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

November 30, 2012

Can your genes be patented?

Filed under: Intellectual property,Myriad Genetics,Personal genomics — Razib Khan @ 7:30 pm

Court to Decide if Human Genes Can Be Patented. So it seems a group of middle aged to very aged lawyers will decide the decades long Myriad Genetics saga. My position on this issue is simple: if you are going to award patents, they must be awarded to acts of engineering, not discoveries of science. See Genomics Law Report for more well informed commentary.

November 29, 2012

Burma’s “Muslims” are kalar Bengali

Filed under: Arakan,Bengali,Islam,Rakhine — Razib Khan @ 8:58 pm

The American media often confuses the subtleties of international ethography. For example, there is a tendency to use the term “Uyghur” and “Chinese Muslim” interchangeably. This is misleading. The largest Muslim ethnic group in China are the Hui, who were rather culturally similar to the Han, except in the many areas where the Islamic religion results in their deviation from Han practice (e.g., they do not eat pork). Though Uyghur religious feelings are real, and their resentment at the government of China does derive from religious persecution, it is also an expression of nationalistic alientation. Uyghurs are ethnic Turks. In short, the Uyghurs are Muslims in the People’s Republic of China (the governmental entity which is the heir to the extra-Chinese territories of the Manchu dynasty; Xinjiang, Manchuaria, and Tibet). The Hui are Muslims of China.

“Burmese Muslims”

A similar nuance is surely important when considering the situation of “Burmese Muslims.” In the article itself the author is peculiarity cryptic about who these people are aside from their religious identity, and their putative foreign origins. Who these people are are Rohingyas. They are the Muslims inhabitants of Arakan state, which extends southeast of Bangladesh. And importantly Rohingyas are descended from and closely related to ethnic Bengalis. Their language is a sister to Sylheti, standard Bengali, and Chittagongian, with a particular affinity to the latter. Additionally, there are other Muslims in Burma who are not Rohingya! Some of these are ethnic Burmans, also called Bamars, who are the majority community with Burma/Myanmar. Aung San Suu Kyi herself reportedly has some Muslim ancestry from the civil servants and soldiers who were to be found around the courts of the kings of old.

There are two issues which need to be highlighted. First, it seems reasonable that the Rakhine people of Arakan worry that the Islamic demographic wave will inundate them. Though Bangladesh now has the same fertility as Burma, until recently Muslim demographic expansion has been a fact on the eastern marchlands of South Asia. The ratio of Rakhine to Rohingya seems to be on the order of 3 or 4 to 1, which is a majority, but not a comfortable one. But there is a clear racial element to the animus here, which would likely not be present if the Muslims were of one of the Sino-Tibetan or Mon people. Following attack, Muslims demonstrate in Rangoon:

“We should either kill all the Kalars in Burma or banish them, otherwise Buddhism will cease to exist,” said another user.

“Kalar” is used to describe perceived outsiders within the country, especially individuals with dark skin, but the term often carries a pejorative tone. In the Burmese edition of the New Light of Myanmar today, the victims of the sectarian attack were referred to as “Kalar” instead of Muslims.

Second, the Rohingya themselves deny strenuously their association with Bengal and Bengalis, because that would give credence to the Rakhine accusation that they are recent migrants into Arakan. As it happens I think in the main the Rakhine are probably right. Though some of the Rohingya date to the long-standing Muslim minority of Arakan which likely dates to the vassalage of the region to the Sultanate of Bengal in the late medieval period, most of the Rohingya probably are the descendants of peasants from Bengal, who were part of the great global migration which brought Tamils to Malaysia further south.

But, when the ancestors of most of the Rohingya were leaving Bengal a self-consciously Muslim and Bengali identity was inchoate at best. Elite culture in Bengal by the late Mughal period was the purview of Urdu speaking elites, and elite Bengali culture arose in the early 19th century with the Hindu bhadralok. The Rohingya detachment from a Bengali identity is to a great extent natural, insofar as their peasant ancestors were never part of the consciousness raising and nation-creation project of the 19th and early 20th centuries, whereby an elite nationalistic and Muslim Bengali identity emerged.


