The cockroach as we know it has been around for ~140 million years. That’s a rather long run. The evolutionary design of the cockroach seems to be well suited to avoiding obsolescence; it’s withstood the test of time. I suspect that the particular example of the roach is often used to illustrate the blindness of evolution because of its lack of aesthetic alignment with the the values of modern humanity. Unlike the elegant wasp or the industrious bee the cockroach seems to have few redeeming characteristics on first blush. The Hutus referred to the Tutsis as cockroaches before and during the Rwanda genocide of 1994. And yet the roach succeeds, it breeds, and it flourishes.

Some of the same class of issues pertain to our own species. What we feel to be edifying, to be aesthetically pleasing, may not comport with the final judgement of history, of evolution. The narrative of man ascending which has become so popular since the Enlightenment turns out to present us with some problems when one realizes that our species seems to have regressed on particularly transparent metrics such as height and cranial capacity since the last Ice Age. But the prevailing wisdom of the ancients that we descend from an Edenic Golden Age also does not seem to necessarily comport with the record at hand either. Just as the past is cloudier than we once perceived it to be, so the future often looks muddled from the perspective of the present. How did man come to be? What should we be? And why should we be? These are a combination of positive and normative questions, and Spencer Wells tackles them in his newest book, Pandora’s Seed: The Unforeseen Cost of Civilization.

Wells is a relatively prominent public intellectual. He came to the fore in the early aughts with his book The Journey of Man: A Genetic Odyssey, which was made into a documentary of the same name, and led to Wells heading National Geographic’s Genographic Project. A geneticist by training the history of the human species has always been one of his passions, and that topic has become the current focus of his career. But while The Journey of Man was a historically inflected work of genetics, Pandora’s Seed is a scientifically inflected work of history; political, social, and economic. There are broad family similarities to Jared Diamond’s Guns, Germs, and Steel, but Pandora’s Seed is both more tightly written and broader in scope. Wells describes the past, posits some tentative predictions about the future, assesses the present, and questions whether we need to reclaim a firmer and clearer grasp of the aims of the well lived life.

The first third of the book is focused on the Neolithic Revolution. Or perhaps more accurately the agricultural innovation. In its broad outlines I agree with Wells’ thesis that the transition to an agricultural lifestyle resulted in greater morbidity because of the shift away from a diversified diet to one based on grains. With the judicious use of charts and illustrations Pandora’s Seed outlines how pre-agricultural sedentarists of the post-Ice Age Natufian culture had to adopt the conscious planting and harvesting of grain due to a change in their environment. That change was the exogenous shock of the Younger Dryas, which saw a reversion back to dryer and colder conditions. The model of adaptation in the face of inclement conditions is persuasive precisely because it so human. In extreme circumstances human populations set in their ways must abandon tried & true traditions which are found wanting and explore the space of possibilities so as to maintain their viability. This ingenuity in the face of resource exhaustion or scarcity has occurred many times in human history. The critical factor distinguishing the present from the past is not the reality of innovation itself, but the rate of innovation.

But at this point I must enter into the record a major caveat, and even object to the veracity, of the story which unfolds in Pandora’s Seed. I will quote the section which raised my eyebrows in full:

…As the land dried out, the wild grain retreated from the lowlands, remaining only in the higher mountain valleys, where it could get enough water. The Natufians had to travel farther and farther from their lowland settlements to gather enough to survive. This would have put tremendous pressure on food supply, and probably esulted in an increased mortality rate in these people accustomed to a land of plenty. It was humanity’s first real encounter with Thomas Malthus’s conjecture that popualtion growth will eventually produce more people than can be supproted by the availalble food supply.

Spencer Wells has a doctorate in biology, and great breadth of knowledge. So perhaps there is some detail or nuance I’m missing here, but the fact is that all organisms are subject to Malthusian laws except in the transient state of resource surplus. The term “carrying capacity” is one which one learns in introductory biology courses for a reason. The hunter-gatherers no doubt pushed up against their carrying capacity. I am aware of arguments that weaning and infanticide constrained hunter-gatherer populations, but even granting such forethought would not abolish the vicissitudes of exogenous disruptions in climate and ecosystem. Even the most culturally anti-natalist tribe would at some point be faced with a situation where circumstances outside of their control would leave the adults above the Malthusian limit of their local territory. Wells argues that for much of human history we were expanding in a transient. But this does not negate the broader point that animals generally move up to the carrying capacity of the local ecosystem rather quickly because of the nature of natural increase. In the course of history exogenous shocks generally produce periodic culls of the herd. Spencer Wells implicitly endorses this reality by his tacit support for the Toba catastrophe theory.

Many of the other arguments which implicitly argue for the superiority of the hunter-gatherer mode of production over the agricultural one are somewhat tendentious, but in those cases Wells usually presents the “other side.” For example he is skeptical from what I can tell of the idea of widespread organized war among hunter-gatherers, but he grants evidence of relatively high mortality rates due to conflicts of a more limited scale, but still significant when judged against the small sizes of the ancient bands. The main big picture reality seems to be that hunter-gatherers were generalists with few material goods. The world of The Gods Must Be Crazy was no utopia, but it illustrated how physical objects of value and scarcity could introduce conflict and tension, above and beyond the mundane realities of human existence (also see The Pearl).

Much of the second half of Pandora’s Seed leaps forward from the Stone Age to the present, and attempts to grapple with the reality that many of our competencies are not much advanced over that of the hunter-gatherer despite the fact that we are embedded in a world of extreme sophistication and specialization. I’m reminded of the old 1990s hit Mo Money, Mo Problems. Over the past 10,000 years our species has ascended up an irreversible ratchet of population density, complexification of society, and specialization of labor. And for what? In some ways Pandora’s Seed presents a profoundly pessimistic case, and verges on being a 21st century update of the idealizations of the Romantics of savage peoples who lived in enchanted worlds without worry. The title of the book seems justified.

