I’ve written about Thierry Legault’s phenomenal imagery of space before; with relatively modest equipment, but excellent foresight, he gets astronomical shots of surpassing beauty.

He sent me a note earlier that he had something new and cool, and he wasn’t kidding: a video of the ISS in 3D!

Coooooooool.

To see it in 3D you don’t need glasses; it’s a bit like those Magic Eye posters. Look at the video, and cross your eyes slightly to merge the left and right images into one. Then hit play (move your mouse into the frame to get the video controls). It may take you a while to get the hang of it, but it’s worth the effort! I found it easiest to do when my eyes were about 50 cm (18 inches) from my monitor; for reference, on my screen the image of the ISS is about 8 cm (3 inches) high.

What you’re seeing here is actually only one video of the ISS. As it orbits the Earth, the ISS actually keeps the same attitude — that is, the same physical orientation. It only seems to rotate because Thierry centered it in the video. Take an orange or something like it in your hand, and move it straight across your field of vision. If you start on the right, you’ll be able to see more of the left side of the orange; as you move it to the left you’ll start to see more of the right side of the orange. It’s as if it’s rotating, but really you’re just changing the angle between you and the two sides of the orange. If you keep your head pointed right at the orange as it passes, you can see this more clearly. Note that it gets bigger as it gets closer, just as the ISS does in the video.

What Thierry did then was pretty tricky: he offset the left video in time a bit from the one on the right. We see 3D with our eyes because the angle from our left eye to an object is slightly different than the angle using our right eye (this effect is called parallax). Our brain processes these slightly different angles to construct an object with depth — it’s how all 3D works, from red-green anaglyphs to movies in the theater. And since the ISS was apparently rotating with time in the video, all Thierry had to do was offset the two videos a bit to trick the brain into thinking it’s seeing two different angles from your eyes; the brain does the rest.

Note that the ISS was over 300 km away when he took these shots on April 24th from France. It was also moving at over a degree per second across the sky, which is pretty fast. To make the animation cleaner, he took every 15 frames and combined them, a standard practice to make fuzzy images somewhat sharper. He also sped the animation up 2.5 times.

This video is extremely well done, and a fantastic exercise in clever thinking. Thierry continues to amaze me every time he does something new… but he’ll have a hard time topping this!

Video used with permission.

You probably are aware that different populations have different tolerances for high altitudes. Himalayan sherpas aren’t useful just because they have skills derived from their culture, they’re actually rather well adapted to high altitudes because of their biology. Additionally, different groups seem to have adapted to higher altitudes independently, exhibiting convergent evolution. But in terms of physiological function they aren’t all created equal, at least in relation to the solutions which they’ve come to to make functioning at high altitudes bearable. In particular, it seems that the adaptations of the peoples of Tibet are superior than those of the peoples of the Andes. Superior in that the Andean solution is more brute force than the Tibetan one, producing greater side effects, such as lower birth weight in infants (and so higher mortality and lower fitness).

The Andean region today is dominated by indigenous people, and Spanish is not the lingua franca of the highlands as it is everyone in in the former colonial domains of Spain in the New World. This is largely a function of biology; as in the lowlands of South America the Andean peoples were decimated by disease upon first contact (plague was spreading across the Inca Empire when Pizzaro arrived with his soldiers). But unlike the lowland societies the Andeans had nature on their side: people of mixed or European ancestry are less well adapted to high altitudes and women without tolerance of the environment still have higher miscarriage rates.

So despite the suboptimal nature of the Andean adaptations vis-a-vis the Tibetan ones, they are certainly better than nothing, and in a relative sense have been very conducive to higher reproductive fitness. And yet why might the Andeans have kludgier adaptations than Tibetans? One variable to consider is time. The probability is that the New World was populated by humans only for the past ~10,000-15,000 years or so, with an outside chance of ~20,000 years (if you trust a particular interpretation of the genetic data, which you probably shouldn’t). By contrast, modern humans have had a presence in the center of Eurasia for ~30,000 years. Generally when populations are exposed to new selective regime the initial adaptations are drastic and exhibit major functional downsides, but they’re much better than the status quo (remember, fitness is relative). Over time genetic modifications mask the deleterious byproducts of the genetic change which emerged initially to deal with the new environment. In other words, selection perfects design over time in a classic Fisherian sense as the genetic architecture converges upon the fitness optimum.*

Another parameter may be the variation available within the population, as the power of selection is proportional to the amount of genetic variation, all things equal. The peoples of the New World tend to be genetically somewhat homogeneous, probably due to the fact that they went through a bottleneck across Berengia, and that they’re already sampled from the terminus of the Old World. A physical anthropologist once told me that the tribes of the Amazon still resemble Siberians in their build. It may be that it takes a homogeneous population with little extant variation a long time indeed to shift trait value toward a local ecological optimum (tropical Amerindians are leaner and less stocky than closely related northern populations, just not particularly in relation to other tropical populations). In contrast, populations in the center of Eurasia have access to a great deal of genetic variation because they’re in proximity to many distinctive groups (the Uyghurs for example are a recent hybrid population with European, South Asian and East Asian ancestry).

So that’s the theoretical backdrop for the differences in adaptations. Shifting to the how the adaptations play out concretely, some aspects of the physiology of Tibetan tolerance of high altitudes are mysterious, but one curious trait is that they actually have lower levels of hemoglobin than one would expect. Andean groups have elevated hemoglobin levels, which is the expected “brute force” response. Interestingly it seems that evolution given less time or stabilizing at a physiologically less optimal equilibrium is more comprehensible to humans! Nature is often more creative than us. In contrast the Tibetan adaptations are more subtle, though interestingly their elevated nitric acid levels may facilitate better blood flow. Though the inheritance patterns of the trait had been observed, the genetic mechanism underpinning it has not been elucidated. Now a new paper in Science identifies some candidate genes for the various physiological quirks of Tibetans by comparing them with their neighbors, and looking at the phenotype in different genotypes with the Tibetan population. Genetic Evidence for High-Altitude Adaptation in Tibet:

Tibetans have lived at very high altitudes for thousands of years, and they have a distinctive suite of physiological traits that enable them to tolerate environmental hypoxia. These phenotypes are clearly the result of adaptation to this environment, but their genetic basis remains unknown. We report genome-wide scans that reveal positive selection in several regions that contain genes whose products are likely involved in high-altitude adaptation. Positively selected haplotypes of EGLN1 and PPARA were significantly associated with the decreased hemoglobin phenotype that is unique to this highland population. Identification of these genes provides support for previously hypothesized mechanisms of high-altitude adaptation and illuminates the complexity of hypoxia response pathways in humans.

