Minggu, 23 Januari 2011

Study of French Canadian founder population

HUMAN GENETICS
DOI: 10.1007/s00439-010-0945-x

Genomic and genealogical investigation of the French Canadian founder population structure

Marie-Hélène Roy-Gagnon et al.

Abstract

Characterizing the genetic structure of worldwide populations is important for understanding human history and is essential to the design and analysis of genetic epidemiological studies. In this study, we examined genetic structure and distant relatedness and their effect on the extent of linkage disequilibrium (LD) and homozygosity in the founder population of Quebec (Canada). In the French Canadian founder population, such analysis can be performed using both genomic and genealogical data. We investigated genetic differences, extent of LD, and homozygosity in 140 individuals from seven sub-populations of Quebec characterized by different demographic histories reflecting complex founder events. Genetic findings from genome-wide single nucleotide polymorphism data were correlated with genealogical information on each of these sub-populations. Our genomic data showed significant population structure and relatedness present in the contemporary Quebec population, also reflected in LD and homozygosity levels. Our extended genealogical data corroborated these findings and indicated that this structure is consistent with the settlement patterns involving several founder events. This provides an independent and complementary validation of genomic-based studies of population structure. Combined genomic and genealogical data in the Quebec founder population provide insights into the effects of the interplay of two important sources of bias in genetic epidemiological studies, unrecognized genetic structure and cryptic relatedness.

Link

The Greater Humanities


Jim Clifford as a part of a roundtable on “The University We Are For” presented this paper calling for substantially more unified “Greater Humanities”. You can see video of Clifford delivering his paper too. Click the timeline to start at 71 minutes in. Expect to wait a minute while the video loads to the cued spot. The talk is fifteen minutes in length.


The point of this conference was to set aside practicality in reimagining the university. Think big. Think utopian. What do we want the university to be? If you could have it all, what would you make the university into?


Clifford accepts this “license to want” as an opportunity to resist being put on the defensive in the never ending contest for scarce resources. Instead he aims to actively combat what he calls “belittlement” or the shrinking of the liberal arts to make way for the practical courses of study that lead to jobs or produce goods for sale on the market.


He imagines a coalition, the Greater Humanities, which he sees as “a deeply rooted configuration of knowledge practices.”



Here’s another sketch map of the Greater Humanities—by disciplines this time, most of them internally divided.

* Literature (a vast archipelago)

* History also very widely extended now (including Art History and Visual Culture, and why not? Archaeology…)

* Philosophy (still divided along “two cultures” lines– hard/soft, analytic/continental. But there are signs of movement along this front?)

* Linguistics (also a divided field: do we need to chose between the traditions of Sapir and Chomsky?)

* All the “studies” inter-disciplines: American Studies, Women’s/Feminist Studies, Ethnic Studies, Cultural Studies, Science and Technology Studies… etc.

* Socio-Cultural Anthropology (my own second home) and Historical Archaeology, Human Geography, Qualitative Sociology, some of Environmental Studies…

* Film, Digital Media, Communications.

* Important sectors of Politics, Economics, and Psychology.

* And what we might call the theoretical “Arts”—including Theatre Arts and performance Studies.

This leaves out a good deal, I’m sure. But the map is, I trust, big enough to make my basic, and rather crude, point.


Drawing these disciplines together is a habitus shared across the humanities, some of the social sciences, some of the arts, and with allies in the natural sciences. Clifford identifies this connective tissue as four “knowledge practices”.



The Greater Humanities are 1) interpretive 2) realist 3) historical 4) ethico-political.


1. Interpretive. (read textual and philological, in broad, more than just literary, senses) Interpretive, not positivist. Interested in rigorous, but always provisional and perspectival, explanations, not replicable causes.

2. Realist. (not “objective”) Realism in the Greater Humanities is concerned with the narrative, figural, and empirical construction of textured, non-reductive, multi-scaled representations of social, cultural, and psychological phenomena. These are serious representations that are necessarily partial and contestable…

3. Historical. (not evolutionist, at least not in a teleological sense) The knowledge is historical because it recognizes the simultaneously temporal and spatial (the chronotopic) specificity of…well… everything. It’s evolutionist perhaps in a Darwinian sense: a rigorous grappling with developing temporalities, everything constantly made and unmade in determinate, material situations, but developing without any guaranteed direction.

