I just knew it. The second I read this abstract I just knew that the Uncommon Descent cranks would dust off their old “Junk DNA” harangue and suggest that if it wasn’t for them, no one would believe that all that non-coding DNA had a purpose. Sal Cordova obliged, and it’s the usual embarrassing misread of our literature.

Heaven forbid that scientists should be so brash as to not infer purpose into everything without studying it first. I’ve been waiting to use “promiscuous teleology” in a post, I guess this is my chance. But that’s not even necessary in this case, this is such an egregious misreading of this result by Cordova that we can nail him just on his lack of reading comprehension and knowledge of biology, let alone his historical revisionism. That is if we’re not assuming he’s being purposefully dishonest – given his history of quote-mining that wouldn’t be stretch.

Let’s start with a timeline of non-coding DNA:

The most important thing to remember about creationists is their complete inability to appreciate a timeline. In this case, the term “Junk” as applied to DNA originated in 1972 with Susumu Ohno. It was kind of a null hypothesis – that there was no obvious function for such huge amounts of non-coding DNA so some of it might just be filler.

Evidence already existed in 1972 for the function of some non-coding DNA. Probably starting from the discovery by Barbara McClintock of transposons it was known that repeat elements and non-coding regions could serve a functional and/or evolutionary purpose.

The creationists however, make it sound as though once Ohno suggested the junk hypothesis, that all biologists just sat on their hands and stopped working on non-coding DNA. However biologists were already intensely studying it – contrary to the rather idiotic assertions of the evolution denialists that ignoring junk was some great “mistake” that we’re trying to recover from.

A decade before this Jacob and Monod figured out the lac operon – and that it was controlled by a promoter or a non-coding region. The terminology of junk, while popularized widely, wasn’t believed. It’s not like all the molecular biologists in the world took the cue from Ohno and just dropped their pipettes and walked away. Non-coding DNA was an active field of study at the time, if anything the only false assumption was that things like promoter regions would only be immediately adjacent to genes – within 100 base-pairs – and that it was then hard to account for all that additional space between genes. That is, until around 1981 with the discovery that upstream promoter elements could be thousands of base pairs away.

Promoter research was intense throughout the 80s, and with the advent of PCR in 1984, molecular methods became exponentially more powerful. Day by day, the function of non-coding elements of the genome was being analyzed and dissected. Promoters were being used to drive expression of transgenes in experimental animals, they were being mutated. Regulatory elements were being discovered as well as the transcription factors they bind. In other words, no one thought that non-coding DNA was really junk. After all, the best way to find the regions that were important was through conservation analysis – which requires that natural selection preserve the most important regions for gene regulation. By comparing a similar sequence across species, the areas of high conservation turn out to be the ones that are responsible for controlling genes, the intervening sequence that his highly mutable is often just spacer. But that’s not the only thing discovered in non-coding DNA, even without funding from the Discovery Institute, rebel scientists studying the junk against the wishes of the Darwinian orthodoxy have discovered in humans things like micro-RNAs, non-coding RNAs that appear to be critical for gene regulation. They’ve discovered various RNA molecules that are critical to protein function, and some that have their own enzymatic functions. For decades following Ohno’s suggestion of the null hypothesis (creationists do have a problem distinguishing between hypothesis and theory) functions of non-coding DNA were being elucidated.

But what does the creationist mind of Sal Cordova think of this timeline? Well, apparently the study of non-coding DNA started in 1997.

Behe 10 years ago, in Darwin’s Black Box (DBB) suggested junk DNA may not be junk after all. Behe has been vindicated by the facts, Miller refuted.

Wow. What a stunning insight from Behe! Decades after every other scientist in the world began to study and decode the function of non-coding DNA, he figured out it might be useful for something. What a genius! Give that guy a Nobel! He predicted, from the future mind you, what would happen in the past! What an accomplishment!

Not content to just let it go at that level of idiocy, Cordova then, true to his nature, quote-mines the article:

Finally, there is at least one other interesting fact in this article: “the ENCODE effort found about half of functional elements in the human genome do not appear to have been obviously constrained during evolution”. This means these designs NOT attributable to natural selection. Features in the genome have been shown not to be likely products of “slight successive modifications”. How I love science!

At least one other? Holy crap is that an understatement. This has got to be the most important paper in transcription in years. As Razib points out in his analysis, there’s enough here for 5 or 6 papers full of interesting facts. But onto his allegation that these results are a sign that, ” these designs NOT attributable to natural selection”. Aside from the obvious promiscuous teleology (hehe), what is Cordova’s major failure in reading comprehension? Can anyone figure it out?

