Yet more iconoclasm.

Toppling Another Evolutionary Icon, ENCODE Suggests Endogenous Retroviruses are Functional

Casey Luskin 

Recently a reader emailed us to ask about how to respond to the argument that some endogenous retroviruses (ERVs) seem to match the standard phylogeny of higher primates, supporting common descent. Endogenous retroviruses are thought to be parasitic junk sequences in our genome that were derived from viral DNA. Evolutionists often cite them as supposed evidence of common ancestry. The reader asked how many ERVs are shared between humans and apes.

These are good questions. ERVs are a favorite with Darwin defenders -- so much so that one particularly uncivil activist, Abbie Smith, even named her popular science blog after them, "ERV."

In response, I suggested that, when analyzing common descent, the number of ERVs shared by humans and chimps is beginning to look like it's not a very important question. An assumption in the question (and in the arguments from supporters of common ancestry) is that ERVs are a type of functionless "junk" DNA. Thus if apes and humans share ERVs in the same position in our genomes, that would seemingly count as evidence for common descent. But what if ERVs aren't junk? What if they are a type of functional DNA? If that's the case, then shared ERVs could easily be explained by common design rather than common descent, and they would certainly no longer be some kind of special argument for common ancestry.

In fact there is good evidence that ERVs as a class of DNA are functional. A 2013 paper in PLOS Genetics using ENCODE data reported that very high percentages of endogenous retroviruses in the human genome are associated with open chromatin -- strong evidence of transcription -- and that they are transcribed non-randomly, suggesting some functional role:

Although emerging evidence suggests that transposable elements (TEs) have contributed novel regulatory elements to the human genome, their global impact on transcriptional networks remains largely uncharacterized. Here we show that TEs have contributed to the human genome nearly half of its active elements. Using DNase I hypersensitivity data sets from ENCODE in normal, embryonic, and cancer cells, we found that 44% of open chromatin regions were in TEs and that this proportion reached 63% for primate-specific regions.We also showed that distinct subfamilies of endogenous retroviruses (ERVs) contributed significantly more accessible regions than expected by chance, with up to 80% of their instances in open chromatin. Based on these results, we further characterized 2,150 TE subfamily-transcription factor pairs that were bound in vivo or enriched for specific binding motifs, and observed that TEs contributing to open chromatin had higher levels of sequence conservation. We also showed that thousands of ERV-derived sequences were activated in a cell type-specific manner, especially in embryonic and cancer cells, and we demonstrated that this activity was associated with cell type-specific expression of neighboring genes. Taken together, these results demonstrate that TEs, and in particular ERVs, have contributed hundreds of thousands of novel regulatory elements to the primate lineage and reshaped the human transcriptional landscape.

(Pierre-Étienne Jacques, Justin Jeyakani, Guillaume Bourque, "The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements," PLOS Genetics (May 9, 2013) (emphases added).)

Again, we see from this that a great number of ERVs are found within open chromatin, strongly suggesting they are transcribed into RNA. Junk-DNA advocates respond that this isn't enough to show function because the transcribed DNA might just be producing "junk RNA." That's a weak rebuttal. As the paper states, ERV-based RNA was produced "in a cell type-specific manner" and was "associated with cell type-specific expression of neighboring genes." In other words, ERVs are being transcribed in a highly non-random manner that correlates with embryological patterns in association with other functional genetic elements. That is strongly suggestive of function.

Junk-DNA defenders rarely address such evidence showing that transcription is not random. For example, we see this in a recent paper in Genome Biology and Evolution by Brunet and Doolittle which critiques the PLOS Genetics paper. They write: "Jacques et al. (2013) for instance used ENCODE DNase I hypersensitivity data to place 80% of ERVs within open chromatin, and TEs in 63% of primate-specific regions." However, because specific functions for each ERV haven't yet been discovered they argue "It seems premature to imagine that a function for TEs as a class has been found!"

Their guilty-until-proven-innocent argument assumes that ERVs are by default non-functional. This reminds me of ENCODE critic Dan Graur who has stated, "If you don't know a function assume as a null hypothesis that it doesn't have function."

Worse, their approach ignores the specific empirical evidence raised in the PLOS Genetics paper, which shows ERVs aren't merely transcribed -- they are transcribed in a non-random, cell type-specific manner that correlates with the transcription of other functional genetic elements and strongly suggests function.

