Isn’t he special!

Credit: Marrabbio2
Credit: Marrabbio2
There’s a nice letter in Nature right now with an understated title, Mating advantage for rare males in wild guppy populations. But if you dig deeper you see some moderately grand claims being made. The key issue is that the authors seem to be implying that negative frequency dependent selection (NFDS) is a major factor in maintaining genetic diversity in populations. A reductio ad absurdum of the problem might be to ask why a superior and ideally fit morph does not dominate the whole planet? A more elaborated question lay at the heart of Charles Darwin’s The Origin of Species. Fundamentally: why diversity? There have been many answers posited (e.g., see W. D. Hamilton’s ideas in regards to sex, Narrow Roads of Gene Land). We needn’t try to tackle the whole problem here, no matter what needs to be written in grant applications. Guppies are sufficient and interesting in and of themselves.

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Right science

220px-JohnvonNeumann-LosAlamos
John von Neumann
About a month back a researcher at Yale published survey results which showed that Tea Party members exhibited more science knowledge than the general public, somewhat to his chagrin. I wasn’t particularly surprised, because the knowledge of science as it relates to political ideology is somewhat complex. Often the right-leaning get lower marks because of strong reactions to questions perceived to be ideological. It’s a rather robust finding that the more intelligent are more ideological, so it is no surprise that a group like the Tea Party would do better on tests which measure underlying cognitive orientation.

This was brought back to my mind by a new piece in The Atlantic which had a “Slate-pitch” sort of title: The Republican Party Isn’t Really the Anti-Science Party. There was some comment on Creationism in the piece, so I wanted to review the data on this mostly ideologically freighted of the standard science questions asked of the public. To do this I used the General Social Survey. To limit demographic confounds I constrained the samples to non-Hispanic whites who responded 2006-2012 (“Selection Filter(s): Race1(1) Hispanic(1)”). Additionally, I partitioned the data into two classes, non-college and college-educated (“Degree(r:0-2;3-4)”). Then I looked at political party identification and ideology (“Partyid” and “Polviews(r:1-2;3;4;5;6-7)”).

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bioRxiv is here

bioRxivFor years many in the biological sciences community have been jealous of the exist of arXiv. This preprint server allows researchers to distribute their work widely to all comers. On occasion when when there have been debates about mimicking arXiv for biology there has been skepticism about the nature of the outcomes (my own rejoinder is that fields where a preprint culture is the norm, such as economics and physics, don’t seem to be doing badly). Now we’ll see if the end is nigh in biological science due to preprints; bioRxiv is live (sponsored by CSHL). The first paper, The Population Genetic Signature of Polygenic Local Adaptation. There’s not much up yet, but there will be.

Vaccination, and social information networks

Preventable
If you have not read Julia Ioffe’s story about getting whooping cough at the age of 31 (also see follow up), you might want to. Here’s some further context, Vaccine Refusals Fueled California’s Whooping Cough Epidemic. This topic has been covered and dissected in great detail by many writers and scientists, so I won’t repeat what you already know in regards to herd immunity. There’s no point in preaching to the choir.

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Selection happens; but where, when, and why?

Distribution of SLC452 variation at SNP rs1426654. Credit, HGDP Browser
Distribution of SLC452 variation at SNP rs1426654. Credit, HGDP Browser
Nina Davuluri, Miss America 2014, Credit: Andy Jones
Nina Davuluri, Miss America 2014, Credit: Andy Jones

One of the secondary issues which cropped up with Nina Davuluri winning Miss America is that it seems implausible that someone with her complexion would be able to win any Indian beauty contest. A quick skim of Google images “Miss India” will make clear the reality that I’m alluding to. The Indian beauty ideal, especially for females, is skewed to the lighter end of the complexion distribution of native South Asians. Nina Davuluri herself is not particularly dark skinned if you compared her to the average South Asian; in fact she is likely at the median. But it would be surprising to see a woman who looks like her held up as conventionally beautiful in the mainstream Indian media. When I’ve pointed this peculiar aspect out to Indians* some of them of will submit that there are dark skinned female celebrities, but when I look up the actresses in question they are invariably not very dark skinned, though perhaps by comparison to what is the norm in that industry they may be. But whatever the cultural reality is, the fraught relationship of color variation to aesthetic variation prompts us to ask, why are South Asians so diverse in their complexions in the first place? A new paper in PLoS Genetics, The Light Skin Allele of SLC24A5 in South Asians and Europeans Shares Identity by Descent, explores this genetic question in depth.

Much of the low hanging fruit in this area was picked years ago. A few large effect genetic variants which are known to be polymorphic across many populations in Western Eurasia segregate within South Asian populations. What this means in plainer language is that a few genes which cause major changes in phenotype are floating around in alternative flavors even within families among people of Indian subcontinental origin. Ergo, you can see huge differences between full siblings in complexion (African Americans, as an admixed population, are analogous). While loss of pigmentation in eastern and western Eurasia seems to be a case of convergent evolution (different mutations in overlapping sets of genes), the H. sapiens sapiens ancestral condition of darker skin is well conserved from Melanesia to Africa.

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The future always advances

The last week has seen a lot of chatter about the slapping down of the diagnostic patent by Sequenom, Judge Invalidates Patent for a Down Syndrome Test:

A federal judge has invalidated the central patent underlying a noninvasive method of detecting Down syndrome in fetuses without the risk of inducing a miscarriage.

The ruling is a blow to Sequenom, a California company that introduced the first such noninvasive test in 2011 and has been trying to lock out competitors in a fast-growing market by claiming they infringe on the patent.

Sequenom’s stock fell 23 percent on Thursday, to $1.92.

The judge, Susan Illston of the United States District Court in Northern California, issued a ruling on Wednesday that the patent was invalid because it covered a natural phenomenon — the presence of DNA from the fetus in the mother’s blood.

The existence of intellectual property is a utilitarian one. That is, these are institutions which are meant to further the cause of creativity and innovation. Is there going to be an abandonment in this domain of the push toward technological innovation? Coincidentally in the last week of October Sequenom put out a press release which heralded some advances in its panel:

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Open Thread, 11/3/2013

Origins-of-the-Irish1After reading Ancestral Journeys, I decided to get J. P. Mallory’s The Origins of the Irish. A bit on the academic side for some, but definitely a good dive into the literature. Mallory is well aware of the latest genetic research, so this is as up-to-date as it gets. It’s a good case study in how multidisciplinary prehistoric studies should be done.

As I’ve suggested earlier prehistory looks to be a good deal more complex than we had previous thought, so expanding beyond single methodological perspectives is probably essential if we really care about truth.

In other news, a short piece in The New York Times refers to Salafis as ‘ultraconservative.’ I think this misleads most people about the nature of Salafism: it is a radical utopian system which recently arose out of Islam’s confrontation with Western derived modernity. It isn’t conserving anything. This aspect of Salafism explains why Saudi Arabia condones the bulldozing of Muhammed’s tomb and celebrates modern monumental architecture in Islam’s holy city.