Archive for March, 2011

The Bantu völkerwanderung

By Razib Khan | March 31, 2011 3:34 pm


Image Credit: Mark Dingemanse

I recall years ago someone on the blog of Jonathan Edelstein, a soc.history.what-if alum as well, mentioning offhand that archaeologists had “debunked” the idea of the Bantu demographic expansion. Because, unfortunately, much of archaeology consists of ideologically contingent fashion it was certainly plausible to me that archaeologists had “debunked” the expansion of the Bantu peoples. But how to explain the clear linguistic uniformity of the Bantu dialects, from Xhosa of South Africa, up through Angola and Kenya, to Cameroon? One extreme model could be a sort of rapid cultural diffusion, perhaps mediated by a trivial demographic impact. The spread of English exhibits this hybrid dynamic. In some areas (e.g., Australia) there was a substantial, even dominant, English demographic migration coincident with the rise of Anglo culture. In other areas, such as Jamaica, by and large the crystallization of an Anglophone culture arose atop a different demographic substrate, which synthesized with the Anglo institutions (e.g., English language and Protestant religion). The United States could arguably be held up as a in-between case, with an English founding core population, around which there was an accretion of a non-Anglo-Saxon stream of immigrants who serial adopted the Anglo culture, more or less. Sometimes this co-option of Anglo-Saxon norms may surprise. “Black English” (i.e., Ebonics) actually seems to be a genetic descendant of lower class northern English dialects. Other distinctive components of black American (e.g., “jumping the broom“) culture can also plausibly be derived back to the British Isles.

So cultural change is in the “its complicated” segment of dynamics. We have to go on a case-by-case basis. For the Bantu expansion though we have a good answer now thanks to genetics: this cultural change almost certainly was accompanied by a massive demographic migration. Thanks to Brenna Henn and company you can even run some analyses on your desktop to confirm the reality of this model. I pulled down the 55,000 SNPs from various African populations, merged with Palestinians, Tuscans, and Maya as outgroups, and pruned down to ~40,000 after removing those which were missing in more than 1% of the cases. The Hadza are also gone, as they’re such a small isolated group who always hogged up K’s all by themselves. I ran a bunch of different ADMIXTURES, from K = 2 to 12. You can see all 12 here, but let’s just focus on the 12th.

Below is a bar plot, somewhat sorted by ADMIXTURE elements. I’ve reedited some of the labels for clarity, adding regions. I’m sure some of you are ignorant of where the Brong people (Ghana) are from as I was before I looked them up. Also, please be careful about ADMIXTURE. There is a “Fulani” ancestral component below, but I’m 90% sure that’s just an artifact of recent Fulani demograhics + their unique genetic admixture.

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CATEGORIZED UNDER: Genetics, Genomics

Mapping ADMIXTURE components

By Razib Khan | March 31, 2011 1:05 pm

Over at Harappa Simranjit has been allowing Zack to post his isopleth maps of the frequencies of ADMIXTURE components by region. He now has his own blog, The Jatt Gene. On unrelated note, does anyone know of an easy way to generate isopleth maps which is open source?

CATEGORIZED UNDER: Genomics

The New York Times "pay wall"

By Razib Khan | March 31, 2011 12:09 am

So what do readers of this blog think? Pay or no pay? It’s useful, and The New York Times is pretty massive in scope, if sometimes lacking in breadth. I love their data-oriented stuff, but I ignore their columnists and a lot of their “analysis,” which is frankly substandard if I know anything about the topic (which suggests to me if I don’t know about the topic, they barely do too). There are certain areas where blogs have a comparative advantage, and I don’t see why an organization with other strengths would even make an attempt.

CATEGORIZED UNDER: Blog

Personal genomics gets very personal

By Razib Khan | March 30, 2011 11:58 pm

Dan MacArthur points me to this nice post over at Daily Kos, Our Genome Decoded: How Companies Like 23andMe Are Advancing the Field of Personal Genomics:

…However, in the past few years several private biotech companies have started offering a “personal genome service” that involves sequencing the most variable portions of our DNA. The goals are straightforward – to give individuals information about their ancestry and inherited traits. While there are definite limitations – both technically and bioethically – to the amount and type of information that can be obtained from personal genome sequencing, in my case the service answered a lingering question about something important to me, and thus was well worth it.

