Archive for September, 2006

Is evolution a universal acid against theism?

By Razib Khan | September 30, 2006 9:44 pm

Check out the data posted by rikhurzen from the GSS.


What do Y & mtDNA tell us?

By Razib Khan | September 30, 2006 2:13 pm

RPM has a post up about Y and mtDNA lineages, and what they can (or can’t) tell us about demographic history. I’m pretty skeptical myself about the broad and detailed deep time inferences some make with these markers (see The Real Eve for an extreme case), but Dienekes points me to a situation where there is some utility to this methodology:

The differential relative contribution of males and females from Africa and Europe to individual African American genomes is relevant to mapping genes utilizing admixture analysis…The European genetic contributions were highest (and African lowest) for the Y chromosome (28.46%), followed by the autosomes (19.99%), then the X chromosome (12.11%), and the mtDNA (8.51%). The relative order of admixture fractions in the genomic compartments validates previous studies that suggested sex-biased gene flow with elevated European male and African female contributions. There is a threefold higher European male contribution compared with European females (Y chromosome vs. mtDNA) to the genomes of African American individuals meaning that admixture-based gene discovery will have the most power for the autosomes and will be more limited for X chromosome analysis.

Similarly, Latin America shows strong signatures of asymmetrical gene flow in relation to the sexes. The key I think is that genetic data is a supplement to what we already know, and refines and confirms our hypotheses, the problem tends to be when genetic data is the sole leg upon which to stand, because as RPM notes assumptions of neutrality might not hold across the time spans and geographical distributions that we wish to survey.


Culture naturally

By Razib Khan | September 30, 2006 1:08 pm

Back in August AlphaPsy had series of posts on ‘naturalism’ in the context of culture. Check them out! (links below) I strongly believe it is important to discuss human affairs with a multi-disciplinary lens, too often the public discourse is presupposed on naive psychology, while elite models tend to fixate on one dimension (e.g., the ‘rational actor,’ a pet historical paradigm, etc.).

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Fisher and population size

By Razib Khan | September 30, 2006 12:52 pm

One of the major dialogues in evolutionary genetics in the 20th century was that between R.A. Fisher and Sewall Wright. It is so seminal that the term Fisher-Wright controversy is often used. One of the major points of disagreemant between Fisher and Wright was the role of population substructure and the relevance of long term effective population size in shaping the trajectory of allele frequencies over time. At my other blog David B is starting a series which addresses this issue. The initial post deals with the period before the publication of The Genetical Theory of Natural Selection.


Katz tale

By Razib Khan | September 29, 2006 4:51 pm

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Tall, to short, to tall (again)

By Razib Khan | September 29, 2006 11:33 am

height.jpgDienekes reports on a paper which chronicles the change height of “Europeans” over the last 20,000 years ago. Anthropologist Henry Harpending once told me that when the first modern humans arrived in European 40-30 thousand years ago they were as slim and towering as modern Nilotic peoples, in other words, they were evolutionary reflections of the African environment. But soon enough the nouveau Europeans shape shifted and developed a more robust physiognomy, with a reduction in median height. As you can see from the graph which I generated the Neolithic Revolution and the introduction of agriculture was the nadir of physical size, and undernourished reality of the farming cultures of Eurasia was a fact of life until the past century. But, note that even today Europeans are not as domineering in stature as they were 20,000 years ago. Humans have a tendency to view evolution as a progressive force, toward more complexity, size and intelligence. But we aren’t sure that this is correct, not only were modern humans larger during the Ice Age, but the largest cranial capacities of any human population can be found among the Neandertals.


Discrete continuity in genetics

By Razib Khan | September 29, 2006 10:09 am

In the post below on skin color within a multiracial family I made the point that genetics is inherited in a discrete fashion. In the post-genomic era, or even the post-DNA era, this seems intuitively clear. Our genetic sequence, our genome, is a string of precisely four base pairs, A, G, T and C. The genome is digital, not analog. Case closed, right?
Not really. One of the main reasons I wrote the post below is the consistent misconception that genetics is blending, that children are a mix of the essences of their parents. This captures the expectation, but the variance. A natural inference of this model is that variation is diminished over the generations as it is homogenized through a process of mixture. Because Charles Darwin held to a system of blending inheritance he had to come up with ingenious ways to perpetuate and replenish variation. R.A. Fisher saw that Mendelianism was a way out, that discrete inheritance preserved information and genetic variation from generation to generation in full, mitigating the need for high mutational rates to battle homogenization, or to conceive of artificial barriers to breeding between demes.
Though it is easy to assert that Mendelianism “naturally” leads to the perpetuation of extant variation, it was harder to come to this consensus. One of the early posts on this weblog dealt with the early 20th century battle between the Mendelians and Biometricians. A large number of the former conceived of themselves as rebels overthrowing the outmoded Darwinian model, while the Biometricians fancied themselves the heirs of Charles Darwin. Under the leadership of Karl Pearson the Biometricians held that the Mendelian model could not account for continuous variation in phenotype, such as the famous bell curve which describes the nature of traits such as height or intelligence. This was nonsense, as some early Mendelians saw, and Will Provine in his book The Origins of Theoretical Population Genetics seems to suggest that one of the main blocks was simply a conflict of personality. Though Karl Pearson was no Fisher, he was a genius in his own right, and the basic reality that discrete processes can approximate continuous ones should have been clear to him.
Get it? If not, click below the fold for some graphs which I believe elucidate the issue pretty clearly.