Here’s what they did. First, Tibetans are adapted to higher altitudes, Chinese and Japanese are not. The three groups are relatively close genetically in terms of ancestry, so the key is to look for signatures of positive selection in regions of the genome which have been identified as possible candidates in terms of functional significance in relation to pathways which may modulate the traits of interest. After finding potential regions of the genome possibly under selection in Tibetans but not the lowland groups, they fixed upon variants which are at moderate frequencies in Tibetans and noted how the genes track changes in the trait.

This figure from the supplements shows how the populations are related genetically:

In a worldwide context the three groups are pretty close, but they also don’t overlap. The main issue I would have with this presentation is that the Chinese data is from the HapMap, and they’re from Beijing. This has then a northeast Chinese genetic skew (I know that people who live in Beijing may come from elsewhere, but recent work which examines Chinese phylogeography indicates that the Beijing sample is not geographically diversified), while ethnic Tibetans overlap a great deal with Han populations in the west of China proper. In other words, I wouldn’t be surprised if the separation between Han and Tibetan was far less if you took the Chinese samples from Sichuan or Gansu, where Han and Tibetans have lived near each other for thousands of years.

But these issues of phylogenetic difference apart, we know for a fact that lowland groups do not have the adaptations which are distinctive to the Tibetans. To look for genetic differences they focused on 247 loci, some from the HIF pathway, which is important for oxygen homeostasis, as well genes from Gene Ontology categories which might be relevant to altitude adaptations. Table 1 has the breakdown by category.

Across these regions of the genome they performed two haplotype based tests which detect natural selection, EHH and iHS. Both of these tests basically find regions of the genome which have reduced variation because of a selective sweep, whereby selection at a specific region of the genome has the effect of dragging along large neutral segments adjacent to the original copy of the favored variant. EHH is geared toward detection of sweeps which have nearly reached fixation, in other words the derived variant has nearly replaced the ancestral after a bout of natural selection. iHS is better at picking up sweeps which have not resulted in the fixation of the derived variant. The paper A Map of Recent Positive Selection in the Human Genome outlines the differences between EHH and iHS in more detail. They looked at the three populations and wanted to find regions of the genome where Tibetans, but not the other two groups, were subject to natural selection as defined by positive signatures with EHH and iHS. They scanned over 200 kb windows of the genome, and found that 10 of their candidate genes were in regions where Tibetans came up positive for EHH and iHS, but the other groups did not. Since these tests do produce false positives they ran the same procedure on 240 random candidate genes (7 genes were in regions where Chinese and Japanese came up positive, so these were removed from the set of candidates), and came up with average EHH and iHS positive hits of ~2.7 and ~1.4 genes after one million resamplings (specifically, these are genes where Tibetans were positive, the other groups negative). Their candidate genes focused on altitude related physiological pathways yielded 6 for EHH and 5 for iHS (one gene came up positive for both tests, so 10 total). This indicates to them these are not false positives, something made more plausible by the fact that we know that Tibetans are biologically adapted to higher altitudes and we have an expectation that these genes are more likely than random expectation to have a relationship to altitude adaptations.

Finally, they decided to look at two genes with allelic variants which exist at moderate frequencies in Tibetans, EGLN1 and PPARA. The procedure is simple, you have three genotypes, and you see if there are differences across the 31 individuals by genotype in terms of phenotype. In this case you want to look at hemoglobin concentration, where those who are well adapted have lower concentrations. Figure 3 is rather striking:

Even with the small sample sizes the genotypic effect jumps out at you. This isn’t too surprising, previous work has shown that these traits are highly heritable, and that they vary within the Tibetan population. There’s apparently a sex difference in terms of hemoglobin levels, so they did a regression analysis, and it illustrates how strong the genetic effect from these alleles are:

My main question: why do Tibetans still have variation on these genes after all this time? Shouldn’t they be well adapted to high altitudes by now? A prosaic answer may be that the Tibetans have mixed with other populations recently, and so have added heterozygosity through admixture. But there are several loci here which are fixed in Tibetans, and not the HapMap Chinese and Japanese. For admixture to be a good explanation one presumes that the groups with which the Tibetans mixed would have been fixed for those genes as well, but not the ones at moderate frequencies. This may be true, but it seems more likely that admixture alone can not explain this pattern. As the Andean example suggests adaptation to high altitudes is not easy or simple. Until better options arrive on the scene, kludges will suffice. It may be that the Tibetans are still going through the sieve of selection, and will continue to do so for the near future. Or, there may be balancing dynamics on the genes which exhibit heterozygosity, so that fixation is prevented.

No matter what the truth turns out to be, this is surely just the beginning. A deeper investigation of the genetic architecture of Andeans and Ethiopians, both of which have their own independent adaptations, will no doubt tell us more. Finally, I wonder if these high altitude adaptations have fitness costs which we’re not cognizant of, but which Tibetans living in India may have some sense of.

Citation: Tatum S. Simonson, Yingzhong Yang, Chad D. Huff, Haixia Yun, Ga Qin, David J. Witherspoon, Zhenzhong Bai, Felipe R. Lorenzo, Jinchuan Xing, Lynn B. Jorde, Josef T. Prchal, & RiLi Ge (2010). Genetic Evidence for High-Altitude Adaptation in Tibet Science : 10.1126/science.1189406

* Additionally, it may be that archaic hominin groups were resident in the Himalaya for nearly one million years. Neandertal admixture evidence in Eurasians should change our priors when evaluating the possibility for adaptive introgression on locally beneficial alleles.

Image Credit: Wikimedia Commons

Bruce Young from the University of Massachusetts is antagonising a spitting cobra. He approaches, keeping outside of the snake’s strike radius, while moving his head from side to side. The cobra doesn’t like it and erects its hood in warning. Young persists, and the snake retaliates by launching twin streams of venom at him from forward-facing holes in its fangs. The aim is spot-on: right at Young’s eyes. Fortunately, he is wearing a Perspex visor that catches the spray; without it, the venom would start destroying his corneas, giving him minutes to seek medical aid before permanent blindness set in.

