Gene Expression

Katz

Fri, 20 Nov 2009 20:55:34 -0500

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The Faith Instinct: How Religion Evolved & Why It Endures

Thu, 19 Nov 2009 05:03:26 -0500

During the first few years of ScienceBlogs there was a lot of talk about religion. Yes, there's talk about religion now, but it's toned down in the wake of the ebbing of the publicity around The God Delusion. Naturally in the wake of the New Atheism a raft of conventional apologetics have been published, The Dawkins' Delusion being a typical example. More recently more nuanced books which wend the middle ground between militant atheism and conventional apologetics have taken center strage. Karen Armstrong's The Case for God approaches this from a philo-theistic angle, while Robert Wright's The Evolution of God is predicated on materialist presuppositions.

Nicholas Wade's The Faith Instinct: How Religion Evolved and Why It Endures is of the same genre as Robert Wright's The Evolution of God, though of its own particular flavor (see Wade's review of Wright's book). In particular, Wade admits that the The Faith Instinct fleshes out aspects of his earlier contribution, Before the Dawn: Recovering the Lost History of Our Ancestors. With his bailiwick at The New York Times in evolution and genetics Before the Dawn is an explicable extension of his reporting. What does religion have to do with evolution and genetics in any constructive sense (as opposed to Creationism)? In Wade's telling quite a bit.

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Firelight

Thu, 19 Nov 2009 00:02:06 -0500

I actually saw this SNL Digital Short parody of the Twilight movie trailer before I saw the real one on YouTube.

Make sure to watch the real thing after the parody, makes it way funnier.

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Ancient DNA & the moa

Wed, 18 Nov 2009 22:54:02 -0500

The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography:

...We synthesize mitochondrial phylogenetic information from 263 subfossil moa specimens from across NZ with morphological, ecological, and new geological data to create the first comprehensive phylogeny, taxonomy, and evolutionary timeframe for all of the species of an extinct order. We also present an important new geological/paleogeographical model of late Cenozoic NZ, which suggests that terrestrial biota on the North and South Island landmasses were isolated for most of the past 20-30 Ma. The data reveal that the patterns of genetic diversity within and between different moa clades reflect a complex history following a major marine transgression in the Oligocene, affected by marine barriers, tectonic activity, and glacial cycles. Surprisingly, the remarkable morphological radiation of moa appears to have occurred much more recently than previous early Miocene (ca. 15 Ma) estimates, and was coincident with the accelerated uplift of the Southern Alps just ca. 5-8.5 Ma. Together with recent fossil evidence, these data suggest that the recent evolutionary history of nearly all of the iconic NZ terrestrial biota occurred principally on just the South Island.

"Subfossil" means that it hasn't totally fossilized and one can extract organic material from the remains.

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Evolution, the Muslim world & religious beliefs

Wed, 18 Nov 2009 17:50:17 -0500

In the post below I pointed to an article which claimed:

It's hard to say exactly how much support the theory of evolution enjoys in the world's Muslim countries, but it's definitely not very much. In one 2006 study by American political scientists, people in 34 industrial nations were asked whether they agreed or disagreed with the idea that human beings evolved from earlier life forms. Turkey, the only Muslim country in the survey, showed the lowest levels of support - barely a quarter of Turks said they agreed. By comparison, at least 80 percent of those surveyed in Iceland, Denmark, Sweden, and France agreed. (The United States ranked second lowest, after Turkey, at 40 percent.) Turkey is widely seen as the most culturally liberal Muslim nation, and on attitudes about evolution, other polling has borne this out: A recent study of religious attitudes found that only 16 percent of Indonesians, 14 percent of Pakistanis, and 8 percent of Egyptians believed in evolution.

I asked the reporter for a citation, and I received one, On being religious : patterns of religious commitment in muslim societies. You can download the PDF at that link (bottom of the page). It has a nice breakdown of religious beliefs, including attitudes toward evolution. But the sample is non-representative:

As you can see the sample is strongly skewed toward the more educated segments of society. On the other hand, they did try and include religious professionals as well, though I'm unclear as to the proportion within the samples. The N's are large, so probably only a few percent. But keep in mind the biases in the sample above when looking at the data below.

So what's the breakdown for evolution?

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Charles Darwin was quite the infidel

Wed, 18 Nov 2009 05:47:29 -0500

There was recently a conference on evolution in Egypt. Some interesting numbers:

Dr Guessoum, who is a Sunni Muslim, said that in countries such as Tunisia, Egypt, Turkey, Pakistan and Malaysia, only 15 per cent of those surveyed believed Darwin's theory to be "true" or "probably true". This stand was equally prevalent among students and teachers, from high school to university. Most alarmingly, he claimed, science teachers were misrepresenting the facts and theories of evolution by mixing it with religious ideologies.

