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Homeopathy made simple | Bad Astronomy

Posted on July 6, 2010 by Danzig

Daryl Cunningham — the man who did this devastating comic strip about antivaxxers — has turned his sights on homeopathy. In just a few dozen panels he describes this alt-med nonsense, shows why it’s nonsense, shows why it’s dangerous, and then provides a dramatic and emotional example of just how and why belief in homeopathy can kill.

His terse description of the Penelope Dingle case hits like a punch in the throat. Homeopathy is dangerous, mostly because it lures people away from real medicine. But it’s also dangerous because it promotes magical thinking, which eats away at all of reality.

Related posts:
- A comic takedown of antivax icon Andrew Wakefield
- British Medical Association: Homeopathy is witchcraft
- Dear media: Hello, it’s me, science
- Homeopathy and the 10:23 project

Must Atheists Also Be Liberals? | The Intersection

Posted on July 6, 2010 by Danzig

The latest episode of Point of Inquiry is something a little different--and I hope in a good way. Here's the write-up:
Recently in Amherst, New York, two of Point of Inquiry’s hosts sat down for a special in-studio episode of the show. One was a conservative (Robert Price), one a liberal (Chris Mooney)—and both were atheists.
The topic they tackled: Is there any necessary correlation between one’s disbelief in God and one’s place on the political spectrum?
The result was a fascinating—and notably civil, and frequently entertaining—conversation ranging across foreign policy, abortion, stem cell research, animal rights, and many other topics. In the end, the discussants actually found not only much disagreement, but also some common ground. You can stream the episode here, and subscribe to Point of Inquiry here. And if you want to join a discussion at the Point of Inquiry forums, visit here...

I Kissed a Nerd (and I Liked it) | The Intersection

Posted on July 6, 2010 by Danzig

I absolutely adore this parody of Katy Perry's I Kissed A Girl by the Damsels of Dorkington, and agree--Big brains are hot! I hope this makes readers smile and wish everyone a very happy holiday weekend!

NCBI ROFL: World Cup Week: Choose wisely, rooting for the winning team DOES make you more manly. | Discoblog

Posted on July 6, 2010 by Danzig

reactionguys Testosterone changes during vicarious experiences of winning and losing among fans at sporting events.

“Basking in reflected glory, in which individuals increase their self-esteem by identifying with successful others, is usually regarded as a cognitive process that can affect behavior. It may also involve physiological processes, including changes in the production of endocrine hormones. The present research involved two studies of changes in testosterone levels among fans watching their favorite sports teams win or lose. In the first study, participants were eight male fans attending a basketball game between traditional college rivals. In the second study, participants were 21 male fans watching a televised World Cup soccer match between traditional international rivals. Participants provided saliva samples for testosterone assay before and after the contest. In both studies, mean testosterone level increased in the fans of winning teams and decreased in the fans of losing teams. These findings suggest that watching one’s heroes win or lose has physiological consequences that extend beyond changes in mood and self-esteem.”

Note from the ladies of NCBI ROFL: We will be on hiatus next week (July 5-9) because we are both traveling to conferences. If you’re going to be at the SMBE meeting in Lyon or the FASEB Biology of Cilia and Flagella meeting in Vermont and want to hang out/buy us a beer/hear about the research we do when we’re not blogging, drop us a line at ncbirofl[at]gmail.com!

WTF is NCBI ROFL? Read our FAQ!

Why Tibetans breathe so easy up high | Gene Expression

Posted on July 6, 2010 by Danzig

I said yesterday I would say a bit more about the new paper on rapid recent high altitude adaptation among the Tibetans when I’d read the paper. Well, I’ve read it now. Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude:

Residents of the Tibetan Plateau show heritable adaptations to extreme altitude. We sequenced 50 exomes of ethnic Tibetans, encompassing coding sequences of 92% of human genes, with an average coverage of 18x per individual. Genes showing population-specific allele frequency changes, which represent strong candidates for altitude adaptation, were identified. The strongest signal of natural selection came from endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1), a transcription factor involved in response to hypoxia. One single-nucleotide polymorphism (SNP) at EPAS1 shows a 78% frequency difference between Tibetan and Han samples, representing the fastest allele frequency change observed at any human gene to date. This SNP’s association with erythrocyte abundance supports the role of EPAS1 in adaptation to hypoxia. Thus, a population genomic survey has revealed a functionally important locus in genetic adaptation to high altitude.

The exome is just the protein-coding part of the genome; so they’re focusing ostensibly on functionally relevant single nucleotide polymorphisms (SNPs). About a month and a half ago a similar paper on Tibetan high altitude adaptations was published in Science (I posted on that too), but their methodology was somewhat different. That group was looking at a set of genes, candidates, which they’d assume might have been under selection and so have functional significance in explaining Tibetan vs. non-Tibetan phenotypes at high altitudes. This second paper takes a more bottom up approach, scanning the genome of Tibetans and Han Chinese, and trying to spotlight regions which exhibit a great deal of between population variance, far greater than one might presume from the total genome genetic distances.

As to that last point…the timing of this has been causing a major problem with archaeologists. The supplements lays out the details a bit more than the press reports, so below is figure 2:

tibhan

It looks like to get a better sense of the model you’ll have to read the cited paper, and I’m not sure that that will satisfy the archaeologists. They did use a large number of neutral markers though, so I’m not too worried about biases in their data set. Some have been confused about the population numbers, but this value in a population genetic context can be counterintuitive, especially over the long term (low values are given much more weight than high values). The small Han value can be easily made less confusing when you consider a massive demographic expansion from a small founder group, as well as persist long term biases in reproductive value within the population (e.g., some males in a given generation are way more fecund than others through polygyny). A higher N for Tibetans may be explained by a more stable population where diverse subsets and across individuals the reproductive value may be more equitable. In other words, an effective population size is a statistic which is bundling together a lot of evolutionary history, and is not a simple measure of perceived census sizes (the Tibetans may also be something of a melange of a diverse set of ancient groups which took refuge in the highlands, while the Han are the descendants of early adopters of agriculture which expanded demographically; so they’re opposite ends of the demographic tunnel).

