Saw Ratatouille today. Never once checked the time. Very good film. So far Yahoo Movie critics & users give it an A-, and it seems like it’ll win the box office. Much recommended (Pixar animation is the bomb obviously, but the story is really good and could only be told in a non-live action context for obvious reasons). This is a movie whose target audience are children and foodies, so definitely a strange and surprising beast. A flavor you won’t forget.

Chris of Mixing Memory has a must read post up about the normal distribution. The man did the tedious work of encoding mathematical notation and symbolism into HTML, so he should take a bow.

Update: iPhone, iPhone, iPhone? Jobs is God? iPhone iPhone iPhone iPhone!!! iPhone. iPhone. iPhone? iPhone-iPhone. iPhone iPhone. Apple Store, wet my pants. iPhone iPhone iPhone. iPhone!!!! iPhone iPhone. iPhone iPhone iPhone iPhone iPhone iPhone iPhone iPhone. Jobs does not exist! iPhone? Jobs is oppressive!!! iPhone. Ah…land line.

There’s a paper to be published on domestic cat phylogenetics in Science tomorrow. National Geographic has a summary, but Forbes has a more thorough treatment. The short of it is that the maternal lineages (mtDNA) of domestic cats seem derived from the Near Eastern varieties . The acculturation of humanity toward domestic cats seems to have taken place gradually between 12,000 and 3,600 years ago, the presence of five distinct maternal lineages suggests that it wasn’t one event, but several simultaneous parallel ones. Sedentary populations rooted around agriculture were the likely necessary environment for the emergence of the cultural co-evolution between cats and humans. Though this study is interesting, please note that the survey of female lineages is a small slice of the total ancestry. Male mediated hybridization wouldn’t be picked up, and the interfertility of domestic and wild cats means there likely has been genetic exchange between the two groups over time.
Update: Nick Wade in The New York Time has more.

John Hawks has the details on a new paper (DOI might not work yet) coming out in PNAS. The researchers trying to reconstruct the Neandertal genome are reporting biases in degradation which is aiding their task. Scientific American has a summary.

Via Sepia Mutiny.

Someone named Schvach Yid left an irritated comment in response to my post about the term Judeo-Christian. He also sent me a short email clearing up the fact that Judaism is more than legalism, and that it is steep to consider Jews non-Western. I think addressing these questions is worthwhile insofar as others might wonder what business a blog whose central theme focuses on evolutionary genetics has with venturing into topics such as the discussion of the history of Judaism and Christianity.

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John Hawks has an excellent decomposition of the story yesterday in The New York Times about paleoanthropology and biology.

John Noble Wilford in The New York Times has a piece titled The Human Family Tree Has Become a Bush With Many Branches, which reflects the current consensus thinking that the hominid lineage was until recently relatively diversified, with a host of species extant contemporaneously (the other view is that many of the “species” we conjecture are just the extant morphological variation of one species across varied local ecological conditions). To be honest the piece seemed to just be throwing a lot of genus and species names at you all the while stirring up the tempest in the tea pot between paleoanthropologists and biologists. Consider:

Now paleoanthropologists say they accept the biologists as allies triangulating the search for human origins from different angles. As much as anything, a rapid succession of fossil discoveries since the early 1990s has restored the confidence of paleoanthropologists in the relevance of their approach to the study of early hominids, those fossil ancestors and related species in human evolution.
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“All biology can tell you is that my nearest relative is a chimpanzee and about when we had a common ancestor,” he said. “But biology can’t tell us what the common ancestor looked like, what shaped that evolutionary change or at what rate that change took place.

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Humans Have Spread Globally, and Evolved Locally (The New York Times):

No one yet knows to what extent natural selection for local conditions may have forced the populations on each continent down different evolutionary tracks. But those tracks could turn out to be somewhat parallel. At least some of the evolutionary changes now emerging have clearly been convergent, meaning that natural selection has made use of the different mutations available in each population to accomplish the same adaptation.
This is the case with lactose tolerance in European and African peoples and with pale skin in East Asians and Europeans.