But then he asks a real question: why? Why to be, as opposed to not to be? With the rise of mass agricultural society such questions were answered definitively by philosopher shamans. At least in their own minds. In China they were called Sages, in India Rishis, and in the West the philosophers, prophets, and Church Fathers. The names may have differed, but this specialized caste spoke and wrote, and the other rentier castes listened and gave nominal fealty to the theories propounded. Over the last few centuries this old world of certainty has collapsed, and a cacophony of voices have arisen, over which looms an operational nihilism. The consumer society which is the apotheosis of “development” is characterized by an all-you-can-eat buffet of gadgets, sensations, and social signalers. Even the religious philosophies which theoretically stood opposed to this sort of gluttony have in part been absorbed or co-opted. Spencer Wells does not come to any conclusion that I can see to resolve this existential Gordian Knot. But a serious conversation needs to be started amongst those of us who no longer bow to the gods, the cosmos, or the ancients. It must be remembered that in some versions of the myth of Pandora hope remains within the jar which she opened.

Over the past two days I’ve given talks at Indiana University and Penn State University. It’s refreshing to speak with so many bright students actively working to make their research more accessible and relevant to broad audiences. Today I’m very much looking forward to spending some time with the Fellows involved in Penn State’s CarbonEARTH program–a terrific initiative supported by the NSF GK-12 grant:

The CarbonEARTH (Educators and Researchers Together for Humanity) Fellowship Program teams Penn State Science, Technology, Engineering, and Mathematics (STEM) graduate students with elementary and middle school science teachers from Pennsylvania’s Philipsburg and Harrisburg school districts. The CarbonEARTH program uses the interdisciplinary theme of carbon, broadly construed, as a unifying platform for student investigation, discovery, training and education.

I tremendously enjoy these campus visits and sense a growing awareness among young scientists that public engagement beyond academia will be necessary to influence and inform the global decision-making process. If the individuals I’ve been meeting are representative of where the science community is headed, the times they are a-changin’.

And I remain optimistic.

Dienekes is now allowing people to “out” themselves in terms of their ancestry on a comment thread over at the Dodecad Ancestry Project. One of the major purposes of the project has been to survey variation in under-sampled groups which could give us insights into human genetic history. Yesterday I pointed to an analysis of Europeans from the British Isles to Russia. Basically Northern Europeans. There wasn’t anything too revolutionary about the nature of the results; rather, it confirmed some patterns we’d seen. Additionally it obviously didn’t resolve issues of timing, though it clarified hypotheses on the margin.

The main benefit of the ADMIXTURE bar plots is that it gives you a gestalt sense of relationships in a quantitative fashion. This is especially important for groups in the Eurasian Heartland, who are in some ways at the center of both genetic and cultural exchange. In the comments above some information was divulged as the provenance of two clusters of samples, Finns and Assyrians. The Assyrians here presumably represents the remnants of Mesopotamia’s Christian majority at the time of the Arab conquests in the 7th century. Prior to the Arab conquests Mesopotamia had been under the rule of the Sassanid Persian dynasty for nearly four centuries, but by early 7th century the Syriac speaking majority by and large adhered to a range of Christian sects (the balance seem to have been heterodox non-Christian Gnostics and Jews), with the ancient Church of the East dominant. Because of the social constraints which Christians were placed under within the Muslim Middle East prior to the modern era these communities may be particular informative as to the demographic impact of the Arab conquests, and the cosmopolitan and international nature of the Muslim polities and how they reshaped the genetics of the Middle East. A good approximation is that the Christian minorities are the dominant parent population of the Muslim majority, but that because of their tendency to withdraw into more isolated regions and their enforced economic marginality they would have not intermixed so much with the influx of slaves, both northern (Turk and Slav), Indian, and African, which characterized much of Mesopotamia over the past 1,400 years.

Below the fold is a slide show. I’ve reedited just a touch (removed a few populations, put the labels in larger fonts, etc.). First the total population set. Then I’ve dropped the Finns and Assyrians, respectively, into the global population set (obscure some which are less relevant).

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First things first: the different ancestral components are popping out of ADMIXTURE and are suggestive inferences base on the data input. They do not necessarily represent real concrete ancestral populations! As I keep pointing out, the purple South Asian element is probably a compound of at least two very genetically distinct ancient groups in about equal measures, one with strong West Eurasian/European affinities, and another a long resident indigenous South Asian group with distant, but definite, affinities to East Eurasians (it may be that the latter South Asian element gave rise to the various branches of East Eurasians and Amerindians further back in prehistory).

The “Northeast Asian” element in the ancestry of the four Finns is not that surprising (though I believe some of these are related). In 23andMe Finns often seem to show trace “Asian” ancestry, on the order of ~1%. Uniparental markers, especially Y chromosomal lineages, have long indicated ancient affinities between the Finnic peoples of Europe and various groups in Siberia. The major question has been whether the migration has been from the west to the east, or the east to the west. And yet perhaps this is the wrong way of looking at it, perhaps both these groups derive from an expansion south of the margins of the glaciers in the wake of the last Ice Age? The Finns clearly physically resemble their fellow Nordics more than the Yakuts. But perhaps this is not to be unexpected when you have mobile low density populations on the margins of more numerous conventional agriculturalists? I believe that the Mercator projection has also caused problems in assessing the plausibilities of connections between circumpolar peoples.

Next let’s move to the Assyrians. As with other such surveys the lack of African ancestry in relation to similar Muslim populations is striking. The Syrian set is probably the best point of comparison. Note the small slices from other populations in the Syrians. I would normally ignore that, but their absence in the Assyrians may be informative. This may be a function of close relatedness of the Assyrians, but I’d give it even odds that a low fraction of exogenous post-Islamic ancestry which is associated with travel within the Muslim lands explains some of the difference between the majority and minority populations (above and beyond the clear African element).

Finally, I’m going make up stories on the fly to generate some discussion (I think the stories correspond to reality more than expectation, but I have very weak confidence in them myself).

- The “Southern European” element which is maximal in Sardinia indicates the very first wave of agriculturalists. The Sardinians may not be purely descended from agriculturalists, but like the composite “South Asian” quantum this represents possibly the very first hybridization due to a rapid demographic pulse driven by agriculture which synthesized with the hunter-gatherers of Western Europe. Like the “Ancient South Indians” I doubt that the Ice Age Europeans of Western Europe are present in “pure” form anymore. The influence of this component can be found far to the east among the Assyrians, but it almost disappears in Afghanistan and Pakistan. I think this may have something to do with R1b1b2.

