Archive for September, 2012

The Bushmen tell us a lot about human evolution because they are humans who have evolved

By Razib Khan | September 21, 2012 12:32 am

When it comes to the human genetics of the Khoe-San there’s a little that’s stale and unoriginal for me in terms of presentation. The elements are always composed the same. The Bushmen are the “most ancient” humans, who can tell us something about “our past,” about “our evolution.” Tried & tested banalities just bubble forth unbidden. I have no idea why. There’s a new paper in Science on the genetics of the Khoe-San, which includes Bushmen, which brought to mind this issue for me because of the outrageous nature of the press releases.

The title of the paper itself is a testament to vanilla, Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History. This is absolutely not surprising. Are you shocked that the Khoe-San have adaptations? Or that African history is complex? The wonder of it all! This paper actually revisits much of the same ground as Pickrell et al.’s originally titled The genetic prehistory of southern Africa. Before Dr. Pickrell executes throw-down on me on Twitter let me concede that I have no creative ideas to offer in terms of an alternative title. Rather, I have an idea: perhaps in the future scientists could explore the evolutionary genetic basis for steatopygia? The trait is not limited just to Khoe-San, my distant cousins the Andaman Islanders also exhibit it. Perhaps this is the ancestral state of the human lineage? This is a situation where the titles just write themselves!

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Steve Sabol, 1942-2012

By Razib Khan | September 20, 2012 10:21 pm

Just found out that Steve Sabol of NFL films passed away a few days ago. I don’t really watch spectator sports anymore, but I remember the important role that Sabol’s films played in my life leading up the week’s games, as you had to wait day by day. I’m no longer in middle school, but I still recall what it was like.

CATEGORIZED UNDER: Uncategorized

Reader survey results

By Razib Khan | September 19, 2012 11:51 pm

I can’t send you to a direct link, so here are the results. Some of the results need to be crunched by me unfortunately. But here’s a sample (yes, I didn’t do much more than the basic R density plot).

CATEGORIZED UNDER: Administration
MORE ABOUT: Reader Survey

Open thread, 9-19-2012

By Razib Khan | September 19, 2012 10:59 pm

Say as you will.

CATEGORIZED UNDER: Uncategorized

The brambly bush of humanity

By Razib Khan | September 18, 2012 11:53 pm

Over at Haldane’s Sieve there are more than preprints posted, there are commentaries from the authors as well. For example, for The genetic prehistory of southern Africa, the first author, Dr. Joseph K. Pickrell, has a extended comment up.

But occasionally you get contributions & perspectives from non-authors which are very interesting. And it is to one of these I want to draw your attention, Thoughts on: The date of interbreeding between Neandertals and modern humans. It’s a comment on The date of interbreeding between Neandertals and modern humans. In the post Dr. Graham Coop contends:

At this point you are likely saying: well we know that Neandertals existed as a [somewhat] separate population/species who are these population X you keep talking about and where are their remains? Population X could easily be a subset of what we call Neandertals, in which case you’ve been reading this all for no reason [if you only want to know if we interbred with Neandertals]. However, my view is that in the next decade of ancient human population history things are going to get really interesting. We have already seen this from the Denisovian papers [1,2], and the work of ancient admixture in Africa (e.g. Hammer et al. 2011, Lachance et al. 2012). We will likely discover a bunch of cryptic somewhat distinct ancient populations, that we’ve previously [rightly] grouped into a relatively small number of labels based on their morphology and timing in the fossil record. We are not going to have names for many of these groups, but with large amounts of genomic data [ancient and modern] we are going to find all sorts of population structure. The question then becomes not an issue of naming these populations, but understanding the divergence and population genetic relationship among them.

This is a bold contention, and I suspect some physical anthropologists will take issue with it. But it’s a testable prediction. We’ll know if it’s panned out in 2020. I may still be blogging between now and then, and so I will now self-importantly label this “Coop’s Conjecture.” Is there anyone who wants to wager some money on Coop’s Conjecture? Any side of the bet you think is a sure thing?

Gene Expression Brave New World Survey

By Razib Khan | September 18, 2012 9:35 pm

A few weeks ago I mentioned that I wanted do another survey. I’ve done a fair number of reader surveys since the mid-2000s of my readership. So, for example, I know that you’re politically well balanced, except for social conservatives (who are very underrepresented). You are also extremely male, pale, well educated, atheistic, and prone to being virgins at a higher clip than your age might suggest. So I didn’t want to overload on demographic questions this time. Rather, I wanted to know about specific responses to specific controversial questions. So I titled it the “Brave New World Survey” this time, because of the focus on uncomfortable questions and the like.

