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• bioRxiv is here

  Posted:Tue, 12 Nov 2013 09:45:21 +0000

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

  The post bioRxiv is here appeared first on Gene Expression.

• Cognitive biases, not science, poses ethical dilemmas

  Posted:Mon, 21 Oct 2013 11:10:59 +0000

  

  A Chimera

  Yesterday I pointed to an io9 post, These Unresolved Ethical Questions Are About to Get Real, on my Twitter feed. It’s interesting (that’s why I tweeted it!), but there were some aspects which I thought were specious, and reflect common intuitions and fears in the public. Two in particular I want to highlight.

  First, “Is it okay to introduce non-human DNA in our genome?” The premise is false. A substantial proportion of the human genome is derived from viruses. Lateral gene transfer in complex organisms is not unknown, and may sometimes be quite functional (arguably endosymbiogenesis and mitochondria is the classic case, but that’s so far back in the past that people aren’t shocked by it). Second, the piece also asks if we “Should we biologically enhance non-human animals?” Last I checked selection was a biological process. Domestication events have radically changed many organisms. The io9 piece spends some time on the possible Uplift of other species, but as a matter of reality coexistence with humans tends to reduce the intelligence of domestic animals (they offload many tasks to us). The narrow exception though is the case of dogs. Yes, they are uniformly less intelligent than wolves, but excel at reading human social cues. We’ve modified them to be our perfect companion animals!

  

  Credit: Lily M

  The only reason these are of note as more than simple confusions is that they’re objections that come up over and over. I recently listened to a radio interview with an activist for organic crops who expressed horror at transgenic organisms. Of course he himself is in some fashion transgenic (being a human, and loaded with viral sequence). Similarly, the idea of animals changing in a manner to be more like man fills us with horror and fascination (Planet of the Apes). But domestic dogs are fundamentally peculiar creatures, whose existence can not be understood aside from the needs of human which they have come to serve. Dogs have even evolved to be able to digest our carbohydrates.

  But the strange can become the familiar. There is little controversy over a process as unnatural as in vitro fertilization. We’ve gotten over it. Similarly, our reactions to our obsequious and often malformed “best friend” is not horror, but affection. As far as transgenics goes, the issue is that humans have a false intuition for how we come into being, and what our essence is. The outlines can be found in books such as Paul Bloom’s Descarte’s Baby. Basically we have an essentialist understanding of Being and nature, and breaking identity apart into reduced elements such as discrete genes is not part of our intuition. Mendelism more generally, and lateral gene transfer more specifically, falsify our intuitions about inheritance and the roots of Being. But they aren’t at the forefront of our thoughts, so you have “gut” responses like the aversion to transgenics.

  The post Cognitive biases, not science, poses ethical dilemmas appeared first on Gene Expression.

• A note on my piece in Slate

  Posted:Sat, 19 Oct 2013 02:00:30 +0000

  

  Credit: 50% to Razib

  Most of you are probably aware that I have a piece that was just published in Slate today, Which Grandparent Are You Most Related to? I’m not used to writing articles for the general interest audience, so I really appreciate Laura Helmuth’s feedback. All errors and confusions in the piece are mine, and there remains one major issue which I did not correct or refine to my satisfaction in the final draft. Michael Eisen pointed out on Twitter that my use of the law of segregation to compute the probability of inheritance from a single grandparent (50% of the autosome vs. 25% as expected) is misleading. I did include a section on recombination in earlier drafts, but couldn’t find a way to elegantly write about crossing over at length without become turgid. In the end I thought my reference to recombination was clear enough to allow one to infer that the true probability was much lower (close to zero as Michael notes), all the while maintaining the illustrative power in relation to the segregation in meiosis of homologous chromosomes. I was wrong, and hopefully this is will serve as a lesson in terms of how to hone my skill at balancing between opaque oversimplification and excessive technical detail. The empirical result of variation across grandparents was probably sufficient in this case.

  The post A note on my piece in Slate appeared first on Gene Expression.

• A golden age of the mind, if you want it

  Posted:Sun, 06 Oct 2013 04:16:07 +0000

  I am old enough to remember card catalogs. They did not make me happy. As a small child I noticed omissions and incorrect classifications so often that for long periods of time I would simply avoid the catalog, and methodically consume books from whole sections of the public library in line with my preferences through tedious manual browsing. I am also old enough to remember when the internet was still  primitive in its data organization and storage capacity (i.e., pre-Google, pre-Wikipedia), and the library was the first, last, and best, recourse toward retrieving data. When Braveheart was released in 1995 I ran down to the local university library to see if I could find more about the protagonist’s biography than was present in Britannica. By chance there was a book available on the life and times of William Wallace, but it was checked out, and there were more than 10 holds ahead of me! This was not an uncommon occurrence in the age before the data rich internet. The reality is what I wanted to know about Wallace is probably found in the Wikipedia entry, but then there was no Wikipedia! These are just a few of the reasons that I have little patience for neo-Luddites such as Nicholas Carr. When I read Carr’s “old man” jeremiads I always wonder, “son, were you even around back in my day?”*

