Archive for February, 2010

Gene Expression Classic moves to WP

By Razib Khan | February 23, 2010 3:08 am

For various reasons it was no longer feasible to run the Gene Expression Classic website on Blogger. So I’ve switched over to WP. Please update your RSS feeds if you are subscribed to that blog:


Still the bridesmaid

By Razib Khan | February 22, 2010 3:56 am

Sweden Beats Finland in Rematch of ’06 Hockey Final.


Canada vs. USA Hockey

By Razib Khan | February 21, 2010 5:11 pm

sp_0710_05_v6.jpgThere’s apparently a game in this sport at the Olympics tonight. Canada is the favorite. Which is awesome, because if the USA loses, no one in the USA will care. But if the USA wins, we’ll get to laugh at the Canadians. Don’t lie, you know Canada is the country that keeps on giving in terms of humor.
Update: Yeah, you guys are funny. LOL.


Culture vs. genes; peoples & places

By Razib Khan | February 21, 2010 2:40 pm

Lost of discussion about Basques below. Some interesting examples which are less speculative.
Hungary = Language changes, genes do not
The intrusion of ethnic Magyars, and later the settlement of Kipchak Turks fleeing the Mongols, within Hungary is historically attested. Additionally, down to the Reformation there were isolated settlements of Turks among the Magyars which maintained their own linguistic tradition. But digging through the literature it is very difficult to find much genetic impact. Anatolian Turks are a milder case; eastern genetic contributions can be found, but it is the minor component, and this may reflect the greater genetic distance of Turks from Europeans/Anatolians than the Ugric groups of the lower Volga.
Bulgaria = Neither language or genes change
Bulgaria is interesting because it resembled Hungary in many ways. An alien ethnic elite on top of a local substrate. In this case though the alien Bulgar elite was Slavicized, leaving only their ethnonym. Again, no genetic impact.
Japan = Language and genes change
This is a case where the preponderance of evidence seems to be that the Yayoi rice-culture bearers arrived from the continent and predominantly replaced the indigenous post-Jomon culture. The Ainu may be a residue of the Jomon natives, and a non-trivial, though minority, component of the Japanese ancestry can be traced back to the Jomon (a Uyghur treatment would clear up the case of Japan, because if admixture did occur in the manner posited above it would should up in the form of decayed linkage disequilibrium. Though the parent populations in this case are much closer than in that of the Uyghurs).
Basques & Brahui = Language does not change, genes do

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Wine, beer & vodka map of Europe

By Razib Khan | February 21, 2010 6:06 am

Original map at Strange Maps.
H/T M. Yglesias


Inside-out, or Outside-in, multi-level selection "vs." inclusive fitness debate

By Razib Khan | February 21, 2010 5:43 am

An interesting exchange in Nature on ways to conceptualize the evolution of virulence. First, Adaptation and the evolution of parasite virulence in a connected world:

Adaptation is conventionally regarded as occurring at the level of the individual organism, where it functions to maximize the individual’s inclusive fitness…However, it has recently been argued that empirical studies on the evolution of parasite virulence in spatial populations show otherwise...In particular, it has been claimed that the evolution of lower virulence in response to limited parasite dispersal…provides proof of Wynne-Edwards’s…idea of adaptation at the group level. Although previous theoretical work has shown that limited dispersal can favour lower virulence, it has not clarified why, with five different suggestions having been given…Here we show that the effect of dispersal on parasite virulence can be understood entirely within the framework of inclusive fitness theory. Limited parasite dispersal favours lower parasite growth rates and, hence, reduced virulence because it (1) decreases the direct benefit of producing offspring (dispersers are worth more than non-dispersers, because they can go to patches with no or fewer parasites), and (2) increases the competition for hosts experienced by both the focal individual (‘self-shading’) and their relatives (‘kin shading’). This demonstrates that reduced virulence can be understood as an individual-level adaptation by the parasite to maximize its inclusive fitness, and clarifies the links with virulence theory more generally….

