tag:blogger.com,1999:blog-100830472010-02-19T16:55:04.615-08:00Gene ExpressionRazibnoreply@blogger.comBlogger3288125tag:blogger.com,1999:blog-10083047.post-76798948594634077852010-02-19T16:40:00.000-08:002010-02-19T16:55:05.150-08:00Armenian genetics<a href="http://armenianow.com/news/21032/armenian_genetic_history">Armenian genes: Scientist in Yerevan launches a project to reveal genetic history of the nation</a>. The description of the science in the piece is <b><i>very</i></b> garbled. But, it would be nice to elucidate the genetics of Armenians in more detail. Their language, like Greek and Albanian, is a singleton in the <a href="http://www.wsu.edu/~gordonl/S05/354/IE-Germanic_files/image002.jpg">Indo-European family tree</a>. Additionally, the Armenian nation has an extremely <a href="http://en.wikipedia.org/wiki/Kingdom_of_Armenia#History">long history</a>. Their identity crystallized in the wake of the Persian and Hellenistic Empires just like that of the Jews.<br /><br />Demographically we know that historically much of eastern Anatolia was dominated by Armenians. Many of the <a href="http://en.wikipedia.org/wiki/Macedonian_dynasty">prominent</a> Byzantine dynasties were of Hellenized Armenian lineages. I would predict that one will likely find that most of the Turks of eastern Anatolia would cluster with Armenians, just as those Turks from the west and coastal Anatolia might cluster more with Greeks, because it seems likely that the ethnogenesis of most Turks in Anatolia was a process whereby Greeks and Armenians assimilated to the identity of a small minority of eastern Turkish invaders.<div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-7679894859463407785?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>Razibnoreply@blogger.comtag:blogger.com,1999:blog-10083047.post-77523373857199006752010-02-16T12:19:00.000-08:002010-02-16T12:54:08.288-08:0010 questions for Peter Turchin<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.gnxp.com/blog/uploaded_images/Turchin_P-750719.jpg"><img style="float:left; margin:0 10px 10px 0;cursor:pointer; cursor:hand;width: 220px; height: 279px;" src="http://www.gnxp.com/blog/uploaded_images/Turchin_P-750717.jpg" border="0" alt="" /></a><br /><a href="http://www.eeb.uconn.edu/people/turchin/">Peter Turchin</a> has appointments in ecology & evolution and mathematics at the University of Connecticut. He is the author of <a href="http://www.amazon.com/Peter-Turchin/e/B001IU2M2K/ref=sr_tc_2_0?qid=1266352405&sr=1-2-ent">five books</a>, three of which, <a href="http://www.amazon.com/exec/obidos/ASIN/0691116695/geneexpressio-20">Historical Dynamics</a>, <a href="http://www.amazon.com/exec/obidos/ASIN/0691136963/geneexpressio-20">Secular Cycles</a> and <a href="http://www.amazon.com/exec/obidos/ASIN/0452288193/geneexpressio-20">War and Peace and War</a>, outline tests of models derived from the new field of <a href="http://cliodynamics.info/">cliodynamics</a>. I have reviewed <a href="http://www.gnxp.com/blog/2008/08/historical-dynamics-and-contingent.php">Historical Dynamics</a> and <a href="http://www.gnxp.com/blog/2008/08/cliodynamics-rise-fall-of-empires-and.php">War Peace and War</a>. Below are 10 questions.<br /><br /><span class="fullpost"><br /><span style="font-weight:bold;">1) Your initial research program was in quantitative ecology. What prompted your switch into modeling historical dynamics?</span><br /><br />At some point I simply realized that most of the big questions in population dynamics were solved, or about to be solved. So I wrote my book on <a href="http://www.amazon.com/exec/obidos/ASIN/0691090211/geneexpressio-20">Complex Population Dynamics</a>, where I synthesized what I thought these answers were, and started looking for some more challenging field. It turned out that the last scientific discipline that has not yet been mathematized was history. At first, I thought that I would simply write some mathematical models for historical dynamics, as a hobby. But once I did that, I wanted to see whether their predictions could be tested with data. To my great surprise, it turned out that there is a lot of quantitative data for historical processes, so testing models and theories is eminently possible. As a result, at this point my main thrust is empirical, rather than mathematical; or, more precisely, I am primarily interested in testing theories with data.<br /><br /><span style="font-weight:bold;">2) You have been at the forefront of creating the new field of "cliodynamics." Is this necessary? It seems that economists have been at the forefront of cliometrics and they have their own theoretical framework. What's the value-add of your specific framework?<br /></span><br />I believe that it is necessary. Historical processes are very complex, they involve not only economic, but also demographic, social, political, ideological, climatological, and many other kinds of factors. Probably because one has to approach history with such a massively interdisciplinary approach, it is the last of social sciences to become amenable to the scientific method. I have a lot of respect for economists, but in many ways it is difficult for them to make progress with history. For example, until recently, they have been hobbled with a bankrupt model of <i>homo economicus</i>. The other problem is that traditional economic theory focuses too much on equilibria, so that also does not predispose economists to deal well with historical dynamics. Both of these barriers are being dismantled right now, but still economists are not in the forefront of the cliodynamic community. We have much greater representation from historical sociologists, anthropologists, and political scientists.<br /><br /><span style="font-weight:bold;">3) In terms of discipline, where have the reactions been most positive and most negative to your project?</span><br /><br />Positive response came from the disciplines named above - historical sociology, social and cultural anthropology, political science, economic and social history, demogrpahy. There has not been really much of a negative reaction. The main defensive mechanism is to ignore us, which is what 95% of historians do. That's fine with me. In fact, I was pleasantly surprised by the positive reception of these ideas among historical social scientists and the (estimated) 5% of historians. It suggests to me that the time of cliodynamics has come. Incidentally, we are launching a peer-reviewed journal this year.<br /><br /><span style="font-weight:bold;">4) I have speculated that the fact that you were born in the former Soviet Union might have made you more open to the concept of a scientific study of history, seeing as how Marxist thought originated as an attempt to scientifically describe the human past and predict its future. Do you think that your current interests might have some relationship to your cultural background, or not?</span><br /><br />Yes, I think that my Russian background was a strong contributing factor, but no, not because of Marxism. You have to realize that before I started my historical project I had completely rejected Marxism, because of my upbrining (my father was a human rights activist in the Soviet Union and was exiled abroad in late 1970s). Only recently, as a result of becoming a social scientist, I learned to appreciate certain insights of Marx and incorporate them into my theories, although I am not a Marxist by any stretch of imagination. The Russian factor, I believe, comes into play because Russians tend to be very broad thinkers. As I think Dostoyevsky once said, the Russian is very broad, I would narrow him down, or something like that. So Russians have a tendency to produce cosmic theories (there is even a philosophical current called Russian Cosmism). In my work I attempt to integrate this Russian tendency with the Anglo-Saxon practicality and empiricism.<br /><br /><span style="font-weight:bold;">5) You make recourse to group selection models in your scholarship. But the work I am familiar with seems to focus on cultural group selection. What do you think of biological level group selection posited by Samuel Bowles for hunter-gatherers, and its possible relevance to agricultural populations?</span><br /><br />I think that group selection mechanisms work at both genetic and cultural levels, and also on gene-culture interactions. The mix of factors have been changing from primarily genetic in the early human evolution to much more cultural today. However, genetic evolution continues, so even today it's not 100% cultural. There is a preprint on my <a href="http://cliodynamics.info/">cliodynamics site</a>, in which I focus on evolution of ultrasociality, our ability to form cooperative groups of millions of individuals, and there my main emphasis is on cultural group selection.<br /><br />One thing that we should not expect is a neat separation between genes and culture. Coevolution of these two information carriers is where the action is.<br /><br /><span style="font-weight:bold;">6) In your models of the rise and fall of agricultural-based polities you seem to emphasize the importance of institutional religions in generating "meta-ethnic" identities. One of the historical quirks which scholars have noted is the rise of world religions between 600 BC and 600 AD, and the relative stability in number of religions after that period. Do you have any explanation for this pattern, or is there nothing to be explained?