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Most of you have probably seen this stylized graphic somewhere along the away (I think it was on PBS at some point). But it’s still cool….

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Biology, DNA 
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I really love the fact that I live in the early 21st century for a host of reasons. That being said, one aspect that’s certainly true is that when it comes to charismatic natural variety and geography there are very few “blank spots” on the map. You can get a sense of what I’m talking about if you browse National Geographic from the early 20th century. Most of the map had been filled in, but there were still nooks and crannies waiting to be illuminated. So I always find stories like this interesting, because they capture a sliver of the wonder that once was so commonplace, Snow Leopard Population Discovered in Afghanistan:

The Wildlife Conservation Society has discovered a surprisingly healthy population of rare snow leopards living in the mountainous reaches of northeastern Afghanistan’s Wakhan Corridor, according to a new study.


The paper is in the International Journal of Environmental Studies, Saving threatened species in Afghanistan: snow leopards in the Wakhan Corridor:

The Wakhan Corridor in northeast Afghanistan is an area known for relatively abundant wildlife and it appears to represent Afghanistan’s most important snow leopard landscape. The Wildlife Conservation Society (WCS) has been working in Wakhan since 2006. Recent camera trap surveys have documented the presence of snow leopards at 16 different locations in the landscape. These are the first camera trap records of snow leopards in Afghanistan. Threats to snow leopards in the region include the fur trade, retaliatory killing by shepherds and the capture of live animals for pets. WCS is developing an integrated management approach for this species, involving local governance, protection by a cadre of rangers, education, construction of predator-proof livestock corrals, a livestock insurance program, tourism and research activities. This management approach is expected to contribute significantly to the conservation of snow leopards and other wildlife species in the Wakhan.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Biology, Conservation 
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BEHOLD, REIFICATION!


In the comments below Antonio pointed me to this working paper, What Do DNA Ancestry Tests Reveal About Americans’ Identity? Examining Public Opinion on Race and Genomics. I am perhaps being a bit dull but I can’t figure where its latest version is found online (I stumbled upon what looks like another working paper version on one of the authors’ websites). Here’s the abstract:

Genomics research will soon have a deep impact on many aspects of our lives, but its political implications and associations remain undeveloped. Our broad goal in this research project is to analyze what Americans are learning about genomic science, and how they are responding to this new and potentially fraught technology.

We pursue that goal here by focusing on one arena of the genomics revolution — its relationship to racial and ethnic identity. Genomic ancestry testing may either blur racial boundaries by showing them to be indistinct or mixed, or reify racial boundaries by revealing ancestral homogeneity or pointing toward a particular geographic area or group as likely forebears. Some tests, or some contexts, may permit both outcomes. In parallel fashion, genomic information about race can emphasize its malleability and social constructedness or its possible biological bases. We posit that what information individuals choose to obtain, and how they respond to genomic information about racial ancestry will depend in part on their own racial or ethnic identity.

We evaluate these hypotheses in three ways. The first is a public opinion survey including vignettes about hypothetical individuals who received contrasting DNA test results. Second is an automated content analysis of about 5,500 newspaper articles that focused on race-related genomics research. Finally, we perform a finer-grained, hand-coded, content analysis of about 700 articles profiling people who took DNA ancestry tests.

Three major findings parallel the three empirical analyses. First, most respondents find the results of DNA ancestry tests persuasive, but blacks and whites have very different emotional responses and effects on their racial identity. Asians and Hispanics range between those two poles, while multiracials show a distinct pattern of reaction. Second, newspaper articles do more to teach the American reading public that race has a genetic component than that race is a purely social construction. Third, African Americans are disproportionately likely to react with displeasure to tests that imply a blurring of racial classifications. The paper concludes with a discussion, outline of next steps, and observations about the significance of genomics for political science and politics.


As with the paper I pointed to yesterday it’s a little dated. We’ve come really far since mid-2010! At the top of this post are some ADMIXTURE plots I generated in ~2 hours yesterday. You have K = 10, with ~250,000 markers. On the left are the results for various populations, and on the right are results for individuals who I’m running for their own interest. The identification numbers are small, but you can make some of them out. The first two are ID001 and ID002, my father and mother respectively. I’m going to break the seal of privacy and tell you that regular reader Paul Conroy is ID010. He looks to be…Irish. There are plenty of other regular readers and friends, family, and Latin American significant others of regular readers on that bar plot. You can “out” yourself if you want on this thread. I will tell you that ID042 is an anonymous Tamil Brahmin, while ID043 is Paul G., an ethnic Assyrian from Iran. ID034 is the anonymous Ashkenazi Jew whose genotype I posted earlier.

Survey results are fine and good, but the public reception and interpretation of genomics is being created anew right now. I spend some time on the best way to gain some insights from ADMIXTURE and PCA because I don’t want to confuse people myself. Most of the reactions have been pretty banal. It turns out that Latin Americans under the presumption that they are “pure Spanish” are not always “pure Spanish.” White Americans yearning for Native American ancestry often have their hopes dashed. White Americans who dismissed the family history of a part-Native American grandparent due to the romanticism about aboriginal blood which they perceived around them, turn out to be part-Native American.

People do have confusions that need to be cleared up, but it isn’t like academics are going to give them that much insight. I know that the above is a working paper, but here’s a sentence that crept into that text: “…Hispanics are mestizo more or less by definition….” No, Hispanics are very specifically constructed as a race-neutral term in the USA. Obviously many Hispanics from the Caribbean also don’t self-identify as mestizo. Honestly, do the authors know any Hispanics?

So what has your experience been with scientific genealogy? I’ve already talked about my own personal journey at length. I think that race as a concept does have biological utility, but the biggest question mark which I move forward with is how oral history can diverge so rapidly from what our genomes tell us. In particular, the tendency to anchor on slices of privileged ancestry. Looking at it every which way I have confirmed to my satisfaction that my mother does have a small, but detectable, amount of Middle Eastern ancestry from her maternal grandfather as the oral histories and textual records tell us. But this dwarfed by a component she shares with my father which ties them to eastern Asia. But neither are aware of any such connection. These are ancestors forgotten, and makes me reflect on how recollection of memes is not always a remembrance of genes. This may not be as sexy an issue as reification of race through personal genomics, but to some extent that issue is so 20th century. Hundreds of thousands are people are just marching ahead into the future, no matter how “fraught” the results generated by obscure algorithms may seem.

(Republished from Discover/GNXP by permission of author or representative)
 
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I’ve been taking about ‘meat things’ for nearly 10 years, so I was really excited by the new Michael Specter piece in The New Yorker about artificially grown meat, Test-tube Burgers. You can’t read most of it online, so I want to copy this small section:

…One study, completed last year by researchers at Oxford and the University of Amsterdam, reported that the production of cultured meat could consume roughly half the energy and occupy just two percent of the land now devoted to the world’s meat industry….

I say real factories because we are all aware I assume by this point of the nature of ‘factory farming’. But mass production of animal stock is an ad hoc kludge. Domesticated animals have been bred for meat production, but they remain organisms with all the range of activities and ends which the term ‘organism’ entails. Raising raw tissue in cultures may seem ‘yucky,’ a point Specter covers in assessing the reaction of some environmentalists and animal-rights activists who don’t seem as excited by the shift from conventional livestock raising to growing tissue as one would expect if they ran the numbers, but it is probably inevitable if it is feasible. The article makes the point that most of the focus on this area seems to be in the Netherlands, but thank god the Chinese are paying attention to this!

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Biology 
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Josh Roseneau, when he’s taking time off from the evolution-creation wars, is poking around his own genome. Some sage advice:

On DNA Day, 23 and Me had a sale on their personal genomics service. They’d do their standard scan of your genome for free, as long as you paid for a year’s worth of their online subscription service.

For the price (nearly free up front, and a modest cost for the online community provided), my wife and I jumped on the deal. Since I got the results back two weeks ago, I’ve been exploring not only the services and information provided by 23 and Me, but the various other tools that individuals have started producing to help analyze and investigate this insight into my ubiquitous but invisible DNA.

My genome, for instance, revealed a genetic predisposition towards late-onset Alzheimers. The odds of getting Alzheimers are still quite small, but elevated because of this particular mutation to the APOE4 gene. This wasn’t a total surprise, given my family history, and as a healthy, young guy with a background in biology and biostatistics, it wasn’t hard for me to put that information into a context and move on. Down the road, I’ll probably keep an eye out for new research on Alzheimers medicines and look into tools for early detection, but I’m not going to kill myself if I forget my keys. (Thanks to the federal Genetic Information Nondiscrimination Act and the Affordable Care Act’s prohibition on “pre-existing conditions” – not to mention the inherent uncertainties in translating this genetic result to a specific outcome – I’m not especially worried about discussing that result in public)

We need to demystify DNA. It’s pretty obvious to me that people perceive genetics to be in the domain of magic, when in reality it manifests itself in the banal realities of correlations within the family, which we’re intuitively aware of. But Josh’s post is more than just personal, he reviews the book Biopunk: DIY Scientists Hack the Software of Life:

Most of the biopunks Wohlsen introduces us to aren’t trying to cure diseases or create genetic tests. They surely wouldn’t mind if they changed the world somehow, but their interest in DIY biology is driven more by a sense of personal exploration and a pure fascination with how things work. The goal, one of these biopunks explains, is to “increase the tinkerability” of biology, “simplifying and domesticating” it to make it accessible to anyone who wants to play with it. Groups like the Bay area’s Biocurious aim to create communal molecular biology labs which anyone can join and tinker in; Biocurious will open its lab this summer in Mountain View, not far from Google and the researchers at NASA’s Ames facility.

But I’m also fascinated because this is the future even for people whose aversion to biochemistry is even greater than my own. Just as everyone in the mid- to late 20th century needed some grasp of physics to be able to think sensibly about nuclear energy, nuclear war, and a host of related issues, the 21st century is sure to be dominated by biology. And DIYbio can play a key role in democratizing science, precisely because it’s more focused on what’s neat than on what’s likely to turn up a new Nobel Prize or a new patent and venture funding for a biotech startup. Its openness will be a great strength as a tool for improving science literacy, and biopunks know it.

I obviously support this movement and its intents (I’ve met a few of the people who are prominent in it). But we need to keep perspective here. This will probably be analogous to the free or open source software movement; the base of tinkers will be much larger than corporations and academic institutions, but it isn’t going to expand to cover the majority of the public. But so what? Most us can probably agree that the ad hoc decentralized elements of the software engineering community have done good just by putting pressure on the margins of staid institutions. Similarly, a minority of biology enthusiasts and hobbyists are going to shape the production and consumption of the plethora of new products we’re going to see coming online within the next few decades. There is often someone in the family who you turn to for tech advice. Now there may be someone in the family who you turn to for personal genomics advice. This is the democratization and decentralization of specialization!