Open Thread, 11-29-2012

Filed under: Administration,Open Thread — Razib Khan @ 1:37 am

Update: You can leave comments now. But, you are forced to register with no third party login option. I know many of you don’t like the last, because you are emailing me about it. If the quantity of responses (<5, vs. the usually of ~50 for an “open thread”) on this thread is a measure I suspect that I’ll have to switch web-discussion mostly to Twitter or Facebook. I balk at registering to comment personally, so I totally understand.

As you may have noticed there are some issues with Discover Blog‘s transition to a new system. But once comments work again, feel free to post here. I’m busy with some other things right now besides the blog, so I’m going to take the current technical issues as an excuse to not post for a few days.

November 28, 2012

Agriculture, South India, Genetics

Filed under: Genetics — Razib Khan @ 6:57 pm

Population Differentiation of Southern Indian Male Lineages Correlates with Agricultural Expansions Predating the Caste System:

Previous studies that pooled Indian populations from a wide variety of geographical locations, have obtained contradictory conclusions about the processes of the establishment of the Varna caste system and its genetic impact on the origins and demographic histories of Indian populations. To further investigate these questions we took advantage that both Y chromosome and caste designation are paternally inherited, and genotyped 1,680 Y chromosomes representing 12 tribal and 19 non-tribal (caste) endogamous populations from the predominantly Dravidian-speaking Tamil Nadu state in the southernmost part of India. Tribes and castes were both characterized by an overwhelming proportion of putatively Indian autochthonous Y-chromosomal haplogroups (H-M69, F-M89, R1a1-M17, L1-M27, R2-M124, and C5-M356; 81% combined) with a shared genetic heritage dating back to the late Pleistocene (10–30 Kya), suggesting that more recent Holocene migrations from western Eurasia contributed <20% of the male lineages. We found strong evidence for genetic structure, associated primarily with the current mode of subsistence. Coalescence analysis suggested that the social stratification was established 4–6 Kya and there was little admixture during the last 3 Kya, implying a minimal genetic impact of the Varna (caste) system from the historically-documented Brahmin migrations into the area. In contrast, the overall Y-chromosomal patterns, the time depth of population diversifications and the period of differentiation were best explained by the emergence of agricultural technology in South Asia. These results highlight the utility of detailed local genetic studies within India, without prior assumptions about the importance of Varna rank status for population grouping, to obtain new insights into the relative influences of past demographic events for the population structure of the whole of modern India.


November 26, 2012

System migration!

Filed under: Uncategorized — Razib Khan @ 11:11 am

Just been notified that comments from now until Wednesday  may not be saved when the system updates on Wednesday.

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 25, 2012

Are you “Driftless”?

Filed under: Politics — Razib Khan @ 11:22 pm

GeoCurrents on the political anomaly of the “Driftless” zone of the upper Mississippi (via GLPiggy). The anomaly has to do with the fact that this area is very white, very rural, and not in the orbit of a larger cosmopolitan urban area (e.g., “Greater Boston,” which extends into New Hampshire). The post goes into much greater detail, but concludes with a request for more information. This is the area where local knowledge might be helpful.

I went poking around old county level presidential election maps, and I can’t see the Driftless blue-zone being a shadow or ghost of any past pattern. But, I did stumble upon again the 1856 presidential election map by county…can there be a better illustration of the “Greater Yankeedom” (the red are Republican voting counties, the first year that the Republicans were a substantial national party):

Addendum: Obviously not the whole North was Yankee. So who were the others? The ancestors of what in the 20th century become “white ethnics,” disproportionately urban Catholics (in this case, mostly Irish and German) were already Democratic leaning by this period. There were also old groups, like the Hudson Valley Dutch, as well as the merchant class of New York City, which were long anti-Yankee in their politics and sentiments. Not only that, but New York City was economically integrated with the South’s cotton economy to a greater extent than other zones of the North. And in places like Pennsylvania there were deep reserves of populist Democrats. Finally, across the southern half of the Midwest states the settlers were actually often from the Upper South states. The “Butternuts.”


“Are you from India”?

Filed under: Uncategorized — Razib Khan @ 5:45 pm

In the social circles that I move in (cosmopolitan, multiracial, liberal, well educated, etc. etc.) I don’t get asked the question “are you Indian?” or “Are you from India?” often. This is a big change from my youth. In the 1980s I was probably asked this nearly every week. Today if I am asked it is usually from a white or black American over the age of 40. That is, of the generation where “Where are you from?” had an exotic valence because not too many of their classmates were from/hard parents from elsewhere.

