In a recent article, I criticised Daniel Fairbanks for his selective disclosure of relevant evidence with regards to the chromosomal fusion evidence for human/chimp shared ancestry. In this article, I want to consider Fairbanks’ central argument in chapter 2 of his book (Relics of Eden — The Powerful Evidence of Evolution in Human DNA), in which he covers jumping genes (transposable elements). In regard to this topic, as we shall learn in due course, Fairbanks not only applies his reasoning inconsistently, but conveniently omits to inform his readers of those papers which (a) serve to substantially undermine his core thesis, and (b) provide extremely potent counter-examples to much of the evidence which he marshalls in defense of it.
What Do Transposable Elements Tell Us About Human Evolution?
Take careful notice of how Fairbanks reasons:
Even more than transposons, retroelements offer intriguing glimpses into our evolutionary past. They can insert themselves anywhere in our DNA and tend to remain stuck in place. The chance of two retroelements independently inserting themselves into exactly the same position in the genome in two different individuals is exceptionally small. It follows that if two individuals have a retroelement at exactly the same location, they must have inherited that retroelement from a common ancestor.
Before we come to examine the strength of this argument in the context of current scientific research, let’s take a moment or two to consider a logical inconsistency which perpetually plagues modern Darwinian reasoning. Fairbanks has effectively excluded the chance hypothesis on the grounds that “The chance of two retroelements independently inserting themselves into exactly the same position in the genome in two different individuals is exceptionally small.” And, indeed, if the process of integration is random (that is to say, not considerably constrained) then Fairbanks is correct here. Though this conclusion is predicated on an assumption which — as we will soon find out — there is good reason to believe to be false, I submit that Fairbanks is being both selective and inconsistent in his utilisation of standards here, on at least two counts.
Firstly, according to the Darwinian story, many remarkable events have elapsed in life’s history, the attribution-to-chance of which seems extremely inappropriate — but Fairbanks and other neo-Darwinians maintain that they happened by chance anyway, almost on a routine basis. One obvious case in point is instances of extreme molecular convergence (where complex features evolve more than once independently). Examples include the remarkable independent evolution of bat and whale echolocation systems and the uncannily apparent independent evolution of similar DNA biosynthesis mechanisms in eubacteria and archaea. I could list dozens of other such examples, and biochemist Fazale Rana has done just that in chapter 21 of the recently published book, The Nature of Nature — Examining The Role of Naturalism in Science (an excellent read, by the way!). Since many complex adaptations seem to have popped up multiple and independent times over the history of life on earth, and since neo-Darwinians don’t seem prepared to accept a non-coincidental explanation of these complex and immensely improbable features, I submit that we have a double standard at play.
The second inconsistency which is worthy of note is Fairbanks’ justification for rejecting the chance hypothesis. As he notes, given the assumption that mobile element insertion is essentially a random process, the probability of two identical independent locus-specific insertions is immensely improbable. But the odds of these elements integrating into the same locus is no more improbable than the two elements integrating into any given two loci, whether they integrate into the same locus or not. The reason why Fairbanks (again, given his assumption) justifiably rejects the chance hypothesis is not only because of the immense improbability of such an event occurring, but also because of a second factor — specificity. Fairbanks justifiably reasons that the observed pattern is unlikely to have arisen from two independent insertion events because of the presence of — wait for it — specified complexity. He thus favours common ancestry, which does not require that two elements independently inserted themselves independently into the same locus by a random process. So why all the fuss when ID proponents reason in a similar fashion?
But be that as it may. Now, let’s turn to an examination of the substance of Fairbanks’ argument for common descent, and assess whether it really holds water. On what assumption is Fairbanks’ conclusion based? His thesis is predicated on the supposition that retroelement insertion is essentially random — or at least sufficiently so as to rule out the independent-insertion hypothesis. Is Fairbanks correct? Actually, no. He isn’t. Consider, for example, this paper by Levy et al. which featured in the journal Nucleic Acids Research in late 2009. The paper’s abstract reports,
Throughout evolution, eukaryotic genomes have been invaded by transposable elements (TEs). Little is known about the factors leading to genomic proliferation of TEs, their preferred integration sites and the molecular mechanisms underlying their insertion. We analyzed hundreds of thousands nested TEs in the human genome, i.e. insertions of TEs into existing ones. We first discovered that most TEs insert within specific ‘hotspots’ along the targeted TE. In particular, retrotransposed Alu elements contain a non-canonical single nucleotide hotspot for insertion of other Alu sequences. We next devised a method for identification of integration sequence motifs of inserted TEs that are conserved within the targeted TEs. This method revealed novel sequences motifs characterizing insertions of various important TE families: Alu, hAT, ERV1 and MaLR. Finally, we performed a global assessment to determine the extent to which young TEs tend to nest within older transposed elements and identified a 4-fold higher tendency of TEs to insert into existing TEs than to insert within non-TE intergenic regions. Our analysis demonstrates that TEs are highly biased to insert within certain TEs, in specific orientations and within specific targeted TE positions. TE nesting events also reveal new characteristics of the molecular mechanisms underlying transposition. [Emphasis Mine]
The researchers documented that these transposable elements routinely preferentially insert into certain classes of already-present transposable elements, and do so with a specific orientation and at specific locations within the mobile element sequence.
