Sunday, December 31, 2006

Human Genetics round-up   posted by agnostic @ 12/31/2006 12:19:00 PM

The new issue of Human Genetics has three articles that may interest GNXP readers. A study on the genetics of height looked at two groups of normal Japanese males (i.e., no cases of Marfan Syndrome), one tall (+2 SD; N =219) and one average (+/- 1 SD; N = 209). A SNP in the FBN1 gene was significantly overrepresented in the tall group, and the number of copies was significantly positively correlated with height within each group too. The mutation doesn't result in an amino acid change.

A study on the genetics of skin color variation looked at loci from Europeans, Africans, and Chinese (HapMap and Perlegen data) and performed tests of Fst (a measure of within-group vs. between-group variation) and decay of haplotype homozygosity (a measure of positive selection similar to the integrated Haplotype Score statistic used in the Voight et al 2006 study). They largely confirmed previous findings, but they also discovered a new locus involved in skin color differences between Chinese and non-Chinese populations, DCT (p. 617, all square brackets mine):

The core SNP was chosen as the SNP within the DCT gene with the most extreme riEHH value [i.e., their measure of positive selection]. This SNP, rs2031526, has a riEHH value within the top 1.7% of the riEHH distribution and has Fst values within the top 0.6 and 0.3% of the Afr–Chn and Eur–Chn HapMap Fst distributions respectively (AC Fst = 0.718; EC Fst = 0.607). Figure 2 demonstrates that the derived A allele in the Chinese is found on a high frequency haplotype with long-range homozygosity, while the Europeans and Africans show substantial breakdown of homozygosity over the same physical distance on the high frequency, ancestral G allele haplotype. Similar results were obtained when other core SNPs with extreme riEHH values from the DCT gene were used (data not shown). Thus, the DCT gene harbors a signature of local positive selection in Chinese using both Fst and LRH-based tests [LRH = Long-Range Haplotype], and is therefore a potential candidate to account for the differences in skin pigmentation between the Chinese and other human populations.

So here we have yet another example of different populations converging on more or less the same phenotype (lightish skin) via somewhat different evolutionary genetic paths. UPDATE: Dienekes links to another new study of convergent evolution of skin color in Europeans and East Asians.

Lastly, a study on the make-up of neutral portions of the African-American genome examined how much Europeans and Africans have contributed. The gist, including numbers, is contained in the abstract. In brief, they found sex-biased gene flow: European male - African female pairings are primarily responsible for admixture, a pattern which the authors note is also common in Native American - European admixed populations in the Americas. And apropos of a recent query at Razib's ScienceBlog, here's what they found on the Native American contribution to African-Americans:

A small contribution from Native American and Asian populations to the founding of African Americans has previously been reported (Parra et al. 2001; Smith et al. 2004; Reiner et al. 2005). In those analyses, the genetic contribution from Native Americans and Asians in individuals is at most 2.6% and generally falls between 1 and 2%. Reiner et al. (2005) showed that there was a greater likelihood that the African American population descended from two populations (as opposed to one, three, or four) which was consistent with our own STRUCTURE analysis, where two populations fit the data best. These analyses showed that it was not necessary to include Native Americans and Asians in the founder populations. Our Y chromosome analysis also supported that there was little contribution from Native Americans since the predominant Y haplogroups found in Native Americans P(xR) were not observed in this sample of African Americans.

Gay sheep, forbidden science?   posted by Razib @ 12/31/2006 03:59:00 AM

Science told: hands off gay sheep:
Scientists are conducting experiments to change the sexuality of "gay" sheep in a programme that critics fear could pave the way for breeding out homosexuality in humans.

You can read the whole article yourself. Randall Parker has been saying for years that genetic engineering will accentuate human differences as parents will choose to invest in alternative enhancements with their finite dollars. The vectors may remain the same, but the magnitudes could increase, as religious parents breed super-religious offspring, secular parents start spawning born atheists, and what not. There is a pretty obvious and straightforward way for homosexuals to calm down their fears that straight parents will genetically engineer out their orientation (ergo, community): breed gay babies. If scientists can understand homosexuality well enough to "cure" it, then they could certainly turn fetuses gay.

2006 Darwin Awards   posted by dobeln @ 12/31/2006 01:23:00 AM

So, they are here. Moral of story: Obey the laws of physics kids! With no further ado - the winners:

Hammer of Doom: A Brazil man tried to disassemble a missile by car, and by sledgehammer...

Copper Kite String: Precautions must be taken to avoid sudden electrocution...

High on Life: Four feet found protruding from a helium advertising balloon...

Score for Goliath: A mythical giant felled by a humble slingshot: a modern speargun versus an underwater leviathan...

Faithful flotation: a pastor who could literally walk on water...

Stubbed out: If a doctor advises that the one thing you must avoid is an open flame, most people ould not strike a match...

Star Wars: Luke vs. Darth Vader, with light sabres made from fluorescent tubes and gasoline...

And if you didn't win this year, you have all of 2007 to make a go for it! Happy new year!

Appendix: Darwin Awards 2006 Demographics:

England - 3 winners
Florida - 3 winners
Gabon - 1 winner
Belize - 1 winner
Brazil - 1 winner

Average winner age: 29 years

Winner gender:
8 men
1 woman

Saturday, December 30, 2006

I'm brown dammit!   posted by Razib @ 12/30/2006 05:38:00 PM

I was in a public place the other day and some small Arab-looking guy was talking really loudly in what sounded like Arabic on the phone. I was reading a book and eventually the guy was like, "Hey, do you speak Arabic?" I was like, "No." And he replied, "Do you speak Mexican?" And I replied, "Uh, no." So he goes on, "Where you from?" I reply, "My family is from Bangladesh." His response? "Is that India?" I say, "Kind of." "I was born in India. Abu Sabbas. You know Abu Sabbas?" I replied, "No." He continued, "It's north of Napali. You know Napali?" I didn't, but I smiled and nodded. "My father was working in India. I'm from Israel." Finally he left me alone.

Friday, December 29, 2006

Speech and motor feedback   posted by amnestic @ 12/29/2006 09:40:00 PM

I am really enjoying Buzsaki's book. The chapter I'm in now is about perturbations of the intrinsic network activity of the nervous system. He examines some of the earliest developing examples of intrinsic neural activity: self-generated activities that help organize the retina to visual cortex mapping and the twitches and kicks of the developing fetus. He is building the point that a nervous system that cannot generate motor output cannot really perceive the world in a meaningful way.

"Only through movement can distances be measured and incorporated into our sensory scheme. For an immobile observer, direction, distance, and location of sensory information are incomprehensible and meaningless concepts."

At another level of analysis he notes that a baby's babbles are self-organized output that is then perturbed by parents via their reaction to babbles that chance upon parts of their own words. Perturbation can reshape the weights of the network and organize them in terms of experience.

It made me wonder about the FOXP2 story. There has been some debate about where exactly the deficit lies in the KE family, the family that has a heritable language disorder. Some have suggested that the main effect of FOXP2 loss is to reduce fine motor control of the face and jaw (and tongue?) that would allow for speech production. I wonder if this motor loss might propagate backwards to a more general loss of language functions. Buzsaki covers some studies in which developing rats are immobilized in one way or the other. The inability to produce motor outputs disallows the creation of coherent sensory maps, presumably because the spontaneous motor programs activate sets of muscles that cause corresponding sets of sensory receptors to be co-activated. At a coarse level, if you move your arm, it might run into something and now the parts of your arm that are near each other get to make coherent sensory input. Cells that fire together, wire together and a somatotopic sensory map is born.

So I think you can see the analogy I am imagining. Since the fine motor control output in KE family members is dysfunctional, the fine sensory perceptions that motor control should map to are also disturbed. I suppose this is one way that a developmental defect that leads to a specific motor problem could affect perception of language as well. Thinking this way would probably still require some sort of magic trick where the sensory patterning fails fairly deep in the hierarchy of language perception processing.

I wanted to make sure I was right about the motor dispute, so I pulled out the latest review. No discussion of intrinsic oscillations and language development, but in case y'all want an update here are some key areas researchers are focusing on:

1) Finding other natural mutations in the FOXP2 gene that lead to a phenotype similar to the original KE family.

2) Using Chromatin-Immunoprecipitation Chip (ChIP-Chip, I dread when they come up with a version of this specifically for our primate cousins) to discover molecular targets downstream of FOXP2. FOXP2 is a transcription factor, which means it binds to DNA. ChIP-Chip allows you to lock the FOXP2 onto whatever DNA it is associated with at the moment, pull those specific pieces of DNA out of solution, and see which pieces of DNA you pulled out by seeing if they stick to other chunks of DNA of which you know the identity.

3) Pursuing the observation that FOXP2 is actively regulated (they make more or less of the protein) during different types of vocal behavior in birds.

4) Pursuing the recent discovery that mice make ultrasonic vocalizations. If we can draw clear analogies between these vocalizations and birdsong or language then we can bring to bear the full arsenal of transgenic manipulations available in the mouse model.

Maybe this review was biased towards certain a certain approach, but I'm not seeing much here in terms of further characterizing the developmental phenotype associated with FOXP2 mutations. Is it not ethical or something? Did the KE family stop breeding? I think it might be worth taking a look at their very early EEGs. Finding a network-level signature for the disorder could provide an intermediate level phenotype and obviate the need to justify analogies between birdsong, mouse vocalizations, and human speech.

Bailey vs. Ann Althouse   posted by Razib @ 12/29/2006 07:55:00 PM

Ron Bailey and Ann Althouse get into it over the Frank-Meyer-is-racist-issue. Virginia Postrel defends Ron. No one who reads this blog will be surprised with my general sympathy for Ron in this matter, in part because I agree with his analysis on the merits (even removing the new data he brings to the table), and in part because there is a non-trivial overlap in our political worldviews. That being said, I don't want to make Ann into the devil, my main exposure to her is via Bloggingheads.TV, and she seems like a nice enough person. I empathize with her discomfort in the various political camps which have coalesced on the American scene. Since Ann is a law professor at the University of Wisconsin I don't doubt that she has some g-mojo. Nevertheless, my own impression of Ann is that she is somewhat thin in her exposure to various flavors of the American ideological spectrum (e.g., her general pose is the heterodox "right-winger" among ultra-Liberals). At one point in this Bloggingheads.TV dialogue with Jim Pinkerton Ann confronts the fact that Jim was an Iraq War Skeptic from a Right-realist perspective (I would point you to a segment, but I don't recall with confidence which one!). That such beasts exist seem to be clearly something of a surprise to her from what I could tell by her facial expression (ironic, considering her own heterodox posturing). Ann's own experience had conditioned her to simply connect anti-War sentiment with Leftism, and here she found herself faced with a reality-based conservative. This was not a critique of the Iraq War in language she understood, that is, the lexicon of social justice and utopian idealism, it was a hard-headed and cynical take on the Darwinian competition between nations and the right and wrong choices which emerge out of the utilitarian calculus.

What I'm trying to say is that Ann Althouse has a finite set of mental schemas. As an A-list blogger and Iraq War hawk who is generally socially liberal without the Maoist Puritanism (e.g., she isn't an ideological feminist) she is preloaded for a particular sort of discourse based on a particular range of common assumptions and disjunctions. A mild paleo-conservative like Jim Pinkerton is a species which Ann doesn't have any defenses or offenses against, and so their "discussion" was somewhat like watching two ships pass in the night. I am bringing this all up because I think Ann was faced with the same issues at the Liberty Conference. I've been to CATO events. There are a wide range of characters, and I mean characters, who show up, from fat cat oil speculators to mainstream journalists to the libertarian math professor from a fundamentalist college. You get all sorts of oddballs as you shift several deviations away from the norm in the American political spectrum, and various questions normally not entertained are now fair game. Again, I suspect Ann was operating in a domain where her mental schemas were ill-fitted, and she obviously couldn't get her bearings. Not only was she not steeped in the abstruse intellectual history of the American political Right before 1964, when conservatives, whether traditionalists like Russell Kirk or libertarians such as Frank Meyer, were in the wilderness and excluded from access to the establishment, but I also suspect that the sea of peculiar background assumptions common to "professional libertarians" was simply lost on her. Discussions about the right to discriminate may seem very bizarre, immoral even, when extracted outside of the context of a matrix of assumptions about liberty, justice and freedom, in other words, what makes the Good Society. Ann might have seen naked dispassion and a cruel lack of historical sensibility, but I suspect that her unfamiliarity with the libertarian subculture, its working assumptions, rendered the debates even more other-worldly than they should have been.

Which leaves me to the final point which I want to reiterate, and that is the role of intellectuals in transgressing manners and mores of society. Humans are social creatures and we are bound by particular conventions, whether it be cultural or biologically informed (or, more usually a synthesis). Men walking around with their penises hanging out of their pants in public would be problematic even though a penis is just a collection of atoms. Nevertheless, in the context of modern performance art it is perhaps more understandable. Whatever you think of art, for most humans the goals of inducing awe, exhibiting virtuosity, or shocking and disgusting, are easily attained. Many artists are good at what they do. But I hold that intellectuals, those who peddel ideas, should be no different in the proper context. We should go where conventional society does not go, explore, entertain, and discuss ideas which are not conventionally discussed. GNXP has done quite a bit of that over the years, and I myself am known personally to many of my friends as the sort that causes a collective dropping of the jaws becaues of a flip assertion or question. This does not mean that intellectual discourse is proper for normal social intercourse, but, I think it has a role to play in modern post-Enlightenment societies. Though Descartes was a Roman Catholic, he entertained the possibility of the non-existence of God (only to later to "prove" His existence). This was blasphemy to many contemporaries, but I believe that Descartes is the archetype of the modern intellectual, taking logic where normal reason dictates that you stop.

As I noted before I believe emotion plays a role in human affairs, and am willing to grant that it is the ends of life. That being said, just as normal social interaction is bounded by a modicum of custom, manners and etiquette, so intellectual discourse must be characterized by emotional detachment for it to truly be effective. Emotions are a powerful tool. When you see another human cry you feel for them, you empathize, and they are humanized. All of a sudden the dance with ideas seems less important and we are brought back to normal convential sociality. Anger, happiness, all these are the ends of life, but they are also tools and weapons of interpersonal manipulation. Ron recounts that Ann broke down and cried at one point. This to me is the real "money shot," I've made people cry or break down myself because of the questions I asked and where I went. It happens. But if you fancy yourself someone of some intellectual daring, you must go where the conventional do not dare, where they cannot. Someone has to.

Of course a meeting of libertarians is bounded by their own rules and bounds of discourse. But when you go into the house of a neighbor with whom you are not familiar you need to be careful to respect their ways and habits even if you are shocked and appalled (barring abominations like child sacrifice!). Many libertarians don't live in reality, they aren't grounded, and their fantasies of the minimal state are more of a "Secondary World" than Middle Earth ever was, but, they have a role to play in the ecology of ideas. The fact that they exist, and that they are who they are, is no crime against humanity.

I've posted on this topic more than once in part because it offers us lessons for this blog "community." It is certainly bounded by rules and conventions, but it is pretty diverse in its own way. The main lesson is that if things posted by the authors of this weblog (not in the comment boxes!) make you want to cry you might withdraw and find some place more congenial. Questions of how the world should be are important, Liberty Conferences are part of the universe, but here I would rather focus on how the world is.

(now you hot ones can go back to your science fiction)

"Western ideals" of beauty look to the South   posted by agnostic @ 12/29/2006 11:29:00 AM

Following a recent suggestion, I was just checking out the Lacey Chabert spread at Maxim's website, where I noticed a hottie ranking of theirs called 2006 Hot 100. Granted, individuals may quibble with aspects of the ranking, but it is presumably the product of many minds with diverse tastes in female appearance, so it's objective enough to get a rough idea of what young American guys find attractive. There is a bias toward current "it" girls, but I doubt the racial variation would be changed much if we looked at "it" girls from five years ago. And because Maxim panders to the lowest common denominator of male interests, it would have to be suicidal to feature a significantly lower proportion of women of a certain appearance if red-blooded males truly desired to oogle women of that appearance (e.g., if it featured few blondes when the average potential reader was blonde-crazy). We can thus test whether the ranking actively glorifies or passively reflects a desire for Nordic features, whose hegemony is a common canard in discussions about standards of beauty and ethnic variation in appearance.

Top 10 by hair color and race below the fold:

10 Christina Milian. Brunette. Cuban.
9 Keira Knightley. Brunette. Scottish, Irish, English.
8 Kate Bosworth. Brunette. English?
7 Cameron Diaz. Blonde. Cuban, English, German, Cherokee.
6 Scarlett Johansson. Blonde. Ashkenazi Jewish, Danish.
5 Stacy Keibler. Blonde. German?
4 Angelina Jolie. Brunette. French, Iroquois, Czech.
3 Lindsay Lohan. Auburn. Italian, Irish.
2 Jessica Alba. Brunette. Mexican, Danish, French.
1 Eva Longoria. Brunette. Mexican.

If Nordic looks reigned supreme, we should expect to see more blondes than 3 of 10, which appears at or below expectation for a majority Northern European country, judging by the graphic at the Wikipedia entry on hair color. On an absolute level, there's no shortage of blondes, so if the media devils really wanted push the "blondes are more beautiful" idea, they could've easily packed the top 10 with them. The racial backgrounds underrepresent the average Northern European phenotype: since Keira Knightley and Lindsay Lohan have the "Black Scottish / Irish" look, that leaves just Stacy Keibler, Kate Bosworth, and Scarlett Johansson who look Nordic.

Turning to the entire 100 (go to the bottom for more detail on the following numbers), those of African and East Asian descent are not well represented. In fact, only 2 of 100 are East Asian, and they rank very low. That's at expectation, since Americans of Korean, Chinese, and Japanese descent make up 2.1% of the population. Vanessa Minnillo ranks highly at 15, but she's mixed Filipina / Pacific Islander and Irish-Italian, not East Asian. Overall, 3 of 100 are African-American. This is quite below their percentage of 13.7% in the general population, and none score very highly. Finally, 9 of 100 have partial African or East Asian ancestry, and they are fairly evenly distributed in the ranking from 90 to 22.

Latin Americans, though, do pretty well. I make no claim about what their neutral markers would tell us about the individuals' racial backgrounds, and I therefore included a couple "half"-Latin Americans for the same reason I included "full" Latin Americans. The point is simply to show how a mixed-race, decidedly non-Nordic group does. There are 14 of 100 who are Latin American (including Daniella Alonso, who I also put in the "part-East Asian" group), which appears at expectation since Hispanics make up 14.1% of the US population as of 2004. However, the Hispanic population surged in the US in the wake of the 1986 amnesty, and since the women in the ranking are mostly in their 20s or older, the Hispanic percentage among their age group is surely lower than 14.1%. So, Hispanics are likely somewhat overrepresented. Furthermore, the lowest-ranking Hispanic clocks in at 71, and 4 of the top 10 are Hispanic, including 1 and 2. The strong performance of Latin Americans in international beauty pageants is nothing new, so one wonders why the Nordic hegemony idea has persisted into the second half of the 20th C. (In this respect, it is like the idea that the WASPs are keeping the Sicilians and Semites under their golf cleat -- perhaps true awhile ago, but clearly false for decades.)

The numbers:

East Asians

98 Yunjin Kim
93 Grace Park


82 Vanessa Simmons
77 Ciara
43 Gabrielle Union

Interracials of African or E.Asian background

90 Chilli (1/2 Af-Am, 1/2 East Indian)
88 Tila Tequila (3/4 Vietnamese, 1/4 French)
84 Amerie (1/2 Af-Am, 1/2 Korean)
79 Halle Berry (1/2 Af-Am, 1/2 English)
53 Moon Bloodgood (Korean, Irish, Dutch)
45 Beyonce (1/2 Af-Am, 1/2 Louisiana Creole)
41 Daniella Alonso (1/2 Puerto Rican, 1/2 Japanese-Peruvian)
40 Alicia Keys (1/2 Irish-Italian, 1/2 Jamaican)
22 Mariah Carey (1/2 Afro-Venezuelan, 1/2 Irish)


71 Roselyn Sanchez
68 Cinthia Moura
60 Shakira
59 Jordana Brewster
55 Vanessa Marcil
41 Daniella Alonso
39 Nadine Velazquez
27 Eva Mendes
19 Jamie-Lynn Sigler
16 Christina Aguilera
10 Christina Milian
7 Cameron Diaz
2 Jessica Alba
1 Eva Longoria

From the archives: see here & links therein.
Update: changed the info on Chilli, Beyonce, and Vanessa Minnillo.

Ali on the radio   posted by Razib @ 12/29/2006 10:58:00 AM

Blogger Ali Eteraz will be on the radio 4:30 PM today PDT (check link for webfeed).

Thursday, December 28, 2006

DevIntel at SB   posted by amnestic @ 12/28/2006 11:58:00 PM

Chris Chatham has moved on over to Seed's megasite finally. You could do a lot worse than reading his entries and the discussion he inspires. Here's some on the potential for enhancing working memory with dopamine system manipulations.

Rome vs. Assyria   posted by Razib @ 12/28/2006 11:25:00 PM

SharpBlue on Rome vs. Assyria. Interesting fact, the last great Assyrian king, Ashurbanipal, could read and write (remember, this is before widespread use of phonetic script, so this was no mean feat). Thanks to Ashurbanipal's library much of the corpus of Sumerian and Akkadian literature came down to us.

YouTube Open Thread   posted by Razib @ 12/28/2006 08:27:00 PM

Post YouTube's that you think are really interesting to GNXP readers in the comments.

