It was a good decade (UPDATE)

Update:  Actually, I was going to put up a post “10 years in blogging.” But right now I don’t have the time, seriously. 10 years is a LONG time though, so I now feel more comfortable talking about events “offline” which date to over half a decade in the past. One thing to note is that my current style of comment moderation crystallized in the mid-2000s because of various time constraints. The fact that I was going to school full time, or had a 65 hour a week job as my firm was coming up to a software release date, and, was in a long distance relationship, was not anyone’s business (did I mention I had freelance web development projects on the side, and was developing a content management system for a client as well?). But it certainly inculcated in me a lack of patience for bullshit. I was cranking out blog posts on Sundays, and in the hour I had after dinner & and my freelance project and before sleep. I recall in the fall of 2006 amusingly some moron left a comment about how I must have a lot of time, since I was posting on Friday evening. …

What turns a blue-eyed girl brown?

I’m questing about for some answers. My daughter is now two months old, and to the left is an image of her eye. As you can see, they are blue. I was not particularly surprised that she was born with blue eyes. Her mother is of Northern European heritage. But, I’ve had both of us genotyped. My daughter is a heterozygote on the HERC2-OCA2 locus, which means that she has a 5% chance of blue eyes, 35% green/hazel, and 60% chance of brown, assuming a European genetic background. Obviously half her ancestry is non-European, so that does not hold (though for gene nerds, I am a homozygote for the “European” alleles of SLC24A5, as are many South Asians).

My question here is simple: of the half-browns with one Northern European parent,  what color were their eyes at birth, and what colors did they change to over time, if they changed at all? I have a friend who is half Bengali and Irish, and he and his brother have green eyes, and were born with green eyes. My friend Jason Goldman has the same genotype as my daughter on the  HERC2-OCA2 locus, but his baby blues disappeared after 2 weeks.

What I want in the comments are details about eye color and transitions, as well as parental ethnicity (I am not too surprised, for example, that one of Nikki Haley’s children has blue eyes as an adolescent).

If you are curious as to why I’m so curious. First, I’m a brown guy who is running around with a little baby with blue eyes. Second, people know of my fixation on genetics. So naturally questions will ensue.

(for further information, her hair color is medium brown; mine is black, her mother’s is blond).

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When little differences matter a great deal

In the comment below Clark alludes to the fact that Jonathan Haidt kept reiterating that even if there were differences between populations due to recent evolution, if it was due to selection on standing variation upon quantitative traits then the between group variation would be dwarfed by within group variation. He didn’t quite say it like that, but I’m sure that’s what he meant. For example, there is now evidence that alleles which can explain the small height difference between Northern and Southern Europeans have been subject to natural selection. Most of the variation obviously remains within the groups; you can’t guess that someone is Italian or Dutch just based on their height. There are many tall Italians, and many short Dutch. But on average there are differences between the groups which can be attributed to genes, and those genes seem to have been targets of selection.

This is good as fair as it goes…but small average differences may not necessarily be marginal. That is because sometimes you select from the tails of a distribution. For example, if you want to ascertain which population will produce more N.B.A. players, …

Jonah Lehrer, science fiction writer

He’s back, and he’s out with a new book, Imagine: How Creativity Works. I am talking of course about Jonah Lehrer, the enfant terrible of cognitive neuroscience. OK, perhaps more Wunderkind. In any case, I was struck by this post on his weblog, The Cost Of Creativity:

There is a serious complication to this triumphant narrative of cliff edges and innovation, however. Because our lifestyle has become so expensive to maintain, every new resource now becomes exhausted at a faster rate. This means that the cycle of innovations has to constantly accelerate, with each breakthrough providing a shorter reprieve. The end result is that our creativity isn’t just increasing the pace of life; it is also increasing the pace at which life changes. “It’s like being on a treadmill that keeps on getting faster,” West says. “We used to get a big revolution every few thousand years. And then it took us a century to go from the steam engine to the internal-­combustion engine. Now we’re down to about 15 years between big innovations. What this means is that, for the first time ever, people are living through multiple revolutions.”

Needless to say, such revolutions aren’t fun. They’re unsettling …

Jonathan Haidt & Robert Wright: crazy delicious

Last night I listened to a very long discussion between Robert Wright, author of The Moral Animal, and Jonathan Haidt, author of The Righteous Mind: Why Good People Are Divided by Politics and Religion. If you have been reading my weblog for years there may not be much new, but if you haven’t, then you’ll encounter a lot of novel information, in particular from Jonathan Haidt. I was intrigued by Haidt’s references to evolutionary and anthropology, and I immediately noticed on Twitter that of the 17 people he follows, two are John Hawks and Paul Bloom. John is a friend, and Paul Bloom has been highly influential in my own thinking about cognitive psychology (see Descarte’s Baby). Additionally, many of the other “shout outs” which Haidt makes are familiar to me as well (e.g., Scott Atran, the neo-functionalism of David Sloan Wilson, etc.).