When it comes to the mass consciousness aspect I think personal genomics and other consumer biotech will play a large role in demystifying DNA, and in the future making the public more open to the possibilities of bioengineering. Those of us alive today are on the cusp of a new age. I think the medium-term shape of that age is highly sensitive to initial conditions, so we should be both hopefully and vigilant.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Biology, Biotech, Personal Genomics 
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ResearchBlogging.orgThe Pith: Biological complexity may be a particular evolutionary path taken due to to random acts of nature, not because there is a selective advantage to complexity.

The title above basically describes the message of evolutionary biologist Mike Lynch from what I can gather. His basic argument is outlined in long form in The Origins of Genome Architecture, though the outline of the thesis is evident over 10 years back (see Preservation of Duplicate Genes by Complementary, Degenerative Mutations). Verbally I think the easiest way to explain Lynch’s framework is that in species with small effective population sizes the creativity of stochastic forces in generating non-adaptive structure and complexity tends to overwhelm the power of natural selection to prune this tendency toward baroque. I reviewed a paper last year which argued that Lynch’s observation of an inverse relation between effective population and genome size was an artifact, that once you controlled for phylogenetic history it disappeared. Suffice it to say this is an area of dispute and active research, so we shouldn’t take any individual’s word for it. This is science on the broadest canvas. Extraordinary general claims need to backed by a generation of publication I’d think.

Lynch is now a co-author on a new letter to Nature (which is open access, so read it!), Non-adaptive origins of interactome complexity. Imagine if you took biochemistry, specifically the nearly impenetrable language of protein interactions, and crossed it with evolutionary genomics. This is what you’d get.


The gist of the letter is in the figure to the left. You see 36 species in order of relative “interactome complexity.” An interactome is a basically a network of biochemical interactions, in this case in particular at the level of protein chemistry. Organisms which we presume to be complex, such as H. sapiens, have a more complex interactome than organisms which we presume to be less complex, such as prokaryotes.

Why does interactome complexity matter? Let me quote from the abstract : “This leads to the hypothesis that the accumulation of mildly deleterious mutations in populations of small size induces secondary selection for protein–protein interactions that stabilize key gene functions. By this means, the complex protein architectures and interactions essential to the genesis of phenotypic diversity may initially emerge by non-adaptive mechanisms.”

You probably know about neutral theory, whereby most evolution on the molecular level is due to substitutions which have neither positive nor negative selective effects. That is, they’re not adaptive. A related model is the nearly neutral theory, where a substantial fraction of substitutions are ever so mildly deleterious. So mild in fact that selection does not “see” these mutations as harmful enough to “purge” them from the genome. This is related to effective population size, which measures the proportion of individuals which matter for purposes of genetics in a set of individuals (if a population is 100, but only 10 breed, then there’s a huge difference between census and effective population size). As effective population size declines the power of random genetic drift becomes more evident. This is simply sample variance, which converges upon zero as N approaches infinite. If you flip a coin 100 times you will expect it to deviate proportionally from expectation (0.50 of both sides) more than if you flipped the coin 1000 times. Low effective population sizes are like the swell of noise against which natural selection is attempting to “make music.”

In this paper the authors seem to be suggesting that these broader population genetic dynamics result in suboptimal functionality on the molecular level as deleterious mutations build up. Complex molecular interactions then emerge through secondary natural selection pressures as a way for the whole Rube Goldberg system from collapsing in on itself. Wheels within wheels. The implication then is that complex organisms evolved not because they were better in a reproductively fit sense in relation to simple organisms, but that organismic complexity is simply a way for collections of simple organisms to not fall apart when subject to stochastic forces which increase the mutational load.

Back in the day my background was in biochemistry, but there’s a reason that I don’t talk about it much in this space. I’m not too excited about the prospect of visualizing the shape and character of a protein and its various subunits (I should have realized something was up when I found that I preferred physical chemistry to biochemistry!). But I’d be curious about the impression of readers who are versed and fluent in the biochemistry to evaluate the claims within. After the criticism of the genome size – effective population size correlation I’m a touch wary about an argument which relies on just 36 species. I also haven’t totally given up on the idea that one could introduce a fitness landscape model here, where organism complexity may initially have been a response to suboptimal fitness, but that after crossing the fitness “valley” the species could then ascend a new “peak.”

Citation: Ariel Fernández, & Michael Lynch (2011). Non-adaptive origins of interactome complexity Nature : 10.1038/nature09992

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Biology, Genome Complexity, Genomics, Mike Lynch 
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John Hawks and Jerry Coyne are mooting the ‘species concepts’ debate, with particular focus on recent human origins (specifically, the relationship of modern humans to Neandertals and Denisovans). Coyne, who coauthored the book Speciation and remains preoccupied with the issue in his academic work, knows of what he speaks. And of course he wouldn’t think that the discussion of species, how to delineate them, and what they are, is a sterile exercise. He has chosen to allocate a significant portion of his life to the topic. I think very few would disagree with Coyne when he contends that “Species are not arbitrary divisions of an organic continuum.” If there is one taxonomic category which has a concrete basis in reality, that would seem to be species. But, I would observe that I’m not sure that species are necessarily so clear and distinct. After all, we know that there is here and there, but where does here end, and there begin?

I’m of a reminded of the classic Zeno’s paradox:

In the paradox of Achilles and the Tortoise, Achilles is in a footrace with the tortoise. Achilles allows the tortoise a head start of 100 metres. If we suppose that each racer starts running at some constant speed (one very fast and one very slow), then after some finite time, Achilles will have run 100 metres, bringing him to the tortoise’s starting point. During this time, the tortoise has run a much shorter distance, say, 10 metres. It will then take Achilles some further time to run that distance, by which time the tortoise will have advanced farther; and then more time still to reach this third point, while the tortoise moves ahead. Thus, whenever Achilles reaches somewhere the tortoise has been, he still has farther to go. Therefore, because there are an infinite number of points Achilles must reach where the tortoise has already been, he can never overtake the tortoise.

The Greeks had a fascination with paradoxes because they perceived that they illuminated deep truths about the true nature of reality which we may have been blind to via sense perception. But sometimes I think that a fixation on species as the taxonomic category to rule them all confuses and calcifies the understanding of evolutionary genetic processes in the eyes of the public. Just as it is difficult to communicate that science is not a collection of facts, that it is a process and a method, so many people seem to take species categorizations as reflecting the true order of the universe. Historically this goes back to the pre-evolutionary taxonomists whose aim was to catalog all of God’s creation. It persists today explicitly among Creationists, who bandy about terms like “kinds,” but are really talking about immutable ideal entities with particular essences. Species on steroids if you will.

A fixation on the species has also confused the public on the issue of microevolution vs. macroevolution. Creationists regularly accept the former and reject the latter, despite the fact that the majority of biologists would probably assert that evolutionary processes are a unified whole, with no difference of scale. The constant usage of the term “microevolution” by the enemies of evolution seems to have even cast that term into some disrepute, I’ll admit to be shocked when a reader was confused as to the non-Creationist usage when I recommended Alan Templeton’s Population Genetics and Microevolutionary Theory. One could argue that the subject of modern population genetics is fundamentally microevolution.

Species are obviously abstractions. But I think an analogy can be made between them and physical objects. At the end of the day we know that the solidity and boundedness of physical objects are perceptions and interpretations filtered through our brains. Fundamentally they’re a bundle of particles and forces, interacting with other particles and forces. We don’t need to deny this deep reality, all the while instrumentally acknowledging the usefulness of categories of physical objections.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Biology, Philosophy, Species concepts 
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This morning I received an email from the communication director of the American Anthropology Association. The contents are on the web:

AAA Responds to Public Controversy Over Science in Anthropology

Some recent media coverage, including an article in the New York Times, has portrayed anthropology as divided between those who practice it as a science and those who do not, and has given the mistaken impression that the American Anthropological Association (AAA) Executive Board believes that science no longer has a place in anthropology. On the contrary, the Executive Board recognizes and endorses the crucial place of the scientific method in much anthropological research. To clarify its position the Executive Board is publicly releasing the document “What Is Anthropology?” that was, together with the new Long-Range Plan, approved at the AAA’s annual meeting last month.

The “What Is Anthropology?” statement says, “to understand the full sweep and complexity of cultures across all of human history, anthropology draws and builds upon knowledge from the social and biological sciences as well as the humanities and physical sciences. A central concern of anthropologists is the application of knowledge to the solution of human problems.” Anthropology is a holistic and expansive discipline that covers the full breadth of human history and culture. As such, it draws on the theories and methods of both the humanities and sciences. The AAA sees this pluralism as one of anthropology’s great strengths.

Changes to the AAA’s Long Range Plan have been taken out of context and blown out of proportion in recent media coverage. In approving the changes, it was never the Board’s intention to signal a break with the scientific foundations of anthropology – as the “What is Anthropology?” document approved at the same meeting demonstrates. Further, the long range plan constitutes a planning document which is pending comments from the AAA membership before it is finalized.

Anthropologists have made some of their most powerful contributions to the public understanding of humankind when scientific and humanistic perspectives are fused. A case in point in the AAA’s $4.5 million exhibit, “RACE: Are We So Different?” The exhibit, and its associated website at www.understandingRACE.org, was developed by a team of anthropologists drawing on knowledge from the social and biological sciences and humanities. Science lays bare popular myths that races are distinct biological entities and that sickle cell, for example, is an African-American disease. Knowledge derived from the humanities helps to explain why “race” became such a powerful social concept despite its lack of scientific grounding. The widely acclaimed exhibit “shows the critical power of anthropology when its diverse traditions of knowledge are harnessed together,” said Leith Mullings, AAA’s President-Elect and the Chair of the newly constituted Long-Range Planning Committee.


Up until the last paragraph this is an anodyne statement. Who could disagree with: “Anthropology is a holistic and expansive discipline that covers the full breadth of human history and culture. As such, it draws on the theories and methods of both the humanities and sciences. The AAA sees this pluralism as one of anthropology’s great strengths.” But the explosion of anger from biologically and scientifically oriented anthropologists on the web is drawn from a deeper layer of lived experience. On a raw level many of them feel that some factions in cultural anthropology are obscurantists who are fluent in rhetoric which they utilize in power-plays and politics. There are anthropologists who do deny the deep insights of the scientific method in illuminating reality. In fact, they reject the naive realism at the heart of science as it is practiced. For them science is a swear-word, and connotes an affinity with oppression and all the negative abstractions in fashion at a given time (e.g., patriarchy, heternormativity, capitalism, Eurocentrism, etc.). Of course as I note above scientific anthropologists are not given to tolerating the verbal circumlocutions and incantations of their non-scientific colleagues with much grace themselves. There is a deep cultural chasm, and these sorts of arguments over words in obscure institutional documents are only triggers for a persistent roiling debate.

