Archive for July, 2007

Google news no like

By Razib Khan | July 31, 2007 8:13 pm

As Kevin Beck points out Google News dropped, but kept the Discovery Institute’s blog. If you have issues this with particular pair of decisions, tell Google.


Copy number variation & being human

By Razib Khan | July 31, 2007 2:28 pm

Gene Duplications Give Clues to Humanness:

All told, the researchers found more than 4000 genes that showed lineage-specific changes in copy number, with the numbers steadily increasing over evolutionary time. Humans, for example, only had 84 genes with increased copy numbers over those of our closet relatives. In contrast, lemurs, which have evolved for 60 million years, have 1180 genes with extra copies. “This is further evidence that genomic differences between humans and other primates is far, far more complex than we originally imagined they might be,” says Ajit Varki, who studies human/chimpanzee differences at the University of California, San Diego. “However, many of the differences may or may not be relevant for explaining ‘humanness.’”

We’ve talked about copy number variation before. Obviously dosage of gene products can be directly impacted by this. We’ve come a long way from non-synonymous base pair changes baby! Though please note that loss of function (fewer copies) might be just as important as gain of function (more copies).


Dell Hell

By Razib Khan | July 31, 2007 3:29 am

Zack talks about his personal Dell Hell. I took had a Inspiron 5100, and it exhibited all the issues he has noted.


Martin Nowak, man of God

By Razib Khan | July 31, 2007 12:19 am

Carl Zimmer has a fascinating profile of Martin Nowak, whose work I have talked about before. Carl saves the best for last:

Dr. Nowak sometimes finds his scientific colleagues astonished when he defends religion. But he believes the astonishment comes from a misunderstanding of the roles of science and religion. “Like mathematics, many theological statements do not need scientific confirmation. Once you have the proof of Fermat’s Last Theorem, it’s not like we have to wait for the scientists to tell us if it’s right. This is it.”


Neandertals & humans gettin' along

By Razib Khan | July 30, 2007 11:07 pm

Were Neanderthals our enemies or lovers?:

One difficulty in working out how these ancient humans rubbed along is that there is a lack of clear evidence of close encounters. That changed two years ago when a paper was published by Prof Paul Mellars, of Cambridge University, and his student Brad Gravina, suggesting the two kinds of human lived together at Grotte des Fées at Châtelperron in France.
The study was criticised but the Cambridge team published a detailed rebuttal. “The importance of the new paper is that it confirms at least 2,000 years of coexistence/overlap between Neanderthals and modern humans in this one small region,” said Prof Mellars. “This is the only direct, unambiguous evidence of this so far.”


Steven Pinker on scientific genealogy

By Razib Khan | July 30, 2007 7:28 pm

Steven Pinker explores The Genealogy Craze in America in TNR. He covers most of the angles, and expands a bit out from a laser-like focus on scientific genealogy toward the relevance of relatedness in the evolution of social behavior.


Foreskin doesn't add "value"?

By Razib Khan | July 30, 2007 9:48 am

Circumcision doesn’t reduce sensation: study:

The study, published in The Journal of Sexual Medicine, looked at a group of 40 men, half of them circumcised. Using sensory testing, the men were monitored at two points on the penis and the forearm while viewing erotic films. Thermal imaging was used to measure sexual arousal.

I think one can criticize this study on the relative coarseness of measure, after all, registering qualia is not a trivial task. Nevertheless, do note that in my previous comment on circumcision I did suggest that “pleasure” might be renormalized by the brain. Remember how good McDonald’s tasted when you are 8 years old?
Related: Circumcision & AIDS, Circumcision – human rights issue?, and Circumcision – HIV vs. pleasure?.


