathered forelimbs of dinosaurs that used them for other purposes, then the wings of flying birds are vestigial. This is the opposite of what most people mean by “vestigial.”²⁹

Coyne also ignores Scadding’s other criticism, arguing that whether the human appendix is useless or not, it is an example of imperfect or bad design. “What I mean by ‘bad design’,” Coyne writes, “is the notion that if organisms were built from scratch by a designer–one who used the biological building blocks or nerves, muscles, bone, and so on–they would not have such imperfections. Perfect design would truly be the sign of a skilled and intelligent designer. Imperfect design is the mark of evolution; in fact, it’s precisely what we expect from evolution.”³⁰

An even better example of bad design, Coyne argues, is the prevalence of “dead genes.” According to the modern version of Darwinism that Coyne defends, DNA carries a genetic program that encodes proteins that direct embryo development; mutations occasionally alter the genetic program to produce new proteins (or change their locations); and natural selection then sorts those mutations to produce evolution. In the 1970s, however, molecular biologists discovered that most of our DNA does not encode proteins. In 1972 Susumu Ohno called this “junk,” and in 1976 Richard Dawkins wrote: “A large fraction of the DNA is never translated into protein. From the point of view of the individual organism this seems paradoxical. If the ‘purpose’ of DNA is to supervise the building of bodies, it is surprising to find a large quantity of DNA which does no such thing.” From the point of view of Darwinian evolution, however, there is no paradox. “The true ‘purpose’ of DNA is to survive, no more and no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA.”³¹

Like Dawkins, Coyne regards much of our DNA as parasitic. He writes in Why Evolution Is True: “When a trait is no longer used, or becomes reduced, the genes that make it don’t instantly disappear from the genome: evolution stops their action by inactivating them, not snipping them out of the DNA. From this we can make a prediction. We expect to find, in the genomes of many species, silenced, or ‘dead,’ genes: genes that once were useful but are no longer intact or expressed. In other words, there should be vestigial genes. In contrast, the idea that all species were created from scratch predicts that no such genes would exist.” Coyne continues:

Thirty years ago we couldn’t test this prediction because we had no way to read the DNA code. Now, however, it’s quite easy to sequence the complete genome of species, and it’s been done for many of them, including humans. This gives us a unique tool to study evolution when we realize that the normal function of a gene is to make a protein–a protein whose sequence of amino acids is determined by the sequence of nucleotide bases that make up the DNA. And once we have the DNA sequence of a given gene, we can usually tell if it is expressed normally–that is, whether it makes a functional protein–or whether it is silenced and makes nothing. We can see, for example, whether mutations have changed the gene so that a usable protein can no longer be made, or whether the ‘control’ regions responsible for turning on a gene have been inactivated. A gene that doesn’t function is called a pseudogene. And the evolutionary prediction that we’ll find pseudogenes has been fulfilled–amply. Virtually every species harbors dead genes, many of them still active in its relatives. This implies that those genes were also active in a common ancestor, and were killed off in some descendants but not in others. Out of about thirty thousand genes, for example, we humans carry more than two thousand pseudogenes. Our genome–and that of other species–are truly well populated graveyards of dead genes.³²

But Coyne is dead wrong.

Evidence pouring in from genome-sequencing projects shows that virtually all of an organism’s DNA is transcribed into RNA, and that even though most of that RNA is not translated into proteins, it performs essential regulatory functions. Every month, science journals publish articles describing more such functions. And this is not late-breaking news: The evidence has been accumulating since 2003 (when scientists finished sequencing the human genome) that “pseudogenes” and other so-called “junk DNA” sequences are not useless after all.³³

Why Evolution Is True ignores this enormous body of evidence, which decisively refutes Coyne’s Darwinian prediction that our genome should contain lots of “dead” DNA. It’s no wonder that Coyne falls back again and again on the sort of theological arguments that Scadding wrote “should be given no place in a scientific discussion of evolution.”

Notes

²⁵ Darwin, The Origin of Species, Chapters XIV (p. 402) and XV (p. 420). Available online (2009) here.
²⁶ Darwin, Charles. The Descent of Man, First Edition (London: John Murray, 1871), Chapter I (p. 27). Available online (2009) here.
Kohtaro Fujihashi, J.R. McGhee, C. Lue, K.W. Beagley, T. Taga, T. Hirano, T. Kishimoto, J. Mestecky & H. Kiyono, “Human Appendix B Cells Naturally Express Receptors for and Respond to Interleukin 6 with Selective IgA1 and IgA2 Synthesis,” Journal of Clinical Investigations 88 (1991): 248-252. Available online (2009) here.
J.A. Laissue, B.B. Chappuis, C. Müller, J.C. Reubi & J.O. Gebbers, “The intestinal immune system and its relation to disease,” Digestive Diseases (Basel) 11 (1993): 298-312. Abstract available online (2009) here.
Loren G. Martin, “What is the function of the human appendix?” Scientific American (October 21, 1999), Available online (2009) here.
R. Randal Bollinger, Andrew S. Barbas, Errol L. Bush, Shu S. Lin & William Parker, “Biofilms in the large bowel suggest an apparent function of the human vermiform appendix,” Journal of Theoretical Biology 249 (2007): 826-831. Available online (2009) here.
Duke University Medical Center, “Appendix Isn’t Useless At All: It’s A Safe House For Good Bacteria,” ScienceDaily (October 8, 2007). Available online (2009) here.
²⁷ Steven R. Scadding, “Do ‘vestigial organs’ provide evidence for evolution?” Evolutionary Theory 5 (1981): 173-176.
Bruce G. Naylor, “Vestigial organs are evidence of evolution,” Evolutionary Theory 6 (1982): 91-96.
Steven R. Scadding, “Vestigial organs do not provide scientific evidence for evolution,” Evolutionary Theory 6 (1982): 171-173.
²⁸ Coyne, Why Evolution Is True, pp. 61-62.
²⁹ Coyne, Why Evolution Is True, p. 46.
³⁰ Coyne, Why Evolution Is True, pp. 81.
³¹ Susumu Ohno, “So much ‘junk’ DNA in our genome,” Brookhaven Symposia in Biology 23 (1972): 366-70.
Richard Dawkins, The Selfish Gene (New York: Oxford University Press, 1976), p. 47.
³² Coyne, Why Evolution Is True, pp. 66-67.
³³ A few of the many scientific articles published since 2003 that document the function of so-called “junk” DNA are:
E.S Balakirev & F.J. Ayala, “Pseudogenes: are they ‘junk’ or functional DNA?” Annual Review of Genetics 37 (2003): 123-151.
A. Hüttenhofer, P. Schattner & N. Polacek, “Non-coding RNAs: hope or hype?” Trends in Genetics 21 (2005): 289-297.
J.S. Mattick & I.V. Makunin, “Non-coding RNA,” Human Molecular Genetics 15 (2006): R17-R29.
R.K. Slotkin & R. Martienssen, “Transposable elements and the epigenetic regulation of the genome,” Nature Reviews Genetics 8 (2007): 272-285.
P. Carninci, J. Yasuda & Y Hayashizaki, “Multifaceted mammalian transcriptome,” Current Opinion in Cell Biology 20 (2008): 274-80.
C.D. Malone & G.J. Hannon, “Small RNAs as Guardians of the Genome,” Cell 136 (2009): 656–668.
C.P. Ponting, P.L. Oliver & W. Reik, “Evolution and Functions of Long Noncoding RNAs,” Cell 136 (2009): 629–641.