As for the last paragraph, it illustrates the selectivity of a discipline which attempts to contextualize, and often has a skeptical relationship toward a positive framework. I believe that race is a social construct. The Hispanic identity, which consists of people of indigenous Amerindian, European, and African ancestry, and all their combinations, has been racialized. The Islamic identity has also been racialized. Benjamin Franklin stupidly contended that only the English and Saxons were true whites, with all other Europeans, including Nordics, being swarthy.

But just because a construct has a social element does not mean it has only a social construct. Because of the Left-liberal anti-racist egalitarian bias of anthropology, the academy in general, and the dominant narrative of Western society as a whole, there is a strong tendency to assert flatly that “race does not exist” as a biological concept. There is no interrogation of the concept of race except to refute its utility. This is not a case of agnostic skepticism washing away illusions, but a case of skepticism applied in a fashion to obtain a clear and distinct objective result which corresponds to reality. When it comes to race many become naive realists who accept that biological concepts can be falsified or verified in a simple and straightforward fashion. There is all of a sudden one Way of Knowing which presents us with indubitable truths.

Here is L. L. Cavalli-Sforza (my question in italics):

7) Question #3 hinted at the powerful social impact your work has had in reshaping how we view the natural history of our species. One of the most contentious issues of the 20th, and no doubt of the unfolding 21st century, is that of race. In 1972 Richard Lewontin offered his famous observation that 85% of the variation across human populations was within populations and 15% was between them. Regardless of whether this level of substructure is of note of not, your own work on migrations, admixtures and waves of advance depicts patterns of demographic and genetic interconnectedness, and so refutes typological conceptions of race. Nevertheless, recently A.W.F. Edwards, a fellow student of R.A. Fisher, has argued that Richard Lewontin’s argument neglects the importance of differences of correlation structure across the genome between populations and focuses on variance only across a single locus. Edwards’ argument about the informativeness of correlation structure, and therefore the statistical salience of between-population differences, was echoed by Richard Dawkins in his most recent book. Considering the social import of the question of interpopulational differences as well as the esoteric nature of the mathematical arguments, what do you believe the “take home” message of this should be for the general public?

Edwards and Lewontin are both right. Lewontin said that the between populations fraction of variance is very small in humans, and this is true, as it should be on the basis of present knowledge from archeology and genetics alike, that the human species is very young. It has in fact been shown later that it is one of the smallest among mammals. Lewontin probably hoped, for political reasons, that it is TRIVIALLY small, and he has never shown to my knowledge any interest for evolutionary trees, at least of humans, so he did not care about their reconstruction. In essence, Edwards has objected that it is NOT trivially small, because it is enough for reconstructing the tree of human evolution, as we did, and he is obviously right.

L. L. Cavalli-Sforza contends that between population genetic variation is not trivially small. This is clear from the fact that one can discern village-to-village genetic distinctions in Europe. Human variation exists, and it is not trivial. It is useful for phylogenetics, significantly impacts salient phenotypes, and, risks for particular diseases. The social construction of race has real biological raw materials. At one end, the transformation of white European converts to Islam through changes in personal appearance into de facto “People of Color” are matters of social construction in totality. In contrast, the blackness of a Dinka from Sudan is a matter of biological categorization. The categorization of Egyptian Arabs with obvious African admixture as “white” in the US Census is a matter of social construction due to bureaucratic contingency, and illustrates the intersection of biological reality and social fluidity. It is well known that when foreign Arabs with obvious black admixture visited the American South there was often a debate as to whether they were subject to segregation, illustrating the tensions between social norms (which would have coded them as black), bureaucratic function (which coded them as non-black usually), and biological reality (where they were an amalgam of a minor black African component with a dominant white Arab component).

Of course it is true that on any given trait variation can span populations. But even in the case given above, of sickle cell, the correlations with ancestry and population are striking. A lower boundary value is that 75% of sickle cell suffers are of mostly African ancestry, despite only 15% of the world’s population being of mostly African ancestry. These statistics refute a platonic model of race, but they do not refute the population-thinking which is at the heart of much of modern biology, pure and applied.

All that said, the word “race” is fraught with a lot of historical baggage. Therefore to study population wide variation you need to focus on “fine-scale population structure” and what not. This trend would be something of interest for cultural anthropologists of science to study. Race is just a word. Even a term as widely accept as species exhibits a fair amount of flexibility on the margins. But the underlying biological patterns, and the instrumental utility of those patterns, can not be denied.

Addendum: I often use “human” or “humankind” where earlier norms would be to use “man” or “mankind.” My main rationale is I don’t want annoying comments objecting to the term. The concept which I’m pointing to is the same no matter the pointer, and so I don’t mind changing it to facilitate my intent to communicate clearly and without undue extraneous baggage.

(Republished from Discover/GNXP by permission of author or representative)
 
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Rosie Redfield has a “must read” post, Arsenic-associated bacteria (NASA’s claims). I won’t excerpt it, read the whole thing. To me it is very interesting that many pieces of her critique are ones I’ve encountered in emails or Facebook postings. She stitches them together into a coherent whole. She’ll be writing a letter to Science. Hopefully they’ll publish it. Even if you don’t have a deep background in microbiology and biochemistry I think it was clear that the authors had jumped to some inferences too quickly.

(Acknowledgement, John Hawks)

Update: Also, Arsenate-based DNA: a big idea with big holes:

So the Sargasso Sea tells us that some bacteria are capable of making DNA at very low phosphate concentrations. The most plausible explanation is that the bacterium GFAJ-1 can make normal DNA at micromolar phosphate concentrations, and that it also has the ability to tolerate very high arsenate concentrations.

This seems like the “boring,” but most plausible, explanation.

Update II: David Dobbs reviews the journalistic response. I think that people who write about science were in a bind because of the structural problems that David points out. When I first skimmed the paper it seemed to claim too much, but I had to keep in mind that it got through peer review. On the other hand as I stated once scientists in a position to critique on a genuinely technical dimension started complaining really loudly on social networking, that changed my own perception really quickly.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Biology 
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ResearchBlogging.org One of the most persistent debates about the process of evolution is whether it exhibits directionality or inevitability. This is not limited to a biological context; Marxist thinkers long promoted a model of long-term social determinism whereby human groups progressed through a sequence of modes of production. Such an assumption is not limited to Marxists. William H. McNeill observes the trend toward greater complexity and robusticity of civilization in The Human Web, while Ray Huang documents the same on a smaller scale in China: A Macrohistory. A superficial familiarity with the dynastic cycles which recurred over the history of Imperial China immediately yields the observation that the interregnums between distinct Mandates of Heaven became progressively less chaotic and lengthy. But set against this larger trend are the small cycles of rise and fall and rise. Consider the complexity and economies of scale of the late Roman Empire, whose crash in material terms is copiously documented in The Fall of Rome: And the End of Civilization. It is arguable that it took nearly eight centuries for European civilization to match the vigor and sophistication of the Roman Empire after its collapse as a unitary entity in the 5th century (though some claim that Europeans did not match Roman civilization until the early modern period, after the Renaissance).

It is natural and unsurprising that the same sort of disputes which have plagued the scholarship of human history are also endemic to a historical science like evolutionary biology. Stephen Jay Gould famously asserted that evolutionary outcomes are highly contingent. Richard Dawkins disagrees. Here is a passage from The Ancestor’s Tale:

…I have long wondered whether the hectoring orthodoxy of contingency might have gone too far. My review of Gould’s Full House (reprinted in A Devil’s Chaplain) defended the popular notion of progress in evolution: not progress towards humanity – Darwin forend! – but progress in directions that are at least predictable enough to justify the word. As I shall argue in a moment, the cumulative build-up of compelx adaptations like eyes strongly suggest a version of progress – especially when coupled in imagination with of the wonderful products of convergent evolution.

Credit: Luke Jostins
Credit: Luke Jostins

One of those wonderful products is the large and complex brains of animals. Large brains are found in a disparate range of taxa. Among the vertebrates both mammals and birds have relatively large brains. Among the invertebrates the octopus, squid and cuttlefish are rather brainy. The figure to the right is from Luke Jostins, and illustrates the loess curve of best fit with a scatter plot of brain size by time for a large number of fossils. The data set is constrained to hominins, humans and their ancestors. As you can see there is a general trend toward increase cranial capacities across all the human populations. Neandertals famously were large-brained, but they exhibited the same secular increase in cranial capacity as African Homo. On the scale of Pleistocene Homo and their brains the idea of the supreme importance of contingency seems ludicrous. Some common factor was driving the encephalization of humans and their near relations over the past two million years. This strikes me as very strange, as the brain is metabolically expensive, and there are plenty of species with barely a brain which are highly successful. H. floresiensis may be a human instance of this truism.

But what about the larger macroevolutionary pattern? Is there a trend toward larger brain sizes in general, of which primates, and humans in particular, are just the most extreme manifestation? Some natural historians have argued that there is such a trend. But, there is a question as to whether increased brain size is simply a function of allometry, the pattern where different body parts and organs tend to correlate together in size, but also shift in ratio with scale. The nature of physics means that very large organisms have to be more robust because their mass increases far faster than their surface area. By taking the aggregate relationship between body size and brain size, and examining the species which deviate above or below the trend line, one can generate an encephalization quotient. Humans, for example, have a brain which is inordinately large for our body size.

And yet there are immediate problems looking at relationships between body and brain size, and inferring expectations. Different species and taxa are not interchangeable in very fundamental ways, and so a summary statistic or trend may obscure many fine-grained details. A new paper in PNAS focuses specifically on various mammalian taxa, corrects for phylogenetics, and also relates encephalization quotient by taxa to the proportion of social animals within each taxon. Encephalization is not a universal macroevolutionary phenomenon in mammals but is associated with sociality:

Evolutionary encephalization, or increasing brain size relative to body size, is assumed to be a general phenomenon in mammals. However, despite extensive evidence for variation in both absolute and relative brain size in extant species, there have been no explicit tests of patterns of brain size change over evolutionary time. Instead, allometric relationships between brain size and body size have been used as a proxy for evolutionary change, despite the validity of this approach being widely questioned. Here we relate brain size to appearance time for 511 fossil and extant mammalian species to test for temporal changes in relative brain size over time. We show that there is wide variation across groups in encephalization slopes across groups and that encephalization is not universal in mammals. We also find that temporal changes in brain size are not associated with allometric relationships between brain and body size. Furthermore, encephalization trends are associated with sociality in extant species. These findings test a major underlying assumption about the pattern and process of mammalian brain evolution and highlight the role sociality may play in driving the evolution of large brains.

