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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….

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 ...

August 19, 2012

Peer of myself

Filed under: science — Razib Khan @ 3:40 pm

Dr. Joe Pickrell has a follow up to his widely discussed post on updating scientific publication for the 21st century. One section jumped out at me, not because it was revolutionary, but because it made explicit a complaint that I had often heard:

The solution to this problem relies on a simple observation–in my field, I am completely indifferent to whether a paper has been “peer-reviewed” for the basic reason that I consider myself a “peer”. I do not think it extremely hubristic to say that I am reasonably capable of evaluating whether a paper in my field is worth reading, and then if so, of judging its merits. The opinions of other people in the field are of course important, but in no way does the fact that two or three nameless people thought a paper worth publishing influence my opinion of it. This immediately suggests a system in which papers are posted online as soon as the authors think they are ready (on so-called pre-print servers). This system is the default in many physics, math, and economics communities, among others, and as far as I can tell it’s been quite successful.

The reality is that often the ...

August 15, 2012

How to get beyond bias in science?

Filed under: science,Science and culture — Razib Khan @ 7:38 pm

Here’s a comment which is interesting, if hard to actually engage with because of the difficulty of the subject matter:

You’re obviously aware of the arguments employed by feminists in the critique of the philosophy of science; that cultural values, in their view patriarchy, could unintentionally contaminate science by affecting how evidence is interpreted and what hypothesises are formed from it. This argument is usually combined with the more fundamental problem of using inductive logic in science, especially biology, and how any cultural norms could be mistaken for biological facts.

My question is how do you separate out the biases from the facts?
What makes you think that the lefts reservations about the studies into sex and race are the result of their own bias and not a legitimate acusation of bias within science? It is obviously not a totally improbable claim considering the long history of racist science in the two previous centuaries.
From my own lay mans knowledge of the subject I’ve got the impression the jury is still out on both innate sex difference and the genetic realities of race.

First, as I keep telling my liberal readers and friends there’s a deep denialism about sex differences that is ...

August 14, 2012

arXiv! arXiv! arXiv!

Filed under: ArXiv,science — Razib Khan @ 7:58 pm

Over the Nielsen Group blog, Time to jump into the arXiv?:

There is one other drawback to the arXiv that makes me, as a potential submitter, very nervous: being scooped.

A paper is “scooped” if someone else publishes the same (or very similar) concept before you get a chance to publish yours. But, wait, if it is on the arXiv, isn’t that documentation that I had the idea first? Well, yes, but… the arXiv isn’t commonly used in Biology yet, so it isn’t clear how important or how much priority will be given to authors who publish there before “traditional” peer review. This is especially concerning if the novelty of the paper is the idea (which is easy to reproduce with the same or different data) versus a method (which is more difficult to replicate). Maybe this isn’t a valid concern, because anonymous reviewers could, one might argue, just as easily “scoop” ideas from a manuscript they have reviewed. Furthermore, perhaps posting ideas/research early might facilitate more collaborations instead of competitions between research groups.

All said, I think that submitting to pre-print servers can be a very valuable tool for facilitating scientific discourse and advances. Will I start submitting there? ...

The art of science

Filed under: science — Razib Khan @ 7:26 pm

Over at Scientific American Blogs Maria Konnikova posts Humanities aren’t a science. Stop treating them like one. The whole write-up leaves me scratching my head, because I don’t really get what the whole point of all the prose is. This is a thesis that is as old as 19th century romantics, and not all too complicated. The author herself has an academic webpage which indicates she works within an analytic framework that’s anything but “soft.” There are huge confusions with terminology, and Jerry Coyne has a response which addresses many of my questions (e.g., what exactly is the alternative to doing statistical tests in psychology? Rely on the impressions and intuition of the researchers and just trust them?). But let me highlight one section:

… Societal conventions change. And is today’s real-world social network really comparable on any number of levels to one, say, a thousand, or even five or one hundred years ago?

Yes, today’s real-world social network probably is comparable to those of the past. There is some science on this issue. Not even rocket science with abstruse statistics. Science which is highly relevant today. Question science, and it may surprise you with what it ...

August 13, 2012

Why you shouldn’t publish in PNAS

Filed under: PNAS sucks,science — Razib Khan @ 6:41 pm

Update: It’s online.

Well, maybe the title is hyperbolic. But it’s been frustrating for years that PNAS seems to have some of the most backward post-publication delay policies/patterns in the business. So, for example there’s a new paper in PNAS which is being covered in the media extensively with a DOI link released, but the paper still isn’t on the website. This allows David Reich free reign to do a little amusing slap-slap without any paper to check him:

….The PNAS paper questioning Neanderthal admixture addresses issues swirling around two years ago but not Reich and Slatkin’s latest work. “It’s been an issue for several years. They were right to work on this,” says Reich. But now “it’s kind of an obsolete paper,” he says.

And of course Reich’s group put their preprint up on arXiv yesterday (though the linked piece above says that it’s already been accepted into PLoS Genetics), so we can slice & dice it while we’re waiting on PNAS.

My primary reason for putting a whole post on this issue, which Ed Yong has mentioned many times, is that Twitter kept buzzing (at least my feed) about when the paper was going live earlier ...

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