Thoughts on the BGI IQ study.

Language Evolves in R, not Python: An apology. Open science is good.

Are Twin Studies “Pretty Much Useless”? One interesting, but unsurprising, aspect of the response to execrable Brian Palmer piece is that several of us in the blogosphere pointed out pretty much the same set of well known findings to refute his weird charges. This isn’t rocket science.

Romney vs. Perry: It’s personal. ‘“I think he had a few exasperating experiences with Perry, and he’s not alone in that,” said one source close to Romney. “I think Mitt thinks Perry is not that bright.”’

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In the comments below a weird fact came to light: it does not seem that liberal/Democrat reduced skepticism toward astrology vs. conservatives/Republicans can be explained just by a secularization, and therefore diminished Christian orthodoxy. There are two reasons for this. First, on a priori grounds most people are religious, liberals and conservatives. The difference between the religious and irreligious on this issue would have to be rather large, and the different apportionment across ideology to be striking, for it to drive the division which seems so robust. Second, within the results it seems rather clear that the gap between liberals and conservatives is most evident amongst the religious of both! In other words, secular liberals and conservatives tend to agree (and be skeptical) in relation to astrology. While religious conservatives are skeptical of astrology, as one would expect from orthodox conservative Christians, religious liberals are not. The table below shows some results.

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Above is the Ngram result for paradigm shift, a ubiquitous descriptive concept which can be quite slippery when applied to contemporary science. For example, every few years there is always a new “revolution” which is going to overturn “Darwinism.” Be it punctuated equilibrium, symbiogenesis, or epigenetics. But over time revolutionary fervor abates, and the orthodoxy remains standing, albeit with modifications and alterations, making it all the more robust.

I thought of this when I saw Andrea Cantor’s comment below in relation to twin studies:

Twin studies underestimate heritability only if you subscribe to the crude notion that the effect of genes is additive, i.e., keeping “environments” the same, the more similar two people are genetically the more alike they will be. This ignores everything we now know about the way genes work.

Genes are not self-activating: they do not turn themselves on and produce traits. Genes do not, in fact, produce anything. Genes are turned on and off by the epigenome in response to environmental inputs. If you are inclined to doubt this, then consider: If all the cells in our body are supposed to contain identical DNA, how do you account for the existence of different tissues and cells types (answer: the epigenome). Twins have been shown to have significantly different epigenomes in the womb. Does this show that twin studies underestimate heritability? Of course not. It shows, rather, that these studies are out of touch with advances in molecular genetics.

You are all committed to a crude, 19th century conception of the relationship between genotype and phenotype. Twin studies are based upon a scientific paradigm that has remained unchanged since the time of Galton. Problem is, recent advances in molecular genetics are bringing about a paradigm shift in the science of genetics.

Twin studies make it seem all so easy: All you need is a large data set that has zygosity status and statistical software and any undergraduate can unravel the biomolecular basis of human behavior.
Would that it were so easy.

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I’ve been following the development of the BGI study on IQ pretty closely. I wanted to note two main caveats people should be aware of with regard to its methodology.

First, as with any case-control study, volunteer bias will be an issue. If the cases are a certain class of very smart people, rather than a representative sample, then genes peculiar to that class of smart people will show up as hits. The BGI study is choosing people who are more math than verbal-oriented; will math-specific genes show up as general intelligence genes? Other confounds along these lines are possible– PhD genes, Ashkenazi genes, curiosity in new study genes, etc..

Second, because the study doesn’t completely control for family environments (possible only by comparing siblings to each other), gene-environment correlations and interactions can cause problems as well. For example, suppose that high IQ parents also confer better environments for their children. Then the IQ gene effects will get an extra “boost” from that environment.

None of this is to downgrade the awesomeness of the BGI study. It should be viewed as an important step in resolving the nature vs nurture controversy. Overeager journalists and bloggers are urged to wait a few more years before we finally resolve the IQ debate.

Someone on twitter was curious about GOP attitudes toward astrology. I left the party breakdown out of the previous post because ideology accounts for most party differences. In other words, conservatives are more skeptical of astrology than liberals, and Republicans more than Democrats, but the second result just seems to emerge from the Republican’s greater conservatism.