A key point is that the authors introduce time as an independent variable, so they are assessing encephalization over the history of the taxon. This is clearly relevant for humans, but may be so for other mammalian lineages. The table and figures below show the encephalization slope generated by using time and body size as the predictors and brain size as the dependent variable. A positive slope means that brain size is increasing over time.

[nggallery id=21]

Two major points:

- Note that the slope is sensitive to the level of taxon one is examining. A closer focus tends to show more variance between taxa. So, for example, humans distort the value for primates in general. Bracketing out anthropoids paints a more extreme picture of encephalization, a higher slope. In contrast, the lemurs and their relatives exhibit less encephalization over time.

- The correlation between proportion of species which exhibit sociality and encephalization of the taxon is strong. From the text:

Encephalization slopes were correlated with both the proportion of species with stable groups (order R = 0.92, P = 0.005, n = 6; suborder R = 0.767, P = 0.008, n = 9; Fig. 2 A and B) and the proportion in either facultative or stable social groups (order R = 0.804, P = 0.027, n = 6; suborder R = 0.63, P = 0.04, n = 9).

The last figure makes it is clear that the correlations are high, so the specific values should not be surprising. Don’t believe these specific figures too much, how one arranges the data set or categorizes may have a large effect on the p-value. But the overall relationship seems robust.

266px-Alienigena
A highly encephalized “alien”

What to think of all of this? If you don’t know, one of the authors of the paper, Robin Dunbar, has been arguing for the prime importance of social structure in driving brain evolution among humans for nearly twenty years. The relationship is laid out in his book Grooming, Gossip, and the Evolution of Language. Robin Dunbar is also the originator of the eponymous Dunbar’s number, which argues that real human social groups bound together by interpersonal familiarity have an upper limit of 150-200. He argues that this number arises because of the computational limits of our “wetware,” our neocortex. Those limits presumably being a function of biophysical constraints.

One interesting fact though is that the median cranial capacity of our species seems to have peaked around one hundred thousand years ago. The average human today has a smaller brain than the average human alive during the Last Glacial Maximum! (see this old post from Panda’s Thumb, it’s evident in the charts) This may be simply due to smaller body sizes in general after the Ice Age. Or, it may be due to the possibility that social changes with the rise of agriculture required less brain power.

Ultimately if Dunbar and his colleagues are correct, if social structure is the most powerful variate in explaining differences in brain size when controlling for phylogenetics and body size, then in some ways it is surprising to me. After all, it does not seem that ants have particularly large brains, despite being extremely social and highly successful. Clearly the hymenoptera and other social insects operate on different principles from mammals. Instead of
developing “hive minds,” it seems as if in mammals greater social structure entails greater cognitive structure.

Citation: Susanne Shultz, & Robin Dunbar (2010). Encephalization is not a universal macroevolutionary phenomenon in mammals but is associated with sociality PNAS : 10.1073/pnas.1005246107

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If you haven’t, check out the Leigh Van Valen obituary in The New York Times. I hadn’t been aware of the breadth of his work, and the disciplinary range he showed over his career.

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• Category: Science • Tags: Biology, Leigh Van Valen 
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Girl_hands_out_flyer_at_Loveparade_03John Hawks, Genomes unzipped, unzipped:

What I wonder is, how much will personal genomics be like nude beaches? I mean, it’s been a long time since the first nude beaches, but most people don’t take advantage of the opportunity. Clearly, there’s variation in different countries! But most people neither feel compelled to see others’ data nor feel comfortable sharing their own.

Well, they used the word unzipped, not me!

Obviously John had his tongue-firmly-planted-in-cheek, but I have wondered about this. How deep is the impact of personal genomics going to be for individuals? If a person gets their genome sequenced and has a list of odds ratios in front of them are they going to bone up on the statistical genetic subtleties of the face value?

That is where genetic counselors come in. The necessity of interpretative experts highlights the difference between nude beaches and personal genomics: personal genomics has more potential societal impact. I know of the nudist/naturist phenomenon only tangentially, but it strikes me as similar to the broader New Age health movement. The focus is on individual health returns. A colon cleanse simply does not have much of broader social effect. Yes, lest my nudist readers strike me down I do understand that there are purported positive social externalities, but set next to personal genomics nudism still strikes me as a fundamentally more individual activity whose benefits redound to the naked individuals, and not the broader clothed society. It does not pick my pocket nor break my leg if my neighbor is a weekend nudist. It is of no concern of mine (in contrast, my experience with public nudity is that it is generally disruptive when unexpected).


pgenI conceive of the social returns to personal genomics as a function of the proportion utilizing it will be defined by an s-curve. When only a few people have been genotyped your understanding of population-wide variation is still spotty. But as you increase your coverage you get a better sense of the variance within the population…but soon enough you enter the phase of diminishing returns.

Here’s a concrete example. In Reconstructing Indian History Reich et al. indicated that it is likely that South Asian castes are endogamous groups which will carry their own recessive risk alleles. In other words, Kayasthas from Bengal may have their own suite of recessive diseases, while Nadars from Tamil Nadu may have a totally different set of risk alleles. In a world with infinite NIH funding there would studies of Kayasthas and Nadars, and doctors and genetic counselors would be aware of what to look for in each group. We don’t live in a world with infinite NIH funding. Let’s assume that 1% of Indian Americans are Kayasthas from Bengal. That’s 30,000 people. If 5% of them make extensive use of personal genomics, then you have 1,500 people with a deep individual knowledge of their personal genomic profile, as well as a set of possible diagnoses or suites of symptons.

We’re still at the individual level. How does this matter on a social scale? Because with modern technology people can form communities online and get a sense of the nature of things from the “bottom-up.” Granted, the information gleaned isn’t going to go through peer review, and “irrational herds” can no doubt emerge. The bigger point is that sum can become more than the parts as motivated individuals pool information in a coordinated fashion. Once there’s some general insight extracted then that will flow to the rest of the group because of interpersonal networks.

This already happens with genealogy. A few highly motivated individuals dig deep into the archives to learn about their own personal history, and once they’ve retrieved the information they freely distribute what they’ve found to their relatives. From one perspective you could say that others are “free riding” on the passion and labor of a few, but you could also characterize this as a spillover effect or positive externality. The consequences of personal genomics are arguably much more substantive than traditional genealogy because of their potential health import.

Note that I’m emphasizing the social good here. Your sample size only needs to be so large to get a good sense of population-wide dynamics. More prosaically, as I noted before the Genomes Unzipped bloggers have opened a window into the genetics of their extended families. If Dienekes analysis is correct Joseph Pickrell and Vincent Plagnol likely have half-Jewish parents. Not that there’s anything wrong with that, though some people are still somewhat reluctant to acknowledge their Jewish heritage even today.

I assume that there will be individual utility as whole populations are sequenced over time. There’s more you can potentially learn by getting yourself sequenced even after ethnic-group or family level risks are ascertained (e.g., what are your distinctive alleles which are de novo mutations?). But this would simply be a classic increase of well being through summing of the parts. And here the analogy to the nude beach would be valid.

Image Credit: Pradeur

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Last month in Nature Reviews Genetics there was a paper, Measuring selection in contemporary human populations, which reviewed data from various surveys in an attempt to adduce the current trajectory of human evolution. The review didn’t find anything revolutionary, but it was interesting to see where we’re at. If you read this weblog you probably accept a priori that it’s highly unlikely that evolution “has stopped” because infant mortality has declined sharply across developed, and developing, nations. Evolution understood as change in gene frequencies will continue because there will be sample variance in the proportions of given alleles from generation to generation. But more interestingly adaptive evolution driven by change in mean values of heritable phenotypes through natural selection will also continue, assuming:

1) There is variance in reproductive fitness

2) That that variance is correlated with a phenotype

3) That those phenotypes are at all heritable. In other words, phenotypic variation tracks genotypic variation

Obviously there is variance in reproductive fitness. Additionally, most people have the intuition that particular traits are correlated with fecundity, whether it be social-cultural identities, or personality characteristics. The main issue is probably #3. It is a robust finding for example that in developed societies the religious tend to have more children than the irreligious. If there is an innate predisposition to religiosity, and there is some research which suggests modest heritability, then all things being equal the population would presumably be shifting toward greater innate predisposition toward religion as time passes. I do believe religiosity is heritable to some extent. More precisely I think there are particular psychological traits which make supernatural claims more plausible for some than others, and, those traits themselves are partially determined by biology. But obviously even if we think that religious inclination is partially heritable in a biological sense, it is also heritable in the familial sense of values passed from one generation to the next, and in a broader cultural context of norms imposed from on high. In other words, when it comes to these sorts of phenotypic analyses we shouldn’t get too carried away with clean genetic logics. In Shall the Religious Inherit the Earth? Eric Kaufmann notes that it is in the most secular nations that the fertility gap between the religious and irreligious is greatest, and therefore selection for religiosity would be strongest in nations such as Sweden, not Saudi Arabia. But as a practical matter biologically driven shifts in trait value in this case pales in comparison to the effect of strong cultural norms for religiosity.

Below are two of the topline tables which show the traits which are currently subject to natural selection. A + sign indicates that there is natural selection for higher values of the trait, and a – sign the inverse. An s indicates stabilizing selection, which tells you that median values have higher fitnesses than the extremes. The number of stars is proportional to statistical significance.


future1

future2

Some of this is not surprising. The age of the onset of menarche has been dropping in much of the world. I suspect this is mostly due to better nutrition, but a consequence of this shift is earlier fertility for some females. The authors are nervous about the robust correlation of higher fertility with lower intelligence, but notice that the pattern for wealth and income is different and more complicated. The key is to look at education. Whether you believe intelligence exists or not in any substantive concrete sense, those who are more intelligent are more likely to have had more education, and there’s a rather common sense reason why investing in more schooling would reduce your fertility: you simply forgo some of your peak reproductive years, especially if you’re female. The higher you go up the educational ladder the stronger the anti-natalist cultural and practical pressures become (the latter is a heavier burden for females because of their biological centrality in child-bearing, but both males and females are subject to the former). As with religion even if the differences have no biological implication because you believe the correlations are spurious or reject the existence of the trait one presumes that parents and subcultures pass on values to offspring. If higher education has anti-natalist correlations we shouldn’t be surprised if subsequent generations turn away from higher education. Their parents were the ones who were more likely to avoid it.

We live in interesting times.

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324_1035_F1To the left is a figure from the 2009 paper The Genetic Structure and History of Africans and African Americans. This paper happens to have excellent coverage of African populations, and the figure is a phylogenetic tree generated from distances between those populations, as well as some non-African ones. I’ve labelled the broad clusters. The Bushmen* branch off first, along with the Pygmies. The other clade represents all other humans, African and non-African. Following the non-Bushmen/Pygmy clade down its branching pattern all non-Africans eventually go their own way, and differentiate into their various groups. South Asians form a clade with Europeans and Middle Easterners. East Asians, Native Americans, and more broadly Oceanians, form their own clade. Outside of Africa you basically have a west vs. east & further east division.

