Today I was curious what people thought of Wired Science Blogs. More honestly, I was really trying to see if anyone else was a little put off by the forced registration to comment. But in the process I ran into this post, In which I notice a trend. The author did some counting before talking, which is always something I respect. Now, I suspect if you have read me closely over the years you can tell I’m not too worked up over lack of proportionality in the science blogosphere, whether it be of sex, race, ethnicity, religion (or irreligion) or politics. I say this as a Right-leaning brown-skinned male who was once termed “the black science blogger” at ScienceBlogs.
But can Discover Blogs get some props here? Once they swap out the DNA logo and put in my head shot it will be clear that we’re much more ethnically diverse here than at the other “celebrity” blog networks! N = 2 far beats out N = 0. And Wired Science Blogs even has a guy blogging for them who has the same surname as Lou Dobbs! How’s that for insensitive, I’m a naturalized American citizen (and look at this title, it makes me feel unsafe on the web! What’s he trying to say?).
Rest assured, Ed Yong and I are here to give voice to the 85% of humanity which is not of European descent, and, love to write about natural science. You can call us the Chindia of science blogging.*
* Indians will object because I was not born in India. Get over it, we all look to the same to everyone else.
Detecting positive natural selection from genetic data. “I’ve tried to avoid the alphabet soup of acronyms for tests for selection in the above discussion.” Eminently readable.
A New Power Broker Rises in Italy. An article about the Northern League. The inclusion of Tuscany indicates a “broad church” vantage point. An indication of the mishmash of policies (from an American perspective): “It is openly hostile to illegal immigration, an increasingly loud theme both in Italy and Europe. One Northern League deputy provocatively threw a pig’s head on the ground where a mosque was planned, defiling the lot. Popular among agricultural workers, it is fiercely opposed to genetically modified crops and European legislation that it fears would inhibit local food traditions.” Seems some Italians are blaming rising obesity rates on Chinese GMOs.
Natural selection happens. It was hypothesized in copious detail by Charles Darwin, and has been confirmed in the laboratory, through observation, and also by inference via the methods of modern genomics. But science is more than broad brushes. We need to drill-down to a more fine-grained level to understand the dynamics with precision and detail, and so generate novel inferences which may then be tested. For example, there are various flavors of natural selection: stabilizing selection, negative selection, and positive directional selection. In the first case natural selection buffets the phenotype about an ideal mean, in the second case deleterious phenotypes and their associated alleles are purged from the genome, and finally, natural selection can also drive a novel trait toward greater prominence, and concomitantly the allelic variants which are associated with the fitter phenotype.
The last case is of particular interest to many because it is often with positive natural selection by which evolution as descent with modification occurs. Over time trait values and the nature of traits themselves shift such that a lineage changes its character beyond recognition. This phyletic gradualism and the scale independence of evolutionary process has been challenged, in particular from the domain of developmental biology (albeit, not all ,or even most, developmental biologists). But ultimately no one doubts that a classical understanding of evolution as change in allele frequency, often driven by natural selection, is part of the larger puzzle of how the tree of life came to be.
One of the phenomena associated with positive directional evolution is the selective sweep. How a selective sweep occurs, and its consequences, are rather straightforward. A genome consists of a sequence of base pairs (e.g., we have 3 billion base pairs). If a new mutation emerges at a particular base pair, a novel single nucelotide polymorphism (SNP), and, that allelic variant is ~10% fitter than the ancestral variant, natural selection could drive up its frequency (the conditionality is due to the fact that in all likelihood it would still go extinct because of the power of stochastic forces when a mutant is at low frequency). So the variant could in theory shift from ~0% (1 out of N, N being the number of individuals in a population, 2N if diploid, and so forth) to ~100%. This would be the fixation of the novel variant, driven by selective dynamics. So what’s the sweep aspect? The sweep in this case refers to the effect of the very rapid rise in frequency of the SNP in question on the adjacent genomic region. What is termed a genetic hitchiking dynamic results if the sweep occurs rapidly, so that nearby regions of the genome also move to fixation along with the favored SNP. But in a diploid organism with sexual reproduction genetic recombination persistently breaks apart associations across the physical genome. Therefore the span of the sequence of genetic markers nearby a favored SNP which form a haplotype is dependent on the rate of recombination as well as the rate of the rise in frequency of the allele, which is contingent on the strength of selection. A powerful selective sweep has the effect of homogenizing wide regions of the genome flanking the favored mutant; in other words the sweep “cleans” the gene pool of variation as one very long haplotype replaces many shorter haplotypes. As an example, in the genomes of Northern Europeans the locus LCT is characterized by a very long haplotype, which itself seems to correlate well with the trait of lactase persistence. The implication here is that the lactase persistence conferring variant arose relatively recently, and was swept up to near fixation by positive directional natural selection.
