Archive for November, 2011

Why some like it hot: awesomeness

By Razib Khan | November 30, 2011 7:33 pm

Mr. Jason Goldman has a post up, On Capsaicin: Why Do We Love to Eat Hot Peppers?. We don’t need no stinkin’ science for this. Do some ethnography with an N = 1: me. Those of us who love spicy food are just awesome! Recently I went to a Thai restaurant for the first time in 4 years which I used to frequent weekly in 2006-2007. Every Saturday I’d go and get a beef salad, which the chef would specially prepare for me by rubbing in a habanero paste into the meat ahead of time. That was the “four star” spicy level. When I reappeared after all this time the host exclaimed, “It’s Mr. four star!” Despite the years much of the staff which had been around back then remembered me. Back in the day sometimes they’d even watch me eat the dish to observe if I’d live to tell the tale. I can tell you similar stories from other restaurants. My very high spice tolerance threshold has reached such a level of virtuosity that people are often taken aback, and strangers will often comment upon it.

My point is that consumption of spicy food isn’t just a experience of the palette, it is deeply social. It is a signal of awesomeness, like having big antlers.

Here are some of Jason’s ideas:

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CATEGORIZED UNDER: Culture
MORE ABOUT: Spice

A consideration of Pacific Biosciences

By Razib Khan | November 30, 2011 6:16 pm

I went to a seminar where a Pacific Biosciences representative was presenting recently. Along with others I arrived early because we thought it would be rather crowded. Not so much. Has the bubble burst?

Zoom in to the last year….

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CATEGORIZED UNDER: Genomics, Personal Genomics

Modern humans in Arabia >100,000 years ago

By Razib Khan | November 30, 2011 5:49 pm

The genetic model of the “Out of Africa” scenario is getting more complex. There may be two waves, as well as the likelihood of admixture between the Neo-Africans and “archaic” hominins, such the Neandertals and Denisovans. From what I can gather the genetic evidence is now converging upon the sequence of events where African populations diverge >100,000 years ago (e.g., a deep separation between the ancestors of the Bushmen and the ancestors of West Africans), and a radiation of non-Africans at most ~75,000 years ago, and more likely ~50,000 years ago. There are still many holes to be plugged in. While we’re waiting on genetics, here’s an interesting paper using archaeological methods in PLoS ONE, The Nubian Complex of Dhofar, Oman: An African Middle Stone Age Industry in Southern Arabia:

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What anime tells us about Japan and America

By Razib Khan | November 30, 2011 1:08 am

A Slate piece on the coming Voltron Renaissance sent me to this interesting juxtaposition of the American cartoon and the Japanese original from which it was culled:

CATEGORIZED UNDER: Culture
MORE ABOUT: Voltron

On structure, variation, and race

By Razib Khan | November 30, 2011 12:30 am

I noticed yesterday that Andrew Sullivan, Ta-Nehisi Coates, and a cast of others were having a roiling debate on race and I.Q. My name came up in several comment threads on various issues. I’m aware of this because I have Google Alerts set for my name. I don’t have the time or energy to get immersed in this particular debate at this moment, but I did review some older material in the course of following links placed elsewhere. In particular, I encourage all of my newer readers to check out my friend Armand M. Leroi’s article in The New York Times from 2005, A Family Tree in Every Gene. Though dated in a few particulars (e.g., we know the locus responsible for most variation in blue eyes now, and it seems likely that Andaman Islanders and Malaysian Negritos are not the original settlers of their domains) I think the general outline has held up rather well. Compare it to the numerous vociferous responses over at SSRN. One wonders at the motivation for what seems like massive retaliation! Here are a few critical paragraphs from Armand’s piece:

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Genetic Creationism

By Razib Khan | November 29, 2011 2:50 pm

Carl Zimmer points me to a piece in a publication called GeneWatch, The Crumbling Pillars of Behavior Genetics. I won’t quote from it because it’s kind of a tired rehash of the confusions and misrepresentations found in The Great DNA Data Deficit: Are Genes for Disease a Mirage?, thoroughly refuted by Luke Jostins and Dan MacArthur (and others at Genomes Unzipped). As I have stated before this sort of attack on genetics is basically similar to Creationism. It’s overloaded with technical and scientific terminology bound to impress the public, but which is just used in a confusing manner, to the point where there’s a big overhead in trying to unpack the logic (as opposed to rhetoric) of the argument. I am broadly convinced that we should be very cautious about results which point to specific genes implicated in a complex trait. But, this is not the “bread & butter” of behavior genetics, which has always been about smoking out the relationship between genetic and phenotypic correlations, and therefore heritabilities. Additionally, as I’ve pointed out there are areas of genomics which are going to be a very important helpmate to quantitative genetic analyses. As noted in the piece behavior geneticists did turn out to be too optimistic about genomics as being relevant to their field. But, the main objections aren’t that novel, and the argument is a repetition of very old conflicts.