In this article, I’m going to tell the story about why I chose to purchase a personal genome service, briefly explain how it works, show my interesting results, and finally, provide some commentary on how these services will impact the fields of genomics and medicine.

One step at a time. I also appreciate that Michelle keeps posting on her ADMIXTURE results.

CATEGORIZED UNDER: Personal Genomics

Bravo for Mormons!

By Razib Khan | March 30, 2011 11:48 pm

Trying to Relish the Big Time, Even When It Brings a Cringe:

The house lights came up and it was intermission at “The Book of Mormon,” the new Broadway musical about a pair of innocent young Mormon missionaries sent to Uganda to spread the faith. John Dehlin, a graduate student who flew in from Utah to see the show with a group of Mormons from around the country, was still riveted to his theater seat, having flashbacks.

“It’s way, way too close to home,” he said, recalling his own missionary years in Guatemala: the shock at the poverty and violence, the pressure from the mission president to baptize more natives, the despair when his mission companion ran off with a local girl — and the Mormon mandate, above all, to repress doubt and remain relentlessly cheery.

A friend in the crowded theater aisle, Paul Jones, passed by and gave Mr. Dehlin a high-five and a hug. “It’s right on,” said Dr. Jones, a dentist from Gilbert, Ariz., “but I cringed a little bit, a couple of times.”

The arrival of a Broadway musical that ridicules their religion, produced by the creators of the scathingly satirical television show “South Park,” is proving to be a cringe-worthy moment for many Mormons.

And yet, even though the very name of the show appropriates the title of the church’s sacred scripture, there have been no pickets or boycotts, no outraged news releases by Mormon defenders and no lawsuits.

This is intentional. Mormons want people to know that they can take it.

Not all religious communities react in the same way. In Birmingham, England, 2004, Theatre attacks Sikh play protest:

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CATEGORIZED UNDER: Religion

The end of Ayla & The Land of Painted Caves

By Razib Khan | March 30, 2011 2:03 am

I read  Jean Auel’s Clan of the Cave Bear in elementary school at a friend’s house during a sleep over. It was next to the bedside, and I decided to pick it up. I’d thought it was a human evolution book from the cover. I read  2/3 of the book by dawn, took a few hours to catch up on sleep, and then finished the rest before the afternoon. I read almost no fiction outside of what was assigned in school as a child, but this was the exception (I also read a lot of Greek mythology, though I’m not sure that counts). The three sequels I finished in middle school when I noticed there were sequels! By the time book 5, Shelter of the Stones, came out in the early aughts I’d lost interest. I’ve moved on, but many have not. The last book, The Land of Painted Caves, is now out. The Los Angeles Times has written a retrospective of the series.

Since Amazon has a 1 to 5 star rating system, I thought I’d plot the results for the first five books. On the y-axis you have the number who gave a particular star value to a given book (the order of the books goes from left to right, book 1 to book 5). I haven’t read Shelter of the Stones, but I agree with the median reviewers on Amazon that The Mammoth Hunters was the most uninteresting of the first four books.

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CATEGORIZED UNDER: Culture

The day of the farmer

By Razib Khan | March 29, 2011 11:01 pm

About five months ago I read Peter Bellwood’s First Farmers: The Origins of Agricultural Societies. Bellwood’s thesis is simple: that the first adopters of farming entered into a period of rapid demographic expansion and by and large replaced non-farming groups. The populations which dominate the world today in this model are then the descendants of the very small set of cultures which ~10,000 years ago triggered the Neolithic Revolution. When Bellwood presented his thesis in the mid-2000s many would have dismissed it out of hand. Today I believe we have to take this model seriously.

There are two primary reasons from my perspective why I am now thinking about Bellwood’s thesis a great deal. First, the archaeogenetic inferences based on distributions of modern allele frequencies which suggested that the Neolithic Revolution in Europe was a matter of cultural diffusion seem far shakier. With such genetic models no longer taken for granted the recent historical, semi-historical, and ethnographic evidence, on farming transitions must be given much more weight. The case of the Bantu expansion in Africa seems to be semi-historical. The Bantu farmers themselves were not literate but their wave of advance was in historical time. Tellingly, the Bantu speaking populations of Southern Africa are genetically more similar to the Fang of Cameroon then they are to the Khoisan to their west! More well documented has been the attempts by Europeans to settle various lands overseas in their colonial adventures. They have been able to marginalize populations which did not habitually practice intensive agriculture relatively easily (note that the locus of Afrikaner settlement was initially around the Cape, where Bantu influence was minimal and Khoikhoi pastoralists were dominant). In contrast, in regions like Mesoamerica where obligate intensive agricultural civilization had deep roots there was no biological replacement, but hybridization.