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Genetics reference

By Razib Khan | September 28, 2006 9:11 am

Check out this Mendelian Genetics reference site, which has an enormous catalogue of links. It doesn’t just talk about Punnett Squares, there’s also a link to a simple introduction to the chi square test.


Brown gaucho & Tangled Bank #63

By Razib Khan | September 27, 2006 9:35 pm

Our old friend Brown Gaucho is hosting Tangled Bank #63. I enjoyed his post, The importance of evolution in medicine. BG is a primatologist-turned-med student, so he knows of what he speaks. But, I do have to take some issue with this contention:

Anatomically and genetically, humans haven’t changed all that much in the past 100,000 years.

Yes, anatomically modern humans emerged over 100,000 years ago, but, that does not suffice to allow us to assume that genetically humans haven’t changed “all that much.” Of course, that depends on how you define “all that much,” but a supercharged immune system forged in the fires of the Eurasian pathogen pool & lactose tolerance don’t show up in the fossil record….


Can you tell if you're black or white?

By Razib Khan | September 27, 2006 10:25 am

twinspic.jpgLast winter a story surfaced about “black” and “white” twins. As you can see by the picture the main difference is in skin color, though genetically full sisters (fraternal twins), one twin has the complexion typical of a northern European, while the other is darker skinned. Contrary to the news reports the darker skinned twin does not seem to exhibit the modal complexion of sub-Saharan Africans, rather, she is several shades lighter. In fact, the photo suggests that she is about the same color as her parents, who are both genetically 1/2 European and 1/2 black.* Seeing as how adults are generally darker than they were as infants it is not unreasonable to assume that “black twin” will be darker than either of her parents by adulthood, just as her sister is lighter than either of them as a child (and will likely remain so). In any case, for the exposition below I will assume that one twin is “black” and the other is “white.”
In light of my recent posts about skin color, I thought this was an appropriate time to use this old story (which according to google remains popular) as an exemplar of Mendelian genetics beyond the single locus, that is, an exploration of variation on traits generated by a confluence of loci. The recent evidence suggests that about 5 loci are responsible for about 90% of the difference of average effect in regards to phenotype (i.e., skin reflectance) for skin color between populations (these are loci of “large effect”). This does not mean that these loci are as relevant for within population differences (or between sex differences within a population), as Europeans and Africans are often “fixed” for those genes in alternative alleles (so when you see variation within Norwegians or Nigerians for skin color, that might be due to very different genetic dynamics which only come into play when the background is controlled for). Keep in mind that this exposition is focused on between population diferences, crudely, what makes us black or white (or, in my case, a rich and sensual brown which is magnetic to the female sex).**

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Cladistics & culture – Wilkins responds, etc.

By Razib Khan | September 27, 2006 3:35 am

Update: Make sure to read the comments, some of them are worthy of posts.
John Wilkins has a long response to my post Cultural Cladistics. Now, John knows several orders of magnitude more about systematics than I do…so he emphasized the cladistics aspect and traced out the misimpressions, fallacies and problems. He begins:

He repeats the usual [redacted] canard that culture isn’t like biology in terms of its evolution. I think it is exactly like it, and that the “analogy” between cultural traditions and species is quite exact. All that differs is the frequency of the various kinds of evolution.