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More than models

By Razib Khan | November 29, 2011 1:16 pm

Slate recently had a series up on the use of mice as “model organisms.” In particular, it put the spotlight of some limitations of extrapolating from a mouse to a man (or other species). This is in some ways biology’s “WEIRD” problem. There are always going to be obvious reasons why we’d want to use mice instead of elephants as model organisms, but we might be entering into an era when the fixation on a few species might abate at least somewhat. With that, I point you to a piece in The Scientist (in its final issue I believe), Beyond the Model – How next-generation sequencing technologies will drive a new era of research on non-model organisms:

Central goals of biology have always been to understand the basis for diversity within and among species, and to understand how the environment can influence the expression of different traits. These emerging genetic approaches enable studies in a greatly expanded number of organisms and potentially allow genetic approaches to be applied in natural habitats. The use of model organisms is not dead, however. The utilization of previously generated resources and continued development of model systems will support and facilitate research in non-models. But with the ability to address molecular mechanisms in the natural world, we can truly begin to understand how all of these factors interact to generate the biological diversity that motivated the early scientists and continues to inspire us today.

There is a reason for the hype that the 21st century will be to biology what the 20th was to physics.

COMMENTS NOTE: Any comment which misrepresents the material in this post will result in banning without warning. So you should probably stick to direct quotes in lieu of reformulations of what you perceive to be my intent in your own words. For example, if you start a sentence with “so what you’re trying to say….”, you’re probably going to get banned. I said what I tried or wanted to say in the post. Period.

CATEGORIZED UNDER: Genetics, Genomics
MORE ABOUT: Genetics, Genomics

When trees turn into brambles

By Razib Khan | November 29, 2011 1:00 pm

Genetics is powerful. The origins of the field predate Gregor Mendel, and go further back to plain human common sense. Crude theories of inheritance in the 19th century gave way in the early 20th to Mendelism, which happens to be a very powerful formal system for predicting the patterns of transmission of information from generation to generation. But I suspect that the popular accolades showered upon genetics would be more muted if it were not for the concrete discovery of the biophysical medium of that pattern of inheritance, DNA. By visualizing strands of DNA packaged into chromosomes one can gain a substantive understanding of Mendelian processes previously somewhat abstracted (e.g., recombination). In concert with the centrality of genetics at the heart of evolutionary science has been the ascendance of its methods in the older field of systematics. The phylogenetic tree is not only intuitive, but it has concrete reality in the sequences of base pairs or structural elements within the genome.

Whatever skepticism there might be about the dynamic phenomenon of evolution, the material aspect of modern genetics rooted in molecular biology is one of he primary wedges by which one can introduce an element of doubt into minds of a skeptic. The correlation between phylogeny and sequence identity of organisms which were previously adduced to exhibit some sort of biological relationship on the tree of life can not be dismissed out of hand. But this mode of thinking has limits, albeit due to the quirks of human psychology.

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Has twitter peaked?

By Razib Khan | November 28, 2011 8:19 pm

I hadn’t given the issue much thought, but that’ what Randall Parker asserted in the comments below.

First, let’s look at Google Trends search traffic with Facebook as well:

Facebook dwarfs twitter, so you can’t tell. So with only twitter:

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CATEGORIZED UNDER: Technology
MORE ABOUT: twitter

The New York Times on violence and Pinker

By Razib Khan | November 28, 2011 8:08 pm

The New York Times has a short piece on Steven Pinker up. Nothing too new to long time followers of the man and his work. I would like to point readers to the fact that Steven Pinker has a F.A.Q. up for The Better Angels of Our Nature: Why Violence Has Declined. He links to my post, Relative angels and absolute demons, as supporting his dismissal of Elizabeth Kolbert’s review in The New Yorker. I have to admit that I find much, though not all, of the coverage of science in The New Yorker to exhibit some of the more annoying stereotypical caricatures of humanists when confronting the specter of natural philosophy.

I should also mention I started reading The Better Angels of Our Nature over Thanksgiving. I’m only ~20% through it, and probably won’t finish until Christmas season gets into high gear, but so far it’s a huge mess. In both a good way, and a bad way. The good way is that it’s incredibly rich in its bibliography, with fascinating facts strewn about the path of the narrative. The bad way is that so far it lacks the tightness of  The Blank Slate or The Language Instinct in terms of argument. This may change. Finally, I think I should mention that Pinker has already addressed some of the criticisms of his methodologies brought up in the comments sections of my posts. Those who have specific critiques probably should read the book, because he seems to try sincerely to address those. Or at least they should address those critiques to people who have bothered to read the book.