A survey of 100 academics and 100 students that he conducted at his own university showed that 62 per cent of Muslim professors and students believed evolution to be an "unproven theory", compared with 10 per cent of non-Muslim professors. "The rate of acceptance of evolution and of the idea of teaching evolution was extremely low," he said. "I wondered, who are all these educated people rejecting evolution? They are even rejecting the fact that it should be taught as scientific knowledge."

I put more stock in the second paragraph since he did that survey himself, though I wouldn't be surprised if the numbers for the first checked out. I did find this Boston Globe article with more concrete numbers:

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From population genetics to linguistics

Tue, 17 Nov 2009 17:38:37 -0500

The relationship between language families and historical population genetics has a long history. In the 19th and early 20th centuries anthropologists were wont to substitute and synthesize the connections discerned in linguistic relationships with those of presumed biological affinities. This resulted in great hilarity. Older works sometimes labeled the Finns a "Mongoloid" people because of their Uralic language. But once the physical substrate of genetic inheritance (DNA) was ascertained some correspondences did emerge.

The figure to the left is from an L. L. Cavalli-Sforza paper, Genes, peoples, and languages. The correspondence between gene families and language families is clear. From the paper:

Most patterns found in the analysis of human living populations are likely to be consequences of demographic expansions, determined by technological developments affecting food availability, transportation, or military power. During such expansions, both genes and languages are spread to potentially vast areas. In principle, this tends to create a correlation between the respective evolutionary trees. The correlation is usually positive and often remarkably high. It can be decreased or hidden by phenomena of language replacement and also of gene replacement, usually partial, due to gene flow.

Genetic variation and languages are both characteristics of individuals & populations. One might imagine that gene flow between groups might be modulated by linguistic affinity between groups, or, linguistic affinity between groups might be modulated by gene flow between the groups. Cavalli-Sforza's colleague Marcus Feldman has asserted that the correlation does indeed emerge out of biases in mating patterns more explicitly of late.

Language and genes are passed from parents to offspring. But, there are clearly differences in terms of the specific constraints on inheritance. When it comes to genes we have both the Mendelian abstraction as well as DNA as a concrete substrate. Parent-offspring transmission is symmetrical (from both parents), subject to mutation, segregation, recombination, etc. Though there are attempts to model language, to my knowledge there is not such robust theoretical understanding of the inheritance of language from parents to offspring, in particular the biological substrate which acquires language (I do not class the arguments about deep structure in linguistics in the same class as Mendelian and DNA models of genetics).

Of course there is the reality of great differences in transmission of language and genes. In the domain of language horizontal transmission is critical to understanding its distribution & evolution (I am aware that horizontal gene transfer is important in biological evolution, but not so much in the scope and species we're talking about). One's parents may speak a different language because language acquisition and fluency is also dependent on peers in a way that genetic variation is not. Additionally, language transmission from parents need not be symmetrical, one may acquire the language of one parent but not the other. One may speak the same language as one's parents, but with a different accent (that one of one's peer group). Interestingly, the exception to this rule of accents are individuals with some socialization dysfunction, such as autism.

There are also similarities between languages and genes. The molecular clock has its analogy in the lexical clock. There is also lexical admixture between languages, for example the heavy load of French-derived terms in modern English, the influence of Slavic upon the Baltic languages. A new paper in PLoS Biology leans on these last similarities to utilize the Structure framework to flesh out the relationships of the language of New Guinea & Australia, what was once "Sahul" during the last Ice Age. The author's summary from Explaining the Linguistic Diversity of Sahul Using Population Models:

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Personal genomics bubble bursting?

Tue, 17 Nov 2009 03:54:09 -0500

Changes in the world of personal genomics. Dan MacArthur has the details on 23andMe changing up its offerings, perhaps signalling that the money gush is long over. And deCode is finally dead. Of course, just because the .com bubble burst doesn't mean that the internet is no longer a part of our lives. New players will likely emerge in the wake of this creative destruction, and old players will adapt to survive.

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The other denialisms

Mon, 16 Nov 2009 19:39:04 -0500

This discussion between Michael Specter & Chris Mooney pointed me to an interesting new book, Denialism: How Irrational Thinking Hinders Scientific Progress, Harms the Planet, and Threatens Our Lives. Instead of Global Warming or Creationism, Specter addresses less pervasively disputatious issues such as genetically modified food, the anti-vaccination movement and the politics of the FDA approval process (at least judging from the discussion). Mooney & Specter also point to the reality that denialism exists in Blue America (though anyone who has followed the dabbling of the Huffington Post in this area would be aware of that stream of thought). When I was in college a friend of mine who active in Leftish causes expressed her disgust with the idea of fish genetic material spliced into tomatoes.* This is a cliche and widely quoted example, so she wasn't being original, but it was clear that she thought that the argument was powerful on prima facie grounds. That is, fish genes shouldn't be in plants. Why? Because they just shouldn't. This genre of argument from intuition and plausibility derived from an emotional response is of the same family as Sarah Palin's Creationism.

