Skeptics of ENCODE’s Discovery of Function

In 1972, geneticist, Susumu Ohno, was the first to coin the term “junk” DNA in reference to  pseudogenes but the meaning expanded to non-coding DNA as well. Ohno stated, “The earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?

Out of a span of 30 years or so, scientists didn’t do much research on what was considered “fossil remains” of DNA.  Then a group of scientists called, ENCODE discovered something very interesting in 2007. DNA is transcribed into RNA!

Ewan Birney, a coordinator of ENCODE said, “The genome looks like it is far more of a network of RNA transcripts that are all collaborating together. Some go off and make proteins; [and] quite a few, although we know they are there, we really do not have a good understanding of what they do.” 

Then on September 5, 2012, the guardian reports…

“Long stretches of DNA previously dismissed as “junk” are in fact crucial to the way our genome works, an international team of researchers said on Wednesday.

It is the most significant shift in scientists’ understanding of the way our DNA operates since the sequencing of the human genome in 2000, when it was discovered that our bodies are built and controlled by far fewer genes than expected. Now the next generation of geneticists have updated that picture.”

80 percent of the genome is now regarded to having function which is a major shift considering most of it was considered junk. The discovery has caused quite a stir with those who advocate “junk DNA” being necessary for evolution (having a critical role in ensuring the survival of biological lineages) while using it for evidence against creationism or intelligent design.

P.Z Meyers has been a skeptic of ENCODE and a huge advocate of junk DNA, (but admires their work) here he writes the following in his blog called, “The ENCODE Delusion.” 

“The vast majority (80.4%) of the human genome participates in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type.”

“That isn’t function. (says PZ Myers) That isn’t even close. And it’s a million light years away from “a critical role in controlling how our cells, tissue and organs behave”. All that says is that any one bit of DNA is going to have something bound to it at some point in some cell in the human body, or may even be transcribed. This isn’t just a loose and liberal definition of “function”, it’s an utterly useless one.”

Nick Matzke in Panda’s Thumb, reiterates what Myers spewed out…

“The science media exploded today with the claim from the ENCODE project that 80% of the genome is “functional”. The creationists are already beside themselves with joy. And the problem cannot be blamed on the science media, although I wish they were quicker to exercise independent skepticism – the 80% claim is right there in the abstract of the Nature article.”

“However, skepticism has arisen spontaneously from all over the scientific blogosphere, facebook, and twitter. You see, most of us scientists know that (a) ENCODE is using an extremely liberal and dubious definition of “function”, basically meaning “some detectable chemical activity”.

“People have pointed out that randomly generated DNA sequences would often be “functional” on this definition. (b) All the evidence for relative nonfunctionality which has been known for decades is still there and hasn’t really changed – lack of conservation, onion test, etc. But I’m beginning to think that certain parts of molecular biology and bioinformatics are populated with people who are very smart, but who got through school with a lot of detailed technical training but without enough broad training in basic comparative biology.”

ENCODE defines function by activity meaning, the transcription into RNA which makes 80% of our DNA functional which is a perfectly logical conclusion. However, PZ Myers suggests in his sarcasm…”Oh, jeez, straining over definitions—ultimately, what he ends up doing is redefining “functional” to not mean functional at all, but to mean simply anything that their set of biochemical assays can measure.” 

ID proponent and scientist says…”Non-protein-coding DNA even provides spacers to regulate the timing of protein production; and focusing light in rod cells in the retinas of nocturnal mammals.”  -Biologist Jonathan Wells.

Skeptics of ENCODE, are just one angry bunch of men because one of their weapons they have used for many years is being taken away from them as a result of better science. There is nothing to suggest that the majority of scientists even agree with them just rumblings on facebook and twitter. That is not to say the majority in the science community is always right, (many times they are wrong concerning evolution) but they have always advocated the majority to creationists as being logically conclusive and right in science. But we know that is nothing more than a straw man’s argument along with circular reasoning.