The time of divergence of a little under 3,000 years is important for the rest of the paper, so I suppose other workers had better replicate their findings in the future. Figure 1 is rather striking, so let’s jump to it:

tibhan2

This chart is simply showing frequencies of SNPs in Tibetans and Han. The two are obviously correlated, as evident by the diagonal. Shading indicates the density of the number of SNPs at a given position. Look to the bottom right, and you see the gene around which much of the paper hinges, EPAS1. It’s an enormous outlier, with SNPs where Tibetans and Han differ a great deal. This is important in regards to looking for genes which may drive adaptation to higher altitudes; if you don’t have different genes then you don’t have different traits. If the Tibetans and Han diverged ~3,000 years ago, then those adaptations may be recent and would have emerged through rapid allele frequency changes (though they observe that it may be drawn from standing variation). The researchers didn’t go looking for EPAS1 as such, rather, it came looking for them. What does it do? From the text:

EPAS1 is also known as hypoxia-inducible factor 2{alpha} (HIF-2{alpha}). The HIF family of transcription factors consist of two subunits, with three alternate {alpha} subunits (HIF-1{alpha}, HIF-2{alpha}/EPAS1, HIF-3{alpha}) that dimerize with a ? subunit encoded by ARNT or ARNT2. HIF-1{alpha} and EPAS1 each act on a unique set of regulatory targets…and the narrower expression profile of EPAS1 includes adult and fetal lung, placenta, and vascular endothelial cells…A protein-stabilizing mutation in EPAS1 is associated with erythrocytosis…suggesting a link between EPAS1 and the regulation of red blood cell production.

Next, they dig into the functional significant of EPAS1 variants, in the literature, and in their current sample:

Associations between SNPs at EPAS1 and athletic performance have been demonstrated…Our data set contains a different set of SNPs, and we conducted association testing on the SNP with the most extreme frequency difference, located just upstream of the sixth exon. Alleles at this SNP tested for association with blood-related phenotypes showed no relationship with oxygen saturation. However, significant associations were discovered for erythrocyte count (F test P = 0.00141) and for hemoglobin concentration (F test P = 0.00131), with significant or marginally significant P values for both traits when each village was tested separately (table S5). Comparison of the EPAS1 SNP to genotype data from 48 unlinked SNPs confirmed that its P value is a strong outlier (5) (fig. S4).
The allele at high frequency in the Tibetan sample was associated with lower erythrocyte quantities and correspondingly lower hemoglobin levels…Because elevated erythrocyte production is a common response to hypoxic stress, it may be that carriers of the “Tibetan” allele of EPAS1 are able to maintain sufficient oxygenation of tissues at high altitude without the need for increased erythrocyte levels. Thus, the hematological differences observed here may not represent the phenotypic target of selection and could instead reflect a side effect of EPAS1-mediated adaptation to hypoxic conditions. Although the precise physiological mechanism remains to be discovered, our results suggest that the allele targeted by selection is likely to confer a functionally relevant adaptation to the hypoxic environment of high altitude.

There are random anomalies in nature, but it seems too perfect that this is the outlier in allele frequencies across two populations which differ in adaptations which relate to many of the traits above.

tibhan3 OK, so they found an outlier SNP. The gene seems to have a reasonable probability of being involved in functional pathways relevant to altitude adaptation. But so far we’ve been focusing on the Tibetan-Han difference. If the two populations separated about 3,000 years ago one assumes that genes with SNPs with huge F_sts, where most of the variation can be partitioned between the groups, not within them, are good candidates for having been driven by selection. But it would be nice to compare with an outgroup. So they compared the Tibetans and Hans with the Danes, who are an outgroup who separated from the East Asian cluster about one order of magnitude further back in time (~30,000 years). Next they generated a “population branch statistic,” (PBS), from the the F_st data (see the supplements). Basically you’re getting a value which describes allele frequency differences normalized to the expected genetic distance as known from population history. I’ve extracted out Panel B from figure 2. T = Tibetans, H = Han, and D = Danes. The smaller tree represents genome average PBS values. It’s what you’d expect, the Danes are the outgroup. Over time genetic difference builds up because of separation between the groups. The Han and Tibetans are very close, as you’d expect from genetically similar populations. But look at the larger tree, the Tibetans are the outgroup by a mile! The Danes and Han differ far less from each other on EPAS1 than they do from the Tibetans. This seems like a clear deviation from the level of allele frequency difference one might be able to generate by neutral random walk processes.

EPAS1 isn’t the only gene which they found, but it was the most significant, and illustrates the nature of the methodological orientation of this group. Sift through the genome and look for something which is totally unexpected, and put a focus on the peculiar diamond in the rough and see what it can tell you. They conclude with the big picture:

Of the genes identified here, only EGLN1 was mentioned in a recent SNP variation study in Andean highlanders (24). This result is consistent with the physiological differences observed between Tibetan and Andean populations…suggesting that these populations have taken largely distinct evolutionary paths in altitude adaptation.
Several loci previously studied in Himalayan populations showed no signs of selection in our data set…whereas EPAS1 has not been a focus of previous altitude research. Although EPAS1 may play an important role in the oxygen regulation pathway, this gene was identified on the basis of a noncandidate population genomic survey for natural selection, illustrating the utility of evolutionary inference in revealing functionally important loci.
Given our estimate that Han and Tibetans diverged 2750 years ago and experienced subsequent migration, it appears that our focal SNP at EPAS1 may have experienced a faster rate of frequency change than even the lactase persistence allele in northern Europe, which rose in frequency over the course of about 7500 years…EPAS1 may therefore represent the strongest instance of natural selection documented in a human population, and variation at this gene appears to have had important consequences for human survival and/or reproduction in the Tibetan region.