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Box office retardiculosity!

Sun, 15 Nov 2009 15:40:45 -0500

'2012' Opening Earns $65 Million:

It is rare for a movie not based on a pre-existing brand, franchise or hit novel to deliver such robust results. Sony said "2012," with a budget of $200 million, had the highest worldwide opening ever for an original movie.

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2012, "retardiculous"

Sat, 14 Nov 2009 15:57:38 -0500

Peter Suderman on 2012, the stupid new film based on the stupid 2012 phenomenon:

And with its never-ending parade of glorious, ludicrous, and utterly improbable catastrophes, it more or less succeeds. 2012 is the sort of movie so aggressively hyperbolic and devoutly over-the-top that it makes traditional descriptive labels obsolete and thus requires the invention of whole new words. My suggestions? How about catastrophaganza--the subgenre to which 2012 (and most of Emmerich's oeuvre) belongs--and retardiculous--a combo word to describe its barfy blend of low-quality yucks; treacly, social-welfare obsessed melodrama; buzz-word-laden psuedo-scientific babble; and gleefully apocalyptic pyrotechnic spectacle.

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Tracing the tribes of American politics

Sat, 14 Nov 2009 03:42:02 -0500

John Emerson points me to some interesting data crunching over at Open Left. The diarist, "dreaminonempty," is analyzing the past few years' election results against demographic variables. What's there not to like? Though I do think the perspective is a bit too The Emerging Democratic Majority. Yes, it does look like the Republicans, as a white Christian party, are in a world of demographic hurt. But, be cautious about projecting current trends too far. By that, I mean that the trends working against the Republicans are clear, but we aren't quite where the Republicans were during the 1970s-1990s where the opposition party had to play on their terms (e.g., the two Democratic Presidents were Southerners who engaged in triangulation). Realignments take time, and by the time all the dynamics play out some of the background assumptions may have changed.

More substantively, below is a comparison of the proportion of votes that the Republican John C Fremont received in 1856, and the proportion of whites who voted for Barack Hussein Obama in 2008 (the % county-by-county here is an estimate since Exit Polls are only statewide).

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Malcolm Gladwell

Sat, 14 Nov 2009 03:06:56 -0500

First, in The New Republic, Malcolm Gladwell's Secret Of Success:

The first sentence here is a classically Gladwellian assertion about what the rest of us think. The rest of the paragraph consists of, more or less, made up numbers and figures which Gladwell claims constitute a "rule". Seriously, read these sentences again. Where does he get these figures? Anyway, the exchange ended on this note:

CHARLIE ROSE: Everyone always has this question when I tell them your story and hand your book out to people, and they say what does that say about gift and superb talent?
MALCOLM GLADWELL: I remain -- I'm uninterested in that topic.

CHARLIE ROSE: Which one? The relation between gift and practice?

MALCOLM GLADWELL: No, I'm not interested in natural gifts. I know they exist and I know there is such a thing as natural talent, but I just feel so what, right?

Apparently there are some things that are uninteresting! The cumulative effect of watching both of these interviews was to make one feel enhanced respect for experts and for the peddlers of conventional wisdom. Here are three guys [he mentions Levitt & Dubner earlier in the post] who style themselves as being unconventional and bold and generally at an angle from received opinion. And yet after watching them talk for an hour, I felt like I was being sold a bill of goods by people who did not know what they were talking about.

Steven Pinker has a more measured and charitable review of Gladwell's new collection of essays:

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The Devil's Helpers

Fri, 13 Nov 2009 17:15:42 -0500

Two Are Charged With Helping Madoff Falsify Records:

Two computer programmers who worked for Bernard L. Madoff's brokerage firm were arrested on Friday on criminal charges of helping perpetuate his long-running Ponzi scheme.

The two men -- Jerome O'Hara of Malvern, N.Y., and George Perez of East Brunswick, N.J. -- were also sued by securities regulators, who said they had helped keep the Madoff fraud running for more than 15 years and took "hush money" to keep it secret.

The criminal and civil complaints accuse the men of creating and maintaining the software that enabled Mr. Madoff to generate a completely fictitious paper trail to conceal his fraud from investors and regulators.

Hopefully the first of many prosecutions.

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The moon is not such a harsh mistress

Fri, 13 Nov 2009 16:32:02 -0500

Dynamic of the Cats as some commentary on the LCROSS landing the moon. The "big news" is the very high confidence now that one can put on the proposition that the moon does have water. Since humans are mostly water by weight, this is very important when assessing the practical difficulties of colonization or settlement. Would have been a drag to lug or synthesize H₂O.

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