It may seem a bit daft to provoke a snake that can poison you from afar, but Young’s antics were all part of an attempt to show just how spitting cobras make their shots. Their venom is a potent defensive weapon, but it’s also completely useless if it lands on the skin or even in the mouth. To work, the cobra must aim for the eyes. Just think about how hard that is. The cobra must hit a moving target that’s up to 1.5 metres away, using a squirt gun attached to their mouth. The fang is fixed with no movable nozzle for fine-tuned aiming. And the venom spray lasts just 50 milliseconds – not long enough to correct the stream after watching its arc.

By taunting cobras from behind his visor, Young discovered their secret. The snake waits for a particularly jerky movement to trigger its attack and synchronise the movements of its heads in the same way. It shakes its head rapidly from side to side to achieve a wide spray of venom. And it even predicts the position of its target 200 milliseconds later and shoots its venom at where its eyes are going to be.

There are several species of Asian and African spitting cobras, and Young had individuals of three – the red, black-necked, and black-and-white spitting cobras. Getting the snakes was straightforward enough; getting them to spit is another matter. It’s very difficult to provoke a cobra to spit at a stationary object – you need a moving target for the best results. That sounds like the sort of job that graduate students normally do, but Young stepped up to it himself. As he wryly writes, “To maximize consistency, the last author served as a target for all trials.”

His visor was fitted with accelerometers that recorded his own head movements, while his colleagues Guido Westhoff and Melissa Boetig filmed the snakes with a high-speed camera. Both films were synchronised with a laser pulse and together, the team recorded data from over 100 spits.

They found that a particular type of head wiggle provoked the snakes into spitting – not necessarily large or long-lasting, but always involving a jerky change of direction. This makes sense for the snake. At the moment when the target’s head changes direction, its movements are probably going to keep in the same direction for a short while. Also, to change direction, the head must briefly slow down before speeding up again, giving the snake more time to predict its future position.

On average, the cobra starts spitting 200 milliseconds after such movements, which is roughly the same as a human’s reaction time between sight and movement. But if it takes that long for the snake to contract its venom-shooting muscles, it’s at a 200 ms disadvantage. How can it possibly gun down a moving target and avoid spitting into empty space?

The answer is simple – even before the first droplets of venom emerge, the cobra is already taking aim. Around 65 ms before, it starts to waggle its head up and down, and from side to side, perfectly tracking the zig-zagging of its target’s face. When it actually starts to spit, it stops this synchronous bobbing and rapidly accelerates its head in the same direction as its target’s. The snake is compensating for its moving bull’s-eye, predicting where it’s going to be 200 ms in the future and ‘catching up’ to it well ahead of time.

Young thinks that the cobra’s calculations would be accurate enough to hit the eyes if it focused its venom jets on a specific point. As it is, the snake increases the odds of hitting its target even further by wiggling its head from side to side while releasing its poisonous payload. The result: a massive chance of a direct hit, and a reeling animal that will think twice about approaching a spitting cobra again.

Reference: J Exp Biol http://dx.doi.org/10.1242/jeb.037135

More on snakes:

• The tentacled snake turns a fish’s defence into a death march
• ‘Wasabi protein’ responsible for the heat-seeking sixth sense of rattlesnakes
• Sanajeh, the snake the ate baby dinosaurs
• The snake that eats toads to steal their poison
• Snake proteins have gone through massive evolutionary redesign
• Immune snakes outrun toxic newts in evolutionary arms races

It’s time for more amazing images to add to your collection, and maybe update your wallpaper.  I can never get enough gorgeous wallpapers to put on my desktop, and these seemed to fit well.

I’ll start off with this one from the GLOBE at Night study for 2010.  It’s their dark sky image, and it makes a beautiful desktop.

Here’s an image from NASA, showing the Vulcepula constellation.  This was presented May 6, 2010, and credit goes to ESA.

Isn’t that incredible?

Another one from ESO.  This is Cerro Armazones at night:

This next image is the Sombrero Galaxy in infrared, brought to you by Hubble.

Next, from the Astronomy Picture of the Day website, PSR B1509-58.  Courtesy of the Chandra X-Ray Observatory and NASA, this is just one of hundreds of beautiful images you can look at here.

And finally this beauty, from the NASA/ESA SOHO project, showing CMEs with aurorae.  SOHO has new information up daily, with special emphasis now on sunspots since we seem to be shaking off a “mini-minimum”.  See more gorgeous images of the Sun at the SOHO home page.

You’ll have to let me know which is your favorite.  I have to say, in this collection the SOHO image is my favorite, with the GLOBE at Night coming a close second.  In my post yesterday about telescopes, I said something about Hubble, et al, “rocking our world” daily with images like these.

Don’t they just?

Not Exactly Pocket Science is a set of shorter write-ups on 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.

Mum’s voice as good as a hug

For many children facing times of stress and worry, there are few things more soothing than a hug or a kind word from mum. Peer into a child’s bloodstream, and you can see this comforting effect manifesting itself at in the molecules that pass by. A simple hug can release hormones that combat stress and strengthen the bond between parent and child but according to a new study, this effect can happen without any contact. The mere sound of a mother’s voice, channelled down a phone line, can trigger the same biochemical changes in a distressed child.

Leslie Seltzer from the University of Wisconsin-Madison asked 61 girls, aged 7-12, to complete a series of exercises involving public speaking and maths challenges, all done in front of an audience. Even many adults would find this stressful and the children were no different. Their saliva betrayed higher levels of the stress hormone cortisol. If mum stepped in, these levels were back to normal within an hour, regardless of whether she was allowed to hug her child or merely to speak to her down the line. Either way, the comforted children also showed raised levels of oxytocin, a hormonal jack-of-all-traders with roles in solidifying social bonds, controlling stress and even, it’s said, love and trust.

Studies in mice have suggested that only touch can release oxytocin, but Seltzer’s work suggests that in humans, a voice can have the same effect. A gentle word from human creates the biochemical equivalent of a supportive nuzzle from a mouse. So far, Seltzer has only looked at communication between mothers and young daughters. It will be interesting to see if a comforting voice can have the same effect on boys or adults, or if it’s delivered by a father, a friend or even a sympathetic stranger.