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8 thoughts on “Skeptics of ENCODE’s Discovery of Function

  1. The first thing to realize is that the controversy over non-functional DNA is that it is of no consequence to evolution.[1] Michael’s earlier post imagined that, since creationism prohibits non-functional DNA, then evolution must require it. This was shown in the comments to be a false dichotomy—the opposite of “prohibit” is “allow,” not “require.”

    But this issue is of fundamental importnce to creationism, because the presence of any non-functional DNA whatsoever in the genome would impugn the perfection of God, showing him up as an incompetent tinkerer. So here we have a clear fork where evolution is indifferent, but a specific outcome is crucial to creationism.

    There are scientific reasons for evolution to investigate DNA that seems to have no function..[2] A record of the former function of pseudogenes is valuable in evolutionary research. Incipient preaptations might be exposed. New classes of promoters and inhibitors may surface. Disease-causing mobile elements may appear, suggesting medical treatments.

    This last group brings up another point. A lot of “junk DNA” is known to have function[3] which causes disease in the organism in whose genome it lives. Transposable elements (TEs) are stretches of DNA that can hop from place to place in the genome.

    They are mutagens—they damage the genome of their host cells. When they insert themselves into a gene, that gene will frequently be damaged to the point of being functionally disabled. When they leave a gene, the gap usually cannot be repaired, again damaging the gene. Long repeats such as Alu sequences hinder chromosome pairing, sometimes leading to chromosome duplication—one of which causes Down syndrome. Other diseases caused by thi form of junk DNA include hemophilia, severe combined immunodeficiency, porphyria,and Duchenne muscular dystrophy. TEs can contribute to aneuploidy in humans and other animals; more and more researchers believe that aneuploidy is a major predisposition to cancer.[4]

    If that were not enough, many TEs have evolved their own promoters, which are often linked to other genes as well, affecting their expression. These unintended linkages can lead to disease and malformed body parts.

    So tell us, Michael, which you prefer—
    (a) a sloppy God who leaves non-functional junk lying around in his designs; or
    (b) a malicious God who puts functional stuff in our genome to damage it.
    .

    =============

    [1] There was some early concern about a “mutational load” imposed by such junk hanging about. However, this led biologists to posit that evolution might also require absence of junk. Turned out this concern was of little consequence to the genome.

    [2] Creationisrs fail to acknowledge that all of the functions that have been discovered or non-coding DNA have in fact been discovered by research by evolutionists. This is hilarious. Occasionally, creationists even calim to have “predicted” function for non-coding DNA. This is even more hilarious.

    [3] And thus would be included in Birney’s 80% figure.

    [4] For a longer list of human diseases from TEs, see Belancio et al., “LINE dancing in the human genome: transposable elements and disease” Genome Med. 1(10): 97,.
    published online 2009 October 27.

  2. In 1972, geneticist, Susumu Ohno, was the first to coin the term “junk” DNA in reference to pseudogenes but the meaning expanded to non-coding DNA as well.

    Wrong on the very first sentence: this is not an auspicious beginning. In fact, one could argue that the errors begin at the title, because ENCODE didn’t discover function, rather they defined it into existence. But more on that presently.

    I think most molecular biologists would be very surprised to find that junk DNA came to indicate all non-coding DNA considering that François Jacob and Jacques Monod had already been honored as Nobel laureates in 1965—that is seven years before Ohno’s paper—for their work on regulatory regions that contain non-coding DNA.

    Out of a span of 30 years or so, scientists didn’t do much research on what was considered “fossil remains” of DNA.

    The insinuation that scientists didn’t do research on non-coding DNA is a complete falsehood that can only be stated with a straight face if one has zero knowledge of half a century of molecular biology. It’s absurd if you think about it for more than a few seconds because by the early 60s, scientists knew what coding DNA did: it codes for proteins. Finding a novel genomic function in that is like expecting a tibia to start doing double duty as an organ of hearing. So where else could they look for new functions except non-coding DNA? And they found many, including coding for ribozymes, tRNA, snRNA in the spliceosome, etc. (DNA that codes for non-coding RNA is technically non-coding itself), introns, telomeres, etc. Some of this work was rewarded with Nobel Prizes (including one for the man Stephen Meyer called a crank, Jack Szostak, in the very year he wrote that particular bit of ad hominem).