  
  This line of thought crossed my mind as I was sitting in the audience at BAPG IX**; the ninth Bay Area Population Genomics meeting. Started by Dmitri Petrov at Stanford, it brings together research groups at from Petrov’s institution, Berkeley, UCSF, and UC Davis which work at the intersection of population genetics and genomics (I noticed a non-trivial UC Santa Cruz contingent this time around, so I suspect it’s getting more popular). BAPG illustrates the fact that the internet changes the way we communicate and consume information, but in a synergistic, not antagonistic, fashion in relation to traditional person-to-person interactions. The core elements of the meetings would be recognizable to someone from 1990 (perhaps replace PowerPoint with transparencies?), presentations and posters. But these two informational centerpieces are embedded in a scaffold of richer transmission and dissemination modalities. I first heard about BAPG through an email notice. Many people no doubt became aware via Twitter and blogs (which may have triggered word of mouth or emails). Prominent researchers in population genomics such as Dmitri Petrov, Graham Coop, and Carlos Bustamante, have robust and accessible internet presences, so you can hear about what their labs are doing from the horse’s mouth, so to speak. Not only can events like BAPG be organized rapidly with minimal overhead because of the ease of the spread of information, but the proceedings are often relayed on Twitter in real time.

  And yet the fact that the BAPG meetings are “in the flesh” reflects two realities. The prosaic one is that this sort of meeting is probably only feasible in the San Francisco Bay region, due to the existence of the Berkeley-Stanford axis, as well as concentration of private sector genomics related firms.*** The deeper truth though is that even academics as comfortable with computation and information technology as population genomicists still thrive on interpersonal contact face to face. They are human. Despite all the worries about the ubiquity of smart phones, tablets, and notebooks (all on display at the meeting!), and their impact on social interaction, there was a copious amount of old fashioned free spirited conversation. WALL-E is not real. Yet.

  The human element can not be abolished, only modified. And unforutnately the scarcity of human interest is often the shortcoming, not the technology. I thought of this while taking in Kelley Harris’ fascinating presentation on the distribution of mutations across the genome. Using 1000 Genomes data Harris found that point mutations are not randomly distributed; they cluster. And, they exhibit unexpected patterns in their proportions of transversions to transitions. As I said, these were very interesting results. But I wondered why it was that Harris was the one who had to discover this. As a Harvard and Berkeley educated mathematical biologist she obviously has some skills and aptitudes, but it isn’t as if there aren’t many competent thinkers across the Bay area working at places such as Google who couldn’t have done the same in their spare time. The data is there. It reminds me of a conversation I had with a very prominent statistical geneticist who I visited with in Cambridge. He wondered why bright minds around the world weren’t excavating the same mathematical and computational gold freely available to his research group.

  I hold that the problem here has to do with the humans, and not what technology is doing to the humans. As outlined in works such as The Lunar Men it seems that the diversion of the energies of those with leisure and inclination toward intellectual pursuits is subject to the whims of fashion and cultural Zeitgeist. The problem is not the technology. Technology is used by people, to serve their interests and preferences. If you have a problem with the preferences of the human race, take that up with the human race, don’t crucify technology for the sins of humanity.

  * I am joking, as I know Carr is older than I am.

  ** For your amusement. The keynote speaker was rattling off a series of population genetic parameters. So the individual directly in front of me was furiously Googling, and for about 30 seconds he was browsing one of my blog entries! I was tempted to tap him on his shoulder and inform him that the author was sitting directly behind him, but I did not do so.

  *** I am aware there is now a southern California equivalent.

  The post A golden age of the mind, if you want it appeared first on Gene Expression.

• The eternal two cultures reprised

  Posted:Fri, 12 Jul 2013 18:00:42 +0000

  

  A humanist

  Over fifty years ago C. P. Snow wrote The Two Cultures. The details of the argument, and his more general worry about the state of his society, are less important than the fact that there has been a persistent and widening chasm in perception, and often in reality, between the two antipodes of intellectualism, the humanities and science. This has not always been so. The great evolutionary geneticist J. B. S. Haldane studied mathematics and “the Greats.” From what I can tell the latter is equivalent to classics. This combination is not unheard of, the eminent UCLA neuroscientist Paul Thompson has a similar educational background (he is also British, like Haldane). The string theorist Edward Witten received his first degree in history, only later shifting toward a focus on mathematics and science. But these are exceptions, not the rule.Most people who end in the sciences began in the sciences, and the majority do not have a liberal arts college undergraduate background.*

  The converse situation is also true in regards to experience and familiarity. Most who are enmeshed in the humanities have only a cursory knowledge of science, and a general unfamiliarity with the culture of science (though more students switch out of science to non-science degree programs than the reverse). In most cases I find the ignorance of science by non-scientists sad rather than concerning, but in some instances it does lead to the ludicrous solipsism which was highlighted in books such as Higher Superstition: The Academic Left and Its Quarrels with Science. Though there is often a focus on fashionable Leftism in these critiques, it may be notable that the doyen of “Intelligent Design” has admitted a debt to Critical Theory. The scientist-turned-theologian Alister McGrath positively welcomes post-modernism in his The Twilight of Atheism: The Rise and Fall of Disbelief in the Modern World. The problem is not ignorance of science, as much as the dismissal and mischaracterization which that ignorance can give birth to in the right arrogant hands.