</span><br /><br />In fact, this is one of the most striking patterns in history, and it fits very neatly with my theories. Rather than repeat myself, let me direct your readers to my recent artcile, a reprint of which is posted here:<br /><br /><a href="http://cliodynamics.info/PDF/Steppe_JGH_reprint.pdf">http://cliodynamics.info/PDF/Steppe_JGH_reprint.pdf</a><br /><br />See p. 201 for my explanation of the Axial Age. And then check out the section on the Middle East during the Axial Age (p. 209).<br /><br /><span style="font-weight:bold;">7) I believe in <a href="http://www.amazon.com/exec/obidos/ASIN/1563247313/geneexpressio-20">China: A Macro History</a>, by Ray Huang, he notes that the interregnums between Chinese dynasties became shorter and shorter. Is this explicable through your models of historical processes?</span><br /><br />Yes, and the same observation was made for other world regions by Victor Lieberman in his book, <a href="http://www.amazon.com/exec/obidos/ASIN/0521530369/geneexpressio-20">Strange Parallels</a>, the second volume of which was recently published. I think that the case for cultural evolution of state capacity is quite convincing - each new state starts not from a blank page, but already equipped with techniques of political integration that were developed during previous attempts. As a result, both the scale of polities and their cohesion tend to increase with time, and interregnum periods become shorter.<br /><br /><span style="font-weight:bold;">8) You observe the importance of meta-ethnic frontiers across history.<br />In the modern world with ease of travel and communication it seems that spatial boundaries are less relevant, as civilizations seem somewhat intercalated with each other (e.g., Western enclaves in the Third World, Muslim diasporas in the West, Chinese in Africa, etc.). Is the concept of a meta-ethnic frontier transferable to the modern context?</span><br /><br />I think it is, although at this point this is purely speculation. The above-mentioned Victor Lieberman has another striking idea, that modern Europeans are really 'White Inner Asians'. So after 1500 the primary locus of cultural evolution shifted from steppe frontiers to European colonial frontiers. We are probably still in the same era, so the most intense evolution occurs where Western societies impinge on other societies.<br /><br />Also don't forget that ethnic and religious diasporas were not an invention of modernity. What is more important is that information flows today are much less local. So a person in Saudi Arabia, a thousand kilometers from Iraq, can see the news about Abu Ghraib in real time, and perhaps with visual material, and decide to become a mujahedeen. So my guess is that the basic dynamic is still playing out, but it's not as localized in space as it was prior to modern communications.<br /><br /><span style="font-weight:bold;">9) Is there insight about the modern post-Malthusian world we can obtain from the secular cycles of the past?</span><br /><br />My working hypothesis is that the two out of three mechanisms of the demographic-structural theory, elite overproduction and state fiscal fragility, continue to operate in the modern world. See the answer to the next question.<br /><br /><span style="font-weight:bold;">10) What's your next big project?</span><br /><br />My main project on which I am currently working is a demographic-structural analysis of American history, from 1780 to the present. So we will see whether the hypothesis, to which I alluded under #9 above, will be borne out by the empirical analysis.</span><div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-7752337385719900675?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>Razibnoreply@blogger.comtag:blogger.com,1999:blog-10083047.post-79542140145375808422010-02-14T08:37:00.000-08:002010-02-14T09:56:14.998-08:00Small genetic effects do not preclude drug development<a href="http://scienceblogs.com/geneticfuture/2010/02/the_end_for_the_decodeme_perso.php?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+scienceblogs%2Fgeneticfuture+%28Genetic+Future%29">Daniel MacArthur points</a> me to <a href="http://www.newsweek.com/id/233494">a Newsweek article</a> on the bankruptcy of Decode Genetics. The author describes (one of) Decode's problems like this:<blockquote>The genetics of illness turned out to be more complex than researchers expected. At deCODE and elsewhere, the new genes linked to common diseases turned out to be rare or to have only small effects on individual risk. That killed any prospect of using deCODE's discoveries to make blockbuster drugs.</blockquote> The leap--that small genetic effect sizes means no prospects of drug discovery--sounds reasonable, but is actually wrong. Here's an example of why:<br /><br />Consider a trait like, say, cholesterol levels. <a href="http://www.nature.com/ng/journal/v41/n1/full/ng.269.html">Massive genome-wide association studies have been performed on this trait</a>, identifying a large number of loci of small effect. One of these loci is HMGCR, coding for <a href="http://en.wikipedia.org/wiki/HMG-CoA_reductase">HMG-CoA reductase</a>, an important molecule in cholesterol synthesis. The allele identified increases cholesterol levels by 0.1 standard deviations, meaning a genetic test would have essentially no ability to predict cholesterol levels. By the logic of the Newsweek piece, any drug targeted at HMGCR would have no chance of becoming a blockbuster. <br /><br />Any doctor knows where I'm going with this: one of the best-selling groups of drugs in the world currently are <a href="http://en.wikipedia.org/wiki/Statin">statins</a>, which inhibit the activity of (the gene product of) HMGCR. Of course, statins have already been invented, so this is something of a cherry-picked example, but my guess is that there are tens of additional examples like this waiting to be discovered in the wealth of genome-wide association study data. Figuring out which GWAS hits are promising drug targets will take time, effort, and a good deal of luck; in my opinion, this is the major lesson from Decode (which is not all that surprising a lesson)--drug development is really hard.<div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-7954214014537580842?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>p-terhttp://www.blogger.com/profile/03756271491303196763noreply@blogger.comtag:blogger.com,1999:blog-10083047.post-82926387389484904002010-02-12T07:17:00.000-08:002010-02-12T07:26:23.471-08:00Homo erectus and EDAR?In <a href="http://whyevolutionistrue.wordpress.com/">Why Evolution is True</a>, <a href="http://whyevolutionistrue.wordpress.com/">Jerry Coyne</a> has the following parenthetical aside about population variation in morphology in <i>H. erectus</i>:<br /><blockquote>(<i>H. erectus</i> from China...had shovel-shaped incisor teeth not found in other populations)</blockquote> This stopped me dead in my tracks: modern East Asian populations have similar tooth morphology, <a href="http://www.cell.com/AJHG/abstract/S0002-9297%2809%2900402-9">caused in part by a positively-selected nonsynonymous change in the gene EDAR</a>. Could this be an example of convergent evolution of tooth morphology in hominins? <br /><br />However, a cursory google suggests that shovel-shaped incisors might be thought to be a trait general to <i>H. erectus</i>, not specific to Asian populations. Can anyone clarify this?<div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-8292638738948490400?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>p-terhttp://www.blogger.com/profile/03756271491303196763noreply@blogger.comtag:blogger.com,1999:blog-10083047.post-60528638320881352272010-02-10T01:03:00.001-08:002010-02-10T01:30:14.084-08:00Low IQ correlated with cardiovascular disease?<a href="http://www.sciencedaily.com/releases/2010/02/100209200754.htm">Second Only to Cigarette Smoking in Large Population Study</a>:<br /><blockquote>While lower intelligence scores -- as reflected by low results on written or oral tests of IQ -- have been associated with a raised risk of cardiovascular disease, no study has so far compared the relative strength of this association with other established risk factors such as obesity, smoking and high blood pressure. Now, a large study funded by Britain's Medical Research Council, which set out to gauge the relative importance of IQ alongside other risk factors, <b>has found that lower intelligence scores were associated with higher rates of cardiovascular disease and total mortality at a greater level of magnitude than found with any other risk factor except smoking.</b><br /><br />...<br /><br />The relative strengths of the association were measured by an "index of inequality," which summarised the relative risk of a health outcome (cardiovascular death) in the most disadvantaged (high risk) people relative to the most advantaged (low risk). This relative index of inequality for the top five risk factors was found to be 5.58 for cigarette smoking, 3.76 for IQ, 3.20 for low income, 2.61 for high systolic blood pressure, and 2.06 for low physical activity.