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July 28, 2017

The Indo-Aryan question nearing resolution

Filed under: Genetics,science — Razib Khan @ 5:50 pm


India Today published my review of the current state of the genetics and genomics of the Indian subcontinent, and what it can tell us about the ethnogenesis of South Asians generally. In the piece I tried to be very circumspect and stick to what we know with a high, if not perfect, degree of certainty. Here I will add some comments where I reduce the threshold of certainty somewhat. That, I’m going to include here my beliefs where I think I’m right, but in some details wouldn’t be surprised if I was wrong.

First, the title is Aryan wars: Controversy over new study claiming they came from the west 4,000 years ago. Writers don’t get to choose titles, and this is not one I would have chosen. But I am not in a position to care or know what draws clicks. Let’s note that this “controversy” is restricted mostly to India. Outside of India it’s not controversial, but a matter of the science, because people don’t have any political or social investment in the topic. It reminds me of debates about genetics and intelligence in the West, where emotions get overwrought and lies fly wildly with abandon.*

Second, there is a reference in the figures to an “Out of India” (OIT)  model. That is, the Aryans migrated out of India, and implicitly the Indo-European languages derive from South Asia. I don’t think this theory has any support at all. That is, I think it is rather clear that proto-Indo-European probably emerged neither in Europe proper, nor in South Asia, but in the Inner Eurasian spaces between. But for an Indian audience ignoring OIT would seem a peculiar lacunae, so there was a reference added to the figure on that account (I pushed back against this, but do not make ultimate decisions on figures).

But I do think it was plausible up until 2009’s Reconstructing Indian History to suggest that most modern South Asian ancestry dates to the Pleistocene. In this framework the Indo-Europeanization of the subcontinent was primarily a cultural one, where small groups of Central Asians imposed their language on the native population. What the genome-wide work has shown is that South Asians are the product of a large-scale mixing process between a population very distant from West Eurasians (“Ancestral South Indians”, ASI) and a population which was indistinguishable from other West Eurasians (“Ancestral North Indians”, ANI).

Since ANI is indistinguishable from West Eurasians I hold it is clearly a West Eurasian population in provenance. Those who reject this position from a scientific perspective believe that there could have been some sort continuous zone of “ANI-like” habitation from northwestern South Asia up into northern Inner Eurasia (and perhaps toward West Asia as well) dating from the late Pleistocene. I do not that believe this is plausible, and I will tell you that prominent researchers who I have brought up this idea to are somewhat incredulous.**

Third, there are major unresolved issues genetically in relation to the dates and the total number of mixing populations. I am quite confident saying around half of the total South Asian genomic ancestry today derives from populations who were living outside of South Asia on the Holocene-Pleistocene boundary 11,700 years ago. Much of that ancestry probably flourished between the Caucasus and Zagros mountains. The remainder somewhere in the vast swath of territory between the Baltic and Siberia (perhaps further south, toward the Pamirs?).

But I am not confident of the relative balances of contribution to the ANI. It does seem that the northern component, which is derived in part from the southern component, is much more prominent in upper castes and northwestern populations. In contrast the southern component is found throughout the subcontinent.

In Genomic insights into the origin of farming in the Near East there is analysis of South Asia in the supplements. The author concludes that ANI can not be modeled as a single population (Zack Ajmal and I were saying this in 2010). The top hits for the sources of ANI tend to be the genomic sample from the Zagros, in western Iran (before subsequent admixture with Levantine farmers), and a population similar to the Yamna culture the steppe. The issue seems to be that later steppe populations which harbor a fair amount of “Early European Farmer” ancestry (e.g., LBK in Central Europe) due likely to back migration aren’t good model fits.

Below are two plots, one showing a scatter of South Asian groups with their Iran_N (a sample from ~10,000 years ago) vs. Yamna (from ~5,000 years ago), and another with the ratios.

   

DO NOT TAKE THE PROPORTIONS LITERALLY.  My intuition that these models are overestimating the proportion of steppe ancestry, but my confidence in my intuition is low.

There are two groups enriched for Iran_N ancestry.

  1. Lower caste groups, especially from South India.
  2. Populations in southern Pakistan.

The reasons I differ. If you have done genetic analysis of the Pakistani populations it seems quite obvious that unlike other groups in South Asia Pakistani groups facing the Arabian sea across from Oman have genuine Near Eastern ancestry. This affinity declines as you go north in Pakistan rather rapidly. Notice though one South Indian group: Jews from Cochin. This population clearly has recent Near Eastern ancestry.

The Kharia are an Austro-Asiatic Munda group. For whatever reason Austro-Asiatic groups seem to consistently have very little steppe ancestry. The Mala are Dalits from South India. The further up you go on the modal Iran_N-Yamna cline you see the populations are either upper caste, or, they are from the far northwest of the subcontinent.

The conclusion I derive from this is that first there was an early migration of West Eurasian populations consisting of Iranian farmers. This group mixed with the ASI element. The Indo-Aryans, who probably correlates with the Yamna-like component, arrived later as an overlay (and nearly half of their ancestry was derived from Iranian farmers). Then many South Asian populations have modifications on this base model of compound ANI + ASI; Munda and Bengali have later East Asian ancestry, while populations on the Arabian sea have Near Eastern ancestry.

Fourth, the story in India Today leans heavily on Y chromosomes R1a1a. It is true we are Lords of the Steppe and destined to drive out enemies before us. But, it is not the primary story. And yet Y chromosomal phylogenies are easy for the public to understand. But they only make sense in light of the above framework. R1a1a is found in South Indian tribal populations. It seems likely that Indo-Aryan paternal lineages were highly invasive across the subcontinent, just as they were in Europe. In many cases they likely extended far beyond domains where Indo-European acculturation occurred.

I’m probably wrong on some of the details. But I suspect the final story will not be so different from this.

Finally, I will mention the cultural element here. There is a fair amount of the discussion of the form “so you are saying the ancestors of Indians are Europeans?” or “does this mean Hinduism is not Indian?”

The piece was about genetics and demography, not my opinions about culture. So I will say this:

  1. The “West” as an entity is no older that Classical Greece. 500 BC. My own personal position, strongly held, is that the West should indicate cultures and societies which descend from the European societies which adhered to the Western Church around ~1000 AD (some nations, like Lithuania, became absorbed into this cultural complex hundreds of years later). So Russia is not the West. And Merovingian Francia is not the West.
  2. Indian civilization of what we term the Hindu variety coalesced in the period between between 500 BC and 500 AD, from before to the Mauryas up to the Guptas. Obviously the period before 1000 BC was important in setting the ground-work, but I do not believe it was Indian as we’d understand it in anything but the geographical sense, nor was it Hindu in any way we’d recognize it today (similarly, Shang dynasty China was not China as we’d understand, which came into being after 500 BC).

These positions mean that I think nationalist passions are in the “not even wrong” category. Indian Hindu civilization is indigenous by definition, since it was synthesized in situ on the edge of historical perception and attestation (for the record, I think Adi Shankara was critical in the completion of a crystalized self-conception of Hindu religio-philosophical thought, but its origins predate him). Similarly, Indian civilization was not seeded by white Europeans because white Europeans were only coming into being in Europe when the Indus Valley civilization was collapsing.