4. Ethico-political. (never stopping with an instrumental or technical bottom line…) It’s never enough to say that something must be true because it works or because people want or need it. Where does it work? For whom? At whose expense? Contextualizing always involves constitutive “outsides” that come back to haunt us– effects of power.



As anybody who has ever struggled to find funding can attest the deepest pockets are to be found in the so-called STEM fields. Clifford contemplates how to respond and finds an answer, of sorts, in the foundational thinkers of social science: Weber, Durkheim, Marx, Freud, and others. They were, “non-reductive, imaginative, yes “humanistic” thinkers, concerned with the unconscious, with indeterminate behaviors and complex, over-determined motivations.”


The revolt against positivism wasn’t then (and isn’t now) a revolt against science. But against a narrow, instrumentalist vision of science, a vision that fetishizes quantifiable, auditable outcomes—immediately useful (to whom?) and marketable (for whose benefit?)



It’s hard to look at the contemporary scene and imagine the university as we know it will remain for much longer. For those of us looking to make our livings as employees at institutions of higher learning the future looks very uncertain. And it does seem that anthropology’s share of the pie is shrinking. You can see it now on the horizon, something is coming for our discipline and the institutions that house it.



What is it? And, if we had a choice, what would we even want it to be?

Climate and the demise of the Western Roman Empire

This paper got a lot of attention, deservedly, in my opinion. Here is a high-level description of the research from the BBC:

A team of researchers based their findings on data from 9,000 wooden artifacts from the past 2,500 years.

They found that periods of warm, wet summers coincided with prosperity, while political turmoil occurred during times of climate instability.
There are theories a-plenty about the Western Roman Empire's demise, and prima facie this seems as good as any. It has a desirable property that, unlike more 'historical process' explanations, there is no indeterminedness of whether something that occurred was a symptom of the decline, or its cause: tree rings are presumably oblivious to human societal organization.

I was recently reading a book on the subject, I believe it was the Grand Strategy of the Byzantine Empire but correct me if I'm wrong, which made the point that the eastern Empire should have been a better candidate for failure for several reasons, including the fact that it was partitioned across three continents, and faced more formidable foes. Did climate do the Western Romans in?

A good test of the theory would be to identify other instances (in space or time) where climate can be linked to social organization; obviously there are not that many candidates with a continuously recorded history that long, and the fact that climate may have unstabilized the Western Empire does not mean that every 'collapse' can be traced to climate.

Science DOI: 10.1126/science.1197175

2500 Years of European Climate Variability and Human Susceptibility

Ulf Büntgen et al.

ABSTRACT

Climate variations have influenced the agricultural productivity, health risk, and conflict level of preindustrial societies. Discrimination between environmental and anthropogenic impacts on past civilizations, however, remains difficult because of the paucity of high-resolution palaeoclimatic evidence. Here, we present tree ring–based reconstructions of Central European summer precipitation and temperature variability over the past 2500 years. Recent warming is unprecedented, but modern hydroclimatic variations may have at times been exceeded in magnitude and duration. Wet and warm summers occurred during periods of Roman and medieval prosperity. Increased climate variability from ~AD 250 to 600 coincided with the demise of the Western Roman Empire and the turmoil of the Migration Period. Historical circumstances may challenge recent political and fiscal reluctance to mitigate projected climate change.

Cliodynamics journal

Here is a new journal whose content seems reminiscent of what a Hari Sheldon might write. From the journal's definition of 'cliodynamics'
‘Cliodynamics’ is a transdisciplinary area of research integrating historical macrosociology, economic history/cliometrics, mathematical modeling of long-term social processes, and the construction and analysis of historical databases.

Here is a Wikipedia page for Peter Turchin, the journal's editor, and his welcome to the new journal. I had previously linked to a paper by Turchin and Scheidel about a possible link between coin hoard size and population.