Natural selection is somewhat stochastic; it can take different tacks to the same process because it doesn’t have infinite power in its search algorithm. Given enough time and gene flow no doubt adaptations would homogenize and converge upon a perfect optimum, but given enough time the universe will devolve into heat death. Evolution has to operate extemporaneously for eternity because the conditions are ever changing. Second, the big headline grabbing assertion about EPAS1 being the strongest instance of natural selection needs to be moduled by the fact that the conclusion was generated assuming the validity of the inferences of a particular model, and models can be wrong. It does seem like the evolutionary change is likely to be recent, I doubt they’d be off by an order of magnitude. But for lactase persistence we’ve extracted genetic material from ancient remains. The conclusion then is much more concrete in this case. Until we get remains from ancient Tibetans and can infer their allele frequencies, there will be some asymmetry in the confidence with which we can make a claim as to when the selection event began.

Citation: Yi, X., Liang, Y., Huerta-Sanchez, E., Jin, X., Cuo, Z., Pool, J., Xu, X., Jiang, H., Vinckenbosch, N., Korneliussen, T., Zheng, H., Liu, T., He, W., Li, K., Luo, R., Nie, X., Wu, H., Zhao, M., Cao, H., Zou, J., Shan, Y., Li, S., Yang, Q., Asan, ., Ni, P., Tian, G., Xu, J., Liu, X., Jiang, T., Wu, R., Zhou, G., Tang, M., Qin, J., Wang, T., Feng, S., Li, G., Huasang, ., Luosang, J., Wang, W., Chen, F., Wang, Y., Zheng, X., Li, Z., Bianba, Z., Yang, G., Wang, X., Tang, S., Gao, G., Chen, Y., Luo, Z., Gusang, L., Cao, Z., Zhang, Q., Ouyang, W., Ren, X., Liang, H., Zheng, H., Huang, Y., Li, J., Bolund, L., Kristiansen, K., Li, Y., Zhang, Y., Zhang, X., Li, R., Li, S., Yang, H., Nielsen, R., Wang, J., & Wang, J. (2010). Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude Science, 329 (5987), 75-78 DOI: 10.1126/science.1190371

Female Baboons Find a Secret to Longevity: Close Girlfriends | 80beats

Posted on July 6, 2010 by Danzig

Apparently, in the animal kingdom, it’s better to be a girl. We have seen that women macaques are superior conversationalists. We learned that lady humpbacks enjoy long-lasting friendships. Now research published in Current Biology shows that baboon ladies with good friends around them may live longer.

At Botswana’s Moremi Game Reserve, Joan Silk of the University of California, Los Angeles and her team spied on 44 female chacma baboons over the course of six years. Among other things, Silk looked at which girls had the most visitors and how often the women picked junk out of each other’s hair. In other words, true friendship. She also tracked each baboon’s circle of friends, seeing how each lady’s top three buddies changed over time.

Silk saw a correlation between sociability and longevity. She divided the baboons into three groups, and found that the least friendly lived 7 to 18 years, while the friendliest group lived from 10 years on (they were still kicking when the study ended). They also found that those baboons who formed stable, enduring bonds were more likely to have long lives than those with flightier friendship habits.

It’s tempting to look for parallels between baboons and humans, and indeed, the researchers engage in a little speculation.

Such findings in a nonhuman primate, the authors write, “suggest that the human motivation to form close and enduring bonds has a long evolutionary history.” … They note that previous research in humans has shown that socially isolated people suffer more from high blood pressure and sleep disorders and have longer wound-healing times. [ScienceNOW]

But back in the animal world, it’s still not clear how these stable friendships could make baboons live longer. It’s possible, they say, that more friendly grooming could mean fewer parasites, or more social interactions could mean more eyes to watch for predators.

“It all depends on what causes the death of female baboons, which is hard to determine because there’s seldom a single cause,” comments New York University anthropologist Clifford Jolly. [Science News]

In this baboon species, males miss out on friendship and its possible benefits. It seems that chacma males never groom each other, and only groom women before sex.

Follow Discover on Twitter.

Image: flickr / Graham Racher

Pocket Science – 2.1 billion year old fossils, and arm-wrestling a sabre-tooth cat | Not Exactly Rocket Science

Posted on July 6, 2010 by Danzig

Gabon fossils are earliest traces of multicellular life… or are they?

These unassuming fossils may be some of the earliest known examples of complex life on Earth, composed of many cells (like animals and plants) rather than just one (like bacteria). They were uncovered in Gabon by a Abderrazak El Albani from the University of Poitiers, and they’re around 2.1 billion years old. They have been preserved in remarkable detail for their age. They are centimetres in length, and El Albani thinks that they’re probably some of the oldest multi-cellular organisms so far discovered. If he’s right, they’re half a billion years older than the previous record-holders.

Leading a team of 21 scientists, El Albani has painstakingly analysed the fossils. Their three-dimensional structure came with radial slits, scalloped margins and a complicated folded centre. To the team, these complex patterns tell us that the fossils were not simply rock formations. Instead, they were the remnants of once-living things that grew through coordinated signalling between different cells. The fossils are also rich in the mineral pyrite, which is the work of decomposing bacteria; again, this suggests that they were once living.