Rate of Evolution in Brain-Expressed Genes in Humans and Other Primates   posted by Razib @ 12/28/2006 07:55:00 PM

Rate of Evolution in Brain-Expressed Genes in Humans and Other Primates:
Our analyses of the rates of protein evolution in these species suggest that genes expressed in the human brain have in fact slowed down in their evolution since the split between human and chimpanzee, contrary to some previously published reports. We suggest that advanced brains are driven primarily by the increasing complexity in the network of gene interactions. As a result, brain-expressed genes are constrained in their sequence evolution, although their expression levels may change rapidly.

...we've always told you that "gene expression" is where it's at :) It's PLOS, so go read the whole thing for free.

PS3 vs. WII   posted by Razib @ 12/28/2006 01:04:00 AM

I stopped playing video games when I was 16. So I don't get a lot of the references of the below comparison... (guess which one likes science fiction)

[below the fold for after work]

Wednesday, December 27, 2006

Althouse is wrong, Goldberg is right   posted by Razib @ 12/27/2006 11:39:00 PM

On this segment Ann Althouse rips Jonah Goldberg for his quasi-defense of a discussion of the ideas and influence of Frank Meyer, the libertarian conservative who was the father of "fusionism" and arguably the man behind William F. Buckley's throne. Althouse was appalled that at a Liberty Fund event to which she was invited a discussion of the great man's ideas did not dwell long enough upon his support for the American South's practice of Jim Crow in the name of State's Rights (perhaps one might say that Southerners supported State's Rights because of Jim Crow, while Meyer accepted Jim Crow because of State's Rights). Althouse's point, from what I can gather, is that Oh my god Frank Meyer was a racist!!!! Goldberg made, I thought, a pretty level-headed response, sometimes one must extract and abstract ideas from their context to explore fully their ramificatins, validity and utility. This does not mean that I don't share Althouse's discomfort, even censure, of Jim Crow and the Right's support of these policies during the 1950s and 1960s. The Zeitgeist has changed, and for the better. Especially for those like myself who happen to have brown skin. Nevertheless, there are two issues that we must address

1) Ideas are not like a stew, each and every one mixed together so that they are fundamentally inseparable, unperceivable without tasting the whole.

2) To examine questions from every angle one must withold judgement, censure or outrage on occasion.

This does not negate emotion, feeling or values. It simply means that different aspects of life, and cognition, have their own purposes. Margaret Sanger was a progressive racialist eugenicist. That doesn't mean that Planned Parenthood is Nazi. Isaac Newton was an alchemical nut. That doesn't mean that his Mechanics and Optics don't exhibit a scientific virtuosity which induces awe. Emotions tell us what is important. Rationality allows us to realize and perpetuate what is important.

The nose knows   posted by p-ter @ 12/27/2006 11:57:00 AM

The paper on the ability of humans to track smells contained a couple interesting references on the human specific loss of some olfactory genes (see an old post here for an interesting correlation between the loss of these genes and the rise of color vision). Apparently, some genes have both functional and non-functional versions that still segregate within the population. So do different populations have receptors for different scents?

The last link is to a paper that typed 51 olfactory receptor genes in 189 people. It's a little unclear where these 189 people come from (though they do refer to African-Americans, so it's apparently a sample of Americans); it would be interesting to type them in a large number of populations (the human diversity panel, perhaps?) and give that hypothesis a whirl.

However, see this paper for an argument that humans actually have a pretty good sense of smell, and some possible explanations for why the loss of olfactory receptors doesn't mean the loss of the sense:
[M]uch of the olfactory system can be removed with no effect on smell perception. The olfactory receptor genes map topographically onto the first relay station, a sheet of modules called glomeruli in the olfactory bulb. Up to 80% of the glomerular layer in the rat can be removed without significant effect on olfactory detection and discrimination. If the remaining 20% of the glomeruli-and the olfactory receptor genes they represent-can subserve the functions of 1,100 genes, it implies that 350 genes in the human are more than enough to smell as well as a mouse.

Tuesday, December 26, 2006

The smell of victory   posted by p-ter @ 12/26/2006 07:20:00 PM

Humans can track smells, and the ability to do so is greatly aided by practice (and the use of both nostrils). Very cool:
Whether mammalian scent-tracking is aided by inter-nostril comparisons is unknown. We assessed this in humans and found that (i) humans can scent-track, (ii) they improve with practice, (iii) the human nostrils sample spatially distinct regions separated by approx3.5 cm and, critically, (iv) scent-tracking is aided by inter-nostril comparisons. These findings reveal fundamental mechanisms of scent-tracking and suggest that the poor reputation of human olfaction may reflect, in part, behavioral demands rather than ultimate abilities.

Evangelical Atheists and the Sciences of Religion   posted by Matoko Kusanagi @ 12/26/2006 07:04:00 PM

I spent some time with the Edge Reality Club today. I hadn't had time to read it yet. It is no surprise to me that Scott Atran is closest to me ideology and analysis. I liked his book far better than any of Harris', Dawkins', and Dennett's books I've read.
The topic of the discussion was Beyond Belief: Science, Religion, Reason and Survival.

The other participants accused Atran of ignoring the fact that religions, and in particular, Islam, actively encourage destructive behavior like suicide bombing, apostate killing, pograms, etc. I dont think he ignores that at all. But he says instead, what can we do with what we know? Im so grateful to find someone who thinks about this the way I do. This is exactly what I mean, when I talk about leveraging Islam to stop the slaughter and help instantiate democracy in Iraq.
Atran on evangelical atheism:
At the conference, Harris and partners ignored the increasingly rich body of scientific research on religion. They ignored the vast body of empirical data and analysis of terrorism — a phenomenon they presented as a natural outgrowth of religion. The avowedly certain but uncritical arguments they made about the moral power of science and the moral bankruptcy of religion involved no science at all. Some good scientists stepped out of their field of expertise, leaving science behind for the unreflective sort of faith-based thinking they railed against. Sadly, in this regard, even good scientists join other people in unreason.

Harris despairs that my approach to dogmatism is to throw up my hands and "make declarations about ‘the basic irrationality of human life and society'." No, I argue that one way to deal with this important problem is to use science and rational processes to study irrational ones and then to leverage that scientific knowledge in ways that can affect public policy, although this second step may have to be more art than science. Harris suggests that if, indeed, irrationality is some vestige of our evolutionary legacy, then we should still be able to master it and perhaps eventually eliminate it from society through reason and vigilance as we are increasingly able to do with rape. I think a better, deeper, more pervasive analogy would be sex: repress it one way and it will pop out other ways.
My critique of Harris and company was that:

(1) An increasing body of scientific research on religion suggests that, contrary to Harris's personal and scientifically uninformed intuitions about what religion consists of, the apparent invalidity of religious thought is insensitive to the kind of simple-minded disconfirmation through demonstrations of incoherence that Harris and others propose.

(2) No data by Harris or others was offered to suggest that the naturalistic worldview they mean to replace religion with would be, or could be, successful; or that such a worldview would generate more happiness, compassion or peace (which most us at the conference hope for).

(3) Evidence supporting empirical claims about negative behavior caused by religious beliefs in general, or Islam in particular, was based on a decidedly selective sample or idiosyncratic interpretation (e.g., Harris tells us that he has read the Qur'an and on his reading, which he may share with some minority of Muslims, the Qur'an literally prescribes, or at least sanctions, suicide terrorism).

(4) Experiments on "sacred values" (which Harris refers to in his reply but misunderstands, and which were presented in more rigorous form before the American Association for the Advancement of Science and the National Security Council at the White House) suggest that arguments by Harris and others about how to best lessen the noxious effects of dogmatism are liable to do more harm than good for his own cause (which is also my own cause and that of most others at the conference).

Now, according to Salam's colleague and co-Nobel Prize winner Steven Weinberg, scientists must rise up to the challenge of liberating humanity from "the long nightmare of religion. " Biologist Richard Dawkins tells us that we need to "come out of the closet" and form a political lobby of committed atheists and scientists to do public battle with religion and other forms of "rubbish" that tyrannize the mind. For neuropsychology student Sam Harris, technological advances in the ability to terrorize and wage war require an uncompromising and unrelenting intellectual struggle to destroy religion — especially, but not exclusively, Islam — and banish unreason beyond the pale of civilization.
I find it fascinating that among the brilliant scientists and philosophers at the conference, there was no convincing evidence presented that they know how to deal with the basic irrationality of human life and society other than to insist against all reason and evidence that things ought to be rational and evidence based. It makes me embarrassed to be a scientist and atheist. There is no historical evidence whatsoever that scientists have a keener or deeper appreciation than religious people of how to deal with personal or moral problems. Some scientists have some good and helpful insights into human beings' existential problems some of the time, but some good scientists have done more to harm others than most people are remotely capable of.

Scott and I are in complete agreement--sho, supernatural and religious beliefs cause dreadful problems. BUT it is biologically, culturally, and psychologically impossible to destroy religion.
What to do? Since we cannot eradicate religion, let's leverage it instead, for benevolent goals.

Here I quote Atran's section on sacred values, and how those values can leverage arbitration and conflict resolution in the face of anti-rational behavior. The classic example of anti-rational behavior is the Palestine/Israel conflict.
Sacred Values And Bounds On Rational Resolution Of Conflict. Dan Dennett seems to argue that because most people are rational most of time, as in properly navigating when crossing the street, then people should be perfectly capable of following and accepting rational arguments against religion if only the repressive social and political support for religion could be jettisoned. Now, unlike in the field of economic judgment and decision making, where basic assumptions of rationality have been scientifically sundered (most prominently by recent Nobel laureates Danny Kahneman and Thomas Schelling), there has been little serious of study of the scope and limits of standard notions of rationality in moral judgment and decision making. There is, however, some evidence that rationality is not standard for religion and morality.

Religious behavior often seems to be motivated by sacred values, that is, values which a moral community treats as possessing transcendental significance that underlies cultural identity and precludes comparisons or tradeoffs with material or instrumental values of realpolitik or the marketplace. As Immanuel Kant framed it, virtuous religious behavior is its own reward and attempts to base it on utility nullifies its moral worth. Instrumental decision-making (or "rational choice") involves strict cost-benefit calculations regarding goals, and entails abandoning or adjusting goals if costs for realizing them are too high. A sacred value is a value that incorporates moral and ethical beliefs independently of, or all out of proportion to, its prospect of success."

Current approaches to resolving resource conflicts or countering political violence assume that adversaries make instrumentally rational choices. However adversaries in violent political conflicts often conceptualize the issues under dispute as sacred values, such as when groups of people transform land from a simple resource into a "holy site" to which they may have non-instrumental moral commitments. Nowhere is this issue more pressing than in the Israeli-Palestinian dispute, which the majority of people in almost every country surveyed (e.g., in the June 2006 Pew Global Attitudes Survey) consistently view as the greatest danger to world peace. Our research team − including psychologists Jeremy Ginges and Douglas Medin, and political scientist Khalil Shikaki − conducted studies indicating that instrumental approaches to resolving political disputes are suboptimal when protagonists transform the issues or resources under dispute into sacred values. We found that emotional outrage and support for violent opposition to compromise over sacred values is (a) is not mitigated by offering material incentives to compromise but (b) is decreased when the adversary makes materially irrelevant compromises over their own sacred values.

In a survey of Jewish Israelis living in the West Bank and Gaza (settlers, N = 601) conducted in August 2005, days before Israel's withdrawal from Gaza, we randomly presented participants with one of several hypothetical peace deals. All involved Israeli withdrawal from 99% of the West Bank and Gaza in exchange for peace. We identified a subset of participants (46%) who had transformed land into an essential value; they believed that it was never permissible for the Jewish people to "give up" part of the "Land of Israel" no matter how extreme the circumstance. For these participants, all deals thus involved a "taboo" trade-off. Some deals involved an added instrumental incentive, such as money or the promise of a life free of violence ("taboo+"), while in other deals Palestinians also made a "taboo" trade-off over one of their own sacred values in a manner that neither added instrumental value to Israel nor detracted from the taboo nature of the deal being considered ("tragic"). From a rational perspective, the taboo+ deal is improved relative to the taboo deal and thus violent opposition to the tragic deal should be weaker. However, we observed the following order of support for violence: taboo+ > taboo > tragic; where those evaluating the tragic deal showed less support for violent opposition than the other two conditions. An analysis of intensity of emotional outrage again found that taboo+ > taboo > tragic; those evaluating the tragic deal were least likely to report anger or disgust at the prospect of the deal being signed.

These results were replicated in a survey of Palestinian refugees (N=535) in Gaza and the West Bank conducted in late December 2005, one month before Hamas was elected to power. In this experiment, hypothetical peace deals (see supporting online materials) all violated the Palestinian "right of return", a key issue in the conflict. For the 80% of participants who believed this was an essential value, we once more observed that for violent opposition the order between conditions was taboo+ > taboo > tragic, where those evaluating a "tragic" deal showed lowest support for violent opposition. The same order was found for two measures ostensibly unrelated to the experiment: (a) the belief that Islam condones suicide attacks; and (b) reports of joy at hearing of a suicide attack (there is neuroimaging evidence for joy as a correlate of revenge). Compared to refugees who had earlier evaluated a taboo or taboo+ deal, those who had evaluated a tragic deal believed less that Islam condoned suicide attacks; and were less likely to report feeling of joy at hearing of a suicide attack. In neither the settler nor the refugee studies did participants responding to the "tragic" deals regard these deals as more materially likely or implementable than participants evaluating taboo or taboo+ deals.

These experiments reveal that in political disputes where sources of conflict are cultural, such as the Israeli-Palestinian conflict or emerging clashes between the Muslim and Judeo-Christian world, attempts to lessen violent opposition to compromise solutions can backfire by insisting on instrumentally-driven tradeoffs and rational choices, while non-instrumental symbolic compromises may reduce support for violence. Further studies with 750 Hamas members and non Hamas controls this past June, show similar results, as do on-going pilot studies among Christian fundamentalists who consider abortion and gay marriage to violate sacred values.

Given these facts, I and others have been assisting in political negotiations that target recognition of sacred values over instrumentally rational tradeoffs. The goal is to break longstanding deadlocks that have proven immune to traditional business-like frameworks for political negotiation that focus on rational choices and tradeoffs. By targeting "sacred values" and "moral obligations" I don't seek to "ignore the role of religion" in people's actions and decisions, though Harris complains this is the reason I introduce sacred values into the discussion. My aim is quite the opposite: to politically engage those deepest held religious beliefs that are matters of life and death for peoples and nations.

This is what I mean when I talk about using the science of religion to solve resistant geo-political conflicts. Like Palestine. Like Iraq. If we understand the mechanism, can't we exploit it?

note: The "sciences of religion" is a tribute to one of my favorite books of Islamic theo-philosophy, the incomparable al-Ghazali's The Resusitator of the Sciences of Religion.

ASPM and flagella   posted by p-ter @ 12/26/2006 04:40:00 PM

In the profile of Bruce Lahn in Science, the following quote, on the possibility that the selective pressure on ASPM could be due to sperm function, stood out to me:
But genome researcher Chris Ponting of the University of Oxford, U.K., notes that microcephalin and ASPM are also expressed outside the brain. In last May's issue of Bioinformatics, he reported that part of ASPM's DNA sequence resembles that of genes involved in the function of flagella, which propel sperm. Earlier work had shown that ASPM is expressed during sperm production. Ponting suggests that natural selection might have acted on flagellar function rather than brain growth.
This would be a striking result, if true. However, I'm skeptical (actually, I'll put the punchline right here: the data provide little, if any, support for this). Let's review:

Ponting's paper is a look at the sequence of the ASPM gene-- it's possible, with this data, to determine the eventual sequence of the protein and see if any regions of the protein ("domains", we call them) are similar to parts of other proteins. If those other proteins have a known function, you might infer that ASPM has a similar function. And indeed, ASPM shares a domain, called ASH, in common with some other proteins. The function of that domain? Well, it's not clear, but as Pontig writes, "[t]hese domains are present in proteins associated with cilia, flagella, the centrosome and the Golgi complex".

This is all well and good, but to jump from a protein possibly "associated with cilia, flagella, the centrosome and the Golgi complex" to saying the selective pressure on the gene is due to flagellar function in sperm is a serious leap indeed. Where does this come from?

Frankly, I have no idea; perhaps I'm missing a key part of the puzzle. But another paper used actual molecular tecniques to look at the distribution of ASPM in neural stem cells. In their words, "Aspm was found to be concentrated at mitotic spindle poles". And what else is found at mitotic spindle poles? Centrosomes, of course, one of the possible locations for ASPM as determined by Pontig. As other centrosomal proteins are known to be involved in brain size, this is perfectly in line with the hypothesis that ASPM is a regulator of brain growth.

I'm not man enough to say the selective pressure on ASPM is definitely not due to a flagellar role in sperm, but for the moment, I ain't buyin' it.

Monday, December 25, 2006

Human monogamy is a farce!   posted by Matt @ 12/25/2006 11:27:00 PM

EDIT: I just found a paper (posted here)estimating the rate of human EPC to be between <1%-30% with a median of 3.7%. In other words, 1 in 25 fathers reading this are raising children that are the product of their partners infidelity...

In a previous post (link) the bold claim was made that there is no biological predisposition towards human monogamy, but instead what drives us toward monogamy-like mating system is culture. There seem to be several independent lines of evidence that supports my position.

  1. Anecdotal evidence. How many of us:
    1. Have never had a friend who cheated?
    2. Cheated ourselves?
    3. Know somebody who was actually cuckolded?
  2. Evidence from parsimony-
    1. There are 5,419 mammal species listed in Mammal Species of the World, the definitive resource. Of these, less than 5% are monogamous. Which is more parsimonious- that we ARE or ARE NOT monogamous?
    2. None of the great apes, our closest living related species, are monogamous
  3. Evidence from the literature.
    1. anybody have some good examples of data that defines human genetic mating system?
  4. Evidence from Adaptation and physiology
    1. Sperm competition
    2. Adaptive sperm allocation
It seems quite logical to me that humans are in fact not monogamous,at least not in the strictest (and biologically relevant) sense, but that instead polygyny might more appropriately represent our biology.

Anybody have problems with this?

Update from Razib: Paternity confidence.

Universal Granules   posted by amnestic @ 12/25/2006 01:47:00 PM

First order of business: RIP James Brown.

RNAs aren't just allowed to roam around the cell unescorted. They are most often found in association with RNA-binding proteins. One of the important stories from the past year was that assocation of RNAs with particular proteins involved in the microRNA interference pathway caused them to be localized to special processing centers in the cell soma called P-Bodies. Another relatively recent buzz follows the discovery that the protein lost in Fragile X mental retardation (FMRP) is an RNA-binding translation-repressor. Yet another area of broad interest has been the association of RNAs coding for synaptic plasticity-related proteins with protein particles attached to molecular motors that crawl up and down dendrites using the microtubule highway.

If you look at the figures from all of these discoveries you will find a lot of pictures of cells containing tiny bright dots. This is the visualization of an RiboNucleoProtein (RNP) granule. If your career didn't depend on it and you liked to dream, you might just go ahead and assume that those granules found in yeast, frog eggs, fly neurons, and mammal neurons were all pretty much the same things and continue to develop your mental model with this concept in mind. Fortunately, all you need is an international collaboration of 17 scientists to confirm your suspicions. Barbee et al just reported that, at least in fly neurons, we can find most of disparate translational repression machines in the very same granules. The summary table is below. Points of interest include AGO2, which is the catalytic center of RNA interference; DCP1, the hallmark of a P-Body; FMRP, the fragile X mental retardation protein; and Staufen, the marker for neuronal granules that can be found travelling up and down dendrites in just the right places to be useful for local protein synthesis.

There are so many pathways leading to RNA degradation these days, I've lost hope of keeping track. Perhaps I'll be able to make time to do a review in the next few months. I just ordered this lovely book. It should be noted that not all granules/particles/bodies were created equal. It is possible to have a granule with FMRP and no Staufen and vice versa. This leaves open the possibility of individual granule identities for specific translational control tasks. The relation of RNA interference to neuronal translational control is moving along surprisingly slowly, but we've had a couple good illustrations so far. One of the most interesting is was the discovery by Ashraf et al. (pdf) that olfactory learning in flies leads to proteasomal destruction of RNAi machinery at synapses and derepression of CaMKII translation. In other words, learning allows a very important synaptic constituent to be made, and the reason it isn't being made all the time is probably because its coding RNA is tied up in one of these repression granules.

I have visions of a gradient of RNP granule identities diffusing away from the focus of synaptic potentiation. Since FMRP seems especially good at repressing depression related proteins it should remain intact at the area of highest calcium influx, repressing depression proteins while repressors of LTP related proteins (i.e. maybe Cup or parts of the miRNA machinery) are destroyed by the proteasome. Further away the relationship flips over such that, within a dendritic neighborhood, an overall excitability is maintained by suppressing potentiation related proteins and allowing production of those that lead to depression. This is just an order that would please me. So far I have not found the science.

Believe the hype   posted by amnestic @ 12/25/2006 12:07:00 PM

I'm caught up in the microfinance hype. Maybe you're looking for something to do with that extra xmas cash. That or tell me what's wrong with it.

Update: Be sure to read the comments before you run off and end up a sucker.

Sunday, December 24, 2006

Merry Christmas! (for real)   posted by Razib @ 12/24/2006 09:41:00 PM

Have a good day everyone.

Saturday, December 23, 2006

T-minus 17 years + 6 months   posted by Razib @ 12/23/2006 10:28:00 PM

About 6 months ago I speculated that Shiloh Pitt was going to be a very beautiful baby considering how hyperattractive her parents were. Well, I was in the supermarket checkout line today and I saw some pictures of her in US WEEKLY. This is the best res photo I could find online, but the spread in US WEEKLY confirms that she is an extraordinarily beautiful child that lived up to my expectations based on her parental phenotypes.