But a few days ago I was introduced to an old high school friend of my wife. To give some background, he’s a cultural Jew who lives in the Pacific Northwest, with a “New Age” orientation (so to speak). He greeted me with the “Are you Indian?” question, to which I responded apathetically with “my family is from Bangladesh.” Nevertheless, he decided to tell me about his friend from Bombay, and also asked me how I thought the chai was (I drink coffee). I found this all somewhat amusing, though tiresome (also, his wife was surprised that I didn’t know much about homeopathy, since it was big in India!). And yet I had a bigger meta issue which I was considering: is really useful to categorize brown folk/South Asians/Indians into one group?

Obviously to some extent it is. Pakistanis may protesteth, but to to Middle Eastern or Southeast Asians they’re just Indians-by-another-name, who happen to be Muslim. Our genetics, cuisine, to some extent language, folkways, unite us. And yet we’re also extremely varied. There is “Indian food” in a general sense, but there is also Indian food in a real regional sense. I don’t know much about Udupi cuisine, and what I know about Tandoori is from visiting Indian restaurants in the USA. There’s a lot of cultural detail about South Asia that I feel I people assume that I am aware of, which I’m not. Some of this could be my ignorance, but I suspect that a lot of it is just the fact that South Asia is diverse.


Going short and going long in terms of blog traffic

Filed under: Arnold Kling,Politics — Razib Khan @ 11:59 am

Arnold Kling took a break from blogging, but is coming back. But under an explicit set of personal guidelines. About This Blog:

I decided to go with my own blog, rather than return to EconLog, because I want to have total control over the blog content. I want to model a very particular style of discourse, as indicated by the tag line “taking the most charitable view of those who disagree.” In June, I wrote

Suppose we look at writing on issues where people tend to hold strong opinions that fit with their ideology. Such writing can

(a) attempt to open the minds of people on the opposite side as the author
(b) attempt to open minds of people on the same side as the author
(c) attempt to close minds of people on the same side as the author

So, think about it. Wouldn’t you classify most op-eds and blog posts as (c)? Isn’t that sort of pathetic?

My goal is to avoid (c). I will try to keep the posts here free of put-downs, snark, cheap shots, straw-man arguments, and taking the least charitable interpretation of what others say. So, if what you most enjoyed about my past blogging efforts were the put-downs, be prepared for disappointment with this incarnation.

I’ve been “around the block” for a long time in blog time. Around ~2002 and forward there was a naive initial moment when the fervor over the “War on Terror” resulted in some post-partisan good feeling, but that faded soon enough. Today the American Left and Right are rather insular when it comes to interaction and linking. Because most of the blogs I follow are science related, any political comments tend to be on the Left liberal end of the spectrum. To me the problem, if there is one, tends to be in the strawman/least charitable interpretation aspect that Kling mentions (aspects of raw and low style are easy to filter). As someone who is not liberal I find it curious when Left liberals fulminate against positions or motives which I don’t really even seen conservatives holding. It seems pointless over the long term, though it can result in greater in-group cohesion, and generate some psychic utils. A converse element are conservative bloggers who rage against ‘secular liberals,’ and routinely false positive me as liberal because I’m secular (the reality is outside of the internet most political liberals are not secular in their religious orientation in any case!).

An interesting issue here is that people who have a particular viewpoint don’t see their own viewpoints as viewpoints at all. Rather, their own viewpoints are positive descriptions of the world. So, for example, I once had an exchange with a reader who suggested that if I express any political viewpoints that would alienate readers, so I should avoid it. When I pointed out that most (though not all) science oriented weblogs seem to express conventional to radical Left liberal perspectives, he conceded the point. Because my own perspectives were at variance with the reader’s, the political posts were very salient, but on other science blogs they probably didn’t register as “political.”

In this vein I had dinner with a long time reader who told me that this weblog had helped shift his own political worldview over the past six years. It was interesting because my own political passions in the proximate sense (i.e., do I care if the president is a Republican or a Democrat?) are attenuated at best to a shadow of what they once were. I have opinions, but my interest in those opinions is rather marginal compared to science or historical topics. Nevertheless you can’t account for how you impact other people.