<br /><br />The investigators note "a number of plausible mechanisms" whereby lower IQ scores could elevate cardiovascular disease risk, notably the application of intelligence to healthy behaviour (such as smoking or exercise) and its correlates (obesity, blood pressure). <b>A further possibility, they add, "is that IQ denotes 'a record' of environmental insults" (eg, illness, sub-optimal nutrition) accumulated throughout life.</b></blockquote><br /><br />Related, <a href="http://www.stanford.edu/~pleslie/calories.pdf">Calorie Posting in Chain Restaurants</a>:<br /><blockquote>...In Table 5 we present estimates of how the effect of calorie posting on calories per transaction differs across sub-groups. The estimates in column (1) are based on the transaction data. Although the anonymous transaction data contain no information about the demographics of the consumers who made each transaction, we do know the store location of each transaction, and census data provide us with zip-level demographics. <b>Using this information, we find that the decrease in calories per transaction was larger in zips with higher income and in zips with more education</b> (i.e., more people with college degrees).</blockquote><div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-6052863832088135227?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>Razibnoreply@blogger.comtag:blogger.com,1999:blog-10083047.post-78337629291329134212010-02-10T00:56:00.000-08:002010-02-10T01:28:20.868-08:00Jersey Shore nicknameWhat's your <i>Jersey Shore</i> nickname? I like "The Prediction" for myself.<div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-7833762929132913421?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>Razibnoreply@blogger.comtag:blogger.com,1999:blog-10083047.post-6874693172502026102010-02-09T23:52:00.000-08:002010-02-10T00:29:28.591-08:00Books & guidance<a href="http://motherjones.com/kevin-drum/2010/02/read-more-books">Read More Books!</a>:<br /><blockquote>If you really want to understand any issue more complex than Brad and Angelina's marital status, there's really no substitute for a book. Not instead of blogs and newspapers and Twitter, but in addition to them. So: read more books! They're good for you.</blockquote><br /><br />I've heard and read about how awesome Charles Darwin was as a thinker, but I had to (re)<a href="http://scienceblogs.com/gnxp/2010/02/charles_darwin_was_a_genius_i.php">read</a> <a href="http://www.amazon.com/exec/obidos/ASIN/0451529065/geneexpressio-20/">The Origin of Species</a> to really <i>grok</i> what was being communicated here. So yes, books are important. The point that the <b>content</b> of what is being examined is critica can't be overemphasized.<br /><br />It seems that disciplines which exhibit a great deal of tight contingency, such as the natural sciences, are easier to digest in purely non-book form, than those more humanistic domains which are messier and less causally clear in the network of the relationship of facts to frameworks. As an example, very little of Charles Darwin's argument in <a href="http://www.amazon.com/exec/obidos/ASIN/0451529065/geneexpressio-20/">The Origin of Species</a> was illuminating as such, it was by and large integrated seamlessly into the body of science if it was worthy, and discarded if it was not. This applies much more forcefully to the physical sciences which have been more strictly formalized. There is also the problem that if you picked up a scholarly book which discussed evolutionary fitness landscapes or the physics of quasars <b>it would probably be unintelligible to you unless you had absorbed the prerequisite scholarship.</b> The structure of learning in extremely contingent disciplines is <i>relatively</i> straightforward. If you want to learn quantum physics, there are necessarily specific math and physics prerequisites. If you want to learn about Russian history from the time of Ivan the Terrible to the rise of the Romanov dynasty, some prior knowledge of late Byzantine history might be useful to understand the cultural-political roots of Russian Orthodoxy, but it is not necessary.<br /><br />When it comes to "softer" disciplines I think books are critical, because it is so easy to mislead yourself on the shape of scholarship. When I occasionally hear Creationists observe that there is a scientific controversy about evolutionary theory, or even more blatantly that evolutionary theory has fallen into disrepute within biology, they are either being lied to, or, they are lying. It is simply impossible to avoid the fact that there is no alternative universe of Creationist scholarship which has a credible scientific framework which explains the pattern and nature of biological diversity. But what about a discipline such as economics, one of the "harder" domains outside of natural science? You'll get a very different perspective if you read <a href="http://gregmankiw.blogspot.com/">Greg Mankiw</a> (PhD, MIT) vs. <a href="http://krugman.blogs.nytimes.com/">Paul Krugman</a> (PhD, MIT). More outlandishly, many individuals with a political ideology of libertarianism are strongly attracted to the <a href="http://en.wikipedia.org/wiki/Austrian_School">Austrian school</a> of economics, despite the fact that this is a totally marginalized heterodox tradition today. In this case, normative preferences generate a positive feedback loop in terms of how one explores the sample space of scholarship. One can debate whether the marginalization of Austrian economics is justified or not (see <a href="http://www.amazon.com/exec/obidos/ASIN/080184391X/geneexpressio-20/">The Eclipse of Darwinism</a>), but it is also an empirical fact that it is marginalized.<br /><br />Reading a wide range of books is a good way to diminish the power of preferences when exploring scholarly landscapes with which one is unfamiliar. When searching for journal articles it becomes easy to get caught in circular networks of citation, or fixating on particular journals which one finds congenial. Additionally, in less contingent disciplines the synoptic vision of a scholar who has dedicated their life to absorbing and reprocessing a mountain of data and generating insight and inference can often be helpful. If they are honest they will sample from the distribution of data in a manner which is not selection biased, something that you as an outsider will likely not be able to do because you do not know the shape of the distribution.<div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-687469317250202610?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>Razibnoreply@blogger.comtag:blogger.com,1999:blog-10083047.post-5675972810129802152010-02-09T01:04:00.000-08:002010-02-10T00:17:42.632-08:00Gene Expression SurveyThat time of the year. Please take the <a href="http://www.AdvancedSurvey.com/default.asp?SurveyID=70954" target="_blank">Gene Expression Survey</a>. I'll put up the analysis and the csv file next week. I have the usual questions, but also added a few more that might seem a bit weird. There are 30 questions total, and you don't need to answer all of them, but as I said the more you answer the more data there'll be. I did a trial run and it took less than 5 minutes; most people can answer a question about their sex or religious identity pretty quickly.<br /><br /><b>Update:</b> You can view the <a href="http://www.advancedsurvey.com/results/public_results.asp?SurveyID=70954">results of the survey here</a>.<div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-567597281012980215?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>Razibnoreply@blogger.comtag:blogger.com,1999:blog-10083047.post-62917353897668975972010-02-08T11:22:00.000-08:002010-02-08T11:25:24.404-08:00Delayed childbearing & autism<a href="http://www3.interscience.wiley.com/journal/123275763/abstract?CRETRY=1&SRETRY=0">Independent and dependent contributions of advanced maternal and paternal ages to autism risk</a>:<br /><blockquote> Reports on autism and parental age have yielded conflicting results on whether mothers, fathers, or both, contribute to increased risk. We analyzed restricted strata of parental age in a 10-year California birth cohort to determine the independent or dependent effect from each parent. Autism cases from California Department of Developmental Services records were linked to State birth files (1990-1999). Only singleton births with complete data on parental age and education were included (<em>n</em>=4,947,935, cases=12,159). In multivariate logistic regression models, advancing maternal age increased risk for autism monotonically regardless of the paternal age. Compared with mothers 25-29 years of age, the adjusted odds ratio (aOR) for mothers 40+ years was 1.51 (95% CI: 1.35-1.70), or compared with mothers <25 years of age, aOR=1.77 (95% CI, 1.56-2.00). In contrast, autism risk was associated with advancing paternal age primarily among mothers <30: aOR=1.59 (95% CI, 1.37-1.85) comparing fathers 40+ vs. 25-29 years of age. However, among mothers >30, the aOR was 1.13 (95% CI, 1.01-1.27) for fathers 40+ vs. 25-29 years of age, almost identical to the aOR for fathers <25 years. Based on the first examination of heterogeneity in parental age effects, it appears that women's risk for delivering a child who develops autism increases throughout their reproductive years whereas father's age confers increased risk for autism when mothers are <30, but has little effect when mothers are past age 30. <b>We also calculated that the recent trend towards delayed childbearing contributed approximately a 4.6% increase in autism diagnoses in California over the decade.