Ebola is very virulent. Swine flu is less virulent than ebola. The common cold is less virulent than swine flu. You get the picture. If a pathogen is very virulent it needs to be very transmissible to be evolutionarily successful (replicate itself); otherwise, it will kill its host before it is transmitted and so kill the golden goose. By contrast, if a pathogen is not very virulent, it can be relatively chilled out in terms of transmission since the host isn’t going to die anytime soon. Models of virulence aren’t of purely academic interest, since they are critical components of an evolutionary understanding of epidemics, and their potential future trajectories.
In any case, the “multi-level” point here is obviously that one can easily imagine conceptually that a fast replicator strain within a host can kill the golden goose. So even though that strain is successful within the host, it will decrease group level fitness. By contrast, those hosts which do not produce fast replicator strains within their population of pathogens will persist and the pathogens will have a better chance of being transmitted. The group level logic here is rather evident, but the authors of the above paper think that one can eliminate the need for this sort of thinking within a traditional individual level inclusive fitness framework.
In any case, I’ll skip the formal analysis and jump to their conclusion:

…Thus, irrespective of the relative strengths of within-group versus between-group selection, individuals are predicted to maximize their inclusive fitness. In contrast, groups are only predicted to evolve traits that function to maximize their fitness in extreme situations where there is no conflict of interest between the members of the group…Put another way, the presence of group selection does not invalidate the idea that the individual is an adaptive unit, and it does not validate the idea that the group is an adaptive unit

This is a standard individual selectionist dismissal of the multi-level selection viewpoint: group selection happens, but it is a rare dynamic which only crops up in marginal cases.
Recently this letter prompted a rely. Multilevel and kin selection in a connected world. In this response the authors basically argue that the equation at the heart of the first paper is just a restatement of the Price Equation. They say:

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CATEGORIZED UNDER: Evolution, Genetics

Amy Bishop & oxidation

By Razib Khan | February 21, 2010 2:15 am

From The Boston Globe, Ambition fueled a smoldering rage:

A friendship of sorts was kindled, based largely on a mutual interest in science. Over coffee and lunch, they would discuss Bishop’s research and McCann’s work in biotechnology.
Bishop never spoke of her husband or growing family.
During one meeting, Bishop listened patiently to McCann for a time before suggesting they switch topics.
“She said, ‘That’s very nice, Isabel, but can we talk about oxidation?‘ ” she recalled, with a chuckle. “That one moment in time encapsulated who Amy was. She just couldn’t connect with people.”

I would elaborate on the emphasized part above, but I’ll leave it to readers as to why this sort of behavior is informative….


Amy Bishop, the Stephen Glass of biology?

By Razib Khan | February 20, 2010 5:26 pm

Ruchira Paul points me to a blogger who’s been digging through Bishop’s recent published works, and there’s a lot of fishy stuff in there. You have to read it to believe it. Here’s the conclusion:

There is no question that Dr. Bishop is smart. But it also seems very evident that she suffers delusions of genuis. Far from establishing a record of accomplishment warranting the grant of tenure, since joining UAH Dr. Bishop took a long nap on her one true laurel — her affiliation with Harvard .
Evidence strongly suggests that Dr. Bishop used her husband, her family and by all appearances the sham ‘Cherokee Labsystems’ to fabricate a record of recent accomplishments. Her use of essentially an online vanity publisher further diminishes her professional stature.
It should have been no surprise to Dr. Bishop that the University easily saw through the smoke and mirrors and that she would not receive tenure. But an oversized ego can be blinding.
It seems clear that Dr. Bishop re-wrote the rules for herself. Rather than face the reality that she needed to conduct real research and publish substantial, scholarly work in peer reviewed journals, Dr. Bishop tried to cheat her way to tenure. And, when that failed, it appears Dr. Bishop premeditated a new plan: if you don’t accept what I publish, you will perish.

Some readers mentioned putting her kids on a paper as a co-author. But it might not have been an isolated incident.


The New York Times on Amy Bishop

By Razib Khan | February 20, 2010 3:20 pm

Covers all the major angles. Nice that there’s a newspaper which can support this sort of reporting (on the other hand). Not surprising that Amy Bishop seems to have some history of delusions of grandeur, she’s claiming that both she and her husband have an I.Q. of 180. That’s 5.3 standard deviations above the mean. Assuming a normal distribution that’s a 1 in 20 million probability. Of course the tails of the distribution are fatter beyond 2 standard deviations than expectation for I.Q., but at these really high levels (above 160) I’m skeptical that most tests are measuring anything real.

