Razib Khan One-stop-shopping for all of my content

November 30, 2011

Why some like it hot: awesomeness

Filed under: Culture,Spice — Razib Khan @ 7:33 pm

Mr. Jason Goldman has a post up, On Capsaicin: Why Do We Love to Eat Hot Peppers?. We don’t need no stinkin’ science for this. Do some ethnography with an N = 1: me. Those of us who love spicy food are just awesome! Recently I went to a Thai restaurant for the first time in 4 years which I used to frequent weekly in 2006-2007. Every Saturday I’d go and get a beef salad, which the chef would specially prepare for me by rubbing in a habanero paste into the meat ahead of time. That was the “four star” spicy level. When I reappeared after all this time the host exclaimed, “It’s Mr. four star!” Despite the years much of the staff which had been around back then remembered me. Back in the day sometimes they’d even watch me eat the dish to observe if I’d live to tell the tale. I can tell you similar stories from other restaurants. My very high spice tolerance threshold has reached such a level of virtuosity that people are often taken aback, and strangers will often comment upon it.

My point is that consumption of spicy food isn’t just a experience of the palette, it is deeply social. It is a signal of awesomeness, like having big antlers.

Here are some of Jason’s ideas:

Perhaps we seek out the painful experience of snacking on chillies while consciously maintaining awareness that there is no real danger to ourselves. After all, people seem to enjoy – and actively seek out – many other sensations that are otherwise undesirable but are ostensibly safe: the sensation of falling provided by rollercoasters or skydiving, the feelings of fear and anxiety while watching horror movies, the physical pain experienced upon jumping into icy water, or even the feelings of sadness that come while watching a tear-jerker. Perhaps it is this cognitive mismatch itself that provides the thrill: like strapping into a rollercoaster or popping Hostel into your DVD player over and over again, the burn of capsaicin only seems to be threatening.

Image credit: Andrew Bushby

A consideration of Pacific Biosciences

Filed under: Genomics,Genotyping,Pacific Biosciences,Personal genomics — Razib Khan @ 6:16 pm

I went to a seminar where a Pacific Biosciences representative was presenting recently. Along with others I arrived early because we thought it would be rather crowded. Not so much. Has the bubble burst?

Zoom in to the last year….

Modern humans in Arabia >100,000 years ago

Filed under: Evolution,Genetics,Human Evolution,Human Evolutionary Genetics — Razib Khan @ 5:49 pm

The genetic model of the “Out of Africa” scenario is getting more complex. There may be two waves, as well as the likelihood of admixture between the Neo-Africans and “archaic” hominins, such the Neandertals and Denisovans. From what I can gather the genetic evidence is now converging upon the sequence of events where African populations diverge >100,000 years ago (e.g., a deep separation between the ancestors of the Bushmen and the ancestors of West Africans), and a radiation of non-Africans at most ~75,000 years ago, and more likely ~50,000 years ago. There are still many holes to be plugged in. While we’re waiting on genetics, here’s an interesting paper using archaeological methods in PLoS ONE, The Nubian Complex of Dhofar, Oman: An African Middle Stone Age Industry in Southern Arabia:

Despite the numerous studies proposing early human population expansions from Africa into Arabia during the Late Pleistocene, no archaeological sites have yet been discovered in Arabia that resemble a specific African industry, which would indicate demographic exchange across the Red Sea. Here we report the discovery of a buried site and more than 100 new surface scatters in the Dhofar region of Oman belonging to a regionally-specific African lithic industry – the late Nubian Complex – known previously only from the northeast and Horn of Africa during Marine Isotope Stage 5, ~128,000 to 74,000 years ago. Two optically stimulated luminescence age estimates from the open-air site of Aybut Al Auwal in Oman place the Arabian Nubian Complex at ~106,000 years ago, providing archaeological evidence for the presence of a distinct northeast African Middle Stone Age technocomplex in southern Arabia sometime in the first half of Marine Isotope Stage 5

Dienekes has extensive commentary up.

What anime tells us about Japan and America

Filed under: Culture,Voltron — Razib Khan @ 1:08 am

A Slate piece on the coming Voltron Renaissance sent me to this interesting juxtaposition of the American cartoon and the Japanese original from which it was culled:

On structure, variation, and race

I noticed yesterday that Andrew Sullivan, Ta-Nehisi Coates, and a cast of others were having a roiling debate on race and I.Q. My name came up in several comment threads on various issues. I’m aware of this because I have Google Alerts set for my name. I don’t have the time or energy to get immersed in this particular debate at this moment, but I did review some older material in the course of following links placed elsewhere. In particular, I encourage all of my newer readers to check out my friend Armand M. Leroi’s article in The New York Times from 2005, A Family Tree in Every Gene. Though dated in a few particulars (e.g., we know the locus responsible for most variation in blue eyes now, and it seems likely that Andaman Islanders and Malaysian Negritos are not the original settlers of their domains) I think the general outline has held up rather well. Compare it to the numerous vociferous responses over at SSRN. One wonders at the motivation for what seems like massive retaliation! Here are a few critical paragraphs from Armand’s piece:

The identification of racial origins is not a search for purity. The human species is irredeemably promiscuous. We have always seduced or coerced our neighbors even when they have a foreign look about them and we don’t understand a word. If Hispanics, for example, are composed of a recent and evolving blend of European, American Indian and African genes, then the Uighurs of Central Asia can be seen as a 3,000-year-old mix of West European and East Asian genes. Even homogenous groups like native Swedes bear the genetic imprint of successive nameless migrations.

Some critics believe that these ambiguities render the very notion of race worthless. I disagree. The physical topography of our world cannot be accurately described in words. To navigate it, you need a map with elevations, contour lines and reference grids. But it is hard to talk in numbers, and so we give the world’s more prominent features – the mountain ranges and plateaus and plains – names. We do so despite the inherent ambiguity of words. The Pennines of northern England are about one-tenth as high and long as the Himalayas, yet both are intelligibly described as mountain ranges.

