Now there’s data–actual data–showing how few climate scientists doubt the existence of climate change. From Science Daily:

The small number of scientists who are unconvinced that human beings have contributed significantly to climate change have far less expertise and prominence in climate research compared with scientists who are convinced, according to a study led by Stanford researchers.

–

Expertise was evaluated by the number of papers on climate research written by each individual, with a minimum of 20 required to be included in the analysis. Climate researchers who are convinced of human-caused climate change had on average about twice as many publications as the unconvinced, said Anderegg, a doctoral candidate in biology.

Prominence was assessed by taking the four most frequently cited papers published in any field by each scientist — not just climate science publications — and tallying the number of times those papers were cited by other researchers. Papers by climate researchers convinced of human effects were cited approximately 64 percent more often than papers by the unconvinced.

–

“I never object to quoting opinions that are ‘way out.’ I think there is nothing wrong with that,” said Stephen Schneider, professor of biology and a coauthor of the paper in Proceedings of the National Academy of Sciences. “But if the media doesn’t report that something is a ‘way out’ opinion relative to the mainstream, then how is the average person going to know the relative credibility of what is being said?”

“It is sad that we even have to do this,” said Schneider. “[Too much of] the media world has just folded up and fired its reporters with expertise in science.”

The Stanford team is prepared for the doubters of anthropogenic climate change to object to their data.

Unfortunately, I am too. Carry on…

(H/T Philip)

The Bad Astronomer’s secret media project has been revealed… Phil will have his own Discovery Channel show called Bad Universe–and I can’t wait to watch!! Check this out:

The summer of our government’s discontent (with personal genetics tests) continues. Yesterday an investigator with the Government Accountability Office reported back to Congress on its undercover investigation of the tests on the market, saying that testing the DNA of GAO staffers returned frequently contradictory and confusing answers.

“Consumers need to know that today, genetic testing for certain diseases appears to be more of an art than a science,” said GAO investigator Gregory Kutz [CBS News].

Here at 80beats, we’ve gone over some of the potential problems with these tests. DISCOVER blogger Ed Yong covers them in great detail in a post he wrote this week after getting his genes tested by 23andMe, including the dearth of data appropriate for interpreting results if you’re of Asian rather than European descent, and deciding whether to peek into the data that says whether you have a much higher than average risk for Parkinson’s disease.

The federal government began to worry about the same things this summer after Walgreens announced plans to sell tests by Pathway Genomics in its drug stores. Then, last month, the FDA announced that it intended to regulate these tests, whereas before they existed in a cloud of regulatory uncertainty—Pathway had told Walgreens the tests didn’t require the government’s OK. Congress got in on personal genomics, too, which led to this GAO investigation.

The GAO report suggests the companies still have a long way to go in drawing accurate conclusions. The agency submitted DNA samples from five staffers to four different genetic testing companies. When considering the same disease, the companies’ results contradicted each other nearly 70 percent of the time, according to GAO. In response to the same patient’s DNA, one company claimed he was at above-average risk for prostate cancer, a second said he was below average and two others said his risks were average [AP].

The FDA is holding meetings this week, trying to decide how it will regulate the tests.

Related Content:
Not Exactly Rocket Science: How I Got My Genes Tested
80beats: FDA: We’re Going To Regulate Those Personal Genetics Tests, After All
80beats: 5 Reasons Walgreens Selling Personal DNA Tests Might Be a Bad Idea
Discoblog: Welcome, UC Berkeley Freshmen! Now Hand Over Your DNA Samples
Discoblog: 23andMe To Customers: Oh Wait, Those Are Somebody Else’s Genes

Image: flickr / nosha

There will be no carbon cap-and-trade provision in this summer’s energy legislation in the Senate. Nor will there be a renewable energy standard (RES)—a mandate that a certain percentage of national energy come from renewable sources. Those are the two major losses for climate-watchers today as Senator Harry Reid and other Democrats announced they would drastically scale back their energy proposals in the face of what looks like an non-winnable fight before the 2010 midterm elections.

Instead, the Senate will consider a much smaller bill before the August recess.

The measure would include money for home energy-efficiency retrofits, for encouraging natural-gas-powered vehicles and for land and water conservation, Reid said [Los Angeles Times].

So what now for the more ambitious ideas to reduce greenhouse gas emissions and adopt renewable energy technologies?

Compromise

David Moulton, director of climate policy at the Wilderness Society, said renewable energy supporters and companies desperately want the shot in the arm an RES could provide. But they might not get it without a compromise proposal.

One way to win additional votes for the measure could be to develop a “big tent bipartisan approach” that would expand the renewable electricity standard to a “clean electricity standard” including nuclear, carbon capture and storage and natural gas [The New York Times].

Push in other directions

Senators John Kerry and Joe Lieberman have produced separate bills that specifically target power utilities for emissions reductions, and that bill might continue.

Reid left open the possibility that efforts to cap carbon emissions in the electric power sector could resume this fall. Sen. John Kerry (D-Mass.), an architect of Senate climate policies, vowed to continue pushing. “Harry Reid, today, is committed to giving us that opportunity, that open door over the next weeks, days, months, whatever it takes to find those 60 votes,” Kerry said. “The work will continue every single day” [The New York Times].

Use the EPA

Obama has pushed the U.S. Environmental Protection Agency to take unilateral action if Congress fails to pass a bill. The EPA has begun issuing rules to cut emissions from cars and requiring power plants to have permits to emit carbon dioxide [Reuters].

However, given that EPA leadership changes from administration to administration, the unclear limits of its authority, and the feeling that Congress ought to make the rules on this important issue, most people see this as an unsatisfying answer. Congressional Republicans even tried to explicitly block the EPA’s power to regulate greenhouse emissions, which the 2007 Supreme Court case Massachusetts v. EPA upheld. That effort last month fell short, but members of Congress may try to revive the issue, fearing the EPA will act now that the legislative branch has failed to do so.

Related Content:
80beats: Skip the Political Babbling: Here’s What the Kerry-Lieberman Climate Bill Says
80beats: Climate Bill Passes in the House, Moves on to Senate
DISCOVER: It’s Getting Hot in Here: The Big Battle Over Climate Science, interviews with Judith Curry & Michael Mann
DISCOVER: The State of the Climate—And of Climate Science

Image: Wikimedia Commons

One of the marvels of Comic-Con is that when a panelist asks the people in the room whether they’d be willing to risk a fatal mechanical failure for the chance to go into space, everyone raised their hands. It’s the kind of place where nerds roam free, geeks can be both predator and prey, and the answer to the question, “How about going to space?” is foreordained.

The panel I’m referring to focused on the question of whether private companies are better suited to taking humanity into space, or whether NASA is doing awesome work and we, as a society, should just keep on keepin’ on. To help answer the question, the panel featured Mark Street (from XCOR), John Hunter (Quicklaunch), Chris Radcliff (San Diego Space Society), Dave Rankin (The Mars Society), Molly McCormick (Orbital Outfitters) and was moderated by Jeff Berkwits (editor and writer).

The group did praise NASA for the Mars Rovers and the Hubble space telescope (referring to the beautiful Hubble pictures, Rankin said, “let it not be said the federal government doesn’t fund the arts”) but generally they brought the hammer down on NASA and its private counterparts like Boeing and Lockheed Martin: NASA is too big, too old, and is constantly trying to perfect old ideas rather than introduce new ones.

And the group praised small “new-space” companies for being willing to fail and try, try again as they strain to bring space tourism to everyone.

But perhaps most interesting was the almost uncontested assertion that space flight will never really be profitable.

“Ninety percent of mass is propellant in space, and it’s $5000 a pound with rockets, SpaceX is is $2000 a pound,” Hunter said. “Going to Mars, that’s one million pounds per person. Each person is going to cost $5 billion in propellant alone.”*

But for all that Hunter threw cold water on the proceedings, he also said money really isn’t why we go into space.

“The only thing that makes money in space is communications satellites. Mining doesn’t pan out,” he said. “You have to go to space for manned exploration for the human spirit. You’re not going to make money there.”

And the members of the panel sagely nodded their heads. For all that these folks recognize the challenges of space flight, and the amount of money and smarts that will be required, they’re generally optimists: Every single one said they expect space tourism will become reality…eventually.

* This quote added later to correct a paraphrase of mine. Thanks to commenters Jadon and eyesoars for the correction.