Reference: Proc Roy Soc B http://dx.doi.org/10.1098/rspb.2010.0567

A nursery for Megalodon, the world’s largest shark

Megalodon was the largest shark of all time: 16 metres in length, 50-100 tonnes in weight, and possessing the strongest bite of any animal. But like every other animal, Megalodon grew from humble and vulnerable beginnings. A new set of fossil teeth suggest that it used a strategy that its living relatives share – baby sharks huddled in shallow waters where they found not only ample food, but also shelter from predators (including, mostly, other sharks). Today, a set of 21 teeth recovered from Panama’s Gatun formation have revealed the clearest evidence yet that the world’s greatest shark used such a nursery.

Catalina Pimiento from the University of Florida uncovered the teeth and confidently classified them as Megalodon chompers based on their shape. However, all of them were surprisingly small. They compared the teeth to other Megalodon specimens from younger and older rock formations to show that the animal wasn’t evolving towards a smaller size as the millennia ticked past. They compared the individual teeth to full sets to make sure that they weren’t just looking at the smaller rear teeth from larger sharks.

Instead, Pimiento says that the teeth belonged to juvenile sharks. Using a model based on great whites, she estimated the length of each tooth’s owner, and found that they fell within the length estimates for juvenile sharks. Even as a newborn, Megalodon could have reached 2 metres in length. That’s still pretty sizeable, but small enough to make a meal for other mega-sharks, including the great hammerhead, the snaggletooth and other adult Megalodons. Today, other sharks including Megalodon’s closest relative, the great white, uses similar nurseries, where pregnant females swim in the company of newborns, who stay there for their first weeks, months or years of life. It’s a strategy that has apparently been around for at least 10 million years.

Reference: PLoS ONE http://dx.doi.org/10.1371/journal.pone.0010552

More from Brian Switek at Laelaps

NASA’s Aqua satellite took this incredible shot of the Iceland volcano Garvenblagentralfamadoran (pronounced "Eyjafjalajökull") on May 10, 2010:

I know I’ve posted several of these, but this is my favorite; we can actually see the ground in this one, instead of clouds and ice. You can also trace the plume from the volcano for hundreds of kilometers as well, showing just why this event is making such a mess of things in Europe. NASA’s Earth Observatory Picture of the Day is a must-see for anyone interested in these incredibly images coming from space.

"The aim of this study was to investigate whether the eating behaviors of people at all-you-can-eat Chinese buffets differs depending upon their body mass. The resulting findings could confirm or disconfirm previous laboratory research that has been criticized for being artificial. METHODS AND PROCEDURES: Trained observers recorded the height, weight, sex, age, and behavior of 213 patrons at Chinese all-you-can-eat restaurants. Various seating, serving, and eating behaviors were then compared across BMI levels. RESULTS: Patrons with higher levels of BMI were more likely to be associated with using larger plates vs. smaller plates (OR 1.16, P < 0.01) and facing the buffet vs. side or back (OR 1.10, P < 0.001). Patrons with higher levels of BMI were less likely to be associated with using chopsticks vs. forks (OR 0.90,P < 0.05), browsing the buffet before eating vs. serving themselves immediately (OR 0.92, P < 0.001), and having a napkin on their lap vs. not having a napkin on their lap (OR 0.92, P < 0.01). Patrons with lower BMIs left more food on their plates (10.6% vs. 6.0%, P < 0.05) and chewed more per bite of food (14.8 vs. 11.9, P < 0.001). DISCUSSION: These observational findings of ...

The USA Patriot Act and the Bioterrorism Preparedness Act, both enacted not long after the 9/11 attacks, contained measures to make it harder for anybody to get their hands on the kind of pathogens one might need to launch a bioterror attack. There was just one problem: The rules also slowed down and constrained our own scientists’ abilities to learn about those pathogens, according to a study out this week in the Proceedings of the National Academy of Sciences.

To be specific, lead researcher Elizabeth Casman found while there was a touch of good news—the laws didn’t appear to deter new scientists from entering the field—the major effect of those acts has been to make research on ebola virus and anthrax much more expensive, and much slower.

The researchers did find an increase in the total number of papers published. But before the laws, 17 anthrax papers appeared per million dollars of funding. With the restrictions, only three papers appeared per million dollars of funding. For ebola, the numbers dropped from 14 to six papers per million dollars. Figures for the control stayed the same [Scientific American].

In other words, a scientific paper on anthrax became five or six times more expensive, and a paper on ebola twice as expensive. And a lot of the problem is simply the exhaustive record-keeping required.

The laws’ new regulations govern the exhaustive documentation of the transportation, guarding, and use of select agents. As a result, they are burying researchers studying select agents with administrative duties, Casman noted. Researchers to whom Casman spoke “all complained of the paperwork,” she said. “A lot of it, they just find overwhelming” [The Scientist].

One might argue that the paperwork headaches are worth it if they keep our samples of deadly pathogens secure (especially after an affair like the Bruce Ivins case, in which the longtime Army researcher was convicted for was the lead suspect in the 2001 anthrax attacks before he died in 2008 in an apparent suicide). But biodefense policy expert Vickie Sutton told Nature that the Patriot Bioterrorism Preparedness acts aren’t securing out lab supplies of ebola and anthrax—they’re just slowing down our own knowledge about them.

For example, regulations require researchers to create an inventory of each sample of a select agent and to document any changes. A missing test tube would draw immediate attention from the US Centers for Disease Control and Prevention, says Sutton. But the system does nothing to prevent the use of samples withdrawn from a live culture to seed a new culture. “You could every day be giving this agent out to someone,” she says. “It’s nonsense” [Nature].

Related Content:
80beats: Bioterror Attack Likely in the Next 5 Years, Congressional Report Says
80beats: Army Biodefense Lab Shuts Down To Check if Anything Is Missing
80beats: Army Researcher’s Alleged Anthrax Attack Raises Concerns Over Biodefense Labs
DISCOVER: Infectious Defense asks whether a determined bioterrorist can be stopped

Image: U.S. Army

Sometimes you have to change your vantage point to really see something.