And that’s the sort of thing I suspect Arnold Kling is aiming for. Long term impact. The main skepticism I have is that are there even enough interlocutors in this domain? He’ll probably have to go solo and slowly accrue a following who shares his own philosophy.

November 22, 2012

Prop 37 vs. Obama (by county)

Filed under: Politics — Razib Khan @ 11:12 pm

Following up my request a reader crunched the numbers (here is his data table) to show the association between supporting supporting Proposition 37 and voting for Barack Obama by county in California:

From what I know this issue really polarized people in highly educated liberal enclaves in the state of California. Many of my Left non-scientist friends supported the measure because of an anti-corporate animus. But, another issue that sometimes came up was transparency and fair play, in a “teach the controversy” fashion. My own contention is on the scientific point there is no controversy.

Prop 37 vs. Obama (by county)

Filed under: Politics — Razib Khan @ 11:12 pm

Following up my request a reader crunched the numbers (here is his data table) to show the association between supporting supporting Proposition 37 and voting for Barack Obama by county in California:

From what I know this issue really polarized people in highly educated liberal enclaves in the state of California. Many of my Left non-scientist friends supported the measure because of an anti-corporate animus. But, another issue that sometimes came up was transparency and fair play, in a “teach the controversy” fashion. My own contention is on the scientific point there is no controversy.

Open Thread, 11-22-2012

Filed under: Open Thread — Razib Khan @ 1:11 am

If you aren’t too stuffed, ask! I plan to get my simultaneous review of The Signal and the Noise: Why So Many Predictions Fail-but Some Don’t and Uncontrolled: The Surprising Payoff of Trial-and-Error for Business, Politics, and Society up over the holiday weekend, but I’m going to be focused on other things besides the blog obviously. That being said, to be frank I don’t personally feel that the regular reader of this weblog would get much value from The Signal and the Noise (Nate Silver interviews Robin Hanson. I didn’t need to read his book to be aware of Robin Hanson’s ideas, he quite freely shares them to all curiosity seekers on the internet and in person).  Uncontrolled adds more value in my opinion because experiments in social science are more difficult, and probably more genuinely ground-breaking (if less sexy), than statistical inference.

Open Thread, 11-22-2012

Filed under: Open Thread — Razib Khan @ 1:11 am

If you aren’t too stuffed, ask! I plan to get my simultaneous review of The Signal and the Noise: Why So Many Predictions Fail-but Some Don’t and Uncontrolled: The Surprising Payoff of Trial-and-Error for Business, Politics, and Society up over the holiday weekend, but I’m going to be focused on other things besides the blog obviously. That being said, to be frank I don’t personally feel that the regular reader of this weblog would get much value from The Signal and the Noise (Nate Silver interviews Robin Hanson. I didn’t need to read his book to be aware of Robin Hanson’s ideas, he quite freely shares them to all curiosity seekers on the internet and in person).  Uncontrolled adds more value in my opinion because experiments in social science are more difficult, and probably more genuinely ground-breaking (if less sexy), than statistical inference.

Back to crunching personal genomic data

Filed under: Personal genomics — Razib Khan @ 12:54 am

Many months ago I told some of my friends that I’d run analyses of their 23andMe data, and report it back to them. A year ago I made the same promise to some of my readers. But life got in the way, and I’ve been very busy. I’m working on scripts to make the whole process efficient for me (if you want to know, I’m trying to get the output to be easy to merge many runs with CLUMPP and then produce DISTRUCT type outputs; I’ve done this with other Admixture outputs, but for various reasons the labeling gets messed up with my ‘personal’ project). But I’ve decided to at least start pushing some of the results live. I won’t be putting it in this space, probably razib.com. But I thought I would get your attention first. I know a lot of ID’s are missing, but I’ll add them later when I can find anything. And yes, I need to get back to African Ancestry too (that site was infested with a backdoor, so I had to yank it). This is all rather basic stuff, but I just don’t have the time to do things in a manual fashion, and the scripts I have for population sets don’t transfer over when I want to give individual friend results as well as population results.

The results in tabular format are here. And all individual results are here. In terms of the tech details, ~140,000 SNPs, ~3000 total individuals in the data set, at K = 11. I will probably be reporting K = 12 to K = 25 from now on (I’m just going to get 10> replicates and merge them).

November 21, 2012

A very special Thanksgiving to one and all!