Well, aside from the obvious hilarity of a creationist using the results of sequence conservation analysis across different mammals for his advantage, the answer of course is in the very next paragraph, which as a creationist quote-miner, Cordova would never bother to report. From the Science Daily article.

According to ENCODE researchers, this lack of evolutionary constraint may indicate that many species’ genomes contain a pool of functional elements, including RNA transcripts, that provide no specific benefits in terms of survival or reproduction. As this pool turns over during evolutionary time, researchers speculate it may serve as a “warehouse for natural selection” by acting as a source of functional elements unique to each species and of elements that perform the similar functions among species despite having sequences that appear dissimilar.

It’s also worth including this passage from the Nature paper.

Surprisingly, many functional elements are seemingly unconstrained across mammalian evolution. This suggests the possibility of a large pool of neutral elements that are biochemically active but provide no specific benefit to the organism. This pool may serve as a ‘warehouse’ for natural selection, potentially acting as the source of lineage-specific elements and functionally conserved but non-orthologous elements between species.

You see, these elements are “functional” in that they do something, but not necessarily to the benefit of the organism. It suggests rather than part of being an integral part of the “design” of an organism, they are merely tolerated. They aren’t harmful enough to effect survivability, and not critical enough for natural selection to maintain them under constraint. They may serve a long-term advantage for natural selection – that has yet to be determined – but they certainly aren’t critical for the function of the organism.

If anything, this is the opposite of what intelligent design would predict. These sequences have a function, it’s just not particularly useful for the organism.

That’s some good quote mining there Sal.
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Comments

  1. #1 TR Gregory
    June 15, 2007

    If I may, I would expand on the statement about Ohno to note that he was not using it simply as default because he did not know what non-coding DNA does — he based it on specific knowledge about a mechanism of non-coding DNA generation (pseudogenization of duplicates).

    Some relevant discussions:

    Function, non-function, some function: a brief history of junk DNA. (Genomicron)

    WIRED on Junk DNA. (Sandwalk)

    Junk DNA gets Wired. (Genomicron)

    More about ENCODE from Scientific American. (Genomicron)

    It’s junk. Get over it. (Pharyngula)

    So Much Junk in the Genome� and the Press. (Panda’s Thumb)

    A word about “junk DNA”. (Genomicron)

  2. #2 CaptainBooshi
    June 15, 2007

    My understanding of the origin of the term “junk DNA” is that it was originally intended specifically for those regions of noncoding DNA for which we knew there was no purpose, and that it fairly quickly was coopted to be synonomous with all noncoding DNA. Have I been wrong all this time? This is very possible, of course, since I am a physicist, not a biologist, and so I might be misremembering something or been mislead at some point.

    It seems to me that promoting this as scientists taking the lead from ID (besides being untrue) is ridiculously contradictory for any crank, since they so often argue that all the ‘evidence’ for ID is being censored by scientist and journals.

  3. #3 Dave S.
    June 15, 2007

    One wonders why Sal gets so excited at this news, since functionality of all genetic material is NOT a prediction of intelligent design. As we are assured time and again, ID makes no statements about the designer. His (Her/Their/Its) motives, abilities, mechanisms, are all beyond the ken of science, so they say.

    Were they being disingenuous then or are they being disingenuous now?

  4. #4 Dave S.
    June 15, 2007

    CaptainBooshi says:

    My understanding of the origin of the term “junk DNA” is that it was originally intended specifically for those regions of noncoding DNA for which we knew there was no purpose, and that it fairly quickly was coopted to be synonomous with all noncoding DNA. Have I been wrong all this time? This is very possible, of course, since I am a physicist, not a biologist, and so I might be misremembering something or been mislead at some point.

    In addition to this thread, you might want to check out T. Ryan Gregory’s site.

  5. #5 ck1
    June 15, 2007

    http://genomicron.blogspot.com/2007/04/word-about-junk-dna.html

    From this long history/discussion:

    “As Comings (1972) put it, “Being junk doesn’t mean it is entirely useless. Common sense suggests that anything that is completely useless would be discarded.” (This is what Sydney Brenner meant by the distinction between “trash” or “rubbish”, which one throws away, and “junk”, which one keeps; Brenner 1998).”

