Thursday, October 07, 2010

Three Conundrums

 
Razib Khan over at Gene Expression is discussing a recent article on epigenetics and other "revolutions" in molecular biology. Check out Razib's postings: Arise the vehicle! Arise the cell! and Epigenetics – what revolution?.

The article in question is by Steve Talbott1 and it's published in The New Atlantis: Getting Over the Code Delusion. Here's how the editors introduce the article ...
Editor’s Note: This is the first in a planned set of essays by Mr. Talbott explaining the significance of a revolution in genetics and molecular biology that has only just begun to receive public attention. Although this essay is at times necessarily tech­nical, we trust that our readers will not find it prohibitively so — and we have appended a modest and informal glossary to help smooth the path.
You all know where this is going, don't you?

Talbot sets up his "revolution" by describing several problems.
A number of conundrums have helped to nudge molecular biology toward a more contextualized understanding of the gene. To begin with, the Human Genome Project revised the human gene count downward from 100,000 to 20,000–25,000. What made the figure startling was the fact that much simpler creatures — for example, a tiny, transparent ­roundworm — were found to have roughly the same number of genes. More recently, researchers have turned up a pea aphid with 34,600 genes and a water flea with 39,000 genes. Not even the "chimps are human" boosters were ready to set themselves on the same scale with a water flea. The difference in gene counts required some sort of shift in ­understanding.
I've addressed this before. Knowledgeable experts in the field were predicting 30,000 genes at least as far back as the late 1960s. Their predictions were very close to the mark [False History and the Number of Genes] [Humans Have Only 20,500 Protein-Encoding Genes] [Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome]. Steve Talbot hasn't done his homework. This isn't a very auspicious beginning.
A second oddity centered on the fact that, upon "deciphering" the genetic Book of Life, we found that our coding scheme made the vast bulk of it read like nonsense. That is, some 95 or 98 percent of human DNA was useless for making proteins. Most of this "noncoding DNA" was at first dismissed as "junk" — meaningless evolutionary detritus accumulated over the ages. At best, it was viewed as a kind of bag of spare parts, borne by cells from one generation to another for possible employment in future genomic innovations. But that’s an awful lot of junk for a cell to have to lug around, duplicate at every cell division, and otherwise manage on a continuing basis.
In this day and age, anyone who equates junk DNA with non-coding DNA isn't worth reading. They've lost all credibility as far as I'm concerned.

Talbott explains the solution later on in his article when he says ...
So what’s going on? These puzzles turn out to be intimately related. As organisms rise on the evolutionary scale, they tend to have more "junk DNA." Noncoding DNA accounts for some 10 percent of the genome in many one-celled organisms, 75 percent in roundworms, and 98 percent in humans. The ironic suspicion became too obvious to ignore: maybe it’s precisely our "junk" that differentiates us from water fleas. Maybe what counts most is not so much the genes themselves as the way they are regulated and expressed. Noncoding DNA could provide the complex regulatory functions that direct genes toward service of the organism’s needs, including its developmental needs.
Anyone who states or implies that there is a significant correlation between total haploid genome size and species complexity is either ignorant or lying.

Larry Moran
Genome Size, Complexity, and the C-Value Paradox
"Organism rise on the evolutionary scale"? Has Talbott done any research at all for this article? His understanding of evolution is no greater than kindergarten level if he believes that there's an evolutionary scale with us near the top.

The idea that noncoding DNA contains sequences that govern gene expression has been with us for fifty years. That's hardly revolutionary. The idea that the amount of junk DNA in a genome equates to complexity has been soundly disproven. The idea that humans might need a million base pairs of DNA to control expression of every gene is ludicrous and has absolutely no evidence to support it. In fact, nobody I know has ever shown that mammalian genes require more regulatory sequences than insect genes or those of crustaceans (water fleas). What we have here is a perfect example of The Deflated Ego Problem.