So, too, it is with the genetic topography of our species. The billion or so of the world’s people of largely European descent have a set of genetic variants in common that are collectively rare in everyone else; they are a race. At a smaller scale, three million Basques do as well; so they are a race as well. Race is merely a shorthand that enables us to speak sensibly, though with no great precision, about genetic rather than cultural or political differences.

But it is a shorthand that seems to be needed. One of the more painful spectacles of modern science is that of human geneticists piously disavowing the existence of races even as they investigate the genetic relationships between “ethnic groups.” Given the problematic, even vicious, history of the word “race,” the use of euphemisms is understandable. But it hardly aids understanding, for the term “ethnic group” conflates all the possible ways in which people differ from each other.

The problem here is the word “race.” It has a whole lot of baggage. So many biologists prudently shift to “population” or “ethnic group.” I don’t much care either way. Let’s just put the semantic sugar to the side. I contend that:

1) Human populations can be easily separated into plausible clusters using a random set of genetic markers

2) The differences between human populations are not trivial

You can say that both positions apply to human races. Or, you can say that race does not exist as a biological concept, and that both positions apply to human populations. Call it what you will, style is secondary to substance. Just as half-siblings and full-siblings are clearly genetically distinct, and those distinctions matter in terms of their traits, so French and Chinese are genetically distinct, and those distinctions matter in terms of their traits.

In the mid-2000s Armand, and at the time myself as well, put a great deal of weight on the importance of the elucidation of population structure for biomedical purposes. How else is one going to get funded by the N.I.H.? At this point I’m not sure that that’s going to be the low hanging fruit in the near term. Rather, I think an understanding of the phylogeny of the human race is a grand story. Population structure in the present is a shadow of histories past. And with the possibility of admixture with archaic lineages and recent adaptations that story has a lot of novel plot elements to keep your attention.

COMMENTS NOTE: Any comment which misrepresents the material in this post will result in banning without warning. So you should probably stick to direct quotes in lieu of reformulations of what you perceive to be my intent in your own words. For example, if you start a sentence with “so what you’re trying to say….”, you’re probably going to get banned. I said what I tried or wanted to say in the post. Period.

November 29, 2011

Genetic Creationism

Filed under: Genetic Determinists,Genetics,Genomics,Human Genetics,Human Genomics — Razib Khan @ 2:50 pm

Carl Zimmer points me to a piece in a publication called GeneWatch, The Crumbling Pillars of Behavior Genetics. I won’t quote from it because it’s kind of a tired rehash of the confusions and misrepresentations found in The Great DNA Data Deficit: Are Genes for Disease a Mirage?, thoroughly refuted by Luke Jostins and Dan MacArthur (and others at Genomes Unzipped). As I have stated before this sort of attack on genetics is basically similar to Creationism. It’s overloaded with technical and scientific terminology bound to impress the public, but which is just used in a confusing manner, to the point where there’s a big overhead in trying to unpack the logic (as opposed to rhetoric) of the argument. I am broadly convinced that we should be very cautious about results which point to specific genes implicated in a complex trait. But, this is not the “bread & butter” of behavior genetics, which has always been about smoking out the relationship between genetic and phenotypic correlations, and therefore heritabilities. Additionally, as I’ve pointed out there are areas of genomics which are going to be a very important helpmate to quantitative genetic analyses. As noted in the piece behavior geneticists did turn out to be too optimistic about genomics as being relevant to their field. But, the main objections aren’t that novel, and the argument is a repetition of very old conflicts.

Addendum: I also feel that in many ways “genetic determinist” is rather like the Left-wing Blank Slate equivalent of Right-wing Creationist’s usage of terms like “Darwinian materialist” or “secular humanist.” It fills the same aspersion-shaped-hole in the heads of the polemicists. The difference though is often, though not always, the terms “Darwinian materialist” or “secular humanist” have some germ of truth (in that many evolutionary biologists are secular materialists who operate with a Darwinian framework in the background). In contrast, though there are scientists who are genetic determinists when it comes to the number of fingers you are expected to have, there are very few scholars who think that behavioral traits are determined purely by genes.

COMMENTS NOTE: Any comment which misrepresents the material in this post will result in banning without warning. So you should probably stick to direct quotes in lieu of reformulations of what you perceive to be my intent in your own words. For example, if you start a sentence with “so what you’re trying to say….”, you’re probably going to get banned. I said what I tried or wanted to say in the post. Period.

More than models

Filed under: Genetics,Genomics — Razib Khan @ 1:16 pm

Slate recently had a series up on the use of mice as “model organisms.” In particular, it put the spotlight of some limitations of extrapolating from a mouse to a man (or other species). This is in some ways biology’s “WEIRD” problem. There are always going to be obvious reasons why we’d want to use mice instead of elephants as model organisms, but we might be entering into an era when the fixation on a few species might abate at least somewhat. With that, I point you to a piece in The Scientist (in its final issue I believe), Beyond the Model – How next-generation sequencing technologies will drive a new era of research on non-model organisms:

Central goals of biology have always been to understand the basis for diversity within and among species, and to understand how the environment can influence the expression of different traits. These emerging genetic approaches enable studies in a greatly expanded number of organisms and potentially allow genetic approaches to be applied in natural habitats. The use of model organisms is not dead, however. The utilization of previously generated resources and continued development of model systems will support and facilitate research in non-models. But with the ability to address molecular mechanisms in the natural world, we can truly begin to understand how all of these factors interact to generate the biological diversity that motivated the early scientists and continues to inspire us today.

There is a reason for the hype that the 21st century will be to biology what the 20th was to physics.

COMMENTS NOTE: Any comment which misrepresents the material in this post will result in banning without warning. So you should probably stick to direct quotes in lieu of reformulations of what you perceive to be my intent in your own words. For example, if you start a sentence with “so what you’re trying to say….”, you’re probably going to get banned. I said what I tried or wanted to say in the post. Period.