</b> <br /></blockquote><br /><br />See <a href="http://www.sciencedaily.com/releases/2010/02/100208102411.htm?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed:+sciencedaily+(ScienceDaily:+Latest+Science+News)&utm_content=Google+Reader">ScienceDaily</a> for more detail.<div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-6291735389766897597?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>Razibnoreply@blogger.comtag:blogger.com,1999:blog-10083047.post-72576659948556233012010-02-06T21:17:00.000-08:002010-02-08T10:11:31.463-08:00Beautiful butterflies & localized adaptationTwo new papers are out in <i>PLoS Genetics</i> which make inferences about adaptation using butterfly species which exhibit <a href="http://en.wikipedia.org/wiki/M%C3%BCllerian_mimicry">Mullerian mimicry</a>. I'll give the author summaries instead of the abstracts.<br /><br /><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000794?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed:+plosgenetics/NewArticles+(PLoS+Genetics:+New+Articles)&utm_content=Google+Reader">Genomic Hotspots for Adaptation: The Population Genetics of Mullerian Mimicry in the Heliconius melpomene Clade</a>:<br /><blockquote>The diversity of wing patterns in Heliconius butterflies is a longstanding example of both Mullerian mimicry and adaptive radiation. The genetic regions controlling such patterns are "hotspots" for adaptive evolution, with small regions of the genome controlling major changes in wing pattern. Across multiple hybrid zones in Heliconius melpomene and related species, we no find no strong population signal of recent selection. Nonetheless, we find significant associations between genetic variation and wing pattern at multiple sites. <b>This suggests patterning alleles are relatively old, and <i>might be a better model for most natural adaptation</i>, in contrast to the simple genetic basis of recent human-induced selection such as pesticide resistance.</b> Strikingly, across the region controlling the red forewing band, a very strong association with phenotype implicates three genes as potentially being involved in control of wing pattern. One of these, a kinesin gene, shows parallel differences in expression levels between divergent forms in the two mimetic species, making it a strong candidate for control of wing pattern. These results show that mimicry involves parallel changes in gene expression and strongly suggest a role for this gene in control of wing pattern.</blockquote><br /><br /><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000796">Genomic Hotspots for Adaptation: The Population Genetics of Mullerian Mimicry in Heliconius erato</a>:<br /><blockquote>Identifying the genetic changes responsible for beneficial variation is essential for understanding how organisms adapt. Here, we use a combination of mapping, population genetic analysis, and gene expression studies to identify the genomic regions responsible for phenotypic evolution in the Neotropical butterfly Heliconius erato. H. erato, together with its co-mimic H. melpomene, have undergone parallel and concordant radiations in their warningly colored wing patterns across Central and South America. The "genes" underlying the H. erato color pattern radiation <b>are classic examples of Mendelian loci of large effect and are under strong natural selection. Nonetheless, we do not see a clear molecular signal of recent natural selection, suggesting that the H. erato color pattern radiation, or the alleles that underlie it, may be quite old.</b> Moreover, rather than being single locus, the genetic patterns suggest that multiple, widely dispersed loci may underlie pattern variation in H. erato. One of these loci, a kinesin gene, shows parallel expression differences between races during wing pattern formation in both H. erato and H. melpomene, suggesting that it plays an important role in pattern variation. High rates of recombination within naturally occurring H. erato hybrid zones mean that finer genetic dissection will allow us to localize causative sites and better understand the history and molecular basis of this extraordinary adaptive radiation.</blockquote><br /><br />Here's a section from the first paper which I found intriguing:<br /><blockquote><b>The results therefore appear to support the 'shifting balance' model for the evolution of Heliconius colour pattern races</b>...whereby novel wing patterns arise and spread through otherwise continuous populations behind moving hybrid zones...The 'Pleistocene refuge' model seems less likely, as recent contact after extended periods of geographic isolation would presumably have left a stronger signal of genetic differentiation between divergent races, perhaps across the genome but especially more strongly in regions linked to patterning loci...</blockquote><br /><br />I have no idea why they necessarily think this validates the shifting balance. You can see David's <a href="http://www.gnxp.com/MT2/archives/000629.html">critique</a> of the model, but reading <a href="http://www.amazon.com/exec/obidos/ASIN/0226684733/geneexpressio-20/">Will Provine's intellectual biography of Sewall Wright</a> it seems that the shifting balance sometimes becomes the evolutionary genetic version of "it's complicated."* What they seem to have done here though is refute a simple model of powerful selective sweeps giving rise to these morphs recently. Rather, these seem to be ancient local adaptations, whose frequencies and genetic architectures are perhaps perturbed by long term exogenous (e.g., environment) and endogenous (e.g., complex frequency dependencies) dynamics.<br /><br />Despite my lack of clarity on a few theoretical issues, I found the papers very interesting, and haven't really processed them fully.<br /><br /><b>Citation:</b> <br /><br />Baxter SW, Nadeau NJ, Maroja LS, Wilkinson P, Counterman BA, et al. 2010 Genomic Hotspots for Adaptation: The Population Genetics of Mullerian Mimicry in the Heliconius melpomene Clade. PLoS Genet 6(2): e1000794. doi:10.1371/journal.pgen.1000794<br /><br />Counterman BA, Araujo-Perez F, Hines HM, Baxter SW, Morrison CM, et al. 2010 Genomic Hotspots for Adaptation: The Population Genetics of Mullerian Mimicry in Heliconius erato. PLoS Genet 6(2): e1000796. doi:10.1371/journal.pgen.1000796<br /><br />* I see one reference to <a href="http://www.gnxp.com/blog/2005/07/through-rugged-roads-of-gene-land.php">epistasis</a> in both papers, and that concept is very important in the shifting balance. Though I assume the <a href="http://en.wikipedia.org/wiki/Linkage_disequilibrium">LD</a> and supergenes might point to that.<div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-7257665994855623301?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>Razibnoreply@blogger.comtag:blogger.com,1999:blog-10083047.post-9326729112035736122010-02-06T00:52:00.000-08:002010-02-06T00:54:30.306-08:00Eliezer Yudkowsky & Razib Khan on bloggingheads.tv<embed type="application/x-shockwave-flash" src="http://static.bloggingheads.tv/maulik/offsite/offsite_flvplayer.swf" flashvars="playlist=http%3A%2F%2Fbloggingheads%2Etv%2Fdiavlogs%2Fliveplayer%2Dplaylist%2F25848%2F00%3A00%2F61%3A00" height="288" width="380"></embed><div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-932672911203573612?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>Razibnoreply@blogger.comtag:blogger.com,1999:blog-10083047.post-64835121375212055632010-02-05T17:59:00.000-08:002010-02-05T18:07:48.999-08:00Hayek vs. KeynesYou've probably watched the Hayek vs. Keynes rap by now:<br /><br /><object width="560" height="340"><param name="movie" value="http://www.youtube.com/v/d0nERTFo-Sk&hl=en_US&fs=1&"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/d0nERTFo-Sk&hl=en_US&fs=1&" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="560" height="340"></embed></object><br /><br />Am the only one who was a little weirded out by the incongruity of John Maynard Keynes kickin' it with the honeys in the back of the limo? It isn't as if he was exactly on the <a href="http://en.wikipedia.org/wiki/John_Maynard_Keynes#Personal_life">down-low</a>. He was a freak, swinging both ways, though not symmetrically....<div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-6483512137521205563?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>Razibnoreply@blogger.comtag:blogger.com,1999:blog-10083047.post-81069744029499264502010-02-05T09:23:00.000-08:002010-02-05T10:42:15.322-08:00Language goes extinct, human race to follow....<a href="http://news.bbc.co.uk/2/hi/south_asia/8498534.stm">Last speaker of ancient language of Bo dies in India</a>:<br /><blockquote>Professor Anvita Abbi said that the death of Boa Sr was highly significant because one of the world's oldest languages - Bo - had come to an end.<br /><br />...<br /><br />"It is generally believed that all Andamanese languages might be the last representatives of those languages which go back to pre-Neolithic times," Professor Abbi said.