Genetic conflict in fish

By Razib Khan | July 28, 2007 2:59 pm

Ancient and continuing Darwinian selection on insulin-like growth factor II in placental fishes:

…We found that IGF2 is subject to positive Darwinian selection coincident with the evolution of placentation in fishes, with particularly strong selection among lineages that have evolved placentation recently. Positive selection is also detected along ancient lineages of placental livebearing fishes, suggesting that selection on IGF2 function is ongoing in placental species. Our observations provide a rare example of natural selection acting in synchrony at the phenotypic and molecular level. These results also constitute the first direct evidence of parent-offspring conflict driving gene evolution.

I’ve discussed genomic imprinting before. Though not restricted to mammals, much of the work has been done on this taxon simply because gestation increases the window during which such conflicts could occur and the relatively high investment the mother makes into the development of the embryo/fetus. John Timmer at Ars Technica covered this paper in detail several weeks ago.

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By Razib Khan | July 27, 2007 9:24 pm

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Paleontology & microevolution?

By Razib Khan | July 27, 2007 3:41 pm

Rapid evolution in early trilobites fueled by high variation:

Webster compiled morphological data for nearly 1,000 of the 17,000 different species of trilobites, a class of marine arthropods that died out by 250 million years ago, from 49 previously published sources. By tracking different morphological features — the number of body segments, for example — Webster found that trilobite species exhibited more variation during the Cambrian than in later periods, he reported in Science July 27. “Once you go beyond the Cambrian, the diversity of forms within any one species drops off,” he says.
Early and Middle Cambrian trilobite species, especially, exhibited greater morphological variations than their descendants. This high within-species variation provided more raw material upon which natural selection could operate, Webster says, potentially accounting for the high rates of evolution in Cambrian trilobites. Such findings may have implications for our understanding of the nature of evolutionary processes, he says.

I don’t know about the nature of the debate within paleontology (paleobiology) with great detail, but it seems that men like S.J. Gould and Niles Eldredge promoted “higher level” evolutionary processes to explain speciation and deep time natural history. This researcher seems to be putting the onus on basal microevolutionary processes.


Evolutionary parameters – migration matters!

By Razib Khan | July 27, 2007 3:22 pm

How bacteria evolve into superbugs:

“Bacteria that can mutate fast will quickly adapt to harsh environments containing antibiotics. Our study showed that a high rate of immigration significantly augments the regular process of genetic mutation commonly used to explain the evolution of antibiotic resistance,” said co-author Dr. Andrew Gonzalez, a Canada Research Chair in Biodiversity and associate professor in the Department of Biology at McGill. Gonzalez explained that the flow of bacteria in the experiment is analogous to the immigration of bacteria-carrying individuals into a hospital, and “the rate at which bacteria are entering a particular environment – not just the fact that they are coming in – is a key factor.”

What species migrates a fair amount? Ultimately, recall that the rate of evolution is proportional extant genetic variation. That variation can be assumed to be “standing genetic variation” (the range already out there which is now subject to direction selection). Or, open can imagine the fountain of mutation always gushing, mostly with deleterious alleles which are purged, but on some occasions producing neutral alleles which remain extant at low frequencies, or positive alleles which increase in frequency (though stochastic dynamics are always operative). But then there is migration, which pools mutants from across multiple demes with permeable barriers. Selection doesn’t see provenance, whether it is a de novo mutation from within the population, or a de novo allelic brought via gene flow. Obviously one assumes that there will be a bias for alleles which drive evolution that arrived via gene flow to be positive and of large fitness effect. In any case, one doesn’t need to read a paper which explicitly fleshes out a population genetic demographic model (e.g., stepping stone, island, etc.): one can intuitively note that human societies have slowly become tied together by migration over the centuries, with some societies being the subject of mass population movements on a regular basis. One can connect the dots on the implications pretty easily….


Apostasy on apostasy?

By Razib Khan | July 26, 2007 10:49 pm

Looks like there might be a recantation of the argument against death for apostasy by the Grand Mufti of Egypt. Abu Aardvark has the details.