  
  This is why I think Virgina Heffernan’s column ‘Why I’m a creationist’ is important as an exemplar of an unfortunate genre. Her slippery prose makes David Berlinski seem the model of precise sincere clear concision. For me Heffernan’s ‘Creationism’ in and of itself causes little offense; plain and sincere falseness is a clean error at least. I am wrong on many things, though I aspire toward correctness in the future. Rather, it is assertions like the following on Twitter:

  

  I invite you to peruse her strange musings further, and please also read Carl Zimmer’s eloquent rationale for why he became somewhat absorbed in l’affaire Heffernan. Like Heffernan Carl has a background in English literature. Unlike Heffernan he does not have an advanced degree, so perhaps he did not fully imbibe such sophistry at the knee of the greats to the same extent? The inability of some humanists to admit that they know not what they know not is what can be very infuriating about interacting with them in their ‘science skeptic’ modality. Though it is cliche to assert that science is a process, rather than fixed truths (the fixed truths are the subjects of study), it is clear that individuals such as Virginia Heffernan have not internalized that basic fact of how science works (see in her column where she bemoans the protean nature of scientific consensus as if it is a bug, rather than a feature!).

  This bizarre perception is particularly ironic coming from humanists, who deal in ambiguity and gray interpretation as their stock-in-trade. There is an incoherent aspect to implying that science is just another subjective narrative, while crucifying it for changing the terms of understanding of the world around us. What is unique about science is not the fact that it is a process (the law is a process!), but that it is contingent and progressive. Science may change, but over the long term it converges upon progressively more precise and accurate models of the world around us. In physics this is illustrated by the refinements of relativity over classical mechanics. In evolutionary biology it is the transition away from tired ‘selectionist’ vs. ‘neutralist’ debates, toward a better understanding of the true distribution of the parameter space than a coarse qualitative labeling of it.

  And yet it is important to set aside rage at grand-standing opportunists like Virginia Heffernan, because scientists could themselves benefit from a greater appreciation of the humanities. Though science is protean as it is progressive, the fixity, clarity, and objectivity of standard orthodox science one receives as one is encultured does on occasion lead to unfortunate cognitive ticks. The problem resides in the reality that scientists are humans embedded in a human world, and too often they confuse the order and regularity of natural scientific processes  which are their subject with phenomena more generally. In understanding the biomolecular nature of DNA or basic Newtonian mechanics budding scientists do not engage in discussion. They learn, and they solve. The period of these problem solving sessions are finite and often delimited, and though they may be taxing they illustrate to scientists and engineers that difficult issues can be resolved by reduction, analysis, and/or computation in real time. This same mentality can be transferred to humanistic endeavors, to unfortunate consequences.

  The humanities are essential in imbuing us with a sense of values, norms, and an aesthetic framework. But perhaps just as importantly they teach us that understanding topics of extreme complexity such as the historical process or literary creativity require humility, and an acceptance that the task may always be unfinished. Even the masters are but children in this enterprise, and final answers are going to be much more difficult than a good set of questions. The power of science and engineering in the modern world is such that it often confuses the primitive primate practitioners of the discipline. They falsely believe it is in fact they, and not the method, that manage to obtain through power of mental acuity a deep understanding of the subject. This is not so. Science works not just (necessary, but not sufficient) because of individual brilliance, but through a cultural system of values in which scientists are embedded, and the plain fact that their subjects of interest are relatively tractable low hanging fruit. Science inspires awe in part because of its relative ease at generating truth outputs. In contrast, the humanities can remind us that there are truly inscrutable depths which we are only dimly grasping on the edge of our perceptions. I would much rather have a discussion about this reality than the sloppy intuitions of self-aggrandizing intellectual narcissists.

  * Going by the fact that only a minority of people graduate from “liberal arts colleges” last I checked.

  The post The eternal two cultures reprised appeared first on Gene Expression.

• What “outreach” in science is

  Posted:Tue, 11 Jun 2013 14:50:55 +0000

  Outreach is a buzz term in academic science right now. Scientists have to publish. And they have to teach. Then there is service (e.g. committees and such). Outreach is now part of the service element. It doesn’t need to be hard or sophisticated. Not only that, outreach can be general (to the public) and specific (to your peers). As an example of what I’m talking about Michael Eisen’s blog is more aimed toward a broad audience, though on occasion he delves specifically into the science which is the bread and butter of his research. Haldane’s Sieve is more tightly focused on researchers working at the intersection of evolution, genomics, and population genetics. But even it expands further out toward biologists who take an interest in specific evolutionary or genomic questions in their own research (e.g., I have known several molecular biologists who had no idea who was behind Haldane’s Sieve, but had read the site because of an interest in a specific preprint).