They were perfectly lovely, the beets Surendra Pradhan and Helvi Heinonen-Tanski grew: round and hefty, a rich burgundy, their flavor sweet and faintly earthy like the dirt from which they came. Unless someone told you, you’d never know the beets were grown with human urine.

Pradhan and Heinonen-Tanski, environmental scientists at the University of Kuopio in Finland, grew the beets as an experiment in sustainable fertilization. They nourished them with a combination of urine and wood ash, which they found worked as well as traditional mineral fertilizer.

“It is totally possible to use human urine as a fertilizer instead of industrial fertilizer,” said Heinonen-Tanski, whose research group has also used urine to cultivate cucumbers, cabbage and tomatoes. Recycling urine as fertilizer could not only make agriculture and wastewater treatment more sustainable in industrialized countries, the researchers say, but also bolster food production and improve sanitation in developing countries.

Urine is chock full of nitrogen, potassium, and phosphorus, which are the nutrients plants need to thrive—and the main ingredients in common mineral fertilizers. There is, of course, a steady supply of this man-made plant food: An adult on a typical Western diet urinates about 130 gallons a year, enough to fill three standard bathtubs. And despite the gross-out potential, urine is practically sterile when it leaves the body, Heinonen-Tanski pointed out.
The nutrients in urine are also in just the right form for plants to drink them up, said Håkan Jönsson, a researcher at the Swedish University of Agricultural Sciences in Uppsala who was not involved in the beet study but has researched urine recycling for over 15 years. Food gives us nutrients like nitrogen as parts of complex organic molecules, but our digestive system strips them down into the basic mineral form that plants need—so “we have done half of the job,” Jönsson said.

A small but dedicated contingent of organic gardeners in the United States and Europe already fertilize with urine at home, and researchers in Scandinavia have run pilot projects to recycle locally collected urine on small farms. But urine recycling may never become a part of large-scale farming in industrialized countries, because implementing it would mean drastically remodeling the sewage system in order to collect and transport liquid waste.

It would also mean swapping regular flush toilets for separating toilets, where a divided bowl and independent set of pipes sort the urine out from everything else. This detail is a roadblock, Jönsson said, because many people don’t want a toilet that looks strange. “Acceptance is a big problem for this kind of system.”

For the recent experiment with beets, the urine was obtained from specialized toilets in private homes. Heinonen-Tanski’s group planted four plots of beets and treated one with mineral fertilizer, one with urine and wood ash, one with urine alone, and one with no fertilizer as a control.

After 84 days, about 280 beets were harvested. The beetroots from the urine- and urine-and-ash-fertilized plants were found to be, respectively, 10 percent and 27 percent larger by mass than those grown in mineral fertilizer. By grinding some beets to powder and subjecting them to chemical analysis, the researchers determined that all the beets had comparable nutrient contents—and according to a blind taste-testing panel, the taste was indistinguishable. The results are published in the February 10 issue of the Journal of Agricultural and Food Chemistry.

Effective fertilization isn’t the only benefit of recycling urine, Heinonen-Tanski suggested in a review paper in the January 2010 issue of the journal Sustainability. The separating toilets that collect urine use less water than flush toilets, she writes, and the simplified waste stream requires less energy in sewage treatment.

“Agricultural and health organizations should encourage people to use human urine as a fertilizer,” Heinonen-Tanski concluded in that paper, especially in areas where wastewater treatment is unavailable or ineffective.

Though he’s skeptical that it will ever happen on a large scale, Jönsson does practice urine fertilization himself: He and his wife use what they collect from their separating toilet to nourish their garden at home in Sweden. The urine one person produces can fertilize about ten square feet of soil a day, Jönsson said—but there’s been less to go around since his three children left home.

“It’s enough for the vegetables and the flowers,” he said, “but I can only fertilize very lightly on the lawn. Otherwise I run out of urine.”

By Mara Grunbaum. This article is provided by Scienceline, a project of New York University’s Science, Health and Environmental Reporting Program.

Image: flickr / B.D.’s World

Not Exactly Pocket Science is a set of shorter write-ups of new stories with links to more detailed takes by the world’s best journalists and bloggers. It is meant to complement the usual fare of detailed pieces that are typical for this blog.

Frogs evolved to jump before they perfected landings

Most frogs are can leap large distances in a single bound, jumping forward with a thrust of their powerful hind legs and landing gracefully on their front ones. But it wasn’t always like this. A study of one of the most primitive groups of frogs suggests that the first frogs landed in an awkward belly-flop. These animals evolved to jump before they perfected their landings.

Virtually all frogs jump and land in the same way. But Richard Essner Jr from Southern Illinous University discovered a unique leaping style in the Rocky Mountain tailed frog. This species belongs to a group called the leiopelmatids, more commonly (and accurately) known as the “primitive frogs”. Using high-speed video footage, Essner showed that the tailed frog’s landings are an awkward mix of belly-flops, face-plants and lengthy skids. Only when it grinds to a halt does it gather its outstretched limbs together. By contrast, two more advanced species – the fire-bellied toad and the northern leopard frog – rotate their limbs forward in mid-air to land gracefully. The tailed frog managed to jump a similar distance, but its recovery time was longer.

These results support the idea that frogs eventually evolved their prodigious jumping abilities to escape from danger by rapidly diving into water. Landings hardly matter when you’re submerged and the ability to pull them off elegantly only evolved later. Essner thinks that doing so was fairly simple – if the tailed frog starts pulling its legs in just slightly earlier, it would land with far more poise. This simple innovation was probably a critical one in frog evolution. The primitive frogs never got there, but they have other ways of coping with their clumsy crash-landings. They’ve stayed very small to limit the injuries they sustain, and they have large shield-shaped piece of cartilage on their undersides to protect their soft vital organs.

Reference: Naturwissenschaften http://dx.doi.org/10.1007/s00114-010-0697-4; Video by Essner; soundtrack by me.

More on frogs: Tree frogs shake their bums to send threatening vibes, pesticide-stricken frogs, ‘Wolverine’ frogs, a lungless frog, and seven habits of highly successful toads

Changing climate fattens marmots

The media is rife with tales of animals from polar bears to corals suffering as a result of climate change. But some species stand to gain from the rising global temperatures. In Colorado’s Rocky Mountains, warmer climes allow the yellow-bellied marmot to awaken from its winter hibernation earlier. With more time available to eat, they become bigger and so do their populations. In just three decades, their numbers have tripled.

Arpat Ozgul from Imperial College London studied a 33-year census of Colorado’s marmots, where individuals have been tracked over their entire lifetimes. These rodents spend the winter hibernating in their burrows. But since 1976, they have been waking up earlier and earlier in the year, presumably because of a rise in warm days. That gives them more time to eat and grow before their next hibernation, and the adults have become around 10% heavier. Ozgul found that being fatter offers many advantages for a marmot – females are more likely to breed, youngsters grow more quickly, and adults are more likely to survive their next bout of hibernation.

It’s no surprise that their population has shot up dramatically, although surprisingly, this wasn’t a gradual process. Their numbers seemed to be fairly stable but they passed a tipping point in 2000 and have skyrocketed ever since. By modelling the changes in their bodies over time, Ozgul concluded that the marmots haven’t changed much genetically – their extra pounds are the result of their response to environmental changes. For example, the bluebells that they like to eat declined after 2000, which might have prompted them to seek other fattier foods.

But Ozgul worries that this boom period has a bust on the horizon – it’s a short-term response to warmer climate. These are animals that are adapted to chilly mountainous temperatures and they don’t fare well in heat. If temperatures continue to rise and summers get longer and drier, their health might suffer and their populations might crash.

More on this story from Jess McNally at Wired and Lucas Laursen at Nature

Reference: Nature http://dx.doi.org/10.1038/nature09210; image by Ben Hulsey

More on climate change and animal populations: The rise of “weedy” mice, the mystery of the shrinking sheep, lost clownfish, marching emperor penguins, and declining amphibians and reptiles

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

Despite the reality that I’ve cautioned against taking PCA plots too literally as Truth, unvarnished and without any interpretive juice needed, papers which rely on them are almost magnetically attractive to me. They transform complex patterns of variation which you are not privy to via your gestalt psychology into a two or at most three dimensional representation which can you can grok immediately. That is why History and Geography of Genes was so engrossing. You recognize patterns which were otherwise unrecognizable. But how you interpret those patterns, that’s a wholly different matter. And how those patterns arise is also not something one can ignore.