What about the third "conundrum"?
Another conundrum — perhaps the most decisive one — has been recognized and wrestled with (or more often just ignored) since the early twentieth century. With few exceptions, every different type of cell in the human body contains the same chromosomes and the same DNA sequence as the original, single-celled zygote. Yet somehow this zygote manages to differentiate into every manner of tissue — liver, skin, muscle, brain, blood, bone, retina, and so on. If genes determine the form and substance of the organism, how is it that such radically different cellular architectures result from the same genes? What directs genes to produce the intricately sculpted and differentiated form of a complex organism, and how can this directing agency be governed by the very genes that it directs?
We've known the basic answer to this "conundrum" for about five decades. Talbott's idea of a revolution is very strange.

Don't bother reading the article in The New Atlantis. There's nothing "new" there and it may make you very angry.


1. Steve Talbott is a Senior Researcher at The Nature Institute. "My primary undertaking right now is a critique of conventional science with a view toward establishing the foundations of a new, qualitative science. The project, which requires an extraordinarily radical assessment of contemporary habits of thought, is headquartered here."

13 comments :

  1. So, is the Nature Institute an Alan-Sokal-inspired attempt to punk those who think that mysticism has something to do with science or are they the mystical equivalents of Social Text?

    It appears, particularly from their holistic explanation of evolution that they are slightly less clued in than the editors of Social Text.

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  2. "My primary undertaking right now is a critique of conventional science with a view toward establishing the foundations of a new, qualitative science."

    The ego is strong in this one.

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  3. Thanks to Larry for braving that vortex of suck so we don't have to.

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  4. I scrolled down to the illustration in the original article, saw that the guy does not know what nucleosome is and decided there is practically no way it's worth reading.

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  5. gillt says,

    The ego is strong in this one.

    So is the irony.

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  6. It's tough for the non-scientist reader to know where to go for reliable info. on epigenetics or evo-devo in book or article form. Are the Sean Carroll books (I have a couple but have yet to read them) worthwhile? If there are better people explaining these fields in a clear manner, who are they?

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  7. As organisms rise on the evolutionary scale, they tend to have more "junk DNA."

    John Mattick, are you there?

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  8. As organisms rise on the evolutionary scale, they tend to have more "junk DNA."
    So the onion is the pinnacle of evolution?

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  9. No, the pinnacle of evolution is a little flower Paris japonica with its genome size 50 times bigger than human.

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  10. Anonymous says,
    Are the Sean Carroll books (I have a couple but have yet to read them) worthwhile?

    I have read one, and I can tell you they are very worthwhile.

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  11. Steve Talbott is a moron. I read his NetFuture columns for years; I never knew anyone who could be so completely clueless on so many issues - although George Gilder has got to be a close second.

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  12. "I've addressed this before. Knowledgeable experts in the field were predicting 30,000 genes at least as far back as the late 1960s."

    So what? Anthro 1 teachiong materials were giving the 100k figure in the early 2000s (I saw them.) What they were thinking in the '60s is meaningless if the consenses had shifted.

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  13. J. M. B. says,

    What they were thinking in the '60s is meaningless if the consenses had shifted.

    The consensus among knowledgeable experts had not shifted. What shifted was uninformed speculation by people who didn't bother reading the scientific literature. Unfortunately, those people were the ones doing the sequencing so they got a lot of press.

    When their uninformed speculation turned out to be wrong they tried to pretend that everyone else had it wrong as well. That's just not true. Throughout the 1990s there were plenty of us who knew that humans had a lot fewer than 100,000 genes. Even if you look at the contest guesses [Facts and Myths] you'll see that the majority of guesses by the sequencers was less than 50,000. Very few people guessed there would be more than 100,000 genes so even the facts are wrong.

    It's amazing to me that your introductory anthropology course would have taught you that there were 100,000 genes in the year 2000. By then we already had the sequences of two chromosomes and we knew that number was way off. Did your anthropology teachers give you a source for that false information?

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