When trees turn into brambles

Filed under: Evolution,Evolutionary Genetics,Genetics,Genomics — Razib Khan @ 1:00 pm

Genetics is powerful. The origins of the field predate Gregor Mendel, and go further back to plain human common sense. Crude theories of inheritance in the 19th century gave way in the early 20th to Mendelism, which happens to be a very powerful formal system for predicting the patterns of transmission of information from generation to generation. But I suspect that the popular accolades showered upon genetics would be more muted if it were not for the concrete discovery of the biophysical medium of that pattern of inheritance, DNA. By visualizing strands of DNA packaged into chromosomes one can gain a substantive understanding of Mendelian processes previously somewhat abstracted (e.g., recombination). In concert with the centrality of genetics at the heart of evolutionary science has been the ascendance of its methods in the older field of systematics. The phylogenetic tree is not only intuitive, but it has concrete reality in the sequences of base pairs or structural elements within the genome.

Whatever skepticism there might be about the dynamic phenomenon of evolution, the material aspect of modern genetics rooted in molecular biology is one of he primary wedges by which one can introduce an element of doubt into minds of a skeptic. The correlation between phylogeny and sequence identity of organisms which were previously adduced to exhibit some sort of biological relationship on the tree of life can not be dismissed out of hand. But this mode of thinking has limits, albeit due to the quirks of human psychology.

I began to think about this when reading Brian Switek’s post, Inside the Columbian Mammoth, Signs of a Woolly Cousin. It’s long and wide-ranging, so let me spotlight the section of particular interest to me:

On an anatomical basis, woolly and Columbian mammoths would be expected to be cousins which diverged from a common ancestor sometime between one and two million years ago. This is not what the genetic investigation found. “[T]he Huntington mammoth mitogenome is largely indiscernible from those of endemic North American WMs [woolly mammoths]”, Enk and co-authors wrote. The genetic readout of the Utah mammoth fell deep within the genetic diversity of woolly mammoths previously sampled from Alaska. This did not appear to be a case of contamination or mistaken identity – at a genetic level, researchers could barely distinguish a Columbian mammoth found in Utah from Alaskan woolly mammoths. What could this mean?

As I said, there’s a lot more detail in Brian’s post, so do read it. But one thing I want to emphasize: I think the results from the mammoth are far less surprising in light of what we’re finding from other widespread large mammals. Consider the polar bears:

The bear family, Ursidae, is believed to have split off from other carnivorans about 38 million years ago. The Ursinae subfamily originated approximately 4.2 million years ago. According to both fossil and DNA evidence, the polar bear diverged from the brown bear, Ursus arctos, roughly 150,000 years ago. The oldest known polar bear fossil is a 130,000 to 110,000-year-old jaw bone, found on Prince Charles Foreland in 2004. Fossils show that between ten to twenty thousand years ago, the polar bear’s molar teeth changed significantly from those of the brown bear. Polar bears are thought to have diverged from a population of brown bears that became isolated during a period of glaciation in the Pleistocene.

More recent genetic studies have shown that some clades of brown bear are more closely related to polar bears than to other brown bears, meaning that the polar bear is not a true species according to some species concepts. Irish brown bears are particularly close to polar bears. In addition, polar bears can breed with brown bears to produce fertile grizzly–polar bear hybrids, indicating that they have only recently diverged and are genetically similar. However, because neither species can survive long in the other’s ecological niche, and because they have different morphology, metabolism, social and feeding behaviors, and other phenotypic characteristics, the two bears are generally classified as separate species.

Long story short: the polar bear as a cluster of phenotypic characteristics may predate the polar bear as a distinctive cluster of genes! Now from John Hawks’ weblog, When anthropological and geological facts collide:

I am concerned with this passage today because of a re-emerging mismatch of evidence from the morphology of Middle Pleistocene humans and the genetics of Neandertals. Some paleoanthropologists have asserted that Europeans of the Middle Pleistocene were the exclusive ancestors of Neandertals. I have in the past written that Middle Pleistocene Europeans were among the ancestors of Neandertals, with sustained gene flow from other populations including Africa. The Sima de los Huesos people, maybe 600,000 years old, resembled the (much) later Neandertals in several aspects of their anatomy, as did other Middle Pleistocene Europeans. The genetic differences between living people and the ancient Neandertal genomes appear consistent with the emergence of distinct African and Neandertal populations only within the last 400,000 years or less.

Such a recent date seems a poor match for the morphological evidence of Neandertal ancestry in Europe. I can think of several ways to make these morphological and genetic comparisons concordant with each other, all of which balance some shift in one body of inference against the other. As long as we can’t pin down the human mutation rate within a factor of two (“What is the human mutation rate?”), there’s a lot of room to make different population models consistent with the genetic data.

I have been told that the most recent genomic data indicating the red wolf is a wolf-coyote hybrid of post-Colubmian vintage is perplexing to some who have accepted the fossil evidence of a far older derivation from the gray wolf stock. But remember that fossils rely on visible phenotypes, which may diverge from what genes tells us. The modern red wolf may simply be the latest instantiation of a constellation of characteristics which have bubbled out of the froth of the morphological background repeatedly for nearly a million years!

With the expansion of genomics from humans to a wide range of species I suspect that we’ll see a lot more blurring of distinctions between species on the margins. This will be particularly true of those lineages with wide and continuous distributions. It will also be most salient and surprising for mammalian populations, where our prejudices about the primacy of a biological species concept are most strongly developed.

In a phylogenetic sense when you shift the grain of analysis to a finer scale the tree of life becomes much more of a bramble in many cases. We understand this intuitively when it comes to pedigrees which we constrain to within our demarcated species. Many of us have the same ancestor over and over in our lineage as we go back into the past. Similarly, why should we presume that closely related lineages have parted for all of eternity when they speciate? If you pull back far enough monophyly is obviously a pervasive phenomenon, but in many scenarios we’re talking on the scale of ten million years, not one million. In hindsight it seems strange that people thought Neanderthals and African hominins could not interbreed despite a maximal separation on the order of ~500,000 years (in reality it seems plausible there was some gene flow between the two lineages in any case prior to the Neanderthal’s absorption into the Neo-African modern populations).