Mostly, I’m tired of arguing with readers about what is, and isn’t, controversial. My readership has a lot of intellectual oddballs (probably because as an atheist brown conservative I am one). So I assume I’m sampling from the extreme end of the pool in terms of openness to heterodoxy, so we’ll see how it shakes out.

I haven’t used this survey software before, so take that as a warning. I put the survey as an iframe below the fold, but it didn’t work too well. So please go to the link here. It’s all one one page, so you should be able to complete it quickly (you can omit questions you want to omit).

When 100 responses come up, I’ll post a summary below the fold. I’ll do so with every hundred. Usually I make it to ~500 responses for this weblog. Also, I’ll try and figure out how to export it once I close the survey (personally information won’t be in the export, so don’t worry).

Update: If it didn’t work when you tried it earlier, try it now. I didn’t set it ‘live’ because I’m stupid.

CATEGORIZED UNDER: Uncategorized
MORE ABOUT: Survey

The feathery Neandertal

By Razib Khan | September 17, 2012 11:11 pm

Birds of a Feather: Neanderthal Exploitation of Raptors and Corvids:

The hypothesis that Neanderthals exploited birds for the use of their feathers or claws as personal ornaments in symbolic behaviour is revolutionary as it assigns unprecedented cognitive abilities to these hominins. This inference, however, is based on modest faunal samples and thus may not represent a regular or systematic behaviour. Here we address this issue by looking for evidence of such behaviour across a large temporal and geographical framework. Our analyses try to answer four main questions: 1) does a Neanderthal to raptor-corvid connection exist at a large scale, thus avoiding associations that might be regarded as local in space or time?; 2) did Middle (associated with Neanderthals) and Upper Palaeolithic (associated with modern humans) sites contain a greater range of these species than Late Pleistocene paleontological sites?; 3) is there a taphonomic association between Neanderthals and corvids-raptors at Middle Palaeolithic sites on Gibraltar, specifically Gorham’s, Vanguard and Ibex Caves? and; 4) was the extraction of wing feathers a local phenomenon exclusive to the Neanderthals at these sites or was it a geographically wider phenomenon?. We compiled a database of 1699 Pleistocene Palearctic sites based on fossil bird sites. We also compiled a taphonomical database from the Middle Palaeolithic assemblages of Gibraltar. We establish a clear, previously unknown and widespread, association between Neanderthals, raptors and corvids. We show that the association involved the direct intervention of Neanderthals on the bones of these birds, which we interpret as evidence of extraction of large flight feathers. The large number of bones, the variety of species processed and the different temporal periods when the behaviour is observed, indicate that this was a systematic, geographically and temporally broad, activity that the Neanderthals undertook. Our results, providing clear evidence that Neanderthal cognitive capacities were comparable to those of Modern Humans, constitute a major advance in the study of human evolution.

Not to be too skeptical, but has anyone done an analysis of a possible change in the nature of publications about the cognitive capacities of Neandertals since it was established that there is a high likelihood of admixture between that lineage and ours (i.e., that that lineage is to some extent ours)? This is where I have to point to Luke Jostins’ loess curve illustrating the increase in cranial capacity of hominins over the past few million years. As Luke notes “brain size increases gradually in all lineages.”

This isn’t to deny that there seem some qualitative differences between the descendants of anatomically modern humans and other hominins. Neandertals, Denisovans, etc., never made it to the New World or Oceania. But there are differences, and there are differences. One model which was rather popular, and which I tacitly accepted, is that modern humans, the “descendants of Eve,” are sui generis. Somehow, somewhere, ~50-100,000 years ago a lineage of geniuses came upon the scene and swept all others away. I don’t accept this proposition anymore. Rather, it may be that 1-2 million years ago the hominin lineages took some irreversible step, and all the parallel and reticulate branches were hurtling toward a new evolutionary equilibrium.

CATEGORIZED UNDER: Evolution
MORE ABOUT: Neandertal

Minor administrative notes

By Razib Khan | September 17, 2012 10:34 pm

I’m a bad man, cluttering this weblog with administrative notices. But sometimes it needs to be done.

1) In case you don’t know, comment threads close after one week. As occurred this week, if you want to continue a thread, the weekly “open thread” is the place to go. That option has the benefit of being less subject to my supervision!

2) Speaking of which, probably every day or so I get a long, passionate, and coherent comment, which I never publish and which results in the banning of the commenter. I suspect most of these are newbies, who surf in via links, tweets, etc. But just in case you are tempted to go off on a rude rant, understand that you might as well just email/Facebook message me. No one’s going to see what you say.