  This isn’t rocket science, so to speak. Information dissemination is pretty easy right now, and that is theoretically one of the major things which drives science. This should be a great time for scientific progress! Is it? In genomics, yes, though that’s not because of more efficient flow of information, as opposed to technology. With that prefatory comment, I think John Hawks’ recent jeremiad is worth reading, Speak up and matter:

  I have little patience for the risk-averse culture of academics.

  The bottom line is: People need to decide if they want to be heard, or if they want to be validated.I have long been an associate editor at PLoS ONE, and once I edited a paper that received a lot of critical commentary. That journal has a policy of open comment threads on papers, so I told disgruntled scientists to please write comments. The comments appear right with the article when anybody reads it, they appear immediately without any delay, and they can form a coherent exchange of views with authors of the article and other skeptical readers.

  Some of the scientists didn’t want to submit comments, they wanted to have formal letters brought through the editorial review process. “Why?” I wrote, when you could have your comments up immediately and read byanyone who is reading the research in the first place? If you want to make an impact, I wrote, you should put your ideas up there right now.

  They replied, “How would you feel if someone published something wrong about Neandertals? Wouldn’t you want to publish a formal reply?”

  I wrote: “In that case, I would probably get a blog.”

  What is the difference between being heard and being validated? It’s whether you are contributing to the solution or to the hindsight.

  Academics are risk averse. I’m thinking here of a friend who expressed a bit of paranoia about maintaining good relations with his Ph.D. adviser because negative comments from that direction can still matter ten years down the line in tenure reviews. Science is highly political, and money and career options are finite. You have to be careful about who you might offend.

  Or do you? What’s the point of doing science if security is what you want? I think scientists need to be careful about personalizing a war of ideas into a war of people, though this is going to happen because science is a human endeavor. But there are many easier jobs than science which pay better. Those jobs require political skills and machinations, but many of them don’t put forward the pretense of a noble elevation of the truth above all.

  One day we all die. On that day if you are a person interested in forwarding science and understanding the world, being true to truth, do you want too many regrets about how you had to “work the system” and cultivate relationships? If that was an overwhelming focus rather than speaking plainly, then you should have gone into a more lucrative career. The world needs more actuaries.

  Addendum: Much of the same could be said about journalism. And science journalism? Well….

  The post What “outreach” in science is appeared first on Gene Expression.

• Managing the sea of data: Mendeley and PubChase

  Posted:Wed, 10 Apr 2013 17:16:59 +0000

  Every few months someone asks me what I use to manage my papers. Stupidly, I don’t use anything. Or I haven’t. Over the past few weeks I’ve been playing around with PubChase and Mendeley. You probably know of the latter, and the fact that it’s been purchased Elsevier. Elsevier is what it is. Mendeley on the other hand is a firm that I have a positive view of, in part because of their culture of openness and support for the free flow of information, but also due to the fact that I’ve known their head of outreach for ten years. You trust people, not things. Mendeley‘s not a charity, and I don’t begrudge them their new resources now that they are under the corporate wing of Elsevier. Whether you’re pessimistic or optimistic about their future, I think caution is warranted.

  PubChase is a new outfit you probably have not heard of. It’s product is a bit beta-ish feeling to me. I’ve been testing it on and off for a while now, because I have known one of the scientists who works for them for about five years. There are a few things missing, which I’ve been curious about. For example, where is the extension to simply add papers via Chrome? When I inquired about this the response I got was that you could import your Mendeley citations into PubChase. Not totally useful for me, but with the controversy over Mendeley‘s new corporate patron, this is probably a good opportunity for PubChase to position themselves as an alternative.

  The ultimate issue here is getting relevant signal from noise. Individual human curation is still useful (ergo, Haldane’s Sieve). I don’t follow too many people on Twitter in part because I don’t want to get overwhelmed. And my focus is more professional than personal, so I have a lot of genomics and evolution people.

  In the future I’m going to look for applications which not only manage the sea of data, but help you navigate it. There are way too many papers I download and only see three or four years later as I’m cleaning out folders.

  Note: EndNote and CiteULike too. Don’t have time to try everything. Though people who use EndNote tell me that they use it partly because they know how to use it well.

  The post Managing the sea of data: Mendeley and PubChase appeared first on Gene Expression.

• Michael Eisen wants peer review comments on his paper

  Posted:Thu, 21 Feb 2013 04:29:58 +0000

  This is great, Please review our new paper: Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression:

  It’s no secret to people who read this blog that I hate the way scientific publishing works today. Most of my efforts in this domain have focused on removing barriers to the access and reuse of published papers. But there are other things that are broken with the way scientists communicate with each other, and chief amongst them is pre-publication peer review. I’ve written about this before, and won’t rehash the arguments here, save to say that I think we should publish first, and then review. But one could argue that I haven’t really practiced what I preach, as all of my lab’s papers have gone through peer review before they were published.