First, let’s start with an easy case. To the left is a PCA plot with four populations. Nigerians, East Asians (Chinese + Japanese), Europeans (whites from Utah), and finally, African Americans. The x-axis is the first principal component of variation, and the y-axis the second. That means that the x-axis is the independent dimension of variation within the patterns of genetic data which explains the largest fraction of the total amount of genetic variation. The sum totality of the variation can be decomposed into an large set of independent dimensions which can be rank ordered from the largest explanatory components to the smaller ones, successively by number. In a human genetic context the first principal component invariably separates Africans from non-Africans, and the second principal component often maps onto a west-east axis from Europe to the New World. Subsequent principal components can often be useful in smoking out fine scale distinctions, or relationships which are confused by the existence of similar but different signals in admixed populations.

The interpretation of this plot is rather easy. You see that African Americans lay along a continuum between Nigerians and Europeans, skewed toward Nigerians, with some outliers toward East Asians. We know from other genetic findings that ~20% of the African American ancestral quanta is European, but, that quanta is not equally distributed across the population. ~10% of the African American population is more than 50% European in ancestry, while 90% is less than 50% European. And so you have a distribution which reflects this variation. As for the outliers, I will speculate and suggest that these are indications of Native American ancestry among some African Americans.

The story I presented above is probably plausible as an explanation of the visual because we have a wealth of historical data to corroborate the plausibility of that narrative. The fit between the results from the technique of analysis of genetic variation and what scholars have long inferred from textual sources is relatively easy. It is far more difficult to look at a PCA plot, and generate a plausible narrative that you yourself accept with a high degree of confidence with little external support. It is with that caveat in mind that I present Toward a more uniform sampling of human genetic diversity: A survey of worldwide populations by high-density genotyping:

High-throughput genotyping data are useful for making inferences about human evolutionary history. However, the populations sampled to date are unevenly distributed, and some areas (e.g., South and Central Asia) have rarely been sampled in large-scale studies. To assess human genetic variation more evenly, we sampled 296 individuals from 13 worldwide populations that are not covered by previous studies. By combining these samples with a data set from our laboratory and the HapMap II samples, we assembled a final dataset of ~ 250,000 SNPs in 850 individuals from 40 populations. With more uniform sampling, the estimate of global genetic differentiation (FST) substantially decreases from ~ 16% with the HapMap II samples to ~ 11%. A panel of copy number variations typed in the same populations shows patterns of diversity similar to the SNP data, with highest diversity in African populations. This unique sample collection also permits new inferences about human evolutionary history. The comparison of haplotype variation among populations supports a single out-of-Africa migration event and suggests that the founding population of Eurasia may have been relatively large but isolated from Africans for a period of time. We also found a substantial affinity between populations from central Asia (Kyrgyzstani and Mongolian Buryat) and America, suggesting a central Asian contribution to New World founder populations.

The studies which came out of the original HapMap had northern Europeans, Yoruba from Nigerians, and Chinese & Japanese. These three populations can tell us a lot, but there’s something lacking in the coverage. The HGDP sample is better. But specifically because of political considerations it was not feasible to collect Indian samples, so Pakistani ones are used in their stead. Additionally, the HGDP sample is a touch biased toward isolated and distinctive populations, such as the Kalash of Pakistan. This genetic distinctiveness is important to catalog because it is fast disappearing. But the Kalash are so unique because of their long history of isolation, so one can’t really use them as a proxy population for Pakistanis, as one could with Sindhis. The POPRES sample seems to complement the HGDP well, but I don’t see it being used so much. Since the next phase of the HapMap has more populations, some of the deficiencies which emerged with the utilization of just three terminal groups (in a World Island context) will soon no longer be an issue.

But until that time it’s nice when studies come out which close some of the gaps in our knowledge of world wide genetic variation. This is one such study. I’m somewhat familiar with the samples already because I’ve seen it in an analysis of Indian populations. It seems that it is somewhat skewed toward South and Southeast Asian populations, but hey, these are groups which need to draw the long straw sometimes as well.

Before I go any further I should mention that they use a SNP-chip with hundreds of thousands of markers. Additionally, they looked at copy number variation. Two rather different types of variation within the genome, probably to double check that the outcomes were the same. Population historical events which shape patterns of genomic variation would presumably have a similar large scale effect on both types of variation. In their results that checked out, or so they claimed, as the paper is a manuscript without the supplements attached.

Though there’s some interesting fine-grained analysis to be had, they draw some macro-scale and deep time inferences as well. First, you probably know the famous fact that 15% of variation in genes is between races, and 85% within races. That’s derived from the Fst statistic, which is basically partitioning between and within population variance across two populations. Obviously the value of Fst varies by the set of populations you’re comparing. That between Mbuti Pygmies and Japanese is far higher than between Chinese and Japanese. Using the HapMap the Fst was 16%. About what you’d expect. To equalize sample sizes with the HapMap they randomly selected individuals from a pooled set grouped by continent from their populations, and calculated Fst. They found values around 11%. Why the difference? Because their data set included populations which were between the three clusters within the HapMap.

This is naturally not a surprising result at all, but it does reiterate one issue which sometimes crops up: Platonism in relation to race. The northern European whites in the HapMaps are the whites par excellence. Turks, who are perhaps more centrally located in the genetic variation of West Eurasian and North African peoples, what used to be termed “Caucasoid,” are “less white.” Similarly, Nigerians are more African than Ethiopians. Chinese and Japanese are more Asian than Burmese. And so forth. When modeling between group differences there is I think a somewhat old-fashioned tendency to consider some populations racial archetypes. That modulates the input which modifies the results somewhat. The analytical technique may be as cold as stone, but they are used by flesh and blood human beings.

There is also some funny business going on with haplotype and SNP heterozygosities which I think needs to be highlighted, and speaks to the fact that SNP-chips are not perfect. They’re tools, and human tools are impacted by arbitrary or instrumental choices humans make. Let me quote:

We also compared the SNP and haplotype heterozygosity values in each population (Figure 2B). These two quantities are generally highly correlated, although there are several exceptions: First, SNP heterozygosity is higher than haplotype heterozygosity in European and Central Asian populations. This may reflect a SNP ascertainment bias, since many of these polymorphisms were historically selected to maximize heterozygosity in European populations. Second, the Pygmy sample shows a low SNP heterozygosity despite relatively high haplotype heterozygosity. This unusual pattern could be caused by stronger effects of SNP ascertainment bias in this population than in others. Indeed, a recent study of Khoisan individuals (another hunter-gatherer group from Africa) showed a similar pattern: despite high SNP heterozygosity (~60%) in whole-genome sequence data, a Khoisan individual showed low heterozygosity on the SNP microarray genotypes (~22%) . Alternatively, this difference could also reflect unique attributes of population history.

In plain English the gene chips were designed with Europeans in mind, so they don’t necessarily pick up all the variation in non-European groups, who are believe it or not genetically different. This issue cropped up (as alluded to in the above text) with the recent paper which sequenced some Bushmen as well as Desmond Tutu. The Bushmen have a lot of variation, this is well known, but they have variation at markers where Europeans don’t, and if Europeans don’t the chips may not look for polymorphism at that locus. This sort of thing probably doesn’t affect broad population relationships, but if you want to zoom in and do analysis which is sensitive to fine distinctions and quantitative differences, then it might be problematic.

Let’s jump to the pretty charts. First, a PCA plot with all of the individuals from all of the populations:

Note that PC 1 accounts for nearly eight times as much variation as PC 2. This speaks to the African vs. non-African gap. Because their data set is relatively thick in “intermediate” groups you see a spectrum. The vertical axis is obviously mostly east-west. And here’s the accompanying bar plot derived from the ADMIXTURE program. K = putative ancestral populations.

With this many populations at K = 12 I think you could write a fantasy novel worthy of Tolkien. K = 4 is more realistic. Among the African populations you see likely Eurasian admixture in some eastern, and it seems Bushmen, individuals. In Eurasia itself you see a clinal gradation of admixture between putative ancestral components that seems to follow longitude rather well.

Because so much of the variation in the total sample is due to Africans, removing them from the picture will allow us to focus more on the relationships of the Eurasian groups. And so that’s exactly what they did. Note that focusing on the Eurasian groups does not mean simply magnifying or zooming in on the Eurasian section of the PCA plot, rather, the plots are regenerated with a subset of the previous genetic variation. In other words, the dimensions will shake out a bit differently.

The first plot shows Eurasian populations as a whole. The second removes Europeans and Near Easterners.

