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Gene Expression

“I don’t have a T.V.” isn’t such a signal anymore….
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So I last had cable television in August of 2004. By the the summer of 2005 we’d phased out the television, period. I became the “well, I don’t have a television….” guy. This causes some issues. I am somewhat spotty in my pop culture awareness. And it’s getting worse and worse the further I am from my television days (though I think I’ve hit the point of diminishing returns in gains of pop culture ignorance over the past few years; there’s only so much crap you can forget!). When I was on vacation recently I naturally turned on the television to see what commercials I missed. There’s a lot of clever stuff out there! I was totally amazed by the Kia Soul Hamster commercial, and was thinking about blogging it, before being told that it was old news. I have a similar issue with video games, which I’ve avoided since adolescence because of the opportunity cost of playing. They’re starting to become so awesome that I have a hard time understanding what I’m seeing on the screen at the electronics store.

But things are changing. The rest of the world is slowly catching up, and I’m falling back toward them. Ownership of TV Sets Falls in U.S.:

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May 4th, 2011 Tags: Television
by Razib Khan in Culture | 1 Comment »
My dreamquest: what has the “phone” become?
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What is this?

I experienced a very strange and perhaps illuminating dream last night. I’ve had an HTC Evo 4G since Christmas (for what it’s worth, Sprint’s customer service has been horrible, but the phone itself is great). Before that I had phones with internet access, but which were more primitive. At this point I probably can’t imagine what life was like without a phone like the Evo. That was evident in my dream.

Here’s what happened. Apparently I had left the phone in my pocket while doing laundry. This meant that it was damaged. For reasons which the dream-gods did not explain to me, as a replacement I received an old school gray Nokia of some sort, the likes of which I hadn’t encountered since the mid-2000s. Here’s the kicker, I looked at my replacement phone, and wondered out loud: “OK, so what am I supposed to do with this phone? All it can do is call people. I don’t even like calling people!”

Obviously I still refer to my phone as a phone. But at this point I don’t see its primary role as sending and receiving phone calls! (in fact, if I want more reliable voice I’ll probably go with Skype due to issues with reception) I am reminded of the origin of the term ‘stationery’.

May 3rd, 2011 Tags: Technology
by Razib Khan in Technology | No Comments »
One root for rice
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ResearchBlogging.orgThe Pith: There was one rice domestication event somewhere in central China about 10,000 years ago. Probably!

Going by the numbers rice is the real staff of life. Rice is the staple for ~50% of humans alive today. So the science of rice is of major pragmatic importance of all humans (even if a major disease which impacts rice doesn’t result in mass starvation, it will probably generate a price spike for all other staples due to Asian demand). One major issue which I’ve kept track of over the years has been the origin of rice agriculture: was it a parallel multi-hearth origination or a single-hearth event? We know that there were at least two instantiations of agricultural civilization in the world without any cultural diffusion: in the New World and the Old. More likely there were at least several independent hearths in the old world which utilized local wild crops. Wheat and barely in the west, millet and rice in the east, etc. But there is also a model that rice agriculture had two independent origins, in India and China, which gave rise to the indica and japonica strains from the welter of wild rice lineages. Some genetics has supported the model of two hearths by reporting a deep time depth to the last common ancestor of these strains, on the order of ~100,000 years. The implication from phylogenetics is that there were two adaptations of local lines, which later converged in morph due to parallel selection pressures.

The interest in this issue has application to our understanding of human history. Peter Bellwood in First Farmers argues that what L. L. Cavalli-Sforza termed the “great human diasporas” have their roots ultimately in distinctive domestication events. Bellwood goes on to suggest that the contemporary genetic and linguistic patterns of variation we see around us are the products of rapid population growth of these ancient agricultural nuclei (the genome blogger Digonenes works within this framework). The implication then would be that two domestications of rice would imply two population pulses. A single domestication would imply one pulse. Therefore there is a connection here between historical human population genetics and agricultural history & genetics. This stands to reason in that our own species is so parasitic on domestic crops.

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May 3rd, 2011 Tags: Evolution, Genetics, Genomics
by Razib Khan in Evolution, Genetics, Genomics | 2 Comments »
Osama bin Laden and the DNA match
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How they determine Osama bin Laden really is Osama bin Laden:

Once samples from all sources are in hand, analysts isolate a bit of DNA from each sample, make lots of copies of it, and then process the copies through a machine that analyzes genetic markers — DNA fingerprints — that have been passed down through a subject’s family. Typically, Bieber said, DNA tests examine around 15 of these markers.

…

It typically takes several hours to complete each step of the analysis process, Bieber said, though he noted that in high-profile cases like this one, law enforcement agencies might already have genetic profiles of the relatives available — which means they’d only have to complete one additional test.

I checked and it seems that there are paternity testing outfits that offer one day turnaround. So I guess it’s not implausible that they could have pulled this off. I assume they still use variable number tandem repeats for DNA profiling?

Update: Yeah, short tandem repeats.

May 2nd, 2011 Tags: DNA, Osama bin Laden
by Razib Khan in Genetics, Genomics | 22 Comments »
A blog and Bin Laden
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Chris Mooney:

The news stream of the country just shifted dramatically. I was up late last night, putting on hold an article deadline, unable to take my eyes off CNN–and remembering what it was like to be in D.C. on 9/11, huddled in a hotel watching the news, and then for more than a month afterwards, as we were all additionally terrorized by the anthrax mailings.

