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Pseudogenes Are Going the Way of Darwin’s “Rudimentary Organs”

Long described as useless leftovers of evolution, pseudogenes are rising from the junk pile as functional entities — so much so, that scientists think a change in terminology is needed.

Wikipedia can be counted on to parrot the Darwinian view. Here’s what they say about pseudogenes:

Gene duplication generates functional redundancy and it is not normally advantageous to carry two identical genes. Mutations that disrupt either the structure or the function of either of the two genes are not deleterious and will not be removed through the selection process. As a result, the gene that has been mutated gradually becomes a pseudogene and will be either unexpressed or functionless. This kind of evolutionary fate is shown by population genetic modeling and also by genome analysis. According to evolutionary context, these pseudogenes will either be deleted or become so distinct from the parental genes so that they will no longer be identifiable. Relatively young pseudogenes can be recognized due to their sequence similarity. [Emphasis added.]

It’s safe to say that many Darwin skeptics have felt intimidated by this apparent genetic evidence for evolution, not sure what to make of it or how to fit it into their own perspective. Prominent Darwin defenders like Kenneth Miller, meanwhile, trumpeted pseudogenes as prima facie evidence against intelligent design. “The human genome is littered with pseudogenes,” he wrote in 1994. Pointless junk like this “cannot be attributed to anything that resembles intelligent design.” He even characterized ID as a “retreat back to into an unknowledge of biology that is unworthy of the scientific spirit of this century” (Life’s Grand Design).

Evidence Against Design?

Hints of unease with the conventional view appear, however, lower down in the Wikipedia article, where an unknown redactor admits that some pseudogenes have been mislabeled, and others appear to have functions. In his book The Myth of Junk DNA, Jonathan Wells wrote extensively about pseudogenes, setting the stage by quoting Miller, Dawkins, Futuyma, Coyne, Avise, Shermer, and even theistic evolutionist Francis Collins. All point to pseudogenes as evidence against design and evidence confirming evolution. In 2009, Jerry Coyne boasted:

[T]he evolutionary prediction that we would 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 and not others…. Our genome — and that of other species — are truly well-populated graveyards of dead genes.

Wells devotes a whole chapter to the subject, noting that at the time of writing in 2011, evidence was accumulating that so-called pseudogenes were expressed and had functions, such as enhancing gene expression, acting as decoys, and conducting RNA interference. The fact that many are highly conserved, he wrote, also showed that they should be considered candidates for exploring unknown functions.

Paradigm Shift

An important paradigm shift was announced in Nature Reviews Genetics this past December. In their paper “Overcoming challenges and dogmas to understand the functions of pseudogenes,” Seth W. Cheetham, Geoffrey J. Faulkner, and Marcel E. Dinger say the time has come to reconsider these bits of code that were long dismissed as junk. The authors do not acknowledge or credit Jonathan Wells or any other ID advocate, as is so typical of Darwin dogmatists. Nevertheless, this could represent a major turning point in thinking by the secular evolutionist community. See an article at Evolution News, “Nature Reviews Genetics — Pseudogene Function Is ‘Prematurely Dismissed,’” for more detail on the significance of this paper.

Given the current environment in academia, a better admission that “Wells was right” could hardly be wished for. But of course, the new paradigm will help understand the “evolutionary origins” of pseudogenes, they say. Whatever. Let them sigh at their disappearing evidence a little longer.

Par for the Course

Pseudogenes and the “junk DNA” myth are not the only times evolutionists have mislabeled phenomena they did not understand. There are at least three other examples that could be cited. One central proof for unguided evolution that was offered for decades was “vestigial organs,” a variation on the junk-DNA myth. The evolutionary process supposedly littered our bodies with useless organs from our animal ancestry, just as it littered our cells with useless genes.