Genome-wide analysis of a long-term evolution experiment with Drosophila. Interesting: “in our sexual populations, adaptation is not associated with ‘classic’ sweeps whereby newly arising, unconditionally advantageous mutations become fixed. More parsimonious explanations include ‘incomplete’ sweep models, in which mutations have not had enough time to fix, and ‘soft’ sweep models, in which selection acts on pre-existing, common genetic variants. We conclude that, at least for life history characters such as development time, unconditionally advantageous alleles rarely arise, are associated with small net fitness gains or cannot fix because selection coefficients change over time.”
Voters Deliver a Reminder to Republicans (and Pundits). Seems like an illustration of Nassim Taleb’s worries about the illusion of robustness. That being said, I think quantitative predictive models such as Nate Silver’s are critical in dampening the swell of irrelevancy which comes from verbal pundits.
So yes, I will be working with the Scientific American editors and staff in conceptualizing, building, launching and then running a new science blogging network. How could I say No when given such a chance? To do what I love and what I think I can do well, and all of that under the banner of a magazine that was published continuously since 1845.
Mike Castle trailing Christine O’Donnell in poll: What’s going on? I remember O’Donnell from her numerous appearances on Politically Incorrect in the late 1990s. She seemed sweet, but kind of dull. The media reports make her out to be a sociopath though. Here’s an old clip.
George C. Williams, 83, Theorist on Evolution, Dies. Nicholas Wade gets a lot of quotes.
David Dobbs over at his new digs has a massive post on the relationship between behavior genetics, genomics, neuroscience, environment, and culture. It’s titled The depression map: genes, culture, serotonin, and a side of pathogens, and he concludes:
In a sense, these studies are looking not at gene-x-environment interactions, or GxE, but at genes x (immediate) environment x culture — GxExC. The third variable can make all the difference. Gene-by-environment studies over the last 20 years have contributed enormously to our understanding of mood and behavior. Without them we would not have studies, like these led by Chiao and Way and Kim, that suggest broader and deeper dimensions to what makes us struggle, thrive, or just act differently in different situations. GxE is clearly important. But when we leave out variations in culture, we risk profoundly misunderstanding how these genes — and the people who carry them — actually operate in the big wide world.
The empire of the boy-king grows! Meet the New Wired Science All-Star Bloggers. David Dobbs and Brian Switek have already set up their domains, but Dr. Daniel MacArthur will be moving in the near future as well. And to think that Dr. Dan was just a commenter over at ScienceBlogs in the spring of 2006 when I first became aware of him. Now he’s a vassal of the prince of neuropundits!
There’s a little more news to come from what I’ve heard, and not from Wired. Soon.
With all the justified concern about “missing heritability”, the age of human genomics hasn’t been a total bust. As I have observed before in 2005′s excellent book Mutants the evolutionary geneticist Armand M. Leroi asserted that we really didn’t have a good understanding of normal variation of human pigmentation. At the time I think it was a defensible claim, but within three years I’d say that most of the mystery had been cleared up. Though there are still some holes to be plugged, and details to be elucidated, the genetic architecture of pigmentation is now understood more or less. By the fall of 2006 Richard Sturm penned a review titled A golden age of human pigmentation genetics, an age I think which in some ways probably was closed with his 2009 review Molecular genetics of human pigmentation diversity. It’s not surprising that many of the traits that 23andMe tells you about have to do with your pigmentation. Of course there’s some limited utility in this, one assumes that most individuals don’t gain much benefit from the knowledge that they have an “85% change of having brown eyes,” though it may be useful in terms of offspring prediction (I would say I have an 85% chance of having brown eyes, but since I’m not European the genetic background isn’t right to make that probability assertion).