Back when they were still alive, the Earth was a radically different place. Oxygen made up a small fraction of the atmosphere and a toxic mix of greenhouse gases choked the air instead. Still, things were on the up. The “Great Oxidation Event” was underway, kick-started about 300,000 years previously by tiny bacteria. These microbes pumped oxygen into the air around them as a waste product of photosynthesis, enriching the atmosphere with the gas that would change the planet’s fate. These rising oxygen levels could have been the trigger that allowed multicellular organisms to survive. Without the oxygen, they couldn’t have achieved a large size.

Of course, it’s possible that the fossils could simply be complex colonies of bacteria, rather than true multicellular organisms. El Albani doesn’t rule out that possibility but again, the fossils’ complex three-dimensional shapes don’t quite fit with the idea of a simple bacterial mat. They also contain chemicals called steranes, which often give away the presence of complex eukaryotic cells. But Philip Donoghue from Bristol University, while impressed with the fossils, thinks that we can’t rule out the bacteria idea yet. The steranes, for example, could have moved into the fossils from surrounding rocks. And some scientists aren’t even convinced that the Gabon fossils were once alive.

Bruce Runnegar, who studies the origins of multicellular life, says, “It is difficult to know if this is some unusually complex [non-living] structure, a feature made by a consortium of individual microbes, or evidence for primitive multicellular life.” Some of the fossils’ shapes – such as the wavy surfaces and radial slits – are sometimes seen when different kinds of fluids mix. “The wavy surfaces are unusual, but not unusual enough to convince me to put my money on these structures being “ancient representatives of multicellular life,” he says.

Reference: Nature http://dx.doi.org/10.1038/nature09166

Read more about these fossils, including opinions from several other scientists, at Nature News and an excellent explanation of why we can confidently say that the fossils at 2.1-billion years old at Highly Allochthonous

Sabre-tooth cats wrestled prey with powerful front legs

From looking at the skeleton of a sabre-tooth cat, it would seem obvious what its main weapons are. But impressive though the huge canines are, they’re only part of its arsenal. Its stocky frame and sturdy front legs are equally important. Julie Meachen-Samuels and Blaire van Valkenburgh from the University of California, Los Angeles, have studied the skeleton of Smilodon fatalis, the most famous of the sabre-tooth cats (they’re not tigers). Using a digital X-ray machine at the Smithsonian Institution, the duo showed that its humerus (the bone between shoulder and elbow) was reinforced by extra-thick bone.

Its outer shell, or cortex, was thickened to a greater degree than any other living cat. In terms of sturdiness, it even outclassed the equally extinct but considerably larger American lion. The extra reinforcement made Smilodon’s front legs very difficult to break, bend or compress. These sturdy limbs also had expanded attachment points for the cat’s relatively large muscles. The hind legs, while still thickened, was still within the range of normal variation for other cats.

This new research fits nicely with the modern image of Smilodon as a subtle killer that hunted in a very different way than modern cats. It combined elements of a wrestler and an assassin, grapping large prey to the ground with its powerful front legs, and killing them quickly with a lethal stab of its famous teeth.

Modern cats inflict death more slowly, with a suffocating bite to the throat. But there is no way that Smilodon could have done the same. Its skull and teeth are surprisingly weak, and might have broken during a protracted struggle. Instead, they were probably used to deliver an incisive and fatal bite to the blood vessels of the neck, after the prey had already been pinned. This specialisation allowed it to tackle very large prey, but it might also have been its downfall. As the largest mammals went extinct during the last ice age, Smilodon’s overpowering tactics would have done little good against smaller, more agile targets.

Reference: PLoS ONE to be confirmed; Image by Dantheman

If the citation link isn’t working, read why here

Gulf Coast Turtle News: No More Fiery Death; Relocating 70,000 Eggs | 80beats

Posted on July 6, 2010 by Danzig

oiled-turtle Things may be looking up, ever so slightly, for the Gulf of Mexico’s endangered sea turtles. A few days ago, environmental groups announced that they were suing BP and the Coast Guard over the “controlled burns” that were intended to burn off oil slicks in the water; the environmentalists said that sea turtles were getting caught in the infernos and burned alive. This morning a judge was prepared to hear arguments on a proposed injunction, but at the last minute the parties declared that they’ve reached a settlement.

The agreement comes in advance of an emergency court hearing set today in New Orleans federal court, where environmentalists sought to force BP to either stop controlled burns or place rescuers on the boats to scoop federally protected sea turtles out of floating sludge patches before the corralled oil is ignited [Bloomberg].

According to Sea Turtles Restoration Project, one of the plaintiffs in the case, BP and the Coast Guard have agreed to station a qualified biologist on every vessel involved in the burns, and to remove turtles from the burn area before setting the blaze. This is good news for the leatherbacks, loggerheads, and Kemps Ridley turtles that make their home in the Gulf. Of course, it would be better news if their home wasn’t saturated with oil and periodically set on fire, but we’ll take what we can get.

Elsewhere in turtle news, conservationists are preparing to collect 70,000 turtle eggs from Alabama and Florida beaches. The ambitious scheme, coordinated by the U.S. Fish and Wildlife Service, is seen as the best chance of preventing a massive die-off of the threatened creatures.
baby-loggerhead

“This is an extraordinary effort under extraordinary conditions, but if we can save some of the hatchlings, it will be worth it as opposed to losing all of them,” said Chuck Underwood of the U.S. Fish and Wildlife Service. “We have a much higher degree of certainty that if we do nothing and we allow these turtles to emerge and go into the Gulf and into the oil … that we could in fact lose most of them, if not all of them,” he added. “There’s a chance of losing a whole generation.” [AP]

In the next couple of weeks, turtle experts will start the painstaking process of excavating up to 800 nests; each egg must be carefully lifted from its nest without rolling or repositioning it, to avoid disrupting the growing embryo inside. Then the eggs will be transported to a climate-controlled hanger at Kennedy Space Center on Florida’s east coast where they’ll stay until hatching. Finally, if all goes well, the next generation of loggerheads and other sea turtles will be set loose in the oil-free Atlantic.