Tolerable jackfruit

By Razib Khan | November 28, 2011 1:33 am

When perusing Asian groceries I occasionally run into cans of jackfruit. Or should I say “jackfruit,” because often what’s inside of the cans resembles jackfruit flavored wax. Real fresh jackfruit is soft and mushy. Unfortunately the preservation process turns canned jackfruit into a turgid and far less flavorful product. That being said, I recently purchased three different brands, and I found that Chaokoh brand wasn’t totally awful. I don’t know if I’d purchase it again, but I am considering it. It’s not real jackfruit by any means, but the flavor is stronger and the waxiness of the fruit flesh less pronounced.

Do readers have any experiences with canned jackfruit?

Image credit: Wikimedia

CATEGORIZED UNDER: Blog
MORE ABOUT: Jackfruit

Genetic distinctiveness vs. genetic diversity

By Razib Khan | November 28, 2011 1:20 am


Meeting the Taino

In the comments below a few days ago someone expressed concern at the diminishing of genetic diversity due to the disappearance of indigenous populations. My response was bascally that it depends. The issue here is whether that disappearance is due to assimilation, or extinction. If a given population is genetically absorbed into another, obviously their genetic diversity is by and large maintained. What disappears are the specific genotypes, the combinations of gene pairs, which are distinctive to that given group. This is the same dynamic at the heart of the ‘disappearing blonde gene’ meme. Unless there is selection at the loci which encode or predispose one to blonde hair the ‘gene’ isn’t going anywhere. Rather, the implicit issue here is that blonde people are intermarrying with non-blonde people, and if the genetic variant has a recessive expression then the frequency of the trait will decrease. Populations with a high degree of homozygosity at the ‘blonde loci’ are distinctive in a very particular manner, but they’re no more or less ‘diverse’ than other populations which don’t manifest the same tendency.

A toy example will suffice. Take two populations, A and B, and one locus, 1, with two variants, X and x. Assume that the two populations are the same size. At locus 1 population A is 100% X, and population B is 100% x. In a diploid scenario then all the individuals in population A will be XX, and in B will be xx. When you add A + B you get a frequency of X of 0.5, and of x of 0.5 (since the two populations are balanced in size).

 

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CATEGORIZED UNDER: Human Genetics, Human Genomics

Evolution is haram!

By Razib Khan | November 27, 2011 8:47 pm

Ruchira Paul points me to this peculiar article, Muslim medical students boycotting lectures on evolution… because it ‘clashes with the Koran’:

Muslim students, including trainee doctors on one of Britain’s leading medical courses, are walking out of lectures on evolution claiming it conflicts with creationist ideas established in the Koran.

Professors at University College London have expressed concern over the increasing number of biology students boycotting lectures on Darwinist theory, which form an important part of the syllabus, citing their religion.

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CATEGORIZED UNDER: Creationism
MORE ABOUT: Creationism, Evolution

Google+, Facebook, twitter

By Razib Khan | November 26, 2011 2:08 pm

It’s been a while…what’s going on with Google+? I think we can conclude it isn’t a Facebook killer in anything like the medium term.  After moving away from Facebook I started posting again because almost all of my friends in “flesh space” simply don’t use Google+. Rather, Google+ has become a more elaborate extension of my twitter circle. I’ve got over 2,100 who’ve added me to their Google+ circles, and only 1,600 twitter followers. But I don’t do post much on Google+ at this point. For someone with my amount of time and interest two social networks seems optimal in terms of complements. That being said, as many have noted Google+ is more than just a social networking platform. Rather, it has to be understood as an extension of giving your whole suite of Google services an identity, specificity, and personality.

With all that said, Facebook is starting to get a little too busy for my taste. Does anyone else feel the same way? Mark Zuckerberg has known how much to “push it” for years, but my own suspicion is that he has to be very careful of a rapid implosion of usage due to feedback loops if he moves beyond a particular threshold.

Addendum: My various web offerings can be found at razib.com. Probably most relevant for you is the total feed.

CATEGORIZED UNDER: Technology
MORE ABOUT: Technology

On the real possibility of human differences

By Razib Khan | November 26, 2011 1:16 pm

I have discussed the reality that many areas of psychology are susceptible enough to false positives that the ideological preferences of the researchers come to the fore. CBC Radio contacted me after that post, and I asked them to consider that in 1960 psychologists discussed the behavior of homosexuality as if it was a pathology. Is homosexuality no longer a pathology, or have we as a society changed our definitions? In any given discipline when confronted with the specter of false positives which happen to meet statistical significance there is the natural tendency to align the outcome so that it is socially and professionally optimized. That is, the results support your own ideological preferences, and, they reinforce your own career aspirations. Publishing preferred positive results furthers both these ends, even if at the end of the day many researchers may understand on a deep level the likelihood that a specific set of published results are not robust.