Naked Mole rats are inbred

By Razib Khan | July 26, 2007 3:44 pm

molerat.jpgViral Epizootic reveals inbreeding depression in a habitually inbreeding mammal:

Inbreeding is typically detrimental to fitness. However, some animal populations are reported to inbreed without incurring inbreeding depression, ostensibly due to past “purging” of deleterious alleles. Challenging this is the position that purging can, at best, only adapt a population to a particular environment; novel selective regimes will always uncover additional inbreeding load. We consider this in a prominent test case: the eusocial naked mole-rat (Heterocephalus glaber), one of the most inbred of all free-living mammals. We investigated factors affecting mortality in a population of naked mole-rats struck by a spontaneous, lethal coronavirus outbreak. In a multivariate model, inbreeding coefficient strongly predicted mortality, with closely inbred mole-rats (F ≥ 0.25) over 300% more likely to die than their outbred counterparts. We demonstrate that, contrary to common assertions, strong inbreeding depression is evident in this species. Our results suggest that loss of genetic diversity through inbreeding may render populations vulnerable to local extinction from emerging infectious diseases even when other inbreeding depression symptoms are absent.

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Evolution, genetics & human nature feed

By Razib Khan | July 25, 2007 2:54 pm

If you find the material on this blog of interest, I highly recommend that you subscribe to Jason Malloy’s de facto clipping service: A far number of the articles I blog about I find via that entry on my RSS….


Bonobos, the "gentle ape"?

By Razib Khan | July 25, 2007 1:47 pm

Check out a long piece on bonobos in The New Yorker. Now, I’ve read a fair amount of Frans de Waal’s work, and I think the piece is making him out to be a little more PC than he is. Nevertheless, I am a bit disturbed by the fact that hasn’t seen a Bonobo in the wild! I just happened to have missed that assumed that though most of his research was based on captive animals, there must have been some field research supplementing it. No. And de Waal’s response it pretty lame:

Captivity can have a striking impact on animal behavior. As Craig Stanford, a primatologist at the University of Southern California, recently put it, “Stuck together, bored out of their minds–what is there to do except eat and have sex?” De Waal has argued that, even if captive bonobo behavior is somewhat skewed, it can still be usefully contrasted with the behavior of captive chimpanzees; he has even written that “only captive studies control for environmental conditions and thereby provide conclusive data on interspecific differences.” Stanford’s reply is that “different animals respond very differently to captivity.”

Frans has to know about the problems that might occur because of a norm of reaction. Environments don’t always have the same linear effect on phenotype as you vary them across different genotypes. Bonobos are complex creatures, just like humans. Just as controlled psychological studies on colleges students are important in smoking out the nature of our own species’ cognitive apparatus, field work by anthropologists is also essential in documenting the extent of variation of behavior in the “wild.” It see no reason why the same principle wouldn’t apply to great apes, even if to a lesser extent.
Update: Here’s an interview with a Bonoboologist.


A reflected light from the nations

By Razib Khan | July 25, 2007 10:13 am

I was putting off commenting on this, and wondering whether I had any value to add. But a reader pointed me to Noah Feldman’s Orthodox paradox, a piece in The New York Times Magazine where the author, a young Harvard law professor, reflects on his journey from the Modern Orthodox subculture into the wider world. The whole piece is worth reading. There is a problem in these sorts of articles insofar as Feldman is such an “insider,” while most of the readers are such “outsiders,” that one is totally dependent on the author for context and situation. For example, most gentiles have difficultly distinguishing between Reconstructionist, Reform, Conservative and Orthodox movements in the United States, let along the distinction between Modern Orthodoxy, and less modern Orthodox movements, the latter of whom are divided between the Hasidic and non-Hasidic. My own impression is that there isn’t a hard & fast line between Modern Orthodox and non-Modern Orthodox. I’ve had friends who call themselves “Conservadox,” and it is no surprise that the Conservative movement has had problems because of this broad scope. To illustrate this I know someone whose Conservative synagogue became a Reconstructionist synagogue, which might seem strange when you know that on the spectrum of religious ideals Reform probably sits somewhere in the middle between Conservative and Reconstructionism. But historically Reconstructionism emerged out of the Conservative movement, not the Reform one, so that makes the jump a bit more intelligible. In any case, the point is that though Feldman’s piece has broad and general relevance to the human condition, there are precise contextual details and differences of interpretation in regards to his narrative which are probably important to keep in mind before making sweeping generalizations.