Friday, December 22, 2006

Merry Christmas!   posted by Razib @ 12/22/2006 10:56:00 PM

It'll be Christmas soon. Unfortunately here in these United States we've been overwhelmed by materialism. So I'll share with you an SNL sketch which brings the focus back to something more personal and intimate (use this search if the video is gone)....

Religion - definitions   posted by Razib @ 12/22/2006 05:37:00 PM

In the post below I got pretty blogged down by the definition of the word religion. This is not new, almost anything is tagged as a 'religion.' Elvis fandom, football, and so forth. Six months ago I spelled out in tedious detail some of the definitions which I allude to contextually when I say "religion."

To repeat:

1) The axis of intuitive supernatural agency. This is basically god(s)-belief, and serves as the lowest common denominator across cultures. Cognitive anthropologists hypothesize that this tendency emerges out of a combination of our social intelligence mixed with theory of the mind, folk physics and other pattern recognition heuristics and modules. One could posit that schizophrenics and autistics occupy two antipodes of this trait, one group seeing agents all around them, another unable to perceive agency even in human beings in front of them.

2) The axis of social ritual and participation. This is basically the liturgical and outward behavorial aspect of religion. Even in "primitive" societies rituals and rites of passage exist, and they are often imbued with supernatural significance. Some people do not take to these rituals for whatever reason (asociality, fear of crowds, etc.) while others thrive on them and the public forum they offer for their charisma.

3) The social functionality. This is basically the phenomenon where church or religious ties serve as an entree into social accepability and smooth the interactions between individuals within a society. It is a reflection of some of the ideas promoted by David Sloan Wilson regarding group selection. Some individuals might not be particularly supernaturalistic or aroused by ritual, but they know that church membership and nominal profession of belief is essential for good standing within a community.

4) The axis of mystical experience of higher consciousness. This is basically an encapsulation of the program of "neurotheology," which attempts to show that religion can be characterized as altered states of brain chemistry. Obviously some people are more mystical in orientation, while others are relatively dead to the dreams of the cosmos. This is obviously related to #1, but I don't think the two are coterminus subsets.

5) The axis of rationality and ideology. This is basically the creeds and doctrines promoted by the "high religions" coupled with the insitutional systems that promote them. Out of this religious mileu come the Five Ways of Aquinas or the Four Noble Truths. This mode of religious expression intersects a great deal with ethical philosophy.

These can be thought of as multiple vectors or traits which sum up to what we perceive in a gestalt manner as "religiosity." All of these are not necessary for religion as I define it. For example, #5 is a development of the last 3,000 years, and at most the last 6,000. #3 is probably a feature which emerged in the last 10,000 years as agriculture resulted in mass societies where non-kin associations became significant. #1 and #2 have always been with us I suspect, and are modal in the human psychology. They're the "default" state, and we atheists are "oddballs" in our deviation from it. #4 is in some ways the opposite pole from atheism, it is perhaps a hyperactive form of #1 so that perception is distorted/heightened (depending on whether you believe there is anything out there to perceive) to an extreme.

When people say that "Therevada Buddhism is non-theist" I tend to express skepticism because I offer that ethnographic literature strongly implies that #1 is powerful enough to overrule the formal creeds imposed by #5 on a day to day level. This means I'm skeptical of the functional impact of belief, because I don't think belief is in most people that powerful aside from being a group demarcator in most circumstances. When Rod Stark offers that the Trinitarian Christian theology offers special functional benefits in One True God I wince, he needs to read some psychology. Most Christians have only a fuzzy idea of the genuine meaning, rooting in Greek philosophy (e.g., the technical meaning of the term "substance"), of the Athanasian Creed. And yet nevertheless, Stark does observe that throughout most societies there is operational limit to the number of gods worshipped in a locale (e.g., no Hindu worships, let alone comprehends, 333 million gods, this as sensible as the Athanasian Creed in terms of typical Hindus actually extracting direct meaning out of divinity). He also notes that over time the raw number of gods in most society have decreased. A simple explanation might be that the extinction of many languages and peoples as empires expanded naturally resulted in a consolidation of "god concepts." The emergence of local "saints" in monotheisms suggests that this consolidation also has a natural break.

In any case, the point of my original post wasn't to espouse a particular view as to the strength of a meme complex, it was to ask what role historical contingency vs. inevitable directionality played. It seems, for example, that the period between 600 and 600 was especially fruitful for the emergence of "world religions." And yet it has been over a thousand years since a real heavy hitter appeared on the scene. Perhaps human social complexes have attained a metastability?

Ultimately the questions I'm asking are so vague and general that they'll spawn a mass of counter-questions. I plan on tightening the constraint in the future.

How nice is that doggie in the window?   posted by Dylan @ 12/22/2006 04:47:00 PM

A link between coat color and certain behavioral traits has reportedly been discovered in a couple of dog breeds.

A dog's colour reflects a pooch's personality, scientists say, at least in one breed, the English cocker spaniel.

The latest study, recently published in the journal Applied Animal Behaviour Science, shows that golden/red English cocker spaniels exhibit the most dominant and aggressive behaviour.

Black dogs in this breed are the second most aggressive, while particolour (white with patches of colour) are more mild-mannered.

Earlier research suggests that hair colour is also linked to behaviour in labrador retrievers.

For this breed, the most aggressive are the yellow ones, the next most aggressive are the black dogs and the least aggressive are the chocolate coloured ones.

The behaviour-hair colour connection is likely due to related genetic coding that takes place during the pup's earliest life stages, according to lead author Dr Joaquín Pérez-Guisado.

"Maybe the link [to coat colour] is due to the fact that the ectoderm [one of the three primary germ cell layers] is where the skin and central nervous system originate in the embryo," he says.

Pérez-Guisado, a Spanish researcher in the Department of Medicine and Animal Surgery at the University of Cordoba, and his colleagues measured levels of dominance and aggression in 51 seven-week-old English cocker spaniel puppies that were either full siblings or half siblings.

The tests looked at how quickly a person could capture a puppy's attention, how well puppies followed the individual, how the dogs behaved while restrained, how they exerted their social dominance and what they did when they were lifted off the floor.

In many cases, the golden-coloured dogs resisted human contact and even tried to bite the tester, while the particolour pups often wagged their tails and seemed to enjoy the attention.

While genes control coat colour and appear to predispose behaviour in certain dogs, Pérez-Guisado says how dogs are raised plays the biggest role in behaviour.

He shows that environmental factors account for 80% of dominant, aggressive personalities while genes only influence 20% of dogs' demeanours.

"It is very important to give the dog an optimum and suitable environment in order to have a dog with a low dominance aggressive behaviour level," he says.

"For that reason, owners are primarily responsible for this undesirable dog behaviour."

I say reportedly discovered because the link to Applied Animal Behaviour Science gives at least the contents of all past issues, but using my browser's "find" didn't turn up any paper by a Dr. Joaquin Perez-Guisado published in 2006-2007. If anyone can find a link to any part of it, please update this post or put it in the comments.

Of course it's impossible to evaluate these claims without reading the paper. This doesn't seem to bode well:

"Maybe the link [to coat colour] is due to the fact that the ectoderm [one of the three primary germ cell layers] is where the skin and central nervous system originate in the embryo," he says.

Whether these findings are true and the actual magnitude of any genetic link between dog personalities and color potentially constitutes an important path to more widespread public acceptance of genetic relationships between physical and behavioral phenotypes. If it's a good enough theory to help you pick out a new Fido for the kids... Or, perhaps more plausibly, the usual fringe crazies on both sides can use bizarre analogies to support their pet paranoias1. Cocker spaniels show that gingers really are a threat to the rest of us!

Via Geek Press.

1 - Pun not intended and only belatedly noticed.

Brownology   posted by Razib @ 12/22/2006 12:15:00 AM

Low Levels of Genetic Divergence across Geographically and Linguistically Diverse Populations from India:
The authors performed an extensive investigation of Indian genetic diversity and population relationships, sampling 15 groups of India-born immigrants to the United States and genotyping each individual at 1,200 genetic markers genome-wide. Populations from India, and groups from South Asia more generally, form a genetic cluster, so that individuals placed within this cluster are more genetically similar to each other than to individuals outside the cluster. However, the amount of genetic differentiation among Indian populations is relatively small. The authors conclude that genetic variation in India is distinctive with respect to the rest of the world, but that the level of genetic divergence is smaller in Indians than might be expected for such a geographically and linguistically diverse group.

Update: Genetic Evidence on the Origins of Indian Caste Populations (from 2001, Bamshad et. al). Control-f "Alu."

Thursday, December 21, 2006

If you cant beat em...   posted by Matt @ 12/21/2006 10:53:00 PM

Scoop out their sperm!!!

I'm writing a series on human behavioral ecology over here, and am currently writing about sperm competition. Obviously, any strategy that enhances your likelihood of fertilization should be strongly favored by natural selection. In particular, I was thinking of probabilistic strategies that enhance the likelihood that your sperm does the job (as compared to rival males sperm). In insects, penile morphology has somewhat frequently evolved to incorporate a complex "sperm scooping" device.
On an aside, I note that the complex penile morphology (sperm scoopers) is conspicuously missing from Dembski's list of "things-too-complex-to-have-evolved" without a designer.
Anyway, I found a paper that describes the human penis as a sperm displacement device (full text here).

Selected Excerpt: "...found that males appear to modify the use of their penis in ways that are consistent with the displacement hypothesis. Based on anonymous surveys of over 600 college students, many sexually active males and females reported deeper and more vigorous thrusting when in-pair sex occurred under conditions related to an increased likelihood of female infidelity."

Man isn't science fun...

Update from Razib: Sperm competition part n, sperm competition.

Lahn profile, part 2   posted by p-ter @ 12/21/2006 10:36:00 PM

Ah, what the hell, I'm putting the full text of the initial profile below the fold (the full sidebar on research into ASPM and microencephalin is here). If anyone is horribly offended by this, I'll take it down. But hey, if they remark that unnamed "bloggers" (well, John Derbyshire is mentioned by name) "jumped on" the race angle, they should be happy to let us jump on this as well:
CHICAGO--In 1993, not long after Bruce Lahn joined David Page's genetics lab at the Massachusetts Institute of Technology (MIT), Page invited all lab members on a 2-day hike in New Hampshire's rugged White Mountains. Page circulated a list of items to pack and stressed bringing enough food and water. Everyone showed up with stuffed backpacks--everyone, that is, except Lahn, who arrived toting only a small shoulder bag. When asked, Lahn pulled out the bag's sole contents: a gallon jar of Chinese pickled eggs.

"That was classic Bruce," Page recalls. "He didn't follow instructions." Lahn's insistence on doing things his way has made him one of the fastest rising stars in genetics and also one of the most controversial. His work with Page to decipher the evolutionary history of the human Y chromosome was a major landmark in genome research. It led directly to a position at the University of Chicago in Illinois, where Lahn achieved tenure in an unusually rapid 5 years, and to an investigator award from the Howard Hughes Medical Institute.

But Lahn's more recent work, seeking to identify the genes behind our species' superior cognition, has sparked skepticism (see sidebar, p. 1872) and plunged this Chinese-American scientist into contentious debates over genetics, race, and intelligence. Two Science papers concluding that purportedly beneficial brain mutations are common in Eurasia but rare in Africa have made Lahn a darling of right-wing commentators seeking evidence of racial differences in cognition. Some scientists say Lahn overinterpreted and sensationalized his findings, and one co-author has distanced herself from one of the paper's more speculative conclusions.

The papers have such serious social implications that they needed to meet a higher standard of proof, says David Altshuler of the Broad Institute in Cambridge, Massachusetts--and they didn't. The links to cognition in particular were "wild speculation," he says. "We have a powerful responsibility to think about how society will interpret [such work]."

Lahn finds the political fallout discomfiting, insisting that he is a staunch antiracist and "extremely liberal" in his personal politics. He says he is a lifetime member of the National Association for the Advancement of Colored People and gives money to Democratic candidates. Yet Lahn is fascinated by differences among people and says he has long wondered whether variations in social status have genetic underpinnings. "You can't deny that people are different at the level of their genes," Lahn says, citing the examples of skin color and physical appearance. "This is not to deny the role of culture, but there may be a biological basis [for differences] above and beyond culture."

Becoming Bruce
Lahn, 38, is slim and handsome, with expressive hands that gesture animatedly as he speaks. He was born in China to two physicists who both suffered from the country's political turmoil. His mother was branded a "rightist" by the Communist Party during the 1950s, leading his maternal grandmother to commit suicide out of shame. His paternal grandfather died in a Communist labor camp. "From early on, I had a sense of what had happened to my family, and that made me a bit of a rebel," Lahn says. "I was hyperactive and always in trouble at school."

Lahn's rebelliousness made him keenly interested in China's social inequalities. He was particularly struck by the privileges foreigners received when they visited China. "I was deeply traumatized by that," Lahn says. He wondered whether there might be a genetic basis for these class differences. "But I didn't know what genes were exactly."

In 1986, Lahn began studying genetics at Beijing University. He soon got caught up in the nascent democracy movement, putting up one of the first wall posters on campus. "We were very naive," he recalls. "We really thought that we had the power to change the government." When Lahn heard he was on a watch list, he decided to leave China and was accepted at Harvard University in 1988.

When he arrived in the United States, Lahn was still going by his Chinese name, Lan Tian. But one day, a McDonald's janitor told him he looked like the late martial arts actor Bruce Lee, and Lahn's friends started calling him "Bruce." Lahn soon adopted it as his legal first name and Anglicized the spelling of his last name.

Lahn thrived at Harvard. Geneticist James Birchler, now at the University of Missouri, Columbia, supervised Lahn's senior thesis. "He had golden hands" in the lab, Birchler recalls, "and he was intellectually fearless and adventuresome."

In 1991, after beginning Ph.D. studies at MIT, Lahn asked Page to take him on as a student. But Page says at first he was not keen to do so: "A number of people in the lab were unsure about whether it was wise. He seemed brash and cocky and too self-confident." Page put Lahn on a small project investigating a rare defect in the human Y chromosome. "But Bruce thought [the project's] range was too limited. He started conducting secret experiments in the lab that he thought I wasn't aware of." Finally, Lahn announced that he wanted to isolate all of the Y chromosome's genes. Page let him go ahead. Within 18 months, Lahn had cloned about half of the dozen genes then known on the male part of the chromosome. Page and Lahn went on to show that the human Y chromosome evolved from a series of rearrangements of the mammalian X chromosome (Science, 29 October 1999, p. 877).

"Bruce had a deadly killer instinct," Page says. "He kept his eye on the prize. And he was very charismatic. … After he left, some of us felt that we would never see the likes of him again."

Tackling the evolving brain
Soon after Lahn's move to the University of Chicago in 2000, he began looking for genes that might explain the evolution of the human brain, motivated in part by his long-standing interest in human differences. In 2004, his team reported that two genes thought to regulate brain growth, called microcephalin and ASPM, appeared to have undergone strong natural selection since the human and chimpanzee lineages split between 5 million and 7 million years ago. These genes are implicated in regulating cell division in developing neural cells, and some mutations in them result in a tiny brain, or microcephaly. But their function in normal humans is not clear, and they are expressed in non-neural tissues as well.

Then, in two papers in Science last year, Lahn reported that variants of the two genes appear to have been strongly favored by recent natural selection (Science, 9 September 2005, pp. 1717 and 1720). That implies that the variants conferred a survival or reproductive benefit, perhaps a cognitive one. In media interviews, Lahn conceded that there was no real evidence natural selection had acted on cognition or intelligence. But both papers pointed out that the mutations arose when key events in human cultural development occurred: The microcephalin variant was dated to about 37,000 years ago, when the first art and symbolism showed up in Europe, and the ASPM variant to 5800 years ago, when the first cities arose.

Lahn's papers also reported the skewed geographic distribution of the genetic variants. Variants in microcephalin turned up in 75% or more of some Europeans and Asians Lahn studied, but in less than 10% of some African groups. The ASPM variant was also much less frequent in Africa.

Bloggers jumped on the news, trumpeting the papers as support for the idea that African Americans have lower intelligence than whites. Two months later, in the conservative National Review Online, columnist John Derbyshire wrote that the research implied that "our cherished national dream of a well-mixed and harmonious meritocracy … may be unattainable."

Among some geneticists, there was consternation. "There was no evidence whatsoever that these [genetic variants] have any effect" on differences between people, Altshuler says, adding that the controversy over the work was "easily anticipated." Harvard geneticist Richard Lewontin goes further, criticizing both Lahn and Science for publishing such speculative links to cultural advances. "These two papers are particularly egregious examples of going well beyond the data to try to make a splash," he says. And archaeologist Scott MacEachern of Bowdoin College in Brunswick, Maine, says the archaeological links in the papers are simplistic and outdated. The symbolic revolution, agriculture, and urbanism developed "over many thousands of years, and none was restricted to Europe and the Middle East," he says.

Even one of the co-authors of the papers, Sarah Tishkoff of the University of Maryland, College Park, has now distanced herself from the attempt to link the ASPM variant to human advances, saying that she didn't see the wording until page proofs.

Lahn points out that the papers include disclaimers, stating, as one of them put it, that it was "formally possible" that natural selection had acted on the genes' roles outside the brain. And in media interviews he emphasized that a number of genes other than microcephalin and ASPM are probably involved in cognition. But he insists that the evidence points to some sort of brain function as the most likely target of selection.

Lahn asserts that some scientists "start with a political agenda and fit the evidence to that." This political bias, he argues, "takes credibility away from an antiracist program that I agree with. … If someday we discover that there are genetic differences in cognitive abilities, would that mean that racism is now justified?"

And some scientists believe that Lahn has shown courage in pursuing his research. "There is widespread fear of this [research] among scientists," says geneticist Henry Harpending of University of Utah in Salt Lake City, who has suggested evolutionary explanations for high IQ scores in Ashkenazi Jews. Even some researchers who scoff at racial differences in intelligence think the research should go on. Geneticist Michael Hammer of the University of Arizona in Tucson says he's not worried about the end result: "I have no serious concerns that Europeans or Asians are going to be proven to be more intelligent, so I say go at it, let the chips fall where they may."

Lahn says the controversy has made him back away "from going after these kinds of questions aggressively," although he continues to test whether the variants affect IQ. He has begun diverting his energies to another high-profile project: stem cells. He became interested in the topic after running into a Chinese colleague at a meeting and is collaborating with a center at Sun Yat-sen University in Guangzhou. He was motivated in part by China's relatively liberal attitude toward this research and also, he says, by his desire to help China modernize.

Time, and further research, will tell if Lahn was right about microcephalin and ASPM. But Page says that few other scientists would have been willing to get involved in such controversial questions in the first place: "That willingness to venture into this territory without his guard up is entirely in keeping with who Bruce is. Anybody who would have packed their bag as instructed for that White Mountain hike would have steered clear of all this."

Monotheism, the thread, the ball of yarn that's hard to untangle   posted by Razib @ 12/21/2006 10:18:00 PM

A clarification on the post below, when I talk about the spread of 'monotheism' I'm talking about the outward spread of groups who espouse an Omni-god. I'm not talking psychologial monotheism, I don't think it makes much sense to really distinguish it from polytheism. To be frank, the Omni-god monotheisms have many gods, some of them are called angels, others are called saints, and in the case of Christianity there's a lot of smoke thrown in the air about the Trinity which is a mystery to all involved. Some might consider Buddhists to be a non-theistic group which is fundamentally different from the Omni-godists. Well, a few years ago I read an article about the aftermath of the Indian Ocean Tsunami where Therevada Buddhist peasants in Sri Lanka explained how their Muslim neighbors were adversely affected by the catastrophe because they didn't accept Lord Buddha. Sound familiar? The Buddhists in question didn't seem to find it relevant that in that locality Muslims were fishermen who live don the coast while Buddhists were inland farmers. Buddhism, the religion of rationality?

So you see, Buddhists do believe in god, they just call it Lord Buddha, or a Bhoddisatva, or some such other thing. Yes, Muslims are monotheists, but saint worship and veneration of Sufis is pretty common in the Muslim world. Hard-core Omni-godists like the Salafists have to take drastic measures like destroying the tomb of the Prophet Muhammad to really batter away at human instincts. Omni-godists sincerely profess a believe in All-god of All-things and All-times, but that sincerity is as relevant as being sincerely convinced that an 8-dimensional Peacock Asteroid is lord of the world. It could be true, but whatever. Hindus might traditionally believe that the godhood is immanent in all things, but they never worship toilets or turds, rather, they focus their spiritual energy on the concept of a god out their, or embodied in an avatar, often using imagery as foci.

Elite religious professionals and the ruling castes need ideology. There is basal religious sentiments which most humans exhibit, so this is good raw material to synthesize with ingroup-outgroup markers. Add a few demarcatory rituals and shibboleths, plus magical words of a sacred nature that are incomprehensible to all, and you have a good recipe for an epidemiologically potent complex of ideas. We know it's potent, higher religious imbued with philosophical baggage and ideology have become dominant in our world. The elites with leisure time like philosophy. The masses are attracted to religion, the beliefs, the rituals, the communal bonding. Mix the two together and have a dragon with a head, philosophy and ideology generate a systematic superstructure through which the religious passions which have always existed by can channeled.