That is all (for now).

Addendum: The first tranche of ancient DNA should be out in a few months. Also, there is another paper on Indian genetics in the work from the usual suspects. There won’t be anything totally surprising (or so I’ve been told).

* By lies, I mean the contention that intelligence is an “invalid” instrument in relation to predictiveness, or, if it is valid, it is not genetically heritable. People routinely lie about these facts in discussion or spread lies because there are socially preferred positions which they conform to. Similarly, many questions about Indian history seem to hinge on widely promoted lies.

** This model needs to also confront the massive mixing of the last 4,000 years. If it is true then it is ASI which is mostly likely intrusive, because it is not creditable that these two populations were in nearby proximity for tens of thousands of years without exchanging genes.

June 19, 2017

Indian genetics, the never-ending argument

Filed under: Genetics,India,Indian Genetics,Indo-Europeans,science — Razib Khan @ 10:44 pm

I am at this point somewhat fatigued by Indian population genetics. The real results are going to be ancient DNA, and I’m waiting on that. But people keep asking me about an article in Swarajya, Genetics Might Be Settling The Aryan Migration Debate, But Not How Left-Liberals Believe.

First, the article attacks me as being racist. This is not true. The reality is that the people who attack me on the Left would probably attack magazines like Swarajya as highly “problematic” and “Islamophobic.” They would label Hindu nationalism as a Nazi derivative ideology. People should be careful the sort of allies they make, if you dance with snakes they will bite you in the end. Much of the media lies about me, and the Left constantly attacks me. I’m OK with that because I do believe that the day will come with all the ledgers will be balanced. The Far Left is an enemy of civilization of all stripes. I welcome being labeled an enemy of barbarians. My small readership, which is of diverse ideologies and professions, is aware of who I am and what I am, and that is sufficient. Either truth or power will be the ultimate arbiter of justice.

With that out of the way, there this one thing about the piece that I think is important to highlight:

To my surprise, it turned out that that Joseph had contacted Chaubey and sought his opinion for his article. Chaubey further told me he was shocked by the drift of the article that appeared eventually, and was extremely disappointed at the spin Joseph had placed on his work, and that his opinions seemed to have been selectively omitted by Joseph – a fact he let Joseph know immediately after the article was published, but to no avail.

Indeed, this itself would suggest there are very eminent geneticists who do not regard it as settled that the R1a may have entered the subcontinent from outside. Chaubey himself is one such, and is not very pleased that Joseph has not accurately presented the divergent views of scholars on the question, choosing, instead to present it as done and dusted.

I do wish Tony Joseph had quoted Gyaneshwer Chaubey’s response, and I’d like to know his opinions. Science benefits from skepticism. Unfortunately though the equivocation of science is not optimal for journalism, so oftentimes things are presented in a more stark and clear manner than perhaps is warranted. I’ve been in this position myself, when journalists are just looking for a quote that aligns with their own views. It’s frustrating.

There are many aspects of the Swarajya piece I could point out as somewhat weak. For example:

The genetic data at present resolution shows that the R1a branch present in India is a cousin clade of branches present in Europe, Central Asia, Middle East and the Caucasus; it had a common ancestry with these regions which is more than 6000 years old, but to argue that the Indian R1a branch has resulted from a migration from Central Asia, it should be derived from the Central Asian branch, which is not the case, as Chaubey pointed out.

The Srubna culture, the Scythians, and the people of the Altai today, all bear the “Indian” branch of R1a. First, these substantially post-date 6000 years ago. I think that that is likely due to the fact that South Asian R1a1a-Z93 and that of the Sbruna descend from a common ancestor. But in any case, the nature of the phylogeny of Z93 indicates rapid expansion and very little phylogenetic distance between the branches. Something happened 4-5,000 years ago. One could imagine simultaneous expansions in India and Central Asia/Eastern Europe. Or, one could imagine an expansion from a common ancestor around that time. The latter seems more parsimonious.

Additionally, while South Asians share ancestry with people in West Asia and Eastern Europe, these groups do not have distinctive South Asian (Ancestral South Indian) ancestry. This should weight out probabilities as to the direction of migration.

Second, I read some of the papers linked to in the article, such as Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia and Y-chromosomal sequences of diverse Indian populations and the ancestry of the Andamanese. The first paper has good data, but I’ve always been confused by the interpretations. For example:

A few studies on mtDNA and Y-chromosome variation have interpreted their results in favor of the hypothesis,70–72 whereas others have found no genetic evidence to support it.3,6,73,74 However, any nonmarginal migration from Central Asia to South Asia should have also introduced readily apparent signals of East Asian ancestry into India (see Figure 2B). Because this ancestry component is absent from the region, we have to conclude that if such a dispersal event nevertheless took place, it occurred before the East Asian ancestry component reached Central Asia. The demographic history of Central Asia is, however, complex, and although it has been shown that demic diffusion coupled with influx of Turkic speakers during historical times has shaped the genetic makeup of Uzbeks75 (see also the double share of k7 yellow component in Uzbeks as compared to Turkmens and Tajiks in Figure 2B), it is not clear what was the extent of East Asian ancestry in Central Asian populations prior to these events.

Actually the historical and ancient DNA evidence both point to the fact that East Asian ancestry arrived in the last two thousand years. The spread of the first Gokturk Empire, and then the documented shift in the centuries around 1000 A.D. from Iranian to Turkic in what was Turan, signals the shift toward an East Asian genetic influx. Alexander the Great and other Greeks ventured into Central Asia. The people were described as Iranian looking (when Europeans encountered Turkic people like Khazars they did note their distinctive physical appearance).

We have ancient DNA from the Altai, and those individuals initially seemed overwhelmingly West Eurasian. Now that we have Scythian ancient DNA we see that they mixed with East Asians only on the far east of their range.

The second paper is very confused (or confusing):

The time divergence between Indian and European Y-chromosomes, based on the closest neighbour analysis, shows two different distinctive divergence times for J2 and R1a, suggesting that the European ancestry in India is much older (>10 kya) than what would be expected from a recent migration of Indo-European populations into India (~4 to 5 kya). Also the proportions suggest the effect might be less strong than generally assumed for the Indo-European migration. Interestingly, the ANI ancestry was recently suggested to be a mix of ancestries from early farmers of western Iran and people of the Bronze Age Eurasian steppe (Lazaridis et al. 2016). Our results agree with this suggestion. In addition, we also show that the divergence time of this ancestry is different, suggesting a different time to enter India.

Lazaridis et al. accept a mass migration from the steppe. In fact, the migration is to such a magnitude that I’m even skeptical. Also, there couldn’t have been a European migration to South Asia during the Pleistocene because Europeans as we understand them genetically did not exist then!!!

I assume that many of the dates of coalescence are sensitive to parameter conditions. Additionally, they admit limitations to their sampling.

Ultimately the final story will be more complex than we can imagine. R1a is too widespread to be explained by a simple Indo-Aryan migration in my opinion. But we can’t get to these genuine conundrums if we keep having to rebut ideologically motivated salvos.

