Razib Khan One-stop-shopping for all of my content

February 29, 2012

Jerry Coyne on race: a reflection of evolution

Filed under: Human Evolution,race — Razib Khan @ 8:53 am

After my post on the ‘race question’ I thought it would be useful to point to Jerry Coyne’s ‘Are there human races’?. The utility is that Coyne’s book Speciation strongly shaped my own perceptions. I knew the empirical reality of clustering before I read that book, but the analogy with “species concept” debates was only striking after becoming more familiar with that literature. Coyne’s post was triggered by a review of Race?: Debunking a Scientific Myth and Race and the Genetic Revolution: Science, Myth, and Culture. He terms the review tendentious, and I generally agree.

In the early 20th century Western intellectuals of all political stripes understood what biology told us about human taxonomy. In short, human races were different, and the white European race was superior on the metrics which mattered (this was even true of Left-Socialist intellectuals such as H. G. Wells and Jack London). In the early 21st century Western intellectuals of all political stripes understand what biology teaches us about human taxonomy. Human races are basically the same, and for all practical purposes identical, and equal on measures which matter (again, to Western intellectuals). As Coyne alludes to in his post these are both ideologically driven positions. One of the main reasons that I shy away from modern liberalism is a strong commitment to interchangeability and identity across all individuals and populations as a matter of fact, rather than equality as a matter of legal commitment. In a minimal government scenario the details of human variation are not of particular relevance, but if you accept the feasibility of social engineering (a term I am not using in an insulting sense, but in a descriptive one) you have to start out with a model of human nature. So this is not just an abstract issue. For whatever reason many moderns, both liberals and economic conservatives, start out with one of near identity (e.g., H. economicus in economics).

I want to highlight a few sections of Coyne’s post:

What are races?

In my own field of evolutionary biology, races of animals (also called “subspecies” or “ecotypes”) are morphologically distinguishable populations that live in allopatry (i.e. are geographically separated).  There is no firm criterion on how much morphological difference it takes to delimit a race.  Races of mice, for example, are described solely on the basis of difference in coat color, which could involve only one or two genes.

Under that criterion, are there human races?

Yes.  As we all know, there are morphologically different groups of people who live in different areas, though those differences are blurring due to recent innovations in transportation that have led to more admixture between human groups.

Why do these differences exist?

The short answer is, of course, evolution.  The groups exist because human populations have an evolutionary history, and, like different species themselves, that ancestry leads to clustering and branching, though humans have a lot of genetic interchange between the branches!

But what evolutionary forces caused the differentiation?  It’s undoubtedly a combination of natural selection (especially for the morphological traits) and genetic drift, which will both lead to the accumulation of genetic differences between isolated populations.  What I want to emphasize is that even for the morphological differences between human “races,” we have virtually no understanding of how evolution produced them.  It’s pretty likely that skin pigmentation resulted from natural selection operating differently in different places, but even there we’re not sure why (the classic story involved selection for protection against melanoma-inducing sunlight in lower latitudes, and selection for lighter pigmentation at higher latitudes to allow production of vitamin D in the skin; but this has been called into question by some workers).

As for things like differences in hair texture, eye shape, and nose shape, we have no idea….

I have no idea if reading Coyne’s earlier work influenced me, but observe that he too emphasizes that human races are a reflection of evolutionary history. Some of my interlocutors believe it is essential to have a tree-like phylogeny with no reticulation (gene flow across branches) to have a reasonable model for race, but I do not. That’s because the focus for me is evolutionary history. I want to understand evolutionary history. Taxonomy is a means to that end. It is not the end.

Coyne has a follow up post which will be of no surprise to reader of this weblog. But I do want to add a few things. 1) For pigmentation we do now understand its genomics relatively well. It seems that light skin emerged at least twice at the two ends of Eurasia, and, that it was a recent emergence (as evidence by markers of selective sweeps). 2) As for hair texture, there is some work which has shed light on this. East Asians in particular carry a variant of EDAR which gives them their distinctive thick straight hair. There has been less work on “woolly hair,” but I suspect that it will be elucidated soon (there are some candidate genes, from linkage studies and animal models). Additionally, I think it is important to note that the dark-skin-as-protection-against-skin-cancer does not make much evolutionary sense. Melanoma strikes later in one’s reproductive years. Rather, I accept that Nina Jablonski has the right of it when she argues that it protects against neural tube defects which arise because of various chemical changes which occur in one’s biochemistry due to exposure to sun. Finally, I think Coyne underestimates the power of even gene genomics using haplotype based techniques in narrowing down on very specific geographical and population origins for segments of your DNA right now. The key is not where you come from, it is how segments of your DNA relate to the full range of segments of other peoples’ DNA.

February 28, 2012

Are Sardinians like Iberians?

Filed under: Anthroplogy,Human Genetics,Sardinians — Razib Khan @ 10:32 pm

Dienekes asks:

In terms of autosomal DNA, the Iceman clearly clusters with modern Sardinians, and also appears slightly more removed than them compared to continental Europeans. Interestingly, at least as far as the PC analyssi shows, Sardinians appear to be intermediate between the Iceman and SW Europeans, rather than Italians. Perhaps, this makes sense if the Paleo-Sardinian language is indeed related to languages of Iberia.

This trend aroused a little curiosity in me too. I’m sure Dienekes & company will be probing these issues a lot in the near future, but I couldn’t wait. I took the IBS data set, which includes a lot of individuals from various areas of Spain, the Sardinians, French and French Basque from the HGDP, and the Tuscans from the HapMap, and threw them together into a pot. I added HGDP Russians & Orcadians (the latter a British group) to make sure there was a North European “outgroup.” In terms of technical details the combined data set had ~220,000 SNPs, not too shabby. Additionally, I decided to run a PCA, where this number of SNPs is more than sufficient.

On a technical note, the Sardinians were swamped in raw numbers by Iberians and Tuscans (over 100 and around 80 respectively). This means that the peculiarities of the Sardinian genetic heritage didn’t show up, rather, what you see are the Sardinians as they arrange themselves in relation to the genetic variation of these more numerous groups. I used SmartPCA to generate the 10 largest independent dimensions of variation. To make a long story short there really wasn’t much variation added from the second dimension on in this relatively homogeneous sample. So below is PC 1 and 2 (E1 and E2).


I’d be curious if someone could replicate this. I’m rather surprised that the Tuscans form such a tight cluster, but then again the IBS sample is very geographically distributed across Spain. The analogy to the HapMap Tuscans might be if Spain was represented by just Galicians. So what you’re really seeing is a lot of Spanish variation, and of course the north-south range in Europe (which is really a southwest to northeast cline). I don’t see a very strong affinity between Basques and Sardinians, but repeated trials indicated that the Sardinians do not cluster with Tuscans when it comes to their position within the Iberian genetic spectrum.

 

Ötzi the Iceman and the Sardinians

Well, the paper is finally out, New insights into the Tyrolean Iceman’s origin and phenotype as inferred by whole-genome sequencing. In case you don’t know, Ötzi the Iceman died 5,300 years ago in the alpine region bordering Austria and Italy. His seems to have been killed. And due to various coincidences his body was also very well preserved. This means that enough tissue remained that researchers have been able to amplify his DNA. And now they’ve sequenced it enough to the point where they can make some inferences about his phenotypic characteristics, and, his phylogenetic relationships to modern populations.