So, back to the question. Why did exclusive universalistic monotheism succeed in Western Eurasia and not Southern and Eastern Eurasia? Here I'm not asking about differences in psychology, European peasants were operationally pagan until the Reformation. There is enough ethnographic literature in places like Germany in the 18th century which show almost immediate reversion to paganism (without knowing what they were doing) by peasants who are without a pastor to "guide" their thoughts. This is why I reject Theresa's idea that European natural individualism was somehow attracted to monotheism because it of a good fit between ideology and psychology, I've already established that the two don't really match at all, there's little variation between groups on the latter, a lot on the former. Also, in any case the the most individualistic European groups were the last to monotheism, and the first to post-Christianity (and operational re-paganism, starting with an abortive attempt in Nazi Germany), so that doesn't work either The most monotheistic groups are in the Middle East, but it seems that a more parsimonious explanation is simply that Omni-godism spread outward as a function of distance from the Middle East.1 Mousy Matt pointed out that the probability of extinction of any given introduction of a favored mutant is rather high. In other words, if Christianity (to use an example) was introduced by the immigration of one individual to China the chances of propogation might be higher than !Christianity, but that doesn't mean that you are probably going to see it go extinct. So I asked Mousy Matt, "what's the level of selection?" The reason is that in Tang China between 600 and 850 (which a religious pogrom rendered extinct most "foreign" religions and reduced in power "indigenous" ones) Christians were a non-trivial presence in the cities. Christianity showed up again a bit during the Mongol period (some of the Mongols were Christians), and again during the late Ming period, and finally again during the 19th century. So does each introduction count as a mutational event? But what about the dispersion of Christians to the various cities of China? Isn't each loci a potentional point of protonation? Finally, there's another Omni-god religion, Islam, which has pretty solid roots in China, and has had them, for nearly 1,000 years. There is some evidence that Chinese lineages in parts of South China were even originally Muslim before full assimilation into a Han identity.

OK, enough for now. I guess the point is that our model can't be one where Omni-god meme complexes float on top of an invariant background fitness level which they have an advantage over. In places like China and India their fitness is constrained, even nullified, by sociological factors. It isn't like Chinese can't become Christian, most Chinese in the United States, many in places like Indonesia, are Christian. When the constraints are removed and the fitness landscape is altered (e.g., becoming Christian was a good way for a Chinese individual to prove that they weren't a Communist in Indonesia) it is a different ball game.

1 - The monotheistic explanation can be tested in East Asia, there are two nations with many Christians, South Korea and The Philippines. I think it can be argued that Filipinos are rather individualistic, and sociologial data shows that Korean Christians are more liberal and individualistic than non-Christians. But both these effects are hard to tease apart from the influence of Spanish and American culture respectively.

Bruce Lahn profile in Science   posted by p-ter @ 12/21/2006 10:18:00 PM

The week's Science has a two-part profile on Bruce Lahn which includes some new information on research into ASPM and microencephalin. One of the two articles in entirely devoted to the flurry of articles disputing various claims about the two genes. Full text below the fold.
Some of Bruce Lahn's provocative claims are running into heavy fire. Last year, the University of Chicago geneticist reported, in two papers in Science, that he had uncovered genes that are still evolving in humans, and he suggested that they confer a brain-related boost--perhaps even a cognitive one. His university even applied for patents on a test that would reveal whether individuals carry the possibly advantageous genetic variants. Some researchers have since argued, however, that selection may have favored the variants for a non-neural function. Others have questioned whether the variants were under recent selection at all. And Lahn's own work with other scientists has failed to correlate variants of the genes ASPM and microcephalin with IQ. At this point, concedes Lahn, "we don't know what the variants do."

Soon after the Science papers were published, Lahn set out to see whether the variants give a cognitive advantage. In one study, Lahn helped controversial psychologist Philippe Rushton of the University of Western Ontario in London, Canada, test whether people who carry the favored variants have higher IQs. Rushton is well known for his claims that African Americans have lower intelligence than whites, and Lahn had found that some genetic variants are common in Europeans and Asians but less frequent among sub-Saharan Africans. But Rushton reported last week at the annual meeting of the International Society for Intelligence Research in San Francisco, California, that he had struck out: The variants conferred no advantage on IQ tests. "[We] had no luck," Rushton told Science, "no matter which way we analyzed the data." Lahn was not a co-author, but his group genotyped the 644 adults of differing ethnicity in the study.

Lahn is a leading author, however, of a similar international study of about 2500 subjects. Most of the results are unpublished, but findings from Australia were presented at a meeting in Brisbane last August. Nicholas Martin's team at the Queensland Institute of Medical Research in Brisbane found no statistically significant correlations between the supposedly favored variants and IQ. In large part due to this raft of negative results, Lahn says, the patenting effort has now been dropped.

If the variants aren't boosting IQ scores, what are they doing? Some mutations in microcephalin and ASPM lead to microcephaly, or very small brains, so Lahn had hypothesized that the variants might influence brain growth in normal people. But that idea was challenged last May by neuroscientist Roger Woods of the University of California, Los Angeles. Woods's team found no correlation between brain volume and the variants in 120 normal subjects, as reported in Human Molecular Genetics. Woods suggested--and Lahn agrees--that the variants might be involved in some more subtle neurological function, with Lahn arguing that a brain-related function is still the most likely target of selection.

But genome researcher Chris Ponting of the University of Oxford, U.K., notes that microcephalin and ASPM are also expressed outside the brain. In last May's issue of Bioinformatics, he reported that part of ASPM's DNA sequence resembles that of genes involved in the function of flagella, which propel sperm. Earlier work had shown that ASPM is expressed during sperm production. Ponting suggests that natural selection might have acted on flagellar function rather than brain growth. "These genes could well have many functions in many parts of the body," Ponting says, "and any one of these could have driven their adaptive sequence changes."

Meanwhile, other researchers have questioned the basic finding that the variants have been under recent natural selection. In a Technical Comment published 14 July online in Science, Sarah Otto of the University of British Columbia in Vancouver, Canada, and colleagues argued that Lahn's findings reflected not a signature of selection but rather the genetic traces of population movements as modern humans migrated out of Africa. And in October, a team led by geneticist David Reich of the Broad Institute in Cambridge, Massachusetts, reported at the meeting of the American Society of Human Genetics that it found no evidence for recent selection on ASPM when it used a method of analysis it considered superior to Lahn's. But Lahn, who is familiar with Reich's results, stands by his conclusions: "Their method has lower resolution … and is less reliable," he says.

All the same, Lahn says he has mixed feelings about the failure to date to correlate the variants of microcephalin and ASPM with differences in intelligence: "On the scientific level, I am a little bit disappointed. But in the context of the social and political controversy, I am a little bit relieved."
It's always been clear (from a scientific standpoint) that the claims of an IQ link were premature, at best (and indeed, there's no talk of it in the papers), and as Dr. Lahn noted in his 10 questions, his other speculations are clearly labeled as such. But the claims that the variants are not at all under selection are probably specious. The technical comment published in Science was essentially crap, and it's impossible to so far impossible to judge the other, unpublished results. Time will tell, time will tell...

Watch what you say, the elders are watching!   posted by Razib @ 12/21/2006 07:22:00 PM

Every time I allude to the male biased readership, one feisty individual emails me to take issue with my assertion. I thought I'd pass on the email since I think some of you might be surprised at who reads our little blog:
I'm a lady (73 years old) and read Gene Expression most every day. I don't usually respond to surveys but would guess you have more "lady" readers than you think.

PLoS One arrives with a bang   posted by p-ter @ 12/21/2006 04:32:00 PM

Evolgen points out that the new open access journal PLoS One is now online. The journal looks to make commenting and ongoing editing a central part of the publishing process, and I certainly wish them luck. Their launch is certainly impressive; here are a couple papers that might be of interest to readers. If you've got any background in any of these areas, get over there and start commenting.

1. "The torture experiment" reprise
One of the most chilling psychology experiments ever performed was the legendary Milgram experiment on obedience, performed in the '60s. The question was this: will a random individual be willing to torture, possibly to death, another randomly chosen individual, simply because a figure of authority tells them to do so?

The answer, strikingly, was yes-- something like 65% of the individuals were willing to, depending on the conditions. You can read the links for the experimental setup; it's really quite an impressive experiment. Of course, being made to think they were killing someone caused some stress in some of the participants, and this kind of study is now considered unethical.

The PLoS One paper describes a way around this-- a virtual reality setup (see the picture). Obviously, the subjects know they're not hurting a real person, but apparently their stress levels are similar to if they were, and the reactions of people to the pleas for mercy were similar in to the original experiment (some giggled). So a virtual reality setup like this could be a possible ethical way to put people in "extreme" social situations.

2. Sexual selection for bigger brains?
The present research examines the evolutionary relationship between brain size and two components of primate sexual selection, sperm competition and male competition for mates. Results indicate that there is not a significant relationship between relative brain size and sperm competition as measured by relative testis size in primates, suggesting sperm competition has not played an important role in the evolution of brain size in the primate order. There is, however, a significant negative evolutionary relationship between relative brain size and the level of male competition for mates. The present study shows that the largest relative brain sizes among primate species are associated with monogamous mating systems, suggesting primate monogamy may require greater social acuity and abilities of deception.

How to make an extra finger   posted by p-ter @ 12/21/2006 10:47:00 AM

While we're on the subject of freaks, let's talk about polydactyly; that is, the presence of one or many additional digits on the hands and/or feet. It's actually a fairly common malformation, and it segregates as a dominant phenotype. But the genetic basis for this phenotype has only recently been elucidated, and the eventual culprit was a great example of an emerging pattern in human genetics.

It all started with the mice--actually a polydactylous line of mice called Sasquatch. The reason for the name is a bit of a mystery to me, but in any case, Sasquatch had extra digits and showed misregulation of a developmental gene called Sonic Hedgehog. So perhaps these two event were linked--could the misregulation cause the phenotype? It's a good hypothesis. But the researchers are geneticists, so they had another question first: what is the genetic basis of the misregulation itself?

This mouse line had been created by the insertion of DNA randomly into the genome, so perhaps the location of the insertion would give some clue as to how this misregulation was caused. The team then found the location of the inserted DNA, and saw that is was in the intron of another gene, over 1 million bases away from sonic hedgehog! So could this just be a fluke accident caused by the insertion of random DNA? That is, could polydactyly in humans really be caused by a mutation a million bases away from the gene involved?

To determine that, you'd have to look at humans, and that's exactly what the next group of authors did. They found a highly evolutionarily conserved region a million bases away from sonic hedgehog and a number of families segregating polydactlyly with single base pair changes in precisely that region. That's striking, but it's still not enough to infer causality-- we're sticklers here, and that's just a correlation. There's one more experiment to do-- take the single base changes from the humans with polydactyly and see if they're enough to cause misregulation of a gene in the mouse. The results are what you see in the picture above-- the top picture is the normal copy of the sequence attatched to a gene encoding a blue dye, so you see blue dye everywhere the gene is expressed. In the bottom, you see the expression pattern of the gene attatched to the mutated sequence-- as you immediately notice, it's expressed all over the hand/paw. So there you have it-- a single base pair change a million bases away from a gene (in fact, in the intron of another gene) is enough to cause a dramatic phenotypic change like an extra finger. Crazy stuff.

So what to take from this? A couple things:
First, small regulatory changes can have big phenotypic effects. Second, determining causality of a regulatory mutation is a pain. Third, the elements that regulate the expression of a gene don't have to be near the gene-- indeed, this one was in the intron of the next gene over.

So how important phenotypically are changes in the spatio-temporal expression patterns of genes? Potentially huge.

Four Stone Hearth 5   posted by Razib @ 12/21/2006 12:23:00 AM

Four Stone Hearth 5.

Wednesday, December 20, 2006

George Packer in The New Yorker   posted by Razib @ 12/20/2006 09:54:00 PM

Of course you should read George Packer's piece in The New Yorker, Knowing The Enemy. The contempt for knowledge common in our government today is a shame of, but let's not cut any slack for academics who won't work within the system which in the end protects them.

Obesity germs, thrifty genes   posted by agnostic @ 12/20/2006 08:43:00 PM

Nature has two studies on the difference in gut microbe composition between lean and obese mice and people (mice study, human study). Read their news department's review here to get the skinny (c'mon, you had to have seen that one coming!). In brief, the balance between two divisions of bacteria -- Bacteroidetes (B) and Firmicutes (F) -- is pronouncedly different in lean and obese mice and people, such that lean ones have a greater proportion of B microbes and a lesser proportion of F microbes compared to obese ones. The F to B ratio in obese humans was about 12 times that of the lean humans, but decreased over the course of a year-long diet (though not reaching the levels of lean subjects). And after mice raised in sterile conditions were given gut microbes from lean or obese mice, the ones given obese microbes gained more weight than those given lean microbes within just 2 weeks (1.3 +/- 0.2 g vs 0.86 +/- 0.1 g, respectively), even though the two groups did not differ in the amount of food they ate -- the obese microbe group simply absorbed more energy from food. Though small absolutely, this difference in weight gain presumably accumulates over longer periods of time.

I blogged here about some studies earlier this year that investigated obesity from an infectious angle, which implicated a human adenovirus. Let me reiterate my skepticism regarding thrifty gene ideas about obesity (more below the fold).

The basic idea is that in times of famine, an allele that increased an individual's ability to harvest more energy from food would have been advantageous, although when thrust into a new environment of abundance, the allele will tend to make its bearers obese. The prediction, then, is that populations for whom famine has been the strongest burden over time should have higher frequencies of such alleles, and thus in the modern world should have a higher frequency of obesity. Because famine arose from agriculture and civilization, the concrete prediction is that Eurasians should be most obese, and non-Eurasian populations falling below depending on when they adopted agriculture. However, in the US, Europeans are least likely to be obese, followed by African-Americans, and then Native Americans and Mexicans. The latter two (New World) groups have not been practicing large-scale agriculture long at all, and thus have not been as subjected to famine as other groups, yet they are the most likely to be obese. See here for obesity rates by gender and race.

Thus, obesity looks like an infectious disease whose microbes have resided longer in Eurasia than in sub-Saharan Africa or the New World.

Note that the microbes involved need not have been disease-causing in Europeans -- if the two Nature studies are to be believed, obesity is associated with a bacterial balance being thrown outta whack. That suggests that the "microbiome" in the gut is like one large co-adapted gene complex. Just as hybrid depression can result from disrupting such complexes, co-habitation of races separated for a long time might introduce gut microbes from one group into another, disrupting the balance of the latter's gut microbiome and/or its interaction with the human system around it. That is, if human guts co-evolve with gut microbes, Native American guts may not know how to work optimally with the new European gut microbes. This clearly isn't all that happens, though, since people of European and Native American ancestry have been living next to each other in the US for centuries, yet obesity has only recently flared to epidemic proportions. But something like this is likely at work, and likely accounts for some of the racial variation in obesity.

Notes & links   posted by Razib @ 12/20/2006 06:44:00 PM

First, a Long post where I say all have to say publically about the "hot chick" topic. As I note at the end, I'd like to move on. I hope that GNXP readers won't waste their time on threads 'defending' me. I excoriate readers enough that I hope that you allot your time more productive ends. I'd also like to thank Chris of Mixing Memory for speaking up on my behalf many a time on several weblogs. A few days ago I stated I was a conservative, and sure enough those who have come and explicitly defended me have been mostly on the Right (Steve, Udolpho & Your Lying Eyes). Nevertheless, Chris is far Left personally but took time out to make sharp deconstructions of pretty nasty smears of my character and false characterizations of the original post (also, I remember when John Emerson and Ikram Saed defended GNXP from accusations of avowed racism at places like The Gay One's weblog). I suppose I shouldn't stereotype, I am again officially in limbo-land politically and will attempt to act the rational actor instead of being emotionally driven.

Second, a question for the ladies: is GNXP so male heavy in its readership because of our sexism? Regular surveys point to the fact 90% of our readers are male. I've always ascribed this to the content. But do the frat-boyish comments and picture posting drive you away? I'm mostly curious, the reality is that I'm (and the Others) not doing GNXP to be popular. We're trying to go where no one has gone before and have fun doing it. If that rubs some the wrong way, well, that's how it rolls. Nevertheless, more data isn't bad.

Third, do any of you wonder why exclusive monotheistic religion become dominant in western Eurasia, but not in South or East Eurasia? Rod Stark has a 'rational choice' model where socially there is selection upon sects so that those who provide the optimal 'goods and services' come out on top. In other words, Christian victory was inevitable. Nevertheless, in China you have a scenario where Christian was introduced in the 7th century, and went extinct (before reappearing twice, first in the 12th century with the Mongol invasion, and second with the arrival of Europeans in the 16th century). In South Asia there have been long resident Christian communities in Kerala, but penetration of exclusive monotheisms like Islam which had elite support was generally limited (about 1/3 of South Asians are Muslim) as the Hindu substrate managed to maintain dominance.

In The Fall of the Roman Empire Peter Heather asserts that The Battle of Teutoburg Forest was not the event which prevented Roman expansion into Germania, rather, the lack of a taxable population base with cities which one could hold was the crucial long term factor. Germanicus' subsequent successful campaigns in Germany attest to this. A good analogy might be the lack of interest in the Pictish country of Scotland, even though Agricola came and conquered throughout the land (many Roman commentators long contended that Britain was conquered for the glory of Claudius and no other reason).

Book review - The Gecko's Foot: Bio-inspiration: Engineering New Materials From Nature   posted by Razib @ 12/20/2006 06:25:00 PM

My review of The Gecko's Foot is out in Science & Spirit. I'll be honest, I'm not happy with the review since I was on a time crunch (I was a back up reviewer and the piece needed to be sent in on a short deadline) & very busy with other things. Nevertheless, the take home message is about right.

Assesing the risk of extra-pair matings...   posted by Matt @ 12/20/2006 09:04:00 AM

A.K.A smelly t-shirt experiment revisited. These experiments basically ask women to evaluate the "sexiness" of a man's body odor. Turns out, women consistently rated odors of men with dissimilar MHC genes to be most attractive. Here is a link to some background info. Similar studies have been done in mice and other primates and show that all else being equal, there is a preference for MHC dissimilarity. Just like in humans, the mechanism for the detection of genotype is olfaction.. Cool stuff.

In a bit of a twist, UNM researchers recently repeated the "sweaty t-shirt" experiment, but asked different questions. Instead of attractiveness, they were interested in looking at sexual receptivity and rate of extra-pair-matings. Results of their findings are here.

The take-home message.. If you're partner doesn't find your B.O., attractive, chances are, they're likely to find someone else's whose is...

Tuesday, December 19, 2006

IQ vs. hotness   posted by Razib @ 12/19/2006 11:07:00 PM

Here is my general model. Ignore the magnitude of the slope, I suspect the covariance between IQ & hotitude is rather modest indeed. Nevertheless, the graph illustrates my general model, a linear increase between 85 and 115, about 75% of the population. Then, a slight linear decrease up the IQ ladder (though beyond 140 you don't have too many people). Finally, below 85, and definitely below 75, a much sharper drop in attractiveness, and increase in phenotypic variance due to macroscale developmental instability.


Cruise control: does holoprosencephaly explain some of Tom's behavior?   posted by Dylan @ 12/19/2006 08:11:00 PM

A common aphorism in the legal world is that the worst thing for a libeled celebrity to do is sue and spread the alleged falsehoods even more widely. So my thanks to Tom Cruise's legal team for bringing the subject of this post to my attention. (For a more pithy and very amusing take, please see Overlawyered.)

As first brought to my attention here, in the wake of the Cruise-Holmes pregnancy announcement a neurologist and Metafilter participant argued in a since deleted comment that Tom Cruise might suffer from mild symptoms of holoprosencephaly. Someone recently started a new thread noting that at some point this comment, apparently a relatively famous and well regarded one by the Metafilter community, had been deleted. By this afternoon, that entire thread had been deleted after the original claims had been reposted and much speculation ensued that Cruise's infamous legal team threatened Metafilter into removing it.

The original claims, which I saw reposted this morning before they were once again deleted, were contemporaneously recorded here:

The wonderful photo of the grinning Cruise illustrates beautifully the reason why I think this report might not be true, or at the very least, might be premature. Check out his teeth. That's right, Cruise has only three incisors - he was born with a fused, midline incisor. He's had dental work, including reshaping and adult braces, to minimize the abnormal appearance of this tooth - in early photos you'll find he almost never smiles, and when he does you can see that the middle incisor is freakishly wide.

Midline incisor can be a forme fruste of holoprosencephaly, a syndrome which in its more severe manifestions can lead to cyclopia, fusion of the frontal lobes, a primitive proboscis instead of a nose (located above the fusion eyeball), and other grisly abnormalities. [Caution: disturbing medical photographs.]

The babies are usually aborted or stillborn, which if you recall was the fate of Nicole's first couple of preganancies (after the first one, she clammed up about it.)

Further evidence of this heritable trait comes from Cruise's history; his biological father was mildly retarded and beat him severely as a child. Mild retardation, with or without violent behaviors, can also be part of an incomplete holoprosencephaly syndrome.

Amusingly, one of the genes found to be mutated in holoprosencephaly is called sonic hedgehog. It is a human analog of a gene first described in Drosophila fruit flies; embryos with the gene knocked out develop a spiky appearance and are non-viable. More than one gene knockout produced this 'hedgehog' appearance; some wag dubbed this member of the hedgehog family "sonic."

In any event, I suspect Cruise might carry one or even a pair of these holoprosencephaly genes, and if so, this pregnancy might not make it. I hope I'm wrong, though; no matter how you feel about Tom Cruise, genetic diseases really suck.