Related: Ancient herders from the Pontic-Caspian steppe crashed into India: no ifs or buts. I wish David would be a touch more equivocal. But I have to admit, if the model fits, at some point you have to quit.

June 17, 2017

Indian media is finally reporting on the Aryan migration into South Asia

Filed under: Genetics,science — Razib Khan @ 2:49 pm

For various ideological reasons in India there has been a strong resistance to the idea that Aryans came from outside of South Asia. When David Reich’s Reconstructing Indian Population History was published 2009 the Indian media had a weird response. For example, Aryan-Dravidian divide a myth: Study.

Though Reich’s paper was equivocal, it was clear to me that it was likely going to be the launching point for a resurrection of the Aryan migration theory. Now Tony Joseph in The Hindu has published a pretty good survey of the literature, How genetics is settling the Aryan migration debate. Nothing new for readers of this weblog, but he some good quotes:

The avalanche of new data has been so overwhelming that many scientists who were either sceptical or neutral about significant Bronze Age migrations into India have changed their opinions. Dr. Underhill himself is one of them. In a 2010 paper, for example, he had written that there was evidence “against substantial patrilineal gene flow from East Europe to Asia, including to India” in the last five or six millennia. Today, Dr. Underhill says there is no comparison between the kind of data available in 2010 and now. “Then, it was like looking into a darkened room from the outside through a keyhole with a little torch in hand; you could see some corners but not all, and not the whole picture. With whole genome sequencing, we can now see nearly the entire room, in clearer light.”

In relation to online debates I have had Indian interlocutors tell me flat out that they believe in the papers published between 2005 and 2010. It is nice to get the scientists who actually published this work now admit that new results overturn the older theories.

Note: I am going to refer to this as a migration, because “invasion” seems to connote too much specificity as to how it happened. But I have a difficult time imagining that it was a peaceful process.

June 9, 2017

The last days of pre-ancient DNA Indian population genomics

Filed under: Indian Genetics,science — Razib Khan @ 7:21 pm

If anyone wants to know about the population genetics of South Asia, I recommend three papers (all are open access):

Genetic Evidence for Recent Population Mixture in India

A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals

The promise of disease gene discovery in South Asia

In the near future ancient DNA will do for South Asia what has been done for Europe, and to a lesser extent the Near East. It will pull back our veil of ignorance. But until then we have genomic inference from larger data sets with a greater number of markers. What can we say now?

– The 2009 work that modern South Asians are broadly a compound of two streams of the out of Africa populations is correct. One is much like other West Eurasians. Another is distantly related to other East Eurasians, with possible affinities to Paleolithic Southeast Asian hunter-gatherers.

– The West Eurasian ancestry of South Asians, the “Ancestral North Indians” (ANI), does likely seem to be a a mixture at minimum between two groups. One element is related to the eastern farmers who first adopted agriculture on the slopes of the Zagros ~10,000 year ago. Another stream is closely related to the Yamna people who flourished on the Eurasian steppe north of the Black Sea ~5,000 years ago.

– The Munda people see to have a distinct Southeast Asian component that ties them with other Austro-Asiatic peoples. Their migration was almost certainly tied to the Neolithic migration of rice farmers.

– The R1a1a-Z93 Y chromosomal lineage found across much of South Asia, and especially the higher castes and the north, increased in frequency within the last 4,000 years. It is almost certainly exogenous to South Asia; ancient DNA from the steppe finds the Z93 in Iranic peoples, but no Indian ancestry in these groups.

November 30, 2016

Razib Khan at the Center of Eurasia

Filed under: Genomics,science — Razib Khan @ 6:41 am
The Eurogenes blog is running a fundraiser. I chipped in mostly to support his continued blogging. I don't agree with everything he posts, but the site is a good and valuable resource. "Genome blogging" hasn't gotten as far as I'd have thought it would have in 2010, mostly because the initial burst of enthusiasm wasn't...

November 28, 2016

Genomics Is Not Magic, There Is No Magic

Filed under: Genetics,science — Razib Khan @ 3:26 am
MIT Technology Review has an article up, Do Your Family Members Have a Right to Your Genetic Code?, which is now part of the genomics-human-interest-piece genre you see regularly. Here you have the exemplar of this sort of narrative: what do you do when one twin gets a test and the other does not, and...

November 26, 2016

Afro-Asiatic and Eurasian Backflow

Filed under: Africa,Genetics,science — Razib Khan @ 11:55 pm
If you follow Y genealogy you know that the distribution of R1ba2 exhibits a peculiar pattern. R1b is the most common haplgroup in Western Eurasia, and shares a deep common ancestry with R1a. It seems to have risen to high frequencies in Europe only during the Bronze Age, though has been found in earlier periods....

The Species Barriers Between Neanderthals and Anatomically Modern Humans

Filed under: Genetics,Neanderthals,science — Razib Khan @ 11:55 pm
A new paper in The American Journal of Humans Genetics, The Divergence of Neandertal and Modern Human Y Chromosomes, reports on possible reasons why we don't see Y chromosomes in modern humans from this archaic lineage, despite exhibiting detectable levels of autosomal admixture. As you might recall the clear lack of deep branching Y and...

The species barriers between Neanderthals and anatomically modern humans

Filed under: Genetics,Neanderthals,science — Razib Khan @ 3:30 pm

gr2A new paper in The American Journal of Humans Genetics, The Divergence of Neandertal and Modern Human Y Chromosomes, reports on possible reasons why we don’t see Y chromosomes in modern humans from this archaic lineage, despite exhibiting detectable levels of autosomal admixture. As you might recall the clear lack of deep branching Y and mtDNA lineages was long one of the major genetic rationales for why gene flow between Neanderthals and modern humans was presumably not very significant. This, despite suggestive evidence from morphological analysis as well as inferences from autosomal data. The problem is that it is harder to do the sort of clean phylogenetic reconstruction via a coalescent model utilizing autosomal data (which recombines, as opposed to the Y and mtDNA, which do not for the regions of interest), so ancient genome sequences were really what was needed to convince most people with these sorts of markers.

This makes us ask: why are Neanderthal Y and mtDNA lineages not found in modern humans which exhibit indications of gene flow from other hominin lineages? After all, the lack of these really led many people off on the wrong track for years. I recall in 2008 going to a talk by Svante Paabo who reported that the Neanderthal mtDNA he had sequenced was definitely very different from anything in the current databases for our species, which confirmed his assumption that there was no admixture into modern populations (Paabo changed his tune very soon after due to the whole genome sequencing obviously). One simple explanation is that because effective population sizes of Y and mtDNA are smaller than autosomal regions of the genome they’ll be more strongly subject to drift, and exhibit higher extinction rates. In other words, it wouldn’t be that surprising of all Neanderthal Y and mtDNA went extinct after admixture because they were a small minority, and most lineages went extinct in any case. Researchers who work in non-human phylogeography who relied on mtDNA in particular can tell of many stories of being led astray by looking at one informative locus.