- The “Northern European” element which is maximal in the Lithuanians is found among the Pashtuns and non-Arab Middle Easterners, but not Arab speakers. It drops off in India very quickly. I don’t think the Lithuanians are the “purest” Indo-Europeans, and I don’t think that this element was necessarily exclusive to Indo-Europeans. But there has to have been some leap-frogging going on, because on average Semitic Middle Eastern groups are more like Europeans than Gujaratis are in total genetic distance, but Gujaratis seem to have a higher fraction of this quantum. And suggestively Punjabis seem to carry the Central Eurasian lactase persistence alleles (I know this from the literature and genome sharing on 23andMe). Again, because these ancestral quanta don’t represent real populations, but are proportions popping out of ADMIXTURE, we shouldn’t take the orange fraction as the “Aryan” ancestry in South Asia. But that seems the most plausible explanation for why it seems at far higher frequency in Indo-European speaking northwest India than it does in the Semitic speaking Fertile Crescent.

- The light-blue “West Asian” fraction gets around. It’s found at the same proportions in Tuscans as Uyghurs, and, you can find it pretty far south and east in South Asia (I have a fair amount of it, as does a Reddy from South India, and the Kannada speakers in the global Dodecad set have some of it too, though less). I assume that it is present at high frequency among the Uyghurs because of the Indo-European speakers. But it clearly doesn’t have an Indo-European origin as such. It has a high frequency among the Cypriots, but not the Sardinians, with modal proportions among various Caucasian groups. I assume it has something to do with agriculture, but seems to have less of an influence in Western Europe than further to the east. The Finns and Lithuanians have a little bit, about the same as South Indians. So again, something which probably hitch-hiked with population movements in the center of Eurasia, but I assume pre-dating the Indo-Europeans.

Tom Rees has a fascinating post up, Why religious Austrians have more children:

On average, the more religious you are, the more kids you’ll have. It’s a widespread phenomenon, seen across pretty much all of the modern world.

The problem is, no-one really knows why this happens.

It could be something about religious beliefs. Maybe they make you more attractive to potential mates, or maybe they drive you to have more kids once you have found your mate.

Or maybe they encourage traditional, rather than modern, approaches to relationships. The traditional role for women is to stay at home and raise children, while hubbie has a career (and the independence and money that goes with it). It works (in theory at least) because divorce is not allowed, meaning that women cannot be left financially adrift.

This post is of interest because of my recent post reviewing Eric Kaufmann’s Shall the Religious Inherit the Earth. Here’s the top line conclusion from Tom’s post:

Berghammer found that people following the ‘traditional’ lifestyle were more to have 3+ children than those following the ‘modern’ lifestyle. What’s more, traditionalist individuals were more likely to be religious (all Catholic in this analysis).

But – and this is the crucial bit – among those who followed a traditional life path, there was no relationship between their depth of religious belief, or their Church attendance, and the number of children they had.

Exactly the same was seen for those following a modern life path. Although this was more popular among non-religious women, those religious women who did follow this trajectory had no more children than the non-religious.

There was also no difference between the religious and non religious in the chances of remaining single and childless.

Berghammer concludes from this that the critical factor in determining fertility is the choice of life trajectory. Once this has been decided, then religiosity has no further effect on fertility.

The model here is then that religiosity shifts the probability of one following a particular life path, but that there is no marginal return on religiosity once that life path is chosen. This sounds broadly plausible to me. It explains how more religious societies such as Greece, Italy, or Spain, could have lower fertility rates than more secular societies such as Iceland or Finland. There are lots of variables which go into determining life path, and the average between society differences can have a big impact on the distribution of fertility. Though within societies the religious on average seem to be more fertile. Or do they? Again we need to be careful as different societies have different correlations.

Here’s some data from the World Values Survey Wave 5. I limited the sample to those age 50 or over.

The Netherlands has the largest disjunction between fertility in those who view religion as important, and those who do not. I suspect this is due to the advanced secularization in the Netherlands, and, the existence of a cultural Bible Belt where higher fertility is normative. What’s going on in South Korea? To understand this you need to know that Europe and South Korea in some ways have gone through inverse cultural processes since World War II. Europe has de-confessionalized as belief in, and support for, institutional religion has collapsed in many regions. In contrast, South Korea has confessionalized, driven by a Western oriented conservative Protestant movement which went from less than 5% of the population to around 25% in two generations. As in many Confucian dominated societies organized religion generally had been viewed suspiciously by the authorities, and institutional Buddhism specifically had been marginalized in Korean public life for centuries (since the rise of the Joseon)). The emergence of Christian (and also Buddhist to a lesser extent) religiosity in South Korea over the past two generations has been particularly notable among the urban middle classes. In South Korea religious affiliation is higher in urban areas, and Seoul is the most Christianity city in the peninsula (while Busan is the capital of Korean Buddhism). So the most “modern” segment of society is the most the religiously devout, and you see the lower fertility among those who are the least secular.

A method to enable a bottlenose dolphin (Tursiops truncatus) to echolocate while out of water.

“The study of site-specific brain activity associated with dolphin echolocation has been hampered by the difficulties inherent in administering radiolabels and performing medical imaging while a dolphin echolocates in an aquatic environment. To overcome these limitations, a system has been developed to allow a bottlenose dolphin to echolocate while out of the water. The system relies on a “phantom echo generator” (PEG) consisting of a Texas Instruments C6713 digital signal processor with an analog input/output daughtercard. Echolocation clicks produced by the dolphin are detected with a hydrophone embedded in a suction cup on the melon, then digitized within the PEG. Clicks exceeding a user-defined threshold are convolved with a target impulse response, delayed, and scaled before being converted to analog and transmitted through a sound projector embedded in a suction cup attached to the dolphin’s lower jaw. Dolphin in-air echolocation behavior, inter-click intervals, and overall performance were analogous to those observed during comparable underwater testing with physical targets, demonstrating that the dolphin was indeed performing an echolocation task while out of water.”

Image: flickr/Beverly & Pack

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WTF is NCBI ROFL? Read our FAQ!

Autism researchers already knew that a variant of gene called CNTNAP2 that appears in about one-third of people is associated with higher risk for developing the condition. A study this week out in Science Translational Medicine puts that genetic marker together with what it appears to do in the brain: cause too many connections inside the frontal lobe of the brain, but too few from there to other brain regions. That could be a key clue in unraveling the learning and language difficulties that frequently appear in autism spectrum disorders.