<br /><br />"The Andamanese are believed to be among our earliest ancestors."</blockquote><br /><br />I have a tendency to eye roll when people come out with these weepy stories about dying languages. When a language dies a people dies, more or less. No doubt there are particular stories, memories passed down which maintain continuity of identity, which disappear. But <b>humans do not necessarily die.</b> If members of obscure tribe X all learn English, or Chinese, tribe X as tribe X disappears, more or less. This is not trivial, I believe most humans would prefer that the cultural forms which pervade their own lives would pass down to future generations. Memory is to a great extent the only form of immortality we've had access to. But for members of obscure tribe X learning a widely spoken language is often a boon, and brings great benefit as they can engage in more fruitful exchanges with the broader human race. The implicit contract that peoples make with their own ancestors extracts too high a cost at some point, and when the present ceases to uphold its pact with the past, the past becomes obscured in the mists.<br /><br />On a specific note about this article, the Andaman Islanders are actually a real concrete human population, they're not "among our earliest ancestors." Additionally, I thought that languages which were purely oral tended evolve faster than languages which were written down. Is it then plausible to make great claims for Bo's antiquity?<br /><br /><b>Related:</b> <a href="http://news.bbc.co.uk/2/hi/in_depth/8500108.stm">The tragedy of dying languages</a>. Larded with specious banalities or outright falsities, but good for a laugh.<div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-8106974402949926450?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>Razibnoreply@blogger.comtag:blogger.com,1999:blog-10083047.post-48003932024850774842010-02-05T01:09:00.000-08:002010-02-05T01:25:50.639-08:00Ibn Khaldun In Our Time<a href="http://www.bbc.co.uk/programmes/b00qckbw">Ibn Khaldun</a> on <i>In Our Time</i>. Excellent program. Khaldun's assessment that the Mamluks of Egypt had developed a system of rule which was robust against the decay of <a href="http://en.wikipedia.org/wiki/Asabiyyah">asabiyyah</a> was born out by 450 years of subsequent history (that is, until the liquidation of the Mamluk ruling caste of Egypt in the 19th century). Unfortunately, the pervasive Islamic system of channeling slaves into the military and bureaucracy from the time of <a href="http://en.wikipedia.org/wiki/Al-Mu'tasim">Al-Mu'tasim</a> in the early 9th century seems to have been a local optimum. Like a Confucian bureaucratic state it was <i>relatively</i> stable and robust, maintaining a modicum of peace and order, but over the long term it produced stasis. These are social systems geared toward squeezing more "efficiencies" (operationally, rents for the elite) out of the system, not reinventing it so as to generate growth in wealth which compounds.<div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-4800393202485077484?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>Razibnoreply@blogger.comtag:blogger.com,1999:blog-10083047.post-28278508014596199492010-02-01T19:40:00.000-08:002010-02-01T20:37:38.449-08:00"Synthetic associations" and sickle cell anemia<a href="http://www.gnxp.com/blog/2010/01/bold-prediction-synthetic-associations.php">Last week</a>, I made a silly error in describing a problem in the sickle cell anemia example given by <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000294">Dickson et al. (2010)</a> as an empirical example of the phenomenon they call "synthetic association". So allow me to take a mulligan, and re-try this:<br /><span class="fullpost"><br />The authors performed an association study in African-Americans, using ~200 individuals with sickle cell anemia as cases, and >7,000 controls. From their description, they simply performed a logistic regression of disease status on common polymorphisms genome-wide. This turned up a large (~2.5Mb) region surrounding HBB (known to harbour the rare disease-causing mutation) as highly associated with the phenotype. This large region of association stands in contrast, they argue, to the known patterns of linkage disequilibrium in the region, which extends over a few kilobases at most. <br /><br />This observation, they argue, is an empirical example of how associations due to rare variants can lead to large blocks of associations at common variants. This effect is due to the fact that haplotypes surrounding rare variants are longer and have had little time to be broken up by recombination. Under certain genetic models, this effect of "synthetic associations" is plausible, however, this example is a poor one for making their case. <br /><br />The reason is that individuals with sickle cell anemia have two chromosomes of African ancestry in the region of HBB, while individuals without sickle cell anemia have approximately the background distribution of European and African chromosomes at the locus--~20% European and ~80% African. To put it another way, let X_d be number of chromosomes of African ancestry of an individual some distance d from HBB (X can be 0, 1, or 2), and Y be the number of chromosomes of African ancestry of an individual at HBB. In the cases, they've conditioned on the fact that Y=2, while in the controls they have not. <b>P(X_d) != P(X_d | Y =2)</b>, so much of their association is likely due simply to differences in ancestry between the cases and controls in the HBB region (recall that admixture linkage disequilibrium in African-Americans <a href="http://www.nature.com/nrg/journal/v6/n8/full/nrg1657.html">extends for megabases</a>). <br /><br />More concretely, any SNP near the HBB locus that happened to be fixed for opposite alleles in Europe and Africa would have a whopping 20% allele frequency difference between cases and controls in their analysis, attributable simply to differences in local ancestry. That's the extreme (and unlikely) situation, but alleles with more modest allele frequency differences between populations will show the same effect. <br /><br />To some extent, this is their point--the haplotype carrying the causal mutation is long. But the effect in this case is massively exaggerated by admixture, and the presentation of this exaggerated effect is misleading. <br /></span><div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-2827850801459619949?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>p-terhttp://www.blogger.com/profile/03756271491303196763noreply@blogger.comtag:blogger.com,1999:blog-10083047.post-68570202901427906582010-02-01T10:33:00.000-08:002010-02-01T13:16:10.822-08:00Half Sigma's flawed post on DTNBP1A while back, Mark and I were working on a comprehensive post which would try to tally the results of the various IQ-gene studies to see what they said about racial differences. We began this quest bright-eyed and hopeful that we would help contribute to ending a calamitous debate that has gone on for way too long. However, as we learned more about genetics, and these studies in particular, we came to realize that it's too early to take IQ-genes seriously.<br /><br />We began with an approach similar to what Half Sigma did 2 years ago with the <a href="http://www.halfsigma.com/2007/11/dtnbp1-gene-and.html">DTNBP1 gene</a>. However, we soon learned that this approach was incredibly flawed and misleading. I wasn't going to write this post, but recently Half Sigma's DTBP1 post was <a href="http://www.halfsigma.com/2010/01/massive-hbdrelated-blog-traffic-today.html">linked from Reddit </a>and tens of thousands of people are viewing it. When I saw that, I frustratedly criticized HS. He responded that I should give a more diplomatic and reasoned response, so here it is:<br /><span class="fullpost"><br /><ol><li><span style="font-weight: bold;">You cannot simply add up SNPs from the same gene or chromosome.</span> Half Sigma simply adds the observed effects of the SNPs to one another, ignoring that the alleles are highly correlated with one another, and not independently inherited, which is referred to as <a href="http://en.wikipedia.org/wiki/Linkage_disequilibrium">linkage disequilibrium</a> (LD). The study that Half Sigma used provides the following table of LD for its SNPs:<br /><table><tbody><tr><td align="center"></td><td align="center">rs2619539</td><td align="center">rs3213207</td><td align="center">rs1011313</td><td align="center">rs2619528</td><td align="center">rs760761</td><td align="center">rs2619522</td><td align="center">rs2619538</td></tr><tr><td align="center">rs2619539</td><td align="center">-</td><td align="center">0.156</td><td align="center">0.111</td><td align="center">0.0</td><td align="center">0.0</td><td align="center">0.001</td><td align="center">0.055</td></tr><tr><td align="center">rs3213207</td><td align="center">1.0</td><td align="center">-</td><td align="center">0.014</td><td align="center">0.334</td><td align="center">0.403</td><td align="center">0.34</td><td align="center">0.076</td></tr><tr><td align="center">rs1011313</td><td align="center">0.916</td><td align="center">1.0</td><td align="center">-</td><br /><td align="center">0.037</td><td align="center">0.033</td><td align="center">0.036</td><td align="center">0.081</td></tr><tr><td align="center">rs2619528</td><td align="center">0.024</td><td align="center">0.955</td><td align="center">1.0</td><td align="center">-</td><td align="center">0.838</td><td align="center">0.737</td><td align="center">0.128</td></tr><tr><td align="center">rs760761</td><td align="center">0.015</td><td align="center">1</td><td align="center">1.0</td><td align="center">0.96</td><td align="center">-</td><td align="center">0.854</td><td align="center">0.166</td></tr><tr><td align="center">rs2619522</td><td align="center">0.04</td><td align="center">0.955</td><td align="center">1.0</td><td align="center">0.867</td><td align="center">0.96</td><td align="center">-</td><td align="center">0.182</td></tr><tr><td align="center">rs2619538</td><td align="center">0.242</td><td align="center">0.823</td><td align="center">0.825</td><td align="center">0.648</td><td align="center">0.772</td><td align="center">0.778</td><td align="center">-</td></tr></tbody></table><br />As can be seen in this table, pairwise LD goes as high as 1.0, meaning that two of the alleles are always inherited together. Adding these SNP's together is therefore like counting them twice.