Ed Yong has a piece in Nature on the problems of confirmation bias and replication in psychology. Yong notes that “It has become common practice, for example, to tweak experimental designs in ways that practically guarantee positive results.” The way this has been explained to me is that you perform an experiment, get a p-value of > 0.05 (significance). You know that your hunch is warranted, so just modulate the experiment, and hope that the p-value comes in at < 0.05, and you have publishable results! Obviously this is not just a problem in psychology; John Ioannidis has famously focused on medicine. But here’s a chart which shows that positive results are particular prevalent in psychology:
Genes are overrated, genetics is underrated
A few days ago Nathaniel Comfort pointed me to this post, Genetic determinism round-up. If you are curious go read Comfort’s whole post. I honestly didn’t enjoy it very much, I think I got what he was saying, but there were all sorts of circumlocutions around the overall message. But I agree one one thing in particular: an emphasis on concrete and specific genes for traits is a motif in science journalism that can be very frustrating, and often misleading. Nevertheless, that’s not the only story. I believe our current culture greatly underestimates the power of genetics in shaping broader social patterns.
How can these be reconciled? Do not genes and genetics go together? The resolution is a simple one: when you speak of 1,000 genes, you speak of no genes. You can’t list 1,000 genes in prose, even if you know them. But using standard quantitative and behavior genetic means one can apportion variation in the population of a trait to variation in genes. 1,000 genes added together can be of great effect. The newest findings in genomics are reinforcing assertions of non-trivial heritability of many complex traits, though rendering problematic attributing that heritability to a specific set of genes.
Abraham’s genetic threads
Every few days my Google Alerts have been dropping in my inbox reviews of Harry Osters’ Legacy: A Genetic History of the Jewish People. The latest is in the The Tablet, A Case for Genetic Jewishness:
For a Jewish genetics researcher, being told in print that ‘Hitler would certainly have been very pleased’ by your work can’t be pleasant. But that’s what happened in 2010 to Harry Ostrer, a geneticist at the Albert Einstein College of Medicine, when he and his colleagues published a study showing that Jews in three different geographical areas had certain collections of genes that made them more biologically similar to one another than they were to non-Jews in the same regions. The work also showed that Jews around the world could trace their ancestry to a group of people who lived in the Middle East 2,000 years ago; that meant, however, that certain genetic signatures could be used to identify Jews, indicating that Jews share a common biological identity beyond their religious affiliation—which is what inspired the Hitler crack.
I don’t plan on reading Legacy because I already read the paper which it is based on, Abraham’s Children in the Genome Era: Major Jewish Diaspora Populations Comprise Distinct Genetic Clusters with Shared Middle Eastern Ancestry. It is now open access, so you can read it too. As implied in the article in The Tablet the biggest finding in this paper is that most of the world’s Jewry seem to share tracts of the genome which are ‘identical by descent’ (IBD). You don’t have to be a geneticist to intuit that being IBD implies relatively recent and elevated shared descent from a common set of ancestors. In particular the authors were looking for segments of the genome where individuals shared the same sequence of genetic markers. Very long sequences indicate a relatively recent common ancestor, while many short ones suggest more distant but numerous common ancestors.
It doesn’t always get “better”
The History News Network has a post up, Now It’s Obama Who’s Our First Gay President!, which hammers home points which I’ve been making implicitly and explicitly about historical processes, especially in the United States:
Today, I know no historian who has studied the matter and thinks Buchanan was heterosexual. Fifteen years ago, historian John Howard, author of Men Like That, a pioneering study of queer culture in Mississippi, shared with me the key documents, including Buchanan’s May 13, 1844, letter to a Mrs. Roosevelt. Describing his deteriorating social life after his great love, William Rufus King, senator from Alabama, had moved to Paris to become our ambassador to France, Buchanan wrote
…
This ideology of progress amounts to a chronological form of ethnocentrism. Thus chronological ethnocentrism is the belief that we now live in a better society, compared to past societies. Of course, ethnocentrism is the anthropological term for the attitude that our society is better than any other society now existing, and theirs are OK to the degree that they are like ours.