The gene produces a protein called CASPR1 and is active during brain development — mostly during frontal-lobe development. “During early development, it is localized to parts of brain that are ‘more evolved’ — areas where learning and language happen, the frontal lobes where really complex thinking takes place,” says Ashlee Scott-van Zeeland, a postdoctoral fellow at the Scripps Translational Science Institute in La Jolla, Calif., and lead author of the study. “[It is] thought to help structure the brain.” [TIME]

To study its effects, Scott-Van Zeeland and company studied 32 kids between 11 and 13 in age. Some were autistic, some not, and many of the non-autistic kids carried the CNTNAP2 gene variant. The scientists examined the children’s brains through fMRI while the kids played a game intended to stimulate brain regions that the gene affects.

Regardless of whether the kids had autism or not, children with the CNTNAP2 “risk” gene showed more activity in the frontal lobe of the brain (specifically, inside the prefrontal cortex) during a “language learning” task than those without the risk gene. In those without the risk gene, activity in the prefrontal cortex decreased during the task. Instead, there was more connectivity between the frontal lobe and other areas of the brain, including the left side of the brain, which is involved with language. [BusinessWeek]

Curious to learn more, the team studied a further 40 kids who did not have autism to see what happened with the gene, Reuters reports. The same pattern emerged: Kids with the risk variant of the gene, though they didn’t have autism, did show the extra connections in the front frontal lobe.

Scott-Van Zeeland said researchers know that autism is caused by more than one gene, but the CNTNAP2 gene helps explain part of the picture. “One third of the population carries this variant in its DNA,” [coauthor Daniel] Geschwind cautioned. “It’s important to remember that the gene variant alone doesn’t cause autism — it just increases risk.”[Reuters]

But while CNTNAP2 is only part of the picture, the team’s findings seem to agree with what’s already known about autism.

The new findings lend support to the “intense world” theory of autism, which has posited that patterns of brain circuitry that result in excessive functioning in some regions may lead to extremes in attention and perception, which can produce both the deficits — and the sometimes extraordinary intellectual talents — that characterize some people with autism. [TIME]

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Image: iStockphoto

New neuroscience research is not only adding to our understanding of math and number processing in the brain, it’s also suggesting a way to improve learning in the math-deficient.

A small new study published in Current Biology involved electrical stimulation of the parietal lobe, a part of the brain involved in math learning and understanding. When this area was stimulated, students performed better on a math problem test. Said study leader Cohen Kadosh:

“We’ve shown before that we can induce discalculia [an inability to do math], and now it seems we might be able to make someone better at maths, so we really want to see if we can help people with dyscalculia…. Electrical stimulation is unlikely to turn you into the next Einstein, but if we’re lucky it might be able to help some people to cope better with maths.” [BBC News]

Dyscalculia is a learning disability similar to dyslexia, in which a person has an innate difficulty with learning or understanding math. People with this condition can have trouble with daily arithmetic, telling left from right, and telling time on analog clocks. Some studies estimate up to five percent of the population suffers from dyscalculia, and about 20 percent have less severe troubles with math.

For the experiment, 15 students were hooked up to a transcranial direct current stimulation (tDCS) machine, which stimulates the brain through the skull with 1 milliamp of electricity, and were given either a positive (right to left) zap to their parietal lobe for 20 minutes, a positive zap for 30 seconds, or a negative (left to right) zap for 20 minutes (five students per group). The current produced a tingling sensation in the scalp, but it didn’t hurt. Then the students were trained to learn the assigned number values of made-up symbols.

To replicate what children go through when they first learn numbers, the researchers presented the volunteers with two symbols at a time and asked them which one had a higher value. At first, the volunteers had to guess, because they had never seen the symbols before. But as the training progressed, those volunteers who remembered their correct guesses began to learn the relative value of all nine symbols. [ScienceNOW]

The students got hundreds of guesses each training day, which the researchers predicted would allow the students to gain an understanding of how the nine symbols ranked.

Each day they were also given a type of mathematical Stroop test: The students were shown two of the symbols where one shape was large and the other small, and were then asked which was bigger in size. The test can be confusing when the higher figure numerically is the smaller figure spatially, but students only have this difficulty if they’ve really learned the sequence of the figures. The researchers judged that students who hesitated in confusion longer had learned the sequence better.

The students who had the 20 minutes of “positive” stimulation at the beginning of each session showed that they’d learned the numbers better than those who were stimulated for only 30 seconds. Both groups did much better than those with the 20 minutes of “negative” stimulation, whose mathematical function was on par with that of a six-year-old. Even six months later, when the students were re-tested, those that received the positive stimulation performed better on the symbols test.

“It is already known that tDCS affects neurotransmitters involved in learning, memory and plasticity, so we presume that these are being manipulated in this study to cause long-term changes in the brain,” says Cohen Kadosh. [New Scientist]

But there are a lot of caveats to the results. A 15-person study is quite small. And though the electrical stimulation seemed to improve the students’ number processing abilities, it didn’t change their other math skills. It’s possible that this type of stimulation could be used to help students learn math better in school, but wouldn’t necessarily help them understand calculus.

Dr Cohen Kadosh, who led the study, said: “We are not advising people to go around giving themselves electric shocks, but we are extremely excited by the potential of our findings and are now looking into the underlying brain changes.” [BBC News]

Some other researchers who weren’t involved in the study say the data looks interesting, but note that the test wasn’t compared with a non-computational task. That makes it hard to tell if the effect is purely mathematical, or if the electrical current was having other effects on memory, learning, or the brain.

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Image: Flickr/quinn.anya

I see a lot of the same, tired, and totally wrong arguments about global warming over and over again whenever I write about it. "The other planets are warming!", "In the 70s scientists said the Earth was cooling!", "The climate scientists were caught faking their data!"

Wrong, wrong, and wrong. It’s almost as if the people making so much noise against the idea of global warming are robots, just repeating their arguments in the hope — sadly, probably correctly — that people will be swayed by repetition.

Software developer Nigel Leck feels the same way, so he created a ‘bot for Twitter that scans for key words used by climate change denialists and tweets automatic rebuttals to the most common "arguments". It’s pretty awesome: it posts a short, pithy debunking with a link to sites for more detail. The ‘bot is called AI_AGW and you can follow it on Twitter (note: it tweets a lot).