But chance may not be what is at work here. Buried in the discussion of the paper:

…polypeptides from several Y-chromosome genes act as male-specific minor histocompatibility (H-Y) antigens that can elicit a maternal immune response during gestation. Such effects could be important drivers of secondary recurrent miscarriages30 and might play a role in the fraternal birth order effect of male sexual orientation.31 Interestingly, all three genes with potentially functional missense differences between the Neandertal and modern humans sequences are H-Y genes, including KDM5D, the first H-Y gene characterized…It is tempting to speculate that some of these mutations might have led to genetic incompatibilities between modern humans and Neandertals and to the consequent loss of Neandertal Y chromosomes in modern human populations. Indeed, reduced fertility or viability of hybrid offspring with Neandertal Y chromosomes is fully consistent with Haldane’s rule, which states that “when in the [first generation] offspring of two different animal races one sex is absent, rare, or sterile, that sex is the [heterogametic] sex.”

The origin of species is obviously one of the founding questions which arose with the emergence of evolutionary biology. Haldane’s rule dates to the 1920s. In mammals the heterogametic sex are males, so these the hybrids which will be selected against (or, they may be sterile). There’s been a lot of research of late on why Neanderthals went extinct, and whether there were speciation barriers in keeping with the biological species concept between our two lineages. This result suggests that there is going to be interesting stuffed coming out of the population genomics of ancient hominins in the near future….

The species barriers between Neanderthals and anatomically modern humans

Filed under: Genetics,Neanderthals,science — Razib Khan @ 3:30 pm

gr2A new paper in The American Journal of Humans Genetics, The Divergence of Neandertal and Modern Human Y Chromosomes, reports on possible reasons why we don’t see Y chromosomes in modern humans from this archaic lineage, despite exhibiting detectable levels of autosomal admixture. As you might recall the clear lack of deep branching Y and mtDNA lineages was long one of the major genetic rationales for why gene flow between Neanderthals and modern humans was presumably not very significant. This, despite suggestive evidence from morphological analysis as well as inferences from autosomal data. The problem is that it is harder to do the sort of clean phylogenetic reconstruction via a coalescent model utilizing autosomal data (which recombines, as opposed to the Y and mtDNA, which do not for the regions of interest), so ancient genome sequences were really what was needed to convince most people with these sorts of markers.

This makes us ask: why are Neanderthal Y and mtDNA lineages not found in modern humans which exhibit indications of gene flow from other hominin lineages? After all, the lack of these really led many people off on the wrong track for years. I recall in 2008 going to a talk by Svante Paabo who reported that the Neanderthal mtDNA he had sequenced was definitely very different from anything in the current databases for our species, which confirmed his assumption that there was no admixture into modern populations (Paabo changed his tune very soon after due to the whole genome sequencing obviously). One simple explanation is that because effective population sizes of Y and mtDNA are smaller than autosomal regions of the genome they’ll be more strongly subject to drift, and exhibit higher extinction rates. In other words, it wouldn’t be that surprising of all Neanderthal Y and mtDNA went extinct after admixture because they were a small minority, and most lineages went extinct in any case. Researchers who work in non-human phylogeography who relied on mtDNA in particular can tell of many stories of being led astray by looking at one informative locus.

But chance may not be what is at work here. Buried in the discussion of the paper:

…polypeptides from several Y-chromosome genes act as male-specific minor histocompatibility (H-Y) antigens that can elicit a maternal immune response during gestation. Such effects could be important drivers of secondary recurrent miscarriages30 and might play a role in the fraternal birth order effect of male sexual orientation.31 Interestingly, all three genes with potentially functional missense differences between the Neandertal and modern humans sequences are H-Y genes, including KDM5D, the first H-Y gene characterized…It is tempting to speculate that some of these mutations might have led to genetic incompatibilities between modern humans and Neandertals and to the consequent loss of Neandertal Y chromosomes in modern human populations. Indeed, reduced fertility or viability of hybrid offspring with Neandertal Y chromosomes is fully consistent with Haldane’s rule, which states that “when in the [first generation] offspring of two different animal races one sex is absent, rare, or sterile, that sex is the [heterogametic] sex.”

The origin of species is obviously one of the founding questions which arose with the emergence of evolutionary biology. Haldane’s rule dates to the 1920s. In mammals the heterogametic sex are males, so these the hybrids which will be selected against (or, they may be sterile). There’s been a lot of research of late on why Neanderthals went extinct, and whether there were speciation barriers in keeping with the biological species concept between our two lineages. This result suggests that there is going to be interesting stuffed coming out of the population genomics of ancient hominins in the near future….

August 6, 2014

The culture of science is the culture of the Left

Filed under: science — David Hume @ 1:52 am

Robert Tracinski, in What Atheists Have To Offer The Right‘s, kindly points to this website. He also goes on to assert:

That leads me to what atheists have to offer to this agenda. One of the problems with citing a religious foundation for freedom and Americanism is that these arguments tend not to appeal to those who don’t share your faith. People will naturally assume that, in order to agree with you, they have to believe in the same particular religious creed you have adopted. And given the vast range of religious belief, that’s a lot to ask for.

I’ve made this argument before. Modern American conservatism has become so culturally captured by the Religious Right that there’s a lot of talk about “Biblically based values” without much reflection that it might turn some people off who don’t share the basis of those values. I do think it is notable that conservatives with broad cultural influence such as George F. Will and David Brooks tend to have a secular affect (Will is personally an agnostic).

Trancinski goes on to talk about the relationship between conservatism and science at some length. I can speak here personally, as I am a scientist and a conservative. One issue is while most liberals may not be scientists, most scientists are liberals. Those who are not are invariably libertarians. I would cop to being conservative, albeit with a strong libertarian streak. And that makes me exceptional. The culture of scientists and culture of religious conservatives are so opposed to each other that a Christian evangelical friend who is an evolutionary biologist once told me he was asked literally every day how he could be a scientist and a Christian. I have been in the room several times where scientists talk about how they can outreach to the broader public, like conservatives, assuming of course that there were no conservatives in the room.

I don’t think this correlation is a logical necessity. It’s just an empirical sociological fact. And we have to deal with it in our political and policy culture. Most scientists exhibit strong domain specific in their cognitive competence, so there’s no reason to think that someone who has a strong command of molecular genetic mechanisms can therefore think cogently about global trade. But many scientists mislead themselves, assuming their powers of ratiocination are generally robust in all areas to which they put their minds. Scientists often are in fact ideally situated to be what F. A. Hayek would term Constructivists.

December 4, 2013

How genetics are rewriting the history of the Caribbean

Filed under: Christopher Columbus,Genetics,Native Americans,science — Razib Khan @ 2:47 am
Over the past century history has been approached from many different angles, despite the stereotype of scholars haunting dusty archives. Adventurers once called antiquarians became archaeologists, and inspired the fictional Indiana Jones. Today it is the turn of the geneticists to put their stamp upon history. By tracing patterns of variation they gain insights as to the [...]

