Genome of DNA Discoverer Is Deciphered.

Related: In defense of the celebrity genome.

Labels: Genetics

Chris of Mixing Memory has a post up titled Are Conservatives Less Creative?. I joked with him that basically creativity is strongly coupled with being mentally on edge, after all, who would really follow their muse on the high risk stakes of a creative career which will likely be characterized by penury? But in any case, check it out. I've seen other stuff which show small correlations like this, but, as I mentioned to him what really matters are the tails. Sure, a statistically significant greater number of Leftish folk might cough up the cash for the rec center finger-painting class, but the more important possibility is that the threshold above which one sees artistic virtuosity might be overwhelmingly dominated by those of Left sensibility. This matters of course over the course of history as art is an essential propagandistic tool. Similarly, the recurrent finding that amongst the high IQ those more verbally adept tend to be on the Left and those with stronger mathematical aptitudes tend to be on the Right is also significant in terms of modeling the trajectory of societal evolution and dynamics.

Labels: Psychology

Sam Brownback offers a cryptic op-ed in regards to his attitude toward evolution (he, one of the three Republican candidates for president who raised their hand when Chris Matthews asked if any of them do not believe in the theory of evolution). As they say, read the whole thing, Brownback is definitely a politician. He seems to have believed that Chris Matthews asked if any of the candidates rejected scientific materialism. Nary a word about common descent in the op-ed, the typical genuflections toward microevolution, and a peculiar objection to both "determinism" and "chance."

Labels: creationism

Read top subtitles....

Labels: video

People who study glia are getting all excited about the 'tripartite synapse' where astrocytes that wrap around the synaptic cleft play an active role in controlling neurotransmission. Well TAKE THAT glia researchers!

Selective Stimulation of Astrocyte Calcium In Situ Does Not Affect Neuronal Excitatory Synaptic Activity

Todd A. Fiacco, Cendra Agulhon, Sarah R. Taves, Jeremy Petravicz, Kristen B. Casper, Xinzhong Dong, Ju Chen and Ken D. McCarthy

Summary

Astrocytes are considered the third component of the synapse, responding to neurotransmitter release from synaptic terminals and releasing gliotransmitters—including glutamate—in a Ca2+-dependent manner to affect neuronal synaptic activity. Many studies reporting astrocyte-driven neuronal activity have evoked astrocyte Ca2+ increases by application of endogenous ligands that directly activate neuronal receptors, making astrocyte contribution to neuronal effect(s) difficult to determine. We have made transgenic mice that express a Gq-coupled receptor only in astrocytes to evoke astrocyte Ca2+ increases using an agonist that does not bind endogenous receptors in brain. By recording from CA1 pyramidal cells in acute hippocampal slices from these mice, we demonstrate that widespread Ca2+ elevations in 80%–90% of stratum radiatum astrocytes do not increase neuronal Ca2+, produce neuronal slow inward currents, or affect excitatory synaptic activity. Our findings call into question the developing consensus that Ca2+-dependent glutamate release by astrocytes directly affects neuronal synaptic activity in situ.

I kid. I'm sure glia are more than support cells. They really are more active and reactive than people had given them credit for. Perhaps if they don't directly affect fast neurotransmission they could modulate glutamate driven synaptic plasticity.

Michael Shermer's Skeptic Society has an interesting article up based on And God Created Lenin: Marxism vs Religion In Russia, 1917-1929, which chronicles the futile attempt by the Communists to exterminate religion. One must make a distinction here between religion and a specific religious system and organization.