Nothing new to readers of this weblog, but Wade does a good job surveying the various angles. Anyone with a model of evolution in their head shouldn’t be surprised, the range of human variation is to be expected; we are a species which spans Arctic and tropical biomes, evolutionary pressures generally reshape populations into localized ecotypes. Dogs are similar except their selection pressure was our species, and our preferences (as opposed to environmental conditions) served as evolution’s sculpting tool.
Note that Wade mentions that selection seems notable on both disease and metabolically salient genomic regions. This illustrates the dynamic and multi-layered texture of evolutionary processes, pathogen resistance is always something which all complex species are always tinkering with as we attempt to stay ahead of the race. In regards to the changes in metabolism Wade alludes to the shift between hunter-gather and farming lifestyles. In most of the world this transition occurred between 5 to 10 thousand years before the present, suggesting rapid and recent evolutionary processes which allow for localized adaptation. Lactose tolerance is another example of this, it seems to have emerged in northern Europe only in the last 5 to 6 thousand years, but is now the dominant phenotype across broad swaths of northwest Eurasia. While particular evolutionary dynamics are always bubbling in the background, others are responses to local conditions in time and space. Shifting from a high protein low starch diet to a low protein high starch diet as populations transitioned between modal hunting and gathering toward agriculture was a definite shock to our metabolic systems. Though there is evidence that peasant populations were always physiologically sub-optimal compared to hunter-gatherers (they were smaller for example, and showed more stress during growth in their bone development) their metabolic systems co-evolved with their lifestyles to produce a “good enough” solution and result in more natural increase than non-agricultural peoples. It is a classic illustration that all evolution cares about is replication, not quality of life or some idealized perfection.
Finally, note that Wade emphasizes the convergent evolutionary patterns throughout the world. Selection operates upon traits, the phenotype, the underlying genetic architecture that produces this is irrelevant. In the case of light skin for example alternative alleles (genetic variants) arose which produced the same phenotype via mutation. This might not be too difficult if you imagine that light skin is simply a loss of function and there are many ways to do that. One can imagine that these mutants were always bubbling in the background but in the higher latitudes the dampening pressure of selection was removed (and perhaps reversed), and out of the random sample spaces of mutants western and eastern Eurasia exhibited different clusters. This is likely to have happened quite a bit in the past 10,000 years as cultural innovations, such as agriculture and mass societies, have swept across the world to a far greater extent than populations. The implication being that cognate selective pressures arose at about the same time across disparate regions.
Related articles on recent human evolution.

On occasion I’ve decided I’ll quickly review some population genetic concepts. These are really “background assumptions,” but sometimes comments make it clear that they’re not in the “common” background. So to the left you see two normal distributions, assume these are quantitative traits. The x-axis is the trait value, while the y-axis is the frequency of that value within a population. As you might note I’ve labeled the two populations “generation 1″ (g1) and “generation 100″ (g100). The implication is that the two distributions represent the “same” population shifted in time. Obviously the population exhibits evolution. You also note that the highest value in g1 is lower than the median value in g100. How could this happen? One could imagine that mutation introduced new variants into the population which changed the trait value, and /or that random genetic sampling processes shifted the allele frequencies over time.

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Agnostic translates an Italian interview with mathematical biologist Martin Nowak. Here are my posts read relating to Nowak’s work. His book Evolutionary Dynamics is one of the best coffee table books for nerds out there (nice sturdy hard cover and glossy pages with helpful charts to navigate the formalism).

Strange. Rise of man theory ‘out by 400,000 years’. I’m skeptical, not that I know anything in detail about palaeanthropology aside from books and a few advanced courses. In any case:

Our earliest ancestors gave up hunter-gathering and took to a settled life up to 400,000 years earlier than previously thought, according to controversial research.
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Professor Ziegert claims that the thousands of blades, scrapers, hand axes and other tools found at sites such as Budrinna, on the shore of the extinct Lake Fezzan in southwest Libya, and at Melka Konture, along the River Awash in Ethiopia, provide evidence of organised societies.
He believes that such sites show small communities of 40 or 50 people, with abundant water resources to exploit for constant harvests.

It seems that if there are 40 or 50 erectines is the sort of community that would need the social intelligence that Robin Dunbar describes in Grooming, Gossip, and the Evolution of Language. Dunbar outlined the general phenotypic parameters of the characteristics of social intelligence (e.g., the outer bound of the number of genuine friends and acquaintances humans can juggle in their mind, on the order of 100 individuals). His work was done before the post-genomic era, so now that we are exploring the genes that code for these methods we may eventually be able to test the plausibility of these paleontological conjectures.

By now you’ve probably heard/read about the relationship of HIV resistance and hominoid evolutionary genetics. The original paper in Science that started it off is titled Restriction of an Extinct Retrovirus by the Human TRIM5α Antiviral Protein; quite a mouthful. Lucky for us Carl Zimmer has an excellent exposition as well as a background primer, while John Hawks offers further thoughts looking at the various hypotheses through the lens of someone with a deep grasp of paleoanthropology.

I’ve always been ill at ease with the term “Judeo-Christian.” As someone from a Muslim cultural background I was minimally familiar with the tenets and principles of the Islamic religion. As someone who was socialized with both Jews and Christians I was reasonably familiar with the outlines of both faiths. When my teachers wouldrefer to the “Judeo-Christian” tradition I simply felt that something was off. Talking to Jews about their religion it seemed, to me, to resemble Islam more than what the Christian children described. Additionally, on occasion my family would purchase kosher food because it was always halal. Unlike Christians both Muslims and Jews tend to avoid pork and circumcise (though Jews obviously have no problem with alcohol). As I grew up I had the experience multiple times of Jews, American and Israeli, attempt to establish a bond with me when first meeting me by emphasizing the relative similarity of Judaism and Islam as opposed to Christianity (the assumption being that I was Muslim). Simultaneously, in my reading I stumbled upon peculiar facts. For instance, while rabbis have long had debates about whether Christian churches are houses of idolatry (e.g., could Jews buy land from Christians and use a former church facility?), there was never any such concern about Muslim houses of worship, because Muslims were incontrovertibly monotheists who did not use images in their worship.

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