Pretty sweet idea! Now we just need one for homeopaths, anti-vaxxers, 2012ers, creationists, chiropractors, UFOers…

The vast majority of people who are infected with HIV go on to develop AIDS. Their bodies become riddled with the virus, their immune systems falter, and they are besieged by life-threatening infections. But not everyone shares the same fate. Around 1 in every 300 people infected with HIV carry genetic trump cards that allow them to resist and control the virus. These “HIV controllers” can live with the virus for years. They never develop AIDS and they live long, healthy lives, even if they never take any medication. Their genetic secrets are slowly being revealed.

Since 2006, a massive group of international scientists have been recruiting and studying a large group of HIV controllers from around the world as part of the International HIV Controllers Study. All of the recruits have been HIV-positive for 10 years. Despite that, the levels of the virus in their blood are around 50 times lower than expected and they have healthy levels of helper T cells, the immune cells that are normally hit by HIV.

Led by Florencia Pereyra, Xiaoming Jia and Paul McLaren, the team compared the genes of almost 1,000 controllers with those of over 2,600 people who haven’t been so lucky at subjugating the virus. After looking at over 1.3 million points around their genomes, the team found that just 313 separate the controllers from the other recruits.

Amazingly, every single one of these variants sits within a specific part of our sixth chromosome, among a set of genes called class I HLA genes. The proteins they produce form part of the internal security checks that defend us from infections. They grab small pieces of other proteins from inside our cells and display them on the outside, waving them under the noses of passing T-cells. If the T-cells recognise these pieces as parts of bacteria, viruses or other foreign invaders, they tell the infected cell to self-destruct and set the immune system on red alert.

All of this depends on a single groove in the HLA proteins. This is the bit that embraces the pieces of other proteins and displays them so prominently to the immune system. If this groove isn’t structured correctly, our defenders don’t get an advanced warning about threats.

True enough, the team found that the groove of a single protein called HLA-B is especially important. At five positions in the groove, the HIV controllers have different amino acids than those whose disease progresses normally. These five amino acids aren’t the only things separating the controllers from the others, but they have a major impact. One of them – the one at position 97 – is “associated with the most extremes of viral load” depending on the… amino acid [there].”

The link between these amino acids and the control of HIV is also very consistent. Pereyra did her protein comparisons using only the Europeans in her study (who formed the largest proportion of the sample). However, the results held true when she focused on the African-American group, and when she repeated the comparison in an independent group of HIV-infected Swiss patients. Again, people with different amino acids at certain key spots in HLA-B proteins were more likely to keep the virus at bay.

It’s still not clear how exactly these genetic variations alter the shape of the HLA proteins, and how these changes affect the ability to control HIV. Nonetheless, the international study is off to a promising start and perhaps, it will help to inspire future vaccines or treatments against this most frustrating of foes.

Reference: Science http://dx.doi.org/10.1126/science.1195271
If the citation link isn’t working, read why here

Ever felt the inclination to go all Armageddon on the whole planet? Well now you can let those feelings loose through a new asteroid impact simulator from Purdue University and Imperial College London.

Sure, the Impact: Earth! simulator is fun to play with, but researcher John Spray told Time that it’s an important research tool as well:

“The calculator is a critical tool for determining the potential consequences of an impact…. It is widely used by government and scientific agencies as well as impact research groups and space enthusiasts around the world.”

The simulator is actually an update to the basic tool already used by astronomers and governments to study how an impact would change Earth, to plan for post-disaster scenarios, and to explore asteroid- and comet-deflection technologies. When our planet was young many more space objects crashed into the Earth; while the barrage has slowed, small bits of debris still frequently fly into our atmosphere, says Time:

It’s still a dangerous cosmos out there, and the Earth gets beaned all the time — with about 100 tons of detritus from comets and asteroids hitting us each day. The overwhelming share of the material — including chunks of rock as big as a car — will incinerate in the atmosphere well before hitting the ground, but about once every 100 years or so, something significant gets through.

At the website you need to define your space object (the diameter, the density), the impact (angle and velocity), the target (what it will hit), and the distance from which you will be observing the impact. Each of these factors affects what will happen to the Earth (and to you) after the impact occurs.

Your apres-impact scores include the size of the crater, changes to the Earth’s rotation, and seismic and radiation effects at your chosen observation point. But the impact crater isn’t the only problem that would result from a moderate sized impact, Jay Melosh, who helped develop the software, told USA Today:

“The chance of a 1 km diameter object hitting the Earth in the next 1000 years is 1 in 1000, so on the face of it, this is not much to worry about. On the other hand, an object of this size, while not a 15 km dinosaur-killer, would have side effects on climate that could lead to global crop failures lasting a few years, so perhaps 90% of humanity would die.”

That’s a good reason to keep on the look out for asteroids, and have a plan able to deflect any threatening objects that come too close.

Related Content:
Bad Astronomy: Amazing close-ups of comet Hartley 2!
Bad Astronomy: Asteroid comparison chart
Bad Astronomy: Video of asteroid near miss from this morning
Bad Astronomy: Hubble captures picture of asteroid collision!
80beats: Two Asteroids Zip Past Today; Meanwhile, NASA Plans Killer Asteroid Defenses

Image: Impact:Earth!

This morning, NASA’s EPOXI mission whizzed by the comet Hartley 2, coming as near as 450 miles to the comet at 8 a.m. and snapping pictures all the while. The icy comet is less than a mile in diameter and has an irregular shape that one NASA researcher recently described as “a cross between a bowling pin and a pickle.”

The images are already streaming in: Head to Bad Astronomy for more pictures and a discussion of what these snapshots tell us about Hartley 2.

This is the second cometary encounter for this spacecraft–under a previous mission called Deep Impact the spacecraft sent an impactor hurtling into the comet Tempel 1, allowing the craft to photograph the excavated debris and the impact crater.