These trees are essential in helping us visualize genetic relationships. Tables of pairwise distances are simply not as informative as representations of the data for the human mind. More colloquially, they blow. Trees and two-dimensional plots are much better representations of the data which we can digest in a more gestalt fashion. We see, therefore we know. Ah, but even the innocent tree can lead a mind astray. Or at least this particular tree. So let’s try something different.


abofig1Here’s a figure from Whole-Genome Genetic Diversity in a Sample of Australians with Deep Aboriginal Ancestry. This tree has a smaller number of populations, but the broad geographical relationships are the same. West Eurasians are one cluster, while East Eurasians, Native Americans and Oceanians are their own super-cluster which divides further. Among the Africans you see that the Bushmen and the Mbuti again exhibit more distance from the other groups. But the biggest difference is that the tree is unrooted, so you don’t immediately orient yourself from outgroup to ingroup in a serial manner.

Now let’s look at a headline inspired by one of the papers: African San people – the world’s most ancient race. Going by the figures which paper do you think it was? It was the first paper of course. There’s a huge problem when these phylogenetic trees are generated that human outgroups, or basal clades, are defined as ‘ancient,’ the ‘oldest,’ or the most ‘antique.’ This is just confusing. Not only that, as a person deeply committed to the dignity of the indigenous peoples I am offended! I generally get irritated or blow a gasket when people make that confusion in the comments, because I think it leads to lazy inferences. One of my main quibbles with The Faith Instinct is that Nicholas Wade used the Bushmen as proxies for ur-humans to reconstruct prehistoric religious practice, implicitly relying on the fact that they’re the basal lineage in most genetic studies as if they’re a fossil which we can use to paint the past.

phytreeIn any case, I was going to recommend to readers that they just refer to ‘basal clades.’ Well, I’m not a taxonomist obviously so I decided to look in the literature, and I found this paper, Which side of the tree is more basal? The tree they use to illustrate the lack of utility of terms like ‘basal clade’ is to the left. Let me quote them:

Both branches originating from a node (i.e. the two sister groups) are of equal age and have undergone equivalent evolutionary change. Whether a group has branched off early (basal) or later in the phylogeny contains no information about this particular group, but information about both this group and its sister group, because both branched off at the same time. By notation we tend to portray one branch (the species/taxa-poor one) as being on the left, and the other (species/taxa-rich) as right – but this infers nothing about their evolutionary development, only about their taxon richness (speciation less extinction) at a given geological period (mostly the present), or, even worse, about the taxon sampling pattern in the particular study. Different taxon sampling leads to different interpretation about ‘the most basal clade’….

Considering clades or taxa as ‘basal’ is not only sloppy wording, but shows misunderstanding of the tree and may have severe semantic and argumentative implications. Declaring one sister group to be basal gives the other sister group a higher or at least a different value (‘the basal clade’ vs. ‘the derived clade(s)’). If the Polyneoptera is the most basal clade of the Neoptera, then the rest of the Neoptera (the Eumetabola) is given a higher value (as the ‘main’ body of the group). Admittedly, it contains more species, but this is not a quality necessarily granting it higher value…..

If the phylogenetic tree in Fig. 1 is correct, Polyneoptera and Eumetabola are sister groups. There is no necessity to term either as ‘basal’. Even if one wants to avoid the little-used name Eumetabola, it is easy to describe the Polyneoptera as the sister group of the remaining Neoptera. Argumentation with sister-group relationships is easy and shows relationships much more clearly than declaring one sister group to be basal. The ‘basal position’ within an ingroup always means ‘sister to the remaining taxa’, so say so!

The argument here is obviously embedded in the milieu of systematics and their particular concerns. But their objection to the term ‘basal clade’ is actually pretty much my main qualm which using terms like ‘ancient.’ I don’t think using ‘sister to the remaining taxa’ is going to be informative to most people, so at this point I don’t know what I’ll use for short hand. Outgroup seems viable.

I don’t really think about systematics in a deep philosophical sense. But the problem of terminology here, and the evolutionary implications therein, have brought home to me utility of a precise and accurate systematic framework in biology.

* The term “San” is like the term “Lapp” or “Welsh,” what others call them, so I’ll use Bushmen.

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• Category: Science • Tags: Biology, Evolution 
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A month ago I pointed to a short communication in Nature Genetics which highlighted differences in the patterns of variation between the X chromosome and the autosome. I thought it would be of interest to revisit this, because it’s a relatively short piece with precise and crisp results which we can ruminate upon.

ResearchBlogging.org Sometimes there is a disjunction between how evolutionary biologists and molecular biologists use terms like “gene.” The issue is explored in depth in Andrew Brown’s The Darwin Wars. Brown observes that one of the problems with Richard Dawkins’ style of exposition is that it did not translate well to the American context. He spoke of genes as units of analysis, from which logical inferences could be made. This was the classical Oxford style of evolutionary biology which Ernst Mayr objected to. In contrast American biologists were used to thinking of genes in more concrete biophysical terms, and tended to miss the theoretical context which Dawkins was alluding to in his arguments. In Dawkins’ defense, it must be remembered that the gene does have its origins as an abstract entity whose biophysical substrate, DNA, was not known for decades. In my post Simple rules for inclusive fitness I outlined a paper which is very much in keeping with the analytic tradition. Start with an abstract model and allow the chain of inferences to be made, and see where it takes you.


But biology is obviously more than just armchair analysis. Though there were always quantitative thinkers such as R. A. Fisher who made great contributions to the field, naturalists and anatomists such as Charles Darwin and Thomas Huxley were the predecessors of the vast majority of working biologists today. Even molecular biologists arguably descend from the laboratories of the physiological geneticists of the early 20th century. With a more robust understanding of the biophysical embeddedness of genetic inheritance in genomic structures a new dimension has been added to analysis from first principles. The fact that genetics is mediated through chromosomes matters.

One obvious aspect in mammals is that males are the heterogametic sex. All males have one X chromosome, while all females have two. This means that an X chromosomal lineage will “spend” 2/3 of its “time” in females, all things equal. This physical reality has been spun out to fascinating effect by evolutionary biologists, outlined in Matt Ridley’s The Red Queen: Sex and the Evolution of Human Nature. In this way the concrete nature of genetics has yielded another axiom to insert into the analytic engine of evolutionary biology.

Of late one finding that has been emerging out of the area of human evolutionary genomics is that the X chromosome may experience selective dynamics differently than the autosome. This possibility turns out to be critical in explaining some strange results reviewed in the communication. The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes:

The ratio of X-linked to autosomal diversity was estimated from an analysis of six human genome sequences and found to deviate from the expected value of 0.75. However, the direction of this deviation depends on whether a particular sequence is close to or far from the nearest gene. This pattern may be explained by stronger locally acting selection on X-linked genes compared with autosomal genes, combined with larger effective population sizes for females than for males.

At issue are some statistics presented in two papers, Accelerated genetic drift on chromosome X during the human dispersal out of Africa and Sex-biased evolutionary forces shape genomic patterns of human diversity. The first group found much less nucelotide diversity, π, on the X chromosome than the second group. From π and D, the divergence between humans and a primate outgroup, they could ascertain a rough proxy of effective population size. The smaller the effective population, the less nucleotide diversity as drift will tend to expunge variation out of the genome. The ratio of effective population size inferred from the X and the autosomes was given by N eX/N eA. The value was on the interval 0.65-0.75 for the first group (depending on the human samples used), and 0.75-1.08 for the second group.

From this the first group concluded that female effective population sizes were smaller for our species. Recall that the X spends more time in females. Naturally from their results the second group concluded that there were more breeding females. In science it is not optimal when two groups come into conflict when looking ostensibly at the same question using similar methods. But, their were subtle differences in their methods which may have biased the results. The first group looked at large regions of the genome, while the second group focused on intergenic regions with recombination. In the second case the aim was to look for patterns of variation away from genes which might have been targets of natural selection (recombination would break apart associations). The logic of the first group was presumably that increasing the proportion of the genome surveyed would mitigate the distorting affect of a few genes which had been subject to natural selection. To check for this they examined the statistics when constraining the data set to regions far away from genes. This did not change their finding.

s1But the second group, which submitted this communication to Nature Genetics, observes that it is not physical distance which is the appropriate variable, but genetic distance. To explore this question they looked at the dependence of π upon genetic distance from genes, and it is clear that the difference in π between the X and the autosome decreases as a function of genetic distance. Obviously the X chromosome has sharply reduced genetic variation near the genes. Why?

The general answer is that the X chromosome experiences selective pressures differently from the autosome. That is a function of the cytogenetics of mammals. Unlike the autosomes a substantial minority of X chromosomes are exposed to the full force of natural selection in the haploid state. To make this concrete males have only one copy of the X, so positive or negative fitness implications would have a much stronger immediate impact. The negative aspect is famous from “sex-linked diseases,” where sons inherit defective genetic variants from their mothers, who are carriers. Since the mothers have two X chromosomes they do not manifest illness. But the positive impact is that if there is a favored allele, and it only expresses recessively, then natural selection is going to be much more efficacious on the X chromosome because a substantial minority of allelic variants will express even at low frequencies. The problem with recessive traits being the primary target of positive selection is that at low frequency the traits almost never express. If, on the other hand, the frequency of the allele rose because of its exposure in males, then that would have a positive feedback loop effect as more and more females would also express the trait in the homozygous state.

In sum the authors conclude that different regions of the X chromosome are telling us different stories. Genic regions are witness to the powerful impact of natural selection upon the genome. In contrast, neutral sites are representative of the demographic history of the species, and in particular its females. I’ll let them finish:

If this hypothesis is correct, multiple evolutionary processes may confound inferences based on wholesale comparisons of full genome sequence data. If we wish to disentangle the history of selection, recombination and demography, a targeted set of carefully chosen regions at sufficient genetic distances from functional elements is needed. Intriguingly, at least for the human X chromosome, the signature left solely by demographic history may be hidden in the small fraction of selectively neutral polymorphisms that reside far from genes.

Citation: Hammer MF, Woerner AE, Mendez FL, Watkins JC, Cox MP, & Wall JD (2010). The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes. Nature genetics PMID: 20802480

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There is a new paper in Nature which is a full frontal attack on the utility of William D. Hamilton’s inclusive fitness framework in explaining eusociality. Martin A. Nowak, Corina E. Tarnita, & Edward O. Wilson are the authors. Wilson is famous in large part for his authorship of Sociobiology: The New Synthesis, and is arguably the doyen of American organismic biology. He is both an active scientist, and, a premier public intellectual. So with that in mind, I notice that Dienekes Pontikos alludes to “E.O. Wilson’s change of mind about group selection.” This is conventional wisdom, but it is I think wrong (though from what I can tell Wilson has not done much to disabuse the press of the notion). In Defenders of the Truth Ullica Segerstrale notes that Wilson did not expunge group selection thinking even in Sociobiology. In Evolution for Everyone David Sloan Wilson recounts that it was in fact E. O. Wilson who pointed out a group selective interpretation of data he was presenting at a conference, helping to push him early on in a rather unfashionable direction. From what I have heard Wilson always believed that the empirical data was not adequately explained by a pure inclusive fitness model, and simply waited until things shook out before pushing back with more theoretically trained colleagues who had the same skepticism.