So ingrained was this idea of vestigial organs, it was common thinking among biologists for a century. Darwin started it, calling them “rudimentary organs” in both the Origin and The Descent of Man. He considered them difficulties for a design view, and predictions of natural selection. Robert Weidersheim made it his life’s work to catalog these evolutionary leftovers. In 1895, he published a list of over 100 body parts he deemed useless and non-functional. His list included the appendix, tonsils, wisdom teeth, and the coccyx. Even as late as the 1960s, tonsils were routinely removed from children on the grounds that they are unnecessary. When inflamed by infection, they can be harmful, but today’s family doctors know that, as part of the immune system, they are best left intact. Similarly, the appendix can be life-threatening when inflamed; but only within the last two decades have scientists come to realize that the appendix serves a vital function — that of “rebooting” the gut biota after diarrhea. Marcos Eberlin has made this point in his book Foresight and on a podcast for ID the Future. Similarly, wisdom teeth are best left in unless they are impacted. Some have argued that bad diet is behind our problems with third molars, not the supposition that the human jaw was shrinking and had no room for them, as Darwinians contended. And for sure, no one would want to sit down without a coccyx or tailbone! Important muscles are anchored to them, including muscles for elimination and childbirth.

Weidersheim’s list of vestigial organs has shrunk to very few today. He had included organs like the pituitary gland, spleen, and thymus gland whose vital functions were discovered later. Evolutionists should have deduced that the argument was flawed anyway; why would natural selection pay the energy cost of keeping useless organs around? The same applies to “junk DNA” — it makes no sense for a cell to keep copying and reading junk. And what is meant by “vestigial” in the first place? Humans can live without fingers, arms, and legs; are those vestigial? Some parts change during life history; they may be important in the embryo and then atrophy in the adult, or become functional after puberty, but are not “vestigial” at other times. Determining what constitutes a function can be subjective. On the whole, the vestigial organs argument is slippery: natural selection predicts many vestiges, but also predicts few vestiges. 

Breaking the Biogenetic Law

The doctrine of vestigial organs overlaps with Haeckel’s “Biogenetic Law” of recapitulation, which basically does the same thing: sends scientists looking for vestiges of evolution in the embryo. But again, why would natural selection pay the cost of keeping useless vestiges of a supposed evolutionary past around for millions of years, generation after generation, if they perform no service to the organism? Jonathan Wells deals with this myth extensively in his books Icons of Evolution and Zombie Science, so readers are encouraged to go there to learn about the rise and fall of Haeckel’s recapitulation theory (which Darwin considered highly significant). Suffice it to say that this dead doctrine still lurks about in some textbooks today.

Vestigial Races

Pursuing the Darwinian myth of non-functionality to the extreme, evolution has also rendered the verdict “junk” on whole groups of organisms. Some of the worst atrocities of the 20th century came from this attitude that spawned eugenics. Undesirable groups have been judged defectives, imbeciles, or “useless eaters.” Do you see the connection with pseudogenes? Underlying all of these damnable doctrines — eugenics, recapitulation theory, vestigial organs, junk DNA and now pseudogenes — is Darwin’s myth of progress, which leaves behind the losers strewn across the battleground in the unending war for survival of the fittest. The awful outcome is depicted in the award-winning documentary short by Discovery Institute’s John West, “The Biology of the Second Reich: Social Darwinism and the Origins of World War I.”

Lessons from History

With Darwin’s suggestion that biology might be littered with useless remnants of natural selection, his disciples went on a wild goose chase to look for them. They weren’t trying to explain the existence of these features; they were looking to support Darwin’s hunch. Once his hunch about evolutionary leftovers became established as a doctrinaire assumption, it became an excuse for scientific laziness. Leftovers could be explained away rather than explained. Who wants to rummage through junk? In each case, history since Darwin has rendered each assumption false. These assumptions delayed significant discoveries, and far worse: they justified horrific atrocities committed in the name of “fitness.”

A proper scientific endeavor should approach a phenomenon by asking what it is there for, not what trash it represents that has been left behind. ID theory is better positioned philosophically and ethically to approach future biological questions, because it assumes “innocent till proven guilty beyond a reasonable doubt.” If something works, it’s not happening by accident. Chance accidents do occur, rendering some genes defective, some organs atrophied, and some individuals disabled. These exceptions prove the rule. They show the harm that results from unguided natural processes. As Michael Egnor wrote here yesterday, “Chance can’t happen — the word has no meaning — in an entirely accidental world. Chance presupposes design.”

Disabilities occur against the backdrop not of a battlefield, but of an interrelated, well-designed community, in which every individual has value as part of a tapestry of design and beauty that arouses awe. If parts of the tapestry are not yet understood, they deserve investigation, not dismissal.

Photo: Charles Darwin in 1855, by Maull and Polyblank, Literary and Scientific Portrait Club, via Wikimedia Commons.