Image: Sea Turtle Restoration Project / Blair Witherington

How to Build a Car for Blind Drivers: With Vibro-Gloves and Air Puffs | Discoblog

Posted on July 6, 2010 by Danzig

A group of new drivers may never watch where they’re going. They won’t need to: Instead, they’ll listen and feel. The National Federation of the Blind and Virginia Tech are developing a car for the blind, and hope to demonstrate a prototype in January of 2011.

Don’t be fooled: Unlike like the do-it-themselves cars that compete as part of the DARPA Urban Challenge, this car will actually let the blind driver take control and drive, and will require the same quick judgments needed by sighted drivers. The only difference will be how these drivers sense what’s around them.

Instead of looking at the car cutting them off or the pedestrian about to step into traffic, the blind drivers must feel them or hear them. Though the final design is still in the works, the car may communicate an obstacle’s presence by audio instructions, vibrating gloves (called DriveGrip), and puffs of compressed air (called AirPix). AirPix is sort of like a map of the road, a flat board with different air jets corresponding to different obstacles.

This vehicle is the next step in an ongoing project at Virginia Tech. Last summer, mechanical engineering professor Dennis Hong and his team unveiled a buggy that used laser tracking systems, audio commands via headphones, and a vibrating vest to tell blind drivers where to go. Several blind volunteers successfully steered the buggy through an unfamiliar obstacle course (see video below).

Mark Maurer, the president of the National Federation of the Blind, came up with this challenge about a decade ago. Even after this new car’s unveiling next January at the Daytona International Speedway, it may still be a long while before blind drivers take to the road. But, Maurer says, that’s not the point. Instead he wants to show that blindness is a difference rather than an insurmountable impairment. He told The Telegraph:

“We’re exploring areas that have previously been regarded as unexplorable. . . We’re moving away from the theory that blindness ends the capacity of human beings to make contributions to society.”

Image: iStockphoto

More markers, or more populations? | Gene Expression

Posted on July 6, 2010 by Danzig

Here’s a letter to The American Journal of Human Genetics worth reading, Genetic Landscape of Eurasia and “Admixture” in Uyghurs:

…In the papers…by Xu and Jin, the genetic structure of Uyghurs was described by 8150 ancestry-informative markers (AIMs). These markers estimated the admixture rate of the Uyghur population to be around 50% East Asian ancestry by comparing Uyghurs to East Asians and Europeans. However, we suspect that the estimate of Xu and Jin may be considerably biased by insufficient reference population coverage….
The difference between the estimate of Xu and Jin (52%) and our estimate (31%) may stem from either the different population coverage or the sample size. We analyzed a different and larger sample of Uyghur individuals (n = 48) than that analyzed by Xu and Jin….Their small sample size may have contributed to their overestimation of the European component to admixture (i.e., to cluster assignment). However, the insufficient population coverage may be more responsible for the difference than the sample size or the number of markers. Concerning the number of markers, it is known that a relatively small but specifically selected number of AIMs can accurately predict ethnicity proportion…As the two papers of Xu and Jin have demonstrated, the estimated admixture rates reported did not change much regardless of whether they were using chromosome 21 data only or the whole genome, and thus a large number of markers may not be necessary to estimate the “admixture” rate of Uyghurs. When we analyzed only the 12 markers with the highest F_ST values in our samples…the Uyghurs had a 30.2% assignment at K = 2 to the Europe and Western Asia cluster. This estimate was not significantly different from the above 31.2% when using all 68 markers. We consider it unlikely that a different set of appropriately chosen SNPs would give a markedly different answer based on unpublished data on some of these same populations….

Basically the authors are arguing that you’d rather have a more diverse range of populations (to get more between population genetic variance) than just keep increasing the number of markers within individuals to really capture geographic diversity. Reference population matters. I know that 23andMe tells South Asians to expect to get back that they’re 70-90% “European,” with the balance “East Asian.” People with only Native American ancestry are going to be 75% “East Asian” and 25% “European.” These sorts of results from the reference populations are pretty misleading in my opinion. If you model the variation of all the world’s populations as the combination of variation of a few reference populations you’re getting a stylized fact which is confusing if you don’t know to interpret it correctly.

Below is figure one, where they show the difference between K = 2 and K = 6 (assume two or six ancestral populations for your data set). The map illustrates the distribution of K = 6, as the intensity of each color represents the current contribution in that region of a K ancestral group.

gr1

Did Hayabusa return empty-handed? | Bad Astronomy

Posted on July 6, 2010 by Danzig

The New York Times is reporting that the Japanese space probe Hayabusa — sent to physically land on the asteroid Itokawa, get a sample of the rock, and return to Earth — may have come back without such samples. While it’s not confirmed yet, it will be disappointing news if true.

Hayabusa was plagued with problems, from faulty engines to a misfiring mechanism designed to force pieces of the asteroid into a collection container. Despite these issues, engineers were able to coax the probe back into an Earth-return orbit and retrieve the sample container after a dramatic re-entry. Apparently there are traces of gas which may be vaporized rock from Itokawa, but no solid chunks. I’m sure they’ll be scouring the container to look for microscopic pieces as well.

hayabusa_itokawa I hope they find some. Itokawa is a rubble pile, an asteroid that has been shattered by collisions and held together by its own gravity. We know very little about such asteroids, and we need to find out more if we should ever see one on a collision course with Earth and want to push it out of the way. And we do want to do that!