An argument can be made that the initial farmers did not have so many advantages over their hunter-gatherer neighbors. So the power and force of the mass agricultural way of life which bore down upon the indigenes of Australia was qualitatively different because the Europeans who arrived were the outer wave of an ancient and ruthlessly efficient civilization of farmers, honed to brutal perfection through the cauldron of inter-group competition over thousands of years. I think the best counter argument against this is the evidence of rapid sweeps of cultural forms in European in prehistory, as well as rapidity of the success of the Bantu agricultural toolkit.

The new genome blogger Diogenes expresses the thesis of agricultural replacement to near maximal levels in the model which he is attempting to test with ADMIXTURE runs. Here are his propositions (formatting reedited for clarity):

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CATEGORIZED UNDER: Anthroplogy, Genetics, Genomics

The excitement of clothed porn stars

By Razib Khan | March 29, 2011 1:59 pm

Porn Stars, Clad? They Seem to Appeal to Indonesian Filmgoers:

Ms. Aoi, and others like her, are the secret of a winning formula stumbled upon by Maxima Pictures, the production house where Mr. Hidayat is an executive producer. For two years, Maxima has made some of Indonesia’s most popular domestic films based on a simple premise: that many in Muslim-majority Indonesia will pay to see foreign porn stars perform — clothed — in local films. Just don’t expect Indonesians to own up to it.

“We’re hypocrites,” said Mr. Hidayat, who is a Muslim. “People know who they are, but they won’t admit it. It’s a love-hate thing.”

This sort of “counter-intuitive” behavior makes total sense in light of the work reported in Paul Bloom’s How Pleasure Works: The New Science of Why We Like What We Like. People consume in a particular context. The hedonic experience can’t be isolated from its history and the prior facts (and expectations) you bring into it. This sort of insight is essential when we start talking about utilitarianism as if it’s a simple calculus.

CATEGORIZED UNDER: Psychology
MORE ABOUT: Pleasure, Porn, Psychology

The limits of computational power – shades of 1982

By Razib Khan | March 29, 2011 1:44 pm

Two Steps Forward, Two Steps Back:

I got my daughter a netbook, so now my computer is doing Harappa Prohect work 24×7.

Also, Simranjit was nice enough to offer me the use of a server. For privacy reasons, I am not going to upload any of the participants’ data there but it is much faster than my machine and hence very useful for running Admixture on the reference data (especially with crossvalidation).

As for steps back, I downloaded the current 1000genomes data (1,212 samples, 2.4 million SNPs). It’s in vcf format. Using vcftools to convert it to ped format will take about 3 weeks. Yes you heard that right. BTW, the good stuff from a South Asian point of view will come later this year with a 100 Assamese AhomF, 100 Kayadtha from Calcutta, 100 Reddys from Hyderabad, 100 Maratha from Bombay and 100 Lahori Punjabis.

Also, I spent most of Sunday evening and night in the ER and got a diagnosis of ureterolithiasis for my efforts. All I can say is: Three cheers for Percocet!!

First, wish Zack well. Second, he has over 70 individuals in the Harappa Ancestry Project data base (in addition to the public data sets). If you’re South Asian, Iranian, Burmese, or Tibetan, here are the details of participation.

CATEGORIZED UNDER: Genetics, Genomics

Genetic paternalists are very patronizing

By Razib Khan | March 29, 2011 11:17 am

An comment below on my post Genetic paternalism & the F.D.A.:

I came across your inflamed post from March 9th and the more I read the more disappointed I became, especially when I read your comment “following twitter, it seems there may be a distinction between raw sequence and interpretation. it may be the latter where there are “gatekeepers.” probably for reasons of liability, public safety, etc. (ergo, FDA). i see the logic, but from a perspective of utility i don’t think that the regs will improve human well being. though that’s probably not the implicit rationale behind “interested parties.””
The distinction there is ABSOLUTELY CRUCIAL. There is a huge difference between providing your raw genomic information, and providing diagnostic interpretation.