The second issue is that we must sometimes dethrone genetics from its determinative role in our understanding of how life is properly cataloged and evaluated. It may be that some phenotypes are recapitulated repeatedly from the ancestral genetic variation pool. This may have happened with the polar bear morph. Perhaps it happened with the mammoth lineages, as the Ice Ages waxed and waned. And perhaps it happened with the hominins of northern Eurasia! In the United States genetic criteria have become critical in application of the Endangered Species Act. Genes are concrete and often clear and distinct. Their physical reality and precision though may deceive us in the end. Does it matter if the red wolf of today is a recent hybrid of the gray wolf and coyote, while the red wolf of 10,000 years before the present was a 10,000 year old hybrid between the gray wolf and coyote?

Image credit: Zephyris, PIRN.

COMMENTS NOTE: Any comment which misrepresents the material in this post will result in banning without warning. So you should probably stick to direct quotes in lieu of reformulations of what you perceive to be my intent in your own words. For example, if you start a sentence with “so what you’re trying to say….”, you’re probably going to get banned. I said what I tried or wanted to say in the post. Period.

November 28, 2011

Has twitter peaked?

Filed under: Technology,twitter — Razib Khan @ 8:19 pm

I hadn’t given the issue much thought, but that’ what Randall Parker asserted in the comments below.

First, let’s look at Google Trends search traffic with Facebook as well:

Facebook dwarfs twitter, so you can’t tell. So with only twitter:

Interesting. Now let’s look with Alexa:

It’s a little more ambiguous using Google Trends estimate of unique visitors:

Finally, Site Analytics:

The New York Times on violence and Pinker

The New York Times has a short piece on Steven Pinker up. Nothing too new to long time followers of the man and his work. I would like to point readers to the fact that Steven Pinker has a F.A.Q. up for The Better Angels of Our Nature: Why Violence Has Declined. He links to my post, Relative angels and absolute demons, as supporting his dismissal of Elizabeth Kolbert’s review in The New Yorker. I have to admit that I find much, though not all, of the coverage of science in The New Yorker to exhibit some of the more annoying stereotypical caricatures of humanists when confronting the specter of natural philosophy.

I should also mention I started reading The Better Angels of Our Nature over Thanksgiving. I’m only ~20% through it, and probably won’t finish until Christmas season gets into high gear, but so far it’s a huge mess. In both a good way, and a bad way. The good way is that it’s incredibly rich in its bibliography, with fascinating facts strewn about the path of the narrative. The bad way is that so far it lacks the tightness of  The Blank Slate or The Language Instinct in terms of argument. This may change. Finally, I think I should mention that Pinker has already addressed some of the criticisms of his methodologies brought up in the comments sections of my posts. Those who have specific critiques probably should read the book, because he seems to try sincerely to address those. Or at least they should address those critiques to people who have bothered to read the book.

Tolerable jackfruit

Filed under: Blog,Jackfruit — Razib Khan @ 1:33 am

When perusing Asian groceries I occasionally run into cans of jackfruit. Or should I say “jackfruit,” because often what’s inside of the cans resembles jackfruit flavored wax. Real fresh jackfruit is soft and mushy. Unfortunately the preservation process turns canned jackfruit into a turgid and far less flavorful product. That being said, I recently purchased three different brands, and I found that Chaokoh brand wasn’t totally awful. I don’t know if I’d purchase it again, but I am considering it. It’s not real jackfruit by any means, but the flavor is stronger and the waxiness of the fruit flesh less pronounced.

Do readers have any experiences with canned jackfruit?

Image credit: Wikimedia

Genetic distinctiveness vs. genetic diversity

Meeting the Taino

In the comments below a few days ago someone expressed concern at the diminishing of genetic diversity due to the disappearance of indigenous populations. My response was bascally that it depends. The issue here is whether that disappearance is due to assimilation, or extinction. If a given population is genetically absorbed into another, obviously their genetic diversity is by and large maintained. What disappears are the specific genotypes, the combinations of gene pairs, which are distinctive to that given group. This is the same dynamic at the heart of the ‘disappearing blonde gene’ meme. Unless there is selection at the loci which encode or predispose one to blonde hair the ‘gene’ isn’t going anywhere. Rather, the implicit issue here is that blonde people are intermarrying with non-blonde people, and if the genetic variant has a recessive expression then the frequency of the trait will decrease. Populations with a high degree of homozygosity at the ‘blonde loci’ are distinctive in a very particular manner, but they’re no more or less ‘diverse’ than other populations which don’t manifest the same tendency.

A toy example will suffice. Take two populations, A and B, and one locus, 1, with two variants, X and x. Assume that the two populations are the same size. At locus 1 population A is 100% X, and population B is 100% x. In a diploid scenario then all the individuals in population A will be XX, and in B will be xx. When you add A + B you get a frequency of X of 0.5, and of x of 0.5 (since the two populations are balanced in size).


Now imagine a scenario where all individuals in population A pair up with someone in population B (assume sex balance in both populations). In the first generation, F1, all the offspring will be heterozygote Xx (hybrids). The frequency of X and x will be 0.5 still, as in the previous generation. But no individual now reflects the genotype of the parental populations, as all individuals are heterozgyote. At the level of alleles, specific genetic variants, you’ve go the same diversity (X and x at locus 1). But at the level of genotype there’s a huge shift. Two genotypes (XX and xx) no longer exist, but a novel one is now fixed in the population (Xy).

A novel combination

Finally, in the F2 generation, the offspring of F1, Hardy-Weinberg will reassert itself. 25% of the genotypes will be XX, 25% xx, and 50% Xx, due to p2 + 2pq + q2 = 1. In this scenario some of the distinctiveness of the parental and F1 generations in terms of genotype are evident, but the diversity in the allelic sense of the parental and F1 states remains the same, X = 0.5 and x = 0.5. Observe that if you’re looking at genotypic diversity the F2 generations are actually more diverse than the parental (because Xy is a different genotype). In other words, in some ways the aggregation of various distinct populations may increase diversity by generating novel combinations.