I don’t know what to say to this exactly…I’ve read Not By Genes Alone by Peter Richerson and Robert Boyd where they use population genetic formalism in the context of culture (much of their works seems to be a extension of the Price Equation), and I see a lot to be gained by this method. Nevertheless, to some extent I feel that asserting that biological and cultural evolution are “exact” in their “analogy” with variations in the frequency of kinds of “evolution” is like saying that physics and biology are “exact” in their “analogy” with only a variation in specific biophysical phenomena. For example, it seems to me that group selection is far more plausible in the case of culture because intergroup difference and within group conformity are quite plausible. Language dialect is a clear example, as are aspects of dress, ritual or diet. Another issue is the omnipresence of “horizontal transfer” in culture, and the importance of peer groups and the tension with “vertical transmission” from parents. In the ideal I do agree that cultural and biological evolution are fundamentally characterized by the same processes (replication, error, selection upon variation, drift, mutation, etc.). But, in terms of analysis the different dynamics mean that they are often easily perceived to be distinct and require alternative mindsets (which I think is born out by problems when biologists like R.A. Fisher try their hand at historical interpretation).
As for the rest about cladistics…well, to some extent, blasphemous as this may sound, that was simply a way for me to introduce the general issues of perception vs. substance when it comes to culture. I am not serious about a general “tree of culture” analogous to the “tree of life,” but rather am interested in more epiphenomenal goings on in regards to how we perceive cultural relations and how that is shaped by local contigencies.


New blog and interesting post

By Razib Khan | September 26, 2006 10:15 pm

Along with Dave I would like to bring to your attention AlphaPsy, a blog devoted to the naturalistical paradigm in cultural anthropology, drawing deeply from the well of cognitive science. Posts like this, exploring the cognitive grounding of our understanding of biology, are typical. Also, I want to point to you this post over at alt.muslim titled The Evolution of Monotheism. I am generally skeptical of the existence of a “religious Left” in Islam, but only because I believe they are thin on the ground, not because they are non-existent. This post is witness to the existence of such a thing within the House of Islam.


It's a white thing

By Razib Khan | September 26, 2006 10:02 pm

colorgraph.gifSandy at Discovering Biology in a Digital World responded to my post about skin color with White People are Mutants. This is an interesting juxtposition with a observation that some might claim that this implies that one is saying white people are more evolved. But it’s more complex than that, as I point out, it seems that before our species evolved dark skin, we were white skinned, underneath our fur, so white people are “back to the future.” Does that mean they are primitive? Or evolved back to primitivity? Obviously not, these sort of categories, “more evolved,” or “advanced,” are really not appropriate in a grand evolutionary scheme. Evolution just is, the only thing it ascends is an abstract, idealized and unreal fitness landscape. A reification which I tend to feel is worthwhile in modelling, but needs to be treated cautiously in the real world where one moment you are on solid ground, and the next moment the mountain of selection moves on you Bugs Bunny style and you are hurtling down from the sky. A fundamental truth which I think is important to comprehend is that almost any scientific finding of relevance to humans can be twisted through rhetorical tricks to support almost any position. Though the process of science is very different from other human systems of thought, it is often very amenable to being leveraged by those systems of thought.
Addendum: In regards to Europeans there is current debate about whether polymorphism on MC1R is due to relaxation of constraint (neutral transient polymorphisms) or positive sexual selection.


Skin deep, why I'm brown and you wish you were

By Razib Khan | September 25, 2006 11:59 am

A year ago, Armand Leroi, the author of Mutants, wrote:

We don’t know what the differences are between white skin and black skin, European skin versus African skin. What I mean is we don’t know what the genetic basis of that is. This is actually amazing. I mean, here’s a trait, trivial as it may be, about which wars have been fought, which is one of the great fault lines in society, around which people construct their identities as nothing else. And yet we haven’t the foggiest idea what the genetic basis of this is. It’s amazing.

Wonder no more Armand! Some have said we are in the golden age of skin color genetics. Nearly 40 years ago quantitative trait loci analysis suggested that 4-5 genes control the variation in skin color which distinguishes Africans from Europeans. And now, new work is pin pointing exactly what those genes of large effect might be. Two recent papers elucidate the underlying genomic architecture which results in human skin color variation, and the general conclusion seems to be that light skin in northern Eurasia is a derived trait which emerged independently in places like East Asia and Europe.* Within a few years a quick genomic sequence might be able to determine the expectation and variance of skin colors in the case of interracial couples.
* Dark skin seems to itself be a derived trait, but far deeper in our evolutionary history, dating to the time when hominids lost their fur.


Blood of the British

By Razib Khan | September 22, 2006 1:57 pm

Two articles are out, one by Stephen Oppenheimer, author of The Real Eve, and another profiling some of Bryan Sykes’1 new research. The headlines are eye-catching, “We’re nearly all Celts under the skin!” The fine print:

Even in England, about 64 per cent of people are descended from these Celts, outnumbering the descendants of Anglo- Saxons by about three to one.
The proportion of Celts is only slightly higher in Scotland, at 73 per cent. Wales is the most Celtic part of mainland Britain, with 83 per cent.