The guts of this paper will not be particularly surprising to close readers of this weblog. The guesses of some readers based on what the researchers hinted were correct: Ötzi seems to resemble mostly closely the people of Sardinia. This is rather interesting. One reason is prosaic. The HGDP sample used in the paper has many Northern Italians (from Bergamo). Why is it that Ötzi does not resemble the people from the region that he was indigenous to? (we know that he was indigenous because of the ratio of isotopes in his body) A more abstruse issue is that it is interesting that Sardinians have remained moored to their genetic past, enough so that a 5,300 year old individual clearly can exhibit affinities with them. The distinctiveness of Sardinians jumps out at you when you analyze genetic data sets. They were clearly set apart in L. L. Cavalli-Sforza’s The History and Geography of Human Genes, 20 years ago. One reason that Sardinians may be distinctive is that Sardinia is an isolated island. Islands experience reduced gene flow because they’re surrounded by water. And sure enough, Sardinians are especially similar to each other in relation to other European populations.

 

But Ötzi’s affinities reduce the strength of this particular dynamic as an explanation for Sardinian distinctiveness. The plot to the left is a PCA. It takes the genetic variation in the data set, and extracts out the largest independent components. PC 1 is the largest component, and PC 2 the second largest. The primary cline of genetic variation in Europe is North-South, with a secondary one going from West-East. This is evident in the plot, with PC 1 being North-South, and PC 2 being West-East. The “Europe S” cluster includes northern, southern, and Sicilian Italians. Now notice the position of Ötzi: he is closest to a large cluster of Sardinians. Interestingly there are also a few others. Who are they? I do not know because I do not have access to the supplements right now. The fact that the Sardinians are shifted closer to the continental populations than Ötzi is also striking. But totally intelligible: Sardinia has had some gene flow with other Mediterranean populations. This obviously post-dates Ötzi; Roman adventurers and Genoaese magnates could not be in his genealogy because Rome and Genoa did not exist 5,300 years ago. These data strongly point to the possibility of rather major genetic changes in continental Europe, and in particular Italy, since the Copper Age.  Juvenal complained that the “River Orantes has long flowed into the Tiber,” a reference to the prominence of easterners, Greek and non-Greek, in the city of Rome. The impact of this is not to be dismissed, but I do not think that it gets to the heart of this matter.

The second panel makes clear what I’m hinting at: Ötzi is actually closer to the “Middle Eastern” cluster than many Italians! In fact, more than most. Why? I suspect that rather than the Orantes, the Rhine and the Elbe have had more of an impact on the genetic character of Italians over the past ~5,000 years. Before Lombardy was Lombardy, named for a German tribe, it was Cisapline Gaul, after the Celts who had settled it. And before that? For that you have to ask where Indo-Europeans came from. I suspect the answer is that they came from the north, and therefore brought northern genes.


A Sardinian

And what of the Sardinians? I believe that the “islanders” of the Mediterranean are a relatively “pristine” snapshot of a particular moment in the history of the region. This is evident in Dienekes’ Dodecad Ancestry Project. Unlike their mainland cousins both the Sardinians and Cypriots tend to lack a “Northern European” component. Are the islanders in part descendants of the Paleolithic populations? In part. Sardinians carry a relatively high fraction of the U5 haplogroup, which has been associated with ancient hunter-gatherer remains. But it is also possible that the preponderant aspect of Sardinian ancestry derives from the first farmers to settle the Western Mediterranean.  I say this because the Iceman carried the G2a Y haplogroup, which has of late been strongly associated with very early Neolithic populations in Western Europe. And interestingly some scholars have discerned a pre-Indo-European substrate in Sardinian which suggests a connection to the Basque. I wouldn’t read too much into that, but these questions need to be explored, as Ötzi’s genetic nature makes Sardiniaology more critical to understanding the European past.

Image credit: Wikipedia

February 26, 2012

Neandertal population structure

Filed under: Human Evolution,Neanderthals,paleontology — Razib Khan @ 6:04 pm

There’s a new paper out, Partial genetic turnover in neandertals: continuity in the east and population replacement in the west. The primary results are above. Basically, using 13 mtDNA samples the authors conclude that it looks as if there was a founder effect for Neanderthals in Western Europe ~50 K years ago, generating a very homogenized genetic background for this particular population before the arrival of modern humans. Perhaps it’s just me, but press releases with headlines such as “European Neanderthals Were On the Verge of Extinction Even Before the Arrival of Modern Humans” strike me as hyperbolic. I’m also confused by quotes like the one below:

“The fact that Neanderthals in Europe were nearly extinct, but then recovered, and that all this took place long before they came into contact with modern humans came as a complete surprise to us. This indicates that the Neanderthals may have been more sensitive to the dramatic climate changes that took place in the last Ice Age than was previously thought”, says Love Dalén, associate professor at the Swedish Museum of Natural History in Stockholm.

There are several points that come to mind, from the specific to the general. First, from what I gather Neandertals were actually less expansive in pushing the northern limits of the hominin range than the modern humans who succeeded them. From this many suppose that despite the biological cold-adapted nature of the Neandertal physique they lacked the cultural plasticity to push the range envelope (e.g., modern humans pushed into Siberia, allowing them to traverse Beringia). One might infer from this that Neandertals were more, not less, sensitive to climate changes than later human populations. Second, there is the fact that as the northern hominin lineage one would expect that Neandertals would be subject to more population size variations than their cousins to the south during the Pleistocene due to cyclical climate change. This is not just an issue just for Neandertals, but for slow breeding or moving organisms generally. The modern human bottleneck is in some ways more surprising, because modern humans derive from a warmer climate. Finally, there is the “big picture” issue that though we throw these northern adapted hominins into the pot as “Neandertals,” one shouldn’t be surprised if they exhibit structure and variation. Non-African humans have diversified over less than 100,000 years, at a minimum the lineages which we label Neandertals were resident from Western Europe to Central Asia for ~200,000 years. Wouldn’t one expect a lot of natural history over this time?

Presumably the authors focused on mtDNA because this is copious relative to autosomal DNA, making ancient DNA extraction easier. I’m a bit curious how it aligns with the inference from the Denisovan paper that Vindija and Mezmaiskaya Neandertals both went through a population bottleneck using autosomal markers. The dates from the paper’s supplements are not clear to me, though it seems possible that they may have sampled individuals where the Vindija population may have been post-resettlement. At some point presumably we may be able to get a better sense of the source population of the Neandertal admixture into our own genomes if the genomic history of this population is well characterized.

What the World Is Made Of

Filed under: science,Top Posts — Sean Carroll @ 12:17 pm

I know you’re all following the Minute Physics videos (that we talked about here), but just in case my knowledge is somehow fallible you really should start following them. After taking care of why stones are round, and why there is no pink light, Henry Reich is now explaining the fundamental nature of our everyday world: quantum field theory and the Standard Model. It’s a multi-part series, since some things deserve more than a minute, dammit.

Two parts have been posted so far. The first is just an intro, pointing out something we’ve already heard: the Standard Model of Particle physics describes all the world we experience in our everyday lives.

The second one, just up, tackles quantum field theory and the Pauli exclusion principle, of which we’ve been recently speaking. (Admittedly it’s two minutes long, but these are big topics!)

The world is made of fields, which appear to us as particles when we look at them. Something everyone should know.


February 25, 2012

Men on the move and women in place?

Filed under: Anthroplogy,Human Genetics,Human Genomics,India — Razib Khan @ 7:22 pm

After posting on Basque mtDNA I wanted to make something more explicit that I alluded to below, that uniparental lineages are highly informative, but they may not be representative of total genome content. This is plainly true in the case of mestizos from Latin America, but we don’t need genetics to point us in the right direction on this score, we have plenty of textual evidence for asymmetry in sexes when it came to admixture events in the post-Columbian era. Rather, I want to note again the issue of South Asia. When it comes to mtDNA the good majority of South Asian lineages are closer to those of East Asia than Western Eurasia. By this, I do not mean to say that that they’re particular close to East Asian lineages, only that if you go back in the phylogeny the South Asian lineages (I’m thinking here of haplogroup M) they tend to coalesce first with East Asian lineages before they do so with West Eurasian lineages.