Filed under: My Girl — Razib Khan @ 7:40 pm

Obama on the age of the earth

Filed under: creationism — Razib Khan @ 5:29 am

Jump to 9:00.

The crowds knows better than you?

Filed under: philosophy — Razib Khan @ 5:23 am

Justin Wolfers & Betsy Stevenson have a piece up in Bloomberg, Crowds Are This Election’s Real Winners. In The Signal and the Noise Nate Silver has a chapter on Wolfers’ belief that prediction markets are superior to the sort of quantitative analysis that is his stock & trade. The belief isn’t based on an intuition. One of Wolfers’ graduate students produced a paper showing that Intrade was actually better than FiveThirtyEight in 2008. Silver demurs in the chapter because he suggests that the model which Wolfers and his student lay out in the paper had some modifications which allowed for one to judge Intrade’s performance superior. I’m willing to accept Silver’s assertion here because I’ve seen enough economic models which are modulated just enough to produce elegant and clean results. That being said, the general tone of the chapter is such that in his heart Silver seems to agree that Wolfers is fundamentally correct in the long term. Prediction markets, when done right, are more powerful than any analytic an individual could cook up.

All that being said, the economist’ faith on the power of mass market signals (“the crowd”) often strikes natural scientists as peculiar. When talking about elections it does seem that the “crowds” are going to be superior to the judgement of individuals or powerful quantitative models (after all, elections are about crowds!).  But there is a long history of the crowd being wrong in the very specific areas of natural science which rely on contingent and formal fameworks to make non-obvious predictions on somewhat complex systems. But that’s because in some areas of the natural sciences humans have a systematic bias due to intuitive psychological tendencies. Aristotle’s model was just more intuitively plausible than those of his skeptics’ for a few thousand years. And quantum theory would never win a crowd-vote. One Bohr is worth a thousand other humans. I think this long history of the worthlessness of mass market intuition across large swaths of the territory of science is why many scientists find technocratic solutions very appealing. The formal reflections of the elect has worked miracles in physics, so why not “social physics” (i.e., economics)?

Obviously there’s a difference between the expertise of a nuclear physicist, an economist, a financial entertainer, and an astrologer. When a physicist speaks about physics, you listen, for they are describing the world. When an economist speaks about economics, you listen, because they are reflecting honestly what economists think about the world. When a financial entertainer speaks, you listen for laughs, because they are mixing substance and style to entertain you. When an astrologer speaks you are a fool to listen, because they are using the artifice of science to sell you nonsense.

Epistemology is hard. There is no “Swiss Army knife” which allows one to know how to know. In some circumstances the utilization of statistics is a matter of style, to firm up a flimsy supposition with the rigorous garb of quantity. The delusion of false precision. But in other domains statistical knowledge is highly informative. And there are areas where one can usefully deploy deterministic models.

The problem that crops up is when one swims in one lagoon of the intellectual pool where a particular suite of tools is useful, it is easy to forget that the utility of that kit may be conditional on the characteristics of that domain. Many physical scientists seem to have a tendency of assuming that there can be a simple and elegant technocratic solution (I believe that this is one reason engineers are attracted to religious fundamentalism). Meanwhile, I have observed before that biologists are often totally wedded to the Malthusian model for humans, when that model has not been fruitful for nearly a century. Biologists may be correct over the long term, but as an economist once observed, over the long term we’re all dead. Finally, economists can see markets everywhere, when sometimes it is not supply & demand, but ecology which is speaking. In A Farewell to Alms I note that Greg Clark argued that the emergence of lactase persistence was a sign of the longstanding high per capita income of Northern Europe, because Northern Europeans could afford to consume large quantities of milk. But of course there are ecological parameters which are relevant for how rational it is to engage in dairy-culture.

In the end, the only solution I offer is trial & error iteration. There is no market, no decision tree, which can guide us here. What works, works. What does not, does not. We muddle on.

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.

The Kindle price

Filed under: Kindle,Technology — Razib Khan @ 7:11 pm

I’ve had a Kindle for a few years now. I read a lot on it. And yet I observed something recently: I’ve stopped going to the library much. This is a big deal for me…probably since the age of 7 I’ve clocked in at least one visit to the public library per week in my life. I never turn books in past due because of the frequency with which I patronize the public or university libraries which I’ve had access to in life. Until recently. Now on occasion books go overdue, because I don’t go very often.

