Archive for April, 2012

What do you think about group selection?

By Razib Khan | April 8, 2012 9:50 pm

I just received a review copy of E. O. Wilson’s The Social Conquest of Earth. One of the reasons why this book is “hot” is that Wilson has recently been revisiting the “levels of selection” debates, and significantly downgraded kin selection in the pantheon of evolutionary dynamics (at least in his mind). There has been a lot of talk on the blogs about Wilson’s ideas, in large part because of his partisan position on the Nowak vs. most other biologists debate, in favor of Nowak.

I don’t know if I’ll have time to review the book (a reality I honestly explained already to the people working at the publisher), but, it did get me thinking: what are the opinions of biologists in relation group selection? My personal experience is that opinions actually vary by discipline and by department. It’s hard to get a real sense, because people tend to be in their own “bubble.” With that in mind, I’ve put together a small survey to assess opinions. My core audience here are people who consider themselves biologists, though I can’t prevent someone with strong opinions from participating obviously!

So, a survey on group selection. You can see the results here.

CATEGORIZED UNDER: Evolutionary Genetics
MORE ABOUT: Group Selection

Another look at mtDNA

By Razib Khan | April 8, 2012 6:55 pm

The new article in The American Journal of Human Genetics, A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root, is open access, so you should check it out. The discussion gets to the heart of the matter:

Supported by a consensus of many colleagues and after a few years of hesitation, we have reached the conclusion that on the verge of the deep-sequencing revolution…when perhaps tens of thousands of additional complete mtDNA sequences are expected to be generated over the next few years, the principal change we suggest cannot be postponed any longer: an ancestral rather than a “phylogenetically peripheral” and modern mitogenome from Europe should serve as the epicenter of the human mtDNA reference system. Inevitably, the proposed change could raise some temporary inconveniences. For this reason, we provide tables and software to aid data transition.

What we propose is much more than a mere clerical change. We use the Ptolemaian geocentric versus Copernican heliocentric systems as a metaphor. And the metaphor extends further: as the acceptance of the heliocentric system circumvented epicycles in the orbits of planets, switching the mtDNA reference to an ancestral RSRS will end an academically inadmissible conjuncture where virtually all mitochondrial genome sequences are scored in part from derived-to-ancestral states and in part from ancestral-to-derived states. We aim to trigger the radical but necessary change in the way mtDNA mutations are reported relative to their ancestral versus derived status, thus establishing an intellectual cohesiveness with the current consensus of shared common ancestry of all contemporary human mitochondrial genomes.

Note that the problem is not restricted to mtDNA. Indeed, in the much larger perspective of complete nuclear genomes in which comparisons are often currently made relative to modern human reference sequences, often of European origin, it seems worthwhile to begin considering, as valuable alternatives, public reference sequences of ancestral alleles (common in all primates) whereby derived alleles (common to some human populations) would be distinguished.

Perhaps the first generation or so of human molecular evolutionary genetics might be thought of as a “first draft.” A serviceable first draft which rendered in broad strokes the gist of the truth as we understand it, but lacking in some essential details.

On a minor note, there are some theoretical reasons why mtDNA did not yield much evidence for archaic admixture, which is clear in the nuclear genomics (e.g., higher rate of change due to lower effective population size, so more rapid extinction of ancient lineages). But perhaps now that the number of complete mtDNA genomes is increasing in size we might start to see “long branches,” which reflect the inferences generated from the ancient nuclear genomes.

MORE ABOUT: mtDNA

Fluff & more

By Razib Khan | April 8, 2012 5:52 pm

CATEGORIZED UNDER: Blog
MORE ABOUT: Fluff, Katz

Doctors and life expectacy

By Razib Khan | April 8, 2012 5:18 pm

A friend pointed me to the following infographic on the concentration of doctors per county. The orange represents “very high need,” and dark blue “very low need.”

Now let’s compare it to life expectancy by county:

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CATEGORIZED UNDER: Medicine
MORE ABOUT: Medicine

Protestant fundamentalists still reject evolution

By Razib Khan | April 6, 2012 4:30 am

Recently over at bloggingheads.tv Matt Lewis broached the issue of science, religion, and politics. Being outside of his bailiwick Lewis seemed to be under some misimpressions. First, he seemed to think that most political liberals were not theists. This is false. In the General Social Survey the GOD variable asks respondents about their confidence in the exist of God. Below are the proportions by ideology for the year 2000 and later who espouse the atheist or agnostic position on the existence of God:

Atheist or agnostic
Liberals 14
Moderates 6
Conservatives 4
Democrat 9
Independent 9
Republican 5

About 1 out of 7 of liberals are an atheist or agnostic. 1 out of 25 conservatives. In contrast, 50 percent of atheists or agnostics are liberal, while only 20 percent are conservatives. Among militant atheists are the proportions are probably even more skewed.

With that out of the way, what about attitudes toward evolution? The GSS asked the EVOLVED question in the year 2006, 2008, and 2010. It asks: “Human beings, as we know them today, developed from earlier species of animals.” The responses are coded as true or false. Below are those who accepted this proposition for various classes of individuals (all political classes are for the year 2000 and later).