Notice again the scale. The vast majority of the variance seems to be east-west. But, there is a noticeable north-south split. For the South Asian population it looks like they had Pakistanis who were farmers of modest means (Arain), high caste South Indians, and very low caste or tribal South Indians. For this Indian sample there’s a problem, and it’s the sample problem which plagued the Up Series, they are looking at the very top and bottom of Indian society and ignoring the middle. Presumably the middle is going to be somewhere in the middle genetically as well, but nevertheless that’s something to consider in a paper which presumes to fill in the patchiness of others. In contrast, the Nepali sample was notably ethnically diverse, including both the dominant Indo-Aryan segment as well as the Tibeto-Burman Newar.

In the first panel there are some curious patterns with the Southeast Asian groups. Culturally, as in language and history, the Thai and Vietnamese have relatively recent roots in the southern regions of modern China. The Dai of Yunnan are the same people in origin as the Thai of Thailand and the Lao of Laos. Both derive from migrations from Yunnan. This is historically attested, even if somewhat fragmentarily. The heartland of the Vietnamese was in the Red River valley and north into southern China, and they spread down the coast and toward the Me kong only within the last 1,000 years. Southeast Asia was not uninhabited during this period. It was dominated by the Khmer Empire, which was slowly consumed by the expanding Thai and Vietnamese polities. Some scholars argue that French colonialism actually preserved an independent Khmer nation, which otherwise would have been divided between Thailand and Vietnam, as Poland was between Germany and Russia. So the Khmer are the indigenous people, while the Thai and Vietnamese are intrusive.

What do the PCA plots tell us? I do not know where the Vietnamese samples were collected. If they were from South Vietnam, then their close position to the Chinese suggests to me that there was substantial demographic replacement or expansion from the Red River valley. In contrast, the Thai are relatively distant from the Chinese. In fact, the Cambodians are somewhat closer to the Chinese! The samples here are small, and the sets overlap, so I wouldn’t put too much stock in that. But, Thailand is geographically closer to South Asia, so isolation by distance models would predict this pattern. It seems that the ethnogenesis of the Thai occurred through the expansion of the Thai identity, likely among Khmer peoples. And it is intriguing that the Iban, an indigenous people of Borneo, are closer to the Vietnamese than they are to the Cambodians. We know that there was substantial migration between coast Vietnam and Maritime Southeast Asia, the Chams of central Vietnam, and dominant in the southern half of the nation before the Vietnamese expansion, are a Malayan people who may have migrated from Borneo.

Shifting to the second panel there’s more here to say about the South Asians. First, geography. The two lower caste groups are actually Dalits from Andhara Pradesh, a South Indian state. Dalits used to be called outcastes, so they aren’t even lower caste, but without caste. The upper caste groups are Brahmins from Andhara Pradesh and Tamil Nadu. Finally, the Irula are tribal people from Tamil Nadu. To me the tribal samples often produce weird results, and I suspect that has to do with population bottlenecks and their demographic isolation. People leave the tribes (becoming part of the Hindu society, or converting to Islam or Christianity), but few join them. The Pakistani sample are Araina, a group of conventional Punjabi farmers who have a made up ancestry from Arabs (obviously made up because they don’t cluster with Near Easterners). Let’s compare to a chart from Reich et al.:

It seems to me that they’re in rough agreement (Reich et al. uses the same two low caste groups for Andhara Pradesh for low caste South Indians by the way). Though South Indian Brahmins speak South Indian languages, and reside amongst other South Indian groups, their genetic heritage is somewhat different. Similarly, tribal peoples are also distinct from caste Hindus. Reich et al. posit that South Asians can be modeled as a composite of two groups, Ancestral North Indians, ANI, and Ancestral South Indians, ASI. Presumably the former are intrusive to the subcontinent in relation to the latter. There seem two clear dimensions along which the ratio of ANI to ASI vary: geography and caste. The proportion of ASI seems to increase from the northwest to the southeast. And, the proportion of ANI seems to increase from tribal to low caste to upper caste. The Pakistani sample does not seem to be from an elite caste (or it does not seem they were converted from an elite caste), but they have more affinity with West Eurasian populations than South Indian Brahmins. It is likely that the latter are intrusive to the south, and have admixed with the local population.

Finally, a word on the Nepali sample. On top of the ANI-ASI mixture, the Nepali groups have varying levels of Tibeto-Burman, and so East Asian, affinity. This is not a surprise if you have met Nepalis. The Assamese, and to a lesser extent Bengalis, also exhibit this pattern of Tibeto-Burman admixture. The Brahmins of Nepal are intrusive like the Brahmins of South India, and like the South Indians they admixed with the local substrate.

Next let’s move to a ADMIXTURE plot.

The selection of a particular K obviously is conditioned by the patterns which “fit” with what you know, and what you expect. With that caution aired, the population represented by red can easily be thought of as a Middle Eastern group which expanded with agriculture. That seems to be what the authors favor. The brown population is the modal Indian ancestral population, which has little presence outside the subcontinent (nice color coding by the way! Brown people are brown). A green color represents a population which the tribal group, the Irula, are heavily weighted on. This reminds me too much of the Kalash. I suspect that the Irula went through some bottleneck or other distinctive event, and some have assimilated to various low status groups in South India.

I’m not a fantasist intent on world-building, so I’ll stop with that in reading the tea leaves of the charts. But there’s an important section which I skipped over, and will move back to now. And that’s the deep time aspect:

A more likely explanation for the OoA bottleneck is that Eurasia was populated by a larger population that had been relatively isolated from other modern human populations for tens of thousands of years prior to the expansion. The first fossil evidence for modern humans outside of Africa is in the Middle East at Skhul and Qafzeh between 80,000-100,000 years ago, which is at least 20,000 years prior to the Eurasian diaspora. If a population of modern humans remained in the Middle East until the expansion into Eurasia, there would have been sufficient time for genetic drift to reduce heterozygosity dramatically before the Eurasia expansion. This “Middle East isolation” hypothesis provides a robust explanation for the relative homogeneity of European and Asian populations relative to African populations (see Figures 3A-B) and is supported by a recent maximum likelihood estimate of 140,000 years ago for the time of Eurasian-West African population separation . Interestingly, a recent study of the Neandertal genome suggests that the non-African individuals, but not the Africans, contain similar amount of admixture (1-4%) with the Neandertals . The authors suggest that the admixture must have happened between the Neandertals with an ancestral non-African population before the Eurasian expansion. Given the fossil, archaeological, and genetic evidence, the Middle East isolation hypothesis warrants rigorous evaluation as whole-genome sequence data become available.

Like the vast majority of genetic studies this work supports the Out of Africa hypothesis. Non-Africans are all branches from a specific African branch. Or more accurately, an African branch which left Africa. The reduction in heterozygosity, a measure of genetic variation, from Africa to Eurasians was large. Additionally, within Africa south of the Sahara there’s little difference in heterozygosity as a function of geography, but outside of Africa it drops off as a function of distance from Africa. A plausible model then is a radiation from a small ancestral population to the four corners of the world, going through a series of bottlenecks along the way. Or at least that’s a model supported by genomic data. But, the drop in heterozygosity is so great a quick separation from the parental African population would require an implausibly small number of founders (less than 10 in one generation). So, to explain the data, they are suggesting here that the original population was not quite so small, but was isolated from the large African population for thousands of years. They assume genetic drift reduced heterozygosity, but if the model is correct I suspect that the way it worked was that bottlenecks due to climatic fluctuations swept clean a lot of the genetic variation. But in the interregnum the isolated population may have interbred with Neandertals. In fact, perhaps they picked up genes from Neandertals when their own effective population was extremely small.

In any case, a wide ranging paper. They manage to tie their results into two other blockbuster papers.

H/T Dienekes

Citation Xing J, Watkins WS, Shlien A, Walker E, Huff CD, Witherspoon DJ, Zhang Y, Simonson TS, Weiss RB, Schiffman JD, Malkin D, Woodward SR, & Jorde LB (2010). Toward a more uniform sampling of human genetic diversity: A survey of worldwide populations by high-density genotyping. Genomics PMID: 20643205

The shepherding moon Prometheus creating waves and building snowballs in the Saturn F - ring. Click for larger. Image Credit: NASA/JPL/SSI

Check out this latest Cassini release. It’s a really cool picture of Saturn’s F-ring showing the wake channels made as the little moon Prometheus moves around it.