</li><br /><li><span style="font-weight: bold;">Group comparisons require replication in both groups</span>. Because different populations have systematic genetic and environmental differences, an effect in one group may not occur in another. The study that Half Sigma uses relies primarily on a (small) sample of Dutch people. It is unclear whether these effects would exist in a population of African ancestry, let alone another European one.</li><br /><li><span style="font-weight: bold;">Candidate-gene association studies are not reliable</span>. This is the most important point. Candidate gene association studies have largely failed to replicate. In fact, there have been no common IQ polymorphisms which have been replicated. Genome-wide association studies, which don't suffer as severely the various biases of candidate-gene association studies like <a href="http://en.wikipedia.org/wiki/Publication_bias">publication bias</a> or the <a href="http://en.wikipedia.org/wiki/Winner%27s_curse">winner's curse</a> have not shown common SNP-associations with IQ.<br /><br />IQ is highly heritable, so the problem is the current methods, not the search for genes. With the development of sequencing technology and huge cohorts, we will be able to see the genes that are really behind normal IQ variation. With replication in multiple ethnicities and races, we will also see to what extent various genes and environments are responsible for group differences. There's no need to make proclamations of victory for hereditarianism or environmentalism in the mean time.<br /></li></ol></span><div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-6857020290142790658?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>ben gnoreply@blogger.comtag:blogger.com,1999:blog-10083047.post-26915757390764183142010-01-31T00:56:00.000-08:002010-01-31T01:07:41.491-08:00Jersey Shore coming backThey've been <a href="http://www.tmz.com/2010/01/31/jersey-shore-cast-season-two-contracts-snooki-situation/">signed</a> for $10,000 per episode the next go around. Years ago <a href="http://yrif.org/">Joel</a> floated the idea of using Reality TV to test theories in social science. Paying the cast of <i>Jersey Shore</i> this much is going to mean that they'll be under serious pressure to produce high quality "product." I assume that means they're crank up the magnitude of their "character." For example, Ronnie Magro will be under pressure to beat up more d-bags next season. "The Situation" is going to have to do the nasty with even nastier.<div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-2691575739076418314?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>Razibnoreply@blogger.comtag:blogger.com,1999:blog-10083047.post-91793482571335873952010-01-29T14:15:00.000-08:002010-01-29T14:26:41.917-08:00Proud to be redA friend pointed me to this <a href="http://www.youtube.com/watch?v=EY39fkmqKBM">YouTube</a> clip of a young red-haired man objecting to the term "ginger," and the opprobrium he's been subjected to since the <i>South Park</i> episode <a href="http://en.wikipedia.org/wiki/Ginger_Kids">"Ginger Kids"</a> popularized ideas such as the possibility that redheads have no soul. I assume the kid is joking. On the other hand, I have read that red-haired males are at some disadvantage on online dating sites, just like non-white males. Have any readers of the red persuasion ever felt put upon due to their rare pigment status?<div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-9179348257133587395?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>Razibnoreply@blogger.comtag:blogger.com,1999:blog-10083047.post-17245176922722812472010-01-29T00:44:00.000-08:002010-01-29T01:11:08.839-08:00Darwin wuz wrong, part nA <a href="http://www.independent.co.uk/arts-entertainment/books/features/did-charles-darwin-get-it-wrong-1882253.html">review</a> of a new book, <a href="http://www.amazon.com/exec/obidos/ASIN/0374288798/geneexpressio-20/">What Darwin Got Wrong</a>. Co-authored by Jerry Fodor, who has been continuing his <a href="http://www.lrb.co.uk/v29/n20/jerry-fodor/why-pigs-dont-have-wings">war against natural selection</a>. I've already read <a href="http://www.amazon.com/exec/obidos/ASIN/1594032009/geneexpressio-20/">Darwinian Fairytales: Selfish Genes, Errors of Heredity, and Other Fables of Evolution</a> (at the suggestion of a reader who found the arguments within incredibly persuasive, convincing me to simply ignore anything that reader ever asserted after finishing the book), so I think I have my quota of philosopher-declaring-evolution-the-naked-emperor under my belt. Meanwhile, there are <a href="http://www.ncbi.nlm.nih.gov/pubmed/19744124">real scholars</a> grappling with the issues which emerged in the wake of the Neo-Darwinian Synthesis and its discontents, and pushing science forward.<br /><br />Yes, Darwin <i>was</i> wrong about many things. But how many scientists will still have such an impact 150 into the future? He's a big enough figure that people can sell books just by putting his name into the title! Only a <a href="http://www.amazon.com/exec/obidos/ASIN/0618711686/geneexpressio-20/">few</a> <a href="http://www.amazon.com/exec/obidos/ASIN/0738205753/geneexpressio-20/">others</a> fall into that class.<br /><br /><b>Note:</b> Here you can read a draft of the <a href="http://www.chd.ucsd.edu/seminar/documents/Fodor.Chapter3.pdf">third chapter</a> of <a href="http://www.amazon.com/exec/obidos/ASIN/0374288798/geneexpressio-20/">What Darwin Got Wrong</a>.<div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-1724517692272281247?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>Razibnoreply@blogger.comtag:blogger.com,1999:blog-10083047.post-85698096571066230232010-01-28T17:36:00.000-08:002010-01-28T17:38:12.063-08:00Peer groups & bourgeois virtues<a href="http://scienceblogs.com/cortex/2010/01/self-control_and_peer_groups.php">Self-Control and Peer Groups</a>:<br /><blockquote>However, according to a new study by Michelle vanDellen, a psychologist at the University of Georgia, self-control contains a large social component; the ability to resist temptation is contagious. The paper consists of five clever studies, each of which demonstrates the influence of our peer group on our self-control decisions. For instance, in one study 71 undergraduates watched a stranger exert self-control by choosing a carrot instead of a cookie, while others watched people eat the cookie instead of the carrot. That's all that happened: the volunteers had no other interaction with the eaters. Nevertheless, the performance of the subjects was significantly altered on a subsequent test of self-control. People who watched the carrot-eaters had more discipline than those who watched the cookie-eaters.</blockquote><br /><br />I assume <a href="http://en.wikipedia.org/wiki/Time_preference">time preference</a> is heritable (at least via its correlation with other traits such as IQ), but, that assumes you control background social and cultural variables.<div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-8569809657106623023?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>Razibnoreply@blogger.comtag:blogger.com,1999:blog-10083047.post-67106448411036674422010-01-28T14:19:00.000-08:002010-01-28T14:36:16.751-08:00Race: A Social Destruction of a Biological ConceptWhat is the single best reference for refuting the notion that "race is only a social construct" for a non-scientist? I don't know. (Suggestions welcome in the comments.) But <a href="http://www.ln.edu.hk/philoso/staff/sesardic/index.html">Neven Sesardic</a> (previously praised <a href="http://www.gnxp.com/blog/2006/05/making-sense-of-heritability.php">here</a>) does a marvelous job in "Race: A Social Destruction of a Biological Concept," (<a href="http://www.ln.edu.hk/philoso/staff/sesardic/getfile.php?file=Race.pdf">pdf</a>) Biology and Philosophy (2010, forthcoming).