Cliodynamics (from the muse Clio, traditionally associated with history) is certainly an interesting concept, which I might summarize as quantitative history. Here are some paper titles from the journal's inaugural issue to give you an idea of what it's supposed to be about:
Articles

A Dynamic Theory of Battle Victory and Defeat
Collins, Randall

Synthezing Secular, Demographic-Structural, Climate and Leadership Long Cycles: Moving Toward Explaining Domestic and World Politics in the Last Millennium
Thompson, William R

Cycling in the Complexity of Early Societies
Gavrilets, Sergey, Anderson, David G, Turchin, Peter

Reports

Why Has the Number of International Non-Governmental Organizations Exploded since 1960?
Turner, Edward A L

Book Reviews

New Patterns in Global History: A Review Essay on Strange Parallels by Victor Lieberman
Goldstone, Jack A

The Silk Road: A Review Essay on Empires of the Silk Road by Christopher I. Beckwith
Hall, Thomas D

Tests in Time: A Review of Natural Experiments of History, edited by Jared Diamond and James A. Robinson
Currie, Thomas E

Accumulation of Knowledge in Theoretical History: A Review Essay on Historical Macrosociology by Nikolai S. Rozov
Tsirel, Sergey V

Regularities in Human Actions: A Review of Bursts by Albert-László Barabási
Zeng, An, Roehner, Bertrand

An interesting set of topics for sure!

Neandertal anti-defamation files, 8


OK, at ScienceOnline2011 I did a little bit of talking about Neandertals represented in art. So this entry in the NAD files truly pains me.


You see, Britney Spears Watcher picked up that story from last year about how digit ratios predict that Neandertals were oversexed.


Neanderthals may be lampooned as slack-jawed low-brows who could just about wield a heavy club on a good day, but in one important respect they outperformed us: in the number of sex partners.


Well, yes, it is a delicious irony for a blog devoted to Britney Spears to refer to anyone as a 'slack-jawed low-brow' with too many sex partners. But that's not what had me concerned. No, it was the accompanying picture:



Neandertal Ken Bump

Dude! They didn't even give him a Ken Bump.


I mean, really -- I know that Britney Spears fans are always looking for quality family-friendly material, but this is just rude. Plus, I think it's sort of obviously one of those times like when they put Oprah's head on Ann-Margret's body.


UPDATE (2011-01-20): Gretchen says it's a Neandertal merkin.


And that, my friends, is Google gold.

No worries, DNA testers


I've started teaching my course in anthropological genetics again this semester. I'll be posting relevant material here every so often, particularly as we continue to make progress on the Neandertal and Denisova genomes.


One thing I do in the course is give the students a very long list of NY Times-level articles, showing ways that genetics has come to influence society (or ways that social factors influence genetic research). The full list is hard to put together -- easy to share PDFs over university network, but hard to extract links. So I'll be working on that because the whole list (featuring Amy Harmon's 'DNA Age' articles from 2008) will be of interest to many readers.


In the meantime, the first article in the series is one from this week, by John Tierney ('Personal DNA tests deliver predictions with few side effects')


[Dr. Eric Topol] and colleagues at the Scripps Translational Science Institute followed more than 2,000 people who had a genomewide scan by the Navigenics company. After providing saliva, they were given estimates of their genetic risk for more than 20 different conditions, including obesity, diabetes, rheumatoid arthritis, several forms of cancer, multiple sclerosis and Alzheimer’s. About six months after getting the test results, delivered in a 90-page report, the typical person’s level of psychological anxiety was no higher than it had been before taking the test.


Although they were offered sessions, at no cost, with genetic counselors who could interpret the results and allay their anxieties, only 10 percent of the people bothered to take advantage of the opportunity. They apparently didn’t feel overwhelmed by the information, and it didn’t seem to cause much rash behavior, either.


In fact, the researchers were surprised to see how little effect it had. While about a quarter of the people discussed the results with their personal physicians, they generally did not change their diets or their exercise habits even when they’d been told these steps might lower some of their risks.


That's an interesting result. Tierney's account accentuates the bottom line conclusion, which is that ordinary, healthy adults are generally unworried by genetic tests that show some long-term health risk.


Should they be worried? That's what I'll ask the class.

Cave of Forgotten Dreams











Another video to share with you, this time the trailer to Werner Herzog‘s Cave of Forgotten Dreams. This is a 3D film shot inside Chauvet-Pont-d’Arc Cave in southern France. These are some of the oldest cave paintings known. The film seems to have good reviews on IMDB and is set to be released on March 25th, 2011 in the UK.


What do you think?



Filed under: Archaeology, Blog, Video Tagged: Chauvet Cave, france, Pont d'Arc, Werner Herzog