CATEGORIZED UNDER: Cognitive Science


By Razib Khan | February 19, 2010 8:37 pm

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By Razib Khan | February 19, 2010 1:50 pm

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The Basques may not be who we think they are

By Razib Khan | February 18, 2010 3:22 am

The language families of Europe fall into a few broad categories. There are the Indo-European languages, which include the Romance, Germanic, Slavic and Celtic subgroups, along with Greek and Albanian. The Iranian languages and most of the languages of India are also Indo-European. Then there are the languages of Finland and Hungary, which are hypothesized to be of a broader Finno-Ugric family. Whatever the validity of this cluster, the relationship of Hungarian and Finnish to languages which are extant deep into Eurasia, beyond the Urals and into Siberia, are not disputed. Turkic and Semitic families have a toehold in Europe via Turkish and Maltese. And finally, you have the Basque dialects. Basque is not related to any other language in the world; it is a linguistic isolate. There have been attempts to connect Basque to languages in the Caucasus, but these are highly speculative conjectures.
So where did Basque come from? A common assumption is that Basque is the autochthonous speech of the Iberian peninsula, perhaps related to the pre-Latin dialects extant to the south and east of the peninsula (the Romans arrived on the scene at a time when Spain was also partially dominated by Celtic tribes). Many go further and assert that the Basques are the pure descendants of the first modern humans to arrive on the European continent, heirs of the Cro-Magnons. Even if this claim is a bit much, many would cede that the Basque populations derive from the hunter-gatherers who were extant on the continent when the Neolithic farmers arrived from the Middle East, and Indo-European speakers pushed in from the east.
RHneg.pngIn terms of historical genetics these assumptions result in the Basque population be used as a “reference” for the indigenous component of the European ancestry which reaches back to the Last Glacial Maximum, and expanded from the Iberian refugium after the ice retreated. One of reasons for the assumption of Basque antiquity & purity are genetic peculiarities of the Basques. Foremost among them is that the Basque seem to have the highest frequency of Rh- in the world, primarily because of the high frequency of the null allele within the population (it is a recessively expressed trait). Rh- is very rare outside of Europe, but its frequency exhibits a west-east gradient even within the continent. It has been suggested that the mixing of Rh- and Rh+ blood groups reflects the mixing of hunter-gatherers and farmers in after the Ice Age. The map above the illustrates the frequencies of this trait, and you can see how the Basque region is cordoned off. It’s an old map because blood group were widely collected in the early 20th century. Because of the early knowledge of this heritable trait you have a lot of weird anthropological theories which hinge around blood group genetics having emerged in the early 20th century. But even as late as the mid-90s L. L. Cavalli-Sforza reported in The History and Geography of Human Genes using classical markers that the Basques exhibited some distinctiveness. Over the years with the rise of Y and mtDNA phylogenetics this distinctiveness has taken a hit. I think the data have a tendency of confirming expectations, or it is often interpreted as such. But the recent story of the R1b haplogroup strongly implied that the Basques are no different from other west Europeans, and are likely the descendants of Neolithic farmers themselves!
A new paper in Human Genetics supports the contention that the Basque are just like other Europeans, A genome-wide survey does not show the genetic distinctiveness of Basques:

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CATEGORIZED UNDER: Anthroplogy, Genetics

NASA will approach girl by 2018

By Razib Khan | February 18, 2010 1:01 am

NASA Scientists Plan To Approach Girl By 2018 


What average genetic variation can tell us (or not)

By Razib Khan | February 17, 2010 11:30 pm

nature08795-f1.2.jpgTo the left I’ve juxtaposed the images of the four Bushmen males whose genomes were analyzed in the recent Nature paper and compared to Desmond Tutu. I’ve added to the montage a photo of a Swedish and Chinese man. The Nature paper looked at the HapMap data sets which had within them whites from Utah, northwest Europeans, and Chinese from Beijing, and compared these populations to the Bushmen and Desmond Tutu. One important point that this paper emphasized was that the rule-of-thumb that African populations have the most extant genetic diversity of all human groups, and that the Bushmen have the most diversity of all (perhaps with the Pygmy groups of Central Africa), seems broadly confirmed:

In the 117 megabases (Mb) of sequenced exome-containing intervals, the average rate of nucleotide differences between a pair of the Bushmen was 1.2 per kilobase, compared to an average of 1.0 per kilobase differing between a European and Asian individual.