The picture is a bit hard to interpet, so  here is a page with movie choices that will help show what is going on, sorry, not great for dial up users, but the description will help along with the main press release below.  Now we know why the ring rarely looks the same every time we see it.

Here’s the Cassini press release to better describe what’s going on:

While orbiting Saturn for the last six years, NASA’s Cassini spacecraft has kept a close eye on the collisions and disturbances in the gas giant’s rings. They provide the only nearby natural laboratory for scientists to see the processes that must have occurred in our early solar system, as planets and moons coalesced out of disks of debris.

New images from Cassini show icy particles in Saturn’s F ring clumping into giant snowballs as the moon Prometheus makes multiple swings by the ring. The gravitational pull of the moon sloshes ring material around, creating wake channels that trigger the formation of objects as large as 20 kilometers (12 miles) in diameter.

“Scientists have never seen objects actually form before,” said Carl Murray, a Cassini imaging team member based at Queen Mary, University of London. “We now have direct evidence of that process and the rowdy dance between the moons and bits of space debris.”

Murray discussed the findings today (July 20, 2010) at the Committee on Space Research meeting in Bremen, Germany, and they are published online by the journal Astrophysical Journal Letters on July 14, 2010. A new animation based on imaging data shows how one of the moons interacts with the F ring and creates dense, sticky areas of ring material.

Saturn’s thin, kinky F ring was discovered by NASA’s Pioneer 11 spacecraft in 1979. Prometheus and Pandora, the small “shepherding” moons on either side of the F ring, were discovered a year later by NASA’s Voyager 1. In the years since, the F ring has rarely looked the same twice, and scientists have been watching the impish behavior of the two shepherding moons for clues.

Prometheus, the larger and closer to Saturn of the two moons, appears to be the primary source of the disturbances. At its longest, the potato-shaped moon is 148 kilometers (92 miles) across. It cruises around Saturn at a speed slightly greater than the speed of the much smaller F ring particles, but in an orbit that is just offset. As a result of its faster motion, Prometheus laps the F ring particles and stirs up particles in the same segment once in about every 68 days.

“Some of these objects will get ripped apart the next time Prometheus whips around,” Murray said. “But some escape. Every time they survive an encounter, they can grow and become more and more stable.”

Cassini scientists using the ultraviolet imaging spectrograph previously detected thickened blobs near the F ring by noting when starlight was partially blocked. These objects may be related to the clumps seen by Murray and colleagues.

The newly-found F ring objects appear dense enough to have what scientists call “self-gravity.” That means they can attract more particles to themselves and snowball in size as ring particles bounce around in Prometheus’s wake, Murray said. The objects could be about as dense as Prometheus, though only about one-fourteenth as dense as Earth.

What gives the F ring snowballs a particularly good chance of survival is their special location in the Saturn system. The F ring resides at a balancing point between the tidal force of Saturn trying to break objects apart and self-gravity pulling objects together. One current theory suggests that the F ring may be only a million years old, but gets replenished every few million years by moonlets drifting outward from the main rings. However, the giant snowballs that form and break up probably have lifetimes of only a few months.

The new findings could also help explain the origin of a mysterious object about 5 to 10 kilometers (3 to 6 miles) in diameter that Cassini scientists spotted in 2004 and have provisionally dubbed S/2004 S 6. This object occasionally bumps into the F ring and produces jets of debris.

“The new analysis fills in some blanks in our solar system’s history, giving us clues about how it transformed from floating bits of dust to dense bodies,” said Linda Spilker, Cassini project scientist at NASA’s Jet Propulsion Laboratory in Pasadena, Calif. “The F ring peels back some of the mystery and continues to surprise us.”

The late Kevin Beurle was made the honorary first author on this paper because of his contributions in developing software and designing observation sequences for this research. He died in 2009.

The Cassini-Huygens mission is a cooperative project of NASA, the European Space Agency and the Italian Space Agency. JPL, a division of the California Institute of Technology in Pasadena, manages the mission for NASA’s Science Mission Directorate, Washington, D.C. The Cassini orbiter and its two onboard cameras were designed, developed and assembled at JPL. The imaging operations center is based at the Space Science Institute in Boulder, Colo.

Being kind of a volcano/earthquake geek, I regularly check in on the recent California earthquake records, the Kilauea activity, and, in the past couple months since the Eyjafjallajokull, the earthquake activity near it that might presage an eruption of Eyja’s big sister, Katla. Historically, eruptions of Eyjafjallajokull are followed by eruptions of Katla, which are an order of magnitude larger. The eruption of Eyjafjallajokull disrupted air travel in Europe for weeks. It’s interesting to consider what a big volcano Katla might do. There is also the fact that Katla erupts every 40-80 years and hasn’t erupted since 1918, making this a potentially bigger buildup to an eruption. Some of the Katla eruptions in the past have gone on for months.

Since I have been watching, the number of earthquakes near Katla has been small, with a few periods of a dozen or so within a 24 hour period. Almost every time I have looked it’s been very quiet, perhaps one or two a day. I was away the previous two weeks, and apparently missed a day with 11 earthquakes on July 10. I checked again today, and I got the map below, with over a dozen earthquakes! Now, clearly, these are all small earthquakes, with magnitude near 1, and there are no reports of steam or ash as yet.

I bet it’s coming, though, fairly soon. The president of Iceland does, too.

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In the caves of Slovenia and Croatia lives an animal that’s a cross between Peter Pan and Gollum. It’s the olm, a blind, cave-dwelling salamander, also called the proteus and the “human fish”, for its pale, pinkish skin. It has spent so long adapting to life in caves that it’s mostly blind, hunting instead with various supersenses including the ability to sense electricity. It never grows up, retaining the red, feathery gills of its larval form even when it becomes sexually mature at sweet sixteen. It stays this way for the rest of its remarkably long life, and it can live past 100.

The olm was once described as a baby dragon on account of its small, snake-like body. It’s fully aquatic, swimming with a serpentine wriggle, while foraging for insects, snails and crabs. It can’t see its prey for as it grows up, its eyes stop developing and are eventually covered by layers of skin. It’s essentially blind although its hidden eyes and even parts of its skin can still detect the presence of light. It also has an array of supersenses, including heightened smell and hearing and possibly even the ability to sense electric and magnetic fields.

The caves of Slovenia and Croatia have provided the olm with safe haven for over 20 million years, but these unchanging habitats are changing quickly. Chemical pollutants leaching into the caves and the attentions of eager black market collectors have seriously hit the olm population, and it is now vulnerable to extinction. Scientists have risen to the challenge by setting up various “cave laboratories” throughout Europe to save and study this iconic species at the same time.

One such laboratory lies in Moulis, France. In 1952, a group of scientists set up several riverbed-like basins in a local cave to mimic the olm’s natural habitat. The animals are protected and regularly fed. Sixty years on, there are more than 400 individuals in the cave, making it the only successful olm breeding programme in the world. And ever since 1958, researchers have been recording births and deaths among the olms on a weekly basis. Thanks to their painstaking census, we now have a unique glimpse into this odd creature and how it lives as long as it does.

Yann Voituron from the University of Lyon has analysed the five decades of data and found that the oldest olms are around 48-58 years old. Still, they show no sign of age-related physical decline. Based on the adults’ survival rates, Voituron calculated that the species lives to an average age of 69 years, supporting reports of captive olms living to 70.

Across different animal groups, the average lifespan can be anywhere from 10-67% of the maximum one. This means that at the very least, the oldest olms should be able to hit a respectable age of around 102 years and it may well live for even longer. Perhaps Voituron’s grandchildren will be able to check up on the same olms that he’s now studying.

Among back-boned animals, the bigger you are, the longer you live (generally speaking – there are exceptions). Whales, elephants and giant tortoises all top the longevity record books, but the humble olm can reach a century while weighing in at a puny 20 grams. The only other amphibian to even approach its lifespan is the giant salamander, which is a thousand times heavier. You can see how unusual the olm is in the graph below in the gallery above, which plots the lifespan of living amphibians against their mass. The olm is the black dot, looming over the clustered throng of white ones.

The deeper mystery here is how the olm achieves such a long life. The standard explanation says that ageing is the result of the very chemical reactions that power our lives. These reactions furnish us with energy but produce highly reactive molecules called free radicals, which damage any DNA or protein that they touch. Over the years, this constant barrage takes a toll on our bodies and ageing is the result; longer lives can therefore be achieved by stopping the onslaught of free radicals, so the story goes.