The New York Times today reports on the work of Diane and Arlen Chase, who spent more than 20 years cutting through the Central American jungle to survey the Ancient Mayan city of Caracol in present-day Belize. But when they were turned on to the possibility of using flyover missions equipped with laser technology that could see to the jungle floor, their research accelerated dramatically.

In only four days, a twin-engine aircraft equipped with an advanced version of lidar (light detection and ranging) flew back and forth over the jungle and collected data surpassing the results of two and a half decades of on-the-ground mapping, the archaeologists said. After three weeks of laboratory processing, the almost 10 hours of laser measurements showed topographic detail over an area of 80 square miles, notably settlement patterns of grand architecture and modest house mounds, roadways and agricultural terraces [The New York Times].

Given such dramatic results, you might think the scientists would have started working from above earlier. After all, learning by bouncing lasers around isn’t new: Satellites have measured the Antarctic ice by reflecting lasers of the sheet and back into space, then measuring how long it took. Scientists have bounced lasers off reflectors that U.S. and Russian moon missions left behind, measuring the moon’s slow progression away from the Earth.

But previous laser measurement techniques suffered when applied to archaeology, and especially trying to see through the thick jungle. Even earlier lidar efforts suffered from poor resolution.

At first, Payson D. Sheets, a University of Colorado archaeologist, was not impressed with lidar. A NASA aircraft tested the laser system over his research area in Costa Rica, he said, “but when I saw it recorded the water in a lake sloping at 14 degrees, I did not use it again.” [The New York Times].

Because of that failure, Arlen Chase tells DISCOVER, many archaeologists didn’t think much about lidar for a while. But, working with biologist John Weishampel, the Chases used a new-and-improved method of lidar called “swath mapping,” in which “you get overlaps on the pass-throughs,” Arlen Chase tells us. As a result, the team was able to get 20 data points per square meter over the entire Caracol area. “It was the first time it was done on this big an area,” Arlen Chase says. “No one knew if it would work.”

But by using this technique, plus doing it during the dry season when there was less prevalent foliage, the team got these great images. According to the Chases, the city of Caracol thrived between about 550 and 900 A.D. And with the size of the city that aerial measurements were able to take, they say 115,000 people could have lived there during its peak.

“Finally, we have a nondestructive and rapid means of documenting the present ground surface through heavy vegetation cover,” Dr. Sheets said, adding, “One can easily imagine, given the Caracol success, how important this would be in Southeast Asia, with the Khmer civilization at places like Angkor Wat” [The New York Times]

Related Content:
80beats: Found on the Moon: A Soviet Laser Reflector That Was Lost for 40 Years
DISCOVER: Uncovering America’s Pyramid Builders
DISCOVER: Royal Tomb Reveals Secrets of the Maya
DISCOVER: 5 Reasons Science Hearts Google

Image: Caracol Archaeological Project

There’s a very long review out which presents a theory for how sauropod dinosaurs could scale up to such enormous sizes, Biology of the sauropod dinosaurs: the evolution of gigantism. ScienceDaily is promoting the likelihood that sauropods did not chew, and so could make do with very small heads which could be supported by long necks, as the big factor. But this is a model with many moving parts. Here’s the verbal list from the conclusion:

(1) Sauropod dinosaurs as the largest terrestrial animals ever represent a challenge to evolutionary biologists trying to understand body size evolution.

(2) The study of the upper limit of body size must address extrinsic as well as intrinsic factors, and it must be determined whether this limit is set by the bauplan of the organisms or by physical and ecological constraints imposed by the environment. Among several possible approaches, we chose the resource perspective because it has been shown that resource availability and maximal body size correlate closely (Burness et al., 2001).

(3) In the interplay of the biology of sauropod dinosaurs with their environment, a unique combination of plesiomorphic features (i.e., inherited from their ancestors) and evolutionary novelties emerge as the key for a more efficient use of resources by sauropods than by other terrestrial herbivore lineages. Plesiomorphic features of sauropods were many small offspring, the lack of mastication and the lack of a gastric mill. The evolutionary innovations were an avian-style respiratory system and a high basal metabolic rate.

(4) We posit that the long neck of sauropods was central to the energy-efficient food uptake of sauropods because it permitted food uptake over a large volume with a stationary body.

(5) In the Late Triassic and Early Jurassic (210–175 million years ago), the combination of biological properties listed above led to an evolutionary cascade in the sauropodomorph lineage characterized by selection for ever larger body size, mainly driven by predation pressure from theropod dinosaurs.

(6)From the Middle Jurassic onward, sauropod dinosaurs dominated global terrestrial ecosystems only to succumb to the catastrophic environmental change at the end of the Cretaceous 65 million years ago.

And here’s a schematic illustrating the interplay of evolutionary forces & constraints:

The paper is open access, so you should read it yourself if you’re interested.

If lightning strikes nearby, you might be in for some incredible hallucinations that resemble what is known as "ball lightning," according to a pair of scientists from the University of Innsbruck in Austria. In the lab, test subjects can experience these visions of shining spheres and lines when they undergo transcranial magnetic stimulation, or TMS, which use huge superconducting magnets create electric fields in the brain up to 0.5 Tesla. (That's a lot; a plain-old bar magnet is only around .01 T.) According to Technology Review:
"If this happens in the lab, then why not in the real world too, say [researchers] Joseph Peer and Alexander Kendl... They calculate that the rapidly changing fields associated with repeated lightning strikes are powerful enough to cause a similar phenomenon in humans within 200 metres."
So when lightning strikes nearby, it can induce fields similar to the ones created by transcranial stimulation. That means you could experience luminous lines and spheres, just like subjects do in the lab.
"As a conservative estimate, roughly 1% of (otherwise unharmed) close lightning experiencers are likely to perceive transcranially induced above-threshold cortical stimuli," say Peer and Kendl. They add that these observers need not be outside but could be otherwise safely inside ...

A man in Boulder — yes, my home town — is trying to meditate the oil leak away. His idea?

"The basic concept is to try and get as many people to visualize that the valve is actually functioning and is working and closing."

This is part of the Intention Experiment, what is basically telekinesis:

Lynne McTaggart, who started the Intention Experiment, has organized more than a half dozen mind-over-matter experiments — most recently to try to improve the water quality in Lake Biwa, Japan — that involve people focusing their thoughts on something in the physical world to make change. She claims to have scientific evidence that it works.

