evolgen

Junk on Junk

I’ve recently come across two articles on junk DNA. The first one, from New Scientist, includes a pretty thorough coverage of recent studies that have identified functions for non-protein-coding regions of the human genome (“Why ‘junk DNA’ may be useful after all”). The article is set up as if it will present the demise of junk DNA, but it paints the accurate picture that a large portion of the human genome is non-functional. And TR Gregory like the article too.

The second article tries to do that, but fails. It’s from The Scientist and entitled Junk Worth Keeping: Is it time to retire provocative descriptors such as “junk DNA”?. This editorial starts out by presenting the evidence for the demise of junk DNA, including a nod to Francis Collins’s belief that there is no junk in the human genome (providing further evidence that Frank knows nothing about evolution). From here, the author attempts to defend the term “junk DNA”, but does so in a very poor manner. While I agree with his conclusion (at least I think I do — it’s hard to parse from stuff on framing and intelligent design), the entire article is just a mess suggesting the author really doesn’t understand what he’s writing about.

Comments

  1. #1 Jonathan Vos Post
    July 15, 2007

    I liked the New Scientist article more than I like most of their science fiction which they pretend is Physics.

    I thought that the New York Times did an okay job on “junk DNA” after the paradigm shift from ENCODE.

    I expect to see a good Scientific American article.

    This is what Scientific Revolution looks like, and what could be more exciting?

    But isn’t it a shame that the mainstream media are ignoring the story? Of course, they hate to admit that they are as ignorant of evolution as are the politicians.

    Thank you, as always, for your bright light shining through the fog, smog, disinformation, and darkness.

  2. #2 RPM
    July 15, 2007

    The ENCODE data are revolutionary in their volume, not in any new phenomena they reveal. There is no scientific revolution going on.

  3. #3 whimple
    July 15, 2007

    Agree there’s no revolution. The revolution that needs to happen is the realization that it is possible to tie up hundreds of researchers and bazillions of dollars doing huge mega-projects that turn out to generate results that just aren’t that interesting. Of course, after blowing through all those resources, they MUST conclude that it’s revolutionary, regardless of whether it actually is or not.

  4. #4 RPM
    July 15, 2007

    Large projects (like ENCODE, HapMap, etc) are important not for the preliminary findings reported in the 1st paper(s). They provide vast amounts of publicly available data, which makes them valuable resources.

  5. “Revolution” may be the wrong word – it is much too political. Let’s just all agree (impossible to disagree with) that there is a “paradigm-shift”, meaning the a set of dogmas were *officially* abandoned. (The ENCODE report by June 14th, 2007 did not break any news; the project went on since 2003-2007 and the dozens of groups in 11 contries were increasingly aware of the unfolding picture through those years. In fact, a large number of discoveries have been published in the process.)

    The extreme significance of the “ENCODE report” is that now the widespread suspicicion is *officially confessed* that modern genetics went out on a limb for decades (since Ohno, 2972) – and the branch is broke, and collapsed.

    I would not hold my breath on the false hope that NIH might suddenly release gezillion dollars (that they don’t have) for revolutionary discoveries (even if they are only called a paradigm-shift). Embarrassment might be one reaseon, why not. Second, their tremendous intertia already compelled to ask double the money already spent ($100 M) just to *continue* the study after 1% “completed”. (This contains zero resources to interpret – “re-think” is perhaps a too strong word, implying prior errors). Third the International PostGenetics Society (http://www.postgenetics.org) aside, there is no organized body for a collective effort.

    The “paradigm-shift” will produce a social revolution. The scientific details that “genes” are not the units of hereditary material, just as the “atom” has proven to be fragmented or fragmentable, the “junk” is not inert but at the least, most if it is active regulatory material – and even the Darwin/Lamarck “dogma” must be tilted back at least to some extent to Lamarkism; the genome changing in a single lifetime may not be understood by the masses.

    However, each and every person, in every society, especially those who are dying, suffering, or can be affected by “Junk DNA diseases” (Alzheimer’s, Parkinson’s, “all if not most of hereditary diseases”; cf. http://www.junkdna.com/junkdna_diseases.html ) will be totally outraged if society (meaning NIH, drug companies, etc, Congress distributing public resources) continue to do as little about such dreaded diseases as presently.

    “Big Pharma” will not wait for any “public outrage”. They are already buying up Intellectual Property of “short repetitive sequences” (most particularly, but not exclusively mircoRNA-s), to the tune of $300-$1,100 M chunks, apiece.

    USA Agencies might not be (already demonstrably are not) the first to move. (Inertia and politics is too big). The IPGS formally abandoned the “Junk DNA” notion half a year before the ENCODE-report in a small struggling Central European country. If an “EU-PostGenetics Initiative” will emerge before an “NIH-PostGenetics Study Program” is not just anybody’s guess – it is also an issue for a vital (I mean literally vital) Global competition.

    How about the Press?

    Science magazine already blew chances to lead – at the least The Scientist picked up the issue; and New York Times is warming up to it, as well. The problem is, that most journalists are still reeling (have been reeling, since 2001, when it first turned out that the human genome has so few genes). Most of them simple don’t understand the issues. For most of them, it hasn’t even dawned that science was (successfully) “framed” into a straightjacket (of 1.3% genes in the human genome) and with the straightjacket ripped off “the emperor is without clothes”.

    However, all this will very rapidly change. Every major paradigm-shift will catapult those who are best prepared for clear understanding, decisive action – and an effective “PR-plan”.

    The two bad news: “May you live in exciting times” and “the revolutions eat up their children”.