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Tripoli 6 are free!

By Razib Khan | July 24, 2007 3:14 pm

Revere has the details.


Neandertals cranium phenotypically neutral?

By Razib Khan | July 24, 2007 2:22 pm

Update II: John Hawks leaves a comment.
Update: Kambiz has much more comment.
Were neandertal and modern human cranial differences produced by natural selection or genetic drift?:

… Here we use a variety of statistical tests founded on explicit predictions from quantitative- and population-genetic theory to show that genetic drift can explain cranial differences between Neandertals and modern humans. These tests are based on thirty-seven standard cranial measurements from a sample of 2524 modern humans from 30 populations and 20 Neandertal fossils. As a further test, we compare our results for modern human cranial measurements with those for a genetic dataset consisting of 377 microsatellites typed for a sample of 1056 modern humans from 52 populations. We conclude that rather than requiring special adaptive accounts, Neandertal and modern human crania may simply represent two outcomes from a vast space of random evolutionary possibilities.

I am generally skeptical of drift as a catchall explanation (it often serves as a deus ex machina, just as sexual selection has become), but from what little I have gleaned from paleoanthropology it seems that some workers contend that the morphological differences between Neandertals and “modern” humans are overemphasized. I’m thinking here body form, e.g., the short & stocky build typical of Arctic peoples. Obviously the consistent patterns of changes in size and proportion of large mammalian species (larger & stockier the further north) across many taxa point to common selective pressures due to environment; but what about cranium? I simply don’t know. I do know that human bone structure and teeth have become less robust over the last 10,000 years, perhaps due to agriculture. This might simply be relaxing the selection for more robust physiques. I hope John takes a minute from his grant application and comments….


Death to the apostates – NOT (?)

By Razib Khan | July 24, 2007 12:57 pm

Ali Eteraz points me to the fact that the Grand Mufti of Egypt seems to have offered the opinion that ‘Muslims can choose their own religion’. This is important, because as Wikipedia says:

All five major schools of Islamic jurisprudence agree that a sane male apostate must be executed. A female apostate may be put to death, according to some schools, or imprisoned, according to others.
Some contemporary Shi’a jurists, scholars, writers and Islamic sects have argued or issued fatwas that either the changing of religion is not punishable or is only punishable under restricted circumstances, but these minority opinions have not found broad acceptance among Islamic scholars.

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Harun Yahya – big fat joke (OK, not fat)

By Razib Khan | July 24, 2007 2:57 am

Most of you could probably guess that my first post on Harun Yahya was meant to highlight what a joke the whole affair was. You see, making fun of Harun Yahya and his fellow travelers is a guiltless pleasure: you get to be snobby and elitist toward those idiotic moronic knuckle-draggers, and, you feel righteous about it because you’re on the side of the angels!. How much of a hilarious incident was this? The first segment of was devoted to it, and the two pundits, neither of whom had a science background, thought it was pretty sneer and smirk worthy. That’s what I told Ali when he asked me what I thought of the article, basically, I’d been laughing my ass off about how stupid those primitive Muslims were. Now, I know that not all Muslims are primitive let alone stupid. Nevertheless, Harun Yahya & company’s “proofs” about the falsity of evolution were so transparently a product of a sub-standard mentality that it isn’t hard to trigger the atheist schemas which attempt to portray all religious people as barely above apes. Fundamentally, Creationism without sophistry is more of a problem for religious people who value their intellects because it is so nakedly propagandistic to the neutral observer.

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