Related Content:
80beats: Holy Hartley 2! What to Know About NASA’s Comet Flyby
80beats: Video: Comet Caught Crashing into the Sun
80beats: Spacecraft-Collected Comet Dust Reveals Surprises From the Solar System’s Boondocks
Bad Astronomy: Ten Things You Don’t Know About Comets
DISCOVER: NASA Takes a Wild Comet Ride

Image:NASA

A decision made Tuesday by San Francisco’s Board of Supervisors may make little kids (and probably some adults) cry. With an un-vetoable vote of 8 to 3, the board banned restaurant chains like McDonald’s and Burger King from giving out toys with “unhealthy” happy meals within San Francisco’s city limits.

The decision is preliminary and will be followed up by a second debate and vote on Tuesday, November 9.

Under the proposed rule, meals deemed healthy can still be packed with action figures. To meet the city’s “healthy” standard a kid’s meal must contain fewer than 640 milligrams of sodium and 600 calories, and under 35 percent of those calories can come from fat. It also has to include a serving of fruit or vegetable with each meal and meet a number of other requirements (pdf).

The majority of McDonald’s Happy Meal options don’t meet these standards, including ALL of the cheeseburger options and any meal with fries. McDonald’s spokesperson told The New York Times they don’t agree with the Supervisors’ stance:

McDonald’s called the bill misguided. “It’s not what our customers want,” said Danya Proud, a spokeswoman for the company, in a statement. “Nor is it something they asked for.”

The restaurateurs aren’t the only ones disappointed in the decision. San Francisco’s Mayor Gavin Newsom (who just won the lieutenant governor’s seat in this week’s election) said he would veto the bill, even though with eight supervisor votes he can’t override the decision. Others aren’t excited that the city government is trying to control what individuals are eating, said chef Henry Dimbleby in his blog for The Telegraph:

Libertarians, needless to say, are not impressed. “This is great,” reads a typical message board entry. “As a parent, I support this 100%. But I was wondering, why stop at telling me what to feed my kids? It would be great if the government would also tell me what time to put my kids to bed and what to clothe them in and what names to give them and how many I can have. That would make being a parent much, much easier and less time consuming. Thanks.”

A very similar ban came out of Santa Clara County (also in California’s Bay Area) in April. The San Francisco board was spurred to act themselves because of the city’s struggle with childhood obesity: Over 30 percent of fifth graders are overweight. The board hopes the ban will encourage kids to eat healthier foods, supervisor Bevan Dufty told the SF Gate:

“If you have to put a Shrek doll with a package of carrots,” Dufty added, “maybe that’s what you have to do, but there hasn’t been a real incentive for this industry to do that, and I think that this legislation in a small appropriate way is a step to say you need to do things differently.”

Related content:
Discoblog: To Catch Hamburglars, McDonald’s Installs DNA-Spraying Security System
Discoblog: NCBI ROFL: I’d like a number 2 value meal, a frosty, and a peer-reviewed publication, please.
Discoblog: Why Do Some People Never Get Fat? Scientists May Have the Answer
80beats: Will the Supreme Court Let California Kids Buy Violent Video Games?
Not Exactly Rocket Science: Fast food logos unconsciously trigger fast behaviour

Image: Flickr/cbgrfx123

Just a reminder to residents of the Elm City and science writers converging here for their annual meeting: here are two public events you don’t want to miss…

1. Great Science Writing at Yale. Friday, 4 pm, Beinecke Library. Jonathan Weiner, Annie Murphy Paul, Richard Conniff, Jennifer Ouellette. Details here.

2. A conservation with Misha Angrist, author of Here Is A Human Being. Saturday, 6 pm, Labyrinth Books. Details here.

The guest this week on Point of Inquiry is blogger, podcaster, and philosopher-skeptic Massimo Pigliucci of “rationally speaking” and CUNY. Here’s the show description:

It’s a longstanding debate in the philosophy of science: Is “demarcation” possible? Can we really draw firm lines between science and pseudoscience?

Massimo Pigliucci thinks so. In his new book Nonsense on Stilts: How to Tell Science from Bunk, Pigliucci attempts to rescue the notion that there are claims we can rule out, and claims we can rule in—a real means of determining what’s science and what isn’t.

Along the way, Pigliucci touches on howlers like creationism and astrology, and borderland areas of research like SETI—and weighs whether science can ever hope to test claims about the supernatural.

Massimo Pigliucci is chair of the philosophy department at CUNY-Lehman College. He was formerly a professor of ecology and evolution at Stony Brook. He’s a prolific blogger and commentator on issues concerning science and skepticism and a prominent battler of creationists and other nonsense peddlers.

Once again, you can listen to the show here, and you can order Pigliucci’s book Nonsense on Stilts here.

UPDATE:  SOLVED by Rob at 1:06 CDT

Happy Saturday to all.  I hope the weather has been nice where you live; I’m having a lovely Indian Summer… the best part of the South/Central United States weather patterns.  Cold nights, mild days, lots of sunshine, and an overall freshness to the air.

Wouldn’t it be great if we could have weather like that more often?

Okay, enough out of me.  Are you ready to tackle the riddle?  I think this one is pretty straightforward, and you should nail it right off.  You will be looking for a thing.

Public image found on PhotoBucket

This thing exists in the real world.

It exists as a single object.

It’s not known for sure if our ancient ancestors knew about this thing.  Maybe… but more than likely not.

There is a subtle, but recognizable beauty associated with this object.

That’s interesting, because usually this “type” of object is rather flashy.

This object is something of the definition of its type.

You need to pay special attention to the images.

especially pay attention to this image

How’s that?  You know where to find me!

(lurking...lurking...lurking...)

News

Most interesting post of the week: Maryn McKenna talks about “vaccine-derived polio”, an “unintended consequence of success”

Holographic telecommunicator. It’s low-res, monochrome and jerky, but seriously, it’s a holographic telecommunicator.

Tom Chivers sets aside his sense of humour to write an amusing explanation of why headlines about a “liberal gene” are being liberal with overstatement.

“The hunt for earth-like planets is an epic endeavour… a perfect case study for the way that science at the bleeding-edge operates. It’s a shame the media aren’t doing a better job of conveying this to public.” Martin Robbins has a planetary gripe.

Welcome to World of WarmCraft. A climate change computer game tries to bring the planetary challenge of global warming to new audiences.

“Evolution in action, audible to the naked ear.” A cool new study on Galapagos finches, a iconic to evolutionary theory as they ever were.

