Slate has some very interesting excerpts from The Big Necessity: The Unmentionable World of Human Waste and Why It Matters posted today. The reality that a great deal of the illness in today's world is caused by fecal contamination is well known. The proximate cause of many minor illnesses is mild food poisoning, but food poisoning itself is ultimately generally caused by poor hygiene.  It seems straightforward to imagine that poor sanitation can be a significant drain on economic productivity. But on this weblog we've also addressed the possibility of pathogens playing a role in changing personalities and temperaments. In Farewell to Alms Greg Clark made the case that the greater mortality due to poor hygiene shifted the death schedule and so relieved Malthusian pressure. In contrast, East Asia was notable for having a rather efficient system of human waste disposal and reuse, and the concomitant lower death rate resulted in more Malthusian pressures and lower per capita wealth. One of the positive developments in the historical disciplines has been the a shift away from narrative annals describing political and social happenings on the elite level, to a more thorough quantitative analysis of the state of mass culture and material condition. Both perspectives are important; in War and Peace and War Peter Turchin reports military historical research which suggests that the presence of Napoleon at a battle was the equivalent of the French having 30% more troops! This suggests that to some extent Great Men do matter, but one must remember that the emergence of parvenu such as Napoleon was conditioned upon the Malthusian economic and social stresses of late 18th century France.

But the Slate piece also puts the spotlight on the particular nature of human psychology and its relation to feces:

Reuse works better when it involves camouflage. This technique is used, appropriately for a militarized country, in Israel. During a presentation at a London wastewater conference, a beautiful woman from Israel's Mekorot wastewater treatment utility, who stood out in a room full of gray suits, explained that they fed the effluent into an aquifer, withdrew it, then used it as potable water. "It is psychologically very important," she told the rapt audience, "for people to know that the water is coming from the aquifer." This is a clever way of getting around fecal aversion. Not having wastewater-and not wasting water-would be better still.

I'm sure this is not surprising to most readers, especially if you have read something like Paul Bloom's Descartes' Baby. One can posit pretty straightforward adaptive reasons for why humans tend to have an aversion to feces and rot; but whatever the ultimate root of these instincts they're pretty universal. Of course, like eating spicy peppers humans seem able to get around these hardwired instincts, or leverage them in some way so as to invert their effect. For example, the application of feces upon wounds had a long history in pre-modern medicine, all the way back to the Egyptians. The detailed inferences can sometimes be surprising, but the point is that though most humans reflectively accept the atomic and molecular understanding of the world, reflexively they are Aristotelians. Intuitions can be overcome or unlearned to a great extent, but if one wishes to reform the human outlook one needs to take into account its a priori biases. The human mind is not amorphous clay which one can mold into any shape in an infinite manner of ways, rather, it is a collection of blocks and units which likely have innumerable combinatorial possibilities, but certainly a finite number subject to various constraints and conditions.

The cultural variation in attitudes which is overlain on human universals illustrates the reality that despite innate tendencies human minds are elastic. Consider:

Sanitation professionals sometimes divide the world into fecal-phobic and fecal-philiac cultures. India is the former (though only when the dung is not from cows); China is definitely and blithely the latter. Nor is the place of excrement confined to the fields. It has featured prominently in Chinese public life and literature for at least a thousand years.

The recycling of "night soil" mentioned in the Slate piece was also highly developed in Tokugawa Japan. Not only did the practice increase crop yields so that a large population was feasible with pre-modern agricultural techniques, but it had a byproduct effect of fostering public hygiene and reducing the disease burden (noted above). As far as the Chinese go, the attitude toward utilization of human waste, as well as other cultural traits such as minimal food taboos, illustrate the deep strain of pragmatic rationalism which many early or proto-Enlightenment philosophers so admired. As for the South Asia tendency to extend and elaborate on human intuitions and tendencies as opposed to channeling toward material ends, if you have nothing good to say, say nothing at all....

Labels: Evolutionary Psychology, History, Psychology

Yann reviews a recent paper, Lactase persistence-related genetic variant: population substructure and health outcomes.

Labels: Genetics

The Whit Stillman film The Metropolitan is viewable online for free (at Hulu).

In 2005, Barry Marshall and J. Robin Warren won the Nobel Prize in Physiology or Medicine for showing that a pathogen was behind the common diseases gastritis and peptic ulcers. Now the 2008 Prize goes to Harald zur Hausen, who showed that pathogens cause the common disease cervical cancer. As far as theory is concerned, these findings are not surprising (PDF). The most recent New Germ Theory winner before these two was Peyton Rous in 1966, whose work on cancer-causing pathogens began in 1911. You might also count Johannes Fibiger's 1926 Prize for what was thought to be a cancer-causing nematode.

And two of the early winners -- Koch in 1905 and Laveran in 1907 -- contributed to the Original Germ Theory of disease. So after 100 years, perhaps people are finally starting to take the idea seriously? Common disease-common variant researchers in human genetics may get more media coverage, including the science media, but the Germ Theory people are cleaning up where it counts.

Labels: pathogens

I think a lot of the reason for the unfounded hyperbole that has been spewed by many people at GNXP and elsewhere (especially by myself) is that this election is just plain ugly...there are no good choices. While no candidate may be Big Brother, O'Brien, HitlerStalinTojo, or the devil incarnate, they are almost certainly amongst the worst candidates Americans have had to choose from in U.S. history (is worst 10 percent reasonable?)

