Paying for pop gen a thing of the past?

Via Haldane’s Sieve, Genetics has a new preprint policy:

POLICY ON PRE-PRINT DEPOSITS

GENETICS allows authors to deposit manuscripts (currently under review or those for intended submission to GENETICS) in non-commercial, pre-print servers such as ArXiv. Upon final publication in GENETICS, authors should insert a journal reference (including DOI), and link to the published article on the GENETICS website, and include the acknowledgment: “The published article is available at www.genetics.org.” See http://arxiv.org/help/jref for details.

Here’s a more thorough list of preprint guidelines by journal. For all practical purposes this means that population genetics can now percolate more freely among the masses. Many of the differences between “draft” preprints and the final manuscript have to do with formatting, etc., from what I have seen. So the content shall flow!

 

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Re-imagining genetic variation

To the left is a PCA from The History and Geography of Human Genes. If you click it you will see a two dimensional plot with population labels. How were these plots generated? In short what these really are are visual representations of a matrix of genetic distances (those distances being general FST), which L. L. Cavalli-Sforza and colleagues computed from classical autosomal markers. Basically what the distances measure are the differences across populations in regards to their genetics. The unwieldy matrix tables can be visualized as a neighbor-joining tree, or a two dimensional plot as you see here. But that’s not the end of the story.

In the past ten years with high density SNP-chip arrays instead of just representing the relationship of populations, these plots often can now illustrate the position of an individual (the methods differ, from components analysis or coordinate analysis, to multi-dimensional scaling, but the outcomes are the same).

 

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Singularity Summit 2012 – be there!

As regular readers know I have been to two previous Singularity Summits (2008 and 2010), and will be at the 2012 event. The speakers look particularly interesting to me this year. I may finally be stupid enough to blurt out to Vernor Vinge how awesome the adolescent me thought Fire Upon the Deep was (I downed a beer with Vinge in 2008, but didn’t say a word to him). Carl will be there again, and we’ll definitely catch up in the “meat-space.” More importantly I have a lot of socializing to do, since I haven’t seen any of my friends from the Berkeley LW community since I left the Bay Area in the summer of 2011. But I hope to meet new & interesting people, as I always have at these events (the social circle overlaps a great deal with BIL). So if you read this weblog and are going to the Singularity Summit and think I’m worth talking to in person just come on up, I’m not very shy. With the prior that you’re actually at the Summit my assumption is that you’re interesting, unless proven otherwise!

Addendum: Some people are curious if I am a “believer” in the Singularity. I’ll be honest and say I don’t think that the idea is necessarily crazy, but I spend my days thinking about genetics far too much to really be a hardcore A.I.-obsessive, which is what is needed to entertain the concept with any seriousness. Rather, my interest is rather in the social milieu where I can temporarily dispense with niceties and get down to the type of verbal blood-sport which I truly relish: engagement with intent not to thrash your opponent, but to wrestle with reality and perhaps squeeze out a few points against it.

The First Men and the Last Men

In the comments below there is a discussion about whether personhood is a continuous or categorical trait. I lean toward the former proposition as a matter of fact, but let’s entertain the second. What if personhood, and in particular consciousness and moral agency, emerged repeatedly over the past two million years in singular individuals? A model I propose is that the reason that ‘behavioral modernity’ exhibited such a long lag behind ‘anatomical modernity’ is that the first conscious human kept killing themselves. After all, imagine that you come to awareness and all your peers are…well, ‘dirty apes.’ You are literally the sane man in the asylum. This is similar the idea proposed, reasonably enough, that a demographic ‘critical mass’ was required for cultural evolution to truly enter into ‘lift-off.’ In any case, perhaps ~50,000 year ago a psychopath was born who could live with the knowledge that their days were to be spent copulating with and eliminating with animals. Animals whom said psychopath could congenially manipulate to increase their own fitness. No sensitive soul, he.

Ultimately obviously my hypothesis is far more science fiction than serious model. But it does get to the heart of something critical: the essence of humanity is not our rational reflective individual faculties, but our powerful social awareness and need for embeddedness. Even a misanthrope like me can recognize this. By our negation of it we recognize that which is the standard. Consciousness and self-awareness did not explode into the world like a shot in the dark in the form of the original human. Rather, groups of proto-humans through their collective actions stumbled upon the configuration of characteristics which connote to us humanity. There was no sentinel, only the passage of countless generations, melting unto each other.

The great Malagasy leap into the unknown

Today there was a short article in Discover on a paper published last spring on the models for the settling of Madagascar. I didn’t pay too much attention when the paper came out for two reasons. First, it focused on Y and mtDNA, and I’ve been playing with Malagasy autosomes. Second, it seemed a ridiculously brutal computational attack on a question which seems to have a straightforward intuitive explanation: yes, Madagascar was settled by a small founding group. With hindsight I may have spoken too soon, or passed judgement too hastily. Looking at the paper the explicit model building of demography does still seem like overkill, but they obtain some important precision here. The phylogenetics and the archaeology align nicely.