This is not to deny that a very specific historically contingent form of diversity in terms of distinctness of particular groups is threatened today. That’s why it was important that the HGDP was overloaded with threatened groups like the Bushmen, Kalash, and Pygmies. These populations may be assimilated soon, and with that assimilation it will be more difficult to extract out historically very important information which will inform us about the human past.

But another issue is extinction instead of assimilation. Wouldn’t this eliminate a lot of genetic variation? Perhaps. I actually considered this issue a few years back with the Star Trek reboot. If you haven’t watched the film, there’s a major spoiler next. So basically on the order of ~10,000 Vulcans survived the destruction of their planet. Culturally the preservation was rather good, because the Vulcan elders, who are the repositories of the culture, were saved. In this way a fully fleshed Vulcan culture could easily reemerge out of the genocide. On the other hand, the vast majority of Vulcans died. Isn’t ths population bottleneck a genetic catastrophe? It depends. If the Vulcans who survived are a relatively random assortment of the population genetically, then the disaster isn’t that bad in terms of genetic diversity.

To get some idea of why, consider the statistic of heterozygosity. This measures the extent of heterozygote states, where the two gene copies differ at a locus, across the population. It’s a proxy for genetic diversity, as more allelic diversity produces more heterozygosity.

The decay of heterozygosity over time due to random genetic drift (without mutation) can be modeled like so:

Ht = H0(1 – 1/(2N))t

The variable “t” is simply the generation time, from an initial time. H0 refers to the initial heterozygosity, and Ht is simply the value at a given time out from that initial value. The N is effective population size. This formula can be used to model population bottlenecks. The Vulcan population reduction from one on the order of billions to 10,000 was basically a massive population bottleneck. The decrease in heterozygosity that you’d expect would be:

Ht = (1 – 1/(2*10,000))1

Ht = 0.99995 of the initial value. Basically almost nothing. Why? Because 10,000 turns out to be a relatively large population. This makes some intuitive sense. If you have a sample size of 10,000, and it’s representative, sample variance isn’t going to be that high. If you have an infinite number of coin flips so that the ratio of heads and tails is 50:50, reducing that to 10,000 flips isn’t going to result in much of a deviation from 50:50.

Let’s look at the effect of population bottlenecks of 20 generations at various values of N. The x axis shows generation time, while the y axis illustrates the proportion of the initial heterozyosity which remains.

This is not to downplay the impact of bottlenecks and demographic stochasticity. Rather, it’s to suggestion that population genetic diversity is relatively resistant to a crash in numbers. The extinction of small tribal groups is a tragedy, but genetically it may not be as much of a problem as we think. Even in groups such as the Bushmen with a great deal of genetic diversity it is likely that most of that diversity is already found within non-Bushmen populations.

Image credits: Ian Beatty and Lesley-Ann Brandt.

November 27, 2011

Evolution is haram!

Filed under: creationism,Evolution — Razib Khan @ 8:47 pm

Ruchira Paul points me to this peculiar article, Muslim medical students boycotting lectures on evolution… because it ‘clashes with the Koran’:

Muslim students, including trainee doctors on one of Britain’s leading medical courses, are walking out of lectures on evolution claiming it conflicts with creationist ideas established in the Koran.

Professors at University College London have expressed concern over the increasing number of biology students boycotting lectures on Darwinist theory, which form an important part of the syllabus, citing their religion.

That Muslim students have Creationist beliefs isn’t too surprising. There’s plenty of evidence of robust Creationist belief as being the Muslim mainstream. Though a minority of Muslims accept evolution in a manner conventional among theistic evolutionists, the majority seem to reject this interpretation. I recently had an interaction over Facebook with a Bangladeshi cousin who queried me whether I accepted “Darwinism,” a theory for which he contended “there was no proof.” I responded that that was one of the most “retarded questions I’d encountered of late,” and that the only reason I continued to talk to him was that he was my relative and it seemed a minimal level of courtesy (I generally “avoid boring people”). The background here is that my cousin comes from a very affluent secular background. My uncle doesn’t pray. This was an issue for my late grandmother, but his sojourn in the Persian Gulf turned him off to organized religion. Also, my uncle’s wife does not cover her hair. Finally, my cousin is sent to a private school where all instruction is in English, and he is very fluent in the superficial aspects of American pop culture. One can extrapolate from that the potential attitude of more genuinely religious Muslims when it comes to evolution.

But the bigger concern here is the walkout. It’s one thing to disagree with a perspective, but a disturbing aspect of some corners of modern academic discourse is the acceptability of shielding oneself from offensive or contradictory opinions. Most of the kids in my high school came from conservative Protestant or Mormon backgrounds and were skeptical of evolution, but they didn’t boycott the class when my biology teacher cursorily touched upon the topic. The fact that university students would behave in such a manner strikes me as particularly disturbing, because they should be held to a higher standard. Secondary education is about learning the basics, but higher education should be about learning to think, and taking in differing perspectives is an essential aspect of that process.

All that being said, it shouldn’t be surprising that British Muslims in particular behave so bizarrely. They’re pretty out of step with the norms of the British public on some “hot button” cultural issues. A few years ago Gallup asked Muslims and non-Muslims in Britain, Germany, and France, a variety of questions. Out of 500 Muslim Britons surveyed exactly 0 accepted the proposition that homosexuality was morally acceptable. This does not mean that no Muslims in Briton accept a tolerant attitude toward homosexuality. Rather, they’re such a small minority than even an N = 500 could miss them! In that context a walkout due to the offensiveness of evolution in the nation which proudly claims Charles Darwin seems less surprising. Cultural diversity is great!