There are two main ways of doing this, but neither applies to the olm. Reducing your metabolism could do the trick. Since free radicals are the by-products of energy-producing chemical reactions, species that opt for life in the slow lane will produce less of them. As a group, salamanders are hardly go-getters, but the olm’s metabolic rate isn’t any lower than that of its much shorter-lived cousins. An alternative is to cope with the steady flow of free radicals with antioxidants that neutralise them. But again, the olm’s antioxidant abilities aren’t anything to shout about.

Something else must be happening in this bizarre creature and for now, it’s a mystery that goes unsolved. Voituron thinks that this tiny salamander will open some promising doors into the biology of ageing for years to come.

It might have something to do with the predator-free nature of the olm’s caves. Species that can escape from an early death often live longer than their peers, including birds and bats that can take to the air, and tree-dwelling mammals that can hide among the branches. Perhaps the safety of the olm’s home has allowed it to evolve an extreme lifespan without sacrificing its metabolism. Indeed, Darwin himself commented on the safety of the olm’s caves in his famous tome On the Origin of the Species:

“Far from feeling surprise that some of the cave-animals should be very anomalous…as is the case with blind Proteus… I am only surprised that more wrecks of ancient life have not been preserved, owing to the less severe competition to which the scanty inhabitants of these dark abodes will have been exposed.”

Reference: Biology Letters http://dx.doi.org/10.1098/rsbl.2010.0539

More on ageing:

• A life in the trees is a longer one
• Balancing amino acids for a longer life
• Secrets of the supercentenarians: Life begins at 100
• Rapamycin – the Easter Island drug that extends lifespan of old mice

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

“This work seeks to understand young adults’ motives for online gaming and extends previous research concerning social interaction in virtual contexts. The focus of the study is on Counter-Strike and World of Warcraft. Drawing on Baudrillard’s concept of simulacra, an analysis of young gamers’ motivation for gaming is carried out. The empirical data was generated employing a mix of qualitative methods such as researcher introspection, observation, and interviews with young adults in two different online gaming centers in Stockholm during 2006 and 2007. The results show that online gaming is foremost motivated by social reasons providing the gamers with a possibility of cooperation and communication. Some of the gamers in the study were motivated by escapism. Online gaming also provides gamers with an experience in which “flow” can be obtained and serves as a “hallucination of the real,” making it possible to do things and try out behaviors that would be impossible to do or try in real life. The gamers felt that online gaming gave them more experiences than real life could provide. For research purposes, this work provides a better understanding of the motivational aspects for gamers.”

Photo: flickr/Pål Berge

Related content:
Discoblog: NCBI ROFL: The ideal elf: identity exploration in World of Warcraft.
Discoblog: NCBI ROFL: Gaming at work positively correlated with multitasking.
Discoblog: NCBI ROFL: Are National Guardsmen the positive or negative control?

WTF is NCBI ROFL? Read our FAQ!

This isn’t The New Yorker, and I’m not writing twenty page essays which flesh out all the nooks and crannies of my thought. When I posted “Linguistic diversity = poverty” I did mean to provoke, make people challenge their presuppositions, and think about what they’re saying when they say something.

I think knowledge of many languages is awesome. I am weak at language acquisition myself, but, as someone with an interest in Bronze Age Near Eastern history I’m obviously invested in people having some comprehension of Sumerian and Akkadian (not to mention Hittite or ancient Egyptian). And I’m not someone who has no interest in the details of ethnographic diversity. On the contrary I’m fascinated by ethnic diversity. Like many people I enjoy reading monographs and articles on obscure groups such as Yazidis (well before our national interest in Iraq) and the Saivite Chams of Vietnam. Oh, wait, I misspoke. I actually don’t know many people who have my level of interest in obscure peoples and tribes and the breadth of human diversity. If you’re the type of person who reads monographs on Yazidis not because it pertains to your scholarly specialty, but because you’re interested in a wide range of facts and topics, and would like to have discussions with someone of similar disposition (me), contact me with your location and if I swing through town we can have coffee or something. I’m interested in meeting like minds who I can explore topics with (and here I’m not talking about someone who is a Hakka and so knows a lot about the history of the Hakka; I’m not Hakka and I know something about the Hakka and I’m not an Oirat I know something about the Oirat, and so forth). All things equal the preservation of linguistic diversity is all for the good, and not only does it enrich the lives of humanity as a whole, it enriches my life in particular because of my intellectual proclivities. But all things are not equal.

First, let me digress and admit that I do not adhere to a plain utilitarianism which does not value the cultural accretions and symbolic residues of history. For a concrete example, consider the destruction of the Buddhas of Bamyan in 2001 by the Taliban. On a concrete material level this was simply the rearrangement of molecular aggregations. We even have the visual sensory representation of the Buddhas before their destruction in the form of photographs. Why the outrage? Naturally Buddhists were outraged because the images of the Buddha had a sacred valence for them. But the world in general was outraged, Buddhist and non-Buddhist. The local Shia Muslims who live in the region, the Hazaras, were aghast at the cultural destruction, as they considered the Buddhas to be part of their heritage. At the time the Hazaras were being subjected to genocidal persecution from the Taliban, who considered them racially alien due to their Mongolian heritage and also heretics because of their Shia faith, so they were in no position to interpose themselves between the Taliban and the Buddhas.

As for the Taliban their concept of the Buddhas of Bamyan is that they were plain stone. Additionally, the Taliban perceived that the Buddhas were blasphemous because they were idolatry, drawing upon a long line of iconoclasm which goes back to the legendary Abraham. Unlike the atheist the Taliban may have perceived in the stone something more than material, rather, the stone may have been an expression of demonic or devilish forces in the world. Even if it lacked malevolent spirit forces, if they were objects of worship by human beings then that naturally violated their conception of the proper order of things.

But there’s a more nuanced context to the destruction of the Buddhas: Afghanistan was suffering through a famine during that period. Though the proximate cause for their destruction seems to have been the influence of the Arabs who were a power in Afghanistan at the time, Arabs who had no cultural affinity for Afghanistan’s pre-Islamic heritage, I have read that one aggravating issue may have been that the leadership of the Taliban was offended that the world seemed more focused on the potential destruction of statues than on the suffering of flesh & blood people. You can extrapolate this sort of objection pretty easily; at the same time that the Buddhas of Bamyan were under threat, tens of thousands were dying weekly in the Congo.

Here is where I must admit that my actions suggest that I am no simple utilitarian, who prioritizes the suffering of flesh and blood above stone and symbol. At the time in 2001 I specifically remember being very concerned about the destruction of the Buddhas, though I did not imbue them with spiritual value. I do not imbue the pyramids of Giza with spiritual value in a deep metaphysical sense, but I would be concerned about their destruction. I am not the only one. How many Egyptians would have to die in local violence to obtain the same world-wide media coverage as a terrorist detonation of a series of devices which destroyed the pyramids? I estimate on the order of millions (and even here, I am not so sure, as the genocide of millions in Africa receives far less coverage than I believe that a destruction of the pyramids would entail).

Human life and suffering are balanced against the aesthetic of life itself, which is more than bread and water. How many millions could have been fed with the funds which went to the Apollo mission? And yet what dollar value could we put on the photo of the pale blue dot? What dollar value on the reality that a human being has stepped foot on another planet? These are difficult questions in some ways because assessments of value and worth need to get the root of one’s implicit calculations. I know many people from the biological sciences who have little use for space exploration. And yet I know many people of marginal academic inclination who perceive much of biological research to be esoteric and without direct utility.

And it is here that biologists can respond that the domain of knowledge leads directly to discoveries in medicine and technology which will enable greater human happiness and well being, no matter what one thinks of the millionth beetle cataloged. On the margin some of these justifications for research based on plausible utility are as ludicrous as the justifications for a manned space mission. But the attempt must be made. Whether the quest for knowledge is worthy or not is not evaluated by some objective abstract criteria; even if researchers sit on granting committees the funds must ultimately come from elsewhere.

Which brings me back to the extinction of languages. The Lousy Linguist is skeptical of my contention that very high linguistic diversity is not conducive to economic growth or social amity. I outlined the theoretical reasons previously. If you have a casual knowledge of history or geography you know that languages are fault-lines around which intergroup conflict emerges. But more concretely I’ll dig into the literature or do a statistical analysis. I’ll have to correct for the fact that Africa and South Asia are among the most linguistically diverse regions in the world, and they kind of really suck on Human Development Indices. And I do have to add that the arrow of causality here is complex; not only do I believe linguistic homogeneity fosters integration and economies of scale, but I believe political and economic development foster linguistic homogeneity. So it might be what economists might term a “virtuous circle.”

