Daniel Fairbanks Cherry Picks Data On Pseudogenes To Prop Up Common Descent
|March 4, 2011||Posted by Jonathan M under Intelligent Design|
In two previous posts (here and here), I raised some objections to the first couple of chapters of Daniel Fairbanks’ 2010 book, Relics of Eden — The Powerful Evidence of Evolution in Human DNA. I encouraged Fairbanks and others to review all the evidence pertinent to the matter at hand. As impressive the array of arguments for common descent may superficially appear at first glance, with only a cursory reading of the relevant literature, upon closer inspection they invariably fall apart.
Given the demonstrable causal impotence of neo-Darwinism to account for the evolution of novel genes and proteins, new body plans, and radical innovations in form, I have thus in recent months become inclined to be rather sceptical of the stupendous claim that all extant taxa are derivative of a single progenitor or common ancestor. If no one can tell us how such evolution from a common ancestor could possibly have occurred, then how can we be so sure that it did occur? In such a case, one would need to marshall some very spectacular evidence for common descent in order to present a persuasive argument. Unfortunately for Darwinists, however, the evidence for common ancestry is paper thin on the ground.
Chapter three of Fairbanks’ book is concerned with pseudogenes, allegedly once-functional relics of our evolutionary heritage. As with all his other “evidences” for common ancestry, Fairbanks — once again — cherry picks all the seemingly confirmatory evidence, while hand-wavingly ignoring all the obvious counter-examples in the scientific literature. Let’s turn our attention to what he has to say.
Are Pseudogenes “Bogus Genes”?
Fairbanks tellingly entitles this chapter “Bogus Genes”, and effectively spends his first six pages re-iterating the old “junk DNA” party line. I do not want to spend much time discussing this, for it has no consequence on my argument. But it might be worth mentioning at this point that Fairbanks is actually wrong here. See, for example, this paper, published in Nature in June of last year (I blogged about it at the time here), in which Poliseno et al. reveal that, “PTENP1 — along with KRAS1P, the pseudogene of the gene KRAS, and potentially other pseudogenes — is not a non-functional relic, but a modulator of gene expression.” The authors of the paper discuss the observed interaction between the RNA encoding for the PTEN tumor suppressor gene and its corresponding pseudogene, PTENP1, demonstrating that this pseudogene acts as a tumor suppressor. A function was also assigned for the KRAS oncogene and the corresponding pseudogene, KRAS1P. As the authors explain,
We also demonstrate that pseudogenes such as PTENP1 can derepress their cognate genes, even when expressed at lower levels (Supplementary Fig. 3a and Fig. 2f–h). We propose that pseudogenesare “perfect decoys” for their ancestral genes, because they retain many of the miRNA binding sites and can compete for the binding of many miRNAs at once.
Typically when I start to talk about functionality for so-called “junk DNA” such as pseudogenes, Darwinists tell me that such instances are the exception rather than the rule, and that I am myself guilty of cherry-picking data. The practical trouble with this argument is that in no conversation am I usually able to discuss more than a handful of documented cases, and the critic is free to simply shift his or her ground with every cited instance, telling me that they still lay claim on the majority of these elements. Alas, I do not have the time or the will to go into all of the wealth of literature which has been accumulating in recent years regarding pseudogene functions. One way of overcoming this difficulty (i.e. the impracticality of discussing more than a few documented examples which leaves us open to the charge of cherry-picking) is to cite review literature. Review articles are great for providing overviews of the current literature and listing many pertinent references and citations in the process.
One such review paper appeared in the Annual Review of Genetics in 2003, authored by Balakirev and Ayala. The paper noted that,
Pseudogenes have been defined as nonfunctional sequences of genomic DNA originally derived from functional genes. It is therefore assumed that all pseudogene mutations are selectively neutral and have equal probability to become fixed in the population. Rather, pseudogenes that have been suitably investigated often exhibit functional roles, such as gene expression, gene regulation, generation of genetic (antibody, antigenic, and other) diversity. Pseudogenes are involved in gene conversion or recombination with functional genes. Pseudogenes exhibit evolutionary conservation of gene sequence, reduced nucleotide variability, excess synonymous over nonsynonymous nucleotide polymorphism, and other features that are expected in genes or DNA sequences that have functional roles. We first review the Drosophila literature and then extend the discussion to the various functional features identified in the pseudogenes of other organisms. A pseudogene that has arisen by duplication or retroposition may, at first, not be subject to natural selection if the source gene remains functional. Mutant alleles that incorporate new functions may, nevertheless, be favored by natural selection and will have enhanced probability of becoming fixed in the population. We agree with the proposal that pseudogenes be considered as potogenes, i.e., DNA sequences with a potentiality for becoming new genes.