  No more. From now on we are going to post all of our papers online when we feel they’re ready to share – before they go to a journal. We’ll then solicit comments from our colleagues and use them to improve the work prior to formal publication. Physicists and mathematicians have been doing this for decades, as have an increasing number of biologists. It’s time for this to become standard practice.

  Some ground rules. I will not filter comments except to remove obvious spam. You are welcome to post comments under your name or under a pseudonym – I will not reveal anyone’s identity – but I urge you to use your real name as I think we should have fully open peer review in science.

  OK. Now for the paper, which is posted on arxiv and can be linked to, cited there. We also have a copy here, in case you’re having trouble with figures on arXiv.

  Peter A. Combs and Michael B. Eisen (2013). Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression. 

  Please leave comments on Eisen’s post.

  Via Haldane’s Sieve.

  The post Michael Eisen wants peer review comments on his paper appeared first on Gene Expression.

• Complex science is very hard

  Posted:Tue, 12 Feb 2013 02:24:37 +0000

  Three articles which illustrate the difficulty of the sort of science which tackles what Jim Manzi would term phenomena characterized by high causal density. First, the simplest one is the report that extrapolating from some mouse models to human biological systems may be problematic. Anyone who has talked to human geneticists who use mouse models is aware that these inbred lineages can be somewhat particular and specific. Order the wrong mice, and all of your experimental designs might be for naught. So the result is not surprising, but it seems useful to have it documented in such a concrete fashion (though this has been reported in the media before).

  Second, a long piece in The Chronicle of Higher Education on the problems in replicating ground breaking research in the area of priming. This may be a case of a robust result which turns out to fade into irrelevance as time passes, and illustrates the fundamental problems of attempting to do sciences on humans; we’re diverse and protean. I think the jury’s out on this, and we’ll wait and see. Fortunately this probably won’t be an issue we’ll be debating in 10 years, as replications will start to occur, or, they won’t.

  Finally, a moderately scathing review in The Wall Street Journal  of the book Blindspot: Hidden Biases of Good People. Here’s the final paragraph:

  There is far from a consensus about the IAT—a meta-analysis, you might say, is overdue. It turns out that the authors themselves published one in 2009, reviewing 184 independent samples and nearly 15,000 experimental subjects. The result: The IAT was very weakly correlated with other measures, failing to account for more than 93% of the data. Interestingly, Ms. Banaji and Mr. Greenwald don’t report this in their book [the authors of Blindspot]. Perhaps a blind spot?

  You surely know about IAT, the Implicit Association Test. You’ve probably even taken a test online, purporting to measure your bias against particular groups (I have). But here is where “inside knowledge” counts. Years ago a friend who was a cognitive psychologist told me privately that he and many others within the field were very skeptical of the utility of these tests to predict anything of substance, even though they were media friendly. This individual has a good track record, as he was the one who alerted me to the serious problems with Jonah Lehrer’s work as far back as 2006.

  Does this mean that you should ignore all science which derives from attempting to infer associations in domains where complexity is the rule? Not at all. But caution is warranted. The reality is that these are the areas where we as humans need to go to discover novel and powerful patterns. But because these are often social or medical domains which have immediate real world consequences we need to be methodologically sound, and not jump the gun. And, unfortunately, excessive immediate and early attention in the media is probably a very bad, perhaps negatively correlated, proxy for how solid a given result will be in the long term.

  The post Complex science is very hard appeared first on Gene Expression.

• Adding more color to science the wrong way

  Posted:Thu, 24 Jan 2013 03:49:28 +0000

  Over at ScienceDaily there is a report on a new paper on affirmative action and academia, Understanding the Impact of Affirmative Action Bans in Different Graduate Fields of Study. The paper is gated, but the regression model used really doesn’t seem to do much more than confirm intuition. The descriptive details are more interesting and straightforward.

  
  Here’s the major point: states which banned affirmative action in higher education seem to see a proportionate drop off in “minority” enrollment in many graduate disciplines. I put minority in quotes because if you read through the paper there is the consistent semantic confusion which elides important dynamics at play. The author admits that Asians are not included in the analysis, because they are a varied group. More precisely: “I do not include Asian American/Pacific Islanders students in my definition of ‘underrepresented’ students of color because the category is too broadly defined to allow me to capture the educational disparities that exist within the various subgroups included in the category.” This seems a dodge. The reality is that “Asians” are not an underrepresented minority, period. Rather, they are an overrepresented minority. If you want to make science reflect America, you better start reducing the number of Asian Americans who are taking the slots of underrepresented minorities! (international students are excluded from this analysis)

  An interesting finding is that the largest effects are in engineering, then the natural sciences, social sciences, and finally humanities. There is no impact on graduate education in business. In other words, banning affirmative action has no impact on the proportion of underrepresented minorities in business graduate school. Why the pattern? The author is straightforward on this point:

  Given that students of color are generally underrepresented at higher score percentiles on standardized tests and generally overrepresented at lower percentiles (see e.g., Bowen & Bok, 1998; Diaz, 1990), it is not surprising that the impact of affirmative action bans is greater in science-related fields like engineering (26%), natural sciences (17%), and social sciences (15.2%), compared to the humanities (11.8%) or education (where the impact is not statistically significant). This is because the overall mean score for standardized tests like the GRE, particularly in the quantitative portion of the test, is generally higher in these fields than in the humanities and education fields. Moreover, as I noted in the hypothesis section, the general characteristics of graduate students in less technically focused fields of education (and similarly humanities) suggest that past work experience may be an important factor that plays into students’ decisions to pursue study in these fields or in faculty’s admissions decisions. These other factors may thus balance the negative impact of affirmative action bans in these fields.