But even if Hayabusa didn’t get any samples, Japan learned a lot of valuable information on how to run (and save!) a space mission of this depth and complexity, and scientists got a lot of info about Itokawa itself. Hayabusa voyaged for seven years in space, and despite these problems I think that the scientists and engineers at the Japanese space agency JAXA should be proud.

Should We Allow a Massive Oil Pipeline from Canada to Texas? | 80beats

Posted on July 6, 2010 by Danzig

oil_sands With the perpetual flow of filthy crude from BP’s oil leak in the Gulf of Mexico, just about anything seems like a better energy solution than deep sea offshore drilling. One new proposal, though, has the potential for similarly disastrous environmental harm.

The Keystone XL is a huge proposed pipeline that could carry oil from Canada’s oil sands on a snaking path through the American Midwest and all the way down to Texas, where it will be refined. The idea has been up for public comment for months, and that period comes to a close soon. So, should we build this thing?

YES

There is one good thing about the project: It would be a source of energy that’s not the Middle East, Iran, Venezuela, or another region or country hostile to the United States.

From an energy perspective, Keystone XL delivers one thing the United States needs: plentiful oil from a friendly neighbor. Most oil companies have invested heavily in Canadian oil sands and are firmly behind it [The New York Times].

The project would bring in another million barrels of oil per day from Canada, which is already our biggest foreign oil supplier.

A study released this month by the Perryman Group, an economic analysis firm based in Waco, concluded that the project could generate as much as $2.3 billion in new spending for Texas during construction and $1.1 billion in property taxes to local and county governments over the pipeline’s operating lifetime [Houston Chronicle].

The oil sands are one of the dirtiest energy projects in the world. The oil is dirty to extract and dirty to refine, plus there are the transportation dangers.

The energy-intensive process emits three times more greenhouse gases per barrel than production of conventional oil, environmental groups say. Friends of the Earth, which opposes the project, estimates that the pipeline would increase greenhouse gas emissions by 38 million tons, equivalent to 6 million new cars on the road [Houston Chronicle].

Oil refining is no clean business anyway, and this oil could be even worse: watchdog groups like Air Alliance Houston say that it causes more emissions of sulfur dioxide and particulate matter. Unsurprisingly, the company behind the project disputes this and also promises that pipelines are the safest way to transport oil. Forgive us, though, if we’re still a little wary of assurances that everything will fine.

At the hearing on Tuesday, Tom Rudolph, a farmer from Circle, Mont., expressed his reservations “as a landowner directly on the route.” He called the draft environmental impact statement “insufficient,” noting in particular the lack of a “complete spill response plan” in the event of a leak. “The disaster in the gulf serves as a warning,” he said [The New York Times].

We should also consider that the Canada-to-Texas route passes through some of the most valuable agricultural land in the United States. In addition, the area is home to the giant Ogallala Aquifer, which provides drinking and irrigation water for the High Plains.

Image: NASA

Ice Ice Baby | Visual Science

Posted on July 6, 2010 by Danzig

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If you have any questions or feedback, please email webmaster@discovermagazine.com. Thank you for reading Discover, and we apologize for the inconvenience.

A Sketch of Science [Science Tattoo] | The Loom

Posted on July 6, 2010 by Danzig

Caitlin tattoo tree Caitlin, a graduate student, writes:

About four years ago, a close friend from college got her first tattoo – something meaningful and marking a particular point in her life – and she asked me if I would ever get one. I said sure, but that at that point in my life there was nothing I could come up with that was meaningful enough to have permanently etched in my skin. That was my first year of graduate school and I was still very unsure of myself and my future.

Four years of graduate school later finds me in the final stages of earning a Ph.D. in evolutionary biology – a place I was not convinced I was cut out to reach at the start of graduate school. After 2009’s year of Darwin celebrations, including my own involvement organizing a conference celebrating 150 years of evolutionary biology, the perfect tattoo came to me in class one day in March, and I found myself at the tattoo parlor by the end of that week.

My tattoo is Darwin’s very first phylogeny, from his Notebook B on Transmutation of Species and it is on my right shoulder. These notebooks contained much of his brainstorming on evolution after returning from the Beagle, and I was able to see this one in person at the American Museum of Natural History’s Darwin exhibit in 2006. I also added his signature and the date which can be found on the inside cover of the notebook.

I chose this particular piece of Darwinia for several reasons. As a perpetual student of science and of nature in particular, I love the slight hesitation and perhaps excitement in the “I think.” I am amazed that Darwin was thinking about phylogenies in 1837, 22 years before the Origin was published – that you can see the seed of his great work (and the preface to the only figure in the Origin) so early in his writings. The phylogeny itself as an image is meaningful because I study speciation, and spend a great deal of time studying, thinking about, and building my own phylogenies. I had also selected it to be part of the cover of the program for the conference I was involved in, and many attendees asked me about it. In short – it carries a lot of meaning to me.

So, my tattoo honors Darwin, the father of my field; it represents my own personal research; and it exemplifies the slight hesitation and excitement of scientific discovery that I hope will stay with me always as I launch my academic career. It is a mark of confidence, in myself, and my chosen profession. I have no doubt that I will never regret permanently etching this image on my skin, and I know that it will serve as a reminder to me that even though the pursuit of scientific knowledge is a long, sometimes daunting journey, I love what I do and I can’t imagine doing anything else.

Click here to go to the full Science Tattoo Emporium.