Porn, a new age, an old age, and all that
I’ve been commenting on internet porn for nearly 10 years. One reason is that as someone who graduated high school in the spring of 1995 I’m probably in the very last cohort of American males for whom pornography was an item subject to scarcity. Those who are 2-3 years younger already experienced a totally different world. The furtive quest to find a friend of a friend whose dad was less than vigilant in guarding his porn stash was a rite of adolescent male passage in my cohort, but would seem totally laughable by 1997. There’s a lot of commentary on the effect of porn on society and sexual relations, but from what I can tell nothing much has really changed between then and now, except that hardcore porn has become harder. Before I see hard data I’m skeptical that American males accept more perversion because of watching porn. Read the Kinsey Reports; farm boys long knew some farm boys lost their virginity to animals.
All this must be kept in mind when reading pieces tinged with moral panic, such as this one in The New York Times, So How Do We Talk About This?, which details the reaction of parents to their children discovering porn. There are few specific elements which strike me as manifestly stupid. For example:
Bonnie, a university administrator in North Carolina with a teenage son and two stepdaughters, realized only after discussing the matter that she and her husband had been sending unintended messages by emphasizing safety and self-protection with the girls and limits with her son.
“Later, we realized how terribly, albeit unconsciously, sexist that was,” she said.
The Malagasy Ancestry Project
Just a heads up, Dr. Joseph K. Pickrell has begun moving on the Malagasy Ancestry Project. More information:
The genetics of the Malagasy people have been essentially unstudied. Analysis of Y chromosome and mitochondrial DNA markers have corroborated the lingustic evidence that the Malagasy result from admixture between southeast Asian and east African populations [1,2]. However, no genome-wide data from Malagasy individuals has been analyzed to date (with the exception of the individuals in this project).
Our goal is to address a number of questions about the genetics of the Malagasy. These include, but are not limited to:
1. What fraction of ancestry in the Malagasy is from Africa rather than southeast Asia?
2. Does this fraction vary geographically and/or ethnically?
3. Who were the populations that first settled Madagascar?
4. Was Madagascar settled once from southeast Asia, or multiple times?
5. Can we use genetics to more precisely date the arrival of African populations in Madagascar?Our approach to this project is to use data contributed from Malagasy individuals who have been genotyped by a personal genomics companies. If you would like to contribute your data, please contact us.
Current results are available from the tabs at the top of this site, and will be updated as the project progresses.
Again, thanks to the people who contributed to genotype the second person. Second, there were several complaints in the origin threads that these individuals were not representative. If this is so, get some genotypes!
The bell curve of personality?
I stopped reading much in the area of personality and behavior genetics a few years back. The main reason is I had a really hard time believing there were very good quantitative measures of many of the traits. A secondary issue, though probably nearly as important, is that some friends were making it clear that they strongly suspected that a lot of the studies in the area of behavior genomics were “underpowered” in a statistical sense. These two issues gnawed at me to the point where I pretty much threw my hands up in the air. Mind you, I accept that personality is substantially heritable. But just because something is heritable does not mean that it is obvious that you’ll be able to detect “the gene” implicated in the variation of the trait. I accepted decades of findings in behavior genetics. But it didn’t seem like we were going anywhere beyond it.
Now a new paper out in PNAS uses genomics to shed light on this issue in the same manner as with intelligence or height. The paper is The genetic architecture of economic and political preferences, and it is free to all. The two primaries takeaways are:
Thanks for the memories
I’m not big into music, being of the aesthetically retarded set, but as I age memory becomes more important, and that is strongly colored by music. The 80s anthems of the Beastie Boys were part of the cultural firmament for me, but at that stage I was more of a Transformers kind of guy. In contrast, So What’cha Want takes me back to the summer of ’92 in a very visceral way. I had come to an age where the Beastie Boys were no longer social white noise, but the rhythm of a life which seemed to roll out before me with possibilities (OK, let’s keep it real, at the time the possibilities were quite proximate and driven by hormonal rushes of puberty).
The great pruning, and the great synthesis
Sahul 10,000 years ago
John Hawks has a very long rumination on the story of blonde Melanesians which came out last week. If I can read between the lines I think some of the implications dovetail with John’s thesis in his 2007 paper on adaptive acceleration. But I’ll leave the deep reading of tea leaves to those better versed in such affairs. Rather, I will comment on two issues. The first is specific. I believe that the TYRP1 R93C allele responsible for blonde hair among the Solomon Islanders is going to be found to be the same one responsible for blonde hair around New Guinea and among some Australian Aboriginals.