  6. #6 MarkH
    June 15, 2007

    Yes, the perception of the DNA as “junk” the way the ID people think of it requires one to ignore Ohno’s point at the time, the type of duplication theory he advanced (it’s in the linked wiki too), and all the research that was ongoing at the time into non-coding DNA. That linked Panda’s thumb article is great, because it also brings up the fact that evolutionary theory had to adjust from a streamlined genome to one that had a bunch of neutral elements and other hitchhikers along for the ride.

    What irritates me most about this though is the suggestion that somehow ID is responsible or predicted anything about non-coding DNA when all sorts of intense research was going on for decades before these idiotic pronouncements.

    I tend to focus on the promoter stuff because that’s what I have the most experience with, but for dozens of reasons we’ve known that all non-coding DNA isn’t “junk” or worthless for far longer than they give credit for. And to make a prediction in 1997 that junk DNA may be functional is, like I say, predicting the past from the future.

    Finally, and the PT article addresses this as well, is that it is obvious that their requirement of a functional, streamlined genome is making inferences about a specific creator. How can they possible know what type of design should be expected unless they make this basic inference?

  7. #7 CaptainBooshi
    June 15, 2007

    Thanks! Glad to know that I wasn’t incorrect. I also noticed that the comment posted over an hour before mine would answered my question before I even asked it, but for some reason, it wasn’t there when I read the article, so sorry for the useless comment.

  8. #8 Dave S.
    June 15, 2007

    I didn’t notice it either CaptainBooshi. Might have been held up for review because of all the links. Or maybe we both need glasses! :)

  9. #9 sparc
    June 16, 2007

    I always wonder what Sal did or does at university. Is he still a student or does he have a regular job? I can’t imagine that he could make a living just by producing ridiculous posts at UD. On the other hand the tendency to spread BS over hundreds of lines might be a sign that he gets paid for this dreck per word.
    BTW, every single post on UD disproves the concept of irreducible complexity: You may remove parts from their BS and it remains BS. You may add parts from other posts of DaveScot, WD or from Behe’s books and it remains BS.

  10. #10 blf
    June 16, 2007

    … every single post on UD disproves the concept of irreducible complexity: You may remove parts from their BS and it remains BS. You may add parts from other posts of DaveScot, WD or from Behe’s books and it remains BS.

    I’m having a hysterical fit of giggling. Thanks…er, I think!

    Now wondering (between giggles) about fractal BS, and what the properties of an atom of BS might be, and the sorts of experiments could be done, and whether or not there a Law of Conversation of BS, or is it just a Law of Ever Expanding BS, and what about Dark BS, and …

  11. #11 ERV
    June 18, 2007

    I was just reading a paper, and they reference an even earlier McClintock paper for functional ‘junk’– 1961.

    Some parallels between gene control systems in maize and in bacteria.

    The paper Im reading:
    “But an increasingly recognized phenomenon is the co-opting of nonautonomous elements as functional noncoding elements (Bejerano et al. 2006; Kamal et al. 2006). This fulfills the vision originally espoused by McClintock, Davidson, and Britten, that TEs, and repetitive DNA in general, may be critical “control elements” in modern genomes (McClintock 1961; Davidson and Britten 1979).”

  12. #12 ERV
    June 18, 2007

    Ugh, I have a comment needing moderation– too many links. Sorry. :P

  13. #13 Jud
    June 20, 2007

    I can see “functional” headed down the same road as “junk.” In the quoted bits, I take “functional” to be used rather sloppily to mean “transcribed.” It’s interesting that DNA without any obvious purpose is being transcribed, but if it’s not under selection, that would tend to show (as the post above states) it has no function in terms of present benefit to the organism.

    The really interesting part is how this plays against ID conjecture re “front-loading,” i.e., that what others call junk is just being held in abeyance until needed by more “advanced” organisms. If this DNA is designed to wait patiently for the next step on the evolutionary ladder, then why isn’t it waiting? Why is it being transcribed now, in us? (And for that matter, if we’re the supposed pinnacle of this design process, why is there any next step at all?)

    Cellular machinery expending the organism’s energy transcribing a bunch of useless stuff doesn’t sound like design to me. (To anyone who wants to argue about usefulness: If it is useful *either* in an evolutionary or in a design sense, why isn’t it being conserved?)

  14. #14 cprs
    May 4, 2009

    Why then did John Mattick also assume a ‘creationist’ perception of non coding DNA, when he claimed, ‘The failure to recognize the full implications of this — particularly the possibility that the intervening noncoding sequences may be transmitting parallel information […] may well go down as one of the biggest mistakes in the history of molecular biology’?

    Mattick,J., cited Gibbs,W., Sci American 289(5): 26–33, Nov 2003; pp 29–30

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