Note that, for those without a subscription, the full PDF article can be downloaded here.
For further discussion of pseudogene function, see Casey Luskin’s discussion of the pseudogene misnomer here, where he notes that even pseudogenes which aren’t transcribed can serve important roles. See also my discussion of “junk RNA” here, in which I draw attention to a Nature news article which reports that “the polished rice peptides could also have implications for how we view pseudogenes, which have long been thought to be defunct relics of protein-coding genes. Pseudogenes often contain many signals that would stop protein synthesis and, as a result, could only encode short amino-acid chains. Maybe this would provide a new way for pseudogenes to have some sort of function.”
I could continue in a similar vein for some time. The bottom line, though, is that Fairbanks is simply wrong when he opts to write off all those pseudogene sequences as non-functional.
What Do Pseudogenes Tell Us About Human Evolution?
Fairbanks subsequently turns his attention to some examples of pseudogene evolution in humans, starting with the unitary pseudogene known as L-gulono-gamma-lactone Oxidase, or just ‘GULO’ for short. This gene ordinarily facilitates the biosynthesis of vitamin C, but in humans this seems to be a genuine case of a ‘broken gene’. This means that other mammals, such as dogs and cats, can have a diet which contains hardly any vitamin C (their bodies produce their own vitamin C). But in humans and all other primates, this gene is dysfunctional, which entails that we must intake vitamin C in order to survive.
Daniel Fairbanks offers the following argument for human/chimp shared ancestry:
Although this pseudogene is highly mutated and utterly useless, humans and chimpanzees have almost identical copies of it. The chimpanzee genome contains the same GULO pseudogene, in the same place in the DNA, and the chimpanzee and human versions are 98 percent identical. The same can be said for almost every other pseudogene in the human genome. With a few notable exceptions, chimpanzees and humans have the same pseudogenes in the same places, and they are, on average, about 98 percent similar.
Remarkably, in support of this, Fairbanks references a paper published in 2003 by Inai et al. in the Journal of Nutritional Science and Vitaminology. What is particularly astonishing about Fairbanks’ citation is that the paper also documents the presence of shared deletions and substitutions in the GULO pseudogene of both humans and guinea pigs! Given that humans and guinea pigs are thought to have diverged at the time of the common ancestor with rodents, if the mutations are truly random, a mutational difference between the rat and guinea pig should not be shared by humans. But many mutational differences were shared by humans. Inai et al. argued that this was indicative of mutation hotspots where certain types of mutations occur with a greater frequency. The paper calculates the likelihood of these same substitutions in both humans and guinea pigs to be 1.87 x 10^-12.
Population Geneticist, Reed A. Cartwright, attempts to evade this in an essay on the Panda’s Thumb website:
However, the sections quoted from Inai et al. (2003) suffer from a major methodological error; they failed to consider that substitutions could have occurred in the rat lineage after the splits from the other two. The researchers actually clustered substitutions that are specific to the rat lineage with separate substitutions shared by guinea pigs and humans. . .
If I performed the same analysis as Inai et al. (2003), I would conclude that there are ten positions where humans and guinea pigs experienced separate substitutions of the same nucleotide, otherwise known as shared, derived traits. These positions are 1, 22, 31, 58, 79, 81, 97, 100, 109, 157. However, most of these are shown to be substitutions in the rat lineage when we look at larger samples of species.
When we look at this larger data table, only one position of the ten, 81, stands out as a possible case of a shared derived trait, one position, 97, is inconclusive, and the other eight positions are more than likely shared ancestral sites. With this additional phylogenetic information, I have shown that the “hot spots” Inai et al. (2003) found are not well supported.
M.D. Sean D. Pitman has responded to this argument on his website. He writes,
It does indeed seems like a number of the sequence differences noted by Cartwright are fairly unique to the rat – especially when one includes several other species in the comparison. However, I do have a question regarding this point. It seems to me that there simply are too many loci where the rat is the only odd sequence out in Exon X (i.e., there are seven and arguably eight of these loci). Given the published estimate on mutation rates (Drake) of about 2 x 10-10 per loci per generation, one should expect to see only 1 or 2 mutations in the 164 nucleotide exon in question (Exon X) over the course of the assumed time of some 30 Ma (million years). Therefore, the argument of the mutational differences being due to mutations in the rat lineage pre-supposes a much greater mutation rate in the rat than in the guinea pig. The same thing is true if one compares the rat with the mouse (i.e., the rat’s evident mutation rate is much higher than that of the mouse).