A more on point response came from John Hawks:

I’m sympathetic to recognizing the real loss that accompanies the disappearance of a language from the world of speakers. The “unique oral history” and “lost in translation” ideas are true as far as they go — the value of folk art and oral history is that they enable social relationships.

But most communities of a few hundred speakers don’t have a Beowulf. Unique perspectives and unique history, to be sure — just as every Rembrandt is unique. But every Rembrandt is not the Night Watch. Most unique perspectives are about the speaker’s life. At some point we can’t learn the stories of all our ancestors anyway, because there are simply too many of them. Obviously I think we should enable people to learn about their history, yet we can’t keep communities pinned like butterflies in a cabinet of curiosities.

Human language communities in prehistory had a few hundred to a few thousand speakers. Those communities shared the same basic social lives and needs. Ninety-five percent or more of all those languages were lost — and those remaining have mostly come from a handful of languages less than 10,000 years ago.

I read in the Rijksmuseum that art historians figure more than 95% of the work of artists from the Dutch golden age had been lost or destroyed over the last 300 years.

John says it with more sensitivity and sympathy for the issue than I did, but I agree 99% with what he is saying here. The only point I might quibble over is that perhaps all groups do have their Beowulf. And yet it doesn’t matter. If the speakers of the language decided to shift to another language, then they are making the choice which increases their own flourishing. Speakers of a few hundred languages are not always in the circumstances of Native or Aboriginal peoples in North America, where they can gain sympathetic hearing for preservation of their folkways from the government and majority population. They need to make the best decision for themselves at the time, and often assimilation is the best of all choices, because the sample space of choices is limited. It is correct that bilingualism, or resistance to linguistic assimilation can persist. Hasidic Jews in New York City have communities where English is a second language and adults, of the third generation born and raised in the United States, have strong accents. But this community’s insulation comes at a cost, their relative poverty.

But for most communities the level of poverty of Hasidic Jews, or the material deprivation of the Amish, is wealth indeed. Many groups in Africa, South Asia and Australasia have not moved far up on Maslow’s hierarchy of needs. Many of these groups live in grotesque poverty, experience radical marginalization, and some of them fear for their individual survival, not just tribal or ethnic coherency. If those in the developed world do value the preservation of these groups and the richness which they add to the world by their very existence, then a concrete program has to be offered. Perhaps a massive direct wealth transfer to targeted ethnic groups which are being assimilated (in India and Southeast Asia conversion to Christianity has been the most efficacious manner in which to preserve ethnic and linguistic identity, so perhaps one should donate to evangelical missionary groups). Or, the selective sponsored immigration of whole tribes and ethnic groups to the West, with an agreement that these groups have a sort of spatial sovereignty similar to Native Americans. In this way they wouldn’t be subject to the same dynamics as they were in their nation of origination.

I don’t care about linguistic diversity enough to support either of these programs. But that’s an expression of my values. And, I think it’s an expression of the values of most humans (granted, most humans do not value knowledge, but they do pay taxes which fund social engineering projects so their opinion counts). For those who do value linguistic diversity, to be taken seriously you need to present more than what it offers you and your own interests when you bear none of the costs of marginalization. Aggregate intangible utility may be maximized by this diversity, but it is simply unjust for that aggregate utility to be gained at the expense of the ones adding the diversity at the cost of their exclusion from the nation-states in which they’ve found themselves.

Addendum: Spencer Wells has noted that there is somewhat the same issue with genotypic diversity, as small groups are absorbed into larger groups. By analogy, one might offer up a program whereby tribal members are encouraged to marry only their own ingroup so as to preserve genetic lineages which may be of intellectual interest, and add diversity to the world. This is naturally the sort of argument many racialists present, though with a slightly different spin.

Image Credits: Wikimedia, CNN, Glenn Fleishman

Two Chinese bodies of water made pollution headlines this week: the Yellow Sea is home to an oil spill, and the Ting River to waste water from a copper processing plant.

The Ting River

The waste water came from the Zijinshan mine in China’s Fujian province. Though earlier this month mine operators blamed weather for waste water entering the river, this week they admitted to and contaminating the river with–as The Sydney Morning Herald puts it–”four Olympic-size swimming pools” worth of waste water containing acidic copper.

Zijin’s board of directors expresses “its deep regret regarding the incident and the improper handling of information disclosure by the company, for causing substantial losses to the fish farmers located at the reservoir downstream of the mine and having a harmful impact on society,” the company said yesterday. [Bloomberg Businessweek]

Chinese police have detained two of the mine’s operators. Meanwhile, acidic copper has reportedly killed 4 million pounds of fish and threatens drinking water.

Reports from China’s official Xinhua News Agency suggest that Zijin is being required only to fix the problem and compensate locals with an offer of three yuan for every kilogram of dead fish. That makes the potential payout about 6 million yuan, [about $900,000]. [Sidney Morning Herald]

The Yellow Sea

Two oil pipelines have exploded in the port city of Dalian and have covered what the AP reports to be around 70 square miles of ocean. That’s not much compared to the 2,700 square miles covered by the Gulf of Mexico spill, but the spill is still a relatively big one in China’s recent history and certainly dramatic given its fiery start.

Images of 100-foot-high (30-meter-high) flames shooting up near part of China’s strategic oil reserves drew the immediate attention of President Hu Jintao and other top leaders. Now the challenge is cleaning up the greasy brown plume floating off the shores of Dalian, once named China’s most livable city. [AP]

Chinese reporters say that the no more oil is entering the sea and that officials have deployed 800 fishing boats to join 24 ships already on scene to stop the oil’s spread before it reaches international waters.

Economic activity in the north-eastern port has been seriously disrupted. Six “very large crude carriers”, with about 12m barrels of oil, were expected to be diverted, possibly to South Korea or other terminals in China with the capacity for such large vessels. Ships carrying imported corn have also been forced to dock elsewhere. Thousands of firefighters have doused the flames and port engineers have staunched the leak, but the clean-up mission will take at least four more days, according to the domestic media. [The Guardian]

Related content:
80beats: Isn’t It Ironic: Green Tech Relies on Dirty Mining in China
80beats: 1/3 of China’s Yellow River Not Even Fit for Industrial Use
DISCOVER: China’s Syndrome—will China be able to curb it’s pollution problem?
DISCOVER: China Promises Pollution Cleanup

Image: Wikimedia / Dalian / ASDFGHJ

Astrocytes, it was long believed, were little more than the scaffolding of the brain—they provided a support structure for the stars of the show, the neurons. But a study out in this week’s Science is the latest to suggest that this is far from the whole story. The study says that astrocytes (whose “astro” name come from their star-shape) may in fact play a critical role in the process of breathing.

Astrocytes are a type of glial cell — the most common type of brain cell, and far more abundant than neurons. “Historically, glial cells were only thought to ‘glue’ the brain together, providing neuronal structure and nutritional support but not more,” explains physiologist Alexander Gourine of University College London, one of the authors of the study. “This old dogma is now changing dramatically; a few recent studies have shown that astrocytes can actually help neurons to process information” [Nature].

Gourine’s team peeked into the brains of rats to figure out the connection between astrocytes and breathing. In humans and in rodents, the level of carbon dioxide in the blood rises after physical activity. The brain has to adjust to this, setting the lungs breathing harder to expel that CO2.

Astrocytes, the scientists found, are key players in this process. When the cells sensed a decrease in blood pH (because the carbon dioxide made it more acidic), they immediately released calcium ions, which the researchers could detect because they’d given the rats a gene encoding a protein that shone fluorescent in the presence of calcium. The astrocytes also released the chemical messenger ATP. That ATP appeared to trigger the nearby neurons responsible for respiration, kicking them into gear.

The astrocytes are no one-trick ponies, though. They could be important not only for breathing, but also for brain circulation, memory formation, and other activities.

The next step is to find a way to inhibit astrocytes in vivo, said Gourine. Then, researchers will be able to test the numerous hypotheses for the functions of astrocytes in the brain. It is likely astrocytes in various regions of the brain serve different functions, said [Cendra] Agulhon, just as many different types of neurons do many different jobs. “Depending on where they are and what kind of neurons they are surrounded by, they will function differently,” she added. “We are just starting to understand how important astrocytes can be” [The Scientist].