Scientific evidence? Really? I wonder if she’s interested in making a quick million bucks.

Look, we’ve seen this before. People have prayed for rain, and tried to pray the stock market into obedience. These efforts fail, always. Or at best they might coincidentally align with some event, but it’s never clear in advance just what event they were aiming at (making it easy for them to claim success after the fact).

I know that people who believe in this sort of thing have their heart in the right place. I’m frustrated by horrific events like the oil leak too, and I wish I could do something tangible. But trying to pray it away won’t work. One believer said this:

"I completely understand that most people would have a healthy skepticism about these things," said Jahnavi Stenflo, also of Boulder, in an e-mail. "To all those skeptics, I would simply ask them to participate in the exercise if they would like to try. … Ultimately, there is nothing to lose in trying to visualize the valve shutting off. It either will help or it will not."

These "What’s the Harm?" arguments are extremely misleading. Of course there is something to lose. This kind of thing has been tested over and again, and shown to be a waste of time. The time spent by the participants is one obvious thing lost. But more than that, what we lose when we do things like this is our ability to separate fantasy from reality. And we do know quite a bit about human behavior: people who will try to meditate the oil leak away will almost certainly not conclude meditation doesn’t work when it fails. Instead they’ll find excuses why it didn’t work, and try it again next time something happens.

The more we wish for something to be true, the more we must hold it up to scrutiny lest we fool ourselves.

I am not saying things like this shouldn’t be tested. The point is, they already have been. Repeatedly. And they never work. If this oil leak is to be stopped, it’ll have to be done using engineering, using science, using actual physical work. And at the moment there’s not much you or I or anyone outside of the engineers at BP can do to help.

However, I’ll add that thinking about the problem is important. When the root causes of the leak are found — and I don’t mean the physical problems, but what failures allowed the situation to arise in the first place, both in the company and in the political environment — we need to make sure that it doesn’t happen again. That means keeping up with the news, being aware of the situation, and contacting politicians so that they hear our voices about it.

That is where thinking makes a difference.

There are about 20,000 gray whales living in the eastern Pacific Ocean today, plus another 200 in a small group in the western Pacific. And, in the Mediterranean Sea, scientists have found one.

Over the weekend, oceanographers saw a solitary gray whale cruising the Mediterranean off the coast of Israel. To say they were surprised would be a vast understatement: gray whales haven’t lived in the Atlantic Ocean or the Mediterranean since their population crashed in the 1700s, possibly because of whaling operations. Yet today a solitary gray whale swims by the shores near Tel Aviv, halfway across the world from where the rest of its species resides (the researchers say they photographed the animal to be sure it wasn’t a different species, like sperm whale).

So what happened to get this whale to the far side of the world? Says Phillip Clapham of the US government’s National Marine Mammal Laboratory in Seattle:

“The most plausible explanation is that it came across an ice-free North-West Passage from the Pacific Ocean, and is now wondering where the hell it is” [New Scientist].

Suppose the whale belongs with that largest group of gray whales that lives in the eastern Pacific. They migrate from their calving waters off Baja California up the coast to the Arctic. But with the decreasing ice cover meaning that the the Northwest Passage is opening up, this lonesome traveler could’ve made it far enough east in those chilly Canadian waters that when it headed back south, it accidentally swam into the Atlantic Ocean. Then, seeking warm waters, it found them in the Mediterranean.

While that seems like an incredible journey, whale expert Nicola Hodgins says that gray whales are well known for making some of the longest migrations in the world each year:

“Over a lifetime, a gray whale migrates the equivalent distance of a return trip to the moon. However, these new images show that this particular whale would have had to beat all previous distance records to end up where it has” [BBC News].

Still, Clapham says, the Northwest Passage journey is far more likely than the alternative explanation: That a relic population of Atlantic gray whales has escaped attention for centuries. The scientists don’t have funding to tag and track the whale to be sure, but Clapham argues that this won’t be the last whale to find its way across the Arctic to points unknown.

Related Content:
DISCOVER: Arctic Thaw, on the opening Northwest Passage
80beats: Will Commercial Whale Hunts Soon Be Authorized?
80beats: Is the Whaling Ban Really the Best Way to Save the Whales?
Not Exactly Rocket Science: Scientists, Film-makers Team Up To Expose Illegal International Trade in Whale Meat

Image: Israel Marine Mammal Research and Assistance Center

Here’s the newly anointed best visual illusion of 2010. No fancy computer graphics. Just cardboard, glue, and some wooden balls. Fabulous.

[Update: Thanks to Sam Mackrill for directing us to the inventor's web site, which includes building instructions.]

Detroit's economy might be seriously suffering, but for one industry, business is booming: Medical marijuana. Since Michigan enacted a law legalizing medicinal marijuana last April, the crop has generated "tens of millions of dollars collectively," according to a statement from Med Grow Cannabis College, located just outside of Detroit:
""With a vast majority of the community in Metro Detroit supporting safe medical marijuana use, many people are looking into the industry as a viable career path," said [president and founder of Med Grow] Nick Tennant."
The school opened in September and has since had more than a thousand graduates. The demand for doctor-advised, medical use of marijuana seems to be growing like a weed, so to speak. And according to Med Grow, the canna-business is an open field with plenty of room for those left unemployed in the state's infamously bad economy:
"With an unemployment rate of over 15%, why not become educated for a career in what could perhaps be Michigan's last true growth industry (no-pun [sic] intended)? For an unemployed Detroit resident, the aforementioned may be his or her last glimpse of hope."
Can Detroit save itself? Looks like it might take a joint effort with a helpful plant. Image: flickr / cannabicas

Pliny the Elder wrote in “The Natural History” on the qualities of amber, “So highly valued is this as an object of luxury, that a very diminutive human effigy, made of amber, has been known to sell at a higher price than living men even, in stout and vigorous health.”