Why are independents so gullible? It probably has to do with their lower average intelligence (this goes for moderates too). So I simply limited the sample to those with at least bachelor’s degrees to control for intelligence:

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I’m still scratching my head over the rather atrocious Brian Palmer piece in Slate, Double Inanity: Twin studies are pretty much useless. It’s of a quality which would make it appropriate for WorldNetDaily. Here are the responses of Jason Collins, Daniel MacArthur, and Alex Tabarrok. The comments at Slate were rather scathing too. I observed over at Genomes Unzipped that many of the assertions in the piece were in the “not even wrong/what does that even mean?” class. Palmer is apparently a freelancer at Slate, and they’re doing a bunch of stories on twins this week. I wonder if they just sent him the assignment with instructions on the slant, and he took it a little too far. Even if it was a polemic it was a shoddy and embarrassing one. My main concern is that many people perceive Slate to be an organ which publishes “smart” and well researched pieces, and they’ll take Palmer’s screed at face value.

The scientific problems with the article are legion. But still: how does something like this get published in a relatively high-end publication? Brian Palmer has editors presumably. If the copy was an undergraduate paper the prose would be relatively polished, but the overall structure of the argument and the naked guilt by association are marks of hurried sloppiness. The attempt to smear twin studies by association with Francis Galton was pathetic and childish. What next, turn against the concept of statistical correlation because Galton introduced it? There has to be more to this story than what we know. Or perhaps the people at Slate just don’t know anything about science.

Over at Culture of Science Sheril Kirshenbaum posts a figure from the NSF displaying what proportion of those without high school educations and those with college educations accept the scientific status of astrology. It’s pretty clear to me that this is the ASTROSCI variable from the General Social Survey. It asks:

Would you say that astrology is very scientific, sort of scientific, or not at all scientific?

It’s also nice that this question was only asked in the latter half of the 2000s. So it’s timely in terms of demographic breakdowns. Speaking of which, here are a whole host of classes and their attitudes toward astrology’s scientific status:

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1) Post from the past: Men at work: hoes, ploughs, and steel.

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The Pith: Evolution is a sloppy artist. Upon the focal zone of creative energy adaptation can sculpt with precision, but on the margins of the genetic landscape frightening phenomena may erupt due to inattention. In other words, there are often downsides to adaptation.

A few weeks ago I reviewed a paper which suggests that Crohn’s disease may be a side effect of a selective sweep. The sweep itself was possibly driven by adaptation to nutrient deficiencies incurred by European farmers switching to a grain based diet. The reason for this is a contingent genomic reality: the positively selected genetic variant was flanked by a Crohn’s disease risk allele. The increment of fitness gain of the former happens to have been greater than the decrement entailed by the latter, resulting in the simultaneous increase in the frequency of both the fit and unfit variants. You can’t always have one without the other.

But that’s just focusing on one gene, though the authors did indicate that this may be a genome-wide feature. A new paper in PLoS Genetics argues that that is the case, at least to some extent. Evidence for Hitchhiking of Deleterious Mutations within the Human Genome:

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The class human or H. sapiens refers to a set of individuals. On the grand scale it’s really not all that clear and distinct. When do “archaic” humans become “modern” humans? Taking into account human variation, what is a “human universal”? A set of organisms are given a name which denotes the reality that they may share common ancestry, and interact behaviorally, and are potential mates. But many of these phenomenon are fuzzy on the margins. Many of the same issues which emerge in the “species concept” debates are rather general up and down the scales of natural complexity. A similar problem crops up when we conflate the history of genes with the history of populations. Such a conflation has value and utility to a first approximation. The story of mitochondrial Eve was actually the history of one particular locus, the mitochondrial genome. But it did tell us quite a bit about the history of the human species, even if in hindsight it looks as if some scientists overinterpreted those findings. One of the major issues I’ve noticed over the past year, with the heightened likelihood of archaic admixture in the modern human genome, is that people regularly get confused by the difference between total genome ancestry, and the evolutionary history of one particular gene.

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