Could this, and not the gay/sham marriage rumors, be the secret about Tom and Nicole's marriage that she's seemed to be keeping? Is this why Tom bought a sonogram machine for personal use - to prevent leaking of rumors or photos if any abnormality had been been discovered? More speculatively, was there some minor cosmetic problem that led to the blackout on Suri appearances for months after her birth while it was corrected? While withholding pictures was hardly strange behavior, I recall that even many close friends had not seen her.

Tom Cruise has been a quasi-popular topic among GNXP contributors and commentors before, most relevantly here, when Nicole Kidman's miscarriages with Tom Cruise were used to eliminate her from speculation over what Oscar winning actress might suffer from what sounded like Androgen Insensitivity Syndrome. Ironically, those miscarriages look like possible evidence for genetic abnormalities on the other side of the relationship.

Finally, I note this post from last year commenting on the original claims of holoprosencephaly. It includes what is apparently the picture that launched this theory, as well as this interesting observation:

What does it say about beauty as a marker of reproductive potential that hardly anyone seems to have noticed Cruise's potentially sterility-denoting genetic anomaly until now? When you also take into account that some of the most strikingly beautiful women are actually genetically male, you have to wonder how much stock to put into the claim that looks tell you anything about reproductive fitness. It isn't exactly as if the typical mother of 10 is or ever was a potential Hollywood starlet either.

[And on an unrelated note, an introduction - I'm GNXP's newest guest blogger. My educational background is actually in economics and law, so my contributions will tend to take a "lay" approach to issues of potential interest to GNXP readers. They will also, at least in the near future, be few in number - I am entering the Army to attend basic training and then Officer Candidate School shortly after the new year.)

Monday, December 18, 2006

A home paternity test?   posted by the @ 12/18/2006 08:21:00 PM

I left a comment on a hilarious post at GNXP-SB in which I suggested the near-term feasibility of a disposable home paternity test.

I can pretty confidently predict that we are less then 5 years from having the technology for a *disposable* home paternity test kit.

Matt was skeptical, and outlined his reasoning in a post here.

An exercise for GNXP readers in the comments thread: is a home paternity test feasible as outlined in this discussion?

Update: Really more important than the "ha ha" home paternity test issue, and the guess what I'm thinking challenge, is the issue of cheap and easy DNA profiling. Assuming I'm right and this is feasible soon, you can expect to start offering up a DNA sample at many more occasions. Previously I predicted and welcomed a universal DNA database[1 2].

Some background:

* The FBI database (CODIS) uses 13 loci to uniquely identify individuals.
* Betagenetics sells home kits (mail in samples). Their advertisement suggests they use 16 loci for more reliable testing.
* The loci tested are STRs - short tandem repeats - alleles of which are discriminated by size.
* Paternity testing appears to involve the comparison of the child, the mother, and the putative father.

I specifically mention CODIS/FBI to point out that there are intermediate applications of the underlying technology which would drive their development -- a disposable DNA profiling kit.

Eventually, whole genome, single molecule sequencing will be possible for negligible costs -- imagine functional nanopore sequencing. Developed into a disposable package, this would a paternity test -- among other things.

In the intermediate-term, is a disposable paternity test feasible?

Flynn on the Flynn Effect   posted by DavidB @ 12/18/2006 03:53:00 AM

From today's UK Times:

It is a common refrain, repeated in response to every new television reality show and every bumper crop of school exam results: society is dumbing down. Scientists have long argued the opposite, pointing to the now widely accepted "Flynn effect", which shows that over the past century average IQ scores have improved across the developed world, irrespective of class or creed. Now the man who first observed this effect, the psychologist James Flynn, has made another observation: intelligence test scores have stopped rising.

The full report is here. There won't be anything very new for regular GNXP readers, but it is useful that the probable levelling out of the rise in IQ scores is getting some mainstream media attention.

Sunday, December 17, 2006

Now It Can Be Told   posted by gcochran @ 12/17/2006 11:00:00 PM

John and I have an article out now on Neanderthal introgression: Dynamics of Adaptive Introgression from Archaic to Modern Humans. It's in Paleoanthropology
The major point is that Neanderthals and modern humans were probably interfertile and most likely interbred - and that we would then have picked up most favorable Neanderthal alleles. Which may have something to do with the cultural ' big bang' that happened not long after.

The argument relies on a simple result of population genetics, due to Haldane - that the probability of success of one copy of a new favorable allele is 2s, when s is the selective advantage, much higher than that of a neutral allele.

As far as I know, this conclusion has not been published before.

You have to wonder why.

Dept of dog bites man: hot chick geeks   posted by agnostic @ 12/17/2006 08:46:00 PM

Oh, of course it's surprising to see a hot girl blathering about science fiction in a wine bar!

Lately Razib's been taking a lot of heat for posting a totally harmless observation that he saw a girl, whose physical attractiveness was in the top 2%, prattling on about science fiction books in a locale where people are supposed to put on their best "I'm cool" face. My initial response is here, but there were several more responses to the original post that completely missed the mark (responses so far from: retrospectacle, bushwell, aetiology, pharyngula, ethics in science, and zuska). So, I figured I'd post a more elaborate rejoinder, chock full of logic and data to counteract the largely fact-free emoting thus far. In brief, Razib was right to be surprised -- surprise!

Rationality and facts below the fold...

Razib's original shock was the result of applying Bayes' Theorem to a real-world situation. Let Hf = "a person X is a hot female," where "hot" indicates top 2% status, and S = "a person X is a hardcore sci-fi geek." Razib heard some babbling about sci-fi first, and then made an unconscious guess / assumption about how probable it was that the speaker was a hot girl. In the above symbols, he computed P(Hf | S) = P(Hf ^ S) / P(S). Now, P(Hf) is easy to calculate: in the 15-64 age group, the male : female ratio in the US is 1 : 1 (cite), and Razib said the girl was in the top 2% for looks, so P(Hf) = 0.01. Not surprisingly, there are no easily found data on the percentage of sci-fi geeks who are also hot girls. I did, however, find lots of data on the sci-fi geek / female intersection. In any event, the only case where such Bayesian reasoning would have been not empirically worthwhile is where hot girl status and sci-fi geek status were independent. We'll look first to see if girl status (hot or not) and sci-fi geek status are independent, and then look at how introducting hotness would affect the results.

I know it will come as a Bayesian shock those who just landed here from Mars, but sex and sci-fi geek status are not independent: males are clearly overrepresented. This is true not only for the readers and consumers of sci-fi but for the producer-creators and editors as well. It is even more true for closely related fields like role playing games (RPGs) like Dungeons & Dragons. This is so obvious that I enumerate the data at the end, where "dog bites man" material belongs. Let's first ask why the observation offended so many? Perhaps on hearing that someone correctly applied Bayesian reasoning to accurately predict whether female X was hot or not given her hardcore sci-fi geek status, she felt she would be assumed to be non-hot by others if her nerd status were known. However, this is no cause for concern, since the most accurate guess we can hazard about a girl's looks is based on just looking at her. If female X is top 2% hot, she will be in no jeopardy of being thought average or ugly simply because she is a huge sci-fi geek.

Another complaint was that Razib was really trying to say he was surprised that an intelligent girl was hot. Of course "intelligent" and "sci-fi nerd" aren't interchangeable, despite overlap. Compare: "I overheard X talking about their business trip to Tuscany, and how well the PR campaign with Vespa was going -- you'll never guess, but X was a hot girl!" In fact, I wouldn't be surprised at all. The median IQ level of PR execs and sci-fi fans is likely not appreciably different, but I'm open to reading data to the contrary. This situation produces no surprise since females are well represented in PR, including quite attractive ones. As Dennis Mangan pointed out, attractive intelligent girls are more likely to join PR-type fields since their good looks are more of an asset there compared to geeky occupations. No one who's been to college will be surprised that there exist smart females, nor that the male-female ratio is close to even as long as one doesn't stray too far from the mean (say, within 1 SD). What's shocking is that this girl had atypical interests even for intelligent females, rather than say, express a fascination with the haute cuisine of the diverse French provinces.

Yet another complaint was that Razib's correct use of Bayesian reasoning would perpetuate a particular stereotype, i.e. that sci-fi geeks and hot people don't overlap much. This stereotype might keep away prospective sci-fi geeks if they were also hot: if the sci-fi community has a deserved reputation for being disproportionately unattractive loners, the hot people might want to steer clear of this hobby. Thus will the stereotype perpetuate its existence. But what, really, is the alternative -- to lie to prospective geeks, or perhaps just keep mum? If so, the prospective geeks will figure out sooner or later that joining a Star Trek club will kill their reputation and leave posthaste, so discussing the stereotype openly will not result in fewer geek members than hiding or denying the stereotype. How did the stereotype begin, then? Did someone roll the dice and the result came up that "sci-fi nerds shall consist almost entirely of non-hot people?" Hogwash. There's something about the hardcore sci-fi existence that appeals to a certain group of people, damn few of whom are hot -- perhaps because sub-hot loners turn to certain hobbies for want of a coterie of same-sex buttkissers and opposite-sex conquests, in virtue of not being very physically attractive while growing up. Similarly, death metal fans are not randomly drawn from the population, and they're biased such that we'd be surprised if we met a Miss Congeniality / Southern Belle type at a death metal concert.

Considering the various complaints, I can't find any reasonable objection to Razib's observation. Again, it must be that one of the faulty objections discussed above, or similar ones, is the real reason that so many got so miffed so easily. It can't be that they actually thought a hardcore sci-fi geek was equally likely to be male as female, let alone introducing the hotness variable. But just to be thorough, here is some data I discovered with ease by Googling. The results won't shock, so if you take them for granted, you'll only be bored by reading further. They are included only to show that dishonesty in the service of calumny will not be tolerated by those of us who still care about keeping "oughts" out of the process of empirical observation. We will call "bullshit."

Starting with the creators and editors of science fiction, here is a long list of stats. Let's consider a few examples. Men and women make up 58% and 38%, respectively, of the Science Fiction Writers of America, and 79% and 21% of the Horror Writers of America. Men and women account for 74% and 26% of professional-market editors for sci-fi-related literature. Men are overrepresented among the winners of nearly all major sci-fi literature awards, whose winners are typically 75% male. (The sole exception is the radical feminist, ideological Tiptree Award.)

As for reader preferences, this study of middle schoolers found notes:

The females reported a stronger interest in Romance, Friendship, Animal Stories, Adventure, and Historical Fiction, while the males reported stronger preferences for the categories of Sports and Science. In addition, the results indicated that the male respondents had a stronger preference for non-fiction than did the female respondents.

This report on the preferences of high schoolers has two tables (Tables 8 and 9) that summarize what genres boys and girls indicate as their favorite. Three surveys were done: one in 1982, another in 1990, and a final one in 1997. The authors don't report all data, just those genres that garnered at least 10% of the responses. Across all three surveys, "science fiction" and "fantasy" never met this threshold among female responses, while "romance" and "mystery" did all three times. At the same threshold, boys consistently liked "adventure" and "sports" -- "science fiction" made the cut twice, and in the year it didn't, "fantasy" did. If we collapse "science fiction" and "fantasy," then boys consistently like such books. The authors also note yet another special case of greater male variance: "Boys show more diversity in the genres they like," and indeed a comparison of Tables 8 and 9 shows that male preferences are more evenly distributed across various genres than female preferences, which are more bunched around the most popular genres. That jibes with most people's personal experience: when you're on the metro or subway, take a look and you'll notice that females tend to conform to a single norm (recently, The Da Vinci Code); whereas males are more fragmented, preferring the manly genres of war, sports, and cars, as well as wimpy geek fare such as sci-fi and popular science.

This review from the American Library Association notes that:

In terms of gender differences, boys showed a markedly higher interest for science, science fiction, nature, and magazines than girls, while girls' responses were considerably higher than boys' for mystery, historical fiction, and friendship and families. The small sample size [N=23; agnostic] makes these differences slightly suspect, but the similarity between this and other studies is noteworthy.


Greenlaw (as cited in Todd 1988) worked with slightly older children (grades 4 to 12). She gave a questionnaire to 1,240 students, asking what they liked to read and how they chose their books. The data were classified according to genre, with the results showing an overall preference for mystery, fantasy, jokes/humor, adventure, and sports. There were marked gender differences as well. Boys chose science fiction, sports, how-to-do-it, and jokes/humor more than girls, while girls more often selected mystery, romance, biography, fantasy, and—by far the greatest gender distinction—poetry.

Most of the other studies reviewed corroborate the main story, but their publication date was pre-Women's Liberation. The fact that they largely agree with the picture afterward shows that changing sex roles in society will not make girls freely choose to read sports, science fiction, and war stories with the same frequency as boys. Badgering and compulsion only are suitable solutions to engineering an equality of preferences.

Nor is the pattern unique to the US. Here is a review of studies from New Zealand, whose apt sub-title is "Identifying the reasons why female high-school students do not like reading science fiction books." If we look at the oldest students (Form 6 = 16-17 y.o.s) in order to best gauge adult preferences, Appendix Item 5 shows that science fiction books rank 2nd of 13 in popularity among boys but 11th of 13 among girls.

Branching out from books, this review on movie preferences shows that males and females are also split when it comes to sci-fi on celluloid. Subjects (264 males, 296 females) were asked to list up to 15 of their all-time favorite movies; the movies were then grouped into Top 25 and All Movies categories. Table 7a shows the Top 25 movies as judged by males and females. The largest sex difference is in "romance" (31% of Top 25 movies rated by females but 4% of those rated by males), and the next largest is in "science fiction: these made up 20% of Top 25 movies rated by males but 4% of those rated by females. As for all movies listed by males and females, "science fiction" shows the largest sex difference: these account for 10.7% of male responses but only 4.6% of female responses.

I'll confess that I'm not very into sci-fi or fantasy, and as I've done this research, I got the hunch that "science fiction" may be a bit broader than non-afficionados assume. It seems like the sex differences should be even greater than the admittedly large gap, but perhaps there are less geeky sub-genres of sci-fi / fantasy that appeal to girls. So I looked at the ultra-geeky sci-fi / fantasy hobby of role-playing games (RPGs) like Dungeons & Dragons. Surprisingly, this was the only area that had easily retrievable market research reports. This summary of market reports confirms that hunch: the study with the most controlled sampling found that 81% of RPG players are male (two less controlled studies found 77% male and 91% male). In one of the less controlled studies, it seems that females were much less likely than males to perform the uber-geek role of DM (I looked it up too; it means "dungeon master," the person who directs the course of a particular game):

Although 9% of the respondents were female overall, just 4% of the respondents classified as DMs were female. Furthermore, 30% of female respondents indicated that they never DM, while just 7% of male respondents indicated this. For the most part, DMing currently seems to be a male occupation.

Lastly, what about the sex make-up of blogs on niche topics? Here is a recent survey by Bloggasm (N = 302 -- pretty big sample for niche bloggers!). Overall, niche bloggers are 69% male. Males exceed this value for the following categories (some of these excessive values may not be significant, including sci-fi): comic books, gadget / tech, music, gay / homosexual, movie / film / TV, sports, law / legal, sci-fi / fantasy / horror, conservative, military, poker, science, and cars. Though males were below 69% for the other categories, females were only clearly overrepresented in the following categories: sex, gossip / fashion, regional interest, feminist, and food. I'll leave it to the attentive reader to discern the patterns.

Thus, investigating the problem from multiple angles converged on a single, obvious conclusion: males are much more likely than females to be interested in geeky hobbies like sci-fi. Anyone for whom this is a novel insight is simply not a good observer of the world around them. Considering that the face that launched a thousand rants was top 2% in good looks only makes the case more surprising: even if hot people, controlling for sex, did not shy away from sci-fi (a dubious assumption), we would still be left with one heck of a statistical rarity.

Variability and determinism   posted by p-ter @ 12/17/2006 03:22:00 PM

This whole Malcolm Gladwell hoopla (which may very well continue-- see his comment here for evidence he still doesn't understand what he got wrong) is proof that statistics is a tough thing for even intelligent people to wrap their heads around. I was reminded of this the other day when trying to explain the concept of heritability. Godless, back in the day, wrote an excellent post on the topic, and I'm only going to rehash a couple of the points in that post.

First, let's consider the study Gladwell cites on car dealers (how this will relate to heritability will become apparent later). The sample consists of a number of individuals (about whom we have collected several pieces of information--their race, age, gender, etc.) along with the price they were quoted on a car. These prices are all different; you could describe the distribution of the prices by its mean and the variance around that mean. The goal of the statistical analysis is to find variables that predict where a given individual's price will land in that distribution. If we look at the population at a whole, we might find that prices for a given can range all over the place, from, say, $500 to $5000-- a whole order of magnitude. To find the effect of a single variable in all that data might be difficult without looking at a lot of people.

But now let's consider the prices given to men in their late twenties, who all dress well and have similar occupations. In this sample, maybe the quoted prices range from $1000 to $1500. There is much less variation in this sample. Assume for the sake of argument that your race perfectly predicts what price you get in this sample, i.e. that white people get price X and black people get price Y. Then all the variance in the sample can be attributed to a single factor-- race. You could say that, in this sample, race accounts for 100% of the variance in price.

But can this finding then be attributed to the population as a whole? That is, could you say that, in the general population, race perfectly determines price? No, of course not-- in the general population there are older people, women, people from different educational backgrounds, etc., and all these things contribute noise (i.e. more variance) to the data. So race will obviously account for much less than 100% of the variance (the exact amount would have to be tested).

Now on to heritability. Let's consider a trait like IQ, whose distribution again has an mean and a variance. Traditionally we want to break the variance of this distribution into two components-- the component due to genetics and the component due to "environment" (i.e. not genetics). The (broad-sense) heritability of the trait is then the genetic variance over the total variance, or the percentage of variance attributable to genetics.

The crucial point is this: heritability is a property of a trait and a population, not of a trait alone. Like race perfectly determined price in the population of upper-class males but not in the population as a whole, if we measure IQ in a population that includes extremely poor individuals, extremely rich individuals, victims of child abuse, and drug addicts, all these things are going to inject additional noise into the data, decreasing the heritability. But if we limit ourselves to upper class individuals who all treat their children similarly, the heritability will be much higher.

This has a consequence that most people aren't aware of--the more we reduce difference in environment between people, the more heritable IQ will become. Presumably, if everyone had exactly the same environment (which is not likely, of course), the proportion of variance due to genetics in the population would approach 100%, while the absolute variance itself would decrease. Heritability is not fixed; it's an attribute of a trait and a population.

Saturday, December 16, 2006

Sharp Blue & analogies   posted by Razib @ 12/16/2006 01:09:00 PM

The whole Razib-is-a-pig blow up resulted in me finding Sharp Blue, a smart blog. Check out his post "Heraclius, Persia and the Arab Conquests," I have issues with it, but anyone who links to the term Dominate gets props.

Also, over at my other weblog I chided Ali for using The Thirty Years War as analogy for sectarian conflicts looming in the Middle East. My main issue is that I don't think the public, even the literate news-watching public, really knows enough about the The Thirty Years War to convey new or novel information. The emphasis is on added information. I think most would get a sense that The Thirty Years War was a massive sectarian conflagration. So, the implication is that we are looking at a massive conflagration in the Middle East. First, I could object that this is a bad analogy in terms of the scale, The Thirty Years War was the World War of its time, but perhaps that's what Ali is implying. Nevertheless, the main issue is that I don't think that for most people it adds anything aside from being a exclamation point reiterating what we already know. In other words, sometimes (most of the time?) analogies are essentially rhetorical devices, kind of like stars and rocket ships in Space Opera, they're background props which enable the story to move forward. On my other blog I said that "For an anology to work like so: X → Y, you need to know a about X to map inferences onto Y, for the nature of Y is unfamiliar and X is familiar." In other words, you have to have a familiar base of information from which you can map structures and data toward a target which is novel or unfamiliar. When I use an analogy on this weblog I try often to attempt this, because many readers here know a great deal about a, b, c, etc., but very little about 1, 2, 3, etc., though they wish to know more about 1, 2, 3. Analogies are an aid to precise conceptualization of new ideas or terms. For example, if I met an evangelical Christian and they asked me what a mosque was, I would use some analogy to an evangelical church. Now, I could start from the basics and explain all the details of the Islamic religion, the role of mosques, prayer leaders and communal worship, but it seems obvious that much of this information can be conveyed by analogy. To this, Ali responded:
so your critique is not that the analogy is wrong but that "the people" don't know enough about the 30 years war for the analogy to be relevant?

that's the nerdiest critique of an analogy i've ever seen.

If you know me well you'd know of course that I don't take "nerdy" as some insult or take down. There is a role for nerdy and non-nerdy in the world, and as I noted in the follow up comments there is a little space for more nerdiness in this world, especially in public policy. In terms of substance what would I offer is that instead of focusing on wars from the 17th century when the average American can barely remember which century Lincoln lived, something from World War II, or perhaps sports or what not, would transmit more genuine informational structure across the two concepts. You can't get something from nothing.

Better living through salt   posted by p-ter @ 12/16/2006 10:35:00 AM

There's an interesting article in the NY Times on the campaign to iodize salt in an effort to raise IQ.
Worldwide, about two billion people - a third of the globe - get too little iodine, including hundreds of millions in India and China. Studies show that iodine deficiency is the leading preventable cause of mental retardation. Even moderate deficiency, especially in pregnant women and infants, lowers intelligence by 10 to 15 I.Q. points, shaving incalculable potential off a nation's development.
Comic strips starring a hooded crusader, Iodine Man, rescuing a slow-witted student from an enraged teacher were handed out across [Kazakhstan].

A logo was designed for food packages certified to contain iodized salt: a red dot and a curved line in a circle, meant to represent a face with a smile so big that the eyes are squeezed shut.