From Zoe Williams, a great interview with Carl Djerassi, the inventor of the Pill and the man who changed the world for women.

Ignoring warnings from 1950s movies, scientists grow giant insects in the lab.

Ah, isn’t it nice when a large international meeting actually produces the right result and everyone largely agrees. 200 countries join forces to stem the loss of Earth’s life. But wait, says George Monbiot. “There is one problem: none of the journalists who made these claims has seen [the declaration]… The evidence suggests that we’ve been conned.”

“For dolphin mothers, successful parenting is as much a matter of having good friends as it is good genes,” writes Brandon Keim.

This is big: the US Government says that genes (human or otherwise) “should not be eligible for patents because they are part of nature.”

More after the jump…

The number of papers being retracted is on the rise, for reasons that are not all bad.

Robin Lloyd and Steve Mirsky have a great writeup of a debate about Rosalind Franklin, one of the co-discoverers of DNA’s structure. In it, Nick Wade espouses the view that Franklin wasn’t wronged because…er… she didn’t know she was being wronged at the time. Right.

Amazon speeds up economics experiments but more importantly, it’s less likely to recruit WEIRD volunteers.

A fascinating Wired feature on the Global Seed Bank: Nature’s backup.

“Hope built on a lie isn’t hope at all.” Beautiful post by PalMD on talking to patients about prognosis

NYT: Europe’s Plagues Came From China. I too have Chinese ancestry, moved to Europe, and killed millions of… no wait.

They all look the same? Here’s why.

Where climate myths come from: a great video from Peter Hadfield, who writes more here.

A history of anti-vaccination movements, dating back to the 1850s.

Diana Gitig at Ars Technica describes a Moebius strip made of DNA origami

Did baby sauropods run on two legs? Did their predators stand around laughing while being cuted out?

“I know that I do not suffer from Autism. I suffer from a lack of understanding and support.” & 25 “things I know about autism” over at Steve Silberman’s blog.

Brian Switek is tired of seeing naked dinosaurs. Maybe he should put his binoculars away, the big perv.

Jesse Bering narrates an evolutionary tale of the fattest ape: us.

“Is it time to start countering climate denial at the local level?” asks Chris Mooney

David Kroll takes a walk in the footsteps of caricatured evil as he puts himself in the shoes of Big Pharma

RIP Leigh Van Valen, evolutionary biologist behind the Red Queen hypothesis

Sometimes, science can go screw itself. Anomalocaris may not have been a superpredator?

“Do mummies have a right to privacy?” asks David Dobbs. That’s the Egyptian kind.

Polar bears: are they threatened or endangered? And either way, are they just screwed?

“Vaccines save lives; fear endangers them. It’s a simple message parents need to keep hearing.”

Heh/wow

Greg Foot is a legend for this: how to make Big Ben strike 13

Ants create a gecko.

From the Daily Mash: “Science cannot defeat cancer AND produce a magical see-through space coat, experts have warned.”

Tired of arguing with anti-science crackpots who can barely pass a Turing test? Nigel Leck was and created a bot to pester climate denialists for him. From Chris Mims.

Want an early Christmas present idea? Buy the Zooborns book. Raising awareness of conservation through the medium of unbearable cuteness.

“Meerkat celebrity Aleksandr Orlov has murdered and partially eaten several of his lower-status co-habitants’ offspring, it emerged last night.” The Daily Mash, of course.

An incredible giant jellyfish caught on video.

Gaah! My brain! An awesome illusion.

George Takei versus a douchebag

The European Wildlife Photographer of the Year 2010

At the NASA Kennedy Space Center shop…

The World Health Organisation’s ICD-10 manual of diseases and health problems includes “Very low level of personal hygiene”, “Bizarre personal appearance”, “Strange and inexplicable behaviour” and “Verbosity and circumstantial detail obscuring reason for contact”

“Psst! Lean closer…. I have a secret… *closer*… you ready?… okay, don’t tell anyone but OWLS DON’T REALLY CARRY POST, YOU MORON”

The Atlas of Science: visualising what we know

Blogging/journalism/internet

Sophia Collins and Shane McCracken organised a great Beyond Blogging event that I’m very sorry to have missed. The event produced five ideas for future activities to improve science communication and I absolutely love the idea of the Media Support Network.

A fascinating debate is raging in the comments of Angela Saini’s piece on whether bloggers devalue journalism.

A timeline for newspaper extinction in every country in the world. The UK’s papers to go within the next decade.

Sharks are “immune to every disease” says the BBC. They also have adamantium claws. They’re the best there is at what they do. One of those statements is true, and it’s not the one by the BBC.

An interesting take on Google and peer review in the public sphere.

James Harding says the Times paywall is a revolution for its journalism. I wonder if the reporters would agree? George Brock has an analysis of the newly released 10,500 subscribers stat.

Another scientist suffers under the yoke of British libel laws.

Invisible ranks: Jenny Rohn on the scarcity of female science ambassadors & pundits, and why it might matter.

Climate scientist Simon Lewis on setting the record straight after he gets misquoted by the Sunday Times’s Jonathan Leake. A valuable lesson on combating shoddy journalism.

Meet Soylent, the crowdsourced copy editor. Hint: it’s people!

You undoubtedly know about this by now, but witness the hilarious and outrageous case of CrookSauce: a tale of an editor with a ridiculous attitude to plagiarism, and what happens when you underestimate the Internet

Congrats to Rebecca Skloot, author of Amazon’s Book of the Year! That’s OVERALL by the way, not in a Science category. This is a massive win not just for Rebecca, but for science, journalism, good writing, racial equality, female role models, and perhaps most of all, for the Lacks family.

November 9 is the 76th anniversary of Carl Sagan’s birth, and is celebrated across the globe as Carl Sagan Day (in general, places that celebrate the day do so on the Saturday previous; so, today!). He did more to bring the wonders of the Universe to the world than any other human being, alive or otherwise, and this day should be a holiday.

In honor of that, I present to you my friend Sara Mayhew’s idea of what she plans to do:

Sounds like a good idea to me. If you’re curious about the apple pie thing, try here. It’s Sagan’s best quote, hands down.

I attended a Carl Sagan Day last year in Broward County, Florida and wrote about the experience. Everything I need to say about Carl and his influence is there, so go read it. Also, that same group in Broward is holding an event this year which will be streamed live.