November 12, 2013

bioRxiv is here

Filed under: bioRxiv,science — Razib Khan @ 1:45 am

bioRxivFor years many in the biological sciences community have been jealous of the exist of arXiv. This preprint server allows researchers to distribute their work widely to all comers. On occasion when when there have been debates about mimicking arXiv for biology there has been skepticism about the nature of the outcomes (my own rejoinder is that fields where a preprint culture is the norm, such as economics and physics, don’t seem to be doing badly). Now we’ll see if the end is nigh in biological science due to preprints; bioRxiv is live (sponsored by CSHL). The first paper, The Population Genetic Signature of Polygenic Local Adaptation. There’s not much up yet, but there will be.

The post bioRxiv is here appeared first on Gene Expression.

January 6, 2013

Why so few Asians in ecology? Not all groups have similar preferences

Filed under: science — Razib Khan @ 12:33 pm

A week ago Keith Kloor had a post up, What Science, Environmentalism and the GOP Have in Common, where he bemoaned the lack of representation of non-whites in these categories. As a matter of fact I think Keith is wrong about science. Even constraining the data set to American citizens and permanent residents people of Asian ancestry are well represented in many areas of science. But not all sciences are created equal. In 2011 there were 158 doctorates which were awarded within the category of ‘evolutionary biology’ for American citizens or permanent residents. Of these 135 were non-Hispanic white, and 5 were Asian. In ‘neuroscience’ the respective figures were 742, 535, and 96. In ‘zoology’ 55, 49, and 0. In ‘bioinformatics’ they were 80, 51, and 17. Finally, in ‘ecology’ the breakdown was 330, 300, and 11. If you are involved in academic biology I’m rather sure that these numbers won’t surprise you too much, even if you’d never thought about it. You can even infer these by walking through the posters at ASHG 2012, and seeing how the demographics of the crowds shift.

We can look at this issue another way. In 2010 US News & World Report listed the top 10 ecology & evolution graduate programs. I went to the faculty websites after typing the university and ‘ecology,’ and then ‘neuroscience.’ Looking at names, and sometimes head shots, I classified everyone as ‘Asian’ (as defined by the US Census) and ‘Not Asian.’ You can find the data here. Please note that the left columns are ecology faculty, and the right are neuroscience.

The raw results are:

University & Department Asian Not Asian % Asian
Berkeley – Ecology 0 46 0.0%
Berkeley – Neuroscience 4 40 10.0%
Harvard – Ecology 3 48 6.3%
Harvard – Neuroscience 21 127 16.5%
Davis – Ecology 8 117 6.8%
Davis – Neuroscience 12 73 16.4%
Chicago – Ecology 3 22 13.6%
Chicago – Neuroscience 11 65 16.9%
Stanford – Ecology 2 17 11.8%
Stanford – Neuroscience 19 74 25.7%
Cornell – Ecology 1 31 3.2%
Cornell – Neuroscience 3 39 7.7%
UTexas – Ecology 3 43 7.0%
UTexas – Neuroscience 7 63 11.1%
Yale – Ecology 0 23 0.0%
Yale – Neuroscience 13 83 15.7%
Princeton – Ecology 0 15 0.0%
Princeton – Neuroscience 2 17 11.8%
Arizona – Ecology 0 54 0.0%
Arizona – Neuroscience 0 20 0.0%

 

And here are charts of % and counts:

Does this matter? In American society, especially from the center to the left of the social-cultural spectrum, there is a premium on diversity. Usually this means specifically cases of racial and gender diversity (again, as I have contended before the nod to class diversity is almost always perfunctory, and there is only marginal concern about ideological diversity). As a rule within these parameters the question about diversity is usually ‘why not,’ in as proportions out of sync with the population immediately prompt questions as to why this might be. My own personal position is at variance with this. Rather, my attitude is more ‘so what?’ I generally don’t care about these things personally. Unlike most my default assumption isn’t that all groups will have the same aptitudes and preferences, and so it is difficult to assess the scope and nature of the idealized demographic mix sans discrimination. In the sciences what is of importance to me is not ‘who,’ but ‘what’? That is, what is being discovered.

The question in regards to Asian Americans with American biological science is of personal interest to me. My own passions lean strongly to evolutionary biology. Any curiosity about genomics and bioninformatics is prompted by population and evolutionary genetic questions. Frankly, this means that I spend a great deal of time around white people, because for whatever reason evolutionary biology is far more white than many other areas of life science. In contrast, if I stumble into a molecular biology or neuroscience seminar the audiences are by nature far more diverse, with diversity being due to the large contingent of people of Asian ancestral background.

I don’t know if this matters in any deep way. I suspect if Asian Americans were as well represented in human evolutionary genomics as they are in cancer research there might be some stronger and earlier focus on questions of ascertainment bias due to early Eurocentric data sets. But this would be only a shift on the margins; it isn’t as if evolutionary biologists aren’t aware of the issue at all. More importantly I wanted to highlight this difference across fields because I think it illustrates the proximate power of preferences and expectations, rather than discrimination or lack of outreach. To give an example of what I mean, my father, who has a doctorate in physical chemistry, once quipped me that ‘it would be nice if you studied neuroscience, then I could just tell people you study the brain.’ Though conveniently for him since my major area of concern is genetics that is something that he can tell his friends which is intelligible, though questions always get back to me about ‘genetic engineering’ and ‘gene therapy,’ suggesting that people assume my topics must be biomedical. For whatever reason most of the young Asian Americans who enter university and study biology of some sort do not tend to gravitate into areas like ecology or evolution. An Asian American acquaintance who is an ecologist has even joked to me that sometimes his friends refer to him as a ‘twinkie‘ on account of his disciplinary focus. I do not believe that the lack of representation of Asian Americans within ecology or evolution has to do with discrimination, nor do I think that biomedical science has less implicit bias against people of Asian heritage. To be succinct, many Asian American youth who pursue graduate school in science may already elicit raised eyebrows because they did not pursue medical school. Going off to study the phylogeny of starfish, or some such thing, would frankly result in even more bewilderment and disappointment.

In this case it seems clear that the problem is not discrimination or bias (though that exists, I don’t think it varies that much across fields), but a cultural preconception as to what science merits one’s professional energies. Evolutionary biologists could go into Korean American churches to argue for the value of their discipline, but even assuming individuals their audience did not hold Creationist beliefs (many would), it would be a hard sell to convince them that abstract and theoretical evolutionary questions are more worthy of attention than projects with a more practical biomedical focus. This isn’t going to convince people who start out with the null hypothesis that variation in discriminatory atmosphere explains variation in representation in fields by race and ethnicity, but, I hope it makes people reconsider different hypotheses.

Addendum: Also, bemoaning the lack of ‘minorities’ in science often seems a case of the ‘How Asians became white‘ phenomenon.

November 26, 2012

There are no shortcuts to knowledge

Filed under: Epistemology,Nate Silver,science — Razib Khan @ 2:53 am

As many of you know, right before the election I made a $50 bet with Hank Campbell that Nate Silver would get at least 48 out of 50 states correct for the 2008 presidential election. I also got one of Hank’s readers to sign on to the same bet. Additionally, a few readers and Twitter followers got in on the wager; they were bullish on Romney’s prospects, and I was not (more honestly, I was moderately sure they were self-delusional, and willing to take their money to make them more cautious about their self-delusional biases in the future). But there’s a major precondition that needs to be stated here: I hedged.