This issue is not endemic to social sciences alone. I have already admitted this issue in medical sciences, where there is a lot of money at stake. But it crops up in more theoretical biology as well. In the early 20th century Charles Davenport’s research which suggested the inferiority of hybrids between human races was in keeping with the ideological preferences of the era. In our age Armand Leroi extols the beauty of hybrids, who have masked their genetic load through heterozygosity (a nations like Britain which once had a public norm against ‘mongrelization’ now promote racial intermarriage in the dominant media!). There are a priori biological rationales for both positions, hybrid breakdown and vigor (for humans from what I have heard and seen there seems to be very little evidence overall for either once you control for the deleterious consequences of inbreeding). In 1900 and in 2000 there are very different and opposing social preferences on this issue (as opposed to individual preferences). The empirical distribution of outcomes will vary in any given set of cases, so researchers are incentivized to seek the results which align well with social expectations. (here’s an example of heightened fatality due to mixing genetic backgrounds; it seems the exception rather than the rule).

Thinking about all this made me reread James F. Crow’s Unequal by nature: a geneticist’s perspective on human differences. Crow is arguably the most eminent living population geneticist (see my interview from 2006). Born in 1916, he has seen much come and go. For those of us who wonder how anyone could accept ideas which seem shocking or unbelievable today, I suspect Crow could give an answer. He was there. In any case, on an editorial note I think the essay should have been titled “Different by nature.” Inequality tends to connote a rank order of superiority or inferiority, though in the context of the essay the title is obviously accurate. Here is the most important section:

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Lynn Margulis, 1938-2011

By Razib Khan | November 26, 2011 1:18 am

The New York Times has an obit. But if you don’t know who she is, really just read the Wikipedia entry.

CATEGORIZED UNDER: Evolution
MORE ABOUT: Endosymbiogenesis

Around the web – 11/26/2011

By Razib Khan | November 26, 2011 1:08 am

I’ve gotten way behind on my RSS…though I caught up a bit over Thanksgiving.

West Hunter. Greg Cochran and Henry Harpending’s blog.

Eurasian Sensation. Liberal Eurasian Australian blogger.

Matt Yglesias moved to Slate. This means that his salary is coming in large part from a firm which he has excoriated in the past. (Slate is owned by The Washington Post Company)

Rod Dreher is now at The American Conservative.

Sorry, Strivers: Talent Matters. “Nor is it to say that it’s impossible for a person with an average I.Q. to, say, earn a Ph.D. in physics.” I think it is possible to earn a Ph.D. in physics with an average I.Q., but only from institutions like Razib-Khan’s-Internet-University, where you pay me $100 for me to send you a printout which purports to give you a Ph.D. in physics. In fact, if someone who is a Ph.D. in physics can send me their G.R.E. scores where they score less than a 550 on the mathematics section, and are willing to go public with this fact (so we can check their scholarly achievements and validate the quality of the institution), I will shell out $250 to this individual. Let’s set the date of expiration for 12/26, so I can budget this expense.

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CATEGORIZED UNDER: Blog

How the worm turns the genic world

By Razib Khan | November 26, 2011 12:25 am

In the middle years of the last decade there were many papers which came out which reported many ‘hard’ selective sweeps reshaping the human genome. By this, I mean that you had a novel mutation arise against the genetic background, and positive selection rapidly increased the frequency of that mutation. Because of the power and rapidity of the sweep many of the flanking regions of the genome would “hitchhike” along, generating long homogenized regions of linkage disequilibrium. If that’s a little dense for you, just understand that very strong selective events tend to result in disorder and distinctiveness in the local genomic region.

But the late aughts and the early years of the teens are shaping up give us a more subtle picture. Instead of classic hard sweeps, researchers are suggesting that there may also be many ‘soft’ sweeps, where selection draws upon the well of standing genic variation. Instead of a novel trait becoming prominent, one tail of the distribution would rise in frequency. The ‘problem’ with this model is that it’s not as tractable as the earlier one of hard sweeps, and selection on quantitative traits with many loci of small effect is more difficult to detect. Its effect on the genome is more subtle and understated, which means that statistical tests often lack the power to grasp onto the underlying dynamics. Naturally this means that there is an extension of statistical techniques to ever greater degrees of sophistication. A new paper in PLoS Genetics attempting to tease apart the various potential selective pressures in the human genome is reflective of that tendency. Signatures of Environmental Genetic Adaptation Pinpoint Pathogens as the Main Selective Pressure through Human Evolution:

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WALL•E + Idiocracy

By Razib Khan | November 25, 2011 7:09 pm

Some ethologists should try and get some research funded to model the “scramble” for “patchy resources” that occurs at Walmart on Black Friday.

(NSFW)

CATEGORIZED UNDER: Blog
MORE ABOUT: Black Friday, Walmart
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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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