Here is a quote from one of the definitive papers on this topic:

Broadly, the average proportion of mtDNAs from West Eurasia among Indian caste populations is 17% (Table 2). In the western States of India and in Pakistan their share is greater, reaching over 30% in Kashmir and Gujarat, nearly 40% in Indian Punjab, and peaking, expectedly, at approximately 50% in Pakistan (Table 11, see Additional file 6, Figure 11, panel A). These frequencies demonstrate a general decline (SAA p < 0.05 Figure 4) towards the south (23%, 11% and 15% in Maharashtra, Kerala and Sri Lanka, respectively) and even more so towards the east of India (13% in Uttar Pradesh and around 7% in West Bengal and Bangladesh).

In Iran, over 90 percent of the mtDNA lineages seem West Eurasian. Though I accepted these findings, I was always a bit concerned that the 40 unit chasm between Iran and Pakistan was so large. Additionally, the autosomal studies seem to show that Pakistani populations exhibited affinities to West Eurasians greater than than would be predicted by being ~50 percent West Eurasian. And, as many of you no doubt know the mtDNA does not align well with the Y chromosomal lineages, which seem to indicate a stronger affinity to West Eurasia.

The 2009 paper Reconstructing Indian History resolved some of these confusions. In it the authors inferred that South Asians were a compound population, about ~50 percent West Eurasian, and ~50 percent South Eurasian, with this latter component having distant, but still closer, affinities to East Asians. In other words, the latter component could be easily aligned with the mtDNA, while the former made sense of the Y chromosomal lineages. According to the above paper the West Eurasian component was present at 70-80 percent fractions in Pakistan at the total genome level. This is considerably above the 50 percent for mtDNA, and made more sense of the visible affinities of Pakistanis to West Eurasians on the phenotypic dimension. But look at the rapid drop off mtDNA fraction.

Here’s a table I generated combining the drop off in ANI and mtDNA across the two papers:

If you don’t know the geography of India, the West Eurasian mtDNA fraction falls off a cliff very quickly in Northwest India. In contrast, the autosomal ANI fraction drops, but not nearly as precipitously. The ratio between the two is 2:3 in Pakistan. In Bengal is 1:5, but it is already 1:4 in Uttar Pradesh, which is closer geographically to Pakistan than Bengal (though arguably more ecologically distinct from Pakistan, the linguistic dialects of Uttar Pradesh are far closer to those of Pakistan than of Bengal). I will let you develop your own the story in this case, as there’s obviously a lot there could be said speculatively. Rather, I simply wanted to illustrate the reality that the differences between patterns in uniparental lineages and autosomal DNA can tell you a great deal, despite their disagreements on occasion.

Finally, I want to end on a somewhat different note:

Elevated frequencies of haplogroups common in eastern Eurasia are observed in Bangladesh (17%) and Indian Kashmir (21%) and may be explained by admixture with the adjacent populations of Tibet and Myanmar (and possibly further east: from China and perhaps Thailand).

These proportions are both higher than anything in the autosomal DNA. My parents are both 10-15 percent Southeast Asian in ancestry. But I am willing to bet that they’re slightly on the high side even for Bangladeshis (going by geography). And as for Kashmiris, these populations do often show some East Asian admixture, but generally not so high as 20%. What explains this? I have posited that rather than being intrusive to Bengal, the East Asian populations (Munda?) may have been already present when Indo-Aryan speaking agriculturalists arrived. This could explain a sex bias in assimilation of these populations toward females. In general my rule of thumb is that later population arrivals are correlated with a male bias in ancestry.

Parkinson’s disease patients & free 23andMe

Filed under: Personal genomics — Razib Khan @ 3:09 pm

Michelle tipped me off to 23andMe’s new initiative to get Parkison’s disease sufferers genotyped. Basically, if you are a sufferer, you get the service for free. The goal presumably to increase the sample size so as to pick up new possible associations. But a question: can you think of a downside for Parkinson’s disease sufferers? A lot of people have genetic privacy concerns, but if you manifest a disease like Parkinson’s I suspect that’s the least of your worries.

Basque maternal heritage & continuity

Filed under: Agriculture,Anthroplogy,Basque — Razib Khan @ 3:02 pm

There’s a new paper in AJHG which caught my eye, The Basque Paradigm: Genetic Evidence of a Maternal Continuity in the Franco-Cantabrian Region since Pre-Neolithic Times (ungated). The first thing you need to know about this paper is that it focuses on only the direct maternal lineage of Basques via the mtDNA. In some ways this is weak tea, since it doesn’t give us a total genome estimate. But there are major upsides to mtDNA and Y. First, because of the lack of recombination it is relatively easy to generate a nice phylogenetic tree using a coalescent model. And second, for mtDNA the molecular clock is considered relatively reliable.

In this specific paper they also expanded the scope of their analysis to the whole mtDNA sequence, instead of just the hypervariable region. Not only did they look at whole sequences, but they also had an enormous sample size. They sequenced over 400 mtDNA genomes from the Basque country and neighboring regions. Haplogroup H peaks in frequency among Basques, and drops off among their neighbors (Gascons, Spaniards, etc.). Because the Basque speak a non-Indo-European language they are usually presumed to be indigenous in relation to their neighbors (or at least more indigenous). Until recently there was a strong presupposition that the Basque were ideal representatives of the pre-Neolithic populations of Western Europe. One common method of analysis would be to use the Basque as a pre-Neolithic “reference,” and simply estimate the impact of a Neolithic demographic wave of advance by using a eastern Mediterranean population as a second “reference” within an admixture framework. But more recent work has muddled the idea that the Basque are the descendants of Paleolithic Europeans. Finally, I suspect we’ll also have to acknowledge complexity in demographic histories. To say that the Basque exhibit continuity with Mesolithic Iberians may not contradict a substantial Neolithic contribution. South Asians for example are one numerous modern group which exhibits sharply divergent affinities if you use Y chromosomes (West Eurasian) or mtDNA (not West Eurasian). Why? The details are prehistorical.


The major takeaway from this paper is that the Basque mtDNA exhibit a pattern of demographic expansion ~4,000 years BP, and ~8,000 years BP. But I think it is important to look at the range of outcomes over their confidence intervals, so I’ve reproduced their second table below:


Table 2. Time Estimates of the Six Autochthonous Haplogroups

Haplogroup N Percentage Rho Standard Error Age (in Years) 95% Confidence Interval
Coalescence Age
H1j1 52 12.4% 1.86 0.49 4845 2324 − 7408
H1t1 34 8.1% 1.94 0.97 5057 99 – 10176
H2a5a1 22 5.2% 1.33 0.65 3422 118 – 6800
H1av1 17 4.0% 1.24 0.52 3213 567 – 5906
H3c2a 14 3.3% 1.27 0.37 3291 1403 – 5204
H1e1a1 12 2.9% 1.23 0.72 3187 −464 – 6927
Splitting Age
H1j1 52 12.4% 2.86 1.11 7514 1764 – 13470
H1t1 34 8.1% 2.94 1.39 7730 554 – 15227
H2a5a1 22 5.2% 2.33 1.19 6094 −6 – 12434
H1av1 17 4.0% 2.24 1.13 5854 65 – 11860
H3c2a 14 3.3% 2.27 1.07 5934 443 – 11619
H1e1a1 12 2.9% 5.23 2.13 14011 2729 – 26000
 

For our purposes the splitting age is important, because it shows when the Basque specific H lineages diverged from other European H lineages. Some of the intervals are huge (look at H1e1a1), so I don’t know what to make of it. I’ll leave further comments to those more well versed in the mtDNA literature, but I would like to say that it is important to remember that we don’t know where the demographic events inferred occurred. It may not have been in the trans-Pyrenees region at all.

More later.