Blogging itself was largely born in the wake of 9/11–the fear and the insatiable demand for news and information, combined with the Internet, set the stage. I started blogging shortly afterwards when I and others created Tapped, the blog of the American Prospect magazine.

People will rightly point out that the tech blogosphere was robust well before 9/11. But I think it is valid to assert that the non-tech blogosphere’s coming of age was really 9/11. Many of the prominent bloggers today (Matt Yglesias and Megan McArdle for example) come out of the “warblogger” milieu of that period (whether pro or anti “warblogger”). Myself, I began blogging a few weeks before Chris at Tapped on a pre-GNXP weblog I had for all of two months, from April to May of 2002. At that point my concerns were Java Server Pages, the War on Terror, and genetic engineering (in particular the anti-genetic engineering arguments of Francis Fukuyama and Bill McKibben). 9/11 had perturbed me from my general isolationist orientation, but over the years I’ve shifted back to my old equilibrium.

Below is a Google Trends result restricted to the USA for the terms blog, magazine, and newspaper.

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May 2nd, 2011 Tags: Osama bin Laden
by Razib Khan in Blog | 2 Comments »
ADMIXTURE, African Ancestry Project, and confirmation bias
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I’ve been running the African Ancestry Project for a while now on the side on Facebook. But it’s getting unwieldy, so I finally set up the website. The main reason I started it up is that there have been complaints for a while now of problems with the 23andMe “ancestry painting” and such for some African groups. For example, a Nubian might be 70% “European.” One might argue that this is due to Arab admixture, but this is clearly not so if you look at the PCA plot. What’s going on? Probably a problem with the reference populations (only Yoruba for Africa), ascertainment bias in the chip (they’re tuned to European variation), and the fact that African genetic variance can cause some issues. I don’t know. But the problem has been persistent, and since most of the other genome blogging projects exclude Africans because they’re so genetically diverse I decided to take it on.

Three groups of people have submitted:

- People of the African Diaspora in the New World

- People from Africa, disproportionately Northeast Africans (Horn of African + Nubia, etc.)

- People of some suspected or known minor component of African ancestry

I’m at ~70 participants now. As one reference population set I’ve been using a subset of Henn et al. as well as some populations from Behar et al. I call this my “thin” set since there are only ~40,000 SNPs. A “thick” set has on the order of 300-400 thousand markers. But fewer populations. I’ve been putting the AAP members through ADMIXTURE in batches of 10, but I also run them all together sometimes for apples-to-apples comparisons. Yesterday I ran AF001 to AF070 from K = 2 to K = 14, unsupervised, with the thin reference. If you want to see all the results, go here. Doing all this myself over and over has given me some intuition as to the pitfalls in this sort of analysis. Especially in the area of confirmation bias.

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May 2nd, 2011 Tags: Admixture, African Ancestry Project, bias, confirmation bias, Science
by Razib Khan in Genetics, Genomics | 4 Comments »
Genetic testing comment period, last day
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I posted a pointer to this a few days ago, but if you care about the regulation of personal genomics the FDA is taking comments on the issue up until today. Here’s the direct link to the comment page. Say whatever you want, up to 2000 characters.

May 2nd, 2011 Tags: Personal genomics
by Razib Khan in Genetics, Genomics | No Comments »
The “law school scam” media bubble
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If you’re like me you have friends and acquaintances who want to go to law school. I often respond sarcastically that “a mind is a terrible thing to waste.” There have long been “law school scam” blogs, but it seems that right now there’s a veritable bubble in media reports on exactly how law schools are screwing their students. Remember, law school debt is not dischargeable in bankruptcy.

First, an article in The New Republic, Served: How law schools completely misrepresent their job numbers:

When we take temporary employment into account, it appears that approximately 45 percent of 2010 graduates of this particular top-50 law school had real legal jobs nine months after graduation. And the overall number is likely lower, since it seems probable that the temporary employment figures for the graduates of almost any top 50 school would be better than the average outcome for the graduates of the 198 ABA-accredited law schools as a whole.

Even this grim figure, however, may be unduly optimistic. All these statistics are based on self-reporting, and neither law schools nor NALP audit the data they publish. In the course of my research, I audited a representative sample of individual graduate responses and found several instances of people describing themselves as employed permanently or full-time, when in fact they had temporary or part-time jobs (I found no instances of inaccuracies running in the other direction). Perhaps some graduates exaggerate their employment status out of embarrassment, or for strategic reasons, but, whatever their reasons might be, this apparently not uncommon practice suggests that the true employment rate should be lowered even further.

This is old news. The New York Times now has a piece up with a new twist, Law Students Lose the Grant Game as Schools Win:

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April 30th, 2011 Tags: Education, Law school scam
by Razib Khan in Culture | 33 Comments »
“Out of Africa” vs. “Multi-regionalism” revisited
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A few months ago I exchanged some emails with Milford H. Wolpoff and Chris Stringer. These are the two figures who have loomed large in paleoanthropology and the origins of modernity human for a generation, and they were keen in making sure that their perspectives were represented accurately in the media. To further that they sent me some documents which would lay out their perspective, in their own words, and away from the public glare (as in, they’re academic publications).

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April 30th, 2011 Tags: Multiregionalism, Out-of-Africa
by Razib Khan in Evolution, Human Evolution | 3 Comments »
The loss of sacred belief?
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