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.

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.

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 disp
ute 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.

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.

A few months ago I posted Discrete continuity in genetics to show how the granular nature of genetic inheritance may still manifest to our perception as continuous variation (i.e., quantitative traits). I used skin color as a model trait because it is easy to relate to, and we are beginning to understand its genetics in detail as I write. To recap, it seems that 3-5 genetic loci control more than 90% of the intergroup variation across populations in complexion. That is, you have a small number of genes which generate the range between black and white skin. These genes come in various flavors, alleles, which in concert sum up to one phenotype. I used a biallelic model which posited 4 loci of independent and additive effect. If a genotype on locus 1 was Aa, I assumed that the quantitative impact would be 1/2 of AA vs. 0 for aa. And so on for each successive locus, resulting in a biological binomial distribution. But, I do not believe that additivity and independence need to be perfect.
I won’t address developmental and environmental variance too much because they are pretty straightforward. In industrialized societies 90% of the variation in height is genetically specified because environmental variation in regards to nutrition is not particularly important, malnutrition has been rendered rather irrelevant (obesity is a problem though). Nevertheless, there is still some environmental component of variation. An acquaintance of mine was rather short in comparison to her sisters and she attributed it to her competitive gymnastics. Additionally, there might be an element of stochasticity introduced during development as a fetus prior to birth. How does this explain skin color? Well, there is still wiggle room even outside the genes of large effect, particularly on the individual level.

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EDIT: I just found a paper (posted here)estimating the rate of human EPC to be between

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.

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.

Have a good day everyone.

Below I spoke of historical perspective, while earlier I referred to Christmas as “universal pagan wine poured into a particular Christian chalice.” I thought I might elaborate upon this.
First, the cultural and historical origins of Christmas are multi-textured. Though Christians assert “Jesus is the reason for the season,” a more precise formulation might be that “Jesus became the reason for the season in the minds of some.” This is important. It is not without rationale that Christian groups like the Jehovah Witnesses reject Christmas, it is not a scriptural festival. Its emergence in the 4th century coincided with the synthesis of Christianity with Roman Imperial culture as the latter took upon the former as the state religion. In 274 the Roman Emperor Aurelian dedicated a temple to the sun god, Sol Invictus, on the 25th of December, Natalis Sol Invictus, “the birth of the invincible sun.” Interestingly, many early depictions of Jesus Christ co-opted solar imagery (e.g., the halo around the Christ). It seems that the thrusting forward of December 25th as the birth of Christ was strongly motivated by co-option of a pre-existing festival. Additionally, holiday merry-making seems to have its classical antecedants in Saturnalia. But this tendency of a mid-winter festival is not limited to Southern Europe. Yule and its cousins play an even greater role in the north than they do in the sunny Mediterranean. The darkness of the mid-winter solstice festivals bloom to usher in the season of hope and lengthening days. Customs like the Yule Log, Christmas cookies and gift exchange all emerge out of this pre-Christian substratum. This is was not unknown to the Christian Church, during the medieval period there were futile attempts to suppress some of these practices. A great enough frustration broke out during the Reformation that groups like the Puritans banned the celebration of Christmas, which was after all a minor holiday next to Easter.
Today the Christmas season has become capitalism’s handmaid. And yet nevertheless there is an economic case against Christmas. But such arguments will, I suspect, be as successful as Christian attempts to co-opt or abolish a fundamentally primal holiday. So long as winter’s darkness passes over us in the Northern Hemisphere our minds will demand a luxury to usher in the new year. It may not be economically optimal, but the human psychology naturally introduces inefficiencies and ‘irrationality’ into the action of Homo economicus. And so in some ways the battle between those who would “defend” Christmas, and those who promote a more inclusive Holidays, is somewhat beside the point, the name is less than the substance that persists. The tendency toward mid-winter holiday is, I believe, evoked from the natural interaction of our cognitive machinery and the seasonal flux of the world around us. The emergence and perpetuation of mid-winter festivals in agricultural societies in the north isn’t a coincidence or an act of cultural diffusion, it is a tendency which our minds are canalized toward. I believe that in general it is best to make the best of our eternal instincts in this matter. Our nature does not insist that we engage in a gross orgy of consumption after all, but neither can we truly honor the Puritan intent to root all acts in scriptural reason, or the economically optimal behavior which would deny the darkening skies above which finally cede ground to the sun. In the end, such exuberant “inefficiencies” are the ends toward which efficient means aim….