February 24, 2012

The data sets in the dark

Filed under: Bangladesh,Genetics,Genomics,Human Genetics,Human Genomics — Razib Khan @ 12:09 pm

Recently I was tipped off to the appearance of a new paper, Genome-Wide Association Study Identifies Chromosome 10q24.32 Variants Associated with Arsenic Metabolism and Toxicity Phenotypes in Bangladesh. This is the section which caught my eye: “Using data on urinary arsenic metabolite concentrations and approximately 300,000 genome-wide single nucleotide polymorphisms (SNPs) for 1,313 arsenic-exposed Bangladeshi individuals.” 300 K SNPs with 1,313 Bangladeshi individuals is a lot! I’m interested in this data set because of the 200+ participants in the Harappa Ancestry Project my parents remain the “unadmixed” South Asians with the highest fraction of East Asian ancestry (10-15 percent). Within South Asia aside from those groups with clear East Asian affinities only peoples of Munda background have the same levels. This data set could answer a lot of questions as to the typicality of my parents (literally within a few hours in terms of data exploration). But this is all you get in the supplements:

 


Zack Ajmal has already sent off an email asking about this data set, so hopefully the results will be positive.

This is a medical genetics study, so all they wanted to confirm is that there wasn’t population stratification due to inbreeding. They confirmed that. It is fine if they don’t want to explore further questions in relation to ancestry, but it would be really depressing if the data set can never see the light of day for those who are interested in asking other questions.

Friday Piano Solo

Filed under: Music — Sean Carroll @ 10:34 am

Keith Emerson has been doing some interesting work on wave mechanics, Fourier transforms, and temporal structure. Here are some of his findings.

Not exactly what you see at the Grammy’s these days. (Not that it was back in 1974, either.)


How common are godless liberals?

Filed under: atheism,Religion — Razib Khan @ 7:43 am

 

I’m going to be speaking at the Moving Secularism Forward conference in Orlando next week. They invited me because I’m a conservative atheist public intellectual, and the three other conservative atheist public intellectuals in the United States were presumably busy. In any case, going over what I’m going to talk about I was double-checking political breakdowns by atheist & agnostic proportions and ideology in the General Social Survey for after the year 2000.

I used the “GOD” variable, which asks people about their belief in God. Those who did not believe, or said there was no way to find out, I classed as “atheists & agnostics.” This means that the total percentages in the population are higher than self-reports; that’s because the word atheism in particular has a negative connotation (I recall that Julia Sweeney’s parents were tolerant of the fact that she did not believe in God, but were aghast that she was an atheist!). “POLVIEWS” what the variable which I crossed “GOD” with. It has seven responses, from very liberal to very conservative, and I just put all liberals and conservatives into one category.

The first table displays what proportion in the whole society atheist & agnostic liberals (or conservatives) are. Since the total proportion of atheists & agnostics is small, naturally these percentages are small. The two subsequent tables just display what percentage of atheists & agnostics are liberal, or what percentage of liberals are atheist & agnostic.

 

All cells combined = 100%
Atheist and agnostic Not atheist or agnostic
Liberal 3.7% 22.8%
Moderate 2.3% 36.0%
Conservative 1.5% 33.5%

Rows = 100%
Liberal Moderate Conservative
Atheist and agnostic 49.7% 30.6% 19.7%
Not atheist or agnostic 24.7% 39.0% 36.3%

Rows = 100%
Atheist and agnostic Not atheist or agnostic
Liberal 14.2% 85.8%
Moderate 6.1% 93.9%
Conservatve 4.3% 95.7%



When I see these results I’m always surprised by the proportions of atheists & agnostics who define themselves as conservative. It seems way too high. I think this is due to libertarians who check the conservative option.

Adam’s end was never in the cards

Filed under: Genetics,Genomics,Human Evolution,Human Genetics,Human Genomics — Razib Khan @ 7:23 am

There has been a lot of talk in the media about a new paper which reports that the Y chromosome is not deteriorating, as had been previously inferred from the data. In the 2004 Bryan Sykes wrote Adam’s Curse: A Future Without Men which used this model as a framing device (and naturally elicited great general interest). You can read some earlier critiques at Gene Expression Classic. I never paid attention to this debate in the details because it seemed ludicrous on the face of it. Bryan Sykes’ was predicting the extinction of males in ~100,000 years. Right, we just happen to be living right before the genomic Götterdämmerung. I don’t think so. Sometimes absurd results which fly in the face of plain history and robust theory are profoundly insightful. But most of the time they’re just false leads.

February 23, 2012

Everything is Connected

Filed under: science,Science and the Media,Top Posts — Sean Carroll @ 10:09 am

They do things differently over in Britain. For one thing, their idea of a fun and entertaining night out includes going to listen to a lecture/demonstration on quantum mechanics and the laws of physics. Of course, it helps when the lecture is given by someone as charismatic as Brian Cox, and the front row seats are filled with celebrities. (And yes I know, there are people here in the US who would find that entertaining as well — I’m one of them.) In particular, this snippet about harmonics and QM has gotten a lot of well-deserved play on the intertubes.

More recently, though, another excerpt from this lecture has been passed around, this one about ramifications of the Pauli Exclusion Principle. (Headline at io9: “Brian Cox explains the interconnectedness of the universe, explodes your brain.”)

The problem is that, in this video, the proffered mind-bending consequences of quantum mechanics aren’t actually correct. Some people pointed this out, including Tom Swanson in a somewhat intemperately-worded blog post, to which I pointed in a tweet. Which led to some tiresome sniping on Twitter, which you can dig up if you’re really fascinated. Much more interesting to me is getting the physics right.

One thing should be clear: getting the physics right isn’t easy. For one thing, going from simple quantum problems of a single particle in a textbook to the messy real world is often a complicated and confusing process. For another, the measurement process in quantum mechanics is famously confusing and not completely settled, even among professional physicists.

And finally, when one translates from the relative clarity of the equations to a natural-language description in order to reach a broad audience, it’s always possible to quibble about the best way to translate. It’s completely unfair in these situations to declare a certain popular exposition “wrong” just because it isn’t the way you would have done it, or even because it assumes certain technical details that the presenter did not fully footnote. It’s a popular lecture, not a scholarly tome. In this kind of format, there are two relevant questions: (1) is there an interpretation of what’s being said that matches the informal description onto a correct formal statement within the mathematical formulation of the theory?; and (2) has the formalism been translated in such a way that a non-expert listener will come away with an understanding that is reasonably close to reality? We should be charitable interpreters, in other words.

In the video, Cox displays a piece of diamond, in order to illustrate the Pauli Exclusion Principle. The exclusion principle says that no two fermions — “matter” particles in quantum mechanics, as contrasted with the boson “force” particles — can exist in exactly the same quantum state. This principle is why chemistry is interesting, because electrons have to have increasingly baroque-looking orbitals in order to be bound to the same atom. It’s also why matter (like diamond) is solid, because atoms can’t all be squeezed into the same place. So far, so good.

But then he tries to draw a more profound conclusion: that interacting with the diamond right here instantaneously affects every electron in the universe. Here’s the quote:

So here’s the amazing thing: the exclusion principle still applies, so none of the electrons in the universe can sit in precisely the same energy level. But that must mean something very odd. See, let me take this diamond, and let me just heat it up a bit between my hands. Just gently warming it up, and put a bit of energy into it, so I’m shifting the electrons around. Some of the electrons are jumping into different energy levels. But this shift of the electron configuration inside the diamond has consequences, because the sum total of all the electrons in the universe must respect Pauli. Therefore, every electron around every atom in the universe must be shifted as I heat the diamond up to make sure that none of them end up in the same energy level. When I heat this diamond up all the electrons across the universe instantly but imperceptibly change their energy levels.

(Minor quibble: I don’t think that rubbing the diamond causes any “jumping” of electrons; the heating comes from exciting vibrational modes of the atoms in the crystal. But maybe I’m wrong about that? And in any event it’s irrelevant to this particular discussion.)