From page 30 of Sociobiology:

…….Nevertheless, Williams’ distaste for group-selection hypotheses wrongly lead him to urge the loading of the dice in favor of individual selection. As we shall see in chapter 5, group selection and higher levels of organization, however intuitively improbable they may seem, are at least theoretically possible under a wide range of conditions. The goal of the investigation should not be to advocate the simplest explanation, but rather to enumerate all of the possible explanations, improbable as well as likely, and then to devise tests to eliminate some of them.

And page 129, the last paragraph in the chapter on group selection (quoted in full so there’ll be no confusions as to whether I’m pulling it out of context):

In conclusion, although the theory of group selection is still rudimentary, it has already providd insights into some of the least understood and most disturbing qualities of social behavior. Like Arjuna faltering on the Field of Righteousness, the individual is forcd to make imperfect choices based on irreconcilable loyalties-between the “rights” and “duties” of self and those of family, tribe, and other units of selection, each of which evolves its own code of honor. No wonder the human spirit is in constant turmoil. Arjuna agonized, “Restless is the mind, O Krishna, turbulent, forceful, and stubbon. I think it is no more aesily to be controlled than is the wind.” And Krishna replied, “For one who is uncontrolled, I agree the Rule is hard to attain, but by the obedient spirits who will strive for it, it may be won by following the proper way.” In the opening chapter of this book, I suggested that the science of sociobiology, if coupled with neurophysiology, might transform the insights of ancient religions into a precise account of the evolutionary origin of ethics and hence explain the reasons why we make certain moral choices instead of others at particlar times. Whether such understanding will then produce the Rule remains to be seen. For the moment, perhaps it is enough to establish that a single strong thread does indeed run from the conduct of terminte colonies and turkey brotherhoods to the social behavior of man.

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In my review of Replenishing the Earth: The Settler Revolution and the Rise of the Angloworld, 1783-1939 I left one aspect of James Belich’s thesis out of my list of criticisms because it wasn’t relevant to most of the argument. He seems to reject, mostly based on incredulity, the idea that there were massive population collapses in the New World when the natives encountered diseases incubated on the World Island (I say “World Island” because it wasn’t only Eurasian diseases, African slaves brought their own suite of lethal ailments which “cleared out” Amerindians from many lowland zones). He points out, correctly, that the Black Death in Europe is estimated to have resulted in a decrease of only ~1/3 from the total population. How then could it be plausible that there may have been population contractions on the order of a magnitude (i.e., the post-collapse population being only ~10% of the pre-collapse population). The skepticism of extreme population decline on the part of indigenes dovetails with the author’s focus on the particular explosiveness of Anglo natural increase, as well as migratory bursts. Heightening the “contrast effect” at the heart of his central thesis.


I think the author’s incredulity only makes sense in light of biological naivete. To a first approximation moderns tend to assume that all populations are interchangeable in our models. Like the economist ignoring individual differences and fixating on H. economicus for analytical purposes this has some utility, but it does miss much of the picture. The Black Death was only one of many epidemics which swept over Europe, so one can presume that European populations were already somewhat robust in the face of a new strain of infectious disease. The revisionist scholarship, which posits mass population collapse, is thoroughly reviewed in Charles C. Mann’s 1491: New Revelations of the Americas Before Columbus. But even today biological differences matter when it comes to disease, for example in relation to swine flu fatalities.

One of the implicit aspects of Belich’s skepticism is that population crash models in the New World are rooted in inferences, not concrete censuses. But I recently stumbled onto a “test case” for contact between Europeans and indigenous people where we have some good data sets, Tahiti.

tahiti2

The initial data point of ~50,000 in 1767 is a low boundary estimate. But the subsequent data points are more concrete, from missionary surveys, or censuses. Even excluding the estimate the pre-contact population of Tahiti island seems to have dropped by one half in a two generation period. This is greater than the average decrease of the Black Death in Europe.

I think the reason for these massive population collapses when isolated groups meet more cosmopolitan ones is simple: they compress many generations of natural selection and immunity acquisition into just a few. In the historical record we know that the 2nd century A.D. witnessed the outbreak of plagues in the Roman Empire, and the subsequent decline and fall was concomitant with the endemic status of malaria in the Italian lowlands. The great Plague of Justinian in the late 6th century has been fingered as the causal factor behind the rise of Islam, the replacement of Celtic Britons by Anglo-Saxons, and the end of the Classical World more generally. Populations isolated from the grinding pathologies of Malthusian agricultural interlude just experienced it in all its glorious misery in a very short burst.

Source: Urbanization in French Polynesia, RC Schmitt, 1962

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• Category: History, Science • Tags: Biology 
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ResearchBlogging.org Despite the reality that I’ve cautioned against taking PCA plots too literally as Truth, unvarnished and without any interpretive juice needed, papers which rely on them are almost magnetically attractive to me. They transform complex patterns of variation which you are not privy to via your gestalt psychology into a two or at most three dimensional representation which can you can grok immediately. That is why History and Geography of Genes was so engrossing. You recognize patterns which were otherwise unrecognizable. But how you interpret those patterns, that’s a wholly different matter. And how those patterns arise is also not something one can ignore.

price_fig1First, let’s start with an easy case. To the left is a PCA plot with four populations. Nigerians, East Asians (Chinese + Japanese), Europeans (whites from Utah), and finally, African Americans. The x-axis is the first principal component of variation, and the y-axis the second. That means that the x-axis is the independent dimension of variation within the patterns of genetic data which explains the largest fraction of the total amount of genetic variation. The sum totality of the variation can be decomposed into an large set of independent dimensions which can be rank ordered from the largest explanatory components to the smaller ones, successively by number. In a human genetic context the first principal component invariably separates Africans from non-Africans, and the second principal component often maps onto a west-east axis from Europe to the New World. Subsequent principal components can often be useful in smoking out fine scale distinctions, or relationships which are confused by the existence of similar but different signals in admixed populations.

The interpretation of this plot is rather easy. You see that African Americans lay along a continuum between Nigerians and Europeans, skewed toward Nigerians, with some outliers toward East Asians. We know from other genetic findings that ~20% of the African American ancestral quanta is European, but, that quanta is not equally distributed across the population. ~10% of the African American population is more than 50% European in ancestry, while 90% is less than 50% European. And so you have a distribution which reflects this variation. As for the outliers, I will speculate and suggest that these are indications of Native American ancestry among some African Americans.

The story I presented above is probably plausible as an explanation of the visual because we have a wealth of historical data to corroborate the plausibility of that narrative. The fit between the results from the technique of analysis of genetic variation and what scholars have long inferred from textual sources is relatively easy. It is far more difficult to look at a PCA plot, and generate a plausible narrative that you yourself accept with a high degree of confidence with little external support. It is with that caveat in mind that I present Toward a more uniform sampling of human genetic diversity: A survey of worldwide populations by high-density genotyping:

High-throughput genotyping data are useful for making inferences about human evolutionary history. However, the populations sampled to date are unevenly distributed, and some areas (e.g., South and Central Asia) have rarely been sampled in large-scale studies. To assess human genetic variation more evenly, we sampled 296 individuals from 13 worldwide populations that are not covered by previous studies. By combining these samples with a data set from our laboratory and the HapMap II samples, we assembled a final dataset of ~ 250,000 SNPs in 850 individuals from 40 populations. With more uniform sampling, the estimate of global genetic differentiation (FST) substantially decreases from ~ 16% with the HapMap II samples to ~ 11%. A panel of copy number variations typed in the same populations shows patterns of diversity similar to the SNP data, with highest diversity in African populations. This unique sample collection also permits new inferences about human evolutionary history. The comparison of haplotype variation among populations supports a single out-of-Africa migration event and suggests that the founding population of Eurasia may have been relatively large but isolated from Africans for a period of time. We also found a substantial affinity between populations from central Asia (Kyrgyzstani and Mongolian Buryat) and America, suggesting a central Asian contribution to New World founder populations.

The studies which came out of the original HapMap had northern Europeans, Yoruba from Nigerians, and Chinese & Japanese. These three populations can tell us a lot, but there’s something lacking in the coverage. The HGDP sample is better. But specifically because of political considerations it was not feasible to collect Indian samples, so Pakistani ones are used in their stead. Additionally, the HGDP sample is a touch biased toward isolated and distinctive populations, such as the Kalash of Pakistan. This genetic distinctiveness is important to catalog because it is fast disappearing. But the Kalash are so unique because of their long history of isolation, so one can’t really use them as a proxy population for Pakistanis, as one could with Sindhis. The POPRES sample seems to complement the HGDP well, but I don’t see it being used so much. Since the next phase of the HapMap has more populations, some of the deficiencies which emerged with the utilization of just three terminal groups (in a World Island context) will soon no longer be an issue.

But until that time it’s nice when studies come out which close some of the gaps in our knowledge of world wide genetic variation. This is one such study. I’m somewhat familiar with the samples already because I’ve seen it in an analysis of Indian populations. It seems that it is somewhat skewed toward South and Southeast Asian populations, but hey, these are groups which need to draw the long straw sometimes as well.

Before I go any further I should mention that they use a SNP-chip with hundreds of thousands of markers. Additionally, they looked at copy number variation. Two rather different types of variation within the genome, probably to double check that the outcomes were the same. Population historical events which shape patterns of genomic variation would presumably have a similar large scale effect on both types of variation. In their results that checked out, or so they claimed, as the paper is a manuscript without the supplements attached.

Though there’s some interesting fine-grained analysis to be had, they draw some macro-scale and deep time inferences as well. First, you probably know the famous fact that 15% of variation in genes is between races, and 85% within races. That’s derived from the Fst statistic, which is basically partitioning between and within population variance across two populations. Obviously the value of Fst varies by the set of populations you’re comparing. That between Mbuti Pygmies and Japanese is far higher than between Chinese and Japanese. Using the HapMap the Fst was 16%. About what you’d expect. To equalize sample sizes with the HapMap they randomly selected individuals from a pooled set grouped by continent from their populations, and calculated Fst. They found values around 11%. Why the difference? Because their data set included populations which were between the three clusters within the HapMap.