    Thus, I try to shut up and focus on my FractoGene book…

    pellionisz_junkdna.com

  6. #6 RPM
    July 16, 2007

    If you’re going to label something as a revolution the least you can do is say what that revolution is. Pellionisz comment has the highest hype to words ratio, while simultaneously having one of the lowest content to words ratios, I have ever seen.

    The scientific details that “genes” are not the units of hereditary material, just as the “atom” has proven to be fragmented or fragmentable, the “junk” is not inert but at the least, most if it is active regulatory material

    Some non-coding sequences are important for regulating transcription and some are important as transcribed, but not translated, RNAs. The majority of the human genome has no function in the eyes of the human organism.

    and even the Darwin/Lamarck “dogma” must be tilted back at least to some extent to Lamarkism; the genome changing in a single lifetime may not be understood by the masses.

    And just because there are changes to the genomes over the lifetime of an organism (both somatic mutations and epigenetic changes), those changes mean nothing in the eyes of evolution if they do not occur in the germ line.

  7. #7 Jonathan Vos Post
    July 16, 2007

    Dr. Andras J. Pellionisz has an interesting web site. If I get his drift, he insists that the genome is fractal in order to build fractal organisms.

    While there are cases where fractal models are good in biology, such as the branching of arteries down to fine capillaries, and the airways in the lung, the fractal genome is not (in my humble opinion) plausible, as presented on that website.

    There may be some sort of hierarchy of genome – chromosome – region – gene – codon but the ENCODE results specifically suggest otherwise. What gets onto RNA depends on the timing within the cell cycle, what’s upstream, what’s downstream, in a very heterarchical way.

    Pellionisz makes a hand-waving argument with computer graphics of fractal plants (branching stems, leaves).

    The point of the latter, hwoever, is that a single parameter, or a couple of parameters define the graphics plant. The fractal reduces the number of variables needed to define the system. Given the billions of nucleotides in each cell of your body, that does not seem to be a useful model.

    Moreso: the codon is divided into 3 nucleotide pairs, each of which is divided into atoms, each of which is divided into nucleons and electrons, with the nucleons divided into quarks and gluons, and so forth, but those are qualitatative changes in the nature of the model itrself, at different scales, rather than a scale-invariant continuation of an infinite recursive process.

    Fractals are wonderful, one of the great inventions/discoveries of the 20th century. But, just because you’re holding a hammer, not everything in nature is a nail needing to be pounded down infinitely.

    Mind you, I’ve been saying for at least 3 decades that “we are fractal organisms who evolved to survive in a fractal cosmos” but that was just a younger me being provocative and poetic, not really offering a scientific model.

    Beware the exclusive dependence on prose, with no equations.

    While I share Pellionisz’ enthusiasm, willingness to think outside the box, and faith that ENCODE reveals a “paradigm shift” [in the strict sense of T. S. Kuhn], I am impelled to ask: what are the specifics of the suggested mathematical model, and what predictions does it provide?

  8. #8 Pellionisz
    August 13, 2007

    “While I share Pellionisz’ enthusiasm, willingness to think outside the box, and faith that ENCODE reveals a “paradigm shift” [in the strict sense of T. S. Kuhn], I am impelled to ask: what are the specifics of the suggested mathematical model, and what predictions does it provide?”

    The “Purkinje neuron predictions of FractoGene” have been experimentally tested, supported and published in the peer-reviewed science journal

    The Cerebellum

    For the fugu, the paper provides experimental support. Shortly after its publication, prediction of the genome size for the guinea pig was supported. For the zebrafish, experimental data should be easily available.

    The “Methylation prediction of FractoGene” has also been put out, unconstrained. It is not limited to the cerebellar Purkinje neurons.

    pellionisz_at_junkdna.com

  9. #9 saurabh
    January 8, 2008

    A bit late, replying to #3 (whimple) – the press is largely irrelevant; I haven’t seen many people in the scientific press calling the ENCODE results a revolution of any sort. It was a pretty mediocre result, and I think most people agree on that. Waste of money? I wouldn’t say that. It did do SOMETHING – provide a lot of interesting data for further studies. And relatively cheap – if a “large” project costs around $1 million, you have a pretty cheap field. Let’s not blow things out of proportion, here. Hell, even the ENCODE 100 RFA only costs $23 million. That is NOT A LOT OF MONEY to spend on basic science research.

  10. #10 ChrisC
    January 9, 2008

    Whether or not there is useless base pair baggage in our genomes, the term ‘Junk DNA’ is a relic of a much more ignorant time in the field of human genetics. Like the author of the article from ‘The Scientist’, I’m not fond on replacing Junk DNA with “DNA of yet-to-be-determined function” but I also doubt that we’ve found ourselves to be wrong for the last time when it comes to branding useless DNA. I seems that further regulatory regions, non-translated RNAs and who knows what else are waiting to be discovered. Even DNA that may prove to be useless today provides evidence of our evolutionary history, or may help fuel our future evolution. So regardless whether or not Junk DNA pays its way for its carriage from one generation to the next or is simply freeloading, we would be remiss to omit it from study.

  11. #11 RPM
    January 9, 2008

    Are there regions of the human genome that we currently define as non-functional but which actually do have function? Most definitely, yes. But those regions make up a small fraction of the non-coding or unknown function regions of the genome. It’s safe to say that the majority of the genome is nonfunctional. But that doesn’t mean that research into the function of regions with unknown functions is not fruitful — it most certainly is.

    In regards to evolutionary history, the non-functional stuff is often the most informative regarding evolutionary history — especially amongst closely related taxa or groups. It tells us about evolutionary relationships and historical demography. It’s actually more informative in that sense because it’s non-functional.