But as the golden age of pigmentation genetics comes to a close and the low hanging fruit is stripped bare, where next? I wonder if it may be altitude adaptations. Like pigmentation altitude genetics has been around for a while, but it seems there’s a recent cresting of papers in the area, focusing in particular on the three canonical high altitude peoples, the Tibetans, Andeans, and the Ethiopians. Last spring two major groups came out with papers on the genetics of Tibetan altitude adaptation, and its evolutionary history, using somewhat different techniques. A new paper in PLoS Genetics builds upon that work (verifying two of the loci as targets of selection in Tibetans implicated in the previous papers), and, adds Andean populations to the mix to assess the possibilities of convergent adaptations. Identifying Signatures of Natural Selection in Tibetan and Andean Populations Using Dense Genome Scan Data:
At the end of World War II, a severe 5-mo famine struck the cities in the western part of The Netherlands. At its peak, the rations dropped to as low as 400 calories per day. In 1972, cognitive performance in 19-y-old male conscripts was reported not to have been affected by exposure to the famine before birth. In the present study, we show that cognitive function in later life does seem affected by prenatal undernutrition. We found that at age 56 to 59, men and women exposed to famine during the early stage of gestation performed worse on a selective attention task, a cognitive ability that usually declines with increasing age. We hypothesize that this decline may be an early manifestation of an accelerated cognitive aging process.
Below the fold on the y-axis malnutrition prevalence, weight for age (% of children under 5), on the x-axis GNI per capita PPP log-transformed (wealthy countries to the right). The size of the bubbles are proportional to population size.
One last week of summer.
Models tell us more than hindsight. Tim Harford, the author of The Logic of Life, defends economics and modeling against a critique of a historian-turned-journalist. My main problem with economists isn’t that the field is formalized and expresses itself in equations. Rather, it’s the tendency to speak with greater force of authority as to the nature of the world than they truly have insight of. A modest amount of knowledge over and above plain common sense is greatly useful, but confusing a modest amount of knowledge for a great amount of understanding is a recipe for disaster (this is clearly evident in the engineering analogy which Harford elaborates upon).
Don’t Believe the Hype About Aborigines, Yiddish, or Ebonics. I’m particularly interested in the section on Guy Deutscher’s new book, Through the Language Glass: Why the World Looks Different in Other Languages. It seems that the book is going to make a big splash, but scientific paradigms don’t usually shift with a book, do they? So has there been a shift in the linguistic literature in the journals over the past ten years?
I was having a touch of insomnia a few days ago, and wasn’t alert enough to do anything intellectually challenging, so I decided to poke around the General Social Survey. I found an interesting variable, POSTLIFE, which asks people if they believed in life after death. I decided to cross-check that against those who were atheists and agnostics, and specifically look at the distribution of WORDSUM scores of those who did, and didn’t, believe in life after death. My hunch before I checked was this: those who believe in life after death despite not believing in the existence of God are going to be less intelligent than those who don’t.
My reasoning was that it was close to philosophically incoherent to reject supernatural agents, but then accept some post-material existence. I know that this is actually not necessarily philosophically incoherent. Asian religious traditions have long had a strand which accepts both immortality of consciousness as well as agnosticism or atheism in relation to supernatural agents, gods. And, there are some secular Western philosophers who make an analytic case for the afterlife despite their lack of belief in the supernatural. But most people are not deeply involved in the philosophical literature on the afterlife, or, Jains.* Rather, I think those who are atheists or agnostics, and, who accept an afterlife, are relying on intuition and not following through deductively on the inferences from their avowed axioms. In other words, I believed they’d be likely to be less intelligent, and habitually make less use of analytic modes of thinking. To double-check on the thesis that the less intelligent are more likely to hold inconsistent views I also looked at self-identified liberals, conservatives, Democrats and Republicans, on specific policy issues and their relationship to intelligence.