Last February a friend told me he was 100% confident that Barack Hussein Obama would be reelected. This prompted me to ask for favorable terms on a bet. The logic was simple, if he was 100% confident, then it shouldn’t be a major issue for him, because he was collecting anyhow. As it happens he gave me 5 to 1 odds, so that I would collect $5 for every $1 he might collect. I told him beforehand that I actually thought that Obama had a 60-70% chance of winning, so I went into the wager assuming I’d be out a modest amount of money. But that was no concern. My goal was now to convince those who were irrationally supportive of Romney to take the other side of the bet. For whatever reason people have an inordinate bias toward their hoped-for-candidate in terms of who they think will win, as opposed to who they wish to win. The future ought gets confused with the future is.* I got people to take the other side, which means that I was going to make money no matter who won.

At this point one might wonder about my comment that I suspected that those who were bullish on Romney were delusional. It’s rather strong, and my reasoning is actually rather strange. Overall I accepted the polling averages. A few years back I was an economic determinist in election outcomes, but Nate Silver had convinced me that the sample size was too small to get a good sense of the real proportion of variation being predicted here. In short, the economy matters, but I stepped back from the supposition that it was determinative (as it happens, purely economic models that were excellent at predicting past elections face-planted this time). So that’s why I relied on the polls. Though I leaned on Nate Silver, I didn’t think he was particularly oracular, and I’d say that I’m mildly skeptical of the excessive faith some put in his particular person. When I put a link up to Colby Cosh’s mild take-down of Silvermania I received a few moderately belligerent comments. This despite the fact that I was willing to put money on Silver’s prediction.


But after soft-pedaling my confidence in polling averages, why did I think the pro-Romney people were delusional? The simple answer is 2004 and 2008. When the polling runs against you consistently and persistently motivated reasoning comes out of the wood-work. There’s a particularly desperate stink to it, and I smelled it with the “polls-are-skewed” promoters of 2012. In 2004 there were many plausible arguments for why the polls underestimated John F. Kerry’s final tally. And in 2008 there were even weirder arguments for why McCain might win. In 2012 it went up to a whole new level, with a lot of the politically conservative pundit class signing on board because of desperation.

The reality is that out of the space of plausible models you can find something congenial to your own proposition. I very studiously avoided reading much about the debates about skewed polls, even in the comments of this weblog. For example, Dwight E. Howell left this note on September 29th:

You might want to go back and look at how accurate polls have been at predicting elections in the past. The track record isn’t great. Even the exit polls in WI were wrong. It appears the Democrats who wanted the governor out stopped and chatted and the people who voted to keep him largely walked on by including a significant number of Democrats who had to have voted for him.

There is also the non trivial question of how many of the various sub groups are actually going to show up on election day. If you assume that blacks will turn out in the same numbers as his last election you get one result. If you note that the black community has not fared well during his tenure in office and he has deeply offended many black Christians you have to wonder if some of these people are going to bother to show up and vote for him. The Jews have to know his position relating to the Jewish state, etc. He pretty much had a solid Catholic vote last time but he’s at war with the Catholic church. What does this all mean? You’ll find out after the votes are counted.

The votes have been counted, and Dwight E. Howell was full of shit. In fact I badgered Howell on Twitter and on these comment boards to put a wager down on the election, and he finally begged off after he couldn’t evade me, claiming he wasn’t a betting man. I have a hard time dismissing the possibility that Howell himself knew he was a delusional crank full of bullshit on some level! And yet what he said wasn’t crazy.

The reality is that I didn’t read most of Howell’s comment until after the election. The same with the very similar comments that came through in Howell’s wake on that thread (I did not post them, I simply skimmed the first few sentences). A similarity of content across the comments suggested that these individuals were just regurgitating plausible nuggets and feeding their motivating reasoning bugs. And that’s why I avoided detailed inquiry into the issues: I didn’t want to bias my own perspective! This was part of the source of Hank Campbell’s confusion as to my somewhat erratic response on Twitter as I frantically tried to make a bet with him on the election: I didn’t really care about Hank’s theories about the polls, I suspected that the polls were right because I strongly scented a lot of bullshit on the Republican side. I wanted to get Hank down on some bet, and I wasn’t too concerned with the details. In contrast to the odor wafting up from the Republicans, the Democrats seemed sincerely and guilelessly accepting of the polls which favored them. My intuition here could have been wrong, or the perceptions of the parties of interest may have been wrong. But that was really the situation and context which motivated my behavior at the time.

After the election was over I actually started reading some of the arguments about why the polls were skewed, and I find that they are extremely plausible to me. And not just me, John Hawks owes me a drink because he simply didn’t believe the turnout models which suggested a demographic more like 2008. The reality is that my instinct was to go with John. I too was very skeptical of the proposition that Obama could turnout the same voters as he did in 2008. And yet he did turnout those voters!

What does this tell me after the fact? The plausibility of any given datum can’t outweigh the aggregate. Dwight E. Howell et al. have a lot of plausible historical data. Granted, you have some obvious bullshit “SHOCK POLL” headlines, but only idiots believe those outliers (there are plenty). Rather, if you have a model, there are plenty of data points you can populate to get the appropriate outcome. That was my suspicion and worry, and I find that I’m highly susceptible to some of the more cogent and eloquent arguments about turnout models (not Dwight’s comment specifically, most of the non-specialists signal that they are just echoing the specialists by garbling and muddling transparently). My initial instinct to not allow myself to info-overload, and then filter it out to the subset which confirmed my model, seems to have been wise.

And importantly I relied on the expertise of others. I’m just not that motivated or interested in horse-race politics (though I am interested in political history, philosophy, and economy). I assumed that “political junkies” of partisan sentiment would keep track of the likely outcomes, and when Right and Republican leaning individuals started making desperate sounding arguments with the intent of converting themselves, I believed that that signaled that Obama was on the rise. Similarly, I also defer to the collective wisdom of the polls. This does not mean that these two are infallible (my judgement of people bullshitting, or, the wisdom of the polls). But it’s better than nothing, and I ended up the richer.

All this brings me to Nate Silver’s  The Signal and the Noise: Why So Many Predictions Fail-but Some Don’t and Jim Manzi’s Uncontrolled: The Surprising Payoff of Trial-and-Error for Business, Politics, and Society. These two authors are class acts, and I follow both of their pronouncements closely. I have long appreciated Silver’s contribution to the broader discourse, and though Jim Manzi may not be as prominent, he is an important voice for empiricism on the modern political Right, which too often seems to simply be a reiteration of old hopeful ideals. But ultimately if you are a long time reader I’d have to say that you should go with Uncontrolled and not The Signal and the Noise.