This is especially interesting since many of the DNA mutations are synonymous. Why should essentially neutral mutations become fixed to a much greater extent in the rat gene pool as compared to the other gene pools? Wouldn’t this significant mutation rate difference, by itself, seem to suggest a mutationally “hot” region – at least in the rat?
Beyond this, several loci differences are not exclusive to the rat/mouse gene pools and therefore suggest mutational hotspots beyond the general overall “hotness” or propensity for mutations in this particular genetic sequence.
Some have noted that although the shared mutations may be the result of hotspots, there are many more mutational differences between humans and rats/guinea pigs as compared to apes. Therefore, regardless of hotspots, humans and apes are clearly more closely related than are humans and rats/guinea pigs.
The problem with this argument is that the rate at which mutations occur is related to the average generation time. Those creatures that have a shorter generation time have a correspondingly higher mutation rate over the same absolute period of time – like 100 years. Therefore, it is only to be expected that those creatures with relatively long generation times, like humans and apes, would have fewer mutational differences relative to each other over the same period of time relative to those creatures with much shorter generation times, like rats and guinea pigs.
What is interesting about many of these mutational losses is that they often share the same mutational changes. It is at least reasonably plausible then that the GULO mutation could also be the result of a similar genetic instability that is shared by similar creatures (such as humans and the great apes).
This same sort of thing is seen to a fairly significant degree in the GULO region. Many of the same regional mutations are shared between humans and guinea pigs…
Why would both humans and guinea pigs share major deletions of exons I, V and VI as well as four stop codons if these mutations were truly random? In addition to this, a mutant group of Danish pigs have also been found to show a loss of GULO functionality. And, guess what, the key mutation in these pigs was a loss of a sizable portion of exon VIII. This loss also matches the loss of primate exon VIII. In addition, there is a frame shift in intron 8 which results in a loss of correct coding for exons 9-12. This also reflects a very similar loss in this region in primates. That’s quite a few key similarities that were clearly not the result of common ancestry for the GULO region. This seems to be very good evidence that many if not all of the mutations of the GULO region are indeed the result of similar genetic instabilities and that are prone to similar mutations – especially in similar animals.
As an aside, many other genetic mutations that result in functional losses are known to commonly affect the same genetic loci in the same or similar manner outside of common descent. For example, achondroplasia is a spontaneous mutation in humans in about 85% of the cases. In humans achondroplasia is due to mutations in the FGFR2 gene. A remarkable observation on the FGFR2 gene is that the major part of the mutations are introduced at the same two spots (755 C->G and 755-757 CGC->TCT) independent of common descent. The short legs of the Dachshund are also due to the same mutation(s). The same allelic mutation has occurred in sheep as well.
I want to make an additional point here. Because the GULO pseudogene is tossed about a lot in these discussions, it might be tempting for one to view it as an isolated incident. Lest I fall vulnerable to the charge of cherry-picking, let me assure my readers that it is not. Let’s take a couple of other examples very briefly.
The human and sheep orthologous P2 pseudogene, for example, share a coincidental premature stop codon without the possibility of common evolutionary ancestry. In addition, one paper, published in the Journal of Molecular Biology and Evolution in 2002 serves to undermine the classic “nested hierarchy” party line, documenting the presence of urate oxidase (Uox) pseudogenes which share convergent ‘mistakes’, without common ancestry. In fact, members of the orang-gorilla-chimp-human clade share the codon 33 premature stop codon, while the one at codon 187 is to be found in humans, chimps and gorillas. Three others (codons 18, 167 and 197) are specific to only one primate. The paper actually reports that “[t]he nonsense mutation (TGA) at codon 107 is, however, more complicated than others. It occurs in the gorilla, the orangutan, and the gibbon, and therefore requires multiple origins of this nonsense mutation, [my emphasis]”
What, then, can we conclude? Thus far, we have examined three key pieces of “evidence” for the human/chimp shared ancestry (i.e. the chromosomal fusion evidence, the orthologous distribution of jumping genes, and shared ‘mistakes’ in pseudogenes) and have found the evolutionary model wanting. I can understand why many people sincerely believe common ancestry to be so well supported (there was a time in my ID-career when I thought this as well). I certainly don’t think they’re being dishonest. One has just to be careful that one reviews all the evidence as part of one’s evaluation. When one systematically and objectively reviews all the evidence, it seems to me that many of the arguments — which appear at first glance to corroborate common ancestry — fall apart upon further inspection.