3) I’ve scheduled open threads to go live once a week. Please use these. I regularly get off-topic questions/comments…but it’s not really feasible for me to track everything. The open thread is useful for odds & ends, and I do respond to a fair number of the queries.

4) I occasionally publish material on other weblogs or sometimes even in regular webzines. If you want to know about that, you might want to subscribe to my total feed (or follow me on Twitter). Normally this wouldn’t be worth mentioning, but sometimes people are surprised when they run into me on another corner of the web.

CATEGORIZED UNDER: Administration

The end of Diaspora

By Razib Khan | September 17, 2012 10:15 pm

I didn’t even notice, Founders of Diaspora, Intended as the Anti-Facebook, Move On. Though I was skeptical about the prospects after one of the co-founders committed suicide. One of the reasons I took an interest is that I gave $50 to the project when it first made a media splash…but honestly I thought the chances of success were always pretty low. The chances of many worthwhile endeavors are low.

CATEGORIZED UNDER: Technology
MORE ABOUT: Diaspora

The great Eurasian explosion

By Razib Khan | September 17, 2012 9:38 pm

Dr. Joseph Pickrell has updated his preprint, The genetic prehistory of southern Africa, with some more material on the Sandawe. I’ve explored the genetics of the Sandawe a bit using ADMIXTURE, so I jumped straight to the section on ROLLOFF:

…To further examine this, we turned to ROLLOFF. We used Dinka and French as representatives of the mixing populations (since date estimates are robust to improperly specified reference populations). The results are shown in Supplementary Figure S22. Both populations show a detectable curve, though the signal is much stronger in the Sandawe than in the Hadza. The implied dates are 89 generations (2500 years) ago for the Hadza and 66 generations (2000 years) ago for the Sandawe. These are qualitatively similar signals to those seen by Pagani et al. [65] in Ethiopian populations. There are two possible historical scenarios that could lead to these signals: either the Hadza and Sandawe both directly admixed with a western Eurasian population about 2,000 years ago, or they admixed with an east African population that was itself admixed with a western Eurasian population. The latter possibility would be consistent with known east African admixture into the Sandawe [16] .

 

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CATEGORIZED UNDER: Genetics, Genomics

Ancestry.com's AncestryDNA won't give you your raw data

By Razib Khan | September 16, 2012 9:18 pm

CeCe Moore points me to an “interesting” fact I had not noticed about Ancestry.com‘s AncestryDNA service (which is not open available to everyone right now):

I re-emphasized to John the importance to the genetic genealogy community that AncestryDNA release our genetic data to us. I mentioned that my colleagues and I were happy to discover that Ken Chahine’s statements to the Presidential Commission for the Study of Bioethical Issues in Washington D.C. on August 1st were in line with our belief that our genetic data belongs to us (video and transcript). During the second session, Dr. Chahine stated that “the customer retains ownership of their DNA and data”. However, we feel that AncestryDNA’s policies do not currently reflect this. John reiterated what I have been told before, which is that they are genuinely considering the best way to deliver this data to us. In response to my persistence, John told me that they are aware that this is important to me, but that they have to take into consideration everyone’s feedback, not just mine. As a result, giving us access to our genetic data is not at the top of their list of priorities. He explained that they read lots of feedback and do a significant number of surveys and focus groups in order to determine what is most important to their customers and, by that process, their priorities are dictated….

 

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CATEGORIZED UNDER: Personal Genomics
MORE ABOUT: Personal genomics

What the substrate tells

By Razib Khan | September 16, 2012 8:26 pm

One of the weird things about genetics is that it encompasses both the abstract and the concrete. The formal and physical. You can talk to a geneticist who is mostly interested in details of molecular mechanisms, and is steeped in structural biology. For these people genes are specific and material things. In contrast there are other geneticists who focus more on genes as units of analysis. In this case genes are semantic labels for the mediators within an intersection of phenomena. Recall that genetics predates the knowledge of its concrete substrate by 50 years! By the 1920s Mendelian genetics had been fused with evolutionary biology to create a systematic framework in which we could understand the patterns of inheritance across the generations. In the 1950s the DNA revolution was upon us, but as W. D. Hamilton recalls this had only a minimal impact on the evolutionary genetic thinkers of the era. With the Lewontin and Hubby allozyme paper in the mid-1960s this sort of benign disciplinary evasion was no longer possible; the field of molecular evolution came into its own.*

Today with genomics these human-imposed artificialities are fading away. Consider the concept of genetic recombination. Originally an abstraction in a formal Mendelian system, today it is of great interest to molecular biologists who are curious as to its exact mechanism and purpose, and genomicists who are interested in the constraints upon the phenomenon due to its physical parameters (e.g., recombination hotspots). If we were to discover alien beings I assume that there would be some sort of genetics in an abstract sense. But would they package their genes in chromosomes? Would their complex organisms tend toward dioecy? I wouldn’t be surprised if the genetics of alien species have their own particular kinks subject to the contingent nature of the physical scaffolding of the process.