The AMA letter http://www.ama-assn.org/resources/doc/washington/consumer-genetic-testing-letter.pdf clearly stated that it was directed to ” direct to consumer (DTC) genetic tests that make medical claims” and it is “the making of medical claims” that puts certain offerings of DTC genetic testing squarely in the FDA’s domain; uninterpreted DTC genetic test results – the raw sequence – are NOT in the FDA’s domain under current regulations. Medical claims are. And I have not heard the FDA claim that they would even try to regulate uninterpreted DTC genetic test results. Have you? (not a rhetorical question)

I found your sloppy, over-emotional post — and the unthinking overreactions by commentors, to be deeply disheartening. How can people claim to be super-smart and bellow about their right to their own information and to be better informed than 99% of MDs (sheesh there is some unsubstantiated overstatement) — how can these people lack the basic common sense, much less decency, to read carefully and think through the actual regulatory issues, before starting to self-righteously holler about being stepped on? Shame on all of you who did that.

Razib – please post an “oops I over-reacted” with respect to this entire over-heated mess that you have poured oil onto. That would show some integrity and thoughtfulness, which we need more of. We do not need more emotional over-reactions to regulatory issues. The dietary supplement people are doing just fine with that.

Before entering into a presumptuous and patronizing lecture, it would have been nice to explicitly admit some conflict of interest here (some MDs arguing for control over this industry did in earlier comments). The IP originates from Joan and Sanford I. Weill Medical College and Graduate School of Medical Sciences of Cornell University. This is the internet. If you’re going to get stuffy and professorial you might want to use your real name.

CATEGORIZED UNDER: Genetics, Genomics
MORE ABOUT: FDA, Paternalism

The flat and the fit

By Razib Khan | March 29, 2011 2:10 am

ResearchBlogging.orgThe Pith: In evolution if you want to win in the long run you don’t want all your eggs in one basket, even if that’s the choicest basket. Sh*t happens, and you better have some back up strategies.

Diversity is a major question in evolutionary biology. In particular, why is there so much diversity, so that the tree of life manifests a multitude of morphs? Might there not be some supreme replicator which emerges from the maelstrom to conquer all before it? This is actually the scenario which unfolds in much of science fiction, with monomorphic grey goo eating everything in its path (a more aesthetically differentiated variant of the super-species emerges in Brian W. Aldiss’  Helliconia Winter). As it is, life on earth does not seem to be converging upon an optimum phenotype for all individuals. In contrast, it seems to be going in the opposite direction broadly speaking (thinking on billion year scales), with the shift from the monotony of communal cyanobacteria to the riotous diversity of tropical forest biomes and coral reefs.

There are many ways you might be able to explain this diversity. Temporal and spatial heterogeneity produces perpetually shifting selection pressures, resulting in transient morphs one after the other. Negative frequency dependent selection, whereby the fitness of a phenotype runs up against its own success. This dynamic is one of the drivers of the Red Queen Hypothesis; the evolutionary arms race in some cases witnessing the resurrection of old techniques against which defenses are no longer recalled. Then there is the possibility that the lack of natural selection as an efficacious evolutionary force could allow for the diversification of phenotypes through  random drift. Finally, it may simply be that the gusher of mutation is powerful enough that novelty overwhelms selection and drift’s attempt to pare it back.

A new paper in Nature offers up another possibility. It does so by examining the fact that biological diversity remains operative even within a homogenized chemostat. A chemostat in this context refers to a controlled environment where inputs and outputs are balanced to maintain constant equilibrium conditions for a bacterialculture. Therefore, an unbeatable strategy should emerge in this medium perfectly tailored to the environmental constants, resulting in a homogeneous biota to match. Empirically this is not what occurs. So some explanation is warranted.

Metabolic trade-offs and the maintenance of the fittest and the flattest:

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CATEGORIZED UNDER: Evolution

Who thinks the sun goes around the earth?

By Razib Khan | March 28, 2011 3:00 pm

My post earlier today prompted a few emails about the bizarre result that a substantial minority of Americans accept that the sun goes around the earth. The General Social Science variable is EARTHSUN, and it asks:

Now, does the Earth go around the Sun, or does the Sun go around the Earth?

