Posting may be light, and/or I may skip link dumps, etc., around the Labor Day weekend. Mostly notifying you so you don’t ask if I’m still alive!

Immunity under natural selection. Focusing on three of the genes which showed signatures of selection in the HapMap 3 paper. It’s interesting to note that only a generation ago many scholars were spending time debating about the adaptive value of blood group antigens and the like because so little was known about the impact of natural selection on the genome (since genomics as such didn’t really exist). Now the swell of results requires labor hours to filter.

Y Chromosomal Variation Tracks the Evolution of Mating Systems in Chimpanzee and Bonobo. Basically, common chimpanzees exhibit more “sperm competition” than bonobos. I think this is a case where common chimpanzees are the outgroup to bonobos and humans. It also puts the spotlight on the necessary nuance in traits like “polyandry.” Imported from human mating systems, they don’t necessarily inform very well for our primate cousins.

The Crystal Ball’s Labor Day Predictions. High probability of Republicans winning the House, modest probability of them winning the Senate. Notes that the two are not independent probabilities. Assuming that the Republicans win the House, the probability of them winning the Senate goes up. 100% probability that the “pundits” are going to discuss the “Death of the Democratic Party” for a few months.

Quants merge with humans. There’s a lot of money to be made in the business of money, so where there’s a will, there’s always a way. The Cowles’ Commission’s finding that stock market newsletters 1) are not effective 2) but will continue to be produced, illustrates the power of human psychology within the context of the rational market.

Burger King Has Suitors From Brazil. Another indication of Brazil’s “ascension graphic.” I still don’t get why Russia is in the list of BRICs. Its demographics look like Japan.

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The Democrats’ New Normal. It’s looking real bad. On the other hand, the Dems passed Health Care Reform. What’s the point of being in power if nothing is achieved? I’m sure the Republicans would have lost bigger if they’d passed Social Security Reform, but they would have achieved a big goal of their party.

Guardian science blogs: We aim to entertain, enrage and inform. They don’t have many science blogs. Yet. But I’m sure they’ll add more, and other “big media” outfits will be adding/expanding in the near future.

Wolves Are Smart, but Dogs Look Back. Makes me think of the empathizing–systemizing theory. Dogs empathize, wolves systemize.

Scientists Square Off on Evolutionary Value of Helping Relatives. Carl Zimmer has a good overview of the controversy which emerged out of the Nowak et al. paper, which seems to take a maximalist position against the utility of kin selection in explaining euosociality. Apparently some “big names” are going to be writing a response, so I’ll be curious. I haven’t bothered going through Nowak et al.’s supplements, so I really can’t say much more than that.

Outlines Emerge of Future State in the West Bank. The thing that stood out was the relative quiescence engendered by economic growth. Idle hands and all.

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Vivienne Raper who analyzed the Wikio Top 100 Science Blogs left a comment below:

I’m now curious to find out why there are no ‘popular’ blogs in certain subjects. Do working condensed matter physicists who want to engage with the public write about astrophysics? Or are astrophysicists the only physicists who want to blog for the public? Or does the public only read astrophysics blogs?

The contrast between astrophysics and solid state physics is a clue to what’s going on I think. Solid-state physics is very important work. Like agricultural science solid-state physics may not have all the public glamor, but it puts bread on the table of our civilization. So why all the love for astrophysics? I think part of the issue is real straightforward. Astrophysics lends itself easily to a visual “hook,” such as the false-color image of the Crab Nebulae to the left. This isn’t necessarily the heart of astrophysics of course, but it’s a way to connect with the broader public in a literally eye-catching manner. Compare the image search results for “solid state physics” vs. “astrophysics. Not a good sign if the first page is overloaded with head-shots of old nerdy white, Middle Eastern, and brown guys. But that’s not the only issue here. I think there’s a “soul factor” at work. To understand what I’m getting at, let’s look at Vivienne’s breakdown by the umbrella categories:

Neuroscience, evolution, and astrophysics speak to normative concerns of our species. That is, they grapple with values. The brain is the seat of our self in a material sense, and neuroscience emerges out of a deep tradition of philosophy of mind which goes back 2,500 years. Evolution has had a fraught relationship with teleology, and some philosophers of biology have quipped that their field to a first approximation can be reduced to philosophy of evolution. Molecular biology is more fundamental in a concrete proximate sense, but evolutionary biology is more fundamental in the ultimate abstract sense. And finally, astrophysics when it bleeds into cosmology rather obviously treads on the ground which was once the domain of mythology, of cosmogony. In a very broad sense these disciplines push against our conceptions of ontology. Astrophysics in the most general sense, neuroscience in a very anthropocentric sense, and evolutionary biology spanning the two extremes.