At face value, there’s no question that what he says here lies somewhere between misleading and wrong. It seems quite plain (that’s the problem with being a clear speaker) that he’s saying that the energy levels of electrons throughout the universe must change because we’ve changed the energy levels of some electrons here in the diamond, and the Pauli exclusion principle says that two electrons can’t be in the same energy level. But the exclusion principle doesn’t say that; it says that no two identical particles can be in the same quantum state. The energy is part of a quantum state, but doesn’t define it completely; we need to include other things like the position, or the spin. (The ground state of a helium atom, for example, has two electrons with precisely the same energy, just different spins.)

Consider a box with non-interacting fermions, all in distinct quantum states (as they must be). Take just one of them and zap it to move it into a different quantum state, one unoccupied by any other particle. What happens to the other particles in the box? Precisely nothing. Of course if you zap it into a quantum state that is already occupied by another particle, that particle gets bumped somewhere else — but in the real universe there are vastly more unoccupied states than occupied ones, so that can’t be what’s going on. Taken literally as a consequence of the exclusion principle, the statement is wrong.

But it’s possible that there is a more carefully-worded version of the statement that relies on other physics and is correct. And we might learn some physics by thinking about it, so it’s worth a bit of effort. I think it’s possible to come up with interpretations of the statement that make it correct, but in doing so the implications become so completely different from what the audience actually heard that I don’t think we can give it a pass.

The two possibilities for additional physics (over and above the exclusion principle) that could be taken into account to make the statement true are (1) electromagnetic interactions of the electrons, and (2) quantum entanglement and collapse of the wave function. Let’s look at each in turn.

The first possibility, and the one I actually think is lurking behind Cox’s explanation, is that electrons aren’t simply non-interacting fermions; they have an electric field, which means they can interact with other electrons, not to mention protons and other charged particles. If we change the ambient electric field — e.g., by moving the diamond around — it changes the wave function of the electrons, because the energy changes. Physicists would say the we changed the Hamiltonian, the expression for the energy of the system.

There is an interesting and important point to be made here: in quantum mechanics, the wave function for a particle will generically be spread out all over the universe, not confined to a small region. In practice, the overwhelming majority of the wave function might be localized to one particular place, but in principle there’s a very tiny bit of it at almost every point in space. (At some points it might be precisely zero, but those will be relatively rare.) Consequently, when I change the electric field anywhere in the universe, in principle the wave function of every electron changes just a little bit. I suspect that is the physical effect that Cox is relying on in his explanation.

But there are serious problems in accepting this as an interpretation of what he actually said. For one thing, it has nothing to do with the exclusion principle; bosons (who can happily pile on top of each other in the same quantum state) would be affected just as much as fermions. More importantly, it fails as a job of translation, by giving people a completely incorrect idea of what is going on.

The point of this last statement is that when you say “When I heat this diamond up all the electrons across the universe instantly but imperceptibly change their energy levels,” people are naturally going to believe that something has changed about electrons very far away. But that’s not true, in the most accurate meaning we can attach to those words. In particular, imagine there is some physicist located in the Andromeda galaxy, doing experiments on the energy levels of electrons. This is a really good experimenter, with lots of electrons available and the ability to measure energies to arbitrarily good precision. When we rub the diamond here on Earth, is there any change at all in what that experimenter would measure?

Of course the answer is “none whatsoever.” Not just in practice, but in principle. The Hamiltonian of the universe will change when we heat up the diamond, which changes the instantaneous time-independent solutions to the Schoedinger equation throughout space, so in principle the energy levels of all the electrons in the universe do change. But that change is completely invisible to the far-off experimenter; there will be a change, but it won’t happen until the change in the electromagnetic field itself has had time to propagate out to Andromeda, which is at the speed of light. Another way of saying it is that “energy levels” are static, unchanging states, and what really happens is that we poke the electron into a non-static state that gradually evolves. (If it were any other way, we could send signals faster than light using this technique.)

Verdict: if this is what’s going on, there is an interpretation under which Cox’s statement is correct, except that it has nothing to do with the exclusion principle, and more importantly it gives a quite false impression to anyone who might be listening.

The other possibly relevant bit of physics is quantum entanglement and wave function collapse. This is usually the topic where people start talking about instantaneous changes throughout space, and we get mired in interpretive messes. Again, these concepts weren’t mentioned in this part of the lecture, and aren’t directly tied to the exclusion principle, but it’s worth discussing them.

There is something amazing and magical about quantum mechanics that is worth emphasizing over and over again. To wit: unlike in classical mechanics, there are not separate states for every particle in the universe. There is only one state, describing all the particles; modest people call it the “many-particle wave function,” while visionaries call it the “wave function of the universe.” But the point is that you can’t necessarily describe (or measure) what one particle is doing without also having implications for what other particles are doing — even “instantaneously” throughout space (although in ways that have to be carefully parsed).

Imagine we have a situation with two electrons, each in a separate atom, with different energy levels in each atom. Quantum mechanics tells us that it’s possible for the system to be in the following kind of state: each electron is either in energy level 1 or energy level 2, and we don’t know which one (more carefully, they are in a superposition), but we do know that they are in different energy levels. So if we measure the first electron and find it in level 1, we know for sure that the other electron is in level 2, and vice-versa. This is true even if the two electrons are a jillion miles away from each other.

As far as I can tell, this isn’t at all what Brian Cox was talking about; he discusses heating up the electrons in a diamond by rubbing on it, not measuring their energies by observing them and then drawing conclusions about entangled electrons very far away. (In a real-world context it’s very unlikely that distant electrons are entangled in any noticeable way, although strictly speaking you could argue that everything is slightly entangled with everything else.) But there is some underlying moral similarity — this is, as mentioned, the context in which people traditionally talk about instantaneous changed in quantum mechanics.

So let’s go back to our observer in Andromeda. Imagine that we have such a situation with two electrons in two atoms, in a mutually entangled state. We measure our electron to be in energy level 1. Is it true that we instantly know that our far-away friend will measure their electron to be in energy level 2? Yes, absolutely true.

But consider the same experiment from the point of view of our far-away friend. They know what the state of the electrons is, so they know that when they observe their electron it will be either in level 1 or level 2, and ours will be in the other one. And let’s say they even know that we are going to make a measurement at some particular moment in time. What changes about any measurement they could make on their electron, before and after we measure ours?

Absolutely nothing. Before we made our measurement, they didn’t know the energy level of their electron, and would give 50/50 chances for finding it in level 1 or 2. After we made our measurement, it’s in some particular state, but they don’t know what that state is. So again they would give a 50/50 chance for getting either result. From their point of view, nothing has changed.

It has to work out this way, of course. Otherwise we could indeed use quantum entanglement to send signals faster than light (which we can’t). Indeed, note that we had to refer to “time” in some particular reference frame, stretching across millions of light-years. In some other frame, relativity teaches us that the order of measurements could be completely different. So it can’t actually matter. It’s possible to say that the wave function of the universe changes instantaneously throughout space when we make a measurement; but that statement has no consequences. It’s just one of an infinite number of legitimate descriptions of the situation, corresponding to different choices of how we define “time.”

Verdict: I don’t think this is what Cox was talking about. He doesn’t mention entanglement, or collapse of the wave function, or anything like that. But even if he had, I would personally judge it extremely misleading to tell people that the energy of very far-away electrons suddenly changed because I was rubbing a diamond here in this room.

Just to complicate things a bit more, Brian in a tweet refers to this discussion of the double-well potential as some quantitative justification for what he’s getting at in the lecture. These notes are a bit confusing, but I’ve had a go at them.