<br /><br /><blockquote><br />It is nowadays a dominant opinion in a number of disciplines (anthropology, genetics, psychology, philosophy of science) that the taxonomy of human races does not make much biological sense. My aim is to challenge the arguments that are usually thought to invalidate the biological concept of race. I will try to show that the way ‘‘race’’ was defined by biologists several decades ago (by Dobzhansky and others) is in no way discredited by conceptual criticisms that are now fashionable and widely regarded as cogent. These criticisms often arbitrarily burden the biological category of race with some implausible connotations, which then opens the path for a quick eliminative move. However, when properly understood, the biological notion of race proves remarkably resistant to these deconstructive attempts. Moreover, by analyzing statements of some leading contemporary scholars who support social constructivism about race, I hope to demonstrate that their eliminativist views are actually in conflict with what the best contemporary science tells us about human genetic variation.<br /></blockquote><br /><br />Nothing new for the GNXP faithful, but the presentation is clear and compelling throughout. He opens with "Those who subscribe to the opinion that there are no human races are obviously ignorant of modern biology." --- Ernst Mayr, 2002. Great quote!<div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-6710644841103667442?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>dkanenoreply@blogger.comtag:blogger.com,1999:blog-10083047.post-77276678299311385652010-01-27T20:55:00.000-08:002010-01-27T21:00:09.463-08:00Maps of white teen birthrate and abortion rates by stateA supplement to the <a href="http://www.gnxp.com/blog/2010/01/teen-birthrates-and-abortion-rates-over.php">previous</a> <a href="http://www.gnxp.com/blog/2010/01/red-state-blue-state-teen-birthrate.php">two posts</a>. Below are maps which are shaded proportionally. Note how New York seems to be the abortion capital of the USA. Total surprise to me. Remember that these data are for white females from the ages of 15-19.<br /><span class="fullpost"><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.gnxp.com/blog/uploaded_images/mapwhiteteenbirthrate-789013.png"><img style="cursor:pointer; cursor:hand;width: 400px; height: 218px;" src="http://www.gnxp.com/blog/uploaded_images/mapwhiteteenbirthrate-789011.png" border="0" alt="" /></a><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.gnxp.com/blog/uploaded_images/mapwhiteteenabortionrate-766470.png"><img style="cursor:pointer; cursor:hand;width: 400px; height: 218px;" src="http://www.gnxp.com/blog/uploaded_images/mapwhiteteenabortionrate-766468.png" border="0" alt="" /></a><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.gnxp.com/blog/uploaded_images/mapwhiteteenabortionratio-766384.png"><img style="cursor:pointer; cursor:hand;width: 400px; height: 239px;" src="http://www.gnxp.com/blog/uploaded_images/mapwhiteteenabortionratio-766382.png" border="0" alt="" /></a></span><div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-7727667829931138565?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>Razibnoreply@blogger.comtag:blogger.com,1999:blog-10083047.post-5278353680364402992010-01-27T19:58:00.000-08:002010-01-27T20:10:56.119-08:00Red State, Blue State, Teen Birthrate, Teen Abortion rateA reader pointed to this <a href="http://www.economist.com/blogs/democracyinamerica/2010/01/teen_pregnancy_and_abortion">post in <i>Free Exchange</i></a>:<br /><blockquote>Here are the 15 states with the biggest percentage drop from 1988-2005 in the ratio of teen abortions—the percentage of teen pregnancies that ended in abortion, not counting miscarriages. Crudely put, these are the states where pregnant white teens stopped having abortions between 1988-2005.<br /><br />1. Kentucky<br />2. Nebraska<br />3. Arkansas<br />4. Oklahoma<br />5. South Dakota<br />6. Tennessee<br />7. Kansas<br />8. Iowa<br />9. Texas<br />10. North Dakota<br />11. Alabama<br />12. Indiana<br />13. Missouri<br />14. North Carolina<br />15. Utah</blockquote><br /><br />I have 2008 exit poll data handy by state, as well as the 2005 birth and abortion data. Abortion ratio = (Abortion rate)/(Abortion rate + Birthrate); basically pregnancy rate minus miscarriages. "Teen" here defines females in the age range 15-19. As you'd expect:<br /><br />1) Whites voting Democrat is correlated with lower white birthrates<br />2) Whites voting Democrat is correlated with higher white abortion rates<br />3) Whites voting Democrat is correlated with higher white abortion ratios<br /><br />#3 is stronger than #2, and I believe that's because teen pregnancy rates are lower in areas where whites are strongly Democrat, so the abortion rates are also going to be lower. The abortion ratio is somewhat normalized to pregnancy rate.<br /><span class="fullpost"><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.gnxp.com/blog/uploaded_images/redbluebirthrate-710536.png"><img style="cursor:pointer; cursor:hand;width: 400px; height: 233px;" src="http://www.gnxp.com/blog/uploaded_images/redbluebirthrate-710532.png" border="0" alt="" /></a><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.gnxp.com/blog/uploaded_images/redblueabortionrate-700218.png"><img style="cursor:pointer; cursor:hand;width: 400px; height: 233px;" src="http://www.gnxp.com/blog/uploaded_images/redblueabortionrate-700216.png" border="0" alt="" /></a><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.gnxp.com/blog/uploaded_images/redblueabortionratio-757192.png"><img style="cursor:pointer; cursor:hand;width: 400px; height: 233px;" src="http://www.gnxp.com/blog/uploaded_images/redblueabortionratio-757189.png" border="0" alt="" /></a><br /></span><div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-527835368036440299?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>Razibnoreply@blogger.comtag:blogger.com,1999:blog-10083047.post-24854879997551567692010-01-27T14:46:00.000-08:002010-01-27T15:37:55.903-08:00Teen birthrates and abortion rates<i>The New York Times</i> has a new article, <a href="http://www.nytimes.com/2010/01/27/us/27teen.html?hpw">After Long Decline, Teenage Pregnancy Rate Rises</a>. The graphic is OK, but it focuses on aggregate teen pregnancy rates (age group 15-19) instead of splitting it out so as to show births and abortions. The <a href="http://www.guttmacher.org/media/nr/2010/01/26/index.html">original report</a> is chock full of tables, but not the charts I was looking for. So I decided to go ahead and create them. All the "teen" data is for the 15-19 age range. The trends are a bit difference from that in the chart because I split up births and abortions, and also added in "abortion ratio," which simply illustrates the proportion of pregnancies which result in abortions excluding miscarriage and stillbirths. The other rates are per 1,000 of females of the given age range. First, the overall trends by time, broken out by race & ethnicity. White = Non-Hispanic white in all that follows.<br /><span class="fullpost"><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.gnxp.com/blog/uploaded_images/pregnancytrendlines-702483.png"><img style="cursor:pointer; cursor:hand;width: 400px; height: 200px;" src="http://www.gnxp.com/blog/uploaded_images/pregnancytrendlines-702451.png" border="0" alt="" /></a><br /><br />Since Latinos have high birthrates, so surprise that their abortion rate is higher than whites. On the other hand, the relatively low abortion <i>ratio</i> vis-a-vis white teens points to some cultural expectations among this group which we'd expect from Roman Catholics (though more generally Catholics don't differ much from Protestants in the United States in regards to abortion, so I think that this is less causal than correlated).<br /><br />There is also state level data, though it is spotty in regards to abortions. I decided to see if the different groups tracked each other in regards to rates. Here's what I found:<br /><br /><p><table frame="VOID" cellspacing="0" cols="3" rules="NONE" border="0" width="500"> <tbody> <tr> <td></td> <td align="right"><strong>Correlation<br /> </strong></td> <td align="right"><strong>R-squared</strong></td> </tr> <tr> <td height="17" align="LEFT"><strong>White Birthrate – Black Birthrate</strong></td> <td align="RIGHT" sdval="0.41" sdnum="1033;">0.41</td> <td align="RIGHT" sdval="0.1681" sdnum="1033;">0.17</td> </tr> <tr> <td height="17" align="LEFT"><strong>White Birthrate – Hispanic Birthrate</strong></td> <td align="RIGHT" sdval="0.44" sdnum="1033;">0.44</td> <td align="RIGHT" sdval="0.1936" sdnum="1033;">0.19</td> </tr> <tr> <td height="17" align="LEFT"><strong>Black Birthrate – Hispanic Birthrate</strong></td> <td align="RIGHT" sdval="0.42" sdnum="1033;">0.42</td> <td align="RIGHT" sdval="0.1764" sdnum="1033;">0.18</td> </tr> <tr> <td height="17" align="LEFT"><br /></td> <td align="LEFT"><br /></td> <td align="LEFT"><br /></td> </tr> <tr> <td height="17" align="LEFT"><strong>White Abortion rate – Black Abortion rate</strong></td> <td align="RIGHT" sdval="0.6" sdnum="1033;">0.6</td> <td align="RIGHT" sdval="0.36" sdnum="1033;">0.36</td> </tr> <tr> <td height="17" align="LEFT"><strong>White Abortion rate – Hispanic Abortion rate</strong></td> <td align="RIGHT" sdval="0.79" sdnum="1033;">0.79</td> <td align="RIGHT" sdval="0.6241" sdnum="1033;">0.62</td> </tr> <tr> <td height="17" align="LEFT"><strong>Black Abortion rate – Hispanic Abortion rate</strong></td> <td align="RIGHT" sdval="0.8" sdnum="1033;">0.8</td> <td align="RIGHT" sdval="0.64" sdnum="1033;">0.64</td> </tr> <tr> <td height="17" align="LEFT"><br /></td> <td align="LEFT"><br /></td> <td align="LEFT"><br /></td> </tr> <tr> <td height="17" align="LEFT"><strong>White Abortion rate – White Birthrate</strong></td> <td align="RIGHT" sdval="-0.44" sdnum="1033;">-0.44</td> <td align="RIGHT" sdval="0.1936" sdnum="1033;">0.19</td> </tr> <tr> <td height="17" align="LEFT"><strong>Black Abortion rate – Black Birthrate</strong></td> <td align="RIGHT" sdval="0.014" sdnum="1033;">0.01</td> <td align="RIGHT" sdval="0.000196" sdnum="1033;">0</td> </tr> <tr> <td height="17" align="LEFT"><strong>Hispanic Abortion rate – Hispanic Birthrate</strong></td> <td align="RIGHT" sdval="-0.07" sdnum="1033;">-0.07</td> <td align="RIGHT" sdval="0.0049" sdnum="1033;">0</td> </tr> </tbody></table></p><br /><br />And the scatterplots, as well as some dot plots which show the <b>ratio</b> of the rates of two minority groups, as a function of geography.