In The Rise of Western Christendom by Peter Brown I was struck by two simultaneous processes as the Roman Empire withdrew from portions of Germany and Britain and the barbarians rushed in. First, there is the archaeological record of the persistence of folk Christianity for centuries (e.g., amongst the presumably post-Roman peasant subjects of the Avars, or the British remnant under pagan Anglo-Saxon rule). But second, there is the almost invariable creeping advance of doctrinal deviation and religious syncretism once the institutional "police" disappear from the scene. This was in clear evidence in portions of Germany which came under Carlognian direct rule after a long period of Merovingian neglect. St. Boniface records nominally Christian priests regularly taking part in pagan cults and garbling the most basic professions of their faith. A more recent example are the Kakure Kirishitan, Japanese "Hidden Christians" who reemerged after the opening of their nation to the West during the 19th century. In the early 17th century hundreds of thousands of Japanese on Kyushu were at least nominal Roman Catholic Christians (Nagasaki was a Catholic city). The victorious Tokugawa Shogunate persecuted and suppressed Catholicism because of its perception as a "foreign" religion and made every Japanese family register with a Buddhist temple. Though the vast majority of Christians seem to have left the religion (many of these were only notional in any case), a small minority kept their religious identity as Catholics under a mask of crypto-Buddhism. Over the centuries they absorbed outward Buddhist motifs and passed on their Christianity orally. By recontact many of these "Christians" needed to be reoriented toward orthodoxy, so deviated had their religion become from its original character without institutional support. Note that though the surface layer of ritual and belief became distorted rather quickly, the basal psychological attachments with the ancestral faith along with the religious impulse still drove these believers forward to put their lives at risk (one can see this clearly among "Hidden Jews" as well).

Earlier, I have pointed to the fact that Russia seems to have gone through religious "awakening" in the last 15 years. This, despite 70 years of state supported atheism. Boris Yeltsin and Vladimir Putin were both baptized into the Orthodox Church & professed believers, a signal as to the direction of the wind. But, I will not reject the assertion that many of these "conversions" are superficial. A few years back I read a piece which pointed out that a disproportionate number of devout Christians during the Soviet period were of Jewish ethnic origin, a group already under suspicion during the later phases of the Communist state which looked toward Russian Orthodoxy as a source of solace. With the reconversion of much of the non-Jewish Russian elite after the fall of Communism many of these Jewish Christians were shocked to observe that those who had once persecuted them on account of their religious convictions were now attempting to marginalize them within the Russian Orthodox Church itself, presumably driven by anti-Semitic convictions. In Evolution for Everyone David S. Wilson holds out the hope that a non-theistic "religion" may serve some of the same group cohesive functional roles (the "horizontal" aspect) without any nod to a supernatural element (the "vertical" dimension). To some extent I think the reassertion of religious identification in places like Russia and Serbia fits this mold in that many people who affiliate with the Orthodox religion are likely only minimally interested in, or believers in, the supernatural. Slobodan Milosevic never disavowed his atheism, but during the late 1980s he built up his power within what was then Yugoslavia by aligning himself with the Eastern Orthodox religion, even attending ceremonies presided over by clerics. Of course, what one generation might do out of expedience another might accept with sincerity. The conversion of the pagan aristocracy of Rome to Christianity in the early 5th century was a forgone conclusion, their own religious traditions to which they had stubbornly clung to in the face of a century of Christian Roman Emperors was simply no longer a viable option in a polity which now proscribed their rituals and persecuted their beliefs. But by the 6th century no doubt the descendants of once proudly pagan families were now sincere and devout Christians (as attested by their patronage of the Church).

The point here is that religious systems and beliefs are embedded within functionally relevant institutional structures. Even if the former are altered or eliminated, the latter are often needful. Observe the cults of personality, mass rallies and cultivation of youth within the Party structure within Communist states which ostensibly have banished religious feeling. Similarly, even with the collapse of the latter as scaffolding the basal religious impulse will seek outlet in the psychology of a great many human beings. The synergy of both have often been powerful and historically significant forces, as attested by the relationship between Christianity and the rise of monarchy in northern Europe or the spread of Islam during the 7th century.

Labels: Religion

Just noticed that Amazon is taking pre-orders for The Stuff of Thought: Language as a Window into Human Nature, Steve Pinker's latest. His website states that Pinker will start his book tour on the publication date listed on Amazon, a little over 3 months from now, so that seems sufficient confirmation. Here is Steven Pinker on The Stuff of Thought from his 10 Questions last year:

(10) Most GNXP readers probably know you for The Blank Slate and your work as a public intellectual. However, your next book (entitled The Stuff of Thought) returns to the themes of language and cognitive science. Now, as you may or may not know, GNXP readers are interested in genetics and evolution; politics, religion, and world affairs; and the past, present, and future of the human species. What can you tell us about your upcoming book that might whet the appetites of GNXP readers?