    Nevertheless, the portion of non-coding DNA with a specifically identified function is still a tiny portion of the genome.

    Then a group of scientists called, ENCODE discovered something very interesting in 2007. DNA is transcribed into RNA!

    That had been known for some time already—about half a century before. Perhaps you mean that they found that noncoding DNA was transcribed into RNA. But that too was known about: I just described the way in which some non-protein-coding DNA is turned into biologically useful RNA transcripts. So perhaps you mean that they showed nonfunctional DNA was transcribed. Well, when you transcribe nonfunctional DNA, you get nonfunctional RNA transcripts that are quickly degraded. (All that work to produce a transcript that doesn’t do anything and which has to be broken down in the cell. Some design.) And it turns out that even this was known about, as I mentioned in the Dawkins thread (Wyers et al. 2005—note the date!). The Wyers paper is evidence that you cannot assume function simply because of transcription.

    Then on September 5, 2012, the guardian reports…

    It is the most significant shift in scientists’ understanding of the way our DNA operates since the sequencing of the human genome in 2000, when it was discovered that our bodies are built and controlled by far fewer genes than expected. Now the next generation of geneticists have updated that picture.”

    Ah, the poor old Grauniad. They’ve got more in error than their typesetting in this case. They are wrong that scientists were surprised by the “unexpectedly small” number of genes. In reality, scientists had predicted this. In the very same paper in which Ohno coins the term “junk DNA”, he also gives an estimate of the number of genes (no more than 30,000) as part of his argument that turned out to be absolutely correct. In reality, we have roughly 20,000 genes. The overestimate of 100,000 genes was just hype getting in the way of science again, this time with the Human Genome Project. And they’re wrong about 80% of DNA being determined to be functional, only this time they’ve fallen for ENCODE’s hype.

    I’ll give you a perfect illustration of what I mean. This appeared in the open-access summary paper on Nature’s website: “These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions.” Now, I may be just be a gruff old traditionalist, but I always understood the words “assign a function” to indicate that you now know what it did. But that is what the ENCODE team cannot say. They did not discover specific functions for the regions under investigation; they just did a series of assays and reported on what showed some level of transient biochemical activity. In their hands, “assign a function” now means that they point at it and say, “Hey, there’s chemistry going on! It’s functional!” By that standard, you can point to an old junker with no tires and no engine up on some cinder blocks and say “Hey, it’s got a function: it’s rusting!” PZ Myers’ comment about defining function as anything their assays can measure is not necessarily sarcasm but is a precise description of what certain members of the ENCODE team did just to raise their media profile (as Ewan Birney admits on his blog in a post that is still weaselly, dishonest, and blatantly self-serving.).

    ENCODE defines function by activity meaning, the transcription into RNA which makes 80% of our DNA functional which is a perfectly logical conclusion.

    How is this a “perfectly logical conclusion”? If they had defined “functional” as exhibiting the property of being duplicated during cell division, then all of the genome would be rendered “functional”. The fact that such an outcome is even conceivable—with different amounts of “function” just depending on how you choose to define the term—shows that it is profoundly illogical and arbitrary and that we should stick to the term “functional” meaning having a sequence that is constrained by organism-level function. By that standard, not only has ENCODE not demonstrated 80% functionality, they haven’t demonstrated any functionalty—that will come, if it comes, in future papers using ENCODE’s data sets as a springboard. Which is all ENCODE should have taken credit for in the first place.

    ID proponent and scientist says…”Non-protein-coding DNA even provides spacers to regulate the timing of protein production; and focusing light in rod cells in the retinas of nocturnal mammals.” -Biologist Jonathan Wells.