But there’s more.
Another paper, appearing in Science at around the same time, documented that, in the water flea genome, introns appear to have been integrated repeatedly into the same loci in different genomes. This led the internationally-acclaimed evolutionary biologist Michael Lynch to note, “Remarkably, we have found many cases of parallel intron gains at essentially the same sites in independent genotypes. This strongly argues against the common assumption that when two species share introns at the same site, it is always due to inheritance from a common ancestor.”
I could continue in a similar vein for some time. For good measure, here’s another paper from PNAS (published in 2000) which explains (with further literature citations) that,
“It has long been appreciated that P elements insert nonrandomly; however, the factors that influence this specificity are not well understood. There is an apparent preference for chromosomal sites that are likely to be accessible in chromatin; euchromatic sites are favored over heterochromatic sites, interbands appear to be favored over bands, and there is a marked tendency to integrate at the 5′-end of genes. Local sequence composition at the site of insertion also appears to play a role. O’Hare and Rubin examined the sequences flanking 18 P element insertions and oted that the 8-bp target sequence that is duplicated on insertion is GC rich.”
Daniel Fairbanks goes on to cite three studies which he thinks constitute good evidence for human/chimp shared ancestry. Let’s look at each in turn.
The first study cited by Fairbanks is concerned with the DNA surrounding a set of genes that encode haemoglobin, documenting the presence of several Alu elements occupying the same places in the same orientations in both species. I have already cited one paper which documents Alu integration preferences. For good measure, let’s throw in another. This paper suggests that,
…a common mechanism exists for the insertion of many repetitive DNA families into new genomic sites. A modified mechanism for site-specific integration of primate repetitive DNA sequences is provided which requires insertion into dA-rich sequences in the genome. This model is consistent with the observed relationship between galago Type II subfamilies suggesting that they have arisen not by mere mutation but by independent integration events.
Or how about yet another paper which was published in the journal, Genetics in 2001? It documents that,
We have identified two hot spots for SINE insertion within mys-9 and at each hot spot have found that two independent SINE insertions have occurred at identical sites. These results have major repercussions for phylogenetic analyses based on SINE insertions, indicating the need for caution when one concludes that the existence of a SINE at a specific locus in multiple individuals is indicative of common ancestry. Although independent insertions at the same locus may be rare, SINE insertions are not homoplasy-free phylogenetic markers. [Emphasis Mine]
The second example which Fairbanks gives is HERV-K, a viruslike retroelement which apparently entered the genome of a common ancestor of humans, apes and monkeys tens of millions of years ago. He cites a study which attempts to construct a phylogenetic tree of humans, chimpanzees, gorillas, orangutans, gibbons, Old World monkeys and New World monkeys based on the presence or absence of the HERV-K element in their respective genomes. The problem? One paper appearing in PNAS in 2005 reports on the convergence of specific ERV sequences in humans and mice:
Together, these data strongly argue for a critical role of syncytin-A and -B in murine syncytiotrophoblast formation, thus unraveling a rather unique situation where two pairs of endogenous retroviruses, independently acquired by the primate and rodent lineages, would have been positively selected for a convergent physiological role. [emphasis added]
Given that out of 30,000 ERVs only 7 of them are known to have integrated at the same locus in humans and chimps, the fact that there is such site preference at all radically undermines the common assumption that these ERV sequences represent potent evidence for common descent.
Then there are, of course, the inconsistent phylogenies. One further paper, appearing in Current Biology in 2001, tells us that,
We identified a human endogenous retrovirus K (HERV-K) provirus that is present at the orthologous position in the gorilla and chimpanzee genomes, but not in the human genome. Humans contain an intact preintegration site at this locus. [Emphasis Mine]
The intact pre-integration site at the locus precludes the possibility of the ERV being subsequently somehow removed from the pertinent locus in the human genome by a process of genetic recombination.
Finally, Fairbanks focuses his discussion on a duplicated segment of DNA with Alu elements on both ends. He notes that humans and chimpanzees have two copies of the CMT1A segment at exactly the same locus in their genome. However, the gorilla and orangutan genomes each have only one copy of the GMT1A segment, in the same position as one of the CMT1A segments in humans and chimpanzees. This might have been a semi-persuasive argument, were it not for the fact that it cherry picks data — again. Quite apart from the numerous evidence which now militates against common descent (not least of which is the sheer lack of a viable naturalistic mechanism to account for it), phylogenetic tree construction based on shared genes is notoriously inconsistent (see here for why). To cut a long story short, it categorically ignores all the genetic evidence which points to different phylogenies.
Are Transposable Elements Useful?
Fairbanks closes chapter 2 by treating his readers to a discussion of “junk DNA”, alleging that “[transposable elements] are useless and, currently, harmless relics of evolution.” To his credit, he does cite one instance of functionality documented in PNAS in 2004, but largely dismisses the rest as “junk DNA”. See Jonathan Wells’ short literature survey over on Evolution News & Views, which should lay this myth to rest. See also Jonathan Wells’ response to Matheson, Hunt and Moran on “junk DNA” here. See also Richard Sternberg’s comments on functions of SINE elements here, here, here and here.