The amber-bound insect you see here is around 95 million years old. Initially this amber was purchased by a Vienna-based mineral dealer in Addis Ababa. Later realizing the potential paleontological value, the dealer sold a big piece to the Natural History Museum in Vienna and several smaller pieces to paleontologists of the University of Vienna. The amber received by Dr. Alexander Schmidt was totally opaque, covered by a dark crust. Dr. Alexander Schmidt: “My colleague Saskia Jancke started to grind and polish the piece randomly to remove the opaque crust, by manual grinding, and stopped (actually, without seeing the insect) a millimeter before reaching the trichogrammatid. We then polished very carefully and it was amazing to see that this wonderful insect was oriented almost parallel to the polished amber surface and that it was not damaged by grinding.”

A tiny trichogrammatid wasp belonging to the hymenopterans order is among the first amber inclusions discovered from the African continent.

Photograph courtesy of Alexander R. Schmidt/PNAS

The world’s coral reefs are disappearing. At least a third of the world’s reef-building species face extinction and in the Caribbean, the average cover of hard corals has fallen by around 80% in the last thirty years. The rich habitats they create are giving way to simpler, less vibrant communities, dominated by seaweeds. But seaweeds aren’t just opportunistic colonisers of waters abandoned by corals – they are coral-killers themselves.

Douglas Rasher and Mark Hay from the Georgia Institute of Technology have found that grazing fish typically keep seaweeds in check. If those fish start disappearing, as they often do because of human hooks, the seaweeds run rampant and corals suffer. Anywhere between 40-70% of the most common seaweed species release compounds that drive away the algae that allow corals to derive energy from the sun. Bereft of energy, the corals ‘bleach’ and die. The message is clear – through overfishing, we are accomplices in seaweed-mediated coralcide.

“Seaweed” is a loose colloquial term for a wide variety of algae, which hail from a few different kingdoms of life. For a while, it’s been clear that they can compete with corals for the same patches of ocean, but the exact nature of that competition has been controversial. To settle the debate, Rasher and Hay set up field experiments in two different reefs, one in Fiji and one in Panama. In both cases, they pit the common coral Porites porites against seven common species of local seaweed. The competitors were lashed against one another using a grid and some rope and left in place for 20 days.

At such prolonged close quarters, the corals became heavily bleached compared to others that were seaweed-free. Their ability to photosynthesise was shot by anywhere from 52 to 90%. Only the parts that actually touched the seaweeds were harmed; the areas on the sides stayed healthy.

It’s possible that the seaweeds damage the corals by shading them from precious energy-giving sunlight, or by cutting into them with sharp edges. But when Rasher and Hay exposed the corals to man-made substances that mimicked the same effects, nothing happened.

Instead, the real reason for the corals’ malaise was a chemical attack by the seaweeds. Rasher and Hay liquidised some of the seaweed species and applied the fat-soluble parts of these extracts to the corals. The result was the same levels of bleaching and disabled photosynthesis as before. This clearly suggests that seaweeds secrete a number of chemicals that damage corals whenever the two competitors touch. Some of the most chemically active species started hurting the corals after just two days of contact.

Rasher and Hay also showed that fish are extremely important for keeping seaweed at bay. In Fiji, they did their field experiments in cages designed to keep hungry fish away. After it was over, they transplanted the seaweeds to two sites. The first was a marine protected area where fishing is banned, coral cover is high and seaweed is rare; there, fishy gardeners cleared away 40 to 100% of the seaweeds, depending on the species. The second site was a heavily fished reef just 300 metres away where seaweed is king and coral is rare. At this location, the surviving fish removed just 0 to 40% of the seaweeds.

So as humans remove fish from a reef, we remove the gardeners that would normally keep seaweeds in check. That gives them an advantage in their chemical competition against corals, damaging the reefs. As the seaweeds become more abundant, the coral density falls, the fish they can support start to dwindle and the seaweeds gain an even greater edge. Rasher and Hay think that even a modest level of fishing can set off this vicious cycle.

And as gardeners, some fish are more valuable than others. The same chemicals that harm corals also deter many grazers from feasting on seaweeds, which makes those that can stomach these morsels that much more vital for the health of a reef. For example, a single species of fish – the streamlined spinefoot – is responsible for eating almost all of the seaweed Chlorodesmis fastigiata. If this one species were to be overfished, the risks to corals could be substantial. It’s yet more evidence to support increasing the proportion of coral reefs that are protected by complete fishing bans.

Reference: PNAS http://dx.doi.org/10.1073/pnas.0912095107

More on corals:

• Clock gene and moonlight help corals to co-ordinate a mass annual orgy
• Bleached corals recover in the wake of hurricanes
• Worrying slowdown of coral growth in the Great Barrier Reef
• Corals survive acid oceans by switching to soft-bodied mode
• Fishing bans protect coral reefs from devastating predatory starfish
• One in three species of reef-building corals face extinction

I've talked in the last two posts about some of Elaine Ecklund's surprising findings about atheist scientists, as discussed on Point of Inquiry (show website here; listen here; download/subscribe here). In this blog post, then, I want to move on to discussing another group that she finds in her survey: spiritual scientists, some of whom are also atheists. This is a topic we discuss beginning around minute 25:20.
The first point about these "spiritual" scientists is that they aren't like spiritual Americans in general. They don't believe in angels and demons. They don't put together an eclectic blend of, say, Christianity, Buddhism, and New Age beliefs.
Rather, as Ecklund observes, they want their spirituality to be of a sort that is entirely consistent with science. And a considerable percentage of them actually overlap with the group of atheist scientists in Ecklund's sample.
For these spiritual but essentially atheistic scientists, "spirituality" involves a sense of awe and wonder at the complexity and beauty of nature. But this raises a pretty big question. Why call it "spirituality" at all? Why use the "S" word, if it does not mean what everyone thinks it means?
Scientific spirituality appears to be an important trend and one we need ...