Also, Ms. Sivryukova's network of local charity women stepped in. As in all ex-Soviet states, government advice is regarded with suspicion, while civic organizations have credibility.

Her volunteers approached schools, asking teachers to create dictation exercises about iodized salt and to have students bring salt from home to test it for iodine in science class.

Ms. Sivryukova described one child's tears when he realized he was the only one in his class with noniodized salt.

The teacher, she said, reassured him that it was not his fault. "Children very quickly start telling their parents to buy the right salt," she said.

Friday, December 15, 2006

I am a conservative   posted by Razib @ 12/15/2006 09:13:00 PM

I'm a little tipsy right now (fair warning). An 11 hour day, 2 hours past its decent termination due to unexcepted events will necessitate such an occurrence. But let me confess something, I am now a much more confident and confirmed conservative and "man of the Right" than I was 36 hours ago. After being slammed by several fellow ScienceBlogers, I am at peace with my political orientation (the post which started it all). For the past few years, since I voted for Kerry in 2004, I have been in a limbo. The Right is not the Right, and the Left is still what it always was. And I seek. I sought. And yet the pact with Satan must be made on some day when the bill comes due. And now I've come to renew my contract, the personal is the political. As my friend Chet Snicker noted, I have a weakness for female beauty, it is a sin in which mine eyes indulge, a glory beneath which I shudder with awe. In it I do see the face of God in whom I do not believe. There are many joys and pleasures in my life, sweets which makes the journey tolerable. Books, conversation, drinks, food. And yes, beautiful women! As I told a friend, if the feminist Left bans due reverence and respect to female beauty (I don't imply here omnipresent and crass hooting & hollering, a fixation upon sex and copulation) 95% of males will vote Republican if the secret ballot still holds. Humans will remain human, that is all they are capable of, even if they be sinners. Gnothi seauton? No, know they friends! Let us climb the hill together and not dance to the tune of the shadows cast by our egos.

Thursday, December 14, 2006

Idea scultping   posted by Razib @ 12/14/2006 09:30:00 PM

Below I suggested that a modest base of knowledge is simply a necessary precondition for smelling crap thrown at your door in some fields. The natural sciences are pretty contingent, the interlocking set of facts have necessary relations so that you can often intuitively "fill in the gaps" and recognize people trying to pass one over on you. There are of course limits to this, most people don't understand Quantum Mechanics, and intuitive physics and folk psychology can be hard to get past. But in something like history or international affairs the necessary relations between the facts are more difficult to establish, and isolated and seemingly unrelated pieces of data float before you in an amorphous mass. It is easy to make mistakes even if you are a specialist, I just read a 1,000 page history of the Crusades and I was a bit irritated when the author confused Nestorian Christians with Jacobites & Copts multiple times. But this author's focus was on medieval Europe, the details of Middle Eastern religious history were outside his domain.

And yet just because theoretical constructs are wobbly and flimsy in history or international affairs does not imply that the full sample space of possibilities is at our beck & call. Below jaim klein offered: "

Malcolm Gladwell gets a course in statistics   posted by p-ter @ 12/14/2006 09:08:00 PM

There's been a somewhat ill-tempered back-and-forth between Steve Sailer and Malcolm Gladwell on the subject of race and racism in the last few days (you can start in the middle with this post and move forwards and backwards from there to get the whole story). The crux of the debate is this story:
In Blink, I tell the story of a study done by the law professor Ian Ayres. Ayres put togother of group of young men and women--half white and half black--and sent them to 242 car dealerships all around Chicago. All were attractive, well dressed, and well-educated. All had the same cover story: that they were professionals from a wealthy part of Chicago. All pointed to the lowest-priced car on the floor and said--"I'm interested in buying this car." Ayres's question was--all other things being equal, how does skin color and gender affect the initial price quoted by a car salesman? His results: white men, on average, got quoted a price $725 above invoice, white women got quoted a price $935 above invoice, black women $1195 above invoice, and black men $1687 above invoice.

Is this discrimination (in the pejorative sense of the word) or is this price discrimination (a morally neutral action: charging each group what it's willing to pay)? Gladwell claims the former, Sailer the latter. The debate is at the links above, so go read it yourself. What I want to focus on is this comment from Gladwell:
Let's go back to the study. The male and female, black and white testers who Ayres sent out to car dealerships all gave the salesmen the same set of facts. They were all roughly the same age (late twenties). They all drove the same kind of car into the lot. They all dressed neatly and conservatively. They identified themselves as college-educated professionals (sample job: systems analyst at a bank). And they said they lived in the upper-income Chicago neighborhood of Streeterville. The car salesman, then, has several pieces of data from which to create his stereotype. He has the gender, race, age, occupation, educational level, and class (or at least a class proxy) of his potential customer. And what did he do? With the black men, he zeroed in on age and race, and ignored everything else.
Why [are the car dealers] so intent on zeroing in on what is only one of many available and relevant facts about the customer? The short answer to that question, I think, is that this is what racial prejudice is: it is the irrational elevation of race-based considerations over other, equally or more relevant factors.
It should be obvious that the imputation of racial prejudice here is absolutely absurd (as was immediately pointed out in the comments). Here's why:

Let's take a look at all the factors Gladwell claims are available for the car salesman to consider: gender, race, age, occupation, educational level, and class. Now let's consider the sample he has to work with (limiting ourselves to black males, as Gladwell does: "with the black men..."). Sex: all male. Age: all late 20s. Occupation: all professionals. Educational level: all college educated. Class: all well dressed and wealthy.

In fact, the only factor that varies in this analysis is race (where he gets the thing about age, I'm not sure). This isn't an accident; the study was explicitly designed that way. So is it at all surprising that race is the only factor that influences anything? Of course not! In fact, when you include women in the analysis, you find that gender plays a role as well (and you see a possibly interesting differential role of gender in the two races). If other variables were included in the sample, they too would likely have been found to play a role in dealer pricing. But they were held constant*. That's why they call it a variable, my friend--it has to vary.

*It occurrs to me that I worded this very poorly originally, though I suppose everyone rearranged the sentence for me unconsciously.

Tools for a better genomics   posted by p-ter @ 12/14/2006 05:41:00 PM

Nature Biotechnology has a primer entitled "What is a support vector machine?" (quick answer: a statistical method for classifying things) for those into that sort of thing. It's a very readable, non-mathematical introduction to the topic. Genomicists are generating more data than has even been seen before in biology, the capability to analyze it is going to advance in leaps and bounds in the coming years.

Foreskin: hot or not?   posted by p-ter @ 12/14/2006 05:28:00 PM

John Hawks casts a skeptical eye on the "circumcision reduces HIV transmission" story. Think how embarrassing it would be if, under pressure from Western governments, African nations start chopping off foreskins willy-nilly only later to find, well, hm, maybe it's not that effective after all. The outrage that would result from that is in itself reason enough to be careful about rushing into things.

Wednesday, December 13, 2006

In praise of calling bullshit   posted by Razib @ 12/13/2006 09:04:00 PM

The comment thread below got me thinking. About 3 years ago I told Randall Parker that I didn't really want to talk too definitively about Islam because I wanted to know more and offer a more thorough and nuanced opinion. Over the years I realized that I was being naive, I'll be dead before I am totally confident about talking about some topics. In regards to Islam my atheism means that I take an instrumental attitude toward knowledge acquisition. I don't think Muslim thinkers are really talking about anything sensible or coherent when they spend 50 pages on tawhid, anymore than I think the Athanasian formula exhibits genuine sense, but I understand that the quasi-concepts that are encapsulated by these words are significant to the people who devote their lives to them. The more I read the more I notice that my ability to discern bullshit is increasing at a far greater rate than my genuine original positive insight. I know what I do not believe more than what I believe.

Consider the following passage from The Coming Anarchy by Robert D. Kaplan:
A recent visit to Azerbaijan made clear to me that Azeri Turks, the world's most secular Shi'ite Muslims, see their cultural identity in terms not of religion but of their Turkic race. The Armenians, likewise, fight the Azeris not because the latter are Muslims but because they are Turks, related to the same Turks who massacred Armenians in 1915. Turkic culture (secular and based on languages employing a Latin script) is battling Iranian culture (religiously militant as defined by Tehran, and wedded to an Arabic script) across the whole swath of Central Asia and the Caucasus. The Armenians are, therefore, natural allies of their fellow Indo-Europeans the Iranians.

When I first read this in 2000 I was dubious about some of the details. A "Turkic vs. Iranian" culture war across Inner Asia? Armenians aligned with their fellow Indo-Europeans, the Iranians? There is obviously a lot of truth here.

1) It is probably true that Azerbaijani Turks are the most secular Shi'ite Muslims in the world. 70 years of Soviet rule will do that to you.

2) I know now that the Azerbaijani government does cultivate relations with Turkey based on common pan-Turkism. Azerbaijan looks to Kemalist Turkey as its ideal.

But there are some serious problems with Kaplan's analysis, some of which I saw then, and some of which I know now. First, there is no "Indo-European" bond between Armenians and Iranians, the common linguistic affinity goes back thousands of years, at least 4-5 thousand years. Iranian languages are closer to the Indo-Aryan tongues of northern India than they are to Armenian. On the other hand, there is a pan-Turkic ethnic identity sealed by a mutually intelligible swath of Turkish languages/dialects stretching from Western China to Turkey. Kaplan is attempting to establish a false dyad between pan-Turkism and non-pan-Turkism. Another major issue is that there are over twice as many Azeris who live in Iran as who live in Azerbaijan. Azerbaijan itself is simply the portion of Iran populated by Azeris which was annexed by the Russian state, the heart of Azeri culture is northwest Iran, in particular the city of Tabriz. So when Kaplan says that Azeri Turks are the most secular Shia in the world, he's wrong. That is, he is simply not telling the truth. I simply can't believe that he doesn't know there are many religious Azeri Turks in Iran, so he was simply trying to pass this paragraph off to an ignorant readership. One of those Iranian Azeri Turks is the current Grand Ayatollah Ali Khamenei! Here Kaplan is trying to emphasize the secularity of the Azeri Turks, but he neglects to point out that the operational leader of the Iranian cultural bloc is an Azeri Turk! Khamenei was Supreme Leader when Kaplan was writing, so he is either deceiving or ignorant. Additionally, if you do the math you see that over 1/4 of the Iranian population is Turkic. In Sons of the Conquerors by Hugh Pope the author notes that Azeri Turks continue to maintain their traditional roles in the military of the Iranian state, and are well represented in the elites from the Supreme Leader on down to the business class. The Iranian nation may at its core be Persian, but Persian speakers form only 60% of the population of Iran.

On this particular topic, the role of Azeris within Iran, I am especially motivated because it seems to me that people are playing shell games with an ignorant public due to ideological motives. I am particularly skeptical of the idea promoted by a few neoconservatives before the 2006 Congressional elections that the ethnic divisions in Iran could be used to fracture the nation. I criticized GNXP reader Jeff Boulier in sharp terms for keeping open the possibility that Azeris could be used to foment divisions in Iran. In our last round Jeff responded:
That doesn't, of course, mean that my opinions are not warped by my priors. I think my opinion is less likely shaped by tribal identification with my political group but, well, my beliefs about the willingness of people to engage in tribal behavior.

Jeff alludes to the fact that I accused him of accepting particular beliefs because his own political tribe espoused them. This is no sin that any of us are free from of course. But Jeff's point about the willingness of people to engage in tribal behavior is a fair one. I agree with the rough theoretical model:

* Humans are socially conformist and are easily induced into tribal behavior based on trivial differences

It follows that tribal behavior based on non-trivial differences (language, religion, etc.) is also common. Tribal behavior can also erupt rather quickly from a serene milieu. Yugoslavia is perhaps a perfect example of this. So why do I object to Jeff's high rating of the plausibility of fomenting division within Iran? Because though I accept his theoretical premise, in the context of international relations or historical events these general truths have enormous error bars. Given enough iterations these truths will beat random expectation, but in any given situation they are very likely to be wrong. And, when you add in specific contextualizing facts a very different inference can emerge. Consider the following....

a) a person's grandparent is Polish, consider the following variable

b) their name is Levy

You are probably savvy enough to know that there is a big difference between Polish Jews and Polish non-Jews. Just saying that someone's ancestor is from Poland might give you a general theoretical model of how they would behave and view the world, but specifying the name makes crisp specific inferences and reduces your error.

In the case of the Azeris of Iran, they are an ethnic minority in a nation where the dominant culture is that of the Persian majority. From this one might conclude that they are resentful of their place. The model of tribalism as a natural property of humans which can be exploited in international relations suggests that inducing division might bear fruit. But, add some more information into the model. Azeris are dominant within the military. The most powerful individual in the nation is an ethnic Azeri. The previous president was of part-Azeri heritage, and Azeris are a prosperous community. Differences of language and ethnic identity still remain, but when you look closer you see that those differences do not take succor from a ground of resentment, segregation and marginalization. As I have pointed out before Turks have ruled Iran for most of the past 500 years (and much of the previous 500). Azeri Turks founded the modern Iranian Shia state during 16th century. I believe these details render the plausibility of a short term expectation of ethnic conflict in Iran to be nearly zero. This does not mean that long term chances of conflict are trivial, but the key is that proximately for public policy considerations this should be taken off the table. Now, the question is whether those who propose this solution actually believed that such division was ever possible, or whether they were employing a coarse theoretical framework because they knew no better. I suspect the former because it seems to me that there were ideological considerations at play, and the polemicists knew that no one was going to check their facts and call bullshit on them.

So back to giving a "nuanced" picture of how the world works. I think that all things are possible under heaven sociologically. Just because today homosexuality is not considered acceptable within Islam does not mean I believe in the future it won't be. Nevertheless, we shouldn't expect a 5 year transformation. Similarly, just because ethnic conflict in Iran is not likely within the next few years does not mean that in a generation such a conflict won't emerge. Just because today the Salafi terrorists call takfir (i.e., non-Muslim) on the Shia does not mean that in the future differences will be set aside because of a "more accurate" interpretation of the Islamic religion. And finally, though evangelical Protestants might naturally be averse to the Mormon Mitt Romney purely on theological grounds in this election cycle, this does not mean that within a generation they might not be as accepting of Mormons as they are of conservative Catholics in the present. It takes time. The key is to not assume that people have changed their minds, it is to remember that with enough time passed they will have forgotten that they ever believed otherwise. You see, white Americans in the southern United States were never racist in the 1960s, it was only their neighbors. The red-hot evangelical fervor for the pro-life movement is simply a fundamental part of their Christianity, forget the fact that Roman Catholic organizations were frustrated at the relative lack of interest from Protestant groups in the anti-abortion in the wake of Roe vs. Wade. Suicide bombers are not suicides, but martyrs. Citizens of a hostile state are not civilians but soldiers by virtue of voluntary participation in the polity. And so on. Self-delusion takes time. Until time can work we must always keep in mind the pattern of delusion.

The mixed race experience   posted by amnestic @ 12/13/2006 08:08:00 PM

MAVIN Foundation builds healthy communities that celebrate and empower mixed heritage people and families.

Our projects explore the experiences of mixed heritage people, transracial adoptees, interracial relationships and multiracial families.

Freaks!   posted by p-ter @ 12/13/2006 04:35:00 PM

This is almost an X-Men worthy mutant: the inability to feel pain. The researchers in this paper found three inbred families in Pakistan with the trait. The description is fascinating:
The index case for the present study was a ten-year-old child, well known to the medical service after regularly performing 'street theatre'. He placed knives through his arms and walked on burning coals, but experienced no pain. He died before being seen on his fourteenth birthday, after jumping off a house roof. Subsequently, we studied three further consanguineous families in which there were individuals with similar histories of a lack of pain appreciation, each originating from northern Pakistan and part of the Qureshi birdari/clan. All six affected individuals had never felt any pain, at any time, in any part of their body. Even as babies they had shown no evidence of pain appreciation. None knew what pain felt like, although the older individuals realized what actions should elicit pain (including acting as if in pain after football tackles). All had injuries to their lips (some requiring later plastic surgery) and/or tongue (with loss of the distal third in two cases), caused by biting themselves in the first 4 yr of life. All had frequent bruises and cuts, and most had suffered fractures or osteomyelitis, which were only diagnosed in retrospect because of painless limping or lack of use of a limb. The children were considered of normal intelligence by their parents and teachers, and by the caring physicians. One author saw and reviewed all six affected individuals and their families.
They then mapped the trait to mutations in SCN9A, a component of an ion channel expressed in pain-sensing neurons. Not only is this study really cool, but it could possibly lead to new painkillers or methods in anesthesia. Hooray for inbreeding!

ADDENDUM: Nick Wade has an article on the study.

Tuesday, December 12, 2006

In answer to my critics   posted by Razib @ 12/12/2006 11:31:00 PM

There were some rather irritable responses to my new Sunni vs. Shia post. I deleted the more childish ones ('just cuz you act smart doesn't mean you are!'). Jaime Klein's comment was funny, but bbartlog's response was even more humorous. I am not going to say much more on this topic than this: Chris Rock used to explain why his female friends were all good looking, "Cuz you never know...."

Virgins without shame   posted by Razib @ 12/12/2006 09:44:00 PM

Virgins and wannabe-virgins sound off.

Wheat from the chaff   posted by amnestic @ 12/12/2006 07:25:00 PM

To prove that someone actually blogs about even nerdier stuff than me, I direct you to the Daily Transcript to learn about the endoplasmic reticulum and how it deals with poorly constructed proteins. My only point of reference in all of this basic cell biology is that I care about eIF2alpha kinases because they provide an interesting way to upregulate some proteins in the face of a global decrease in translation. I have a pet theory that the sort of stimulation that leads to synaptic plasticity is a form of cellular stress that could locally activate some of these same processes. I recommend following his links to the introductory material. There are a lot of abbreviations to get down.

PSD95-Spines   posted by amnestic @ 12/12/2006 06:38:00 PM

The Svoboda paper in the November issue of PLOS Biology (to differentiate from the Svoboda article in the December issue) forces us to really take seriously the idea that the synapse is dynamic. It is easiest to imagine a synapse sitting with say 10 AMPA receptors and then following learning or potentiation 20 more receptors are inserted. There the synapse sits with 30 receptors, newly strengthened. The truth is that AMPA receptors are constantly being removed and replaced as are other members of the post-synaptic density. Synaptic potentiation probably takes the form of something like a brief moment when the rate of receptor insertion is greater than the rate of receptor removal followed by a return to equal rates with a larger number of receptors in the turnover pool. The post-synaptic density (PSD) is a structure containing neurotransmitter receptors of different sorts, signaling proteins, actin cytoskeletal components, and scaffolding proteins that hold the whole shoot'n'match together. PSD-95 is a scaffolding protein. It binds multiple PSD constituents including Stargazin which binds AMPA receptors.

One theory holds that PSD-95 marks the spot that AMPA receptors can cycle in and out of, so synaptic strength is set by the number of 'slots' provided by PSD-95 rather than a fixed population of AMPA receptors. The implication is that PSD-95 levels in the synapse will be more stable and could provide the mechanism for memory maintenance since high AMPAR turnover rates obviously can't do the job. But we run into a sort of homunculus problem. We have a little man that can tell the AMPARs where to go, but who tells the little man where to go. This problem is easiest if PSD-95 is planted at a synapse once and stays there without degrading. This isn't the case, though as Gray et al. show.

And how they show it is way nice. They have a form of GFP that is photactivatable (paGFP). They fuse it to PSD-95 in an expression plasmid and put it in mice's heads using in utero electroporation. I've never heard of it before either. They open up a pregnant mouse mom, pull out the uterine horn, grab fetal mouse heads in between a special pair of electric tweezers, inject their plasmids into the lateral ventricle, and give a little stimulation to disrupt cell membranes to let the plasmid in. Amazingly, it works. Although they don't mention how many fetuses they trashed in the process. One insane technique per paper isn't enough though. Once the injected fetuses grow up, a small segment of their skull is removed and replaced with a glass window so the dendrites containing paGFP can be visualized over many days in a living animal.

When you look at the dendrites you don't see anything until you blast the GFP with a laser to turn it on. Since lasers are very precise (and this technique requires the meeting in space of two different laser pulses) they are able to activate GFP in individual spines. They proceeded to activate PSD95-paGFP and measure how long it takes to disappear from the spine, thus gauging the retention time of PSD95 at a given synapse. It takes longer than GFP by itself suggesting that binding interactions help retain PSD-95 in the PSD, but it still takes less than an hour. Where does it go when it leaves? It's not time to be degraded yet. PSD-95 has a half-life of ~36 hours. Instead, it goes barhopping. If the dendrite is Bourbon St, then PSD-95 is a reveler stopping in this spine for a sec, that hotel for a minute, and on and on until the cops finally catch it and toss it in the proteasome.

If our master controller architectural component, PSD-95, isn't there directing traffic, how does the synapse maintain its strength? Well, we have a glimpse at a solution because Gray et al. studied the movement as a function of spine size. Larger spines capture diffusing PSD 95 better and they hold onto it longer. Now here is an area where my understanding is going to be a little fuzzy. In my reading, we know that spine shape doesn't seem to be much of a barrier to diffusion because GFP on its own diffused out of synapses with a half-second median retention time. However, Gray et al. go to great pains and even produce a stimulation to suggest that spine geometry can influence retention time. In one of the papers they cited (Bloodgood and Sabatini, 2006), a spine was considered diffusionally isolated if the equlibration constant between spine and dendrite was greater than two seconds. Two seconds seems negligible to me compared to the apparent retention time of PSD-95, but to be honest I don't want to take the time to deal with all of their models and equations. If anyone else wants to take a crack at it and tell me what you find, please be my guest.