Addendum: The link is from a British publication. Therefore, I’m open to the possibility that aspects were exaggerated or fabricated. On the other hand, evolution skepticism from British Muslims has been widely reported in other sources, so I think it is plausible overall.

November 26, 2011

Google+, Facebook, twitter

Filed under: Technology — Razib Khan @ 2:08 pm

It’s been a while…what’s going on with Google+? I think we can conclude it isn’t a Facebook killer in anything like the medium term.  After moving away from Facebook I started posting again because almost all of my friends in “flesh space” simply don’t use Google+. Rather, Google+ has become a more elaborate extension of my twitter circle. I’ve got over 2,100 who’ve added me to their Google+ circles, and only 1,600 twitter followers. But I don’t do post much on Google+ at this point. For someone with my amount of time and interest two social networks seems optimal in terms of complements. That being said, as many have noted Google+ is more than just a social networking platform. Rather, it has to be understood as an extension of giving your whole suite of Google services an identity, specificity, and personality.

With all that said, Facebook is starting to get a little too busy for my taste. Does anyone else feel the same way? Mark Zuckerberg has known how much to “push it” for years, but my own suspicion is that he has to be very careful of a rapid implosion of usage due to feedback loops if he moves beyond a particular threshold.

Addendum: My various web offerings can be found at razib.com. Probably most relevant for you is the total feed.

On the real possibility of human differences

I have discussed the reality that many areas of psychology are susceptible enough to false positives that the ideological preferences of the researchers come to the fore. CBC Radio contacted me after that post, and I asked them to consider that in 1960 psychologists discussed the behavior of homosexuality as if it was a pathology. Is homosexuality no longer a pathology, or have we as a society changed our definitions? In any given discipline when confronted with the specter of false positives which happen to meet statistical significance there is the natural tendency to align the outcome so that it is socially and professionally optimized. That is, the results support your own ideological preferences, and, they reinforce your own career aspirations. Publishing preferred positive results furthers both these ends, even if at the end of the day many researchers may understand on a deep level the likelihood that a specific set of published results are not robust.

This issue is not endemic to social sciences alone. I have already admitted this issue in medical sciences, where there is a lot of money at stake. But it crops up in more theoretical biology as well. In the early 20th century Charles Davenport’s research which suggested the inferiority of hybrids between human races was in keeping with the ideological preferences of the era. In our age Armand Leroi extols the beauty of hybrids, who have masked their genetic load through heterozygosity (a nations like Britain which once had a public norm against ‘mongrelization’ now promote racial intermarriage in the dominant media!). There are a priori biological rationales for both positions, hybrid breakdown and vigor (for humans from what I have heard and seen there seems to be very little evidence overall for either once you control for the deleterious consequences of inbreeding). In 1900 and in 2000 there are very different and opposing social preferences on this issue (as opposed to individual preferences). The empirical distribution of outcomes will vary in any given set of cases, so researchers are incentivized to seek the results which align well with social expectations. (here’s an example of heightened fatality due to mixing genetic backgrounds; it seems the exception rather than the rule).

Thinking about all this made me reread James F. Crow’s Unequal by nature: a geneticist’s perspective on human differences. Crow is arguably the most eminent living population geneticist (see my interview from 2006). Born in 1916, he has seen much come and go. For those of us who wonder how anyone could accept ideas which seem shocking or unbelievable today, I suspect Crow could give an answer. He was there. In any case, on an editorial note I think the essay should have been titled “Different by nature.” Inequality tends to connote a rank order of superiority or inferiority, though in the context of the essay the title is obviously accurate. Here is the most important section:

Two populations may have a large overlap and differ only slightly in their means. Still, the most outstanding individuals will tend to come from the population with the higher mean. The implication, I think, is clear: whenever an institution or society singles out individuals who are exceptional or outstanding in some way, racial differences will become more apparent. That fact may be uncomfortable, but there is no way around it.

The fact that racial differences exist does not, of course, explain their origin. The cause of the observed differences may be genetic. But it may also be environmental, the result of diet, or family structure, or schooling, or any number of other possible biological and social factors.

My conclusion, to repeat, is that whenever a society singles out individuals who are outstanding or unusual in any way, the statistical contrast between means and extremes comes to the fore. I think that recognizing this can eventually only help politicians and social policymakers.

You can, and should, read the whole thing. Let’s make it concrete. Imagine the following trait with two distributions (i.e., two populations):

- Mean = 100 and 105 (average value)
- Standard deviation = 15 (measure of dispersion)
- Let’s assume a normal distribution

Let’s plot the two distributions:

Observe the close overlap between the two distributions. Most of the variance occurs within both sets of populations. Now let’s impose a cut-off of about ~130 on the curves:

Now the similarity between the two curves is not as striking. As you move to the tails of the distribution they begin to diverge. In other words, the average of the two populations is pretty much interchangeable, but the values at the tails differ. Now let’s move the cut-off to 145:

The difference is now even more stark. Let’s compare the ratios of the area under the curve for the two populations as defined by the cut-offs:

Value at 100 = 1.26 (any given individual in the blue population is 1.26 times more likely to be above 100 than in the red population)
Value at 130 = 1.83
Value at 145 = 28

A major caveat: quantitative traits are only approximately normally distributed, and there tends to be a “fat tail” dynamic, where deviation from the normal increases as one moves away from the mean. Concretely, this means that the ratios at the tails are probably not quite as extreme, as there are more individuals in all populations at the tails than you’d expect.