One of the most successful achievements of the “post-genomic era” has been the elucidation of the genetic architecture which undergird the variation in human pigmentation. I like to point out that in 2005 the geneticist Armand Leroi observed in his book Mutants that we didn’t know the genetics of normal variation in relation to the trait of skin color. In 2010 one couldn’t plausibly write that. We know the genes which control the vast majority of the interpopulational variation in human complexion. This is not due to human ingenuity, but the fortuitous hand that nature dealt us. Pigmentation is a very salient phenotype, evident by the classification of genetically very distinct populations in Africa, India and Oceania as “black.” But in terms of a genetic research project it has long been one of the ways to explore patterns of inheritance in model organisms such as mice, in particular in relation to coat patterns and pigment. And luckily for us, many of the genes which are implicated in pigment variation produce similar changes across diverse taxa. Additionally, the genetic architecture of human pigmentation variation is such that most of the variance is concentrated among a few loci of large effect. Concretely, it seems that well over 50% of the African-European difference in skin color as measured by reflectance of visible light is attributable to two genes, SLC24A5 and KITLG. In Europeans around 75% of the dichotomous variation between those with blue and non-blue eyes may be due to changes in the genomic region across HERC2 and OCA2 (these two genes are very near each other). These are the veritable low hanging fruit, amenable to studies with even small sample sizes and modest statistical power, so strong are the effects of the genetic variables.

And why is pigment important? Obviously there are social ramifications. But pigmentation is likely a major target of natural selection as well, as I suggested in relation to Neandertals. The results are sometimes confusing, but it does seem that pigmentation related loci are enriched in relation to those genomic regions which turn up as positive in tests of natural selection. Additionally, looking at variation around those genes which are correlated with lighter skin across Eurasia it also seems that it may be that our own lineage has become somewhat paler within the last 20,000 years, perhaps even more recently. And the same may have been true for our possible Neander-kin.

At the current rate in regards to pigmentation the age of revolutionary science may soon be over. Extraction of ancient DNA will probably resolve the rate and nature of evolutionary change, while further typing of current populations will flesh out our understanding of the variants responsible for normal human variation. To do that requires more than simply larger sample sizes or improved genomic techniques, it also requires better measurement. The utilization of reflectance indices in studies of study skin color are a step in the right direction, but a new paper in PLoS Genetics points the way toward the same in the study of eye color, Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci:

We measured human eye color to hue and saturation values from high-resolution, digital, full-eye photographs of several thousand Dutch Europeans. This quantitative approach, which is extremely cost-effective, portable, and time efficient, revealed that human eye color varies along more dimensions than the one represented by the blue-green-brown categories studied previously. Our work represents the first genome-wide study of quantitative human eye color. We clearly identified 3 new loci, LYST, 17q25.3, TTC3/DSCR9, in contributing to the natural and subtle eye color variation along multiple dimensions, providing new leads towards a more detailed understanding of the genetic basis of human eye color. Our quantitative prediction model explained over 50% of eye color variance, representing the highest accuracy achieved so far in genomic prediction of human complex and quantitative traits, with relevance for future forensic applications.

The main improvement was decomposing the elements of pigment variation which contribute to the phenotypes which we observe and recognize in a gestalt manner through inspection. In particular, they focused on two parameters, hue (H) and saturation (S). It seems to me that H correspondences to the quality of color, and S to the quantity of color. Figure 1C shows how the eye color categories map onto the quantitative metrics (it is somewhat confusing that red = brown, but I assume brown is less useful for display purposes as a contrast with blue or green).

The r-squared here is such that ~60% of the variation of H can be explained by variation of S. In other words, the two are correlated. This is clear in the plot above, as you see a distribution which moves from brown to green to blue. In fact the researchers could take the variation in H and S, yank out the independent dimensions of variance, and find that one dimension accounted for 90% of the variation.

What they found by treating eye color as a quantitative phenotype, instead of a categorical one, is that though the primary loci already known to affect variation still showed up in their associations, there were secondary loci which now emerged. This makes sense, as the original procedure whereby what is really a continuous trait was transformed into several distinct categories removes information. Smaller effect loci which impact the change in trait value only on the margins would naturally not show up when you removed variation on the margins so as to collapse the trait into a few broad classes. In other words, if loci X had an effect large enough to shift eye color from blue to brown (as HERC2-OCA2 does) then it would show up. But if loci Y only affects trait value slightly it will be unlikely to shift the trait across categories, and so it would not be discovered.

Table 3 shows the effect of different variables, primarily SNPs on the different loci of interest. Beta simply is a measure of the effect of a variable within a linear model. The bigger the beta, the larger the effect on the variable you wish to predict (here, eye color).

SNPs within HERC2 and OCA2 are still the primary variates, as we’d expect. But other loci also affect the trait on the margins, effects only discernible with a better measurement of the trait. Additionally, there is some evidence that they have independent effects on the two dimensions of the trait in question. With more modest effects and less clear phenotypic measures (at least to human intuition) I would be cautious about overemphasizing these results, but clearly they’re in the right direction when it comes to filling in the smaller pieces to the puzzle of eye color.

And these aren’t simply academic questions. They’re of strong forensic interest. Many of the pigment related markers are very good at distinguishing populations, and, they allow us to accurately reconstruct the appearance of perpetrators for crimes where we only have genetic material. With the model they have here they can explain more than 50% of the variation in the two dimensions that they define of H and S. The effect sizes of the marginal loci are modest already, so one might be running into diminishing returns, but from what I gather this is already a significant improvement over eyewitness recollection in relation to eye color. Pigment is hopefully just the tip of the iceberg, perhaps at some point in the future we could predict the rough outlines of someone’s whole physiognomy so that computer reconstructions of appearance could rely primarily are retrieved genetic data.

Citation: Liu F, Wollstein A, Hysi PG, Ankra-Badu GA, & Spector TD (2010). Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loc PLoS Genetics : 10.1371/journal.pgen.1000934

Earlier today I noted a weird situation in Alabama, with a teacher-union-funded ad attacking a candidate for governor for believing in evolution, and the candidate declaring himself a defender of creationism in the schools. I wondered who would speak up for science in Alabama. But I’d be remiss not to point out that good research in evolutionary biology does get done there. For example:

Beatrice Hahn studies the evolution of HIV from chimpanzee-infecting viruses.

Marshal Abrams studies the philosophical foundations of fitness.

Phillip Harris studies the evolution of diversity in freshwater fishes.

John Yoder studies the evolution of new organs.

Steven Secor studies the evolution of digestion in reptiles and amphibians, and what they surprisingly say about the evolution of our own species.

Jeannette Doeller and David Kraus have designed an innovative course on integrating evolution and medicine.

I could go on (and please feel free add other scientists in the comment thread). Suffice to say, there’s good stuff going on in Alabama. Too bad it’s not better known there.