So now we're back at the homunculus problem. Who is gonna tell PSD-95 which spines it should hang out at the most? We can go searching for another protein that is retained in spines longer and has a half-life of months or years. I can even think of a couple good candidates, but I think the quest is in vain. I predict that we will not find a single protein that can account for lifelong changes in synaptic strength and therefore childhood memories. I know just enough about dynamic systems now to make an ass of myself on the internet, but my feeling is that this sort of analysis is going to have to be brought to bear on the PSD. We don't need a master controller, we need a stable system-state between several constituents. I've cycled through a number of metaphors in my head, but I think maybe a decent image at least is a table with hundreds of legs cemented in the ground. You can remove and replace all of the legs over some period of time as long as you leave three or four. You could remove the table top and replace it with a new one. You could even dissolve the cement and replace it as long as you don't do all of these things at once. PSD-95 has many binding partners in the PSD. If one is removed, the structural integrity could be maintained. If you hold your friend's place in line they can go pee. If you change the guard, he can get some relief and the palace is still protected. We don't need an immortal homunculus to achieve lifelong memories.

Monday, December 11, 2006

Gee are oh double you   posted by amnestic @ 12/11/2006 08:22:00 PM

Most excitatory synapses in the brain occur on dendritic spines. Stronger synapses contain more AMPA receptors. Stronger synapses also tend to occur on larger spines. Spine size and AMPA receptor content have been linked, but never quite like this. Park et al. showed that all the things you expect to induce increases in synaptic strength/AMPAR content (calcium, NMDAR activation, theta burst stimulation) also cause localization of recycling endosomes to spines and fusion of those endosomes with spine membrane. This increases the spine surface area. Endosomes are little balls of membrane with lots of proteins stuck in them (sort of like synaptic vesicles). At least sometimes they carry AMPA receptors, so now they have a dual purpose. When they fuse with the membrane they make the spine larger and insert AMPARs at the same time.

You can ignore all the above and just take a look at these spines dancing.

The hotter points indicate that the inside of an endosome has opened up and probably fused with the cell membrane. When the white dot appears a form of long-term potentiation is being induced. I don't understand why the hotspots aren't right on the membrane instead of appearing just inside, but I can live with it.

A difference of opinion   posted by amnestic @ 12/11/2006 07:47:00 PM

This is pretty funny. Sound required.

Sunday, December 10, 2006

What Makes Us Human   posted by Razib @ 12/10/2006 11:59:00 PM

What Makes Us Human?, on The Discovery Channel:
Back in the 19th century, scientists studying microcephaly - a condition that severely stunts brain growth - were convinced that they had found an evolutionary missing link.

DEC 16 2006
@ 08:00 PM

DEC 17 2006
@ 12:00 AM

With Armand Leroi.

MAO-A and personality   posted by agnostic @ 12/10/2006 09:40:00 PM

Human Genetics has an article (Rosenberg et al 2006) on variation at the monoamine oxidase A gene -- the warrior gene -- and phenotypic personality variation in normal males. Presumably only males were chosen since previous studies (reviewed at OMIM) found a sex-by-genotype interaction, such that associations were noted in males but not females. Unlike previous studies, this one sought to uncover links between genetic variants and the full spectrum of personality traits measured by the NEO-PI (the Big Five questionnaire). In brief, no associations were found with any facets of Openness or Neuroticism; an impressive link was found between the VNTR and the facet of Agreeableness called "Straightforwardness," as well as with the facet of Extraversion called "Activity;" and a less robust link was found between haplotype and the facet of Conscientiousness called "Order."

If you read the article, I would treat as significant any result to which they've applied a Bonferroni correction to reflect 5 independent hypotheses being tested (1 per trait investigated). I assume they had their arms twisted by a referee or someone to also report corrections to reflect 30 hypotheses being tested -- 6 lower-level facets per 5 personality traits -- but the way that questionnaires are designed is so that the facets of traits like Agreeableness all intercorrelate. For example, the hypothesis that an allele correlates with being antagonistic is not independent of the hypothesis that it correlates with mistrusting the motives of others, since these facets of Agreeableness correlate with each other.

It is known that the MAO-A locus has been under positive selection*, and because its effect on phenotype is to generally make people less Agreeable, one assumes there are alleles at modifying loci that have co-evolved to keep the individual from becoming too much of a nasty SOB. In the comments to a recent post on interracial offspring at my personal blog, the subject of hybrid depression came up. Here would be an interesting case to test: if a child were born to parents from population A, in which the "warrior" variant has high frequency, and population B, in which the variant has low frequency, the kid might inherit the "warrior" variant but none of the modifying alleles. It would be like a bad cop paired with -- not a team of "good cops," in the sense of seasoned partners who serve to check the loose cannon -- but with a team of Alaskan mall cops, over whom the bad cop would run roughshod. Alternatively, the kid might inherit the "docile" variant but would also inherit the modifying alleles from the parent with the warrior variant. Thus, there would be a team of restraining cops with no bad cop to contain, perhaps resulting in an overly meek and credulous phenotype. Technically, this latter scenario should fall under hybrid vigor, since the value would be above expectation based on additive factors; I just find it hard to infuse "born sucker" with a positive connotation.

*For free full text of the article, click on "Full text (PDF)" at the link here. A replication of the finding of positive selection is here.

Organizations and cannabinoids   posted by amnestic @ 12/10/2006 03:18:00 PM

For theoretical and physiological reasons, there is a strain of neuroscience that considers the brain as something like a democracy. Consider as an example the decision that a neuron makes whether or not to fire an action potential. An action potential is sparked when the voltage difference between the inside and outside of the cell near a special portion of the axon reaches a threshold value. A given neuron receives thousands of inputs, some excitatory and some inhibitory. In a simplified view, excitatory inputs make the inside of the cell more positive, moving closer to the threshold, while inhibitory inputs move the cell further from action potential threshold. In a sense, each excitation is an 'aye' and each inhibition is a 'nay'. The axon hillock keeps a running tally of the votes and fires off a potential whenever the 'ayes have it'.

With neurons it isn't so much a sense of whether the ayes will win but when they will. How fast can the ayes get the potential all the way up to threshold? Well, if they act independently they may never get there. One of the best ways for a constituency to be heard is to all deliver the same message at once. The votes that arrive synchronously will certainly all be counted in the same tally. If I write my representative over and over again asking them to create a more rational marijuana policy, this might have some small effect on their thinking, but probably wouldn't convince them to vote my way even if I wrote them every day for 2 years. If those same 730 inputs came in all at once from different sources, the content would be a little less individual, but the policy effect would presumably be greater. That's why, even if I have my own individual perspective on the best policy, I get involved with and support larger organizations that can organize to achieve my goals.

Neurons achieve synchrony through oscillatory behavior. The most extensive study of neuronal oscillations has been in the hippocampus. If you stick an electrode into the extracellular space surrounding hippocampal neurons while rats engage in exploration of a novel space you will note that the potential fluctuates rhythmically at about 10 Hz. Neurons are most likely to fire when the extracellular potential is at its lowest (the trough). The source of these oscillations is an area of intense investigation and what is known already is more complicated than I want to go into here, but the effect of these oscillations is simple enough to understand: during the trough, many neurons are likely to fire at once. Thus, the oscillations provide an organization that neurons can join and add their voice to a larger consensus. If many of these neurons converge on a downstream target, they can greatly influence that target's firing behavior.

It has been very difficult to study these population/ensemble behaviors in the intact brain because you must record more than one neuron at once to ask whether they are synchronized. Recently a collaboration between the McNaughton and Buzsaki groups, two of the dopest labs in recording and analysis of many neurons at once, produced a report concerning the effect of cannabinoids on network activity in the hippocampus. The most prominent active ingredient in marijuana is a cannbinoid, delta-9-tetrahydrocannabinol (THC). It can bind two types of receptors in the brain: CB1 and CB2 receptors. There are synthetic agonists and antagonists that specifically affect CB1 allowing more in-depth analysis of this receptor subtype. Most of the experiments in the M&B paper were performed with a CB1 receptor agonist, but some of the effects were replicated using THC at "palliative and recreational" doses, suggesting that effects in this paper can be generalized to effects of actual marijuana use.

The major finding was that CB1 agonism (THC administration) disorganizes neuronal ensembles. The average firing rate is hardly affected. Neurons keep talking. They walk up the mall to the Lincoln memorial, but they do it one by one. This effect was initially detected as an across the board decrease in the power of oscillatory field potentials. The chants quieted down.
Crowd: Eat the cheeseburger, astro boy! Eat the cheeseburger, astro boy!
Trotter: Enough... if you're trying to start a riot, I suggest you choose a simpler chant.
Ensemble behavior can be analyzed using cross-correlograms. You use one neuron's spike as a reference, brand it as t=0, and then count the number of spikes from neuron 2 in time bins in relation to t=0. If two neurons are firing synchronously, there will be a large peak at 0 ms reflecting the large number of spikes from neuron 2 that coincide with spikes from neuron 1. Here is a rather dramatic visualization of a rat's hippocampus on a CB1 receptor agonist:

THC "destroys assembly organization". This is a very interesting subtle effect that couldn't have been detected using single neuron recordings. It doesn't effect the overall behavior of an individual neuron, but instead controls network-level phenomena. While the impulse may be to look at this report in terms of the effect of marijuana use, I think it is important to also understand that this receptor system provides the very unique potential of a tool for specifically understanding neuronal networks. Using these drugs we can begin to determine just exactly what behaviors and aspects of cognition rely on ensemble behavior rather than single neuron or simple population coding.

That said, I can't resist the metaphor. It is not clear exactly how CB1 receptor activation produces these network changes. What little is known suggest that cannabinoids may act presynaptically, perhaps reducing overall neurotransmitter release from the principal neurons of the hippocampus. It reduces their output and shuts them up. Likewise, the effect of on a drug law reform advocate is to effectively quiet their voice. In my experience, motivation, cognitive capacities, and credibility are reduced with any degree of extended use. The ability to organize and assemble is lost and some become so paranoid (imagining government lists of petition signatories and political organizers) that they refuse to speak up. To produce strong organizations capable of influencing a system, brain or otherwise, CB1 receptor agonism is to be avoided.

Lactose tolerance by a different stroke   posted by Razib @ 12/10/2006 02:10:00 PM

Convergent adaptation of human lactase persistence in Africa and Europe:
A SNP in the gene encoding lactase (LCT) (C/T-13910) is associated with the ability to digest milk as adults (lactase persistence) in Europeans, but the genetic basis of lactase persistence in Africans was previously unknown. We conducted a genotype-phenotype association study in 470 Tanzanians, Kenyans and Sudanese and identified three SNPs (G/C-14010, T/G-13915 and C/G-13907) that are associated with lactase persistence and that have derived alleles that significantly enhance transcription from the LCT promoter in vitro. These SNPs originated on different haplotype backgrounds from the European C/T-13910 SNP and from each other.

Nick Wade has an article in The New York Times.


Sunni vs. Shia - let me school you   posted by Razib @ 12/10/2006 01:21:00 PM

So the people in power still don't know the difference between Sunni and Shia. I am willing to step up for my country, I'll give anyone who cares in Washington, D.C. a free seminar on what little I know gleaned via the arduous sacrifice of overdue public library book fines (is interlibrary loan only a feature of the West coast?). The only precondition is that my airfare and accomodations are taken are of. So, I don't know the inner workings of the Usuli vs. Akbari debates in the 18th century, true that, but I do have a grasp of basic demographics and historical connections. It helps in catching people lie!

Saturday, December 09, 2006

Religion is merely a contemporary issue?   posted by the @ 12/09/2006 01:07:00 PM

NPR: Harvard Reconsiders Core-Course Requirements

Harvard University is rethinking what future graduates should be required to know. The latest plan stresses general knowledge about "how the world works," rather than academic methodology. The idea is to make classes more relevant to the modern world.

Perhaps it's just a bit of biased editing, but the NPR clip makes the opposition sound stupid. I especially note the prof who appears to be arguing that knowledge of religion is a passing fad like horses and buggies. I also have to disagree with the notion that top scientists can't be expected to teach a survey course -- at least if they're any good at teaching.

Update: In the comments, epicurus points out an op-ed by Pinker that sheds some light on the reasoning behind the criticism of the religion requirement. While I still know very little about the report in question, Pinker's criticism of the stated reasoning behind the science requirement appears apt: "My first reservation pertains to the framing of the 'Science and Technology' requirement, which aims too low." On religion:

Again, we have to keep in mind that the requirement will attract attention from far and wide, and for a long time. For us to magnify the significance of religion as a topic equivalent in scope to all of science, all of culture, or all of world history and current affairs, is to give it far too much prominence. It is an American anachronism, I think, in an era in which the rest of the West is moving beyond it.

Friday, December 08, 2006

Tech question   posted by amnestic @ 12/08/2006 12:54:00 PM

Let's see how well this 'electronic community' thing works. If anyone out there has tried radioactive amino acid labeling in hippocampal slice cultures could you pls drop me a line via the contact form or in the comments?

Sorry, guys...   posted by DavidB @ 12/08/2006 12:23:00 PM

From the BBC News Service:

A survey of more than 1,000 men in India has concluded that condoms made according to international sizes are too large for a majority of Indian men.

Full report here.

Thursday, December 07, 2006

A revolution in earwig penis biology   posted by p-ter @ 12/07/2006 12:23:00 PM

File this under: things to mention at dinner parties when describing what biologists do.

This week's Nature has an news item on an article on earwig penises (penii?). Some species apparently have two, but (obviously?) use only one at a time. But which penis to use? Some species switch it up, but some are right-penised (i.e. they prefer to use the one on the right). The paper proposes an evolutionary scenario for how the single-penised earwigs evolved from the doubly-endowed ones--through a step in which the behavioral preference for the right penis led to loss of the unused left penis (see the figure).

Splicing mpeg4   posted by Razib @ 12/07/2006 12:34:00 AM

I want to splice up the Beyond Belief talks and put up some "highlights" on YouTube. Anyone know of a freeware app for XP that'll do this? Or a cheap one that's not a rip-off in terms of functionality.

Wednesday, December 06, 2006

Failed mongrel prophet   posted by Razib @ 12/06/2006 08:39:00 PM

Since Chet told me that he was going to start his own weblog after his guesting stint is over at GNXP SB, and that that weblog would focus in part on Austrian economics, I decided to look up von Mises on Wiki out of curiosity (I was a libertarian, I know von Mises, but I am not one of the 132 people in the world alive today who has read all of Human Action). I found out that von Mises was a consultant for the Pan-Europa Movement, which was headed by one Count Richard Nikolaus von Coudenhove-Kalergi. This man was a mischlinge, his mother was Japanese! Here are some of his opinions:
"The man of the future will be of mixed race. Today's races and classes will gradually disappear owing to the vanishing of space, time, and prejudice. The Eurasian-Negroid race of the future, similar in its appearance to the Ancient Egyptians, will replace the diversity of peoples with a diversity of individuals."
"Instead of destroying European Jewry, Europe, against its own will, refined and educated this people into a future leader-nation through this artificial selection process. No wonder that this people, that escaped Ghetto-Prison, developed into a spiritual nobility of Europe. Therefore a gracious Providence provided Europe with a new race of nobility through spiritual grace. This happened at the moment when Europe's feudal aristocracy became dilapidated, and thanks to Jewish emancipation."

Being an F1 hybrid Coudenhove-Kalergi couldn't comprehend that the nature nature of genetical inheritance implies that heritable variation will be maintained. This also means that ills like racism will still be around despite admixture. Consider this description of the problems of racism in multiracial Dominican Republic:
In one Dominican family, one child can be considered black and the other white. Though siblings, their different skin colors make them two different races. Because of this unique structure, I was forced to live and deal with prejudices in new ways. I could not avoid problems by living with a "black" family. There were no black families. I had to live within a community that rejected me.

South Asians can relate to the fact that intrafamilial variance on phenotype does not negate societal preferences for particular looks.

Four Stone Hearth IV   posted by Razib @ 12/06/2006 08:21:00 PM

Yann has Four Stone Hearth IV up.

The banality of eugenics   posted by Razib @ 12/06/2006 08:10:00 PM

Armand Leroi has a new review article out which argues that neo-eugenics is here. I comment on it over at my other weblog (you can download Armand's essay at a link provided over at the other entry, I'd provide the link here but PDFs are kind of big so I might as well make you work for the bandwidth hit).

The Children of Lysenko   posted by Razib @ 12/06/2006 08:04:00 PM

ScienceBlogs has a spate of posts on the Tripoli 6 again. Check them out, spread the word. Nature has a paper out which vindicates the claims of innocence of the scientists caught up in this case.

Tuesday, December 05, 2006

Hawks on Neandertals & feminism   posted by Razib @ 12/05/2006 09:36:00 PM

Nick Wade just wrote up an article on the relationship between Neandertals and divison of labor. John Hawks hurls a cannon of a post at this hypothesis.

Dendritic spines! Good God! What are they good for?   posted by amnestic @ 12/05/2006 09:23:00 PM

We got the first half of the synaptic activity a couple weeks ago. Recall that when one neuron is inspired to talk to another one it releases neurotransmitters into the synapse. Sites of neurotransmitter release can be very precisely lined up with clusters of receptors on the other side of the divide. The receptors are highly organized with other binding and signaling proteins into a large architecture referred to as the post-synaptic density. Neurotransmitters float across the relatively short and confined chasm to the receiving neuron where they bind to neurotransmitter receptors. Binding of neurotransmitter to the receptor produces two general classes of events: 1) It causes the receptor to change shape such that it forms a channel allowing certain ions to flow through (ionotropic receptors) or 2) it causes the receptor to change shape such that enzymes on the intracellular side of the post-synaptic membrane are activated (metabotropic receptors). One transmitter, such as glutamate, can have both ionotropic and metabotropic effects. The effect is a property of the receptor, not of the transmitter. Glutamate has, for instance, three classes of ionotropic receptors with different ion permeabilities: AMPA-type, NMDA-type, and kainate-type, and three groups of metabotropic receptors: I-III.

Glutamate is the main transmitter for fast excitatory transmission, the sort of thing you measure in EEGs, the sort of speed you expect to handle information processing. The majority of this transmission occurs via AMPA receptors located in the post-synaptic density. Post-synaptic densities occur very often at the heads of dendritic spines. A neuron is a polarized cell having two types of processes: axons and dendrites. Major excitatory neurons in the hippocampus and the neocortex usually have one axon (that can branch many times to allow multiple synaptic partners) that serves as an output and many dendrites that serve as inputs. The dendrites are covered in dendritic spines. So in the image graciously provided by wikipedia below, you can see what the structure of a neuron on the post-synaptic side looks like. An axon from another neuron would likely be passing nearby and produce a presynaptic specialized structure called a bouton adjacent to the spine head. Spines are dynamic structures. You can imagine them wiggling around, shrinking and extending, widening and thinning, etc..

There have been a number of recent investigations into the function of dendritic spines. A fairly widely accepted account is of the spine as a biochemical compartment. If neurotransmitter action causes calcium to flow into a spine head you might want to keep it right there next to the synapse that triggered the influx so the inevitable enzymatic signaling functions are performed in an input-specific manner. Calcium can turn on and off a lot of enzymes, in case that's not clear. You wouldn't necessarily want it floating up and down the dendrite all willy-nilly. Kasai and colleagues have done beautiful work showing that spines of different shape and size can have different calcium compartmentalization features. They suggest that spines which restrict diffusion are more likely to undergo biochemical signaling leading to synaptic plasticity, producing subsets of learning vs memory spines. Others have called into question this role for spines, pointing out that calcium diffusion can be restricted in neurons that don't even have spines because of a high-density of calcium binding proteins and a general molecular crowding in dendrites.

The Yuste group in particular has repeatedly made this point and in a series of papers this year suggested a role for spines in electrical isolation of synaptic inputs. They adopted the use of a recently synthesized novel class of chemicals that can insert into cellular membranes and, upon precise laser stimulation, fluoresce in a voltage-dependent manner. They can thus visualize the electrical signals at spine heads and have made the suggestion, predicted by much older theories of spine function, the spine necks act as resistors reducing charge flow into the main dendritic shaft. For reasons I won't go into, isolating the electrical signals in individual spines changes the nature of excitation in neurons, allowing all excitatory signals to be simply summed instead of added up in a complex sublinear fashion. It is not clear how the electrical function works. The resistor property is neck-length dependent, but the effect on summation is not.

I have recently come across two other attributes of spines. One is that spines cause anomalous diffusion along the main dendritic shaft. I quote so as not to pretend to know too much, "Anomalous diffusion arises when the random walk performed by molecules is influenced by their previous positions in space." At face value, this is confusing because you would expect any movement to be dependent on the prior position, else I could teleport if I didn't disintegrate first, but I have been beaten into submission by fancy Monte Carlo simulations and graphical solutions of diffusion equations and I will believe whatever Santamaria et al. tell me. What I take away from it is that as important signaling molecules drift up and down the dendrite they sometimes take a sidetrip into a dendritic spine and get trapped there for a while, especially if the spine head is pretty big and the neck is pretty small. This generally makes the flow of molecules up and down the dendrite seem more erratic. A similar trapping idea comes across in a recent Svoboda lab paper. I think I want to discuss this paper separately because they do some crazy things to get the images they are working with and it can take us down into the nitty grit of postsynaptic density constituents. Related to the current discussion, they suggest that spines with larger postsynaptic densities contain more receptors and thus stronger synapses and that one way to maintain the difference between strong and weak synapses over time in the face of degradation of constituents is for larger spine heads to trap important post synaptic density molecules better. This structural method is only one possibility of how the trapping could occur suggested in the paper. It's PLOS, so go read it if you can't take the suspense.