  Notice the term “students of color.” In this context it’s obvious that she’s talking about underrepresented minorities, but people might be confused and think engineering is “lily white.” It isn’t. Additionally, there is the standard convention whereby the Latino/Hispanic ethnicity is contrasted with the white race, when about half of American Latinos identify as white, and a substantial minority have far less “color” than the Asian students excluded from this analysis (to the point of being omitted from data tables!). In any case the overarching variable is the quantitative GRE. What would happen if affirmative action was enacted, and the quantitative GRE standard was relaxed for underrepresented minorities?

  Consider the Marcus Cole effect:

  Let me illustrate my point. I am willing to bet that I am the only member of this list who feels compelled to put his standardized test scores and National Merit award on his CV. Why do I do this? For those of you who do not know me personally, it is not a matter of braggadocio. Every September I have to deal with nearly 60 prima donna first year law students whose first and only (initial) reaction to my skin color is that they have been cheated out of a “real” Contracts professor, and are stuck with an “Affirmative Action” instructor. Many of them come around when, as some “gunners” often do, they look up my CV and find that I have outscored virtually every single one of them on the test around which they have centered their lives, the LSAT. Others usually come around by mid semester when they have had an opportunity to compare my teaching to that of their other instructors. If numbers (standardized test scores and teaching evaluations) could obscure my skin color, my life would be heavenly.

  Academic science is a test case in vulgar Social Darwinism. Only a minority of graduate students end up with the academic job that most initially desire. There’s a lot of luck and social intelligence which goes into this, but smarts matter. In many of the more mathematical sciences there are often introductory core sequences, and one reason to set the bar for the quantitative GRE high is that graduate schools are not excited at the prospect of students flunking out due to low aptitude or preparation. Do you want your civil engineer to have received a passing grade for effort? I doubt it.

  Laced throughout the paper is the assumption that America needs a diverse scientific work force which includes blacks and Latinos to compete with the rest of the world. I don’t think that that’s true. Are the Chinese diversifying their scientific establishment in such a manner? But even granting a value to diversity, I think one can make the argument that that value varies by discipline.

  In an area like literature cultural priors matter. Discussion and exchange of perspectives are the bread and butter of many humanities programs. In an area like mechanical engineering cultural priors don’t matter. Most people don’t care about the ethnicity or sex of the engineers who help maintain and produce the superstructure of modern civilization. They want their engineers to be competent. In fact, if your engineer has a “different perspective” because of their cultural background they’re likely to be a crank.

  Academic treatments like this presume that differences in ethnic proportions across disciplines can be changed by fiat. It isn’t so easy. I have reported before that cultural preferences and expectations can influence the disciplinary path one takes. When you add the extra layer of lesser academic aptitude or preparation the goal of proportionality seems farcical to me.

  Some of the points made the paper are well taken. Ethnicity and cultural background do matter in the social ecology of science. I have noticed a trend of labs tending to be somewhat skewed in ethnicity, likely because of the nature of social networks in employment opportunities. But simply increasing the number of first year engineering graduate students won’t change that a bit, because they’ll be filtered out by the time they’re up for a tenure track position.

  The post Adding more color to science the wrong way appeared first on Gene Expression.

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

  Posted:Sun, 06 Jan 2013 20:33:52 +0000

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

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

  The raw results are:

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

   

  And here are charts of % and counts:

  

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

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

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

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

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

  The post Why so few Asians in ecology? Not all groups have similar preferences appeared first on Gene Expression.

• There are no shortcuts to knowledge

  Posted:Mon, 26 Nov 2012 10:53:00 +0000

  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.

   

  The post There are no shortcuts to knowledge appeared first on Gene Expression.

• Iterating science, supercharged

  Posted:Wed, 21 Nov 2012 03:17:09 +0000

  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 post Iterating science, supercharged appeared first on Gene Expression.

• Richard Lewontin against the age

  Posted:Tue, 20 Nov 2012 05:35:14 +0000

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

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

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

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

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

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

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

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

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

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

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

  Image Credit: Wikipedia

  The post Richard Lewontin against the age appeared first on Gene Expression.

• A dangerous man

  Posted:Thu, 11 Oct 2012 10:32:00 +0000

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

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

  Shortly after the start of classes this fall, Daniel HoSang, a professor of political science and ethnic studies at the University of Oregon, sent an email to a handful of faculty. Hsu, he wrote, “has taken a keen personal and professional interest in projects with strong Eugenicist overtones.” Because of Hsu’s position of authority at MSU, he said, he felt compelled to warn them.