There are several reasons why I suspect this. First, these Oceanian populations do seem to be a distinctive clade. There are some disagreements among geneticists as to whether they are the descendants of the first settlers of Oceania in totality, or whether they’re a compound lineage. The natural historical details need to be teased apart, but there’s no doubt that they’re a distinct and separate phylogenetic lineage in relation to other human populations (with some admixture from Austronesians in the case of Melanesians). Second, the phenotype of rather light hair, and dark skin, is striking and parallel among all these populations. It is not entirely impossible that random genetic drift could stumble upon an architecture which results in such a suite of characteristics, but I’m generally skeptical of this possibility of having occurred several times in the same human lineage, when it seems relatively rare in other populations (the loci associated with light eyes and light hair in Eurasians seem to have some effect on skin color as well, so it is difficult, though not impossible, to have very dark skin and light hair). Third, as noted in John’s post, this seems an “old” variant. A new mutation which rose rapidly in frequency should have a lot of associated markers flanking it (ergo, high linkage disequilibrium). Again, we need to take into account the joint information here; there seem several Oceanian populations where the allele is at high, but still minor, frequency (assuming it is the same allele). Oceanian populations, especially those verging toward Melanesia, have low effective population sizes. If this is an old variant I am curious as to why it has not fixed in any of the daughter populations (recall that if it did fix, and admixture recently drove it below ~100 percent, there would be a lot of linkage disequilibrium). Therefore, I think we have to seriously consider the possibility that balancing selection is maintaining this polymorphism in the Oceanian populations. This does not entail that the selection is targeting the hair color phenotype, though it may.
Reification is alright by me!
Long time readers know that I’m generally OK with reification as long as we don’t take it too seriously. And we do that all the time. An “object” is really only an “object” in a human-sense. Reduced down to particle physics it is an altogether different entity. But on the human-scale asserting that a chair is indeed a chair, rather than cellulose, etc., (or now, polymers), and further down basic macromolecules, is a useful “fudge.” Similarly, I’m generally skeptical of the idea that we have a clear & distinct model for what a “species” is. The framework is very different when you’re talking about prokaryotes, as opposed to plants, as opposed to mammals. The question is not species, but what utility or instrumental value does the category or class species have?
For most of the stuff I’m concerned with, the messy shapes of reality which are the purview of biological science, we are all fundamentally nominalists in our metaphysic. We may accept that we’re idealists in the sense of cognitive or evolutionary psychology, but human intuition does not make it so. The categories and classes we construct are simply the semantic sugar which makes the reality go down easier. They should never get confused for the reality that is, the reality which we perceive but darkly and with biased lenses. The hyper-relativists and subjectivists who are moderately fashionable in some humane studies today are correct to point out that science is a human construction and endeavor. Where they go wrong is that they are often ignorant of the fact that the orderliness of many facets of nature is such that even human ignorance and stupidity can be overcome with adherence to particular methods and institutional checks and balances. The predictive power of modern science, giving rise to modern engineering, is the proof of its validity. No talk or argumentation is needed. Boot up your computer. Drive your car.
It all started with talk.origins (and Usenet)
Chatting with Dan MacArthur on twitter about the old days of Usenet, and arguing with Creationists in the days of yore (MacArthur actually flipped a Creationist!). Here’s a toast to the innocence of that bygone age around the turn-of-the-century….
(separate “shout out” to those who remember me from soc.history.what-if)
Finding fake roots
I haven’t watched much of Henry Louis Gates Jr.’s Finding Your Roots series. It seems like Gates has kind of created a mini-empire in genealogical series on PBS. More power to him, but it hit diminishing returns for me a long time ago. But I see clips online here and there. And something which I saw really kind of disturbed me. From what I can gather Gates regales his subjects with their DNA results, and tells them their ancestral quanta fractions. Nothing too amazing. But it seemed clear to me that when Gates referred to “European”, “Asian” and “African” ancestors, he was communicating to the audience that these quanta really represented those exact populations!