The subtitle of the book is "Language as a Window Into Human Nature," and The Stuff of Thought deals with many aspects of human cognitive and social evolution--how a mind that evolved to think about rocks and plants and enemies can invent physics and math and democracy; why people impose taboos on topics like sex and excretion and the divine; why they threaten and bribe and seduce in such byzantine ways. I also discuss many real-world applications of semantics--words that have impeached one president and that many feel should impeach another; language that continues to embroil the Middle East; whether Democrats can win back the White House by winning the metaphor wars; whether language traps us in a self-referential circle (as the postmodernists believe) or offers us contact with truth and reality.

Labels: Psychology

Note: The authors have a website which summarizes their research (via Language Log).

Speaking in tones? Blame it on your genes:

People who carry particular variants of two genes involved in brain development tend to speak nontonal languages such as English, while those with a different genetic profile are more likely to speak tonal languages such as Chinese.

In tonal languages, which are most common in South East Asia and sub-Saharan Africa, subtle differences in pitch can change the meaning of vowels, consonants and syllables. Nontonal languages, which prevail in Europe, the Middle East and North Africa, use pitch only as a way of conveying emphasis or emotion.
...
He cautioned, however, that the research had so far found only an association that appears to be more than chance, and that more work was needed to confirm a causal effect.

I first started hearing stuff this sort of research (i.e., the correlations between particular alleles and language forms) in 2006, so I'm not too surprised. We'll see how this pans out, look for it in PNAS.

But, which alleles on which genes? From Scientific American:

The new research, published this week in Proceedings of the National Academy of Sciences USA ties this difference to two genes, ASPM and Microcephalin. The exact functions of both genes are still open to debate, but they are known to affect brain size during embryonic development. "They presumably have something to do with brain structure, because there are deleterious mutations of the genes that lead to microcephaly" (a condition in which a person's brain is much smaller than the average size for his or her age), says senior study author, Robert Ladd, a professor of linguistics at the University of Edinburgh in Scotland.
...
Ladd and Dediu compared 24 linguistic features-such as subject-verb word order, passive tense, and rounded vowels-with 981 versions of the two genes found in the 49 populations studied. Most of the language contrasts could be explained by geographic or historical differences. But tone seemed to be inextricably tied to the variations of ASPM and Microcephalin observed by the authors. The mutations were absent in populations that speak tonal languages, but abundant in nontonal speakers.

First, note that the authors here imply that derived (more recent) forms of the genes in question under strong selection are connected to the spread of non-tonal languages around 6,000 years ago. There's a lot of question begging here, are tonal languages ancestral? Is this association causal? But look, there's one thing that jumps out at me from a cursory examination of the various times suggested here: it sees possible that the rise to prominence of non-tonal languages (assuming their derived character) dovetails with the posited expansions of Indo-European and Afro-Asiatic languages around the core of the World-Island (Eurasia + Africa).

Here is the wiki info on the geography of tonality:

In Europe, only Norwegian, Swedish, Scottish Gaelic, the Limburgish language (according to some a dialect of Dutch), Lithuanian, Serbian, Croatian, and some dialects of Slovenian possess tonality, and only Lithuanian regularly marks it in text other than in dictionaries. The tones of Lithuanian are believed to be especially authentic, as they agree for the most part with the tones of Vedic Sanskrit, its ancient cousin. Another Indo-European tonal language, spoken in the Indian subcontinent, is Punjabi.

Most languages of sub-Saharan Africa (notably excepting Swahili in the East, and Wolof and Fulani in the West) are tonal. Hausa is tonal, although it is a distant relative of the Semitic languages, which are not.