While there has been a lot of hyperbole against all candidates, there has been also a lot of unfounded praise and optimism, I think in hopes that there is a bright spot somewhere amongst these four candidates. I think this is where some commentators and posters such as myself have been driven to hyperbole.

In any case I apologize to anyone who had to dredge through my inappropriate, polemical, and unfocused posts. Time to go back to science or at least non-tabloid grade history.

Labels: apology to readers, commentator peacekeeping, politics

Over at evolgen, more on the cis vs. trans debate:

...First, there is an excess of trans variation within populations. And, second, cis changes tend to be additive, while trans changes are dominant/recessive. That means recessive trans mutations can segregate in populations without phenotypic effects, while cis changes are exposed to selection from the get go (either purged by purifying selection or fixed by positive selection).

Labels: Genetics

The video of deep ocean fish in this news report is fantastic (for broadband browsers).

Many recent posts on this site have been dedicated to genome-wide association studies, in which variants across the genome are tested for their association with a phenotype. These studies, if successful, identify a relatively small candidate region that presumably contains some sort of polymorphism that plays a role in the phenotype. Identifying that causal polymorphism is far from trivial.

A recent study on cleft lip provides a glimpse into how these sorts of follow-up might proceed. The authors had earlier shown (through a candidate gene study) that SNPs in IRF6 (a transcription factor) were associated with cleft lip. In particular, a non-synonymous SNP in the gene was repeatedly and reliably associated with the phenotype. In this follow-up study, however, the authors find another, non-coding SNP that shows the strongest association with the phenotype.

The authors are then able to show that this SNP falls in a binding site for another transcription factor, and that the region is an enhancer element that drives expression of IRF6 in the developing face. They don't show that the SNP changes expression patterns, but it's still a pretty impressive piece of work, and exemplifies the extensive experimental work that will be needed to ultimately refine the glut of genome-wide association signals being published.

Labels: Genetics

Evolutionary emergence of responsive and unresponsive personalities:

In many animal species, individuals differ consistently in suites of correlated behaviors, comparable with human personalities. Increasing evidence suggests that one of the fundamental factors structuring personality differences is the responsiveness of individuals to environmental stimuli. Whereas some individuals tend to be highly responsive to such stimuli, others are unresponsive and show routine-like behaviors. Much research has focused on the proximate causes of these differences but little is known about their evolutionary origin. Here, we provide an evolutionary explanation. We develop a simple but general evolutionary model that is based on two key ingredients. First, the benefits of responsiveness are frequency-dependent; that is, being responsive is advantageous when rare but disadvantageous when common. This explains why responsive and unresponsive individuals can coexist within a population. Second, positive-feedback mechanisms reduce the costs of responsiveness; that is, responsiveness is less costly for individuals that have been responsive before. This explains why individuals differ consistently in their responsiveness, across contexts and over time. As a result, natural selection gives rise to stable individual differences in responsiveness. Whereas some individuals respond to environmental stimuli in all kinds of contexts, others consistently neglect such stimuli. Interestingly, such differences induce correlations among all kinds of other traits (e.g., boldness and aggressiveness), thus providing an explanation for environment-specific behavioral syndromes.

Related: Heritability of the Ultimatum Game, Chimps, the ultimatum game & time preference and Altruism and Risk-Taking: Kinda Heritable.

Labels: Evolution, Evolutionary Psychology

Leading geneticist Steve Jones says human evolution is over. Steve Jones has an appointment in the Galton laboratory, and has written several books on human genetics (e.g., Y: The Descent of Man and Darwin's Ghost: The Origin of Species Updated). But he says things like this:

"Small populations which are isolated can evolve at random as genes are accidentally lost. World-wide, all populations are becoming connected and the opportunity for random change is dwindling. History is made in bed, but nowadays the beds are getting closer together. We are mixing into a glo-bal mass, and the future is brown."

First, we're nowhere close to panmixia.* Second, there is going to be a large variance around the expectation. Even if you remove new mutations, there are a lot of variants out there for selection to pick up from the extant genetic background I would think. The future will not be brown for the same reason that people in an English village do not all have the same hair color despite there being a lot of intermarriage.

Lots of other things to point to that leave you confused in that piece, but I'll leave it as an exercise for the readers....

* And what about the lack of importance of population size as a parameter effecting substitutions in Neutral Theory? I know there are ways you can object to this, but Jones' quote seems to garble many issues here.

Update: I emailed an academic who I suspected would know if Jones was being quoted out of context or misrepresented. But they say that this is probably an accurate representation of his views (and they also seem to think that his coherency leaves a bit to be desired).

Update II: Here is Chris Stringer's rebuttal to Jones:

But Professor Chris Stringer, research leader in human origins at the Natural History Museum, London, said the idea that evolutionary pressures were no longer taking their toll on humanity was true of only western civilisation.

He said: "The argument that modern life has stemmed the effects of evolution is true in some areas, such as the way in which medicine has improved health and wellbeing, and the fact I am not out in the cold and wet, but sitting in a nice, warm office with heat and clothing. But that is very much something that applies only in developed, western countries. You only need look to Africa to see how HIV/Aids is still having an enormous impact on selection, and I believe that genetics will continue to play a part in our evolution."

*roll eyes* Someone should tell these guys that you don't need to die to not reproduce.

Labels: Genetics

New episode of South Park this Wednesday. As always you can watch it online.

Think Gene has a new digg-like site up, news.thinkgene.com. Worth checking out.

Beyond Belief III is going down right now, the 3rd to the 6th. Free registration is soldout, but it looks like there are still some pay slots. If you're in the San Diego area you might be able to attend....