Though the authors of the article talk about future directions, I think we will find that the Malagasy originate from a small group of Malayo-Polynesians who did find themselves stranded on Madagascar (later to absorb African admixture). This is not controversial. Rather, when I came to this position with enough solidity I began to look at the cultural anthropology of Madagascar. In particular, what do the Malagasy remember of about their own past in Southeast Asia? From what I could tell (the literature on Madagascar is not too rich in English) the Malagasy don’t recall much. This is important, because it tells us just how fragile oral memory can be when you have a major geographical and demographic rupture. The influence of Sanskrit is apparently evident within Malagasy, attesting to the early period if Indic influence in Southeast Asia. But the Malagasy are not part of Dharmic or Islamic civilization. They are the people forgotten by time. I think what little we know about the Malagasy can shed on light memories and legends preserved by peoples who we suspect were migrants into the only homelands they knew (e.g., how could the Aryans be exogenous if they didn’t record any memory of lands before India?).

The delta quadrant of American politics & culture

Apparently when he was a consultant Mitt Romney would praise the merits of ‘wallowing in data.’ I agree with this, you can’t get more data than you need. Therefore I highly commend Public Religion Research Institute‘s survey of the “white working class.” More specifically, do read the full PDF. It’ll take you some time, but just trade that in for commenting on a weblog! Of course the results are strongly contingent upon the definition of what the white working class is. In this survey they fix upon the white population which does not have a college education (though may have some college) and is not employed in salaried labor. This seems like serviceable definition. The incomes range from low to lower upper middle class, with a mode in the lower middle class, so you get a broader cross-section of non-elite white America than Honey Boo Boo, which is to working class white America what the “ghetto life” is to working class black America.

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Quartz, kind of a big deal?

A site called Quartz is going to go live today. I have been hearing a lot about it in the media (e.g., The New York Times). One of the people who launched ScienceBlogs, Chris Mims, is involved. I’ve seen a guideline for its freelance writers, and I have to say that I’m impressed by the flexibility and openness to variation and personalization that it communicates. Not sure if it is revolutionary, but I suspect that it will be quite the content machine. And the emphasis on tablets and mobile access via a browser, rather than an app, is probably the best way to optimize readership.

Humanity isn't, it becomes

John Hawks prompts to reemphasize an aspect of my thinking which has undergone a revolution over the past 10 years. I pointed to it in my post on the Khoe-San. In short, the common anatomically modern human ancestors of Khoe-San and non-Khoe-San may not have been people. Rather, people may have evolved over the past 100-200,000 years ago. Of course the term “people” is not quite as scientific as you might like. In philosophy and law you have debates about “personhood”. Granting the utility of these debates I am basically saying that the common ancestor of Khoe-San and non-Khoe-San may not have been persons, as well understand them. Though, as a person myself, I do think they were persons. At this point I am willing to push the class “person” rather far back in time.

As I suggested earlier there is an implicit assumption that personhood is a shared derived trait of our species. Or at least it is a consensus today that all extant members of H. sapiens are persons. Since Khoe-San are persons, the common ancestor of Khoe-San and non-Khoe-San must also be persons if personhood is a shared derived trait. But, we also know that there are many aspects of realized personhood on a sociological or cultural scale which seem to diminish the further back in time you go. For example, the Oldowan lithic technology persisted for ~1 million years. A common modern conception of persons is that persons in the aggregate are simply never so static. Persons have culture, and culture is protean. Therefore, one might infer from the nature of Oldowan technological torpor that the producers of that technology were not persons.

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Reader survey results, biologists vs. non-scientists

There are now over 400 responses to the survey. Here is a link to the responses in CSV format. If you import this into R, an extra parameter in regards to encoding may be necessary:

responses=read.csv("responses.csv",sep="t",header=TRUE,fileEncoding = "UCS-2LE")

I decided to separate the respondents into two categories, biologists and non-scientists (therefore, excluding other types of scientists from further analysis). You can see the filtered responses for biologists and non-scientists yourself. Below are some comments on interesting differences.

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Further survey results

I have now reformatted the responses into a csv file. So you can do something boring like create a scatterplot with Excel, as above. Or, you can import into R and dig for more interesting patterns. Here is an updated to the PDF which shows you the simple non-crossed results.

Also, out of curiosity I separated respondents into geneticists vs. non-biologists (so I exclude biologists who are not geneticists from this analysis). First, here are the non-biologists on race:

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