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The ecstasy and agony of prenatal information

By Razib Khan | September 16, 2012 6:34 pm

Slate reposts a piece from New Scientist, Do You Really Want To Know Your Baby’s Genetics? It is arranged as a series of questions which might arise from the new information. For me my frustration with this sort of discussion is rooted in reviewing old articles about “test-tube babies” in major newspapers from the 1970s and early 1980s. Today in vitro fertilization is banal and commonplace, but many of the same concerns were voiced back then which you see cropping up now in regards to personal genomics. My issue is not concern as such, but its inchoate character. It is not uncommon for me to encounter people pursuing postgraduate work in science who express the opinion that “it’s scary,” the “it” being genetic information. When further queried the fear is generally layers upon layers of formless disquiet, some confusion about the specific details, as well as a default stance toward the “precautionary principle.”

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CATEGORIZED UNDER: Personal Genomics

Nature's Oracle finally out in 2013

By Razib Khan | September 16, 2012 2:03 pm

Jerry Coyne alerts me to the fact that Ullica Segerstrale’s Nature’s Oracle: A Life of W. D. Hamilton is finally near publication. Specifically, early 2013. Coyne has looked at he pre-publication text, so it is probably in revision, though the meat has already been laid upon the bones. Hamilton was one of the preeminent evolutionary biologists of the second half of the 20th century. Though to my knowledge he never wrote an autobiography as such the details of his life was liberally strewn out across dozens of books. You can find them in Segerstrale’s Defenders of the Truth: The Sociobiology Debate, or The Darwin Wars. He makes a cameo appearance in Robert Trivers’ Natural Selection and Social Theory, as well as The Price of Altruism, a scientific biography of Hamilton’s collaborator George Price.

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CATEGORIZED UNDER: Evolutionary Genetics

Intelligence challenged people and free speech

By Razib Khan | September 15, 2012 6:23 pm

 

In the post below I took the time out to link to the GSS, as well as posting my exact queries. As payment for this consideration the first comment was absolute drivel. I understand people have political opinions, but I’m not too interested in your opinions. You may be interested in your opinions, but I’d rather have more data. Most people don’t know enough for me to have interest in their opinions (most != all, many readers do have opinions in their specialties which I seek out).

I was trying to make a point that anger and even violence in reaction to actions which offend are actually comprehensible as the modal human response. The community reacts to punish those who violate taboos. The taboos may differ, but the response to the action of violation is normal and natural. A primary issue that needs to be considered is that taboos differ from society to society, so one is often not conscious of the act of violation (e.g., if you show the bottom of your shoes to people when you sit down, that’s an offensive act in some societies).

An implication here is that American norms of free speech near absolutism, enforced through the fiat of the courts because of their interpretation of the applicability of the Bill of Rights, are radically non-intuitive to most people. The only reason that they are intuitive to many Americans is that we are acculturated over time. This is clear when you look at differences of intelligence and education. In short, less intelligent and educated Americans are much more skeptical of allowing social deviants to speak. This is true even in cases where they are more likely to agree with the deviant in question (e.g., these groups have a more pro-military bent, and yet are more accepting of the concept of censure of pro-military opinions).

I have limited all the results to the year 2000 and later. Additionally, I classify those who score 0-4 on the WORDSUM vocab test as stupid, those who score 5-8 as average, and those who score 9-10 as smart. WORDSUM has been reported to have a 0.7 correlation with general intelligence. In this data set 20% of individuals scored 0-4, 69% 5-8, and 12% 9-10.

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CATEGORIZED UNDER: Data Analysis
MORE ABOUT: GSS, Speech

Who tolerates anti-American preaching from Muslims?