I assume that the geneticists Gates works with explained to him the falsity of this typology. I also understand that the television format results in natural license. But Henry Louis Gates Jr. has produced lots of these shows now. He has the leisure to unpack the concepts for the lay audience. As it is, it seems he is repeating misconceptions of model-based clustering algorithms. Misconceptions mind you which persist even within the biological community. But that doesn’t make it any better.
For those who aren’t getting the essence of what I’m saying, above are my 23andMe results. I’m 60 percent European, 40 percent Asian. But those fractions were produced assuming that I could only be a combination of Northern European, East Asian, and West African! Computational algorithms do not return results of the form “I’m sorry, but the input is going to generate useless output.” So they came back with these results, which are highly misleading. Adding another reference population from South Asia makes the results much more plausible. The take-home is that the terms for each quanta are only mnemonics. They should never be taken literally.
Genetics and genomics projects galore!
Thought I would pass these on. A graduate student at Rice is trying to raise some funds for research, Genopolitics: Your Genes Affect How You Vote!. The methodology is a twin study:
To test this, I’ll track how genes affect attitudes during the 2012 US Presidential election by running several surveys of twins. Why twins? Well, there are two kinds of twins: identical twins (called monozygotic, or MZ) and fraternal twins (called dizygotic, or DZ). MZ twins share 100% of their DNA, but DZ twins share only about 50% of their DNA just like normal siblings. Every twin is born around the same time as his or her co-twin, so each pair of twins shares a common upbringing. If politics is mostly about upbringing (as traditional theories would have us believe), then fraternal (DZ) twins should be just as similar on average as identical (MZ) twins. But if genes do play a role in political attitudes alongside upbringing, then DZ twins should be less similar to each other than MZ twins, since MZ twins share more of their genes. So by tracking attitude changes during the election, if the attitudes of identical twins change together more than the attitudes of fraternal twins, this would suggest that genes play a role in political attitude change.
Secod, Genomes Unzipped put up a very complimentary review of openSNP. I just went in and added a bunch of phenotypes for me. I’d say openSNP is one of those attempts to bridge the space between the type of people who find 23andMe a bit overwhelming, and those who are comfortable using plink and phasing their genotypes.
Every tribune a Rick Santorum!
After the power of Islamists in Tunisia and Egypt made itself felt, and current domination of Iraq by Shia political parties, and the likely strength of Islamists in Libya, the media finally has become more cautious about pushing any narrative which makes them look as prescient as Paul Wolfowitz about the nature of the Arab body politic. So, for example, this article surveying the Islamist strands within the anti-Assad coalition in Syria. The problem for the Islamists is that Syria is “only” on the order of 75 percent Sunni, and they do not want to project the image of chauvinist exclusivity which has come to the fore in Egypt, lest the religious minorities dig in in their strongholds (e.g., along the coast). But I think it needs to be pointed out here that in Iraq the Shia Arabs are only somewhat more than 60 percent of the population. In other words, there is no question that a democratic order will result in the regression of minority rights in Syria if the Islamic Brotherhood wishes this to the the nature of things.
Bell Beakers and R1b
Over at Dienekes blog he has a post up about the extraction of R1b from a male who lived in Germany 4-5,000 in the past. This is important because R1b is one of the two most common male lineages (on the Y chromosome, passed from father to son) in Europe, and, it has inexplicably been underrepresented or absent in the ancient DNA samples. The other modal lineage is R1a (it too is underrepresented).
I have a pretty good grasp of variation on the autosomal dimension. A modest familiarity with uniparental lineages, Y and mtDNA. And finally, a rather weak understanding of archaeological patterns. Since mtDNA tends to be found at very high concentrations in subfossil remains you’ll get a good yield of that in the near future (as in the paper Dienekes covers). Y chromosomal information is more difficult. The problem with autosomal information is that you need more of it to make robust genealogical inferences (due to confounding with selection, as well as recombination breaking apart haplotypes), though if you manage to hit a functional region that can be very informative.
Razib Khan’s degrees are in biochemistry and biology. He has blogged about genetics since 2002, previously worked in software development, is an Unz Foundation Junior Fellow and lives in the western US. He loves habaneros.