The reason they are confusing is because they start off talking about the exclusion principle and indistinguishable particles, but when it comes time to look at equations they only consider single-particle quantum mechanics. They have a situation with two “potential wells” — think of two atoms, perhaps quite far away, in which an electron might find itself. They then consider the wave function for a single electron, ψ(x). And they show, perfectly correctly, that the lowest energy states of this system have nearly identical energies, and have the feature that the electron has an equal probability of being in either of the two atoms.

Which, as far as it goes, is completely fine. It illustrates an interesting example where the lowest-energy state of the electron can be really spread out in space, rather than being localized on a single atom. In particular, the very existence of the other atom far away has a tiny but (in principle) perceptible effect on the shape of the wave function in the vicinity of the nearby atom.

But this says very little about what we purportedly care about, which is the Pauli exclusion principle, something that only makes sense when we have more than one electron. (It says that no two electrons can be in the same state; it has nothing interesting to say about what one electron can do.) It’s almost as if the notes cut off before they could be finished. If we wanted to think about the exclusion principle, we would need to think about two electrons, with positions let’s say x1 and x2, and a joint quantum wave function ψ(x1, x2). Then we would note that fermions have the property that such a wave function must be “odd” in its arguments: ψ(x1, x2) = -ψ(x2, x1). Physically, we’re saying that the wave function goes to minus itself when we exchange the two particles. But if the two particles were in exactly the same state, the wave function would necessarily be unchanged when we exchanged the particles. And a function that is both equal to another function and equal to minus that function is necessarily zero. So that’s the exclusion principle: given that minus sign under exchange, two particles can never be in precisely the same quantum state.

The notes don’t say any of that, however; they just talk about the two lowest energy levels in a double-well potential for a single electron. They don’t demonstrate anything interesting about the exclusion principle. The analysis does imply, correctly, that changing the Hamiltonian of a particle somewhere far away (e.g. by altering the shape of one of the wells) changes, even if by just a little bit, the energy of the wave function defined over all space. That’s connected to the first possible interpretation of Cox’s lecture above, that heating up the diamond changes the Hamiltonian of the universe and therefore affects the wave function of every electron. Which also has nothing to do with the exclusion principle, so at least it’s consistent.

In terms of explaining the mysteries of quantum mechanics to a wide audience, which is the point here, I think the bottom line is this: rubbing a diamond here in this room does not have any instantaneous effect whatsoever on experiments being done on electrons very far away. There are two very interesting and conceptually central points worth making: that the Pauli exclusion principle helps explain the stability of matter, and that quantum mechanics says there is a single state for the whole universe rather than separate states for each individual particle. But in this case these became mixed up a bit, and I suspect that this part of the lecture wasn’t the most edifying for the audience. (The rest of the lecture still remains pretty awesome.)

Update: I added this as a comment, but I’m promoting it to the body of the post because hopefully it makes things clearer for people who like a bit more technical precision in their quantum mechanics.

Consider the double-well potential talked about in the notes I linked to near the end of the post. Think of this as representing two hydrogen nuclei, very far away. And imagine two electrons in this background, close to their ground states.

To start, think of the electrons as free particles, not interacting with each other. (That’s a very bad approximation in this case, contrary to what is said in the notes, but we can fix it later.) As the notes correctly state, for any single electron there will be two low-lying states, one that is even E(x) and one that is odd O(x). When we now add the other electron in, they can’t both be in the same lowest-lying state (the even one), because that would violate Pauli. So you are tempted to put one in E(x1) and the other in O(x2).

But that’s not right, because they’re indistinguishable fermions. The two-particle wave function needs to obey ψ(x1, x2) = -ψ(x2, x1). So the correct state is the antisymmetric product: ψ(x1, x2) = E(x1) O(x2) – O(x1) E(x2).

That means that neither electron is really in an energy level; they are both part of an entangled superposition. If you zap one of them into a completely different energy, nothing whatsoever happens to the other one. It would now be possible for the other one to decay to be purely in the ground state, rather than a superposition of E and O, but that would require some interaction to allow the decay. (All this is ignoring spins. If we allow for spin, they could both be in the ground-state energy level, just with opposite spins. When we zapped one, what happens to the other is again precisely nothing. That’s what you get for considering non-interacting particles.)

But of course it’s a very bad approximation to ignore the interaction between the two electrons, precisely because of the above analysis; it’s not true that one is here and one is far away, they both are equally distributed between being here and being far away, and can interact noticeably.

Since electrons repel, the true ground state is one in which the wave function for one is strongly concentrated one one hydrogen atom, and the wave function for the other is strongly concentrated on the other. Of course it’s the antisymmetrized product of those two possibilities, because they are identical fermions. The energies of both are identical.

Now when you zap one electron to change its energy, you do change the energy of the other one, in principle. But it has nothing to do with the exclusion principle; it’s just because you’ve changed the amount of electrostatic repulsion by changing the spatial wave function of one of the electrons.

Furthermore, while you instantaneously change “the energy levels” available to the far-away electron by jiggling the one nearby, you don’t actually change the position-space wave function in the far-away region at all. As I said in the post, you’ve poked the other electron into a superposition rather than being in an energy eigenstate. Its wave function (to the extent that we can talk about it, e.g. by integrating out the other particles) is now a function of time. And the place where it’s actually evolving is completely inside your light cone, not infinitely far away. So there is literally nothing someone could do, in principle as well as practice, to detect any change as a far-away observer.


Ending the Ice Ages

Filed under: Ice Age — Razib Khan @ 1:58 am

We Are All Panamanians:

When the Isthmus of Panama rose from the sea, it may have changed the climate of Africa–and encouraged the evolution of humans.

The emergence of the Isthmus of Panama has been credited with many milestones in Earth’s history. When it rose from the sea some 3 million years ago, the isthmus provided a bridge for the migration of animals between North and South America, forever changing the fauna of both continents. It also blocked a current that once flowed west from Africa to Asia, diverting it northward to strengthen the Gulf Stream. Now Steven Stanley, a paleobiologist at Johns Hopkins, says that that change in currents may be behind yet another major event: the evolution of humans. When the isthmus rearranged the ocean, he says, it triggered a series of ice ages that in turn had a crucial impact on the evolution of hominids in Africa.

Question: do we have enough nukes to re-open the isthmus?

The race question: are bonobos human?

Filed under: Genetics,Genomics,Human Genetics,Human Genomics,race — Razib Khan @ 1:05 am

Recently Jason Antrosio began a dialogue with readers of this weblog on the “race question.” More specifically, he asked that we peruse a 2009 review of the race question in the American Journal of Physical Anthropology. Additionally, he also pointed me to another 2009 paper in Genome Research, Non-Darwinian estimation: My ancestors, my genes’ ancestors. Normally I don’t react well to interactions anthropologists who are not Henry Harpending or John Hawks. But Dr. Antrosio engaged civilly, so I shall return the favor.

I did read all the papers in the American Journal of Physical Anthropology special issue, as well the Genome Research paper. My real interest here are specific questions of science, not history or social science. But I will address the latter areas rather quickly. I am not someone who comes to this totally naked of the history or social science of the race question. I’ve read many books on the topic. And as a colored person who has moderate experience with racism I get rather bored and irritated with excessively patronizing explanations of how racism afflicts us coloreds from white academics (non-white academics who focus on this subject are usually careerists or activists who don’t have to make much pretense toward scholarly substance and can be duly ignored, at least in my experience). The main point which I think we can all agree upon is that colloquial understanding of race has only a partial correlation with any genetic understanding of race. I myself have ranted against the confusions which have ensued because of the conflation of the two classes, and it is certainly a legitimate area of study, but it is not my primary concern. And importantly, I have no great primary interest in battling racism.

