Copy number variation & being human

Gene Duplications Give Clues to Humanness:

All told, the researchers found more than 4000 genes that showed lineage-specific changes in copy number, with the numbers steadily increasing over evolutionary time. Humans, for example, only had 84 genes with increased copy numbers over those of our closet relatives. In contrast, lemurs, which have evolved for 60 million years, have 1180 genes with extra copies. “This is further evidence that genomic differences between humans and other primates is far, far more complex than we originally imagined they might be,” says Ajit Varki, who studies human/chimpanzee differences at the University of California, San Diego. “However, many of the differences may or may not be relevant for explaining ‘humanness.'”

We’ve talked about copy number variation before. Obviously dosage of gene products can be directly impacted by this. We’ve come a long way from non-synonymous base pair changes baby! Though please note that loss of function (fewer copies) might be just as important as gain of function (more copies).

Eugenics, schmgenics

Ezra & Ross as still arguing about the definitions for eugenics and what not. Clearly there is a lot of baggage associated with the “e-word.” In any case, in an email exchange with Armand Leroi about the use of the term “eugenics” to refer to selective abortions of individuals whose fitness verges upon zero (and so aren’t going to have a long term impact on the gene pool anyhow) it seems clear that his own view of the term is more liberal than Ezra or mine. And when someone in John Brockman’s stable talks, we should listen because these are the public intellectuals who have disproportionate impact on our understanding of scientific terms (another Brockmanite, Dawkins, was the one who introduced eugenics as one of his “Dangerous Ideas”). I suspect operationally more people would align with a broad usage of the term, though “eugenics” has too many negative associations for it to be resurrected I would bet. But in any case, as I have suggested the semantical argument is besides the point, no matter if x, y & z are instances of eugenics, x, y & z are already penetrating the domain of normalcy. As many of Ross & and Ezra’s readers note part of Ross’ objection surely has to do with the fact that he is opposed to abortion on principle, which is a proximate process via which selection for traits can occur. How would he feel about the screening of unfertilized gametes? One can imagine super-wealthy social conservatives going to the extent of not destroying life in such a manner. For Dune nerds you know that the Bene Tleilax perceive themselves to not be violating the injunctions of the Butlerian Jihad (which do include bans on particular genetic technologies), but they certainly violate the spirit of the law. Conversely, I assume that most pro-abortion rights liberals are not down with the creation of Aryan supermen, but genetic technology is going to be advanced enough soon that two parents who want blonde and blue-eyed children and have the genetic potentiality for such offspring can load the die. I have noted in email to friends that with the knowledge of the genetics of skin color many South Asian couples could now load the die so that their offspring would be selected from the lighter skinned range of the probability distribution (the extant variance of the South Asian genetic architecture naturally results in offspring that deviate from the expectation a lot). These are questions which I think are more interesting than the definition of eugenics.

Update: The Elf weighs in. I think she hits it about right, though this is a sprawling issue, made worse by the fact that there are disagreements about the term. The only qualification I would have is that some Lefty/progressives with a strong sympathy toward Deep Ecology and China’s population policies might be the sliver of a connection that conservatives might be looking for between the past and the present (albeit, this is a very small group from what I can tell).

Related: Notes on Eugenics.

Malthusian me?

In the comments below in regards to eugenics I made an argument that rationing is going to be inevitable in national health care systems as the information we have about the propensity (or inevitability) of diseases outruns the ability to treat those diseases. In particular, I believe that it may come to the point where though one can treat something in theory with medical technology the costs may simply be prohibitive. The argument I’m making smells a lot like Malthusianism, insofar as I believe that genomic diagnostic technologies will decrease in price in a manner that scales downward to a far greater extent then the treatments for those diagnosed probabilities for the total sample space of possibilities. But of course, we know how Malthusianism worked out when it came to the argument about population & food production, so I’m not sure about this. We (humans) have a tendency not to account for future innovation. In the near-term (less than 20 years) what do those who know about the costs of medicine think?

Martin Nowak, man of God

Carl Zimmer has a fascinating profile of Martin Nowak, whose work I have talked about before. Carl saves the best for last:

Dr. Nowak sometimes finds his scientific colleagues astonished when he defends religion. But he believes the astonishment comes from a misunderstanding of the roles of science and religion. “Like mathematics, many theological statements do not need scientific confirmation. Once you have the proof of Fermat’s Last Theorem, it’s not like we have to wait for the scientists to tell us if it’s right. This is it.”

Neandertals & humans gettin’ along

Were Neanderthals our enemies or lovers?:

One difficulty in working out how these ancient humans rubbed along is that there is a lack of clear evidence of close encounters. That changed two years ago when a paper was published by Prof Paul Mellars, of Cambridge University, and his student Brad Gravina, suggesting the two kinds of human lived together at Grotte des Fées at Châtelperron in France.
The study was criticised but the Cambridge team published a detailed rebuttal. “The importance of the new paper is that it confirms at least 2,000 years of coexistence/overlap between Neanderthals and modern humans in this one small region,” said Prof Mellars. “This is the only direct, unambiguous evidence of this so far.”

GWA for multiple sclerosis

The latest phenotype to get the scrutiny of a genome-wide association study is multiple sclerosis: three separate reports (ok, only one of them is genome-wide) point to variation in various immune system genes as predisposing to the disease. The effects of one of the variants seems to be non-additive– one group reports that the heterozygotes for the “causal” allele seem to actually be protected, while the homozygotes have a higher risk.

There are a number of reason why this could be the case– linkage disequilibrium patterns and the existence of multiple predisposing alleles can lead to odd patterns of risk, even flipping the apparent effect in some cases. Another possibility, of course, is that there’s some interesting biology there. More research, as they say, is needed.

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Eugenics, what's in a term?

Ross Douthat is concerned with the “New Eugenics.” He linked to my summation of some of the data which Armand Leroi has collected on the rise of selective abortions & genetic screening. Ezra Klein isn’t buying Ross’ characterization of course; actually, like Ezra I think there are serious differences between the old eugenics which emerged from the biometrical school (which became quantitative genetics) and the new eugenics which is predicated on the ubiquity of genomic & fertility technology. Nevertheless, in the proximate sense, for example in our life spans, it might not make much of a difference whether the selective abortions are of heritable traits or those with would result in sharply reduced fitness anyhow (like Down Syndrome). It seems to me that to some extent the Left, which does not fear reproductive technology, is allergic to the term eugenics because of its historical resonances. I’m not going to argue over a word. But, I will offer that Richard Dawkins, no Ross Douthat, is willing to bring up the term in reference to the trends in genetics. I think that sentiments and dynamics reminiscent of the old eugenics is pretty much inevitable now that “we have the technology,” it really doesn’t matter what you call it.

P.S. And once we get government backed health care in the USA I’m pretty sure that the element of coercion will come into play (perhaps we’ll call it “incentives for terminative preventative care” or something).