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CATEGORIZED UNDER: Creationism
MORE ABOUT: Creationism

Genes are probability, not destiny

By Razib Khan | April 4, 2012 10:53 pm

On my Facebook feed some geneticist friends of mine were passing around an article in The New York Times, Study Says DNA’s Power to Predict Illness Is Limited. The article is based on a paper, The Predictive Capacity of Personal Genome Sequencing. In its turn this paper, as well as the write up in The New York Times, has been widely criticized in the genomics and genetics community. On the other hand, Luke Jostins cautions that perhaps one lesson statistical geneticists should take away from this is that they should do a better job communicating to the public.

I’m with Luke in spirit. But I wonder: how much more difficult is it to think in terms of probabilities rather than binary outcomes? Because that is the ultimate issue. Even geneticists sometimes talk in “nature vs. nurture,” as if the two are oil and water poured in exact ratios into a basin. Of course the reality is that nature and nurture interact, and one shouldn’t discount either. Instead of talking about disease, perhaps it might help to focus on a quantitative trait like height. This is ~90 percent heritable. That is, ~90 percent of the phenotypic variation can be explained by genetic variation.

The fact that Kobe Bryant’s father was a journeyman professional basketball player no doubt resulted in his son’s sights being set rather high in that arena. That is nurture. But as it happened, Kobe also inherited height from his father. That is nature. Talking about the two as if they are at cross-purposes misleads.

Recall that height is ~90 percent heritable on the population level. But it turns out that the standard deviation of identical twin height differences is still ~35-40 percent that of random siblings! What I want to see next, an article in The New York Times: “Identical twins not always identical in height; genes don’t explain everything.”

CATEGORIZED UNDER: Human Genetics

Game of Thrones is racist!

By Razib Khan | April 1, 2012 6:01 pm

I wasn’t going to post more today, in light of the April Fool’s joke I played on you. But here’s me going at it again. Lots of stuff I wouldn’t normally stumble upon hits me via Pulse, and today I see this in Salon, Is “Game of Thrones” too white? – Fantasy fiction might have racial problems, but they’re just a reflection of America’s broader battles. Here’s the problem I have, imagine this subhead: “Fantasy fiction might have class problems, but they’re just a reflection of America’s broader battles.” You see, in epic fantasy fiction the class structure is a pyramid, with a few who have, and the vast majority who do not have (let’s take urban fantasy and the like off the table for this discussion). But that’s OK, it’s a feature, not a bug. That’s because epic fantasy is playing with the furniture of the past, and that furniture is riddled with a class system predicated on radical inequality.

The author of the Salon piece concludes:

Ultimately, A Song of Ice and Fire, like the Lord of the Rings, is the work of a brilliant and conscientious writer who is nonetheless writing in his own time and place. The United States in 2012 is, far too often, and even with a black president, still a culture rich in racist stereotypes and xenophobic fear-mongering. Expecting a writer to remain entirely unstained by this is expecting a person to live underwater without getting wet. If we still find troubling racial assumptions and caricatures in fantasy – whether on the page, or on the big or small screen — this probably tells us more about our culture-wide problems than it does about a single writer’s, or a single show’s issues. A Song of Ice and Fire is indeed our American Lord of the Rings, and if Westeros has its race problems, they are simply a powerful reflection of America’s.

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CATEGORIZED UNDER: Culture
MORE ABOUT: Game of Thrones

It was a good decade (UPDATE)

By Razib Khan | April 1, 2012 12:48 am

Update:  Actually, I was going to put up a post “10 years in blogging.” But right now I don’t have the time, seriously. 10 years is a LONG time though, so I now feel more comfortable talking about events “offline” which date to over half a decade in the past. One thing to note is that my current style of comment moderation crystallized in the mid-2000s because of various time constraints. The fact that I was going to school full time, or had a 65 hour a week job as my firm was coming up to a software release date, and, was in a long distance relationship, was not anyone’s business (did I mention I had freelance web development projects on the side, and was developing a content management system for a client as well?). But it certainly inculcated in me a lack of patience for bullshit. I was cranking out blog posts on Sundays, and in the hour I had after dinner & and my freelance project and before sleep. I recall in the fall of 2006 amusingly some moron left a comment about how I must have a lot of time, since I was posting on Friday evening. Apparently cron jobs and scheduled posts were strange and exotic concepts to the idiot. If there’s anything that’s become a motto for this weblog that emerged during that period f my life, it’s this: don’t be stupid or lazy. I try not to be stupid, and if I could manage to blog with all the various things that have gone on my life in the past, you can manage to not insult me with idiotic commentary born of lack in forethought or consideration.

In any case, I plan on blogging away. I do have lots of offline responsibilities, with my daughter foremost. But I started talking about “retiring” from blogging in 2004 to my co-bloggers at GNXP classic. It hasn’t happened yet. I have a big mouth. Though expect variance in posting frequency to continue.

Go back to original post:

You may have noticed that I put up a great many posts up over the last 24 hours. There’s a reason for that. In April of 2002 I began a blog. That was a long time ago. I’ve met post-docs at conferences who read me in high school! My blogging ‘career’ started on a lark. I was playing around with designing a content management system to learn Java Servlets. I sent my website link to a few friends to test it for bugs, and Steve Sailer linked to me, which resulted in new traffic. In May of 2002 somehow I got on Glenn Reynolds‘ blogroll. This was back when blogrolls meant something! In June of 2002 I joined the new ‘Gene Expression’ group weblog, though I stipulated that I was not going to be the ‘front person.’ Let’s just say that it didn’t quite work out that way….

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CATEGORIZED UNDER: Blog
MORE ABOUT: The End
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Gene Expression

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