What does this entail concretely? As Crow noted above if you sample from the tails of the distribution then very modest differences between groups become rather salient. Consider long distance running. To be successful in international competitions one presumably has to be many, many, standard deviations above the norm. One can’t be a 1 out of 100, or 1 out of 1,000. Rather, presumably one should be 1 out of hundreds of thousands, at a minimum. This would be the fastest ~100,000 or so people in the world (out of 7 billion). With this in mind, we should not be surprised a priori at the success of the Kalenjin people of Kenya in this domain. They may have both the biological and social preconditions which allow their distribution of talent to be moderately above that of the human norm. Even a marginal shift can make a huge difference at the tails. 1 out of 100,000 is 4.26 deviation units above the mean. Increasing the mean of a population by half a standard deviation units (e.g., if 100 is the mean, 15 is the standard deviation, then for the population with the higher mean you’d be at 107.5) results in a disproportion in ratio of above 8:1 at 4.26 units (as measured in the first population). This is modest, about 1 order of magnitude, but consider possible gene-environment correlations and synergies that might ensue when you have a critical mass of very fast individuals. This could amplify the effect of a difference in distributions on a single variate (more importantly I suspect, consider that virtuosity in many domains requires an intersection of aptitudes many units deviated from the norm across many traits).

In the early 2000s James F. Crow was responding to the Human Genome Project. As has been thoroughly covered elsewhere human genomics has probably underwhelmed in terms of outcomes 10 years out. But it is often the case that with new technologies we overestimate the short-term change which they will effect and underestimate their long-term consequences. I believe with the rise of mass genomics, a radical increase in population coverage and full genome sequencing, we may finally start to adduce the underpinnings of quantitative traits. We already have indirect methods, but I believe that by 2020 we will have direct means at our disposal. We’ll have a good sense how deeply humans are commensurable on a population genetic level. I doubt it will change much in our values, but it may entail some rhetorical adjustments.

Lynn Margulis, 1938-2011

Filed under: Endosymbiogenesis,Evolution — Razib Khan @ 1:18 am

The New York Times has an obit. But if you don’t know who she is, really just read the Wikipedia entry.

Around the web – 11/26/2011

Filed under: Blog — Razib Khan @ 1:08 am

I’ve gotten way behind on my RSS…though I caught up a bit over Thanksgiving.

West Hunter. Greg Cochran and Henry Harpending’s blog.

Eurasian Sensation. Liberal Eurasian Australian blogger.

Matt Yglesias moved to Slate. This means that his salary is coming in large part from a firm which he has excoriated in the past. (Slate is owned by The Washington Post Company)

Rod Dreher is now at The American Conservative.

Sorry, Strivers: Talent Matters. “Nor is it to say that it’s impossible for a person with an average I.Q. to, say, earn a Ph.D. in physics.” I think it is possible to earn a Ph.D. in physics with an average I.Q., but only from institutions like Razib-Khan’s-Internet-University, where you pay me $100 for me to send you a printout which purports to give you a Ph.D. in physics. In fact, if someone who is a Ph.D. in physics can send me their G.R.E. scores where they score less than a 550 on the mathematics section, and are willing to go public with this fact (so we can check their scholarly achievements and validate the quality of the institution), I will shell out $250 to this individual. Let’s set the date of expiration for 12/26, so I can budget this expense.

Is Newt Gingrich as smart as he thinks? He’s obviously not dumb like Rick Perry, or ignorant like Herman Cain. But I think Newt is a “high verbal” type who can impress the dull more than actually get anything done. I believe that Mitt Romney is somewhat higher in I.Q., but more critically he probably has a better practical skill set. Newt is not one known for contingency and coherency, and that’s a problem.

The Curious Case of Freida Pinto. Frieda Pinto is famous internationally, but obscure in India. Part of this is the inordinate attention paid to Slumdog Millionaire in the West, but part of it is that she’s probably too conventionally Indian looking to really stand out in Bollywood (too dark skinned), but is conventionally Indian looking enough in the West to be ‘exotic’ (just dark skinned enough to obviously be non-white).

Atheists launch campaign to get unbelievers to ‘come out’. Just so you know, I’m an atheist.

In Quiet Part of Russia, Putin’s Party Loses Steam. Unless you’re willing to go “North Korea,” economic growth matters to any ruling class.

Talk cancelled. In the long run it doesn’t matter.

A Blow to Pinstripe Aspirations. My first thought is “fuck them.” Second thought, start a company if you’re that smart! If you’re not really that smart, but can fake it, go work for a company that makes something or produces a genuine service.

Ancient sect fights to keep culture alive in U.S. Mandaeans don’t have critical mass. Excessive fixation on endogamy does not work unless you are willing to engage in self-segregation like the Hasidic Jews do.

Worth remembering (when comparing ‘the US’ to ‘Europe’). A nice post illustrating the data which supports one of my pet peeves: comparing totally different administrative units in qualitative terms on the same quantitative metrics.

Man eats world’s hottest pepper; vomits, hallucinates, and is generally laid low.

‘My daughter deserved to die for falling in love’. For Abdel-Qader Ali there is only one regret: that he did not kill his daughter at birth. ‘If I had realised then what she would become, I would have killed her the instant her mother delivered her,’ he said with no trace of remorse. Stories like this are tragic, but unless the West wants to engage in neocolonialism it has to accept that these are the dominant views in some parts of the world, and will be until economic and social development changes them. Such human interest pieces should continue to be written to remind us what we may become in the process of barbarization and cultural devolution, but it is unlikely that they will affect any great change. Millions of young women will live under a reign of tyranny for several generations, and there is nothing we can do to change this in the cases of most (I suspect the same system is what is driving men to have sex with men in the Muslim world).

The White Stuff. I still like Three Colors: Red, but then Irene Jacob was more striking at her peak than Julie Delpy or Juliette Binoche.

‘Meow’trage at Algonquin. Hotel cat banned from lobby!

That rotting smell is college sports.

Ernest Borgnine. He’s still alive! Was born in 1917.

Libyan Fighters Catch Qaddafi’s Last Fugitive Son. How they treat him will be the measure of the ‘nation.’

The Duggars Demonstrate Life History Trade-Offs Around Quality Versus Quantity of Offspring.

As ultra-Orthodox flex muscle, Israel feminists see a backsliding. Numbers are at issue. The Ultra-Orthodox are now a modest minority, not a marginal one. That being said, they’re subsidized by the rest of society. Would they persist if they were fully economically integrated and active?