Pimm on the Oil Spill Wildlife Crisis | The Intersection

Posted on July 6, 2010 by Danzig

Just because I am no longer at Duke, doesn't mean I don't keep tabs on Stuart Pimm and the rest of the family. Recently Stuart spoke to the Endangered Species Coalition about the oil spill in the Gulf of Mexico describing how it's been so devastating to wildlife, why scientists cannot predict the long-term ecological damage, and the scale of restoration that will be required. This is a sad, but very important podcast and I encourage readers to listen here. You can also read more from Stuart on biodiversity at his terrific National Geographic blog.

Lefties Cry Discrimination Over iPhone’s Faulty Antenna | Discoblog

Posted on July 6, 2010 by Danzig

iPhone-4 Believe me, there are many inconveniences that come with being left-handed: Your childhood art projects look like they were accomplished by jittery beavers on account of those damn right-handed safety scissors, and simple kitchen tools like can-openers and soup ladles can become the enemy. But now we lefties can add in a high-tech complaint: The iPhone 4’s antenna problems are particularly troublesome to the likes of us.

The iPhone 4’s sales have been spectacular since it debuted last week, but consumers immediately noticed a glaring problem with the metal band that wraps around the phone’s perimeter and acts as an antenna; holding the phone in certain ways interfered with the antenna and could lead to dropped calls. In response, Apple advised customers to “avoid gripping it in the lower left corner” when making or receiving a call. That’s when a U.K. group called the Left-Handers Club got irate.

According to The Telegraph, spokeswoman Lauren Milsom issued a blistering statement:

“It seems ludicrous to suggest that 10 per cent of potential users should be told they have to adopt a less natural hand hold to use this latest technology. I would strongly suggest that Steve Jobs employs left-handers in his design and testing team in future, and urgently address this issue to ensure the phone is fit for purpose.”

Lefties are reportedly not the only ones upset about the apparent design flaw. One couple that’s suing Apple says their phone’s faulty antenna has caused them “emotional distress,” and class-action lawsuits are starting to spring up.

Image: flickr / Jorge Quinteros

Cassini’s slant on the rings | Bad Astronomy

Posted on July 6, 2010 by Danzig

Check out this latest image from Cassini at Saturn!

[Click to embiggen.]

Oh, wow! This was taken when the spacecraft was almost in the plane of the rings, which are incredibly thin. You can see several different rings, including the broad A ring in the middle and the thin F ring on the outside. There are also two moons: Janus (the larger one, above) and Prometheus (smaller, below). Janus is about 180 km (110 miles) across, which isn’t terribly big, but Prometheus is even smaller: 120 km (75 miles).

This picture made me smile not only because it is carved out of raw coolness, but also because it’s the complement of an earlier image from Cassini (to the right). The earlier shot is of the moon Epimetheus, which shares an orbit with Janus, and Pandora, which shares an orbit with Prometheus! So the two images go together like a pair of gloves, each showing one of a pair of orbit-sharing moons.

Also, in the big image, take a look at the thin F ring: follow it from the far side to the near side. Just as you pass the bottom left and start moving to the upper right, do you see two spots where it appears thicker, like it’s lumpy? Well, it is lumpy! Pandora and Prometheus are the ring’s shepherd moons, using their gravity to keep the ring particles tightly in place. But when they pass any given point in the rings, their gravity leaves a wake behind, almost like a boat’s wake. That deforms the ring a bit, and you can see that in this image as a thickening in the ring. The animation I’ve inserted here actually shows that as it happens.

Amazing, what can be seen in a single image from Saturn. Especially if you have other images to back it up.

I like this new image a lot. Hmmm, have I found my new desktop picture? Why yes, yes I have.

Tip o’ the CICLOPS to Carolyn Porco.

Related posts:
- A little weekend Saturn awesomeness
- Cassini eavesdrops on orbit-swapping moons
- Dr. Tongue’s 3D House of Prometheus
- The bringer of fire hiding in the rings

Brilliant & Reclusive Russian Mathematician Doesn’t Need Your Prize Money | 80beats

Posted on July 6, 2010 by Danzig

Grigori Perelman isn’t much for prizes. This week Perelman, one of the world best and strangest mathematicians, proved it again by turning down a $1 million dollar prize from the Clay Mathematics Institute Millennium Prize for solving one of the most troubling math problems of the last century.

The Poincaré conjecture, named after prominent French mathematician Henri Poincaré, involves a complex problem in the field of topology — an important area of math that studies the enduring properties of objects that are stretched or otherwise deformed, but not torn or otherwise reconstituted. Scores of prominent mathematicians tried to solve it over decades but failed, leading to its characterization as the Mount Everest of math [Washington Post].

In 2003 Perelman put forth his solution to the conjecture, but not in the traditional way of putting it through the peer review process. Instead, he simply emerged from the shadows and threw his work up on the Internet with in a rebellious, “ta-da,” and waited for the world to catch up.

After a brief barnstorming tour in the United States, during which he refused interviews, Dr. Perelman returned to Russia, leaving the world’s mathematicians to pick up the pieces and decide whether he had really done it. A worldwide race to retrace, explicate and check Dr. Perelman’s proof ensued. In the meantime, Dr. Perelman quit his post at the Steklov Mathematical Institute, moved in with his mother and ceased communicating with the outside world [The New York Times].

Therefore, confirming what Perelman had achieved took several years of work fraught with difficulty understanding his methods (and rivalry with mathematicians like Shing-Tung Yau), as documented in a great New Yorker piece on Perelman from 2006.