The world may be a poorer place without him, but it’s much, much better place for having had him once in it.

A few days ago I was propounding to an old friend my hypothesis that social networks of cultural affinity are determinative in both the nature and trajectory of attitudes and norms within subcultures. In more plain language, you come to an opinion on many issues through your peer-network. The number one predictor of conversion to a “New Religion Movement” (NRM) is a prior personal connection to someone in an NRM.

Consider the issue of abortion. In the late 1960s and early 1970s it was not a salient issue for much of the American Right. Historians of Catholicism remember well the forgotten period in the late 1960s when periodicals of the evangelical Protestant movement such as Christianity Today looked favorably upon the decriminalization of abortion, overseen by men such as governor Ronald Reagan in California. This all changed in the late 1970s with the rise of the social wing of the New Right; the Catholic Right-to-Life movement was suddenly joined by a swell of evangelical Protestants. By the 1980s a pro-life stance was almost entailed by an assertion that one was a socially conservative Protestant. Things were very different in the early 1970s, when Richard Nixon’s concerns about abortion were more about consequence (permissiveness) than principle (sanctity of life). George H. W. Bush’s switch from a long-standing pro-choice position (his father was a treasurer of Planned Parenthood) to a pro-life one before his nomination to the Vice Presidential slot of the Republican ticket in 1980 was a sign of the times.

Did all this occur because conservatives thought more deeply on the issue of abortion? I don’t think so. There are plenty of theories why abortion became more salient for conservative Protestants years after Roe vs. Wade, that’s not my primary interest here. Rather, I suggest that an initial trend was amplified by positive feedback loops driven by the need for social conformity. This operates on the implicit level, people may sincerely believe that their opinions derive solely from their own inner logics, but the social and cognitive science does not support that position. There are of course outliers and non-conformists who find themselves out of line with the new orthodoxies; Barry Goldwater on the Right and Nat Hentoff on the Left would be cases when it comes to abortion.

All that is ultimately preamble. This mode of thinking explains why I am not totally sanguine about the existence of large minorities of Muslims in the West. I do not believe that Islam, or any religion, is necessarily “thick” with a lot of specific detail of belief or practice. Rather, I believe it emerges through social consensus and conformity. The idea that a Western Islam rooted in Western cultural presuppositions is somehow novel is ahistorical. In 18th century a sophisticated Chinese Muslim intellectual culture developed in Beijing which was rooted in Chinese presuppositions despite an explicit Islamic outlook. See The Dao of Muhammad. In the 18th century the collapse of the Turkic polities and Ottoman hegemony on the steppes to the south of the Russian Empire led to a long term attempt to formulate an Islam which was compatible with rule under a a Christian monarch. See For Prophet and Tsar: Islam and Empire in Russia and Central Asia.

The Chinese case turned out to be something of a false dawn. With the collapse of the power of the Ching dynasty in the 19th century, social chaos and persecution of minorities including Muslims, and the integration of worldwide civilizations through modern transportation networks, Chinese Islam went through several phases of “reform” which re-aligned it with more Middle Eastern cultural presuppositions. The sophisticated intellectual system of Chinese Islam rooted in a wholly indigenous lexicon was to a great extent marginalized, as world normative Islam came to be the standard. World normative in particular being variants of Islamic practice and belief accepted as orthodox in the Turco-Persian-Arab world. If the number of Chinese Muslims in the 19th and early 20th centuries had been in the tens of millions, and not millions, the result may have been different. Indian Islam gives us a possible window into this, as the Deobandi movement has broad affinities with the Salafi reform of the Arab world, but is genealogically independent.

The unfortunate reality is that Islam as it is practiced in the Middle East is a pretty scary sight to non-Muslims. It is most manageable when under the vice of near totalitarian secularism, as in Syria. In contrast, a more populist direction in Iraq in the last 10 years has produced a great religious cleansing. This generation shall not pass before Iraqi Christianity and Mandeanism become extinct, ending thousands of years of cultural history. In the early 1990s I recall reading that Mahathir Mohammed was going to make a push for greater prominence of tolerant Southeast Asian Islam (this means that Islam is the favored religion in Malayasia, but non-Muslims are not in fear for their life in any circumstances because of their religion to my knowledge). Whatever happened to that? There are plenty of nations, such as Senegal, which practice a form of Islam which is congenial to most Westerners. But to my knowledge Muslims who are “seekers” are not likely to emulate Senegalese Islam, which is at peace with the idea of pluralism of parity. The Middle East is the gold standard (this finds peculiar expression in Indonesia, where I have read that Muslim reformists attempt to claim South Arabian genealogy for the earliest Muslims. Many histories generally suggest that in fact Gujarati Muslim traders were the dominant, though not exclusive, influence in the early years. But Indian Islam is much less prestigious than Arab Islam).

A more radical thesis which I hope to elucidate at some point in the future is that these dynamics are pervasive not just in the present: rather, persistent inter-generational social networks operate like shadows underneath the cultural patterns we see before us. This is obvious when it comes to religious, linguistic, or national identities. Who you socialize with in those cases is clearly conditional and predicted by who your forebears socialized with. But I suspect that there are several “dark” social networks present for ever explicit one. These may not not be as important on a per unit basis as the explicit ones, but they may be numerous enough to affect great change on the margins.

Discovery on March 11, 2009. Click for larger. Credit: NASA/Bill Ingalis.

Unless things politically change and there is no reason to believe they will.  The shuttle Discovery will be making its last trip to space on Tuesday. This is a little bit of a delay from the original schedule.  Right now the launch is scheduled for November 2nd (Tuesday) at 16:17 EDT (that’s 4:17 pm EDT).

There are a few issues namely helium and nitrogen leaks in the right hand Orbital Maneuvering System (OMS) pod before launch, but the delay should enable the problems to be fixed.

Here are some of the interesting statistics from a very nice retrospective on the NASA site — Discovery:

• Took four years to build
• Has been to space 38 times
• Was the first spacecraft to retrieve and return a satellite to Earth
• Has carried 246 crew members, more than any other space vehicle
• Has spent 352 days in orbit
• Has circled the Earth 5,623 times
• And traveled 143 million miles.

Get wallpaper sized versions of the image at the top of the post at NASA.