Related Content:
DISCOVER: The Brain, all of our mentally stimulating columns
DISCOVER: The Dark Matter of the Brain
The Loom: The Dark Matter of the Brain, Continued
80beats: Star-Shaped Brain Cells May Provide Actual Food for Thought

Image: Wikimedia Commons

I don’t have real value to add on the ScienceBlogs controversy. The only thing I want to mention is that there are some nascent superstar weblogs on that network which aren’t big names, yet, but perhaps will be. You can miss them coming in via the front page because they don’t crank out 10-15 posts per day, but they make them count when they do post. Two new weblogs which have caught my attention are Thoughtful Animals and Observations of a Nerd. There are others too if you poke around (your disciplinary focus may differ).

At this point I think for some people ScienceBlogs is not a the optimal venue. Obviously I was one of those people, as I left in late March. But for other people the reach of a prominent network still has utility. No need to throw the baby out with the bathwater. So by all means, let’s keep track of the SB Diaspora, but there are also diamonds in the rough who aren’t budging.

Replacing a traditional needle with a fingernail-sized patch may one day make some immunizations painless and possibly more effective. A study published in Nature earlier this week shows that a patch–a square of “microneedles” that are too short to register a typical shot’s sting and that dissolve in the skin–effectively immunized mice against a strain of the flu virus.

The researchers have yet to test the patch on humans, and that next step could take a few years; the move from a successful animal trial to a human trial isn’t a small feat. Still, many see this patch’s promise. As Paul Offit, director of the Vaccine Education Center and chief of infectious diseases at Children’s Hospital of Philadelphia, says:

“The caveat is, this needs to be extended to humans…. It’s not uncommon for vaccines or vaccine delivery systems to look very promising in experimental animals, then fail in humans. But there is every reason to believe this kind of technology could be applicable to children and adults.” [HealthDay News]

If the patch proves successful in human studies, here are some reasons it might quickly catch on.

Less Packaging

Traditional flu immunization shots deliver vaccines via metal, hypodermic needles. The leftover? A contaminated needle that goes straight to the biohazard bin. Researchers have designed this patch’s microneedles to disappear after application. They are made from a “bicompatible polymer” that holds the vaccine directly. After immunization, the needles dissolve into the skin itself as they deliver the vaccine, leaving only a watersoluble backing. Explains study coauthor Richard Compans:

“With respect to [the previous] vaccine delivery, we worked with solid metal needles…. The current technology is different because the vaccine is contained in the needle itself, and there is no needle left after the process.” [Tech News Daily]

Less Pain

As their name implies, microneedles are short–shorter than .03 inches each. That’s too short to trigger the pain associated with a traditional shot. The patch has a grid of 100 of the tiny needles as opposed to one large metal one.

Each microneedle is 650 microns long, about as tall as 10 human hairs stacked on top of each other…. They are arrayed in a grid-like pattern on a patch that’s easy to stick on your arm. [Los Angeles Times]

More Protection

There may be other benefits from a shot not going as deep. The study tested three groups of mice: one given no flu vaccine, one given a flu vaccine in the traditional way, and one given the vaccine via the microneedle patch.

Infecting the mice with the flu virus thirty days after immunization, both the mice vaccinated traditionally and with the patch successfully fought off the virus. To test how long the vaccine worked, the researchers then vaccinated a different three sets of mice. Three months later, the mice vaccinated with the patch actually performed better than the needle-immunized mice–more easily clearing the virus from their lungs.

Researchers suspect that the reason may be skin cells’ different immune reaction to virus attackers, which they encounter more often than muscle cells do (where traditional flu shots deliver the vaccine).

Skin, it seems, may trigger the immune system better than muscle, according to Richard Compans, professor of microbiology and immunology at Emory University School of Medicine: “The skin is a particularly attractive site for immunization because it contains an abundance of the types of cells that are important in generating immune responses to vaccines.” [CNET]

Less Postage?

Although traditional delivery systems for standard vaccines are working in many places, the researchers think that a patch vaccine might allow a more rapid and effective response to unexpected outbreaks. Instead of asking people at risk to go to a central location like a flu clinic, doctors could mail them a do-it-yourself patch.

[Coauthor Mark R.] Prausnitz says it’d be much easier if people could either vaccinate themselves or have someone less skilled vaccinate them instead of requiring a doctor or nurse. If the patches are one day approved by the FDA, Prausnitz envisions people ordering patches through the mail or at their local pharmacies.”The technology is ready to take the next step into humans,” says Prausnitz. “Our main barrier is getting funding.” [NPR]

Related content:
80beats: Ice-Loving Bacteria Could Give Humans a Vaccine Assist
80beats: New HIV Hope? Researchers Find Natural Antibodies That Thwart the Virus
80beats: Vaccinating School Kids Can Protect the Whole “Herd” of Community Members
80beats: This Week in Swine Flu: Vaccines Arrive, and Doctors Combat Myths

Image: flickr / El Alvi

While I was at TAM 8, Hemant Mehta and Robin Ferguson from The Friendly Atheist and interviewed me about the JREF, my Sooper Sekrit Project, and many things skeptical. It was too long to transcribe, so they put it up as a recording.

If you’re wondering about my razor joke right at the very start, I was poking fun at their recording device, which looks much like my shaver. But we covered a lot of ground, including PepsiGate, Skeptologists, and of course my talk at TAM 8 which has caused, to my bemusement, so much controversy. I’ll have more about that later, but for now you’ll hear something about it in this interview.

A female kingfisher plunges into a pond in southwestern England hot on the tail of a tasty little fish. These birds’ eyes have special filters thought to reduce glare, giving them a clearer view of underwater prey from above. A third eyelid, called a nictitating membrane, protects their eyes when they strike the water at high speed.

Photographer Charlie Hamilton James placed the camera in a waterproof box and set it up in the pond, wired to an infrared trigger that fired when something crossed its path. This image was the result of several weeks of patient monitoring. James: “When shooting wildlife my aim is to show the subjects as they exist in their environment. This is particularly the case with kingfishers, which are more often than not shot close up with wide-angle lenses in order to show them in their river landscape.”

Charlie Hamilton James/Nature Picture Library

While I was away last week on vacation, the New York Times published my feature on the hidden jungle that each of us carries, known as the microbiome. I was very happy to come home to a lot of kind notes, tweets, and various communications about it. Yet I would never claim that my article delivered the Big Scoop on the subject. After all, we’ve known about the microbiome ever since Antonie Philips van Leeuwenhoek scraped his teeth over 300 years ago and discovered wee animacules in the scum. And as I wrote in my book Microcosm, Theodor Escherich discovered his eponymous Escherichia coli over a century ago in a quest to catalog the good microbes in babies’s guts, hoping to thereby identify the ones that were killing the children in droves. Even in the age of molecular biology, the microbiome has been well-chronicled. Jessica Snyder Sachs wrote a book back in 2007 called Good Germs, Bad Germs: Health and Survival in a Bacterial World that I heartily endorsed (and still do).

So why write a story now? That’s a question that science writers have to ponder a lot. Much of the most interesting science does not explode with a single experiment or the unearthing of a single fossil. It’s a stately unfolding, a long-running collaboration/competition. For me, the time seemed ripe thanks to a couple recent papers that catalogued vast amounts of DNA in the collective genome of our microbial lodgers. Scientists have long known that the genes in the microbiome outnumber human genes by perhaps 10 or 100 to 1. But now we’re finally getting a database of that genomic richness.

And then, at a recent conference, I heard about a fecal transplant that saved a woman’s life. I knew I had my lede. But I called my editor to make sure that I could kick off the article that way, given that so many readers peruse the Times over breakfast. You never know. To anyone who experienced a fascinated nausea, my apologies.

In the days since my article came out, a series of new papers on the microbiome have been published. Today the Times published an editorial about one of them, a study of the incredible diversity of bacteria-infecting viruses we carry. Even identical twins harbor different sets of viruses. And yesterday, Caltech researchers described how multiple sclerosis may be the result of the way bacteria manage our immune systems.

Still, I’m glad I didn’t wait for all the good science to emerge. I would still be waiting 20 years from now.

PS–Here is a list of links for my Times article:

The fecal transplant paper

Genomes of the microbiomes

A catalog of 3.3 million genes

Bacteria teaching the immune system

The paper on how microbes infect us at birth

The microbes of the lungs

[Image: A beautiful bacterial colony]