The answers are “Earth around the Sun,” “Sun around the Earth,” and “Don’t Know.” A substantial minority of Americans answer #2. What’s going on here? This isn’t something limited to America. The same question has been asked internationally. I’ve underlined the geocentrism/heliocentrism question below:

I apologize for the small font. What you’re seeing though is that substantial minorities, on the order of 1/7th to 2/5th of people in the regions above give the wrong answer on whether the earth goes around the sun, or vice versa. Is geocentrism rampant? No, I don’t think so. My explanation is that many people don’t think scientifically habitually, so scientific facts aren’t background priors which pop up reflexively. On surveys which require a rapid first-blush reaction you may give the “intuitive” result, and only later realize that your answer was of course wrong. If you sat down and talked to most of the Americans who answered that the sun goes around the earth and showed them a solar system model and asked them about it I think they would be able to give the correct answer once properly primed in such a fashion.

Below is a side show generated from the GSS which measures reflexive geocentrism by demographic. I’ve combined the categories in the vocabulary test where N < 100 with their adjacent values. Remember that it is on a 0 to 10 scale, and correlates 0.70 with general intelligence. The educational category is broken down by the highest attained qualification.

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CATEGORIZED UNDER: Data Analysis, GSS
MORE ABOUT: Geocentrism

Genetics as the myth buster: Indian edition

By Razib Khan | March 28, 2011 1:17 pm

Whenever Zack Ajmal posts a new update to the Harappa Ancestry Project he appends some data to his ethnic database. This sends me to Wikipedia, because how many people are supposed to know what a “Muslim Rawther” means? Well, if you are a Muslim Rawther, and perhaps from Southern India, you would. But South Asian ethno-linguistic categories and hierarchies are notoriously Byzantine, and I have difficulty making sense of them. This isn’t too surprising in my case, as my family’s background is relatively mixed in the very recent past (e.g., Hindus and Muslims, and people of various caste backgrounds), so we’re not the sort who can go at length about our pure ancestry and all that stuff. Unfortunately, Wikipedia isn’t always useful, because the people editing the entries on particular South Asian ethnic groups are often people from those ethnic groups, so you get a lot of extraneous information, and a particular slant on how awesome and high achieving the group (also, sometimes there’s funny stuff about how notoriously good looking that particular caste!). On occasion there are other sources which are informative. For example, Zack has several individuals from the Tamil Nadar caste. I know a little about this group because 1) I have a friend whose family is Nadar (he’s American, so saying he’s an American Nadar is pretty worthless), 2) The New York Times profiled the group last fall.

When Zack noted that a group termed Tamil Vishwakarma had submitted entries, I went to Wikipedia. That was the first time I’d heard of the group. This is what I found:

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CATEGORIZED UNDER: Genetics, Genomics

The Republican fluency with science

By Razib Khan | March 28, 2011 12:44 am

The Audacious Epigone has a post up, Republicans are more scientifically literate than Democrats or independents are, where he reviews pro vs. anti-science attitude by party in the General Social Survey. He concludes that in fact Republicans are more scientifically literate across the issues than Democrats. Jason Malloy saw this trend four years ago in the GSS, and to some extent so have I. One point to keep in mind is that a few specific politicized scientific issues are very much the outliers in exhibiting tight partisan valences in opinion.

So another question: are conservatives more scientifically literate than liberals? If scientific literacy correlates with being Republican, and being Republican correlates with being conservative, shouldn’t scientific literacy correlate with being conservative? Not necessarily. Such correlations are not transitive. Generally what I’ve seen in the survey data is that Republicans tend to be more pro-science than conservatives. I think part of it is the voting by economic position which has become less stark in our culture, but still remains a force. In any case, my table to accompany AE’s is below. I used his variables:

ASTROSCI, SCIBNFTS, EXPDESGN, ODDS1, HOTCORE, RADIOACT, BOYORGRL, LASERS, ELECTRON, VIRUSES, CONDRIFT, EVOLVED, EARTHSUN, SOLARREV, EATGM, ICESHEET, SCITEST5, GRNTEST1, GRNTEST5.