Before we get to the tables, some methodology. I used WORDSUM, which has a 0.7 correlation with IQ. I recoded WORDSUM so that in terms of intelligence you have the following classes:
Low (0-3) – 11% of the sample, 6% non-Hispanic whites
Below Average (4-5) – 27%, 25% non-Hispanic whites
Average (6) – 22%, 21% non-Hispanic whites
Above Average (7-8) – 27%, 34% non-Hispanic whites
High (9-10), 13%, 15% non-Hispanic whites
For the religion related questions I used the whole GSS data set. For the politics related questions I limited to non-Hispanic whites, which also constrains the data set to the 2000s (politics tends to be racially polarized more than religion, so I wanted to remove the racial variable). The rows in each column below add up to 100%, so what you’re seeing are the intelligence distributions within each class. So, if you see 22% in the Low category, that means that the class has twice as many people in that category than the general population. Please note that ~20% of the population rejects an afterlife, a higher proportion than those who are irreligious, or atheists or agnostics. A substantial number of religious people don’t believe in an afterlife, just as a substantial proportion of atheists and agnostics do.
A few days ago I was listening to an interview with a reporter who was kidnapped in the tribal areas of Pakistan (he eventually escaped). Because he was a Westerner he mentioned offhand that to “pass” as a native for his own safety he had his guides claim he was Nuristani when inquiries were made. The Nuristanis are an isolated group in Afghanistan notable for having relatively fair features. His giveaway to his eventual captors was that his accent was clearly not Nuristani, and master logicians that the Taliban are, the inference was made that he was likely a European pretending to be Nuristani.
I thought about this incident when looking over the supplements yesterday of Reconstructing Indian population history. On page 19 note S2 figure 1 includes the Kalash of Pakistan. These are the unconverted cousins of the Nuristanis who were not forcibly brought into the religion of peace in the late 1800s because their region of the Hindu Kush was under British rule, who naturally imposed their late 19th century European value that populations should not be converted by force to a particular religion (Nuristan means “land of light,” whereas before Afghans called it Kafiristan, “land of the unbelievers”). Despite the fair features of the Kalash, which has given rise to rumors that they are the descendants of Alexander the Great’s soldiers, they cluster with Central and South Asian populations, not Europeans. Like the Ainu of Japan it seems superficial similarities to Europeans, at least in relation to the majority population around them, has resulted in an inordinate expectation of total genome exoticism, when in reality a few particular loci are producing the distinctiveness.
Figure 1 from the 2007 paper, Genetic Evidence for the Convergent Evolution of Light Skin in Europeans and East Asians, brings home the point:
Last week there was an article in The Washington Post that caught my eye, Scientists find evidence discrediting theory Amazon was virtually unlivable. The headline flattens a complex and roiling debate within academia. A generation ago the forests of the Amazon basin were seen as a pristine climax ecosystem. In the 1990s and 2000s that view started shifting, with the maximalist revisionisms recounted in Charles C. Mann’s 1491: New Revelations of the Americas Before Columbus. The general thesis is that the much of the Amazon was a managed ecosystem run for the benefit of a large population, but that the social systems collapsed under the weight of European diseases introduced after 1492. Naturally there are still some holdouts from the older paradigm who are deeply skeptical of the emerging consensus. From the article:
The number of scientists who disagree has diminished, but influential critics remain, none more so than Betty J. Meggers, director of Latin American archaeology at the Smithsonian Institution. She said the new theories are based more on wishful thinking than science.
“I’m sorry to say that archaeologists like to produce sensational refutation of previous theories,” said Meggers, whose 1971 book, “Amazonia: Man and Culture in a Counterfeit Paradise,” holds that the region is unfit for large-scale habitation. “You know, this is how you get your promotions.”
Last spring I posted ‘Beyond visualization of data in genetics’ in the hopes that people wouldn’t take PCA too far in assuming that the method was a reflection of reality in a definite fashion. Remember, PCA visualizations are showing you two, and at most three, dimensions in genetic variation within the data set at any given time. The fine print is important; e.g., “PC 1 15%”, “PC 2 4.5%”, etc., which points to the magnitude of the dimensions within the data. You see the largest, and likely historically most significant on a population wide scale, genetic variances, but there’s still a large remainder left over. But when I look at referrals from message boards people obviously aren’t careful with what PCA is telling them.