In other words, genetic distance measured as nucleotide substitutions would show that two random Bushmen of this particular subgroup (see comment) are more disparate than two random European and Chinese individuals! But if you asked someone to cluster these individuals by phenotype I suspect they’d say that all the individuals in the first row belong together, while the two individuals in the second row are distinctive.

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CATEGORIZED UNDER: Evolution, Genetics

Amy Bishop & the dampening effect of demographic variables

By Razib Khan | February 17, 2010 9:17 pm

Wow, the Amy Bishop post attracted a lot of comments. I’ve been hearing/reading a lot about Bishop’s brushes with the law over the years over the past few days. One of the issues seems to be that she didn’t have a traceable record, and that probably was one reason prosecutors were lenient in 2002 when she was charged with being verbally & physically abusive to another woman at an IHOP. This bit from a mechanic at a car dealership who was held up by Bishop in 1986 struck me:

“I yelled, ‘What are you doing’ and she screamed at me to put my hands up. So I put my hands up, ” recalled Pettigrew, 45, in an interview at his home in Quincy yesterday.
Pettigrew said Braintree police briefly questioned him and several other employees, but authorities never contacted him again. Now, after the deaths in Alabama, Pettigrew wonders why authorities didn’t follow up more aggressively.
“It was almost like they wanted to put it on the shelf and forget about it,”said Pettigrew, whose encounter with Bishop was first reported by the Boston Herald. ‘I think if that happened to me I’d be wrapping up a long prison sentence. But with this, it seems like they just wanted it to go away.”

What Pettigrew is alluding to here is sex & class; if he, a working class male, was in the same situation as Amy Bishop it seems likely that the scales of justice would been measured out a bit differently. His whole life would have taken a totally different track. By contrast, it seems that Bishop’s socioeconomic status, and likely her sex (since women are not perceived to be as fundamentally violent), buffered her from the consequences of her actions. In fact to a great extent Bishop got off scot-free. She finished her education, received a Ph.D., and secured a place in the upper middle class. All the while bizarre incidents characterized her life, from the bomb mailed to one of her doctoral supervisors, to her assault on another mother at a restaurant. Many people may now conclude that it is all too coincidental, that these incidents arose from the common variable of Amy Bishop. But her social environment may have dampened both the consequences, and, the extent of the chaotic outbursts. It may be an exemplar of how innate predispositions and biases interact with one’s environment. What I’m saying is that Amy Bishop may have been an orchid gone wild; she was lucky to have been born into the circumstances that she was, because those with fewer familial resources would have gotten into trouble far earlier. Or was she lucky?


The Bushmen & the Bantu

By Razib Khan | February 17, 2010 1:13 pm

There’s a new paper out in Nature which details the genomes of several Bushmen, and how they relate to other humans, and one particular Bantu speaking individual, archbishop Desmond Tutu. It’s open access, Complete Khoisan and Bantu genomes from southern Africa. I haven’t read the whole thing, but it is probably best to check out Ed Yong’s very thorough review first. Here’s an interesting point Ed brings up:

Most surprising of all, many of their unique SNPs are actually fairly recent developments. The Bushmen are one of the oldest human groups on the planet and you might expect their genes to reflect humanity’s most ancestral state. But not the SNPs – Schuster found that only 6% of !Gubi’s newfound SNPs matched the equivalent sequences in the chimpanzee genome; by comparison, the same positions in the human reference genome are an 87% match for the chimp one. They can’t be ancestral sequences. They must have turned up after the Bushmen dynasty diverged from other human populations, and they provide hints about the history of this most ancient of human lineages.