  His concerns were equally about positions Hsu had taken in his blog five years ago: that race is “clearly” a valid biological concept, that whether there are more-than-superficial differences between groups (in areas such as cognitive ability, personality and athletic prowess) is an open question.

  Thankfully, Steve has a blog, where he elaborates the back story. What’s going on here? Is Steve Hsu a bad, bad, man? In his blog post Steve outlines his position, and to me he seems rather punctilious in regards to constraining the purview of his speculations. Yes, he goes far too far for some, but his transgressions are matters of positive facts about the world, rather than normative issues on what actions to take on those facts (and even then, he is generally equivocal about facts). Steve had a tenured position as a physicist at a research university, and has been a successful entrepreneur. Why is he dabbling in science which to be honest rather on the fringe and pushing the boundaries? Because Steve is interested in how the world is. Either that, or he’s a very clever psychopath who can convince you that the questions he moots are derived from genuine curiosity, rather than some true self-interested motive. And if he’s a psychopath he’s a rather stupid one for a theoretical physicist, because there’s no margin to be gained in arousing the ire of the ethnic studies kommissars.

  Our lives are ephemeral, and we see through the mirror darkly. But the world is. It was before we were, and it always will be. The petty politics of the human race are of little concern on such a grand scale. And yet as individual human beings we have to acknowledge that we’re social beings, and peer effects are powerful. We seek esteem, and don’t want to transgress taboos. You can make the argument that truth and justice win out in the end, but many people can live and die before truth and justice win out. And sometimes the truth isn’t something we can handle very well. Jeffrey Goldberg was famously wrong about many details about the geopolitics of Iraq in the early 21st century, but that has had little negative impact on his career (while his critics, who were vindicated, by and large remain as marginal as they always were). In much of the former Soviet Union the leaders in positions of power are the same apparatchiks who were the foot-soldiers in imperial Communism. As easily as donning a new suit they’ve gone from being Leftist atheist internationationalists to traditionalist Orthodox nationalists. Communism was a failed ideology, and yet it marched on for three generations. In China Mao Zedong is still part of the pantheon of greats, despite the fact that the nation-state he founded has turned its back on his ideology. Human social norms have their own logic and inertia. Reality can wait, and it does.

  One can make a case that Steve should have lain low and kept plugging away at his specific projects in theoretical physics. Such is the world of many scholars. The easiest way to avoid politics is to not draw attention to oneself. But what’s the point of it all then? Why are you a scholar? The reality is that most scholars are pedestrian in the production of scholarship. Only a few will live on in memory. Why not be bold, and ruffle some feathers? Fame may come, though it probably will not.

  My point in posting this is not to demand that everyone become an idealist, jumping into the fray where angels fear to tread. People have lives to lead, and mortgages to pay. But perhaps it would be easier to pay a mortgage if you went and pursued an M.D.? If you’re a failed scholar because politics trips you up, would you really trade that in for external professional success, at the cost of what’s really gnawing at you in terms of the way the world works? People have to balance the various priorities in their lives obviously.

  A constant condition throughout all of this is that man is a political animal. So if you are controversial, be aware, and have back up plans. I’m not telling people here that they should be martyrs for an ideal. That’s not fun. But writing boring papers on topics that you’re not interested in is not fun either. Most people are boring as it is. Why contribute to that mountain of banality? Aim for some fun before you expire. If your idea of fun offends some people, then you have to figure out how much the esteem, contempt, or rage of “some people” impacts your own mental state. Me, I could care less. Your mileage may vary.

  And good luck to Steve!

  The post A dangerous man appeared first on Gene Expression.

• The real end of science

  Posted:Wed, 03 Oct 2012 06:02:32 +0000

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

  That is all well and good. The basic building blocks for many inventions and institutions existed long before their instantiation. But nevertheless the creation of institutions and inventions at a given moment is deeply contingent. Between 1600 and 1800 the culture of science as we know it emerged in the West. In the 19th and 20th centuries this culture became professionalized, but despite the explicit institutions and formal titles it is bound together by a common set of norms, an ethos if you will. Scientists work long hours for modest remuneration for the vain hope that they will grasp onto one fragment of reality, and pull it out of the darkness and declare to all, “behold!” That’s a rather flowery way of putting the reality that the game is about fun & fame. Most will not gain fame, but hopefully the fun will continue. Even if others may find one’s interests abstruse or esoteric, it is a special thing to be paid to reflect upon and explore what one is interested in.

  Obviously this is an idealization. Science is a highly social and political enterprise, and injustice does occur. Merit and effort are not always rewarded, and on occasion machination truly pays. But overall the culture and enterprise muddle along, and are better in terms of yielding a better sense of reality as it is than its competitors. And yet all great things can end, and free-riders can destroy a system. If your rivals and competitors and cheat and getting ahead, what’s to stop you but your own conscience? People will flinch from violating norms initially, even if those actions are in their own self-interest, but eventually they will break. And once they break the norms have shifted, and once a few break, the rest will follow. This is the logic which drives a vicious positive feedback loop, and individuals in their rational self-interest begin to cannibalize the components of the institutions which ideally would allow all to flourish. No one wants to be the last one in a collapsing building, the sucker who asserts that the structure will hold despite all evidence to the contrary.