There are numerous tonal languages in East Asia, including all the Chinese "dialects", Thai, Vietnamese and Burmese (but not Mongolian, Cambodian, Malay, standard Japanese or standard Korean). In Tibet, which is riven by harsh geography, the Central and Eastern dialects of Tibetan (including that of the capital Lhasa), are tonal, while the dialects of the West are not. Much speculation has been generated over the reasons for this partial tonogenesis.

Some of the native languages of North and South America possess tonality, especially the Na-Dene languages of Alaska and the American Southwest (including Navajo), and the Oto-Manguean languages of Mexico. Among the Mayan languages, which are mostly atonal, Yucatec, with the largest number of speakers, has developed tones.

Finally, from the authors' website:

The next step is to do experiments in which we look for evidence of the nature of the predisposition or bias. The work of Patrick Wong and his colleagues provides one possible lead here: they have shown that some monolingual adults find it much harder than others to learn an artificial language vocabulary that makes use of tone or pitch distinctions, and that the differences between these groups show up in subtle differences of brain structure as well. If we could show that these differences also reflect differences in genetic make-up, it would go some way to showing that the correlation we have found is based on a real causal link.

Related: This is Bruce Lahn's brain on ASPM and MCPH1. ASPM, Microcephalin, and intelligence. Developmental cell biology of ASPM. Brain size & genes.

Labels: Genetics

Recently Razib walked readers through a scenario where a population passing through a bottleneck would, by sampling error, experience a change in allele frequencies and thereby convert some of the variance due to dominance into additive genetic variance -- the kind that matters most for a population to respond to selection. If we recall the Breeder's Equation -- R = S*h^2 -- the increase in the population mean for a trait (R) equals the mean of the sub-population selected for breeding (S), multiplied by a fraction between 0 and 1 that shows how fully the potential for change is exploited by selective breeding (h^2). This fraction is called the heritability and equals the fraction of the entire phenotypic variance that is accounted for by just additive genetic effects. Clearly, this fraction increases as additive variance increases.

To review a key difference between additive vs multiplicative scenarios, the components in an additive case don't interact, or the context in which they appear doesn't matter. Since such effects are blind to all other contingencies, they matter most in trying to breed a trait in a desired direction. Non-additive effects throw sand in the gears: for instance, if the alleles within a particular locus interact, we have dominance. The other type is due to epistasis, or the interactive effects between loci. Since these effects blunt the power of directional selection, we ask what if we could magically convert the retarding type into the promoting type? Razib's post linked above has already showed how, in detail, this could happen when a bottleneck converts dominance variance into additive variance. Now, to see how a bottleneck could convert epistatic variance into additive variance, consider the following table*:

---- AA -- Aa -- aa
BB.. 8....... 6...... 4
Bb.. 2....... 4...... 4
bb.. 1........ 1..... 3

Let's call the locus with the A and a alleles locus 1, and that with the B and b alleles locus 2. We'll say the entries correspond to a phenotype that depends on the genotypes at both loci, and that fitness is positively correlated with this phenotype. Consider locus 1: the A allele is associated with greater fitness if you look just at the first row, where it interacts with just the BB genotype. In fact, A's effect is perfectly additive: each copy of A adds 2 units to the baseline, and the heterozygote's value is the average of those of each homozygote. If the b allele were lost somehow, then the only possible genotype at locus 2 would be BB (only the top row would show up), and the greater fitness of A combined with its non-trivial heritability (i.e., greater additive variance) would then drive A to fixation. The trouble is that when A teams up with the Bb and bb genotypes, its effect is non-additive and it's associated with lower fitness. We therefore have epistatic variance in this trait: the fitness of the alleles at locus 1 depend on the larger genetic context in which they appear.

For readers not used to this jargon, consider a real-world case of the market success of musical styles. Let's say that locus 1 represents the musical styles, such that AA is a pure classical, Aa is classical-jazz fusion, while aa is pure jazz. Now, locus 2 represents the critics, such that BB prefers classical and increasingly winces as he hears more jazz intrude into a style; Bb prefers music that has even a hint of jazz; while bb is a jazz purist. Here, the success of a particular style depends on who's judging it, and since the judges have dissimilar opinions, a diversity in musical styles will be maintained.