    Spacers were explicitly discussed as a class of functional noncoding DNA in Ohno’s original 1972 paper, where he referred to them as “partitioning sequences”. Wells wants to pretend like this is news when in reality he’s simply throwing up chaff in order to distract us from the biological reality that the positive arguments for junk DNA have never been refuted, and that function has not been established for more than a small portion of the genome. Moreover, of the noncoding DNA that has been established to be functional, not even one base pair of it was demonstrated to be functional as a result of creationist or intelligent design research.

    Skeptics of ENCODE, are just one angry bunch of men because one of their weapons they have used for many years is being taken away from them as a result of better science.

    LOL! (And I literally did laugh out loud at this.)

    You all really need to get over yourselves. Though a minority of us interest ourselves in the subject of creationism as a hobby, on a day-to-day basis in the scientific world creationism doesn’t merit even a passing thought. The issue of function vs. no function for junk DNA is one that’s being hashed out within the scientific community and among scientists. ID creationists have nothing to say on this score that’s of the slightest interest whatsoever or at all likely to nudge the debate into productive lines of research for a solution. We don’t need junk DNA as a weapon, because there’s nothing to whack at. Creationism is just a paper tiger.

    Citation:
    Wyers, F., Rougemaille, M., Badis, G., Rousselle, J.C., Dufour, M.E., Boulay, J., Régnault, B., Devaux, F., Namane, A., Séraphin, B., Libri, D. and Jacquier A. (2005) Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121:725-37.

  3. Olorin:
    So tell us, Michael, which you prefer—
    (a) a sloppy God who leaves non-functional junk lying around in his designs; or
    (b) a malicious God who puts functional stuff in our genome to damage it..

    Michael Behe in Edge of Evolution argues that resistance to antimalarial drugs is bestowed by the Hand of God—erm, the Designer, so if his argument holds then my money is on option (b). ;-)

  4. Nullifidian, the above alternatives were presented to Michael as a fairly elementary problem in theodicy. Since Michael knows as little theology as he does science, he probably would not even rise to the bait.

    Behe, however, proposes a non-theological escape in When Bad Things Happen to Good People[1]—
    ,blockquote>
    “Maybe the designer isn’t all that beneficent or omnipotent. Science can’t answer questions like that. But denying design design simply because it can cause terrible pain is a failure of nerve, a failure to look the universe fully in the face.”

    His purpose here is undoubtedly to “prove” that ID is not religious,[2] but he does at least confront the issue squarely.

    Since my highest grad degree is in law, I am sensitive to how Michael frames issues. Then it is (sometimes) enjoyable to present the consequences of his claims. Michael never thinks through the logical implications of what he says.

    ================

    [1] The Edge of Evolution, pp. 237-239.

    [2] Behe causes creationists to squirm.He’s a qualified life scientist unwavering in design advocacy; yet he clearly accepts old age and common descent, and sometimes questions divine attributes. (In fact, Jonathan Wells is the only qualified scientist at the Discovery Institute who is a young-earther.)

  5. So tell us, Michael, which you prefer—
    (a) a sloppy God who leaves non-functional junk lying around in his designs; or
    (b) a malicious God who puts functional stuff in our genome to damage it..

    False dilemma. This just shows your level of understanding of theology. What’s the third option as advocated by the bible Mr. ‘I go to church’ Olorin?

  6. Chazing is correct. The third option is that the wisdom of God passes all understanding.

    Michael, please add a third choice to the list. Would you prefer—
    (a) a sloppy God who leaves non-functional junk lying around in his designs;
    (b) a malicious God who puts functional stuff in our genome to damage it; or
    (c) a deceptive God who denies us knowledge that could help us.

  7. Michael, please add a third choice to the list. Would you prefer—
    (a) a sloppy God who leaves non-functional junk lying around in his designs;
    (b) a malicious God who puts functional stuff in our genome to damage it; or
    (c) a deceptive God who denies us knowledge that could help us.

    As expected, you just confirmed your level of theological stupidity. You rarely disappoint.

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