All this thinking about dendritic spine functions got me thinking about how they must've evolved in the first place. Which function was selected for or is it possible to select for multiple functions at once? Of course, the solutions aren't mutually exclusive. I can't seem to discover what the most distant organism that has these structures is. I found one abstract that says that planarians have them. Before spines develop their characteristic shape they resemble and are called filopodia. Single-celled organisms even have filopodia, so I think that's going too far back. When did filopodia start to specialize? Where is the first synapse? On a spine or no? Does anybody out there know? If not, maybe we could reconstruct it by doing molecular phylogeny on proteins known to induce spine formation. One of these is called Shank. Perhaps there are others and a compelling story can be told about the order in which the constituents were initially produced.

Monday, December 04, 2006

The Arabs of Brazil   posted by Razib @ 12/04/2006 07:17:00 PM

Today I read an article in Slate which noted, '"Nasrallah's ultimate goal for Hezbollah, many in Lebanon believe, is the Iran model. They know it cannot be implemented right now, but, in the long run, "if Christians keep leaving the country in big numbers, as they are doing now, well, it might happen," one Lebanese gloomily told me.' First, no one seems to think that Shia form more than 40% of Lebanon's population, and the marginal and dispossessed proportion at that. In contrast, in Iran Shia form 90% of the population, and the Sunni groups like the Kurds and the Balouch have never been that vigorously part of national life in comparison to the Shia groups. So Nasrallah's dreaming, though certainly one-man-one-vote would be good for the Shia and will be when in comes. That being said, I was intrigued by the idea of Christians leaving Lebanon. I have known many Lebanese Christians in my time. When I was younger my best friend was part Lebanese Christian, and I socialized with their family quite a bit. Good people and all that. But I wonder, might it not be good for Lebanese Christians to go live somewhere else? It isn't like they aren't succeeding, and the Middle East is just kind of nutso. I was checking out the Wikipedia article on Lebanon when I noted this: "The number of those inhabiting Lebanon proper was estimated at 3,874,050 in July 2006...There are approximately 16 million people of Lebanese descent, spread all over the world, Brazil being the country with the biggest Lebanese community abroad." Wow! This isn't as extreme as the Irish or the Scottish, but the imbalance between the small "homeland" community vs. the Diaspora is enormous. Some of these of course will be part Lebanese, but the size of the Overseas community is impressive. Of course on second thought this makes sense, there are millions of Arab Americans, the vast majority of whom trace their ancestry to greater Syria-Lebanon. But what about Brazil? Well, here are two articles on the Arabs of Brazil. The numbers I'm seeing for Lebanese Brazilians seem to range between 5 and 10 million out of 188 million Brazilians! If you add other Arabs the number of "Turcos" in Brazil is even greater. I'm having a hard time believing that there are so many Arabs in Brazil, haven't been able to find a good Census of this community for Brazil (they don't look that different from southern European whites obviously, and seem assimilated and successful), but if the data is wrong it is repeated on many websites. I'd be interested in the input/data from Brazilian readers. In my research I uncovered the woman to your left, she, 1/2 Japanese 1/4 Lebanese & 1/4 Swiss. Here's some stuff from Wikipedia that I found interesting....

* Abdala Bucaram (Lebanese origin), former President of Ecuador
* Alberto Dahik (Lebanese origin), former Vice President of Ecuador
* Antonio Saca (Palestinian origin), current President of El Salvador
* Jamil Mahuad (Lebanese origin), former President of Ecuador
* Carlos Menem (Syrian origin), former President of Argentina (a convert from Islam to Catholicism)
* Said Musa (Palestinian origin), current Prime Minister of Belize
* Julio Cesar Turbay (Lebanese origin), former President of Colombia

Red wine; maybe not resveratrol   posted by amnestic @ 12/04/2006 06:11:00 PM

For those of you faithfully taking your resveratrol supplements, may I suggest a little procyanidin addition to your regimen? Heard about it on the Nature Podcast.

Oenology: red wine procyanidins and vascular health.

Corder R, Mullen W, Khan NQ, Marks SC, Wood EG, Carrier MJ, Crozier A.

Regular, moderate consumption of red wine is linked to a reduced risk of coronary heart disease and to lower overall mortality, but the relative contribution of wine's alcohol and polyphenol components to these effects is unclear. Here we identify procyanidins as the principal vasoactive polyphenols in red wine and show that they are present at higher concentrations in wines from areas of southwestern France and Sardinia, where traditional production methods ensure that these compounds are efficiently extracted during vinification. These regions also happen to be associated with increased longevity in the population.

Here's a Wine List. Mind you the authors of the study declare competing financial interests.

In my country, we have problem   posted by p-ter @ 12/04/2006 09:00:00 AM

When radio host Jerry Klein suggested that all Muslims in the United States should be identified with a crescent-shape tattoo or a distinctive arm band, the phone lines jammed instantly.

The first caller to the station in Washington said that Klein must be "off his rocker." The second congratulated him and added: "Not only do you tattoo them in the middle of their forehead but you ship them out of this country ... they are here to kill us."

Another said that tattoos, armbands and other identifying markers such as crescent marks on driver's licenses, passports and birth certificates did not go far enough. "What good is identifying them?" he asked. "You have to set up encampments like during World War Two with the Japanese and Germans."

At the end of the one-hour show, rich with arguments on why visual identification of "the threat in our midst" would alleviate the public's fears, Klein revealed that he had staged a hoax. It drew out reactions that are not uncommon in post-9/11 America.

From here, via Hit and Run.

I've said it before, and I'll say it again: most people are effing idiots. One thing keeping policies like these from actually being implemented now is the bizarre quasi-religious reverence for the Constitution present in our country. In some places, the proper reaction to "that's not constitutional" is "well, then it's about time to change the constitution". Somehow, luckily, the elite in America has convinced the masses that our Founding Fathers were infalliable, God-like uber-democrats. It's enought to prevent shit like this (a crescent-shaped tattooo? C'mon now.), though it's worth noting that, even with these guidelines, people have been able to justify a lot of obviously unconstitutional insanity (see internment, Japanese). But without Constitution-worship, would America be an even more populist (I obviously consider this word a pejorative) country than it is now? Absolutely.

This post is also an excuse to link to the catchiest song ever written about throwing Jews down wells.

Sunday, December 03, 2006

Mendel's Garden #9   posted by Razib @ 12/03/2006 09:13:00 PM

Mendel's #9 .

Come out and smell a couple of cigarettes   posted by p-ter @ 12/03/2006 07:12:00 PM

Association between genes on chromosome 11 and nicotine addiction. Abstract:
Nicotine dependence (ND) is a moderately heritable trait. We ascertained a set of 1615 subjects in 632 families [319 African-American (AA) and 313 European-American (EA)] based on affected sibling pairs with cocaine or opioid dependence. Subjects were interviewed with the Semi-Structured Assessment for Drug Dependence and Alcoholism (SSADDA)...There was relatively weak evidence for association of the flanking DRD2 and NCAM1 markers to ND, but very strong evidence of association of multiple SNPs at TTC12 and ANKK1 in both populations (minimal P=0.0007 in AAs and minimal P=0.00009 in EAs), and in the pooled sample, as well as strong evidence for highly significant association of a single haplotype spanning TTC12 and ANKK1 to ND in the pooled sample (P=0.0000001). We conclude that a risk locus for ND, important both in AAs and EAs, maps to a region that spans TTC12 and ANKK1. Functional studies of these loci are warranted. These results provide additional information useful in evaluating the many earlier discrepant findings regarding association of DRD2 with substance dependence.

Technology always wins   posted by Razib @ 12/03/2006 02:27:00 AM

I don't have a TV because it seems such a time sink. Nevertheless, over the past few years I've felt the creep of media convergence. Now I found this site, not quite as bad as channel surfing...but it's getting there.

Saturday, December 02, 2006

The idea of ideas   posted by Razib @ 12/02/2006 11:27:00 PM

TNR has a review of a book titled There Is No Crime For Those Who Have Christ: Religious Violence in the Christian Roman Empire. It surveys the relationship between violence and coercion as the persecuted sect of Christianity transformed into the universal religion of the imperium. Two important points:
Because the title of persecuted church was so powerful, there were plenty of candidates for it. Gaddis begins with the Donatists, but goes on to chronicle the numerous confrontations, whether Christological, ecclesiological, or political, that produced the fractured religious landscape of the late Roman Empire. Anomoians versus Homoians versus Homoousians; monks versus bishops; Alexandria, Antioch, Rome, and Constantinople against one another.... The violent conflicts and scandals of this era of "robber councils" and militarized monks are the caffeine that carries Gibbon through many pages of his great work, and they energize Gaddis as well
The point of Michael Gaddis's book is surely not that Christianity has a propensity for violence, or that its professions of love are hypocritical. Its point is simpler, more banal, and, although it is mentioned almost in passing, much more important: that "Christian scripture and doctrine contained the basis both for violence and for the condemnation of violence." The same could be said of every rich scriptural tradition in the world. The great Christian theologians of late antiquity seem not to have forgotten this ambivalence; and neither, at a time when religions are again beginning to test their moral muscles against one another, should we.

Over the past few years I've asserted that explicitly worked out ideas often matter less in terms of their inferences than we might think. In the domain of religion, that means the doctrine and theology matter less in ordering society and making decisions than we might assume if we view religion as an axiomatically determined system which consists of entailed propositions. In politics, this means that the specific political philosophies are often less important than the fluid alliances that emerge out of social tribalism over a local time scale. This has tended to make me far more skeptical of naive functionalism in the domain of culture and history than in the past. Causative hypotheses in this paradigm tend be ad hoc. Consider that Confucianism was once assumed to be the reason than East Asia lagged the West economically and politically (early 20th century), but with the rise of the Asian economices in the late 20th century it was the source of dynamism (e.g., Confucian family values and hard work), but after 1998 it was the root of Crony Capitalism. This sort of coupling between ideas and consequences has a tendency to explain everything, and therefore nothing.

In The Corner John Derbyshire recently quipped whether it would have made a difference if Christianity was Quaternary (as opposed to Trinitary). Some scholars would offer that it does make a difference. Rodney Stark has posited that Christian Trinitarianism is an optimum for reason, freedom, individualism and all the good things we love (see One True God). I don't believe Stark, the main reason reason being that psychologists tend to find that religionists the world over tend have an internal self-conception of God in a henotheistic sense, whether they be notionally unitary, trinitary, polytheistic, monistic, etc. I don't believe at taking people at their word, self-perception and conception is a tricky business. Ask half of the 98% of humans who perceive that they are above average in intelligence. And yet to be serious, it does make a difference whether Christianity is Trinitarian or Quaternarian in a fundamental way, these are issues which have resulted in people getting killed.

Consider the difference between Alawites, Shia and Sunnis. Most of you might find the differences of little interest (e.g., the semi-literates who occasionally opine that the differences are irrelevant to a nuclear bomb). I tend to think tit is all mumbo-jumbo myself. That being said, I don't have much patience for people who aren't interested in the difference but who still offer opinions on Iran or Syria, because though the differences aren't really important on a functional level (e.g., I don't believe that Shiism entails a greater otherworldiness vs. Sunnism, resulting in a less conducive culture for capitalism), they are important to the people who espouse them. The issue is not the character of the tribal markers, but that they serve as markers. If Mickey Kaus knew what Alawites were he wouldn't say something as idiotic as asserting that Syria was a "Sunni regime," ergo, it wouldn't have influence on the Shia (in the area of facts, Syria has also had a long standing alliance with Iran going back decades, and the Iranian Islamic regime lost a lot of credibility amongst other Islamists when he looked the other way when Syria gutted thousands of Muslim radicals and their families in Hama in 1983). Recently a ScienceBlogger made the mistake of asserting that Iran was an Arab country. This is a common mistake, nevertheless, it isn't really one we can accept anymore seeing as how the ethnic geopolitics of this region now have important ramifications for our own republic (USA). Why would this matter? Consider....

Iranians are Arab Shia
Iraqis are 75% Arab, of whom the vast majority are Shia
Iran has an influence on the Arab Shia


Iranians are non-Arab Shia
Iraqis are 75% Arab, of whom the vast majority are Shia
Iran has an influence on the Arab Shia

You see, you just went from a situation where Iranians and Iraqi Shia are ethno-linguistically and religiously identical, to one where they have a strong religious connection, but a minimal ethno-linguistic one. The identity of Iran is that of a Persian nation, Farsi speaking, with a large and powerful Turkic minority. Though Iranian Shia and Iraqi Shia are religiously the same (Twelver Shia), they don't speak the same language. That is relevant I would think, language presents barriers. During the Iran-Iraq War the Iranian leadership assumed that the Shia of southern Iraq would welcome their co-religionists when the Islamic regime went on the offensive and encircled Basra. Wrong. The Iraqi Shia weren't keen on Iranian rule, though they certainly didn't flourish under Sunni autocracy, they dug in and repelled their Shia co-religionists.

It's complicated. And yes, rather boring, and the differences are trivial really. Nevertheless, they do matter. If you can't be bothered to comprehend these differences, well, leave it to others who can to manage your foreign policy. Or for that matter, comment on this blog on foreign policy related threads. Speak of what you know, wasted ASCII characters are a shame. Nevertheless, when you do know, be careful about taking ideas seriously in and of themselves.

The more things change...   posted by amnestic @ 12/02/2006 09:20:00 PM

I've been trying to resolve homeostasis and plasticity in my head. Those who are interested in homeostasis suggest that neurons have an optimal excitability. Following a perturbation of that parameter, control mechanisms come online and tune the neuron back to a characteristic firing rate. The level of excitability is controlled by ion channels which could be gated by neurotransmitters, voltage, or intracellular signaling. On the other hand, the goal of plasticity is to alter a cell's firing characteristics. For instance, place cells in the hippocampus fire when a rat is in a particular location (the place field for that cell). If place fields remain constant over the course of several recording sessions the place field stability becomes somewhat analogous to a memory.

Some have suggested that homeostasis works in parallel with plasticity to produce a high signal to noise ratio. If excitability is increased at some inputs to a neuron it will be decreased proportionately at others, so the neuron maintains an overall firing rate. This seems at odds with the idea that a memory can be encoded by changes in a cell's firing rate though. To be concrete, say a neuron develops a new stable place field and the rat is confined such that it spends a majority of its time in that location. Will homeostatic mechanisms eventually resolve the cell's firing rate back to the original level? It seems unlikely. It seems more likely to me anyway that when a certain level of plasticity is desired, the signal must be sent to reset the neuronal thermostat to a new desired level. Plasticity without disrupting homeostasis is doomed to sputter out.

An interesting empirical question would be to ask on what timescale the homeostatic detector integrates. How long does it take a neuron in vivo to detect a change in firing rate and return to baseline? It can't be instantaneous or no signals could be encoded via firing rate, but if it takes very long the neuron would become useless for coding any new information as the signal saturates. Some studies have suggested a timescale on the order of 24 to 48 hours; Schuman and co have been able to make one brand of homeostasis visible over the course of about 3 hours. Could cellular homeostasis mechanisms be an explanation for forgetting? Are forgetting curves smooth or marked by peaks at the times that these mechanisms dominate?

Homeostasis reading:

Homeostatic control of neural activity: from phenomenology to molecular design.
Homeostatic plasticity and NMDA receptor trafficking.

"You are not the father"   posted by Razib @ 12/02/2006 08:07:00 PM

Speaking of fertility, check this out....

Selection and neurodegenerative disease   posted by p-ter @ 12/02/2006 03:57:00 PM

When the paper on genome-wide copy-number polymorphism came out, I noted something interesting--the MAPT locus, known to be in an inversion under selection, was also the site of a copy-number polymorphism. I suggested this might provide an explanation for why the H2 haplotype was under selection.

A new paper adds another bit of data to the story--the H1 haplotype shows significantly greater expression of MAPT than the H2 haplotype. MAPT is a protein known to form deposits that are characteristic of neurodegenerative diseases like Parkinson's and Alzheimer's. So now the hypothesis is clear: the H1 haplotype has an duplication of the MAPT locus, which leads to subtly higher levels of MAPT, which in turn lead to subtly higher levels of neurogenerative disease in carriers. Thus, the H2 haplotype has a selective advantage.

Things that would provide support for this hypothesis:
1. Proof that the duplication of the MAPT locus is on the H1 haplotype (the technology used to identify the copy-number polymorphism can't properly phase the haplotypes).
2. Evidence that the change in copy number is indeed the cause of the change in gene expression at the MAPT locus.
3. A large association study between MAPT copy number and neurodegenerative disease.

A story to watch...

Jaakkeli says....   posted by Razib @ 12/02/2006 12:37:00 AM

From the mouth of Finns....
It seems like the high American total fertility rate is purely a result of a) recent immigration of high-fertility groups and older presence of minorities with higher birth rates and b) an artifact how the total fertility rate responds to the different age patterns in fertility, not a difference in eventual child number. White Americans have simply average European fertility. Those who believe otherwise invariably turn out to have just swallowed a silly self-congratulatory/doomsday myth (pick one depending on whether you're an Europe-hating American or an America-hating European) without doing any fact-checking.

To eliminate total fertility rate illusions, it's easy to just look at completed fertility rates. This gives old data, but it should be recent enough to test ideas about secularity and birth rate. For women born in 1960 (in baby-making age mainly during the 1980s and the 1990s, we should see secularisation differences here) the top 10 of OECD baby makers are, with babies per woman...

1. Iceland 2.46
2. Ireland 2.41
3. New Zealand 2.36
4. Slovak Republic 2.18
5. Poland 2.18
6. Australia 2.12
7. France 2.10
8. Norway 2.09
9. Sweden 2.04
10. Czech Republic 2.03

I bet someone expected to see the United States there. Well, I told you that it's a silly myth! The Americans are not far behind with 2.02, but they're still beaten by some super-atheists and even the supremely decadent French (who really do have high birth rates - no, it's not just the Muslim immigrants!). Especially interesting is how white English-speaking Protestant Urheimat UK is so close with its 1.97 - since the US most likely had a bigger boost from minority birth rates, it seems like a good guess that UK and US white birth rates were almost exactly the same and practically the same as the OECD average of 1.96.

The total fertility rate underestimates eventual fertility whenever the age of mothers is increasing [if this is not obvious to someone, well, those punks shouldn't be discussing birth rates as if they know anything! you can't discuss fertility rates meaningfully if you don't even know what a fertility rate is!] and it's obvious that this DOES have a correlation with religion: countries with higher religiosity have higher youth birth rates. So, the supposed higher morality of the US is actually a statistical artifact caused by the US failure to stop teenage pregnancies and European success in it. No kidding. (Average age at first childbirth in 2000 was 24.90, compared to eg. 29.10 in the UK.) Current low Eastern European total fertility rates are in many cases caused mainly by rapidly rising ages of mothers (EE countries have consistently had young mothers as some bizarre communist legacy that I don't understand at all, and now they're turning Western European).

Obvious prediction: if the US ever does manage to either massively limit immigration or cut into the teenage pregnancy rate, total fertility rates will plummet and clueless commentators who don't understand how easily illusions pop up in total fertility rates will launch into equally silly and pointless doom-mongerism/schadenfreude about how the Americans are going to vanish because they're too decadent to make babies and how the US will soon be taken over by the Amish. Or something equally dumb.

Friday, December 01, 2006

Common disease, common variant   posted by p-ter @ 12/01/2006 05:38:00 PM

Crohn's disease is a common autoimmune disorder, and a model "complex" disease (one which involves a number of genetic and environmental factors). A couple genes contributing to the phenotype have been identified, but are insufficient to explain the population frequency of the disease.

A new study undertook genome-wide association using over 300,000 SNPs in the genome to identify other genetic risk factors, and came across one in the gene IL23R, a subunit of a receptor for a cytokine. The story here is two-fold: first, this is the first genome-wide association for Crohn's disease. Second, and more importantly, is the frequency of the putative causal variant (a nonsynonymous mutation in the gene): in the general population, the at-risk allele has a frequency of 93%. As the authors state:
Our discovery of an uncommon protective allele, or conversely, a very common predisposing allele, reflects a major theme in complex genetics; namely, that functional genetic variation exerts a continuum of susceptibility, neutral, and protective effects. Furthermore, alleles conferring protection against one disease may result in increased risk for another .
Complex phenotypes do not lend themselves well to headlines trumpeting "the gene for Crohn's disease" or "the gene for intelligence". The genes involved in these sorts of phenotypes will be involved in a number of processes, which ultimately play a role in the generation of a number of phenotypes. Selection acts on all of these phenotypes, so deciding a priori that a mutation involved in disease is necessarily deleterious in an evolutionary sense is not necessarily a fruitful approach.

Comment on Eyferth   posted by the @ 12/01/2006 05:50:00 AM

Ron Bailey covered the Flynn-Murray debate at Reason. An insightful comment was left on the Reason blog:

Doesn't the German study seem obviously flawed? GIs who knock up their temporary girlfriend while stationed abroad are obviously not a random sample. Indeed, they are heavily selected for a particular IQ range (smart enough to get into the military, dumb enough to have an unwanted child). All this study seems to show is that if you select the parents to be roughly equal, the kids will be too. That's not much of an insight.

Flynn seems to have reached the same underlying conclusion: "smart enough to get into the military, dumb enough to have an unwanted child". But he applied this reasoning only to the Black GIs. I see no reason that if true it wouldn't apply to both groups.