This is naturally not a surprising result at all, but it does reiterate one issue which sometimes crops up: Platonism in relation to race. The northern European whites in the HapMaps are the whites par excellence. Turks, who are perhaps more centrally located in the genetic variation of West Eurasian and North African peoples, what used to be termed “Caucasoid,” are “less white.” Similarly, Nigerians are more African than Ethiopians. Chinese and Japanese are more Asian than Burmese. And so forth. When modeling between group differences there is I think a somewhat old-fashioned tendency to consider some populations racial archetypes. That modulates the input which modifies the results somewhat. The analytical technique may be as cold as stone, but they are used by flesh and blood human beings.

There is also some funny business going on with haplotype and SNP heterozygosities which I think needs to be highlighted, and speaks to the fact that SNP-chips are not perfect. They’re tools, and human tools are impacted by arbitrary or instrumental choices humans make. Let me quote:

We also compared the SNP and haplotype heterozygosity values in each population (Figure 2B). These two quantities are generally highly correlated, although there are several exceptions: First, SNP heterozygosity is higher than haplotype heterozygosity in European and Central Asian populations. This may reflect a SNP ascertainment bias, since many of these polymorphisms were historically selected to maximize heterozygosity in European populations. Second, the Pygmy sample shows a low SNP heterozygosity despite relatively high haplotype heterozygosity. This unusual pattern could be caused by stronger effects of SNP ascertainment bias in this population than in others. Indeed, a recent study of Khoisan individuals (another hunter-gatherer group from Africa) showed a similar pattern: despite high SNP heterozygosity (~60%) in whole-genome sequence data, a Khoisan individual showed low heterozygosity on the SNP microarray genotypes (~22%) . Alternatively, this difference could also reflect unique attributes of population history.

In plain English the gene chips were designed with Europeans in mind, so they don’t necessarily pick up all the variation in non-European groups, who are believe it or not genetically different. This issue cropped up (as alluded to in the above text) with the recent paper which sequenced some Bushmen as well as Desmond Tutu. The Bushmen have a lot of variation, this is well known, but they have variation at markers where Europeans don’t, and if Europeans don’t the chips may not look for polymorphism at that locus. This sort of thing probably doesn’t affect broad population relationships, but if you want to zoom in and do analysis which is sensitive to fine distinctions and quantitative differences, then it might be problematic.

Let’s jump to the pretty charts. First, a PCA plot with all of the individuals from all of the populations:

indo1

Note that PC 1 accounts for nearly eight times as much variation as PC 2. This speaks to the African vs. non-African gap. Because their data set is relatively thick in “intermediate” groups you see a spectrum. The vertical axis is obviously mostly east-west. And here’s the accompanying bar plot derived from the ADMIXTURE program. K = putative ancestral populations.

indo2

With this many populations at K = 12 I think you could write a fantasy novel worthy of Tolkien. K = 4 is more realistic. Among the African populations you see likely Eurasian admixture in some eastern, and it seems Bushmen, individuals. In Eurasia itself you see a clinal gradation of admixture between putative ancestral components that seems to follow longitude rather well.

Because so much of the variation in the total sample is due to Africans, removing them from the picture will allow us to focus more on the relationships of the Eurasian groups. And so that’s exactly what they did. Note that focusing on the Eurasian groups does not mean simply magnifying or zooming in on the Eurasian section of the PCA plot, rather, the plots are regenerated with a subset of the previous genetic variation. In other words, the dimensions will shake out a bit differently.

The first plot shows Eurasian populations as a whole. The second removes Europeans and Near Easterners.

indo3

Notice again the scale. The vast majority of the variance seems to be east-west. But, there is a noticeable north-south split. For the South Asian population it looks like they had Pakistanis who were farmers of modest means (Arain), high caste South Indians, and very low caste or tribal South Indians. For this Indian sample there’s a problem, and it’s the sample problem which plagued the Up Series, they are looking at the very top and bottom of Indian society and ignoring the middle. Presumably the middle is going to be somewhere in the middle genetically as well, but nevertheless that’s something to consider in a paper which presumes to fill in the patchiness of others. In contrast, the Nepali sample was notably ethnically diverse, including both the dominant Indo-Aryan segment as well as the Tibeto-Burman Newar.

In the first panel there are some curious patterns with the Southeast Asian groups. Culturally, as in language and history, the Thai and Vietnamese have relatively recent roots in the southern regions of modern China. The Dai of Yunnan are the same people in origin as the Thai of Thailand and the Lao of Laos. Both derive from migrations from Yunnan. This is historically attested, even if somewhat fragmentarily. The heartland of the Vietnamese was in the Red River valley and north into southern China, and they spread down the coast and toward the Me kong only within the last 1,000 years. Southeast Asia was not uninhabited during this period. It was dominated by the Khmer Empire, which was slowly consumed by the expanding Thai and Vietnamese polities. Some scholars argue that French colonialism actually preserved an independent Khmer nation, which otherwise would have been divided between Thailand and Vietnam, as Poland was between Germany and Russia. So the Khmer are the indigenous people, while the Thai and Vietnamese are intrusive.

What do the PCA plots tell us? I do not know where the Vietnamese samples were collected. If they were from South Vietnam, then their close position to the Chinese suggests to me that there was substantial demographic replacement or expansion from the Red River valley. In contrast, the Thai are relatively distant from the Chinese. In fact, the Cambodians are somewhat closer to the Chinese! The samples here are small, and the sets overlap, so I wouldn’t put too much stock in that. But, Thailand is geographically closer to South Asia, so isolation by distance models would predict this pattern. It seems that the ethnogenesis of the Thai occurred through the expansion of the Thai identity, likely among Khmer peoples. And it is intriguing that the Iban, an indigenous people of Borneo, are closer to the Vietnamese than they are to the Cambodians. We know that there was substantial migration between coast Vietnam and Maritime Southeast Asia, the Chams of central Vietnam, and dominant in the southern half of the nation before the Vietnamese expansion, are a Malayan people who may have migrated from Borneo.

Shifting to the second panel there’s more here to say about the South Asians. First, geography. The two lower caste groups are actually Dalits from Andhara Pradesh, a South Indian state. Dalits used to be called outcastes, so they aren’t even lower caste, but without caste. The upper caste groups are Brahmins from Andhara Pradesh and Tamil Nadu. Finally, the Irula are tribal people from Tamil Nadu. To me the tribal samples often produce weird results, and I suspect that has to do with population bottlenecks and their demographic isolation. People leave the tribes (becoming part of the Hindu society, or converting to Islam or Christianity), but few join them. The Pakistani sample are Araina, a group of conventional Punjabi farmers who have a made up ancestry from Arabs (obviously made up because they don’t cluster with Near Easterners). Let’s compare to a chart from Reich et al.:

indiareich7

It seems to me that they’re in rough agreement (Reich et al. uses the same two low caste groups for Andhara Pradesh for low caste South Indians by the way). Though South Indian Brahmins speak South Indian languages, and reside amongst other South Indian groups, their genetic heritage is somewhat different. Similarly, tribal peoples are also distinct from caste Hindus. Reich et al. posit that South Asians can be modeled as a composite of two groups, Ancestral North Indians, ANI, and Ancestral South Indians, ASI. Presumably the former are intrusive to the subcontinent in relation to the latter. There seem two clear dimensions along which the ratio of ANI to ASI vary: geography and caste. The proportion of ASI seems to increase from the northwest to the southeast. And, the proportion of ANI seems to increase from tribal to low caste to upper caste. The Pakistani sample does not seem to be from an elite caste (or it does not seem they were converted from an elite caste), but they have more affinity with West Eurasian populations than South Indian Brahmins. It is likely that the latter are intrusive to the south, and have admixed with the local population.

Finally, a word on the Nepali sample. On top of the ANI-ASI mixture, the Nepali groups have varying levels of Tibeto-Burman, and so East Asian, affinity. This is not a surprise if you have met Nepalis. The Assamese, and to a lesser extent Bengalis, also exhibit this pattern of Tibeto-Burman admixture. The Brahmins of Nepal are intrusive like the Brahmins of South India, and like the South Indians they admixed with the local substrate.

Next let’s move to a ADMIXTURE plot.

indo6

The selection of a particular K obviously is conditioned by the patterns which “fit” with what you know, and what you expect. With that caution aired, the population represented by red can easily be thought of as a Middle Eastern group which expanded with agriculture. That seems to be what the authors favor. The brown population is the modal Indian ancestral population, which has little presence outside the subcontinent (nice color coding by the way! Brown people are brown). A green color represents a population which the tribal group, the Irula, are heavily weighted on. This reminds me too much of the Kalash. I suspect that the Irula went through some bottleneck or other distinctive event, and some have assimilated to various low status groups in South India.

I’m not a fantasist intent on world-building, so I’ll stop with that in reading the tea leaves of the charts. But there’s an important section which I skipped over, and will move back to now. And that’s the deep time aspect:

A more likely explanation for the OoA bottleneck is that Eurasia was populated by a larger population that had been relatively isolated from other modern human populations for tens of thousands of years prior to the expansion. The first fossil evidence for modern humans outside of Africa is in the Middle East at Skhul and Qafzeh between 80,000-100,000 years ago, which is at least 20,000 years prior to the Eurasian diaspora. If a population of modern humans remained in the Middle East until the expansion into Eurasia, there would have been sufficient time for genetic drift to reduce heterozygosity dramatically before the Eurasia expansion. This “Middle East isolation” hypothesis provides a robust explanation for the relative homogeneity of European and Asian populations relative to African populations (see Figures 3A-B) and is supported by a recent maximum likelihood estimate of 140,000 years ago for the time of Eurasian-West African population separation . Interestingly, a recent study of the Neandertal genome suggests that the non-African individuals, but not the Africans, contain similar amount of admixture (1-4%) with the Neandertals . The authors suggest that the admixture must have happened between the Neandertals with an ancestral non-African population before the Eurasian expansion. Given the fossil, archaeological, and genetic evidence, the Middle East isolation hypothesis warrants rigorous evaluation as whole-genome sequence data become available.

Like the vast majority of genetic studies this work supports the Out of Africa hypothesis. Non-Africans are all branches from a specific African branch. Or more accurately, an African branch which left Africa. The reduction in heterozygosity, a measure of genetic variation, from Africa to Eurasians was large. Additionally, within Africa south of the Sahara there’s little difference in heterozygosity as a function of geography, but outside of Africa it drops off as a function of distance from Africa. A plausible model then is a radiation from a small ancestral population to the four corners of the world, going through a series of bottlenecks along the way. Or at least that’s a model supported by genomic data. But, the drop in heterozygosity is so great a quick separation from the parental African population would require an implausibly small number of founders (less than 10 in one generation). So, to explain the data, they are suggesting here that the original population was not quite so small, but was isolated from the large African population for thousands of years. They assume genetic drift reduced heterozygosity, but if the model is correct I suspect that the way it worked was that bottlenecks due to climatic fluctuations swept clean a lot of the genetic variation. But in the interregnum the isolated population may have interbred with Neandertals. In fact, perhaps they picked up genes from Neandertals when their own effective population was extremely small.