In the short term the Kindle has been a boon. But I’m not sure if it’s good for us in the long term. I’d rather pay more for a device which allowed for easier usage of different formats, as well as looser distribution policies.

Mine eyes have seen the glory; we are as gods!

Filed under: creationism — Razib Khan @ 6:52 pm

Earlier today Erick Erickson of RedState put up a long and meandering post titled “I Believe and Am Thankful”. As you might infer from the title it elaborates Erickson’s own theological position, and his stance toward the expression of faith in the public square. Because I am an atheist I disagree with many aspects of his position, and because I am not a liberal I agree with other elements of his argument. But there was one portion of which alarmed me a great deal, because I believe it displays an epistemological superificiality which is all too common. Erickson’s first paragraph is:

Marco Rubio is getting beaten up by the press for not decisively and convincingly saying he thinks the world is billions of years old. It has become the new litmus test in the media. Believing what was believed to be literally true for a few thousand years is now nutty. Christian homeschool kids, often taught that the world is not as old as some believe and who routinely kick the rear ends of the ivy prep kids in academics, are considered stupid.

There are two components to my reaction. One is rather general and abstract, while the other is specific. I will begin with the abstract. The fact is that you would be foolish to accept what people believed for “thousands of years” in many domains of natural science. When it comes to the ancients or the moderns in science always listen to the moderns. They are not always right, but overall they are surely more right, and less prone to miss the mark. In fact, you may have to be careful about paying too much attention to science which is a generation old, so fast does the “state of the art” in terms of knowledge shift. That was part of my critique of Richard Lewontin. A great evolutionary biologist of the 1960s, today Lewontin seems far behind the times, tackling issues near and dear to the 1970s, when we live in the post-genomic era.

Science is iterative. It is sloppy, but it does progress. We know so because it is through science we send men to the moon, and it is upon science that the material foundations of our civilization rest. You shall know it by its fruits, as science becomes engineering it moves from the abstract to the concrete, from the plausible and possible to the certain. It is a vast and abstruse contingent system of models, hypotheses, theories, laws, and data strewn about. But, it is arguably the greatest intellectual achievement of modern civilization. We may see through the glass darkly, but science is the bright flare in the night, illuminating a portion of existence, making it clear, precise, and crisp.

A generation ago there arose a movement within the scholarly community of anti-science obscurantists. The phenomenon was documented in works such as Higher Superstition. Though an innovation of the Post Modern cultural Left, this skepticism of scientific positivism, the progression of knowledge, has bled over to the cultural Right. In particular, through Phillip E. Johnson a critical theory inspired movement to ‘teach the controversy‘ arose. Modern Intelligent Design is clearly genetically descended from Young Earth Creationism, but has accrued to itself traits which arose in the milieu of the anti-science Left. In particular, a focus on skeptical critique, rejection of a modernist positive view of the universe, as well explicitly political attacks on science (See Alister McGrath’s Twilight of Atheism for an elaborated argument for why the death of modernism implies the revival of religion).

Science is special because there is no ancient wisdom. The ancients were fools, by and large. I mean no disrespect, but if you wish to design a rifle by Aristotelian principles, or treat an illness via the Galenic system, you are a fool, following foolishness. Science is the true ladder to heaven, anyone who has practiced it can not be help be amazed by its miraculous powers of prediction.

Non-scientific domains are not like this. A lawyer sees in the Corpus Juris Civilis a document which is different in degree, not kind. It is not obvious to me that modern ethics has progressed appreciably in substance as opposed to taste beyond Aristotle. The Iliad is still poetic greatness, in whose shadow moderns dwell. New Age reflections generally pale in comparison to the Bhagavad Gita. Marcus Aurelius’ Meditations can speak still to us down the ages.

There are many domains of knowledge which are permanent things, but science is not one of those. Rather, science is defined by the permanence of its object of study, the external world all around us. History shifts as history accrues. And the truisms of one age of economic history are not those of the subsequent.

The fool hath said in his heart, science is an idol. And yet it is not! For true men do suborn science for their own ends, making it subservient to their perversions. But that is no reflection on science, it is a reflection on men. And that is the important insight that American conservatives need to internalize.

