Arise the vehicle! Arise the cell!

By Razib Khan | October 6, 2010 3:00 pm

A quick follow up to my post Epigenetics arise! Adam Keiper, the editor of The New Atlantis, has graciously sent me a copy of the article, Getting Over the Code Delusion. I’ve also been told that the piece will be free to all on the website at any moment, so I invite readers to check it out when that occurs [it’s online].

First, I want to add that Mr. Keiper doesn’t believe that the Wikipedia entry for The New Atlantis is particularly accurate. William Kristol for example has never been published in The New Atlantis, while the Wikipedia entry says he has. I would add though that many of the people associated with the magazine may broadly be considered “conservative.” Not that there’s anything wrong with that, I too may broadly be considered “conservative”! Others associated with the publication, such as Robert Zubrin, are not known for their politics from what I know.


As for Steve Talbott’s essay, it’s a peculiar beast. It weighs in at 25 pages, but it’s only the first of a series. Getting Over the Code Delusion is to a large extent a primer on molecular genetics, cytology, and genomics for the uninitiated. That’s a tall order. It’s really hard to avoid pitfalls of oversimplification in the space provided, so I’ll let readers judge where Talbott misleads or misunderstands in the details. Another definite aspect of the piece which is a bit out of the ordinary is its literary quality, which one does not usually find in primers of this sort. Consider:

…Noncoding DNA could provide the complex regulatory functions that direct genes toward service of the organism’s needs, including its developmental needs.

That suspicion has now become standard doctrine….

I think coventional technical writing would have avoided a word like “doctrine” (and I think it also misleads as to the disputes around issues such as the importance of cis-regulatory elements, which are not quite settled). But Talbott’s audience does not necessarily consist of individuals who get Science and Nature in the mail every month (or have academic access). So a more thorough judgement probably will have to await the whole series.

But I think I can already glean the gist of where Talbott is going: he wants to dethrone the centrality of the genetic sequence in our understanding of how life emerges and is specified. He is right to point out that debates about the importance of gene regulation, higher order genomic structures, and epigenetics, throw a monkey-wrench into a cool reductionist system where the mapping between genotype and phenotype is going to be easy to unravel. In this Steve Talbott is following many others who have objected to the image of genes as “puppet masters” which control our destinies. Included in this set is Richard Dawkins, who felt that the publicity materials around The Selfish Gene, and misunderstandings by other academics, resulted in a distortion of his underlying message. But in any case the science is still very much in flux. The old order may have fallen, but nothing has risen to replace it. Talbott nicely reminds us that 20 years ago mainstream scientists were engaging in genetic triumphalism with the success of family based linkage studies in adducing variants associated with recessive diseases such as cystic fibrosis. But my main worry is that the triumphalists of our age are again speaking too soon. Science is always full of surprises.

Addendum: One impression I get from Getting Over the Code Delusion is that the author is eliding the distinction between deterministic processes understood on a molecular genetic scale, and statistical associations on the scale of populations and the level of genomics. Prediction need not be conditional on perfection, and clearly systematic patterns and processes can emerge from a seemingly chaotic welter. That’s what developmental genetics certainly teaches. Also, early in the piece Talbot seems to be diminishing the importance of the sequence identity between the chimpanzee and the human, asking that “…we could have done the obvious and direct and scientifically respectable thing: we could have observed ourselves and chimps, noting the similarities and differences.” I think this sort of common sense objective phenetics when it comes to humankind’s closest relatives is not so easy to come by. A history of the taxonomic and evolutionary confusions as to the nature of relations among the homonid lineage are such that this was one area where phylogenetics informed at the sequence level was very useful. Perhaps it’s been overplayed, but it was, and is, a very significant finding, and the perceptions of broad phenotypic differences don’t refute that reality.

CATEGORIZED UNDER: Genetics
  • http://www.iSteve.blogspot.com Steve Sailer

    It’s hard for people to keep straight in their head the difference between “A influences B” and “A determines B.”

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  • DK

    he wants to dethrone the centrality of the genetic sequence in our understanding of how life is specified

    When someone attempts that, it’s not a bad idea for that someone to familiarize himself with basic concepts and terms to start with.

    “… nucleosomes as spools around which DNA is wrapped”, “a nucleosome spool with DNA wrapped around it” – when the guy can’t even get the correct definition of something he makes central in the article, what are the chances that there will be anything interesting there? Sheesh.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    “… nucleosomes as spools around which DNA is wrapped”, “a nucleosome spool with DNA wrapped around it” – when the guy can’t even get the correct definition of something he makes central in the article, what are the chances that there will be anything interesting there? Sheesh.

    that’s why i say link to the definitions of molecular biological stuff. let someone else take the fall if there’s an error.

  • biologist

    As far as I can tell, the existence of epigenetic mechanisms doesn’t change anything that we *should* have already known about the social implications of genetics (i.e. what people care about).

    Quantitative genetic methods that estimate a substantial contribution of genetic variation to phenotypic variation do not now and has never told us anything about actual or counterfactual causal mechanisms involved. They have also never told us much about development other than what we already knew must be true — there will be genes involved in some way.

    Nothing we’ve learned in the last 30 years about molecular biology makes any difference at a general level to those conclusions. What it mostly does is make clearer that the causal mechanisms behind phenotypic variation in complex traits are probably themselves really really complex.

    As soon as you realize that complex traits have non-Mendelian inheritance patterns — something that’s been abundantly clear for many many decades — everything else follows and epigenetics only adds new dimensions to the causal mechanisms that might be involved.

    Whether a trait is amenable to manipulation (and at what stages of development) is an interesting and very challenging question, but there’s no revolution in our understanding of biology involved in asking it. The only way to see a revolution is to ignore all of the incremental changes in understanding that have happened between decades.

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  • http://natureinstitute.org Steve Talbott

    DK quotes from my article in The New Atlantis, “Getting Over the Code Delusion”:

    “… nucleosomes as spools around which DNA is wrapped”, “a nucleosome spool with DNA wrapped around it” – when the guy can’t even get the correct definition of something he makes central in the article, what are the chances that there will be anything interesting there? Sheesh.

    This is rather disgusting. First, DK does not make his point clear. Second, he proceeds from this unclarity to a condescending dismissal. And third, he is wrong if he is saying there is some sort of inconsistency in the phrases quoted. Karolin Luger, who first published the nucleosome structure, happened to remark in one of her later papers about the common misuse of the term “nucleosome”, mentioning that “the nucleosome actually *includes* the DNA”. Both of my remarks can and should be read as reflecting that understanding. I refer to nucleosomes as “spools around which the DNA is wrapped”, and I refer to the nucleosome spool “with DNA wrapped around it”. Finally, even if my language embodied the confusion rampant in the technical literature, it would hardly be a matter worth mentioning, for the same reason Luger doesn’t harp on the point: people don’t have much difficulty understanding what is being said. Why trivialize the discussion?

  • http://natureinstitute.org Steve Talbott

    In order to avoid further petty criticism, I should add that the nucleosome “spool” is more formally referred to as the nucleosome “core particle”, and that the structure Luger is commonly said to have determined is that of the core particle. (Her paper was entitled, “Crystal structure of the nucleosome core particle at 2.8 Å resolution”.) However, she said a good deal about the DNA as well. And, for whatever it’s worth, the image from her that I used in my article shows the DNA double helix, in stick-figure representation, wrapped around the spool.

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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