In lieu of a conventional blog post here a list of comments, reacting mostly to Haidt’s various assertions.

– The biggest “bombshell” that Haidt drops is his empirical finding that when people of a given political ideology, going from very liberal to very conservative, are asked to model the opinions of other people …

Post-Neolithic revenge of the foragers

If I have something to share, why not share it? Over the past few weeks I’ve been ruminating on some of the possible intersections between historical population genetics and anthropology, especially in light of the discussion that I’ve had in the past with Robin Hanson about ‘farmers vs. foragers’. Entering into the record that such a dichotomy is too stark, and only marginally useful (i.e., I think it is important to separate farmers and foragers in to their own sub-classes, as some farmer types may share more with some forager types, and so forth), it may be that after the first wave of the Neolithic expansion the descendants of the foragers “bounced back” in many regions of the world. It does seem that ancient European hunter-gatherers have left modern descendants. They were not totally swamped out. Using autosomal patterns some genome bloggers have inferred the same pattern, and perhaps even a counter-reaction by “Mesolithic” populations which adopted some aspects of the “Neolithic” cultural toolkit.

But here let me come back to the Turks. Are they the descendants of farmers who expanded out of the valleys of eastern …

Cultural Folkways in Flux

A fascinating post over at The Crux, Votes and Vowels: A Changing Accent Shows How Language Parallels Politics. Here’s the section which I might quibble with though:

Labov points out that the residents of the Inland North have long-standing differences with their neighbors to the south, who speak what’s known as the Midland dialect. The two groups originated from distinct groups of settlers; the Inland Northerners migrated west from New England, while the Midlanders originated in Pennsylvania via the Appalachian region. Historically, the two settlement streams typically found themselves with sharply diverging political views and voting habits, with the northerners aligning much more closely with agenerally being more liberal ideology.

But first, here is a map of the dialects in question:

 

Now compare to a map of Yankee settlement in the mid-19th century:

I do not object to the argument that old historical patterns in the USA redound down to the present in surprising and often cryptic ways. I refer to this as the “dark matter” of American history; deep structural patterns which shape the cultural geography of the …

Revenge of the herders

Let me make something explicit: I believe that the model outlined in First Farmers is too simple, and that extant patters of linguistic and genetic variation need to accept the likelihood of multiple population reorganizations across vast swaths of Eurasia within the last 10,000 years. The classic case in point are the Turks. Because of their exotic character vis-a-vis the populations which they displaced and assimilated we can peg rather easily their expansion. Between 0 and 1000 AD they began to make themselves felt across a broad expanse of Eurasia from the eastern fringes of Europe to the western fringes of China, and south toward the world of Islam. Between 1000 and 1800 the Turkic peoples took over much of Eurasia for various periods of time (e.g., the Ottomans, Safavids, and Mughals, were Turkic, while the Golden Horde which imposed the Tatar Yoke were mostly Turkic, not Mongol). It is notable to me that Turkic peoples contributed ~10 percent to the genetic ancestry of modern Anatolians. This is a significant achievement, because Anatolia has been a densely populated seat of agricultural civilization for almost the whole history of agriculture! …

The real secret history of the Mongols?

Thank god for steppe hyper-patriarchy; it’s a model which we can test. Dienekes points me to a paper, The Y-chromosome C3* star-cluster attributed to Genghis Khan’s descendants is present at high frequency in the Kerey clan from Kazakhstan, which is notable for increasing sample coverage of the distribution of “Genghis Khan haplotype.” As you might recall in 2003 a paper reported that a particular Y-chromosomal phylogeny was extremely common in Central Eurasia, and, that it had expanded rather rapidly starting approximately ~1,000 years ago. The natural supposition was that this was connected to the rise of Genghis Khan, from whom male-line descent in particular has become a matter of pride and prestige across the former domains under his rule. Subsequent researchers have supported this finding insofar as the distribution of the haplotype does tend to drop off among the “Western Mongols,” who were for various reasons marginal during the time of Genghis Khan, and whose ruling class were subsequently diminished in part due to their lack of a Genghiside pedigree.

 

The new paper above presents the novel result that the Kereys of Kazakhstan have the highest …

Nature Precedings closes up shop

Here’s the announcement:

As of April 3rd 2012, we will cease to accept submissions to Nature Precedings. Nature Precedings will then be archived, and the archive will be maintained by NPG, while all hosted content will remain freely accessible to all.

Looking forward, NPG remains committed to exploring ways to help researchers, funders, and institutions manage data and best practices in data management, and we plan to introduce new services in this area.

We have truly valued your contributions as authors and users to Nature Precedings and hope that you will actively participate in this research and development with us.”

This comes on the heels of Dr. Joseph Pickrell’s first author submission of a preprint. Correlation? Yes. Coincidence? I’ll let you decide.

In other news the existence and flourishing of arXiv puts a whole different spin on “physics envy.” And, just to reiterate, if I post about a paper, and you don’t have access email me and I will send you the paper.