  Deluded as most graduate students are, they by and large are driven by an ideal. Once the ideal, the illusion, is ripped apart, and eaten away from within, one can’t rebuild it in a day. Trust evolves and accumulates it organically. One can not will it into existence. Centuries of capital are at stake, and it would be best to learn the lessons of history. We may declare that history has ended, but we can’t unilaterally abolish eternal laws.

  Update:

  

  The post The real end of science appeared first on Gene Expression.

• A social science of the obvious

  Posted:Mon, 03 Sep 2012 10:13:45 +0000

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

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

  And so it is with social science phenomena. For example, I can say that most of personality variation within a population is accounted for by genes and non-shared environment. But what does this mean? It could mean that 20% is accounted for by variation in genes and 60% by non-shared environment, with 40% shared environment. Or, it could mean that 40% is accounted for by variation in genes and 40% by non-shared environment, and 20% shared environment. These are not distinctions without difference. The ‘science’ here is less a counter-intuitive framework of prediction and projection than a clarification and precision of broad trends which might be unsurprising, with the ‘non-obvious’ aspect only coming to the fore when quantities are integrate into larger frameworks. So, for example the prediction that heritable inequality may actually increase when you maximize environmental inputs.

  The post A social science of the obvious appeared first on Gene Expression.

• Peer of myself

  Posted:Sun, 19 Aug 2012 23:40:37 +0000

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

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

  The reality is that often the “peers” are not peers. How else to explain the publication of the longevity study in Science, now retracted? Or the non-canonical RNA editing? (presumably this is less common of a problem in specialized journals). And sometimes the feedback of peers can indicate that they don’t really know what they’re talking about. For example, I was once told that the authors of a phylogenetics paper which used Bayesian methods were asked to reanalyze their data with a max likelihood framework (jump to the last sentence of this section to see why this is peculiar).

  The theory of classical peer review made sense in the pre-internet age. But now there are a plenty of reasons why we might need to revisit this.*

  * Not to mention that “peer review” is a somewhat subjective concept. Richard A. Muller has gotten into a back & forth on this issue whether his latest work has undergone peer review. He claims it has, others claim not. I suspect most traditional biologists would be skeptical of Muller’s claim, but physicists would accept it.

  The post Peer of myself appeared first on Gene Expression.

• How to get beyond bias in science?

  Posted:Thu, 16 Aug 2012 03:38:03 +0000

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

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

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

  First, as I keep telling my liberal readers and friends there’s a deep denialism about sex differences that is ideologically motivated on the Left. For me the most obvious illustration of this is when people on the Left are quite happy to talk about sex differences. Here’s a very long article in The Guardian, Testosterone and high finance do not mix: so bring on the women Gender inequality has been an issue in the City for years, but now the new science of ‘neuroeconomics’ is proving the point beyond doubt: hormonally-driven young men should not be left alone in charge of our finances…. This was triggered by Michael Lewis’ speculation about the roots of the financial crisis in Iceland. To my knowledge Lewis did not get tarred and feathered as an ‘essentialist.’ But that’s because he followed Althouse’ rule: make sure your model of sex differences portrays males in an unflattering light.

  But I don’t want to talk about racism and sexism in science. Rather, scientists tend to be liberal and atheist. How can the American public, a plural majority of whom are religious and conservative, trust the findings of a profession which is odds with them on matters of politics and God? Well, what’s the alternative. Do you want to go with faith healers and Flood geologists? Scientists are human, and science is a human enterprise, but as a culture and method toward understanding the world it’s about as good as you get in this world. Mind you, that’s a really low bar, but science gave us antibiotics and men on the moon. Not too shabby. By their fruit you will recognize them.

  The post How to get beyond bias in science? appeared first on Gene Expression.

• arXiv! arXiv! arXiv!

  Posted:Wed, 15 Aug 2012 03:58:06 +0000

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

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

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

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

  It doesn’t matter to me at this point that people might have qualms. Once sufficient consciousness is raised and critical mass is achieved, then you’ll see a stampede. Some fields in biology may be late into the shift toward preprint distribution, but for the purposes of a lot of the stuff I cover on this weblog I doubt that will matter. When it comes to evolutionary biology that isn’t being funded by pharma or private foundations I don’t think there’s much holding people back aside from the worry about being scooped.

  I don’t know much about academia and its intrigues personally, but I have heard of instances of reviewers squatting on a paper until someone else associated with the reviewer publishes (yes, people know who is reviewing in many cases, or suspects). This is a form of scooping, but it occurs in the shadows, and there’s always deniability. Who knows how we can quantify this sort of behavior? But it’s something to that we need to keep in mind when we’re worried about the pitfalls of open access and preprint distribution.

  The post arXiv! arXiv! arXiv! appeared first on Gene Expression.

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