But suppose that, due to the whims of fashion in criticism, the pool of critics was suddenly depleted of those who valued jazz at all, leaving only the classically minded critics (BB). Then we would quickly see jazz musicians removed from the concert halls and record stores, replaced by pure classical musicians. This loss of diversity in the pool of critics wouldn't have to result from caprice -- maybe somebody important in the world of criticism fired all of the critics even somewhat sympathetic to jazz.

To bring this back to genetics, the loss of the b allele at locus 2 could result from a population bottleneck, which increases sampling error, or it could result for more selective forces. We already see that b is associated with lower fitness (values descend as you move down any of the three columns), so it could also be lost due to selection against it. In the past 10,000 years, it has been possible for a few people to affect large numbers of others -- maybe a satrap decides that he doesn't like people with blue eyes and tries to kill them off. Or perhaps an imperial ruler or ruling elite make good on a promise to execute anyone who steals. By purging a locus or loci of their diversity in any of these ways, any other loci that had been interacting with the suddenly homogenous loci are now more free to undergo directional selection. Crucially for humans, the new socio-cultural and institutional structures that came into being only after agriculture probably rubbed out some diversity at loci that were only of marginal importance in a hunter-gatherer society, but whose diversity could not be tolerated in an agricultural one. This applies equally to loci affecting traits above the neck as well as below.

* Shamelessly using the same numbers as Table 2.3 on p.21 of Mazer & Damuth (2001). Evolutionary significance of variation, in Fox, Roff, & Fairbairn (eds.). Evolutionary ecology: Concepts and case studies. New York: OUP.

Labels: epistasis, Evolution, Genetics

Kambiz @ Anthropology.net has an excellent review of the case of the Chinese warlord with "European" ancestry.

Labels: Genetics

'Smart' mice teach scientists about learning process, brain disorders

Mice genetically engineered to lack a single enzyme in their brains are more adept at learning than their normal cousins, and are quicker to figure out that their environment has changed, a team led by researchers at UT Southwestern Medical Center has found.
...
The group is also beginning a search for drugs that might create the same effects without genetic manipulation and monitoring the animals' health and behavior over time.
...
The key in this study was being able to "knock out" the gene for Cdk5 only in the brain, and only when the mice were adults. This technique, only recently developed and called conditional knockout, allows much more sophisticated experiments than traditional knockout, which entirely eliminates the gene.
...
Normally, Cdk5 works with another enzyme to break up a molecule called NR2B, which is found in nerve-cell membranes and stimulates the cell to fire when a nerve cell signaling molecule, or neurotransmitter, binds to it. NR2B previously has been implicated in the early stages of learning.

The new research showed that when Cdk5 is removed from the brain, the levels of NR2B significantly increase, and the mice are primed to learn, Dr. Bibb said.

Evolved biological systems aren't optimal...just good enough. Knowing how the system works should lead to interventions that improve function. In the coming decades there should be nutritional, drug, training, genetic, and cybernetic enhancement of brain function.

Labels: brain

Redefinition / turnin' your play into a tragedy / exhibit level degree on the mic / passionately - Kweli

Nature has an Insight section up ostensibly about epigenetics starting with an article by Adrian Bird suggesting a re-definition. It's free. I think the term is useful to the extent that you can predict something about a phenomenon or mechanism by knowing that it is 'epigenetic'. Bird's suggestion is to make the term less useful and more inclusive. The last section is labeled 'Refining a definition' when in fact he is doing just the opposite:

...there might be a place for a view of epigenetics that keeps the sense of the prevailing usages but avoids the constraints imposed by stringently requiring heritability. The following could be a unifying definition of epigenetic events: the structural adaptation of chromosomal regions so as to register, signal or perpetuate altered activity states. This definition is inclusive of chromosomal marks, because transient modifications associated with both DNA repair or cell-cycle phases and stable changes maintained across multiple cell generations qualify.