 

By this, I do not mean to imply that I support racism, or am personally against battling racism. When it comes to racists, broadly defined, I am not personally a great fan (as can be attested by my pattern of bans and rebukes). And when I say racism, I don’t just mean white people behaving badly. I mean people who express racial nationalist sentiments in a crude and crass manner, and are often inappropriately assertive about the righteousness of their views (e.g., a few commenters have complained that I, an Indian [yes, I'm not technically Indian], should not talk so much about Westerners. Of course I view myself a Westerner, but to a racialist this is simply not even wrong. Naturally this is a chasm in world-views which is not reconcilable. Please note that some “anti-racists” would also agree I am not a Westerner, though mostly because they view that term as referring to evil white colonialists). Nevertheless, when it comes a study of human variation, or history, and the like, my primary aim is to enter into a state of intellectual Epoché. Whether Charles Darwin, Francis Galton, or R. A. Fisher, were, or were not, racists is of minor concern to me. I am not saying that it is irrelevant, but the fixation on racial prejudice is not part of my bailiwick. As I allude to above there are whole departments devoted to the presumed oppression of coloreds by Mighty Whitey, and I leave them to their joyful intellectual romp.

But for many people ferreting out racism is more of a performative act. There’s a big difference between revealed preferences and avowed preferences. For example, most Americans espouse a love of diversity. But they sure don’t love diversity when it comes to who they date. These include many people who I know personally, who are diversity loving progressives, but who seem to fall into the trap of disaggregation. Since I don’t love diversity and don’t care about that issue I don’t bring it up with them often. But it’s what I call a revealed preference. Or, to give an amusing example, I said something offensive in one of my posts apparently a few years back, which prompted one outraged reader to leave a long shocked rant about my racism. The comment was trashed, and the reader banned. Nevertheless, I traced their Facebook account. The individual was a young white professional resident in San Francisco. And, their friends list was visible. I did a quick spot check, and estimated that ~90 percent of their San Francisco friends were white. In contrast, about ~50 percent of San Francisco’s population is white. I’m not going to accuse anyone of racism, but there are quite interesting revealed preferences in the world (I saw this when I lived in Berkeley, where a few times I was the only non-white at a party where people were trashing how little diversity there was in Oregon when they found out that that was where I was from). Most people like associate with “their own kind,” however that is defined.

That’s an observation. Not a judgement. I wish more people would withhold the judgement sometimes. Because I don’t really care about diversity and all the the standard shibboleths common among the progressive set, I do sometimes like to point out the naked emperors here and there. Frankly a lot of the humanistic and social science literature on race strikes me as performative as well. There are some nuggets of truth, but they’re usually trivially obvious. Segregation and genocide are generally agreed upon as bad. When the nuggets of truth are not trivial, they’re often strongly normative. Moral tales told, not positive descriptions of reality. I, for example, do not favor affirmative action, and do not care if academic departments reflect the racial diversity of society at large. This is not a common viewpoint in some circles. If you are on a university campus, I invite you to go look at the headshots of the graduate students in ecology & evolution, and then look at neuroscience. Count the number of Asians. You may see an interesting pattern!

So let’s move to the science. Do races exist in human biology? Is it a useful concept? That depends on criteria in both cases. The reality is that I’m not sure I know what a species is in an axiomatic sense, let alone race (many biologists don’t, that’s why there’s a whole area devoted to studying the issue of the definition). Rather, for me species are evaluated instrumentally. Is the classification of a set of individuals as a species useful in illuminating a specific biological question? Species are human constructions, categories which are mapped upon reality. That doesn’t make them without utility. Many of the same “where do you draw the line?” questions asked of race can be asked of species. In a deep ontological sense I don’t believe in species. But in a deep ontological sense I don’t accept the solidity of a brick (most of the volume is space of any object of course!).

Moving onto specific objections, some observe that genetic variation is clinal. This has a basis in fact, more or less. But the distribution of grades is also clinal. Nevertheless, professors generally look for “natural breaks,” and then distribute A’s, B’s, and C’s, accordingly. In concrete terms groups like the Tuareg and Uyghur are equidistant between West Eurasians and Africans and East Asians, respectively. But look at the map of the Old World’s population density. The variation in gene frequencies may be clinal, but that ignores the reality that the genetic clusters themselves have different weights varying as a function of space. The Tuareg are few. The “donor” populations on either side of the Sahara are many. If you want to look for “natural breaks,” you look to the empty spaces, where there will be populations, but very few.

Additionally, there is the question of history. We know that the Uyghur are a new population, which emerged in the past 2,000 years due to admixture between a resident West Eurasian population, and Turkic groups. We know this both through genetics (decay of linkage disequilibrium) and history. There is also a great deal of circumstantial evidence that the West Eurasian forebears of the Uyghurs, the Tocharians, were long distance migrants from the west. So who were the indigenes of the Tarim? It may be that due to the local ecology the center of Eurasia has long been relatively underpopulated in relation to the peripheries, with the emergence of new lifestyles (e.g., oasis agriculture, nomadism) resulting in the ethnogenesis of groups which arose recently to occupy the midway position between Europeans and East Asians.

This does not mean that I believe that before 5,000 BC the gene flow between East Asia and Western Eurasia was zero. Rather, I think there are lots of data which imply that it was simply very low (the East Asian admixture among Tatars in Russia, and the West Eurasian admixture among Mongols, both show evidence of being relatively recent, due to the rise of horsemanship). This is in contrast to the more genuine cline and isolation-by-distance you see from Europe down to the Middle East, and to a lesser extent South Asia. Actually, until recently I would have said into South Asia without qualification, but I am now convinced that South Asia itself has been the scene of an admixture event of huge scope within the last 10,000 years.

Much of the discussion that Jason Antrosio alludes to discusses the problems which have emerged from hypothesis based admixture inference programs, such as Structure, frappe, and Admixture. The main issue is that many people read them naively. This includes people in the academic community. But this does not mean that no one understands the problem. I’ve talked to evolutionary genomicists who have complained about the misinterpretations, and I am quite aware of the artifacts which can flow out of the software. Anyone who has used Admixture knows very well the problems. For example, South Asians often emerge as a distinct cluster, but the research above indicates that they are a stabilized hybrid! This is why I told some of Antrosio’s commenters to be careful about hitching their wagon to isolation-by-distance and clinal variation; there is some evidence that many of the world’s populations extant today are the product of relatively recent hybridizations between previous rather distinct groups. There’s no need to invoke Platonic original races. Rather, it may simply be that in the random lottery of cultural adoption some groups invented agriculture, and replaced many populations which exhibited a clinal variation.

And that’s the key: racial typologies are coarse reflections of genuine history. In other words, race is a reflection and reification of genuine lower level dynamics, it is not the prior phenomenon. This sidesteps many of the technical complaints which arise in the papers Antrosio linked to. I can quibble with them well enough though. For example, figure 2 in the Genome Research paper relies upon a rather shitty (in relative terms) genetic relatedness statistic, IBS, in my opinion. Don’t take my word for it, play around with data sets in Plink and you’ll see what I mean. It tends to be history-blind. My parents, who are South Asian, but with a non-trivial East Asian component, are often clustered with a host of other South Asians who also have non-trivial East Asian components. This is a real result, but it ignores the history that all that is common across these individuals is a particular admixture pair. It’s not a “real” cluster, reflecting real shared history.

A more interesting concern is the fact that in most trees non-Africans tend to be on their own branch, while Sub-Saharan Africans tend diversify into distinct basal branches. The question ensues: are Sub-Saharan Africans several distinct races? Using evolutionary history as a measure I would say yes! This is definitely one area where social expectations have led us astray. It turns out that it may be that the Bushmen/non-Bushmen separation is only 1/3 as long ago in the past as the Neanderthal/modern human separation. In fact, the Bushmen may predate, and not be part of, the “Out of Africa” event. Along with the Pygmies and Hadza there seems to be a very ancient differentiation between the agriculturalist and hunter-gatherers in the African continent.