It was astonishingly brief for such an ambitious piece of work; logic sequences that could have been elaborated over many pages were often severely compressed. Moreover, the proof made no direct mention of the Poincaré and included many elegant results that were irrelevant to the central argument. But, four years later, at least two teams of experts had vetted the proof and had found no significant gaps or errors in it. A consensus was emerging in the math community: Perelman had solved the Poincaré. Even so, the proof’s complexity—and Perelman’s use of shorthand in making some of his most important claims—made it vulnerable to challenge. Few mathematicians had the expertise necessary to evaluate and defend it [New Yorker].

Perelman turned down the 2006 Fields Medal, and now has officially turned down the Clay prize as well. The reason, according to the reclusive Perelman, is that he built on the work of the American mathematician Richard Hamilton, who deserves as much credit as him. The Clay leaders tried to convince Perelman he should accept, since all great work is built on the shoulders of giants. But, true to form, the eccentric genius stays quiet and hidden away in Russia.

Related Content:
80beats: Can a Google Algorithm Predict Nobel Prize Winners?
80beats: How the Russian Spies Hid Secret Messages in Public, Online Pictures
DISCOVER Interview: The Math Behind the Physics Behind the Universe
DISCOVER: Top Math Stories of 2006, featuring Perelman’s achievement

Image: American Mathematical Society

Tibetans May Be the Fastest-Evolving Humans We’ve Ever Seen | 80beats

Posted on July 6, 2010 by Danzig

Tibetan_lady Clearly, the people of Tibet must have evolved quickly to tolerate a life spent living at the top of the world. How quickly? A study out in this week’s Science, which compared Tibetans to Han Chinese to see the differences in their DNA, says that the two groups may have diverged no more than 3,000 years ago. If natural selection has changed Tibetans in such a short time, it would be the fastest known example of human evolution. But not everybody is buying this time line.

As DISCOVER noted when a similar study by another team came out in May, natives of the Tibetan plateau seem to survive the altitude because their bodies make less hemoglobin. It’s somewhat counter-intuitive:

In theory higher levels of haemoglobin would be beneficial, because this would improve oxygen transport. But high levels could make the blood thicker and less efficient at carrying oxygen, says Jay Storz of the University of Nebraska-Lincoln [New Scientist]. (Storz writes the accompanying commentary in Science.)

Looking at the differences in genes that regulate that, the team found vast differences between the Han and the Tibetans, with one version appearing in 87 percent of Tibetans studied but only 9 percent of Chinese. However, the assertion by the scientists at the Beijing Genome Institute—that their findings mean the two group broke apart just three millennia ago—has ruffled archaeologists who believe that the Tibetan plateau has been continuously occupied for much, much longer: more like 7,000 to 21,000 years.

For more about all of this, check out Razib Khan’s post at Gene Expression.

Image: Wikimedia Commons

Big bruiser stars form like their wimpy little siblings | Bad Astronomy

Posted on July 6, 2010 by Danzig

Astronomers using the UK’s Infrared Telescope (UKIRT) have made an important discovery: massive stars form much like lower mass stars do.

That doesn’t seem surprising, does it? Ah, but it is. It turns out that massive stars are different than the hoi polloi like the Sun, and it’s a bit puzzling that they can form at all!

As I’ve written many times before, stars form from clouds of gas and dust. A cloud can be huge, light years across, its massive gravity balanced by internal heat. But collisions between clouds or nearby exploding stars can disturb that equilibrium, compressing the cloud. Random eddies and whorls in the cloud can be accelerated, amplified by the collapse, giving the entire complex an overall rotation. Random collisions between pockets of matter inside the cloud slowly rob them of energy, causing them to move inward, falling toward the cloud’s equator. What was once a giant amorphous mass is now a relatively rapidly spinning disk of material.

The disk gets denser toward the center. As the material compresses there, it heats up. Eventually, if enough matter piles on, the temperature and pressure at the very center can be enough to fuse hydrogen into helium, and a star is born.

But there’s more to this story. Massive stars are far hotter than lower mass stars. As the material from the disk accretes onto the protostar, the protostar gets hotter. If it gets too hot, it’ll blow away the disk, preventing the star from gaining any more mass. Yet we see more massive stars. How do they form then? Is it the merging of two lower mass stars, or some other process? Any scenario like that would mean that massive stars form differently than lower mass stars, and we should be able to see that.

Enter the UKIRT observations. It’s really hard to see what’s going on deep in the heart of a star-forming cloud, because they’re opaque to optical light. Infrared light, however, gets out. Astronomers used UKIRT to look at 50 high-mass young stellar objects, as they’re called, to see if they reveal themselves to be different than lower mass stars.

The result they found surprised them: these hefty stars form pretty much like lighter-weight stars.

The key to this was the presence of jets, beams of matter and energy blasting out from the poles of the stars. These jets are focused by a lot of forces, but critical to them is the presence of the disk of material from which the star forms. They saw these jets coming from massive young stars (like in the picture above; the red glow is from material in the jets) and they look pretty much like they do in their low mass star counterparts. Not only that, the jets seen in massive stars are well-defined and don’t appear to depend in any way on the amount of energy the star is producing; fiercely hot and bright stars make jets as easily and as nicely as relatively calmer stars.

A study last year indicated that instabilities in the cloud as it collapses help the massive stars form, but that was done in a computer by modeling the physics. These new observations show that this process may yet be correct, since there’s no need to make a massive star by colliding smaller ones, for example. It’s not proof, but it doesn’t contradict the earlier test either.

Still, what’s clear is that whatever process is going on in the heart of a star-forming cloud appears to work the same way for stars up to a mass of at least 30 times the Sun’s mass (the astronomers didn’t observe any stars more massive than that). This is good news! The puzzle of the formation of massive stars just had another puzzle piece fall into place.

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