WHATEVER.jpgSykes and Oppenheimer tell the tale of the resettlement of northern Europe, and specifically the British Isles, by Iberian emigrants who ventured north. In both these stories the authors refer to them as “Basques,” the sole modern indigenous non-Indo-European people of Western Europe. But of course, 10,000 years ago there were no “Basques,” and it is not even guaranteed that the Basque language existed, as such (the modern Basque dialects might be descendents of one particular local dialect which spread and marginalized other languages). Both Sykes and Oppenheimer give relatively high estimates for the proportion of modern British ancestry that is attributable to the first settlers who came back north after the Ice Age, on the order of 3/4. Other works would probably ratchet it down a bit, perhaps 1/2. I think that overall though most workers believe 3/4 is closer to the reality. The other 1/4 are a melange of other groups, from Middle Eastern farmers to Norman aristocrats, though more of the former than the latter. There are varied numbers for the numbers of Anglo-Saxon settlers, and both these researchers tend to understate the impact. But, we can be sure of two things
a) The number of Anglo-Saxons was non-trivial. Whether it is 5%, or 50%, it is still significant in terms of the number of people who moved in just a few numbers. Elite language replacement usually leaves a strong substratum trace, but this is not evident in English (Oppenheimer’s explanation is that southern England was not Celtic speaking to begin with, though most would strongly disagree with this assesesment).
b) There is a strong geographical bias, with the North Sea coastal regions like East Anglia, “The Saxon Shore” of old, being the locus of the newcomers’ demographic expansion.
Uniparental markers (Y and mtDNA) can only tell us so much, specifically, they tell us histories of the genes, not the “peoples.” Of course, national narratives are what we are looking for, but the genes don’t always cooperate so occassional massaging of the “Results” section in the “Discussion” occurs….
1 – The author of The Seven Daughters of Eve.


Kat – kaptive

By Razib Khan | September 22, 2006 12:13 pm

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Cultural Cladistics

By Razib Khan | September 22, 2006 12:26 am

Which is the correct tree?*
One could argue that this is fallacious insofar as Judaism is the “ancestor” of both Islam and Christianity, but my own opinion is that the Jewish traditions of this day and age (including “Orthodox” Judaism) are very different from ancient Judaism (the transition from ancient to modern Judaism might be analogized to anagenesis, while the relationship between Christianity and ancient Judaism is more like cladogenesis). In the United States the term “Judeo-Christian” became popular after World War II as the “Protestant-Catholics-Jew” alignment was used to characterize the piety of the American republic (the core of the “civic religion”). But my own experience with Jews is that substantively they are skeptical of the “Judeo-Christian” concept because it is Muslims who are, unlike Christians, uncontestably monotheists. Though the contingencies of history place Judaism and Christianity in alliance, there is a tacit implication from many of my acquaintances that in many ways Judaism and Islam are far more similar.

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Nerd/Geek/Dork – my breakdown

By Razib Khan | September 21, 2006 11:18 pm
Pure Nerd
82 % Nerd, 17% Geek, 30% Dork
For The Record:

A Nerd is someone who is passionate about learning/being smart/academia.
A Geek is someone who is passionate about some particular area or subject, often an obscure or difficult one.
A Dork is someone who has difficulty with common social expectations/interactions.
You scored better than half in Nerd, earning you the title of: Pure Nerd.

The times, they are a-changing. It used to be that being exceptionally smart led to being unpopular, which would ultimately lead to picking up all of the traits and tendences associated with the “dork.” No-longer. Being smart isn’t as socially crippling as it once was, and even more so as you get older: eventually being a Pure Nerd will likely be replaced with the following label: Purely Successful.


Take the test yourself

Update: Jake is pure m*ther f*cking evil. John is human.


Tripoli (Benghazi) Six "411"

By Razib Khan | September 21, 2006 11:10 pm

Mike Dunford has the low down on how to help by doing something. If you have a blog, consider linking and bringing attention to this matter. Mass action is crucial!


The history of evolutionary genetics

By Razib Khan | September 21, 2006 11:50 am

The first chapter of Evolutionary Genetics: Concepts & Case Studies gives a quick sketch of the arc of the field that the book covers via exposition of topical and current issues. Michael R. Dietrich focuses on the series of controversies which serve as “hinges of history.” I have addressed the controversy between the biometricians & Mendelians before, below are the “highlights” over a longer period based on the outline constructed by Dietrich in his chapter, From Mendel to molecules: A brief history of evolutionary genetics.
darwin.jpgCharles Darwin brings forth an evolutionary theory predicated on natural selection. He emphasizes heritable continuous variation within populations assuming a blending model of inheritance. Darwin’s ideas are greeted with fury and adulation, and he becomes the world’s most famous biologist.
Gregor Mendel performs his experiments and formulates his discrete model of inheritance, elucidating the laws of independent assortment and segregation. Unlike Darwin Mendel’s work is ignored and quickly consigned to the irrelevant bin.

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Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

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