For me these details of history are fascinating. But going back to normative concerns: is there a worry that Bushmen will be dehumanized if it is understood that they are not part of the modern human expansion event circa ~80,000 years before the present? Unfortunately, I don’t think that science matters much in this case. The Bushmen have been dehumanized for hundreds of years. The Pygmy of Central Africa have also been dehumanized. All without science. An understanding of our evolutionary history is informative, but I doubt it is the prime motor for the great injustices of history. The 19th century race science which modern biologists and anthropologists revile (to a great extent, rightly) did not give rise to the race system of the West. Look at the history, and you see that its genesis predates Darwin by decades. Science may have been a supporting argument, but this was thesis looking for talking points.

The Bushmen are human. The Bonobos are not. Why? I don’t think it has been definitively proven that modern humans and Bonobos are not inter-fertile. Granted, the separation between the Bonobos and humans are about two orders of magnitude greater than Bushmen and other humans, but there is some evidence that Bushmen have admixture from archaic lineages diverged nearly 1 million years into the past, pushing elements below a magnitude! Where do you draw the line? Species are a typological concept, but usually as a pure categorical typology the class is useless. Rather, it’s a tool, a framework. What you do with a tool, well, that’s a different thing altogether….

February 22, 2012

Neutrinos and Cables

Filed under: science,Top Posts — Sean Carroll @ 1:16 pm

I’m a little torn about this: the Twitter machine and other social mediums have blown up about this story at Science Express, which claims that the faster-than-light neutrino result from the OPERA collaboration has been explained as a simple glitch:

According to sources familiar with the experiment, the 60 nanoseconds discrepancy appears to come from a bad connection between a fiber optic cable that connects to the GPS receiver used to correct the timing of the neutrinos’ flight and an electronic card in a computer. After tightening the connection and then measuring the time it takes data to travel the length of the fiber, researchers found that the data arrive 60 nanoseconds earlier than assumed. Since this time is subtracted from the overall time of flight, it appears to explain the early arrival of the neutrinos. New data, however, will be needed to confirm this hypothesis.

I suppose it’s possible. But man, that would make the experimenters look really bad. And the sourcing in the article is just about as weak as it could be: “according to sources familiar with the experiment” is as far as it goes. (What is this, politics?)

So it’s my duty to pass it along, but I would tend to reserve judgment until a better-sourced account comes along. Not that there’s much chance that neutrinos are actually moving faster than light; that was always one of the less-likely explanations for the result. But this isn’t how we usually learn about experimental goofs.

Update from Sid in the comments: here’s a slightly-better-sourced story.

Update again: and here is the official CERN press release. Not exactly admitting that a loose cable is at the heart of everything, or even that the result was wrong, but saying that there were problems that could potentially invalidate the result.


February 21, 2012

Loss-of-function & variation in load

Filed under: Genetics,Genomics,Human Genetics,Human Genomics,Personal genomics — Razib Khan @ 9:58 pm

Greg Cochran pointed out something that I’d been considering about the MacArthur et al. paper: if the average human (OK, non-African human) has ~100 loss-of-function variants, then the standard deviation should be ~10. That’s because the distribution is presumably poisson, and variance = mean, and the square root of the of the variance (~100) is the standard deviation (~10). In plainer English there should be a substantial variation in the number of loss-of-function variants within a population, and across siblings. Though by definition these loss-of-function variants don’t kill you, in general there is the assumption that this class of mutants does exhibit some fitness drag (e.g., the fitness of a heterozygote for a variant which is lethal as a homozygote genotype may be ~0.90). A quick back of the envelope calculation implies to me that there is a 1 out of several hundreds of thousands probability that two siblings may exhibit a range of 60 loss-function-variants. But a 40 unit gap is more like a 1 out of one thousand chance.

This variance in mutational load has been the hobby-horse of intellectuals for a while now. Armand Leroi suggested that it correlated with beauty. Geoffrey Miller with intelligence. In the near future presumably we’ll get to see if there’s anything real in this. And obviously we don’t need to leave it to scientists. We’ll all know the summary statistics about own genomes, and probably be able to intuit rough patterns…if they exist.

Books Made From Electrons!

Filed under: Science and the Media,Technology,Top Posts,Words — Sean Carroll @ 8:47 am

[Updated to provide a better link for DtU overlord Carl Zimmer.]

The conventional presentation of a book — words and images printed on sheets, bound together in a folio — is a perfected technology. It hasn’t changed much in centuries, and likely will be with us for centuries to come.

But that doesn’t mean that other technologies won’t be nudging their way into the same conceptual space. Everyone knows that the practice of publishing is being dramatically altered by the appearance of ebooks — a very broad designation for book-length content that is meant to be read on an electronic device. At the simplest level, an ebook can simply be a text file displayed by a reading program. But the possibilities are much more flexible, allowing for different kinds of images, video, interactivity with the user, and two-way connections with the outside world. The production and distribution process is also much easier, which opens the door to books that are faster, shorter, longer, and quirkier than the usual set of hardbacks and paperbacks. If I put my mind to it, I could meander through this blog’s archives, pick out a few posts, and have an ebook published by this evening. It would suck — editing and presenting a good collection requires effort — but it would be published.

In the current state of the market, one question is: how do you find good ebooks to read, ones that don’t suck? Into this breach leaps Download The Universe, a new website devoted to reviewing ebooks about science. Not just “science books with electronic editions,” but books that only exist in the e- format. (Apparently we have already passed through the awkward hypenation phase, and gone from “e-book” right to “ebook.”) Because it would be embarrassing not to, we also have a Twitter account at @downloadtheuni.

This brand-new project has been led by our inestimable blog neighbor Carl Zimmer, who has assembled a crack editorial team consisting of some of the world’s leading new-media science journalists and also me. We’ll be contributing regular (one hopes) reviews of ebooks old and new, all with a science focus. Suggestions welcome, of course.

The world is going to change, whether we like it or not. It always feels good to help channel that change in constructive ways.


February 20, 2012

The future of the world

Filed under: Uncategorized — Razib Khan @ 10:47 pm

May be Mumbai.

Money vs. Science

Filed under: Environment,Science and Politics,Top Posts — Sean Carroll @ 4:35 pm

Everyone who has been paying attention knows that there is a strong anti-science movement in this country — driven partly by populist anti-intellectualism, but increasingly by corporate interests that just don’t like what science has to say. It’s an old problem — tobacco companies succeeded for years in sowing doubt about the health effects of smoking — but it’s become significantly worse in recent years.

Nina Fedoroff is the president of the American Association for the Advancement of Science (AAAS), which is holding its annual meeting right now. She is not holding back about the problem, but tackling it directly. From a weekend article in the Guardian (h/t Dan Gillmor):

“We are sliding back into a dark era,” she said. “And there seems little we can do about it. I am profoundly depressed at just how difficult it has become merely to get a realistic conversation started on issues such as climate change or genetically modified organisms.”

Tim F. at Balloon Juice points to this flowchart at Climate Progress that illustrates how the money and message gets sent around to sow doubt about scientific findings. (Okay, it’s not really a flow chart, but you get the point.) I was also struck by a link to an older article by Ian Sample, which put the problem in its starkest terms: the American Enterprise Institute was offering $10,000 to scientists and economists who were willing to write op-eds or essays critiquing the IPCC climate report — before it was published. Money goes a long way.

Relatedly, here’s Ruth Bader Ginsburg trying to push the Supreme Court away from its ruling in Citizens United, the notorious case that led to the creation of SuperPACs by deciding that corporations were persons, and not letting them advertise anonymously would be a grievous violation of their free-speech rights. We’ll see how well she does. Scientists, meanwhile, need to keep speaking out about the integrity of our field. When researchers are attacked and their jobs threatened by politicians who disagree with their results, it’s time to stand up for what science really means.


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