First, I will touch upon an issue that may seem superficial to many: style. Jim Manzi may not have the most limpid of prose. He is of course spending a great deal of time on epistemology, history of science, and quantitative business strategy. But Silver is a far better blogger than he is a narrative nonfiction writer. Many of the chapters in The Signal and the Noise have a formulaic quality, insofar as the focus is clearly on the ideas, but there are often pro forma biographical introductions of important thinkers. There are writers who do this well. I doubt I would; I’m more interested in ideas than the people generating them. And I suspect so is Silver. He almost certainly finds Futarchy more fascinating than Robin Hanson. The main exceptions tend to be in areas where Nate Silver has some personal connection. The chapters on the quantitative revolution in professional sports scouting and gambling are more lively, with more loving attention to the dramatis personae. And that makes sense if you have some priors in hand: Silver comes out of a quantitative sports analyst background, and, he was a professional poker player at one point.

But more importantly as a work of popularized statistical inference The Signal and the Noise probably would not add much novel data or cognitive tools to the typical core reader of GNXP. Most of you are presumably aware of Bayesian probability, and the abuses of modern Frequentism. If this is Greek to you, then I would recommend The Signal and the Noise!  And perhaps check out the Less Wrong Wiki. If you don’t know that economists are notoriously bad at predicting recessions, or that political prediction models based on a few economic or social indices are notoriously good at predicting the past but bad at predicting the future, then The Signal and the Noise may also be for you. And reading this book reiterated to me that Nate Silver is a great blogger whose Weltanschauung is broadly similar to mine. But The Signal and the Noise did not present to me any grand revelations. It was an exploration of topics which I developed interests in in striking parallel with Nate Silver over the aughts. I suspect this is a function of the change in our relationship to data due to the power of computers in terms of both storage and analysis. Silver is a reflection of the age, a herald, not a prophet. We are part of the same army.

Jim Manzi’s Uncontrolled is a somewhat different work, insofar as within the author explicitly outlines the relatively constrained scope of his ambition. The core of Manzi’s argument is that public policy would benefit from more randomized controlled trials (also known as randomized field trials). This seems a plainly sensible project, but Manzi’s assertion is that too often enormous public policy ideas are proposed, and then implemented on a massive and indiscriminate scale. Whether the policy was ever effective or not can often be litigated, because there was never a “control.” In the end Uncontrolled is a plea for experimentation, epistemological humility, and incremental gains on the margin. Obviously Manzi is not presenting himself as Prometheus. Rather, this is a small vision executed on a massive scale. Manzi has seen this work in the business work, and he wants to translate these private sector successes to the public domain.

But perhaps what Uncontrolled does better than convince you of the efficacy of randomized controlled trials in public policy is that there are limits to the power of elements of the scientific method in particular domains. This is the old hierarchy of knowledge idea, so Manzi is treading over ground familiar to many. In short, physics is easy, and economics is hard. Grand general theories with a few variables have generally failed in economics where they have succeeded in physics. That is not due to the lack of ingenuity of economists (many of whom come from a physics background!), but simply due to the fact that economic phenomena are much more complex than many physical phenomena. In Manzian terms they have “high causal density.” There are so many possibilities that simple models and obvious large correlations are not going to be robust or existent.

This goes back to why I was very cautious about reading too much about the skepticism of polls before the election. There are so many possibilities it is incredibly easy to conjure up a plausible skepticism of the received wisdom, and present an alternative. True aficionados who wallow in the data can filter the good from the bad, but we civilians rarely can. Importantly I would like to add that this is something Silver acknowledges in The Signal and the Noise. Formal quantitative analysis supplemented by qualitative knowledge trumps quantitative analysis alone. If the pundits who criticize the quants have true knowledge, they will only benefit. If they don’t have true knowledge, as Philip Tetlock has reported, then they have much to fear.

All things leads us to the common sense conclusion that the process to attain knowledge is hard. Powerful math and statistics can give us only so much. Experiment without theory is not illuminating. A theory devoid of empirical data is not persuasive. Randomized experiments without any guiding model or hypothesis may be lacking in insight. These are the outward aspects. But what about the personal  strategies for attaining knowledge? If one is focused on one’s domain, one need not over-think this. Presumably, you know your shit. But when you move out of domain your need to be very careful, because you are on alien topography. One suggestion I might make is be careful of looking too hard for data confirming your prejudices; it is all too easy if you are clever. Rather, look only modestly, and withdraw quickly if you don’t find what you are looking for. If it was all that clear and obvious, it would have been clear and obvious to you initially. The bold and plain truth does not hide.

* For those inquiring about Intrade, it is not that easy to deposit money into that system if you are American. Try it.

 

November 20, 2012

Iterating science, supercharged

Filed under: science — Razib Khan @ 7:17 pm

Science is about “updating” with new information. But people are attached to their propositions, and shifts in paradigms can take a very long time, often dependent more on human lifespans than the constellation of the data. But please see this post by Luke Jostins’ over at Genomes Unzipped. He has “updated” his own view of his recent Nature paper on inflammatory bowel disease. This is rather awesome, because yes, there was some talk about the balancing selection aspect of the paper at ASHG, and now Luke has gone and amended his own position.

The reality is that emotions are a big deal in science. But in theory we simply look at the evidence. Bridging that gap, and shifting the balance to the latter, is very important in keeping the enterprise honest, fruitful, and attractive to young scholars. I’m hoping that the more rapid dissemination of information via projects like Haldane’s Sieve will aid in the rate of iteration.

November 19, 2012

Richard Lewontin against the age

Filed under: science — Razib Khan @ 9:35 pm

Richard Lewontin’s fame rests in part on his pioneering role in the development of the field of molecular evolution, and secondarily due to his trenchant Left-wing politics. Several readers have already pointed me to his rather strange review of two new works in The New York Review of Books. The prose strikes me as viscous and meandering, but some of the assertions are rather peculiar. For example:

The other exception to random inheritance is not in the chromosomes, but in cellular particles called ribosomes that contain not DNA but a related molecule, RNA, which has heritable variation and is of basic importance to cell metabolism and the synthesis of proteins. Although the cells of both sexes have ribosomes, they are inherited exclusively through their incorporation in the mother’s egg cell rather than through the father’s sperm. Our ribosomes, then, provide us, both male and female, with a record of our maternal ancestry, uncontaminated by their male partners.

Harry Ostrer, who is a professor of genetics at Albert Einstein College of Medicine, and Raphael Falk, who is one of Israel’s most prominent geneticists, depend heavily on our ability to trace ancestry by looking at the DNA of Y chromosomes and ribosomes….

There is no mention of ribosomes in Legacy: A Genetic History of the Jewish People. I know, because I used Amazon’s ‘search inside’ feature. Rather, there’s a lot of reference to mitochondrial DNA and mtDNA, which is what Lewontin truly meant. Or at least I hope that’s what he meant. Because Lewontin is an eminent evolutionary biologist I assume they felt like they didn’t need a science editor, but perhaps they need to reconsider that.


