The ENCODE War Continues

You remember how, back in September, there was much hype about how the release of data from the ENCODE project supposedly showed that junk DNA was  “dead”? At the time many scientists had other ideas, and the idea of writing a paper disputing this was floated at least once. An important problem, however, was that the junk DNA claims were not themselves made directly in the published journal articles – could you really write a paper slamming statements made to the media? Over the last few months it’s been shown that this was no hurdle for some, with at least three ENCODE-critical papers having been published in that time:

  1. The C-value paradox, junk DNA and ENCODE, (Eddy, Current Biology) pdf
  2. Can ENCODE tell us how much junk DNA we carry in our genome? (Niu & Jiang, Biochemical and Biophysical Research Communications)
  3. On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE (Graur et alGenome Biology and Evolution) open access
  4. Is junk DNA bunk? A critique of ENCODE (Doolittle, PNAS)

The Wednesday article – which is by Nathaniel Jeanson and Brian Thomas (J&T), and is called The Resurrection of ‘Junk DNA’? – is about the third of these. This is the one you may well have heard about already, as it has gained a fair bit of fame for its nastiness. For example:

Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that (at least 70%) of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these “functional” regions, or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly (1) by employing the seldom used “causal role” definition of biological function and then applying it inconsistently to different biochemical properties, (2) by committing a logical fallacy known as “affirming the consequent,” (3) by failing to appreciate the crucial difference between “junk DNA” and “garbage DNA,” (4) by using analytical methods that yield biased errors and inflate estimates of functionality, (5) by favoring statistical sensitivity over specificity, and (6) by emphasizing statistical significance rather than the magnitude of the effect.

(Emphasis added.) Needless to say, this is far more overtly critical than you would normally see in an academic journal.

The main criticism being put forward here comes down to “if 80% of the genome is functional, why is it that all but about 10% couldn’t care less about being mutated beyond all recognition? Surely if it’s functional it should matter if it gets mucked up.” (The 70% is found by assuming that the 10% is all part of the 80%, which still leaves 70% which is vulnerable to mutation yet still somehow important.) This is just one of many problems that are yet to be explained by those who claim that junk DNA is “dead.”

Importantly for us, this is one criticism that young Earth creationists can just shrug off. To recap, creationists despise junk DNA – to them it means that we were created imperfect, containing “junk” from the beginning, which the say contradicts God’s assertion that his creation was “very good.” Naturally, they have seized on the ENCODE claims: in September Jeffrey Tomkins claimed that the ENCODE papers “proclaim[ed] that the human genome is irreducibly complex and intelligently designed,” which they certainly did not.

Creationists love attacking junk DNA not just because it contradicts their beliefs but also because they think it’s a core evolutionary doctrine: if junk DNA is false, evolution must be too. This idea is debatable – the ENCODE authors certainly don’t think so – but that is what this paper alleges. You can see why the creationists would come to the conclusion that it doesn’t challenge their views, but supports them. They should probably take a look at some of the other problems, like the C-value paradox from the first paper listed.

There are, however, a couple of points in the paper that J&T object to.

The Genome Biology and Evolution study authors further vented their grievances against the ENCODE results when they wrote, “The human genome is rife with dead copies of protein-coding and RNA-specifying genes that have been rendered inactive by mutation.” When first discovered, secular researchers assumed that these gene “copies” were junk. Without even testing whether or not the copies were useful, they named them “pseudogenes,” a word that means, “false-genes.” “By definition, they [the pseudogenes] are nonfunctional,” wrote the study authors. But to cite pseudogenes as evidence for evolution based on the definition of pseudogenes as relics of evolution is merely to beg the question. And experimental results continually identify important functions for pseudogenes, showing they are not evolutionary relics but design features.

J&T’s claim that pseudogenes are identified “without even testing whether or not the copies were useful” is analogous to objecting to calling a car broken based simply on it looking wrecked (including discovering that the axle has snapped clean in two), without actually testing the ignition. Some pseudogenes have been found to be functional: this doesn’t mean that all of them are.

Then we have:

“ENCODE’s biggest scientific sin was not being satisfied with its role as data provider; it assumed the small-science role of interpreter of the data.” Since when is interpreting results from lab experiments a sin? Do interpretations somehow become sins when they counter Darwinian dogma?

ENCODE was supposed to collect a huge amount of data for other researchers to sift. That’s not something that will make headlines, however, and they have been accused of making the junk DNA connection simply in order to get into the newspapers. “Sin” is a bit of a strong word, but they certainly made a mistake when they did something they weren’t intended to do, and did it very poorly.

You can blame assignments and general exhaustion for why I, once again, haven’t posted in a week. I’ll try to get on top of it all soon…ish.

4 thoughts on “The ENCODE War Continues

  1. Pingback: Spanking #ENCODE | The OpenHelix Blog

  2. Creationists allege circular readsoning by evolutionists.

    Hold the front page.

    Ewan Birney was on BBC Radio 4 recently, along with another scientist named Chris Ponting (I think the programme is still available online, though possibly not in New Zealand). Note that when Birney first starts speaking it’s not made clear that it’s Birney not Ponting – also I couldn’t catch part of Birney’s final remarks, made over the telephone, at the end.
    There were also P Z Myers and Don Prothero blog posts around 27 Feb about the Graur et al paper.

  3. “You can blame assignments and general exhaustion for why I, once again, haven’t posted in a week. I’ll try to get on top of it all soon…ish.”

    Stay on top of your assignments and your rest. Getting some down time and perhaps some recreation is important and will diminish the weight that can come with juggling those assignments and your daily life. Take care of yourself first and us muggles secondarily. I assure you, and I believe others will agree, we have more than enough patience. It’s actually pleasant to check in daily and after a time discover a new post like it’s an unexpected treat. It adds to the “yay!” factor.

    TL;DR – Go forth and learn.

      “What good are transposable elements (TEs)? Although their activity can be harmful to host genomes and can cause disease, they nevertheless represent an important source of genetic variation that has helped shape genomes”.

      Of course, the ICR appear to be mangling this:
      “The term mobilome refers to a category of transposable DNA segments—sections of DNA that in some cases can excise themselves and move around in the genome (called transposable elements), sometimes taking other pieces of DNA with them. One area of research related to the mobilome—that is completely destroying one of the sacred cows of evolution—is the idea that transposable elements are nothing but useless ‘junk DNA.'”;
      “… the past decade of research has clearly shown that transposable elements play vital and purposeful roles in regulating how genes and the genome function. Moreover, they specifically play key roles related to the type of context in which a cell is located (i.e., tissue type).In fact, a high-profile research paper titled “Transposable Elements Re-Wire and Fine-Tune the Transcriptome” was just published in the journal PLoS Genetics [link above]…”;
      If “transposable elements are key to life” rather than ‘junk’, does this rule out the theory of evolution (it MAY imply design but could that not be theistic evolution)?


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