He wants to allow transience and yet use epigenetics to explain stable phenomena:

A growing idea is that functional states of neurons, which can be stable for many years, involve epigenetic phenomena, but these states will not be transmitted to daughter cells because almost all neurons never divide.

Without such epigenetic mechanisms, hard-won changes in genetic programming could be dissipated and lost;

With this refinement, epigenetics is everything and nothing. The only thing you can infer about an epigenetic event is that it doesn't change the DNA sequence. Bird wants to claim that a unifying trait is that epigenetics is 'responsive' rather than 'proactive'. I don't understand. If you're going to introduce new terms, why not choose to bring into to broader use the distinction between meiotically and mitotically heritable or force people to be specific about which chromatin modification they are referring to instead of saying 'epigenetic modifications'? Responsive and proactive are more loosely defined concepts destined to muddy waters and lead away from insight.

Labels: Epigenetics

The Science article, Childhood Origins of Adult Resistance to Science, has now been re-packaged for Edge. I have read Paul Bloom's work before so none of this is surprising, though I would offer that he has the cognitive psychologist's bias, so to speak, of not addressing the impact of the variation of human intelligence on the ability of people to comprehend scientific concepts. Even if you can't reproduce all the findings of a given science, high IQ people often have a large database of facts they can cross-reference, a toolkit of rough & ready heuristics and raw analytic power through which concepts can be filtered. The less intelligent often can't make recourse to these cognitive faculties, so the power of authorities looms large and there must be an extra sensitive focus on their credibility. Interestingly, I've found that google actually makes stupid people even more efficiently stupid, they simply proceed to use the search engine to collect an enormous assemblage of moronic sources to reinforce their beliefs. Of course, there's the reality that smart people are often quite stupid outside of their knowledge domain, though eminence within their own field often results in self-deception as to the source of their beliefs outside of their area of expertise (i.e., they attribute their positions to reasoned analysis when in many cases they are simply expressing the beliefs of their social set).

Labels: Cognitive Science

Over at my other weblog I have a long response to the Edge piece which argues for the power of the Secularization Hypothesis, roughly, that with modernity there comes a falling away from supernaturalism. In short, the authors dig into some data, but like those who make arguments about the inevitable conquest of secularity by religion, their narrative is characterized by selection bias. That is, where the data is powerfully in favor of their argument they draw upon surveys, where it is not powerful or argues against their case they just quote impressions about how non-religious people really are, and sometimes they just pull data out of context (e.g., focus here on South Korea). In any case, I'm just here to remind people of a little history: atheism and theism have basically always been around. The finally victory of either will likely not be won in the human future, as retreat seems to herald future advances. The relative power of atheism or theism varies over time and space, but neither morph ever seems to fix. The sample space of data is so large that like a high school essay it isn't that hard assemble a list of data which support your thesis. It is natural then that the various camps will have their court propagandists outlining their case. But this just really masks the true variation and diversity on this character and its multi-dimensional nature.

Labels: Religion

European Man Found in Ancient Chinese Tomb, Study Reveals. This is a follow up on an earlier story, worth reading for a lot of quotes. One might ask why the Chinese look so "Chinese" with this ancient evidence of gene flow. Well, non-trivial gene-flow is not the same as a non-trivial flow of peoples. The low level introgression of selectively favored alleles via isolated matings may be genetically significant, but leave little overall signatures on the genome (ergo, ancestry and other characters keep on a truckin' as before). I recall once reading an ethnography of the Hui people, roughly, Chinese speaking Muslims, where local villagers presented an old man with a large nose, a full beard and round eyes and declared that "this is a true Hui man!" Even though generations of intermarriage has resulted in the bleeding into the Chinese Muslim population (presumably founded by Central Asians who settled during the Yuan dynasty of the 13th and 14th century) of the general cultural and genetic character of the surrounding Han population (and likely some flow in the other direction too) these people still remember what they once supposedly looked like.