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.gnxp.com/blog/uploaded_images/hispanicwhitebirthratescatt-724217.png"><img style="cursor:pointer; cursor:hand;width: 400px; height: 399px;" src="http://www.gnxp.com/blog/uploaded_images/hispanicwhitebirthratescatt-724214.png" border="0" alt="" /></a><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.gnxp.com/blog/uploaded_images/blackwhitebirthratescatter-724117.png"><img style="cursor:pointer; cursor:hand;width: 400px; height: 399px;" src="http://www.gnxp.com/blog/uploaded_images/blackwhitebirthratescatter-724115.png" border="0" alt="" /></a><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.gnxp.com/blog/uploaded_images/hispanicblackbirthratescatt-791912.png"><img style="cursor:pointer; cursor:hand;width: 400px; height: 399px;" src="http://www.gnxp.com/blog/uploaded_images/hispanicblackbirthratescatt-791909.png" border="0" alt="" /></a><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.gnxp.com/blog/uploaded_images/blackwhiteabortionscatter-792009.png"><img style="cursor:pointer; cursor:hand;width: 400px; height: 399px;" src="http://www.gnxp.com/blog/uploaded_images/blackwhiteabortionscatter-792007.png" border="0" alt="" /></a><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.gnxp.com/blog/uploaded_images/hispanicblackabortionscatte-711632.png"><img style="cursor:pointer; cursor:hand;width: 400px; height: 399px;" src="http://www.gnxp.com/blog/uploaded_images/hispanicblackabortionscatte-711630.png" border="0" alt="" /></a><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.gnxp.com/blog/uploaded_images/hispanicwhiteabortionscatte-711538.png"><img style="cursor:pointer; cursor:hand;width: 400px; height: 399px;" src="http://www.gnxp.com/blog/uploaded_images/hispanicwhiteabortionscatte-711536.png" border="0" alt="" /></a><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.gnxp.com/blog/uploaded_images/hispanicblackabortionscatte-725389.png"><img style="cursor:pointer; cursor:hand;width: 400px; height: 399px;" src="http://www.gnxp.com/blog/uploaded_images/hispanicblackabortionscatte-725387.png" border="0" alt="" /></a><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.gnxp.com/blog/uploaded_images/hispanicwhitebirthrateratio-767175.png"><img style="cursor:pointer; cursor:hand;width: 400px; height: 399px;" src="http://www.gnxp.com/blog/uploaded_images/hispanicwhitebirthrateratio-767172.png" border="0" alt="" /></a><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.gnxp.com/blog/uploaded_images/hispanicwhiteabortionratio-723251.png"><img style="cursor:pointer; cursor:hand;width: 400px; height: 399px;" src="http://www.gnxp.com/blog/uploaded_images/hispanicwhiteabortionratio-723249.png" border="0" alt="" /></a><br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.gnxp.com/blog/uploaded_images/blackwhitebirthrateratio-767047.png"><img style="cursor:pointer; cursor:hand;width: 400px; height: 399px;" src="http://www.gnxp.com/blog/uploaded_images/blackwhitebirthrateratio-767045.png" border="0" alt="" /></a><br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.gnxp.com/blog/uploaded_images/blackwhiteabortionratio-725292.png"><img style="cursor:pointer; cursor:hand;width: 400px; height: 399px;" src="http://www.gnxp.com/blog/uploaded_images/blackwhiteabortionratio-725290.png" border="0" alt="" /></a><br /><br />Looking closely at the data <b>it seems that that local state law/and/or/culture matters a lot for teen abortion ratios.</b> Vermont for example has a very high abortion ratio. Might look at it later....<br /><br /><b>Note:</b> I excluded DC from the state level analysis because it's a bizarre outlier. White teen birthrates of 1 per 1,000, black & Hispanic above 100.<br /></span><div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-2485487999755156769?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>Razibnoreply@blogger.comtag:blogger.com,1999:blog-10083047.post-54131549489899636702010-01-26T20:48:00.001-08:002010-01-27T07:17:11.700-08:00A bold prediction: "synthetic associations" are not a panaceaThere's a bit of press surrounding the interesting <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000294">result from David Goldstein's group</a> that, in certain situations, a number of "rare" (defined as an allele frequency less than 5% [1]) variants influencing a trait can lead to an association signal at "common" SNPs. This phenomenon they authors call a "synthetic association". <br /><br />The authors claim this is potentially the cause of many of the associations found in genome-wide association studies (with common SNPs), as well as a potential solution to the "missing heritability problem" (this isn't mentioned in the paper itself, but rather in <a href="http://www.nytimes.com/2010/01/26/science/26gene.html">a Times article describing it</a>). In other words, this could be a panacea for all the ills of the human genetics community. Unfortunately, this seems rather unlikely. <br /><br />1. There are a range of parameter values for which "synthetic associations" are plausible--where the effect of the rare variants is small enough to have avoided detection by linkage studies but big enough to show up via correlation with common variants. This range of parameters is kind of small--from Figure 2, it looks like maybe a set of mutations at a gene with a genotypic relative risk greater than 2 but less than 6. Will this be the case for some loci? Sure, that sounds plausible. Is it going to explain everything? No, of course not. <br /><br />2. It has been pointed out (rightly) that diseases that are selected against should have their genetic component enriched for rare variants. Goldstein himself has made this argument about diseases like schizophrenia. So if schizophrenia has all these rare variants, and rare variants cause rampant "synthetic associations" at common SNPs, why hasn't anyone picked up whopping associations using common SNPs in schizophrenia?<br /><br />3. The sickle cell anemia example, as presented in the paper, is extremely misleading. It seems the authors did a simple case control test for sickle cell in an African-American population. Recall that African-Americans are an admixed population, with each individual carrying large chunks of "European" and "African" chromosomes. Anyone will sickle cell will have at least one block of African chromosome surrounding the beta-globin locus, while those without will have two chromosomes sampled from the overall distribution of chromosomes in the population--15-20% of which, approximately, will be of European descent [2]. <b>So any SNP with an allele frequency difference between African and European populations in this region will show up as a highly significant association with the disease due to the way they've done the test</b>, and these associations will extend out to the length of admixture linkage disequilibrium--well, well beyond the LD found in African populations alone. <a href="http://www.plosbiology.org/article/slideshow.action?uri=info:doi/10.1371/journal.pbio.1000294&imageURI=info:doi/10.1371/journal.pbio.1000294.t001#">The presentation of this example in the paper</a>--the large block of association contrasting with the small blocks of LD in the Yoruban population--is a bit silly. <br /><br />If I had to guess, and put a concrete bet on how this will play out, let's take the associations listed in their <a href="http://www.plosbiology.org/article/slideshow.action?uri=info:doi/10.1371/journal.pbio.1000294&imageURI=info:doi/10.1371/journal.pbio.1000294.t001">Table 1</a>, which they call candidates for being due to synthetic associations. My bet: none of them are. Ok, maybe one. <br /><br /><br />[1] These sorts of thresholds are important to watch--in a year people will be calling things at 1% frequency "common" if it suits them for rhetorical purposes.<br /><br />[2] Corrected from: "... will have two large blocks of "African" chromosomes surrounding the beta-globin locus, and everyone without will have at least one European chromosome in the same area"; see comments.<div class="blogger-post-footer"><img width='1' height='1' src='https://blogger.googleusercontent.com/tracker/10083047-5413154948989963670?l=www.gnxp.com%2Fblog%2Findex.php' alt='' /></div>p-terhttp://www.blogger.com/profile/03756271491303196763noreply@blogger.com