The paper itself uses the phrase “the oldest known lineage of modern human.” It’s pretty ubiquitous as a description for the Bushmen and related peoples. But as you probably know, I don’t think it’s that helpful, though the usage of the term “lineage” makes the topology of the phylogenetic tree clear at least. Perhaps more evidence of derived alleles in “ancient populations” will shift the definitional ground a bit….
Citation: Schuster et al., Complete Khoisan and Bantu genomes from southern Africa, doi:10.1038/nature08795


What genes can't tell us about lactase persistence

By Razib Khan | February 17, 2010 5:26 am

Lactase persistence results in the ability to break down the lactose sugar in milk as an adult, lactase being the enzyme which breaks down lactose. If one can not digest that sugar, and still consumes milk, then one exhibits the symptoms of lactose intolerance. Originally diagnosed as a disease it has come to light that 2/3 of the world’s population is lactose intolerant, and, that this is probably the ancestral “wild type” (I would be interested if readers could name a mammal which exhibited lactase persistence aside from humans). Lactase persistence is a relatively new trait which emerged in the wake of cultural changes which were triggered by the Neolithic Revolution, primarily the domestication of cattle, goat, etc., and their utilization as a source of milk. The latter does not always entail from the former; the Gond tribe of India apparently has utilized cattle & goat for meat, but avoids drinking milk as adults (presumably they’re lactose intolerant).
The ability to digest milk as an adult is a phenotype has been elucidated in terms of its genetics rather well in the past ten years, at least in relation to a host of other traits of interest such as height & weight. A few genes of large effect generate a dominant phenotype whereby lactase continues to be produced into adulthood, and, there are alternative genetic architectures which can lead to this persistence. In other words, there are different instances when mutations arose which conferred lactase persistence.
So as far as human genetics questions being illuminated in the “post-genomic era,” lactase persistence is probably one of the successes. And yet there is much we don’t know. A new paper addresses the issue by attempting to connect the dots in the holes of our knowledge, A worldwide correlation of lactase persistence phenotype and genotypes:

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CATEGORIZED UNDER: Evolution, Genetics

Incipient replication (dilution factor 1/2)

By Razib Khan | February 16, 2010 8:46 pm

Congratulations to Dr. Daniel MacArthur & the Mrs.

10 questions for Peter Turchin

By Razib Khan | February 16, 2010 3:52 pm

At my other blog 10 questions for Peter Turchin. Turchin is an ecologist-turned-quantitative historian.


Saint relic might not be real, who would have thought….

By Razib Khan | February 16, 2010 3:59 am

Analysis of the Putative Remains of a European Patron Saint-St. Birgitta:

Saint Birgitta (Saint Bridget of Sweden) lived between 1303 and 1373 and was designated one of Europe’s six patron saints by the Pope in 1999. According to legend, the skulls of St. Birgitta and her daughter Katarina are maintained in a relic shrine in Vadstena abbey, mid Sweden. The origin of the two skulls was assessed first by analysis of mitochondrial DNA (mtDNA) to confirm a maternal relationship. The results of this analysis displayed several differences between the two individuals, thus supporting an interpretation of the two skulls not being individuals that are maternally related. Because the efficiency of PCR amplification and quantity of DNA suggested a different amount of degradation and possibly a very different age for each of the skulls, an orthogonal procedure, radiocarbon dating, was performed. The radiocarbon dating results suggest an age difference of at least 200 years and neither of the dating results coincides with the period St. Birgitta or her daughter Katarina lived. The relic, thought to originate from St. Birgitta, has an age corresponding to the 13th century (1215-1270 cal AD, 2σ confidence), which is older than expected. Thus, the two different analyses are consistent in questioning the authenticity of either of the human skulls maintained in the Vadstena relic shrine being that of St. Birgitta. Of course there are limitations when interpreting the data of any ancient biological materials and these must be considered for a final decision on the authenticity of the remains.

Of course, people are still debating about the Shroud of Turin.
Citation: Nilsson M, Possnert G, Edlund H, Budowle B, Kjellström A, et al. (2010) Analysis of the Putative Remains of a European Patron Saint-St. Birgitta. PLoS ONE 5(2): e8986. doi:10.1371/journal.pone.0008986


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