Labels: Genetics

According to a news article in Nature (subscriber only), some scientists are "alarmed" that a number of high-profile scientists and public figures are going to be the first people to have their genomes sequenced (the published public sequence is a mish-mash of a number of people, and the now-public Celera sequence, though largely Craig Venter, was also from more than one person).

For those unaware of this, 454 Life Sciences is currently in the process of sequencing James Watson's genome, Craig Venter claims to have an analysis of his finished sequence in review at PLoS Biology, and the X Prize in Genomics will be given to the first person to efficiently sequence a number of genomes, including those of "celebrities such as television journalist Larry King, cosmologist Stephen Hawking, Google co-founder Larry Page, Microsoft co-founder Paul Allen and former junk-bond trader Michael Milken".

Some quotes from those who don't like this:

"This is almost like recreational genomics, or the molecular equivalent of a whole-body scan, for those who have boundless curiosity and cash," says Kathy Hudson, director of Johns Hopkins University's Genetics and Public Policy Centre in Washington DC. "It will be sort of a sad statement if that's what we end up getting out of the Human Genome Project."

..

"If all the sequences obtained over the next year or two are done on scientists with strong financial positions, that will send a message quite contrary to what the genome project aimed to achieve," says Francis Collins, head of the US National Human Genome Research Institute (NHGRI) in Bethesda, Maryland.

...

"I'd hate the availability of single-genome sequencing to be based purely on money and fame," says Michael Ashburner, a geneticist at the University of Cambridge, UK. "Just doing famous or very rich people is bloody tacky, actually."

I'll grant that celebrating sequencing the genomes of a bunch of celebrities is pretty tacky. Fair enough. But these critcs are entirely missing the point.

1. I haven't thought to hard about this, but can anyone think of a major technology that was not first used by the rich? Cars, comupters, the internet, air travel, any major medical technology-- all of these things were first available to those with the money to buy them. After the frontier has been broken and the technology proven, it will be improved, made more cost effective, and eventually be available to the more general public. In the article, a comparison is made between sequencing your genome and getting a private space flight, with the implication that both are ridiculous luxuries for the rich. The explcit goal of the X Prize for space flight, of course, is "to make space travel safe, affordable and accessible to everyone through the creation of a personal spaceflight industry." The same principle is at work here.

2. Many people are wary of genetic technologies and what they bring. There are issues with privacy, with "genetic discrimination", with what to do if you know you could pass on a genetic disease, etc. These are not issues to be taken lightly, but the critics above seem to think that the first people to have their genomes sequenced should be the people that have no idea what genetics is. According to the article, one institutional review board required that any person having their genome sequenced in a given study had to have at least a masters degree in genetics. That's not a bad idea, because in the end, the best way to show you think that something is safe and effective is to do it to yourself first. If the first people having their genomes sequenced were individuals with no knowledge of genetics, there is no doubt the scientific community would be accused of taking advantage of ignorance get people to participate, of using less-educated people as guinea pigs, of scientific irresponsibility, and worse. Damned if you do, damned if you don't...

N.B. if anyone wants to sequence my genome (one hell of a genome, if I do say so myself), please be in touch.

Labels: Genetics

Who's Your Daddy? Paternity Battle Between Brothers (who are identical twins). Pretty bizarre story.

Labels: Genetics

The idea that a species will undergo diversifying selection as it begins to colonize an environment made up of many niches never seen before -- adaptive radiation -- is pretty intuitive. It's obvious enough qualitatively that you'd figure it out on your own if thinking about biology were your day job: the forms of life around us seem so different mostly because they are adapted to different habitats. That idea should probably scale down to sub-populations of a single species. What biologists get paid to do is flesh out the finer-grained quantitative details of how that happens, how much diversity will be maintained by what conditions, and so on. We talk a lot here about recent human evolution (that is, after the invention of agriculture), and so it's worth knowing some of the key points that emerge from quantitative studies of adaptive radiation.