I think the anti-alternative medicine category also emerges from the same dynamic, but mainly not to appeal to it, but to battle it. Modern scientific medicine does not jive with the deep intuitions of many people of how bodily processes work, They wish for a more “holistic” and “natural” model. I use the quotations because these sorts of terms are more figures of speech in this context than anything substantive. If there was a “holistic” and “natural” alternative engineering discipline then engineering weblogs would no doubt sprout up to battle intuitive pseudo-science.

Mathematics is a strange discipline because I think it too falls into the category of a soulful science. But as Keith Devlin observed in The Millennium Problems translating deep cutting edge mathematics to the general public can be very difficult, because there is less room to use metaphor and analogy than in the natural sciences. Technical hurdles are not barrier if analogy and visuals can substitute, but this does not seem so easy for many deep mathematical questions.

I believe therefore the issue here is to a large extent demand side. People get worked up over controversy, and emotionally invested in topics which cross the threshold of deep emotional commitment. Whether we are simply another primate, or sui generis and a Special Creation, fits that bill. More practical, and very important in an economic sense, endeavors may not fit the bill.

Note: I think other factors are at work as well. Climate science is popular because of its high profile in public policy right now and the potential existential implications. There are probably other hidden factors too. Why is neuroscience blogging more well developed than psychology blogging (or at least so a psych blogger has complained to me)? Neuroscience is a young field which is maturing right now, and perhaps it simply has the right demographic profile which allowed it to bloom very quickly in the next technological context. And I also think fMRI images are preferable to another stock photo of rats in a maze!

Image Credit: NASA

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Hope you had a good weekend! Winter is not quite coming…but summer is ending.

Phoneme Inventory Size and Demography. Some original data analysis in this post! Turns out that phoneme segment length is positively correlated with population density. Too often culture is viewed as something we can only have a qualitative understanding of, but these sorts of analyses show that there are ways to get a quantitative grasp of the sea of memes (if this post was of interest, see the blog Replicated Typo).

Why Isn’t the Missing Heritability Nearly Neutral and Tightly Networked?. Interesting idea that we’re missing causal variants because of selection bias on the set of SNPs which current gene chips detect. The past 10 years have been awesome in genomics, but what’s going to happen when whole genome sequencing becomes the norm?

Bring Your Genes to Your Life Insurance Sales Representative. Brad DeLong makes the argument for single-payer as a way to obviate the conundrums which will emerge when genetic profiling of disease becomes more efficacious. This is an area where I think the marketing of personal genomics companies have given people the wrong impression of how powerful the techniques are currently. But the time will probably come when there’s a lot more juice to squeeze out of the prediction algorithms. And yet one issue that DeLong assumes is that your genetic endowment is a lottery. That it’s something we can’t control in generation t + 1. That’s false. Parents will be able to screen. If health care is totally socialized, should we also socialize some aspects of the decision making process in relation to procreation? Rights without responsibilities?

Iranian Jews in America: Torn Between Homelands. In the 2004 movie Crash both of the Persian leads were played by Iranian Americans who also happen to be Jewish, Shaun Toub and Bahar Soomekh. Here’s Bahar Soomekh, “Just because I’m in Hollywood doesn’t mean that I forget that I’m Persian or that I’m Jewish. Judaism is not only my religion—it’s my identity.” Remember that only a minority of Iranian Americans are self-identified Muslims.

In Search of Time. A cognitive trick to stretch out your perception of time? Perhaps.

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What do science bloggers blog about? My study of the Wikio Top 100:

As a former scientist, I like evidence-based blogging so I needed a dataset to test my theory that ‘all top bloggers are biologists’. To get a randomish sample of big science bloggers, I did a dodgy analysis of the blogs in the Wikio Top 100 science bloggers ranking.

Here’s the breakdown of bio bloggers topicality:

The large number of neuroscience bloggers has always perplexed me. Any idea what’s going on there?

A minor note: could someone at Wikio update my blog’s address? I tried to do it let myself but it wouldn’t let me. Would be nice to get that before I drop off the list of top 20 science blogs.

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Update: Results so far….