How the worm turns the genic world

In the middle years of the last decade there were many papers which came out which reported many ‘hard’ selective sweeps reshaping the human genome. By this, I mean that you had a novel mutation arise against the genetic background, and positive selection rapidly increased the frequency of that mutation. Because of the power and rapidity of the sweep many of the flanking regions of the genome would “hitchhike” along, generating long homogenized regions of linkage disequilibrium. If that’s a little dense for you, just understand that very strong selective events tend to result in disorder and distinctiveness in the local genomic region.

But the late aughts and the early years of the teens are shaping up give us a more subtle picture. Instead of classic hard sweeps, researchers are suggesting that there may also be many ‘soft’ sweeps, where selection draws upon the well of standing genic variation. Instead of a novel trait becoming prominent, one tail of the distribution would rise in frequency. The ‘problem’ with this model is that it’s not as tractable as the earlier one of hard sweeps, and selection on quantitative traits with many loci of small effect is more difficult to detect. Its effect on the genome is more subtle and understated, which means that statistical tests often lack the power to grasp onto the underlying dynamics. Naturally this means that there is an extension of statistical techniques to ever greater degrees of sophistication. A new paper in PLoS Genetics attempting to tease apart the various potential selective pressures in the human genome is reflective of that tendency. Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution:

Previous genome-wide scans of positive natural selection in humans have identified a number of non-neutrally evolving genes that play important roles in skin pigmentation, metabolism, or immune function. Recent studies have also shown that a genome-wide pattern of local adaptation can be detected by identifying correlations between patterns of allele frequencies and environmental variables. Despite these observations, the degree to which natural selection is primarily driven by adaptation to local environments, and the role of pathogens or other ecological factors as selective agents, is still under debate. To address this issue, we correlated the spatial allele frequency distribution of a large sample of SNPs from 55 distinct human populations to a set of environmental factors that describe local geographical features such as climate, diet regimes, and pathogen loads. In concordance with previous studies, we detected a significant enrichment of genic SNPs, and particularly non-synonymous SNPs associated with local adaptation. Furthermore, we show that the diversity of the local pathogenic environment is the predominant driver of local adaptation, and that climate, at least as measured here, only plays a relatively minor role. While background demography by far makes the strongest contribution in explaining the genetic variance among populations, we detected about 100 genes which show an unexpectedly strong correlation between allele frequencies and pathogenic environment, after correcting for demography. Conversely, for diet regimes and climatic conditions, no genes show a similar correlation between the environmental factor and allele frequencies. This result is validated using low-coverage sequencing data for multiple populations. Among the loci targeted by pathogen-driven selection, we found an enrichment of genes associated to autoimmune diseases, such as celiac disease, type 1 diabetes, and multiples sclerosis, which lends credence to the hypothesis that some susceptibility alleles for autoimmune diseases may be maintained in human population due to past selective processes.

The authors utilized “Projection to Latent Structure multiple regression with an Uninformative Variable Elimination algorithm (UVE-PLS).” I know what multiple regression is, and the general logic which underpins the family of such methods. But I don’t really know what UVE-PLS is in its specifics, so I can’t speak with any intelligence on this technical issue. I assume as per most multiple regression the authors are attempting to tease apart the predictive power of various independent variables upon a dependent variable. In this case, the dependent variable happens to be the pattern of genetic variation, the single nucelotide polymorphisms (SNPs). It isn’t surprising that the biggest predictor of variation happens to be demographic relationship. That is, adjacent populations with recent common ancestors are going to share more genetic variants than those which are distant. The key is to control for this confound, and then see how genes vary according to other factors.

In this analysis they found that diet and climate seem to be less important than genes relating to immune response to pathogens, in particular those implicated in response to parasitic worms. Why worms? The argument they give is that these organisms are not quite so protean as bacteria and viruses, and also tend to be somewhat localized. Their relative sluggishness in adaptation means that humans presumably have some fighting chance in developing defenses, and their spatial stability also implies that human adaptations can differentiate nicely as a function of geography, as may be in the case in genes which are targets of local selection. I’m not quite sure about this idea that we’ve been able to adapt to parasitic worms better though. Rather, I just wonder if human adaptations to viruses and bacteria are simply not easily detectable by these methods. Or, as implied in the piece it may be that these are less locally conditioned, so you see a whole host of generalized adaptations which aren’t geographically constrained.

This is obviously not going to be the last word by any means. They focused on the data sets that were available and computationally manageable in 2011. Over the next 10 years researchers will be combing whole genomes of many individuals in many populations. They’ll come back with gold. It seems a forgone conclusion that loci implicated in response to pathogens are going to be rich candidates for bouts of natural selection. What is perhaps going to be more interesting is the question of what other traits are shaped by natural selection? The unequivocal list is rather short right now. Lactose tolerance, pigmentation, malaria, etc. It’s bound to get longer. The question is now human longer….

Citation: Fumagalli M, Sironi M, Pozzoli U, Ferrer-Admettla A, Pattini L, et al. 2011 Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution. PLoS Genet 7(11): e1002355. doi:10.1371/journal.pgen.1002355

November 25, 2011

Frieda Pinto: suburban Mumbai girl

Filed under: Uncategorized — Razib Khan @ 7:27 pm

The Curious Case of Freida Pinto:

…Theater director and filmmaker Feroz Abbas Khan [Gandhi, My Father] is one of them. “For me, Freida Pinto is a spectacular accident, a dazzlingly lucky by-product of a hugely successful film that grabbed popular imagination I have to admit that, like most, I remain mystified by all the attention she is receiving from the West. Strictly, as a director, I find absolutely nothing in her that is either extraordinary or interesting in terms of personality, talent or looks. She appears like someone available by the truckloads anywhere in suburban Mumbai! In Slumdog too, what great shakes did she do? I am sorry, but I just don’t get it …”

Thank god for the color of her skin which also must have played a part. The Katrinas and Kareenas are fair-skinned and Pinto is spot-on when she feels she could be a misfit in that environment….

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