Toward that end, here is a free journal article from PNAS by Gavrilets & Vose which has pointers to the lit and is brief / very readable (although if you want, you can skip their "model" and "methods" sections and focus on "results and interpretations" and "discussion"). Since it's pretty short, I'll let readers peruse it themselves rather than report its contents, but one thing's worth noting: speciation in their model occurred in huge initial bursts. This is yet more evidence that it's foolish to argue that natural selection "hasn't had enough time" to differentiate human populations within 10,000 years, since adaptation doesn't creep steadily. See also the review and simulation articles by H.A. Orr to this effect. Clearly, to the extent that we've moved from one form of society to another more quickly over this time period, these bursts are probably occurring more frequently than in pre-agricultural times. If anything, the only thing that there "hasn't been enough time for" is the settling down of the adaptive process toward a steady state.

Now, the non-math-phobes will have noticed a few phrases lifted from math lingo in the previous paragraph -- the rate of change is increasing (acceleration), are we in a steady vs transient state, etc. But how many here -- not least of which is me -- would know what to do with the jargon of knots, braids, links, or anything else from the field of topology? The only incorporation of these kinds of ideas that I've seen is the chapter on evolutionary graph theory in Martin Nowak's Evolutionary Dynamics. Maybe there are similar articles or book chapters out there, but the point is that there is a mostly unsettled niche begging to be exploited by biologists whose math toolkit contains more than "engineering math" (i.e., non-expert levels of calculus & differential equations, linear algebra, and statistics & probability).

That's no slight to knowing this much math -- but since these tools have been applied for so many decades, it makes it harder to create something original using them. If you were the first to learn, say, knot theory and apply it to biology, you'd blaze a new trail. Even if you personally didn't perform optimally in this area, your intellectual descendants would become increasingly adapted to it and really exploit it (you'd still get credit as the progenitor). Hell, you wouldn't even need to invent new math -- you could absorb what's already understood in math, and maybe roughly how it's used in applications (which would probably be in physics). All you'd have to do is use a bit of analogical reasoning to figure out what pattern in biology it looks like -- or perhaps predict a biological phenomenon that's currently not known, and investigate that.

Edison didn't give much of a role to inspiration, but we could go farther and say that sometimes inspiration is 99% canny opportunism: taking already invented tools to excavate a virgin mine in your own neck of the woods. Most "big ideas" in evolutionary biology are like this: the diffusion equation to model the spread of alleles through a population, game theory to study altruism, extreme value theory to deal with a mutation more beneficial than all extant alleles, and so on. I'm just harping on topology because of a neat little pop-math book I just read called Knots (review by Derbyshire; review by knot theorist). You'd better start settling now, since the corresponding niche in physics appears very crowded, and many of them must feel pressure to migrate to biology where they'd find it much easier to make a name for themselves.

Labels: Evolution, mathematics

FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity. The "Brief Communication" in Nature is open access. Here's a popular press summation.

Related: The HapMap and copy number variation. Potentially massive human genetic variation detected.

Labels: Genetics

It may be obvious that people tend to trust their intuition over data, but some counterintuitive facts or forces are questioned (i.e. evolution), while other are not (i.e. electricity, the non-flatness of the earth). This review (entitled Childhood Origins of Adult Resistance to Science-- I can't tell if the title is deliberately clever or entirely serious) takes a look at why, concluding (perhaps unsurprisingly) that resistance to scientific information is exacerbated in societies "where nonscientific ideologies have the advantages of being both grounded in common sense and transmitted by trustworthy sources." I tried to pick out some select quotes, but instead I'm just putting the whole thing below the fold. It's a fascinating article, and very well-written:

Scientists, educators, and policy-makers have long been concerned about American adults' resistance to certain scientific ideas (1). In a 2005 Pew Trust poll, 42% of respondents said that they believed that humans and other animals have existed in their present form since the beginning of time, a view that denies the very existence of evolution (2). Even among the minority who claim to accept natural selection, most misunderstand it, seeing evolution as a mysterious process causing animals to have offspring that are better adapted to their environments (3). This is not the only domain where people reject science: Many believe in the efficacy of unproven medical interventions; the mystical nature of out-of-body experiences; the existence of supernatural entities such as ghosts and fairies; and the legitimacy