Too harsh - 3.0%
About right – 15.0%
Not harsh enough, though he shouldn’t be ostracized – 26.0%
He should be ostracized from science - 56.0%

The editor of Cognition believes that Marc Hauser was guilty of fabrication in light of what he’s seen in the Harvard report on Hauser’s misconduct. Marc Hauser is on on leave, and will be supervised in his research in the future. But, he continues to teach extension courses. It doesn’t seem as if his work on human moral cognition is under a cloud. There are other researchers working in the same area who have been able to replicate his general findings. Rather, it seems that it was the work on cotton-top tamarins which is under scrutiny, in large part because Marc Hauser was the only one who was doing that sort of research on that organism.

In the end this is about a violation of trust. Alison Gopnik told Nicholas Wade that “It’s always a problem in science when we have to depend on one person.” Science is a famously a self-regulating culture. The system works because science is about something real, and scientists are constrained by the data. But, science is also a human enterprise so conscious and unconscious bias enters into the system. The question is whether the system works well enough that scientists trust their colleagues to report truthful results. If every scientist had to check in on every other scientist I suspect that the system would collapse because there aren’t enough labor hours to go around. Science is very competitive, and many people work many hours for only modest renumeration. Careers hang in the balance, and many are weeded out. People accept this because there is at least a perception of a minimal level of fairness. Finally, on a social scale the economic growth which our society depends on is driven in large part by scientific innovation. The culture of science is the engine upon whom billions depend.

My first thought about what has happened with Hauser is that he is “too big to fail.” He’s at Harvard, and, he has powerful friends. It reminds me of what a friend of mine told me about what occurred at a major tech corporation he had worked at. Apparently there had been an incompetent hire who lasted for years because no one wanted to take responsibility and fire him, because the very fact that managers actually hired him was a negative reflection on their discernment if someone eventually passed judgement on this individual. So there wasn’t an incentive to bite the bullet, and the incompetent employee was moved from department to department for years.

But I’m curious what readers think. Below is a survey asking what you think of the magnitude of Marc Hauser’s punishment in relation to his infractions. I’ll update the results at the top of this post every day for a week.

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Have a good weekend.

The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes. This is in my RSS, but not on the Nature site, so here’s the snip I have: “The ratio of X-linked to autosomal diversity was estimated from an analysis of six human genome sequences and found to deviate from the expected value of 0.75. However, the direction of this deviation depends on whether a particular sequence is close to or far from the nearest gene. This pattern may be explained by stronger locally acting selection on X-linked genes compared with autosomal genes, combined with larger effective population sizes for females than for males.” Looks interesting.

Journal: Hauser fabricated data. Scientists can be “too big fail” it seems.

Epistasis: Obstacle or Advantage for Mapping Complex Traits? They argue that it’s an advantage, and you can squeeze more juice by taking into account gene-gene interactions.

Genome-wide association study identifies variants in the CFH region associated with host susceptibility to meningococcal disease. There’s a model that unexpected deaths from infections which should be benign or asymptomatic are actually due to genetic variation. Specifically, these deaths run in families. Was there a time when everyone was symptomatic? It seems that this is a case where looking at indigenous populations who haven’t been as exposed to pathogens would be of interest.

Does Your Language Shape How You Think? It seems more a matter of degree if so.

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Essential Science Fiction Movies. People always put Metropolis on the list, or bemoan the fact that they haven’t seen it. What do you think of it? I quite enjoyed, but much of the greatness of the film seems to be that it prefigured so much of what was to come.

The Real Estate Collapse. Jonah Lehrer suggests that the problem with prices not declining (or at least listed prices) has a lot to do with loss aversion/sunk cost fallacy. I agree. On the other hand, many Americans who are older bought into the idea that real estate was the “safe” place to put their savings, and now are looking at taking a big loss. If you have 15-30 good years left it might be really hard to simply “move on” when you don’t have the time left to rebuild equity.

Our advice re: donations for Pakistan flood. The idea is to get the most bang-for-your-buck. From what I have heard ~20 million people have been impacted by the floods. I guess it gives you a sense of what a Pakistani peasant’s life is worth to the world.

Generation X More Loyal to Religion. This looks more likely to just be the law of diminishing returns. The disaffection of the Baby Boomers from organized religion correlates with a relaxation of social norms. The distribution of religiosity among Gen-X probably more accurately reflects their individual preferences.

This Hauser thing is getting hard to watch. David Dobbs reviews some of the issues with l’affaire Hauser. Basically everyone who is a blogger of note seems to be getting emails from people who wish to remain anonymous. Draw whatever conclusions you want to from that.

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