It is entirely true that secular liberal journalists will attempt to goad conservative politicians into expressing opinions which reveal themselves to be in thrall to rubes. But there is no evading the fact that there is a simple response: accept that science says what it says, and move on. Equivocation and evasion do no good, and the reality is that if you fight science, you will lose. Science at any given moment is wrong, but this is a game that the house always wins, and history will not be on your side. The tide rises with science, and you will not hold it back by force of will.

When it comes to many aspects of heredity and behavior I’m confident that the modern cultural Left which still pines for the “blank slate” will have their reckoning. You can put off reality only so long, and the long war against the world as it is is always one of strategic retreat. Evolutionary biology is not novel or new science, it is old as biology goes, having come into form in the 19th century. It predates genetics, and certainly predates molecular biology. It is like a theoretical scaffold on other disciplines, it may not impinge on a day to day scale, but it illuminates quirks of function or structural features which would otherwise seem capricious.

All political persuasions are a mix of norms and assumptions about the way the world is arranged. When you make false assertion about the nature of things, you will make worthless inferences. The cultural Left which denies non-trivial differences between the sexes engages in faulty social engineering, because the science is not robust. Similarly, the cultural Right which denies the biological nature of much homosexuality does a disservice to its ultimate project of fostering virtue. Note that any assumption of what is does not here necessarily entail what ought to be. But it is much easier to achieve an ought if you accurately characterize the is.

Erick Erickson in this post makes much of the fact that secular liberals are relativists, and inconsistent hypocrites. Without disputing these assertions I would suggest that Erickson’s attitude toward Young Earth Creationists, indulgent, even respectful, falls into the same trap. He pulls his punches as to whether they are wrong, shifting into the shades of gray. But the objective reality is that Young Earth Creationists are wrong, and this is science known to a high degree of certitude. Erickson and his fellow travelers have no problem asserting the rightness of their religion, and the falseness of the atheists, but when it comes to established science they become as slippery as a doyen of Science Studies. Truth becomes subjective, malleable, a casual instrument in the culture wars. Science, another superstition of old white men? Perhaps, but a true one!

Knowledge is hard. We, as individual humans are stupid. Science is sloppy and noisy. But science got us to the moon, and science gave is antibiotics. Erick Erickson can talk about the miracles of his God made flesh, but we live in the age of miracles. What tech savvy conservatives who do not speak truth to Creationism are doing is analogous to the behavior of affluent upper middle Marxist academics, who enjoy the accoutrements of bourgeoise life, while giving lip service to the revolution. By their actions you shall know what lurks in their hearts! Their mouths speak lies for the convenience of the moment.

Finally, I want to take a step back and also observe that this whole argument rests on a false historical premise: that modern conservative Protestant fundamentalism was the Christian orthodoxy for the past 2,000 years. It is not. It was not. True, there has always been a strain of Christianity which was naively literalist, but for most of the history of the religion the fixation on the Bible as science manual would have seemed somewhat strange, in part because science did not truly exist. Modern Protestant fundamentalism is intuitively coherent, and we see its forebears during the Reformation. Interestingly, Catholic apologists immediately pointed to the inconsistent nature of portions of the Bible as one argument against the Protestant claim for sola scriptura.* But this is a new argument, not an old one, and the battle between science and religion in this case is a clash of two moderns, not a modern an ancient.

So here we are. Modern American conservatism must bend a knee to a manifestly false model of the world, because of a manifestly false perception of the history of the Western tradition. Where can it lead us? One thing that it leads us to is that we have to have this discussion every four years, as secular liberal journalists know very well that many elite conservatives do not agree with the grassroots on matters of fact when it comes to evolution. It is a useful wedge. There is a simple way to put this to bed: be unapologetic about what the facts of science are, and do not equivocate to the base. They have nowhere else to go, and the reality is that evolution is a far less pressing matter than tax rates or abortion in any case. Many elements of the Democratic base accept without too much grumbling the social liberalism of the party’s political elite. Could it be that much more difficult for conservative grassroots to accept that the conservative elite accepts modern science?

* I do not mean to imply here that pre-modern Christians were all believers in the old earth. Rather, I mean to suggest that the modern discussion about Biblical conflicts with science makes little sense before 1800, because serious Christians thinkers did not imagine the debate in these terms at all.

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