By Razib Khan | September 15, 2012 10:45 am

Obviously the news over the past week has been filled with the events in the Middle East, and the broader Muslim world, in reaction to an anti-Muslim film. I think the most eloquent commentary is from The Onion (NSFW!!!), No One Murdered Because Of This Image. That being said, there are some serious broader issues here. A friend of mine who lives in India (he is Indian American, though raised for several years in India, so not totally unfamiliar with the culture) has expressed to me his frustration with having to defend American liberalism in a society where American liberalism is an abstraction, rather than concrete. The frustration has to do with the fundamental divergence in basic values. For example, his interlocutors have argued to him (he is a practicing Christian of libertarian political orientation) that if someone committed an act of blasphemy against his faith of course he would react in anger and violence. And yet of course the clause “and” is false, though he is greeted with skepticism when he asserts he wouldn’t react violently. As a matter of fact I can attest to the reality that he wouldn’t react angrily necessarily, because in interactions where I’ve made casually blasphemous comments he’s only rolled his eyes. Just as Americans have a vague, even misleading, understanding of the broader historical forces which engender resentment of American hegemony in the broader world, so many non-Americans lack a proper awareness of the broader historical forces, and cultural reality, of the particular American radicalism and extremism in the domain of free expression.

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CATEGORIZED UNDER: Anthroplogy, Geography, GSS
MORE ABOUT: GSS

Predicting someone's face: look at their parents

By Razib Khan | September 14, 2012 12:55 am

A few years ago there was a paper out which illustrated that standard Galtonian method of regression of offspring upon parents still predicted height far better than the most modern genomic techniques. The issue is that height is a quantitative trait whose variation is controlled by variants at hundreds, and likely thousands, of loci. Generating a useful prediction for one individual from a “bottom-up” genetic model is daunting because of the overwhelming number of variants. This is in contrast to pigmentation traits, which been found to be well characterized by a few large effect quantitative trait loci. That is, one gene can account for a substantial minority of the variation within the population of the trait. In regards to eye pigmentation in Europeans the majority of the blue vs. non-blue eye color difference can be accounted for by one locus, HERC2-OCA2. Not so for height, intelligence, and now it seems likely, facial morphology.

A Genome-Wide Association Study Identifies Five Loci Influencing Facial Morphology in Europeans. The issue I’m alluding to is found buried in the paper:

Moreover, our data also highlight that the high heritability of facial shape phenotypes (as estimated here and elsewhere), similar to that of adult body height…involves many common DNA variants with relatively small phenotypic effects. Future GWAS on the facial phenotype should therefore employ increased sample sizes as this has helped to identify more genes for many other complex human phenotypes such as height…and various human diseases.

Am I on crack, or are we not going to really get much yield from hunting for specific genes in most cases? Granted, there may be populations like pygmies who are well deviated on some trait, so we’ll put a finger on particular variants which shift the trait value a lot. Additionally, like height I wouldn’t be surprised if we find some evidence for selection on facial morphology related genes. But this seems to dampen the likelihood of robust individual prediction. The limits of forensic genetics? Say it ain’t so!

CATEGORIZED UNDER: Anthroplogy, Genetics, Genomics
MORE ABOUT: Phenotype, Prediction

ADMIXTOOLS is out

By Razib Khan | September 13, 2012 8:58 pm

The time for commentary uninformed by DIY exploratory analysis is fast coming to a close. The alpha version of ADMIXTOOLS is out. It’s a moderately large download, 166 MB in compressed format. Do note that most of this consists of data files, not the program itself. I uploaded a zip of the README files if you are hesitant. Dienekes has a preview. I probably won’t poking around until this weekend.

If you are confused as to why this is a big deal, please see my post. We’re nearing Adam-biting-the-apple territory for regular people on the street willing to devote some computing time to exploring questions.

Update: From the comments:

For future googlers, the only thing you need to do to compile on a mac (Mac OS X 10.6.8) is add a single line to the Makefile. Replace:

libnick.a: dirs tables $(OBJ)
ar -r libnick.a $(OBJ)

with

libnick.a: dirs tables $(OBJ)
ar -r libnick.a $(OBJ)
ranlib libnick.a

then make clean and make all. Should compile fine.

CATEGORIZED UNDER: Genetics, Genomics
MORE ABOUT: ADMIXTOOLS

Bane loses control

By Razib Khan | September 13, 2012 12:36 am
CATEGORIZED UNDER: Uncategorized
MORE ABOUT: Bane

An ontology of genetic diversity

By Razib Khan | September 13, 2012 12:23 am

Implicit in the title The Origin Of Species is the question: why the plural? In other words, why isn’t there a singular apex species which dominates this planet? One can imagine an abstract system where natural selection slowly but gradually sifts through variation and designs a best-of-all-replicators. And yet on the contrary it seems that our planet has exhibited an overall tendency of going from lower to higher diversity. The age of stromatolites may be the last epoch when we had the best-of-all-replicators.

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CATEGORIZED UNDER: Evolution, Evolutionary Genetics
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Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!
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