For political ideology, it’s pretty simple: POLVIEWS(r: 1-3 “Liberal” ; 4 “Moderate”; 5-7 “Conservative”)

The percentages given are the correct science answer, or the more pro-science answer. If you want to know my criteria for that, don’t ask, just go to the General Social Survey website and enter in the variables above, and you’ll see the results and understand clearly how I categorized things.

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CATEGORIZED UNDER: Data Analysis, GSS
MORE ABOUT: Data Analysis, GSS

It's about heritability….

By Razib Khan | March 27, 2011 2:25 pm


I’m going to promote a comment:

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CATEGORIZED UNDER: Behavior Genetics, Genetics, Genomics

The decline of web 2.0

By Razib Khan | March 27, 2011 1:56 pm

In 2006-2007 I worked at a firm which had its own web application, and “web 2.0″ was a big term in the marketing materials. This article in DealB%k, Is It a New Tech Bubble? Let’s See if It Pops, made me wonder what happened to that term.

Here’s Google Trends:

CATEGORIZED UNDER: Technology

Guest posts @ Sepia Mutiny

By Razib Khan | March 26, 2011 10:15 pm

Since it doesn’t show up in my total content aggregator (RSS), and I don’t know how to author filter Movable Type posts easily, I thought I would point to my guest posts over at the Sepia Mutiny weblog:

Speaking of a demonstration in Pakistan….

The decline of Hindi among American brown folk

A civilization of regions

Do that Guju you do!

The undersampled 1 billion (genetically that is)

If you don’t know about the blog, here’s the Wikipedia entry. I’ve been commenting on that site since its inception in the summer of 2004, as two friends were co-founders.

Addendum: I push all the stuff in my total content aggregator to my twitter account, Gene Expression Facebook page (though this includes GNXP.com posts not by me), and my Facebook page. I’ve also got a NetworkedBlogs page which you can subscribe to or something. Probably other things I’ve forgotten about to be honest (e.g., here’s my Talk Islam author page. Don’t contribute there anymore).  Also, I should mention that Razib on Books has its own domain, razibkhanbooks.com. Everything posted there is pushed into the total content aggregator, and the “posts” will usually be pointers to this weblog anyhow, but here’s the specific feed if you care (someone inquired, so someone cares!).

CATEGORIZED UNDER: Blog
MORE ABOUT: Blog, Sepia Mutiny

Another genome blogger….

By Razib Khan | March 26, 2011 7:53 pm

Reader “Diogenes,” with ADMIXTURE in hand, and way more knowledge of archaeology than I can comprehend, now has a blog. Why am I starting a blog…:

I named my blog Artemis since I believe the “Neolithic” which shaped our world for the last 10,000 years is now ending. Demeter’s shackles are broken.

I’m starting my own Project playing with ADMIXTURE and other programs. I’m not a scientist (even though I work in a field related to biology), but I’ll try to substantiate my thoughts whenever possible.

His interest seems to be the Neolithic Revolution/Evolution in Europe.

CATEGORIZED UNDER: Anthroplogy
MORE ABOUT: Admixture, Genomics

Friday Fluff – March 25th, 2011

By Razib Khan | March 25, 2011 7:54 pm

FF3

1) First, a post from the past: 10 questions for Jim Crow. Arguably the doyen of modern population geneticists. Take a look at who he’s had as graduate students or post-docs, and there’s a high probability there is someone you know of, you’ve met, or you know of by reputation (at least if you have some association with pop gen).

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CATEGORIZED UNDER: Blog
MORE ABOUT: Friday Fluff

Darwin, eh?

By Razib Khan | March 25, 2011 10:29 am

At The Intersection Sheril Kirshenbaum posts some rather stark data from Gallup and a Canadian outfit on the differences in attitudes toward evolution between Americans and Canadians. Those Tories are different! The answers seem very similar to those on offer for the General Social Survey’s “CREATION” question. I thought I’d compare Canadians to various American demographics. The question was asked in 2004 of over 1,400 Americans. I find it somewhat ironic in that I think there has been some question as to the Prime Minister of Canada, Stephen Harper, and his attitude toward evolution. Harper is a member of the Evangelical Protestant Christian and Missionary Alliance (and apparently has appointed known Creationists to various government positions, something controversial or notable in Canada). In contrast, Barack Hussein Obama is famously more grounded in evolution than angels.

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CATEGORIZED UNDER: Creationism
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