In general, SINEs (and thus Alus) allow genetic information to be retrieved in multiple different ways from the same DNA data files depending on the specific needs of different cell types or tissues (in different species-specific contexts). In particular, Alu sequences perform many taxon-specific lower-level genomic formatting functions such as: (1) providing alternative start sites for promoter modules in gene expression–somewhat like sectoring on a hard drive (Faulkner et al., 2009; Faulkner and Carninci, 2009); (2) suppressing or “silencing” RNA transcription (Trujillo et al., 2006); (3) dynamically partitioning one gene file from another on the chromosome (Lunyak et al., 2007); (4) providing DNA nodes for signal transduction pathways or binding sites for hormone receptors (Jacobsen et al., 2009; Laperriere et al., 2004); (5) encoding RNAs that modulate transcription (Allen et al., 2004; Espinoza et al., 2004; Walters et al., 2009); and (6) encoding or regulating microRNAs (Gu et al., 2009; Lehnert et al., 2009).
In addition to these lower-level genomic formatting functions, SINEs (including Alus) also perform species-specific higher-level genomic formatting functions such as: (1) modulating the chromatin of classes of GC-rich housekeeping and signal transduction genes (Grover et al., 2003, 2004; Oei et al., 2004; see also Eller et al., 2007); (2) “bar coding” particular segments for chromatin looping between promoter and enhancer elements (Ford and Thanos, 2010); (3) augmenting recombination in sequences where Alus occur (Witherspoon et al., 2009); and (4) assisting in the formation of three-dimensional chromosome territories or “compartments” in the nucleus (Kaplan et al., 1993; see also Pai and Engelke, 2010).
Moreover, Alu sequences also specify many species-specific RNA codes. In particular, they provide: (1) signals for alternative RNA splicing (i.e., they generate multiple messenger RNAs from the same type of precursor transcript) (Gal-Mark et al., 2008; Lei and Vorechovsky, 2005; Lev-Maor et al., 2008) and (2) alternative open-reading frames (exons) (Lev-Maor et al., 2007; Lin et al., 2008; Schwartz et al., 2009). Alu sequences also (3) specify the retention of select RNAs in the nucleus to silence expression (Chen et al., 2008; Walters et al., 2009); (4) regulate the RNA polymerase II machinery during transcription (Mariner et al., 2008; Yakovchuk et al., 2009; Walters et al., 2009); and (5) provide sites for Adenine-to-Inosine RNA editing, a function that is essential for both human development and species-specific brain development (Walters et al., 2009).
Contrary to Ayala’s claim, Alu sequences (and other mammalian SINEs) are not distributed randomly but instead manifest a similar “bar-code” distribution pattern along their chromosomes (Chen and Manuelidis, 1989; Gibbs et al., 2004; Korenberg and Rykowski, 1988). Rather like the distribution of the backslashes, semi-colons and spaces involved in the formatting of software code, the “bar-code” distribution of Alu sequences (and other SINEs) reflects a clear functional logic, not sloppy editing or random mutational insertions. For example, Alu sequences are preferentially located in and around protein-coding genes as befits their role in regulating gene expression (Tsirigos and Rigoutsos, 2009). They occur mainly in promoter regions–the start sites for RNA production–and in introns, the segments that break up the protein-coding stretches. Outside of these areas, the numbers of Alu sequences sharply decline. Further, we now know that Alu sequences are directed to (or spliced into) certain preferential hotspots in the genome by the protein complexes or the “integrative machinery” of the cell’s information processing system (Levy et al., 2010). This directed distribution of Alu sequences enhances the semantic and syntactical organization of human DNA. It appears to have little to do with the occurrence of random insertional mutations, contrary to the implication of Ayala’s “sloppy editor” illustration and argument.
References, of course, can be found at the original page.
Actually, one very recent paper in Genome Research documented a global genomic function for the mouse B1 SINE — the analogue of Alus — noting that B1 SINEs have “potent intrinsic insulator activity in cultured cells and live animals.”
I could go on and on in a similar fashion. But hopefully enough has been said to demonstrate that Fairbanks’ casual dismissal of the majority of these sequences as “nonfunctional junk” is somewhat premature.
And so concludes my discussion of chapter 2 of Relics of Eden. We have seen how, once again, common descent is being propped up by carefully and selectively cherry-picking which data to report, making much of confirmatory data; disregarding the substantial anomalous data and counter-examples. Since neo-Darwinians are not even close to proposing a plausible naturalistic mechanism for the purported pattern of hereditary continuity, wouldn’t it be wise to treat the latter proposition with a degree of reserved scepticism? Neo-Darwinism is pending its ultimate demise within academia — it’s hard to say when it’s coming, but what is very clear is that it is coming! It is, at the present time, unclear whether common descent will be able to survive the sinking. Only time will tell. We do indeed live in a very exciting time in the history of science.