In any case, a wide ranging paper. They manage to tie their results into two other blockbuster papers.

H/T Dienekes

Citation Xing J, Watkins WS, Shlien A, Walker E, Huff CD, Witherspoon DJ, Zhang Y, Simonson TS, Weiss RB, Schiffman JD, Malkin D, Woodward SR, & Jorde LB (2010). Toward a more uniform sampling of human genetic diversity: A survey of worldwide populations by high-density genotyping. Genomics PMID: 20643205

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Sometimes in a narrative you have secondary characters who you want to revisit. What do to do after the story is complete? An convenient “work-around” to this problem is to find the story rewritten from the perspective of the secondary character. In broad strokes the picture is unchanged, but in the finer grained shadings different details come into sharper relief. Though the exterior action may be unaltered, it gains different context, and the interior motive may radically alter, as the nature of subjective perspective matters so greatly in the last instance. In many ways Oren Harman’s The Price of Altruism reads to me like a narrative rewritten from the perspective of a character who was a supporting protagonist in other stories. George Price, almost a novelty act elsewhere, now becomes the primary point of view character.

I could almost say that Harman, a historian of science, has given us a novel from a “shared universe” of stories. That universe is the real world. The other stories are the lives of great scientists, and the plot consists of the working out of their ideas. In the acknowledgments Harman alludes to the wide range of works where fragments of George Price’s life filters through. I have read many of the mentioned works, The Darwin Wars, Defenders of the Truth, and Narrow Roads of Gene Land. In all of these George Price cuts a quixotic figure, mercurial, brilliant and exceedingly eccentric. His plain biography already peculiar. Price began his career as a chemist, shifted to journalism and became what we today would term a professional “skeptic,” then entered into a period of productivity as an evolutionary theorist of some major impact, and finally spent his last years attempting to live the life of a serious Christian who followed God’s commands to the best of his abilities. He died tragically, committing suicide in his early 50s in 1975, homeless, destitute, and serious ill.

Much of what I already know comes through the memories of William Hamilton in his collections of papers, titled Narrow Roads of Gene Land. In Narrow Roads of Gene Land Hamilton admits that he did not perceive in totality the implications of Price’s eponymous equation when he first encountered it (in particular, he did not initially comprehend that the two elements within the Price equation allowed for the possibility of group selection as you move up the nested hierarchies of organization and reassign the elements to ascending levels). In The Price of Altruism Oren Harman reiterates this reality, but, importantly he emphasizes that Price felt that it was Hamilton alone in all the world who had perceived the equation’s nature upon first encountering it. The back story, which is told in Narrow Roads of Gene Land, is that George Price had difficulty in getting his papers in this area published because the referees simply did not see the implications. Hamilton, perceiving the importance of Price’s ideas, connived to gain publication by making his own work conditional on the acceptance of Price’s paper (which he cited). As Hamilton already had a reputation the game worked.

The necessity of these strategies makes more sense in light of Price’s unconventional background and affect. In evolutionary biology Price was self-taught, and he entered the field in large part because he was interested in the topic, and perceived that he was going to make some difference in the world. He arrived in London in the late 1960s, impressed people at the Galton Laboratory and managed to obtain a research grant and desk, and became an important stimulator of and collaborator with both William Hamilton and John Maynard Smith, arguably Britain’s two most prominent theoretical evolutionary biologists at the time. Price’s relationship to John Maynard Smith is referenced in Hamilton’s own biography, as well as third person narratives such as The Darwin Wars and Defenders of the Truth, but The Price of Altruism fleshes out many of the details. While Price extended Hamilton’s original work on inclusive fitness, for Maynard Smith he served more as a prod and collaborator as they explored the intersection of game theory and biology which eventually led to the ideas outlined in Evolution and Theory of Games. The “hawk” and “dove” morphs made famous by Richard Dawkins in The Selfish Gene go back to Maynard Smith’s work, but the terms themselves were of Price’s invention according to Harman. If I read Harman’s chronology correctly Price was already a fervent Christian by this time, having left atheism in the same period as he launched his career as an evolutionary biologist, and there is some hint that the term “dove” may have been influenced by his particular religious leanings. This possibility seems all the more amusing in light of Dawkins’ later career as an atheist polemicist. Price’s last contribution to evolutionary biology was an explication of Fisher’s fundamental theorem of natural selection. This formalism has been the subject of so much deep analysis, such that I think Price’s interest in it prefigured his later stab at Biblical textual analysis!

The Price of Altruism is a biography of a scientist, so naturally there’s a great deal of science. The meat and heart of the work is George Price’s life trajectory, with all its travails (many) and triumphs (few, but lasting and of importance). Yet the story begins with an exploration of the lives and opinions of men who seem of a different age, Thomas Huxley and Peter Kropotkin. Huxley and Kropotkin were archetypes, who anticipated two streams of evolutionary ecology and social theory which battled it out through the 20th century. Huxley was a man who saw nature as “red in tooth and claw,” the working out of amoral competitive forces, and human virtue as having emerged out and above nature, just as he had risen up from his working class origins to eminence. Kropotkin reflected a Russian viewpoint which saw cooperation as the norm, and competition as the deviation. For him virtue emerged from our natural tendencies. Lee Alan Dugatkin covers much of the same ground in The Altruism Equation. Great men who you meet elsewhere inevitably make cameo appearances in Harman’s narrative; R. A. Fisher, the brilliant cipher, J. B. S. Haldane, the hereditarian Marxist, and Sewall Wright, the American (also see The Origins of Theoretical Population Genetics). The bright lights of Price’s generation also make prominent appearances; William Hamilton and John Maynard Smith, their characters manifesting no great surprises, but also the schizophrenic genius Robert Trivers, with whom Price perhaps shares a great deal excepting his dark ending, as well as E. O. Wilson.

All of these individuals have an interest in evolutionary biology, but biology of a behavioral sort. Though molecular evolutionists such as Richard Lewontin and Motoo Kimura are references in The Price of Altruism, they’re ancillary to the thrust of the book’s central idea (though Lewontin seems to serve as a type, the brilliant scientist who saw the import of Price’s equation too late to engage in a productive exchange with George Price himself). Evolution, like theoretical physics, spans may domains of subject, from the aggregations of millions of individual life forms, to evolution of elements within individual genomes! The Price equation’s generality is such that it does speak to the phenomena which bubble just above the level of organizations of the substrate, DNA itself. But George Price’s focus was on higher, not lower, levels of organizations, human societies. Oren Harman makes this clear, for he brings to light Price’s correspondence with Paul Samuelson, one of the greatest economists of the 20th century. Before Price left for London and began his collaboration with Hamilton and Maynard Smith on altruism, he fancied reconstructing the basis of 20th century economics. By the end of his life Price suggested that he was going to go back to this initial impulse, and attempted to renew his correspondence with Samuelson in the hopes of obtaining a research fellowship of some sort. Price also engaged with the behavioral psychologist B. F. Skinner, though as with many of his encounters it seems that the two soured on each other, in part due to Price’s impolitic tendencies.

George Price’s aim was to explain human cooperation, altruism. In short, goodness. This is the domain of angels, but his analytical bent mean that he could not let the phenomenon lay. He had to break it down, reconstruct its fundamentals, and elaborate on how and why goodness, altruism, manifested itself in the world. From the details reported in The Price of Altruism I would have to admit that Price himself was a Janus-like figure, often being in a manifestly selfish fashion, abandoning his family to follow his intellectual bliss, and yet also radically altruistic, allowing himself to be exploited by the dregs of the London underclass near the end of his life because scripture told him so (or his reading of scripture). What I had previous read did not emphasize Price’s selfishness, his need to satisfy his own wants, and place his own elective priorities ahead of the mandatory ones which decency bound him to honor (e.g., supporting his wife and daughters). Harman has a rich catalog of George Price’s selfish actions and the small vendettas which wracked his soul. No saint was he. Much of what Harmon recounts was simply not evident from other sources. Perhaps in Hamilton’s case he wished to highlight the positive aspects of a good friend who had died tragically. More plausibly I suspect that Hamilton was simply not aware of the selfish sequence of acts which led George Price to the Galton Laboratory in the late 1960s. And it was during this period that George Price became a zealous Christian and a radical altruist. Hamilton’s perceptions may simply have been colored by the slice of Price’s life to which he was privy.

Oren Harman wonders at the end of the book if George Price may have been rather far along the asperger’s spectrum. If so, combined with his fierce intelligence, one is not surprised that Price exhibited a fixation on why and how humans behaved, and why and how it came to be that humans did not seem to be rational psychopaths. Though I do not know if, and honestly do not believe, that George Price was a rational psychopath, in The Price of Altruism Oren Harman paints a picture of a man with immediate urges and impulses, earthy hedonic priorities, and a strong tendency to discount the costs which his choices may have for those close to him. George Price was not the first man to not be a good father, but he was one who perhaps wondered why there were good fathers and bad fathers, those who followed their bliss despite the consequences to their progeny, and those who sacrificed so that their children could enjoy the comforts and pleasures which they elected to forgo. The science is well elucidated in works such as Unto Others, The Origins of Virtue and The Evolution of Cooperation. The Price of Altruism is rather a case study not of the theory of altruism, but of the concrete embodied human experience which eventually gave fruit to an important slice of the theory of altruism. From the small details of his day-t0-day actions, to the arc of his life, George Price played out some of the implications of his own intellectual edifice, both through contradiction and confirmation.

Recommended Reading: The Darwin Wars, The Evolutionists, A Reason for Everything, Narrow Roads of Gene Land, Natural Selection and Social Theory, The Origins of Theoretical Population Genetics, Sewall Wright and Evolutionary Biology, R.A. Fisher: The Life of a Scientist, Defenders of the Truth, Unto Others and The Selfish Gene.

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Earlier this week I pointed to the controversy which has erupted around the widely reported new paper, Genetic Signatures of Exceptional Longevity in Humans. Newsweek did the most thorough early reporting, but now The New York Times has published a follow up story covering the scientific criticisms to the original paper’s methodology. There’s nothing new in The Times‘ piece as such, but it shows that concerted scientific objection to the reception or interpretation of a particular finding which is widely disseminated in the media can yield results. Too often the mainstream media ends up serving as a glorified press release service, but in this case scientists are making their voices heard, and the media narrative is adjusting to the underlying discussion in the scientific community.

I’ve been told there may be more coming out which may shed light on this controversy next week. Stay tuned…

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• Category: Science • Tags: Biology, Genetics, Longevity 
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