Dan Graur shares Brunet and Doolittle's dubious, assumption-filled approach. He claims that "transcription is fundamentally a stochastic [random] process," but as I explained previously in response to the ENCODE critics, ENCODE shows transcription isn't random:

ENCODE didn't merely study the genome to determine which DNA elements are biochemically active and making RNA. It also studied patterns of biochemical activity, uncovering highly non-random patterns of RNA production--patterns which indicate that these vast quantities of RNA transcripts aren't junk.... ENCODE's results suggest that a cell's type and functional role in an organism are critically influenced by complex and carefully orchestrated patterns of expression of RNAs inside that cell. As Stamatoyannopoulos observes, ENCODE found that "the majority of regulatory DNA regions are highly cell type-selective," and "the genomic landscape rapidly becomes crowded with regulatory DNA as the number of cell types" studied increases. Thus, as two pro-ENCODE biochemists explain, "Assertions that the observed transcription represents random noise . . . is more opinion than fact and difficult to reconcile with the exquisite precision of differential cell- and tissue-specific transcription in human cells."

ERVs fit exactly the same pattern. If they are functional, then they don't provide any kind of special evidence for common ancestry, even if they do fit into a nested hierarchy. Here's my view of how evidence can count for or against (or neither for nor against) common ancestry:

(1) Shared functional biological similarity that fits a nested hierarchy (i.e., a treelike pattern): Explained equally well by common design or common descent.

(2) Shared non-functional biological similarity that fits a nested hierarchy: Best explained by common descent.

(3) Shared functional similarity that doesn't fit a nested hierarchy: Best explained by common design.

Defenders of common ancestry would have you think that ERVs belong in category (2). But the best genetic evidence now suggests they belong in category (1), thus toppling another evolutionary icon. If ERVs are functional, that means even if they do fit into a nested hierarchy, they are equally well explained by common design as by common descent.

Implicit admissions that Darwin had good reason to doubt.

More Admissions of Cambrian Explosiveness
Evolution News | @DiscoveryCSC

In these days of anti-ID “consensus,” don’t expect to find science journals publishing overt statements like, “Well, what do you know! Stephen Meyer and the intelligent design people were right!” Darwinian natural selection must remain omnipotent. Observational evidence, however, is more powerful than the language used to suppress it. Here are a couple of examples.

Rapid Arthropods

We reported two years about Marble Canyon, a remarkable Cambrian fossil deposit in British Columbia that rivals the famous Burgess Shale in significance. More extensive and detailed than its famous neighbor 26 miles to the northwest, Marble Canyon will likely provide years of discoveries to illuminate the Cambrian explosion. The site is of special interest because it was announced a year after Darwin’s Doubt (2013) was published.

Meet Tokummia, a creature found at Marble Canyon. The Calgary Sun calls it an “ancient arthropod with gnarly claws.” By all appearances, this four-inch animal was highly complex, possessing over 50 pairs of jointed legs, a shell, antennae, pincers, eyes, and mouth parts (implying a gut). Undoubtedly it was capable of sexual reproduction and partial metamorphosis, as are other arthropods. It is assigned a date of 508 million years old.

Jean-Bernard Caron, the discoverer of the Marble Canyon fossil trove (who also found a vertebrate fish there), with colleague Cédric Aria from the University of Toronto, studied 21 specimens of Tokummia. They tried to figure out where it fits in the evolutionary scheme. Writing in Nature, they conclude that it might have represented the start of the taxon Mandibulate (“biting things”). The Editor’s Summary offers hope that a gap has been partially filled:

Fossils from the famous 508-million-year-old Burgess Shale in Canada have been vital for shaping our understanding of the origin and early evolution of arthropods, the group of invertebrate animals recognized by their segmented bodies with jointed limbs and an exoskeleton. In recent years, research has found support for a single group of arthropods known as mandibulates that comprises insects, crustaceans and myriapods (centipedes and millipedes) but excludes chelicerates (spiders, scorpions and their allies). Few fossils have been found to illuminate the earliest mandibulates. Cédric Aria and Jean-Bernard Caron now show that this gap is partially filled by the arrival of the Burgess Shale fossil Tokummia katalepsis, whose anatomy allows the reconstruction of the anatomical and evolutionary history of this important animal group. [Emphasis added.]
It’s hard to find, however, more than mere suggestions that certain protrusions on the face of this animal might suffice to “partially” fill the gap. They present a theory story that modern mandibulates emerged from larval forms:

The presence of crustaceomorph traits in the Cambrian larvae of various clades basal to Mandibulata is reinterpreted as evidence for the existence of distinct ontogenetic niches among stem arthropods. Larvae would therefore have constituted an important source of morphological novelty during the Cambrian period, and, through heterochronic processes, may have contributed to the rapid acquisition of crown-group characters and thus to greater evolutionary rates during the early radiation of euarthropods.
Pause to understand what they are saying. This statement does nothing more than push the lucky mutations into the larva instead of the adult. Instead of the adult constituting “an important source of morphological novelty” (i.e., body luck), the larva becomes the source. Then, through “heterochronic [different-time] processes,” some things evolved more rapidly than others. Presto! You “greater evolutionary rates” in the Cambrian, speeding up the “acquisition” of arthropod traits. A more vacuous suggestion could hardly be concocted: basically, “some things happened, and some of them happened faster.” Now, watch how some things happened over and over:

The integration of larval taxa in the phylogeny (Extended Data Fig. 10 and Supplementary Discussion) suggests that morphological traits typically associated with crustaceans or their larvae (large labrum, segmented cephalic exopods, antennule-like frontalmost appendages) have occurred across multiple euarthropod clades (Cheiromorpha, Artiopoda, Pycnogonida) with non-mandibulate adult morphologies.
From there, they launch into full-bore storytelling mode. Putting the lucky mutations into the larvae open up wondrous possibilities:

This implies that crustacean-like characters appeared early in the evolution of euarthropods, as a result of adaptation to ecological niches specific to ontogenetic stages, and may have persisted across the ancestors of major clades before their paedomorphic appearance in adult mandibulates. Because ontogenetic niches create new characters upon which natural selection can act intraspecifically, the emergence of specialized larval forms may have constituted an important catalyst for the rapid evolution of euarthropods during the Cambrian period, and a notable source of morphological novelty for the first mandibulates.
Imagine that lucky mutations appeared in larvae, which exposed them to new “ecological niches” where natural selection could act. Those that stayed young-looking as adults (paedomorphs) “emerged” as new kinds of arthropods. That “emergence” triggered “rapid evolution.” This explanation is indistinguishable from magic. It should be dismissed as a non-scientific affirmation of presumptive Darwinian belief.

What’s more interesting for design advocates is their admission of “rapid evolution of euarthropods during the Cambrian period,” and “rapid acquisition of crown-group characters,” viz., the Cambrian explosion. You can’t hide an explosion in post-hoc distractions like “emergence” and “acquisition” and “arrival”. Like all the other Marble Canyon fossils, Tokummia appears in the rock record fully formed as a complex, successful animal.

Elsewhere in their paper, they admit to serious problems in the evolutionary story of arthropods, the most diverse and successful animals in all of nature:

Retracing the evolutionary history of arthropods has been one of the greatest challenges in biology.
Protocaridids are retrieved with Canadaspis and Odaraia (in Hymenocarina, emended) as part of an expanded mandibulate clade, refuting the idea that these problematic bivalved taxa, as well as other related forms, are representatives of the basalmost
The origin of the mandibulate body plan, …which encompasses myriapods, crustaceans and hexapods, has remained poorly documented.
These results, which had been influenced by an interpretation of the heads of large bivalved Cambrian arthropods as two-segmented, have fuelled a number of macroevolutionary hypotheses about the emergence of arthropod body plans and the evolution of frontal appendages, most notably with the objective to resolve the arthropod head problem.
The only fossil taxa put forward as the earliest crown mandibulates have been euthycarcinoids, historically problematic Palaeozoic centipede-like arthropods with multisegmented legs.
How the morphological characters and anatomies of the most successful animal body plan came into place has thus remained largely unknown.
(Regarding the “arthropod head problem,” see here.)

It’s clear that putting lucky mutations into larvae is not going to solve any of these problems. Meyer’s book stands unanswered.

Unrelated Ediacarans

What about earlier Ediacaran organisms? Can they be considered ancestral? Meyer dealt with one called Parvancorina on page 89, refuting suggestions that it had superficial resemblances to an ancestral trilobite-like body plan.

A new paper in Nature Scientific Reports focuses on another topic, a suggestion that Parvancorina displayed an early instance of rheotaxis (active alignment with a fluid current). The evidence, however, is circumstantial and admittedly open to interpretation. The authors do not present any evidence of organs, genes, or tissues capable of controlling movement.

Of more interest to us is their affirmation of Meyer’s view, that the Ediacaran animals bear no ancestral relationship with the Cambrian animals. Here, in regard to one of the leading candidates of such a relationship, these authors say, “Apart from possessing a bilaterally symmetrical body, there are no unequivocal morphological characters to support placement of Parvancorina within the Euarthropoda or even the Bilateria.”


These papers show that four years after Meyer’s book, and 13 years after his paper in the Smithsonian journal, evolutionists are still failing to come up with plausible evolutionary hypotheses for the sudden appearance of the Cambrian animals. As paleontologists hold these stunning fossils in their hands, they need to stop the storytelling about magic appearances, the desperate attempts to force-fit the fossils into mythical evolutionary trees, and take seriously Meyer’s proposal that intelligent design provides the best explanation.