Regular readers will know that I am not a fan of Richard Lewontin, and feel that his influence on intellectual life is generally pernicious. Though the review above is riddled with confusions, the primary aspect of Lewontin’s oeuvre since the mid-1970s that I sense is one of conscious obfuscation, not blundering delusion. Consider what L. L. Cavalli-Sforza told me 6 years ago:

7) Question #3 hinted at the powerful social impact your work has had in reshaping how we view the natural history of our species. One of the most contentious issues of the 20th, and no doubt of the unfolding 21st century, is that of race. In 1972 Richard Lewontin offered his famous observation that 85% of the variation across human populations was within populations and 15% was between them. Regardless of whether this level of substructure is of note of not, your own work on migrations, admixtures and waves of advance depicts patterns of demographic and genetic interconnectedness, and so refutes typological conceptions of race. Nevertheless, recently A.W.F. Edwards, a fellow student of R.A. Fisher, has argued that Richard Lewontin’s argument neglects the importance of differences of correlation structure across the genome between populations and focuses on variance only across a single locus. Edwards’ argument about the informativeness of correlation structure, and therefore the statistical salience of between-population differences, was echoed by Richard Dawkins in his most recent book. Considering the social import of the question of interpopulational differences as well as the esoteric nature of the mathematical arguments, what do you believe the “take home” message of this should be for the general public?

Edwards and Lewontin are both right. Lewontin said that the between populations fraction of variance is very small in humans, and this is true, as it should be on the basis of present knowledge from archeology and genetics alike, that the human species is very young. It has in fact been shown later that it is one of the smallest among mammals. Lewontin probably hoped, for political reasons, that it is TRIVIALLY small, and he has never shown to my knowledge any interest for evolutionary trees, at least of humans, so he did not care about their reconstruction. In essence, Edwards has objected that it is NOT trivially small, because it is enough for reconstructing the tree of human evolution, as we did, and he is obviously right.

The key is “for political reasons.” The title of The New York Review of Books piece by Lewontin is “Is There a Jewish Gene?” Titles are often placed there by editors, but in this case I wouldn’t be surprised if this Lewontin was responsible for this. Much of his line of attack against modern genetics which displeases him is to construct a strawman of monogenic models, when the reality is that polygenic variation is widely acknowledged and understood, within the academy! Not so in the public and popular press, and Lewontin fans the flames of that confusion, because he knows that there isn’t a “Jewish gene,” or an “intelligence gene.”

Also, I actually saw Harry Oster speak at ASHG, and it seems likely to me that Richard Lewontin is not painting an accurate portrait of the book he is reviewing here. Oster’s view of genetics and ancestry is subtle and nuanced. In any case, of the myriad issues which Lewontin mangles, the primary one I need to point out is that the most powerful evidence for the genetic affinity of the Jewish people is not in uniparental markers, as asserted in the review, but autosomal genomic tracts which indicate descent from a relatively small number of people over and over across the past 1,000 years. This is where Lewontin’s thought experiment of dilution over the generations falters; the strong stamp of Jewishness which binds Ashkenazim in particular manifests in the fact that genealogies coalesce over and over again toward the same relatively small number of people 500-1,000 years ago. This is a major avenue of research. If Richard Lewontin had gone to ASHG 2012 he would have been treated to a lot of “Jewish genes.”

Finally, what ultimately vexes me about Richard Lewontin is that it seems clear that for him the ought has more priority than the is, insofar as is derives from the ought. I happen to agree on a normative basis with him about the low value of genetic connection being a valuable ground toward common affinity and fellow feeling. I’ve made my own personal opinion on this rather clear. But that does not mean that because I do not personally value genetic relationships much that those relationships do not exist. In other words, just because you don’t value something does not negate its existence, and just because you value something does not mean that it exists. I don’t value racial solidarity at all, but I believe human races do exist. Some of my friends value their personal relationship with God, but I don’t believe that this exists (that is, I don’t believe that God exists). Of course, there is a class of phenomenon which you can value, but doesn’t exist, but can exist. 18th century abolitionists valued a world where slavery was de jure abolished. That would not exist for centuries, but it does now exist.

It doesn’t gain us anything to assert that what is, isn’t. All that vain hope does is make the reckoning all the more shocking. I am not particular exercised by obfuscation at this point, because in the end reality wins out. Lewontin can laugh off the idea of a Jewish gene, but this isn’t 1972 anymore. People can compute exactly how Jewish they are today.

Image Credit: Wikipedia

October 11, 2012

A dangerous man

Filed under: Genetics,Genomics,Human Genetics,Human Genomics,science,Steve Hsu — Razib Khan @ 2:32 am

I was a little sad when I heard my friend Steve Hsu had accepted a position at Michigan State some months back. My reasons were two-fold. First, I swing by Eugene now and then, and I wouldn’t have the opportunity to drop in on his office. Second, it seemed that Steve was becoming an Administrator. To some extent I feel like that’s going over to the dark side. But ultimately it’s his decision, and Steve has a lot of things going on at any given moment, and I’m hopeful he’ll continue to be involved in the production of scholarship in some form (he’s more of a scholar than most as it is).

Now apparently his move has resulted in submerged tensions coming to the fore. You can read the article in The Lansing Journal, New director’s experience a plus for MSU, but his controversial views concern some. Let’s qualify who these “some” are:

Shortly after the start of classes this fall, Daniel HoSang, a professor of political science and ethnic studies at the University of Oregon, sent an email to a handful of faculty. Hsu, he wrote, “has taken a ...

October 2, 2012

The real end of science

Filed under: Anthroplogy,Culture,science — Razib Khan @ 10:02 pm

Fifteen years ago John Horgan wrote The End Of Science: Facing The Limits Of Knowledge In The Twilight Of The Scientific Age. I remain skeptical as to the specific details of this book, but Carl’s write-up in The New York Times of a new paper in PNAS on the relative commonness of scientific misconduct in cases of retraction makes me mull over the genuine possibility of the end of science as we know it. This sounds ridiculous on the face of it, but you have to understand my model of and framework for what science is. In short: science is people. I accept the reality that science existed in some form among strands of pre-Socratic thought, or among late antique and medieval Muslims and Christians (not to mention among some Chinese as well). Additionally, I can accept the cognitive model whereby science and scientific curiosity is rooted in our psychology in a very deep sense, so that even small children engage in theory-building.

That is all well and good. The basic building blocks for many inventions and institutions existed long before their instantiation. But nevertheless the creation of ...

September 3, 2012

A social science of the obvious

Filed under: science — Razib Khan @ 2:13 am

I’m reading Jim Manzi’s Uncontrolled: The Surprising Payoff of Trial-and-Error for Business, Politics, and Society right now. No complaints, though that’s no surprise, as I’m familiar with the broad outline’s of Manzi’s work, and have found much to agree with him on  in the past (though there are issues where we differ, never fear). That being said, I did ponder one aspect of Manzi’s characterization of science: that it makes non-obvious predictions. This is not controversial, and I don’t want to really quibble with it too much. But in the context of social science in particular I think one of the gains of ‘science’ is the clarification of obvious predictions.

To illustrate what I’m talking about, the inverse-square law defines the decay of the intensity of light from a radiation source. Is this non-obvious? The precise decay function isn’t obvious, but the general trend is clearly obvious. Intensity decreases with distance. We know this intuitively. But it is obviously a gain to quantitize and formalize this phenomenon, as it can then be integrated algebraically into a broader system.

And so it is with social science phenomena. For example, I can say that most of personality variation within a population is ...

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