As an illustration, in the 23andMe user interface you can “compare genes” genes across people who you “share genes” with. This comparison operates over ~550,000 single nucelotide polymorphisms out of 3 billion base pairs (you can constrain it to traits, but I’m going to talk about the comparison to the whole data set below). For example, a man of European descent shares 83.2% with his daughter, who is Eurasian (the mother is Burmese, with some recent Indian admixture). Another man of European descent shares 84% with his daughter, whose mother is also European (in fact, both parents are western European). The “gene sharing” with other people of European descent of these two men is in the 75-74% range (for reference, a Chinese person is 71%, and Nigerian 68.5%). On the PCA plot the European and his Eurasian daughter are very far apart, while the European man and his European daughter cluster together. What you’re seeing on the PCA chart is population level information, not the genetic uniqueness within families and across parents and offspring.
Well, it’s that day again. Nine years on, what’s changed? After Iraq, and the new quagmire in Afghanistan, it seems that our laser-like focus on what & who caused 9/11 is no longer with us. I can’t believe we haven’t caught Osama bin Laden yet. Look at what Eric Raymond is blogging about now vs. what he was blogging about in 2002. For the best I think.
The whole affair with the Turkish commenters gives you a window into some of the stuff that I see, which I do not allow through the mod queue (and usually results in the banning of users). The quantity was greater than the usual, though the Jewish genetics posts invariably draw in a lot of crazies. Even the random post on Uyghur genetics will attract nationalists enraged that I suggested that Uyghurs have a connection to the Han Chinese.
In the interests of “mixing it up” I’ve decided to try something different on Fridays (I’ve been blogging for eight years, but I’ll admit I haven’t been the most innovative of online content generators so far). I’m going to merge the cat pictures with other assorted potpourri. I envision regular features, so, for example, every week I’ll have a link to an old post worth revisiting.
1. First, a post from the past: Breeding the breeder’s equation.
Jerry Coyne notes that George C. Williams died a few days ago. I’d heard he was ill. Michael Ruse has an obituary up. Williams’ book Adaptation and Natural Selection prefigured Richard Dawkins’ The Selfish Gene.
Update: Please see Carl Zimmer’s reflections and recollections.
Years ago an evolutionary biologist mentioned to me almost offhand that with the emergence of genomics and the necessity to master computational techniques a lot of the labor hours which may have gone into a more thorough understanding of specific organisms had gone by the wayside. He believed that his Ph.D. advisor was going to take a lot of knowledge with him when he retired because there was just no time to devote to discussing details of specific organismic life history, anatomy, and behavior. I obviously think that the sacrifice has been worth it, the new methods are powerful and answer long standing questions (or hold promise to do so), but something has no doubt been lost. Biological variation is such that a gestalt “big picture” sense of the lay of the land is useful. Much of biology is a historical science, and like history the details are of the essence. But unlike history biology is a natural science, and amenable to experimentation and observation, as well as laced with a more thorough formalization (yes, I am aware of cliometrics). The mileage one gets out of theory in biology is far greater than in history, as evidenced by the high prestige of an evolutionary framework, and the obscurity of cliodynamics (and the relative marginal reputation of Arnold Toynbee).
But evolution purely as logic often fails. The old debate between the balance & classical schools in evolutionary genetics was upended by empirical findings in molecular evolution in the 1960s, which subsequently stimulated neutral theory. Natural science has to extend itself through a long-term dance between system building and empirical verification or falsification. The seeds of new systems don’t come from a vacuum, rather, the prior set of observations and experiments lay the groundwork and serve as points of embarkation.
The combination of biology’s variation and its reliance on theories, heuristics, and rules-of-thumb (e.g., 19th century biology’s love affair with “laws”), often leads to perplexing surprises when a more systematic or deeper read of the data flies in the face of expectations. So it is with a new paper in PNAS which upends some specific relationships between mammalian characteristics and encephalization, as well as some more general prejudices. Brain size, life history, and metabolism at the marsupial/placental dichotomy: