Here’s an excerpt from my third post at the Techonomy blog–which is on how technology and humanity are “coproduced.” You can read the full post here.

At the official opening plenary session of Techonomy, Kevin Kelly–a co-founder of Wired, and author of the forthcoming book What Technology Wants–made what I considered a pretty profound remark. “The first animal we domesticated was humans,” Kelly said. He went on to describe how we “physically changed ourselves through agriculture, through cooking…we’re both masters of technology and also the children of technology.”

Kelly sounded, in this statement, as though he’d read a book that I recently recommended and blogged about, and whose author I interviewed for BBC 2’s “The Culture Show”: Harvard anthropologist Richard Wrangham’s Catching Fire: How Cooking Made Us Human. It’s hard to think of a better example than cooking if you want to show how human beings and technology are “co-produced,” which I take to be Kelly’s argument.

In Wrangham’s account, our ancestors discovered fire and cooking at some hard-to-fix point in the past—but farther back than most scientists had previously assumed. At this point, the power of this innovation then dramatically drove human evolution.

Cooking food was a game changer….READ ON.

In my review of Replenishing the Earth: The Settler Revolution and the Rise of the Angloworld, 1783-1939 I left one aspect of James Belich’s thesis out of my list of criticisms because it wasn’t relevant to most of the argument. He seems to reject, mostly based on incredulity, the idea that there were massive population collapses in the New World when the natives encountered diseases incubated on the World Island (I say “World Island” because it wasn’t only Eurasian diseases, African slaves brought their own suite of lethal ailments which “cleared out” Amerindians from many lowland zones). He points out, correctly, that the Black Death in Europe is estimated to have resulted in a decrease of only ~1/3 from the total population. How then could it be plausible that there may have been population contractions on the order of a magnitude (i.e., the post-collapse population being only ~10% of the pre-collapse population). The skepticism of extreme population decline on the part of indigenes dovetails with the author’s focus on the particular explosiveness of Anglo natural increase, as well as migratory bursts. Heightening the “contrast effect” at the heart of his central thesis.

I think the author’s incredulity only makes sense in light of biological naivete. To a first approximation moderns tend to assume that all populations are interchangeable in our models. Like the economist ignoring individual differences and fixating on H. economicus for analytical purposes this has some utility, but it does miss much of the picture. The Black Death was only one of many epidemics which swept over Europe, so one can presume that European populations were already somewhat robust in the face of a new strain of infectious disease. The revisionist scholarship, which posits mass population collapse, is thoroughly reviewed in Charles C. Mann’s 1491: New Revelations of the Americas Before Columbus. But even today biological differences matter when it comes to disease, for example in relation to swine flu fatalities.

One of the implicit aspects of Belich’s skepticism is that population crash models in the New World are rooted in inferences, not concrete censuses. But I recently stumbled onto a “test case” for contact between Europeans and indigenous people where we have some good data sets, Tahiti.

The initial data point of ~50,000 in 1767 is a low boundary estimate. But the subsequent data points are more concrete, from missionary surveys, or censuses. Even excluding the estimate the pre-contact population of Tahiti island seems to have dropped by one half in a two generation period. This is greater than the average decrease of the Black Death in Europe.

I think the reason for these massive population collapses when isolated groups meet more cosmopolitan ones is simple: they compress many generations of natural selection and immunity acquisition into just a few. In the historical record we know that the 2nd century A.D. witnessed the outbreak of plagues in the Roman Empire, and the subsequent decline and fall was concomitant with the endemic status of malaria in the Italian lowlands. The great Plague of Justinian in the late 6th century has been fingered as the causal factor behind the rise of Islam, the replacement of Celtic Britons by Anglo-Saxons, and the end of the Classical World more generally. Populations isolated from the grinding pathologies of Malthusian agricultural interlude just experienced it in all its glorious misery in a very short burst.

Source: Urbanization in French Polynesia, RC Schmitt, 1962

Here’s an excerpt from my second post at the Techonomy blog–which is on the morning’s workshop about the global spread of information and communication technologies. You can read the full post here.

Unlike my fellow blogger Marshall Kirkpatrick, I don’t have anything too astute to say about the opening pre-conference workshop of Techonomy—hosted by the World Economic Forum and entitled “How to measure the impact and transformational power of technology?”

But I do have a remark on how sophisticated conversations like this one often get mashed into meaningless by media coverage–which is why we need ideas-oriented conferences like Techonomy in the first place.

The morning’s workshop centered on a regularly released World Economic Forum report—better described as a brick, really; this thing is massive—entitled the “Global Information Technology Report.” If that sounds wonky, it is. But it’s also a crucial document for tracking just how countries are doing when it comes to getting their citizens online, and upgrading and improving their information and communications technologies.

Whenever the “GITR” comes out, observed its co-author Soumitra Dutta, the press uses its release as an occasion for tech horse race stories—e.g., Sweden ranked # 1 in “networked readiness,” Singapore # 2, and so on. Woo hoo. Journalists cover such data almost like they would a presidential campaign….KEEP READING.

Recreational drug users call it “Special K.” Large, frequent doses of the anesthetic ketamine can give users vivid hallucinations, but a recently published study hints that the drug may have a medicinal use: temporarily treating depression brought on by bipolar disorder.

The small, proof-of-concept study appears in the journal Archives of General Psychiatry. National Institutes of Health researchers randomly gave 18 depressed patients ketamine or a placebo on two different days, two weeks apart. They used a much smaller dose of the drug than the amount used for recreation or anesthesia, but within 40 minutes 71 percent of the patients who received ketamine showed a significant improvement in mood, which lasted for three days, as measured using a psychiatric depression rating scale.

The quick response time is unusual for the drugs typically used to treat bipolar disorder’s depression, such as lithium or antidepressants like Prozac, and many of the study’s patients had failed to respond to other treatments. On average, the study participants had tried seven antidepressants and 55 percent of participants had failed to respond positively to the extreme measures of electroconvulsive therapy (ECT)–seizures brought on by electrical current. Ketamine’s apparent success may have to do with the neurotransmitter, glutamate:

Does the unconventional drug ketamine work better? The best answer is that it works differently. Many antidepressants relieve depression by altering levels of the neurotransmitter serotonin in the brain. Ketamine dissociates patients from negative thoughts and feelings by preventing another neurotransmitter, glutamate, from interacting with a receptor in the brain that usually processes it. Brain autopsies have suggested that glutamate activity is associated with bipolar disorder, and past studies have shown that severing the glutamate-receptor link can rapidly lift symptoms in people with major depression within two hours. [Time]

Though ketamine’s therapeutic effects were only temporary, scientists hope that with more research they may be able to incorporate the drug into treatments.

Ketamine could improve treatment of bipolar illness and depression in a variety of ways, [coauthor Carlos A.] Zarate said; for example, as a means to jump-start standard drug treatment, or as an anesthetic before ECT. “It’s opened the floodgate of many different directions of research, and all of them are quite encouraging,” said Zarate, who along with a co-author has filed for a patent on the use of ketamine in depression. Those rights would be assigned to his employer, the National Institutes of Health. [Reuters]

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Image: flickr / Carly & Art

This is wildly good news! Through Vaccine Central I learned that a major polio outbreak in Tajikistan has been stopped!

How? Through vaccination.

Yup. The first reports of polio were confirmed in April — 413 of them. However, that ended in late June, when no new cases were reported. That is credited to the thousands of doctors and nurses who not only vaccinated at least 97% of the children in each region of the mountainous country, but also flooded the area with multi-lingual informational leaflets, posters, and banners.

And they succeeded! With no new reports, it appears this outbreak was stopped cold.

And with the AVN in Australia getting hammered repeatedly in the press, I can now have some hope that the movement here in the United States, spearheaded by Jenny McCarthy, will die off as well. Vaccinations work, and they save a lot of lives.

A brutal Mount Everest storm might have doomed legendary climber George Mallory. How do we know? Because it’s there—in his team’s meteorological records.

Mallory was the man who, according to legend at least, responded to a question about why he’d want to climb Everest with the immortal reply, “Because it’s there.” But he and his partner, Andrew Irvine, never returned from their 1924 attempt to summit the world’s highest peak. Their lost expedition spurred decades of curiosity about their fate, a curiosity that only intensified when explorers found Mallory’s body in 1999.

For a paper published in the journal Weather, scientists have scoured the meteorological measurements taken at the expedition’s base camp at 16,500 feet and recorded in the logs. Despite the fact that those logs were brought back to Britain in 1926, the researchers argue that they haven’t been part of the discussion of Mallory’s downfall, even though the answer could be right there on the decades-old pages.

The researchers analysed barometric pressure measurements and found that during the Mallory and Irvine summit attempt, there was a pressure drop at Everest base camp of approximately 18 millibars (mbar). Lead author GW Kent Moore, from the University of Toronto, Canada, described this as “quite a large drop”. He said: “We concluded that Mallory and Irvine most likely encountered a very intense storm as they made their way towards the summit” [BBC News].

A storm on Mount Everest is bad news for climbers by itself. But the drop in pressure also depletes the oxygen that’s so precious when you’re so high up.

Dr John Semple, an experienced climber and the chief of surgery at Women’s College Hospital in Toronto, said: “Mount Everest is so high that there is barely enough oxygen near its summit to sustain life and a drop of pressure of 4 mbar at the summit is sufficient to drive individuals into a hypoxic state” [The Telegraph].

Even if Moore is right, his storm hypothesis still can’t answer the real burning question about the lost expedition: whether Mallory and Irvine achieved the top of Everest before they died. The 1999 explorers found Mallory’s body more than 26,000 feet up. If he had reached the summit, it would have predated Sir Edmund Hillary’s 1953 ascent by nearly three decades.

For more about Mallory, check out the new documentary The Wildest Dream, which follows both the 1924 ascent and the 1999 mission that finally found him.

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Image: Wikimedia Commons

Want to attract a good mate and ward off unknown relations? Secrete a smelly substance from that gland on your chest and rub it all over. At least that’s what a mandrill might do: A recent study suggests that the baboon-like primates may use their smelly secretions to distinguish compatible mates from family.

After taking swabs from mandrill sternal glands, researchers genotyped each sample to determine the monkey’s major histocompatibility complex (MHC)–a unique genetic signature related to the animal’s immune system. They also, using a sorting technique called gas chromatography–mass spectrometry, determined each secretion’s chemical makeup, and thus its stink bouquet.

As the study’s leader Leslie Knapp of Cambridge University told the BBC, more “genetically diverse” mandrills, i.e. unrelated, have different MHCs and chemically-speaking different scents:

“[I]t seems that the odour is something that tells us some really important things about the genes of a mandrill.”

If this all sounds familiar, perhaps that’s because some researchers have said the same thing about humans. We somehow–even though researchers can’t seem to pin down human pheromones–seem to pick out one another’s genetic diversity when sniffing out good mates. Related studies have even examined whether birth control messes with our and animal’s don’t-mate-with-me-cousin beacons, which could hypothetically lead to inbreeding.

As Knapp told the BBC, the animal’s colorful face markings also seem important for attracting mates and communicating status. But to complicate matters on our end of the primate family tree, another recent study hinted that, for humans, faces that resemble our own or our parents’ drive us wild, narcissistic lot that we are.

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Image: Wikimedia / Robert Young

Today DISCOVER blogger Ed Yong reports on a project called Foldit, in which citizen scientists playing a slick computer game helped to unravel the complex structure of proteins, and in doing so got the game into the prestigious journal Nature.

There are plenty of great ways for non-professional scientists to help out scientific projects. DISCOVER previously brought you the ways to donate your computer’s free time to projects like SETI@home and Stardust@home. But what if you want to use your own brainpower in the aid of science? That can be arranged, as there are plenty of more active ways to contribute to crowdsourced science.

1. Mapping the place where Genghis Khan was buried

This summer archaeologist Albert Yu-Min Lin led an expedition to Mongolia in search of the lost tomb of Genghis Khan—but not before putting out the call for a little help.

Lin’s team provided high-resolution satellite photography of the area they plan to survey. On the mission’s website, volunteers can sign up to scan the images for anything that could help the team on its quest: roads, rivers, or perhaps even the outlines of where long-gone structures once stood centuries ago.

2. Amateur Martians

As we noted yesterday with the Spirit rover’s apparent demise, the rovers and orbiters NASA has sent to Mars have been a smashing success. The only problem is, those robot explorers have sent home more data than NASA’s people can map on their own.

You can help: Play “Be a Martian,” a game set up through the Jet Propulsion Lab. Players earn points and badges by finding the most interesting martian craters for study, or by matching up high-resolution images of the red planet’s surfaces to wider photos taken from above—thereby improving maps of Mars.

3. Fixing that little oil spill down south

With a temporary cap in place and the more permanent “static kill” and relief well measures on their way, we hope that BP is on the cusp of shutting down its oil leak into the Gulf of Mexico for good (fingers crossed). But even if they succeed, the gargantuan task of cleanup remains.

You can help. When BP asked the public to submit ideas for fixing the spill, it got 300,000 responses. Certainly many were kooky, but as the DISCOVER blog The Intersection noted, one proposed scheme seems very similar to the container cap on the leak now. And the X-Prize foundation, which offers multi-million dollar prizes for things like the best lunar craft or high-mileage car, said it would consider such a lucrative prize for the right idea to clean up BP’s mess.

If you’re no Kevin Costner and don’t have an oil cleanup machine in your garage, scientists still could use some help in the long recovery that’s only just beginning. One man, Drew Wheelan of the American Birding Association, sought help this summer to count the ghost crabs on the Gulf Coast, which are imperiled by the oil but harder to count than turtles or birds.

4. reCAPTCHA

You might have already helped reCAPTCHA without even knowing it.

The project, started in 2008 and acquired by Google last year, is helping to digitize old documents like books and The New York Times archive by using talents you have that computers don’t. CAPTCHAs are those squiggly letters and numbers that websites ask you to interpret to prove you’re not a spambot. And the degraded text in old newspapers tends to look a little like CAPTCHAs, making it difficult for computers to digitize them.

So, when computers can’t figure out a word, they ask us. The word or phrase is put into a CAPTCHA, where humans read it with 99 percent accuracy.

5. Galaxy Zoo – classifying galaxies (and more)

Computers have a hard time understanding messy old letters running into each other, and they have a hard time understanding messy old galaxies running into each other, too.

The people behind the Galaxy Zoo project want to understand galactic collisions, and how those collisions helped to provide the variety of galaxy types we see across the universe. So the system shows a volunteer an real image of two galaxies merging into one, surrounded by my computer-simulated images of different types of galactic smash-ups. You, the volunteer, choose the closest match. And when person after person does this with galaxy collision after galaxy collision, a better view of the universe’s evolution comes into view.

Galaxy Zoo volunteers have already turned up a new kind of galaxy, called “green pea” for its appearance. Professional astronomers alone probably couldn’t have scanned enough images to notice this, and computers’ talents aren’t well suited to spotting these oddballs.

We humans notice a surprise.

Follow DISCOVER on Twitter and Facebook.

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Images: GeoEye; Wikimedia Commons

My friend Glenn Schneider is an astronomer, and also a little bit nuts. He’s an umbraphile, an eclipse-chaser. But he’s not just any guy who travels the world to watch solar eclipses, he gets neck-deep into them. He actually chartered a plane and organized an incredible trip to see the total solar eclipse a few weeks ago — I wrote about this as he was planning it.

Glenn sent me a note to say that the trip was a complete success! They had more than nine minutes of totality to watch — that’s literally more than is ever possible on the ground, because a plane can "chase the shadow", counteracting the rotation of the Earth. He has some details and some great pictures on his site. Check this out:

The blue streamers above and below the Sun (and the dark spot below the Sun) are not real, but artifacts produced by the plane window and the camera. Still, that’s incredible. Sigh. I swear, one of these days I’ll go with him. I’ve still never seen a total solar eclipse. Some day…

Here’s an excerpt from my first post at the Techonomy blog–just introducing myself. You can read the full post here.

This is my first post on the Techonomy blog, so I mainly want to introduce myself. I’m Chris Mooney, a blogger for Discover and author of several books about the relationship between science and politics, and how things sometimes go dramatically splat in this area.

So I may seem, in some ways, an odd duck at Techonomy—except for the following fact.

As someone who’s extensively covered climate change, evolution, and stem cell battles (among others), I’ve learned there’s a fundamental dynamic here. Something in science or in technology comes along and dramatically changes our lives—and then people resist it. They fight back against the future, or change, or just plain reality.

Grasping this dynamic has in turn led me to look for the next set of issues that are bound to create similar tensions. That’s where Techonomy comes in….READ ON.

Opportunity's first dust devil. NASA/JPL-Caltech/Cornell University/Texas A&M

The Mars Exploration Rover Opportunity captured this dust devil on camera.  This is the first one for Opportunity in the six and a half years on the planet.  Spirit has seen dozens of them.  I thought sure Oppy had seen one but no, not according to the press release.

This particular dust devil was seen on July 15th while the rover was taking pictures with its panoramic camera to do a bit of drive planning.  The dustier conditions near Gusev Crater where Spirit has been working are likely more favorable to create the phenomenon.

Just a day before the dust devil was spotted, conditions near Opportunity were windy enough to blow some dust off the solar panels and increased the power output by 10 percent.  Opportunity took a series of pictures on Sol 2220 (in April) which were put together to give a 360 degree view of the area, looks pretty desolate – click here to view it.

It’s not every day that people can get published in one of the world’s leading scientific journals by playing computer games, but Foldit is no ordinary game. The brainchild of Seth Cooper from the University of Washington, Foldit taps into the collective efforts of tens of thousands computer gamers to solve scientific problems.

The goal of the game is to work out the complicated three-dimensional structures of different proteins. Proteins are feats of biological origami; they consist of long chains of amino acids that fold into very specific and complicated shapes. These shapes can reveal how proteins work but solving them is fiendishly challenging. To do it, scientists typically need to grow crystals of purified protein before bouncing X-rays off them. Foldit takes a different approach, using the collective efforts of causal gamers to do the hard work. And its best players can outperform software designed to do the same job. Best of all, you don’t need a PhD to play Foldit, or any scientific training at all. The controls are intuitive, tutorial levels introduce the game’s mechanics, colourful visuals provide hints, and the interface is explained in simple language. While protein scientists concern themselves with “rotating alpha-helices” and “fixing degrees of freedom”, Foldit players simply ‘tweak’, ‘freeze’, ‘wiggle’ and ‘shake’ their on-screen shapes. It’s telling that barely an eighth of the players work in science, and two-thirds of the top scorers have no biochemistry experience beyond high school.

Foldit’s success relies on the fact that it doesn’t shallowly flirt with interactivity – it’s a true game. Cooper designed it to “attract the widest possible audience… and encourage prolonged engagement”. For a start, that meant making it competitive. Players are scored based on the stability of the structures they end up with and a leader board shows how they rank against other gamers.

There’s also a social side – gamers can chat on online forums, work in groups to solve puzzles and share solutions on a wiki. Of course, there’s the thrill of contributing to genuine scientific research, but that motivates less than half of the community. The rest do it for the achievement, the social aspects and largely, because the game was fun and immersive.

And just like real game development, everything was tuned according to feedback from the players. Tools were added and refined, the difficulty of the tutorials was tweaked to stop frustrated beginners from leaving, and puzzles were matched to the skills of the players.

Foldit’s origins lie within Rosetta, a piece of software designed to solve protein structures by simulating and testing thousands of different folds. Rosetta is an example of ‘distributed computing’, where volunteers run the program on their home computers when they don’t need it. They effectively donate their computing power to speed up the laborious task of solving protein structures. But the volunteers wanted to use their biological computers – their brains – as well as their man-made ones. They suggested an interactive version of the programme and in May 2008, they got their wish with Foldit.

To test the usefulness of the approach, Cooper challenged his gamers with ten puzzles – proteins whose structures were solved but weren’t on any public database. Even so, the Foldit players did themselves proud. They outperformed the original Rosetta software on five of the puzzles and matched it on three of them. And in the two cases where Rosetta actually beat the players, it still didn’t get anywhere near the right answer.

The human gamers had many advantages that gave them the edge. The players used a far wider range of strategies than Rosetta does, and some specialise in the early, middle or late stages of the game. And they were also good at working out where to begin. In one game, when they were given ten possible starting structures, they picked the one that was closest to the actual answer. Armed with the same starting set, Rosetta couldn’t do as well.

The humans also had the massive advantage of long-term planning. Rosetta uses a “rebuild and refine” method to gradually arrive at the most stable structure through tiny tweaks. But it won’t investigate a potentially interesting move if it means making the protein temporarily less stable. The gamers had no such problems. They were quite happy to substantially unravel the protein because they knew that they could put it back together in an even better state.

“Computers are obviously superior in the ability to crunch numbers, but lack the intuitive sense of knowing when to crunch numbers, or which tool to best use at a certain point in the game,” says CharlieFortsConscience, one of Foldit’s gamers. “The experience and intuition part of the gameplay, for me, is being able to look fresh at a puzzle structure and note which areas ‘don’t look right’.”

But even experience and intuition has its limits. Some puzzles proved too much for them. While some could solve the hardest of challenges – folding a full protein from its extended chain of amino acids – most struggled. Cooper thinks that he’ll get the best outcomes by blending the best of both human creativity and computer power. If Rosetta can take them half-way, gamers can finish the job with aplomb.

Cooper was so impressed with the players’ strategies that he thinks he can use them to design better algorithms for later versions of Rosetta. As he says, “Our results indicate that scientific advancement is possible if even a small fraction of the energy that goes into playing computer games can be channelled into scientific discovery.” It’s a perfect example of what Clay Shirky describes as the “cognitive surplus” – the free time and mental energy that’s spent on leisure pursuits. Thanks to the Internet, this valuable resource could be channelled into something more productive.

In the meantime, the gamers themselves can smile at the fact that they’ve been published in the prestigious journal Nature. They’re final authors on Cooper’s new Nature paper, listed anonymously (as seems fitting) as the “Foldit players”.

Reference: Nature http://dx.doi.org/10.1038/nature09304

More on computer science and video games:

• Sniff-detector allows paralysed people to write messages, surf the net and drive a wheelchair
• Photo-recognition software catches tigers by their stripes
• Using our powers for good – how web security software can help to transcribe old books
• Brain-training games get a D at brain-training tests
• RCT: video games can hamper reading and writing skills in young boys by displacing other activities

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

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Around 105 million years ago, Tanzania was home to a very strange creature. It was about the size of a cat and had features that wouldn’t look out of place on a mammal – a slender frame, long legs, a short skull and a variety of teeth for cutting and grinding its food. But this was no mammal – it was a crocodile.

The newly discovered Pakasuchus has many trademark features that clearly mark it out as a crocodilian – the group that includes modern crocs and alligators. But it was very different to these living relatives, and some of its features were so mammal-like that its name even means “cat crocodile”.

Consider its skull. All modern crocs have a snout full of consistently conical teeth. They snap at their prey with a powerful bite, before swallowing them whole. But Pakasuchus had a diverse set of chompers including piercing canines and grinding molars. It even had shearing teeth like those of cats and other meat-eating mammals. This ancient croc clearly ate its prey in a very different way. It’s dramatic proof that living crocodiles are just a thin branch of what was once an incredibly varied lineage, which came in many shapes, sizes and lifestyles.

Pakasuchus lived in the mid-Cretaceous period, when the gigantic supercontinent called Pangaea has begun to split up into separate land masses. In the Northern Hemisphere, small mammals were on the rise, exploiting all sorts of fresh ecological opportunities while dinosaurs loomed overhead. But in the Southern Hemisphere, small mammals were relatively rare and crocodiles came to fulfil the same roles using very similar adaptations.

Patrick O’Connor from Ohio University led a team that unearthed the little crocodile at Tanzania’s Rukwa Rift Basin. He named it Pakasuchus kapilimai after the Kiswahili word for ‘cat’, the Greek word for ‘crocodile’, and the late Professor Saidi Kapilima, who was an important part of the excavation. The team found several specimens of Pakasuchus but one in particular was in stunning condition.

The animal’s mouth was tightly shut when it died, so O’Connor used a medical scanner to study the details of its unusual jaws and teeth. The scans revealed that Pakasuchus only had 13 teeth, far fewer than its modern relatives. The teeth were very diverse, as the movie below show. And its molars fit together extremely well, and could grind and shear food with the aid of a mobile jaw. These traits are a standard part of a mammal’s hardware but they’re completely unprecedented in crocodiles.

Pakasuchus bizarre features don’t end in its mouth. It had long slender legs and nostrils on the front end of its snout, which suggests that it lived on land. Modern crocodiles, which primarily hunt in water, have short legs (they use their tails to swim) and their nostrils are on the top of their snout to allow them to breathe more easily at the surface.

Pakasuchus also lacks the heavy bony plates, or ‘osteoderms’, that are found on virtually all other crocs, whether living or extinct. Its tail is the only place that retains this body armour. O’Connor thinks that this species was an active hunter that sacrificed its cumbersome protection in favour of agility and speed.

By comparing Pakasuchus’s entire skeleton to those of several other crocodilians, O’Connor discovered that it belongs to a large extinct group called the notosuchians. This lineage is famed for its diversity. Pakasuchus was the only one with molars that met, but the others had their own weird adaptations. They included plant-eating Chimaerasuchus; Notosuchus with a possible pig-like snout and fleshy cheeks; Armadillosuchus with its banded, armadillo-like body armour; the bizarre, rabbit-toothed Yacarerani; and Anatosuchus with a broad, duck-like snout.

All of these species were medium-sized land-living creatures with features and habits that are decidedly unlike the typical crocodile. They were a highly successful part of the Cretaceous ecosystem, eking out lifestyles that mammals were sharing in the opposite hemisphere. Perhaps the eventual coming of mammalian competitors, or a significant environmental change, sealed the fate of these bizarre crocs. Whatever the case, it’s clear that today’s species are just the very tip of a once-diverse lineage.

Reference: Nature http://dx.doi.org/10.1038/nature09061

More on crocodiles:

• Crocodiles signal hatching time by calling from inside their eggs
• Stealthy alligators dive, rise and roll by moving their lungs

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

The Silurian Period, 425 million years ago: As volcanic ash rained down on proto-England, a sea blob named Drakozoon gave its last. Now, using a computer model, scientists have finally witnessed what the soft-bodied ancient looked like in 3D.

Researchers first found a Drakozoon fossil six years ago in Herefordshire Lagerstätte, home to England’s mother-load of soft-bodied fossils. Such fossils are rare since most of these creatures decompose before a fossil can form.To capitalize on the find, a team chopped the Drakozoon fossil into 200 pieces, photographed those slices, and used a computer to construct a rotatable image of the old softy.

They found that Drakozoon, which was little more than a tenth of an inch long, had a hood that it wrapped around itself to ward off predators, and had tentacles for snaring microscopic food bits out of neighboring water. The researchers also noted that Drakozoon had eight ridges on the sides of its body, what they believe could be vestiges of an evolutionary step up from creatures with repeating body segments, similar to modern-day caterpillars. The critter was described in the journal Biology Letters.

Mark Sutton, from the Imperial College London’s earth science and engineering department, said in a college press release:

“Excitingly, our 3D model brings back to life a creature that until recently no one knew even existed. . .”

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Image: Imperial College London

Sure, a laser can shine finely-tuned light to do anything from scanning your barcodes to correcting your vision, but soon that precise hero may meet its match: Physicists have recently imagined a device that can absorb light of certain frequencies, an “anti-laser.”

Absorbing light may not seem all that impressive, since after all, anything that appears black works as an absorber. Your driveway, however, is not the anti-laser. A paper in the Physical Review Letters lays out the plans for this device which can absorb light wave clones (same frequency, phase, and polarization) that some lasers emit. The pickiness of this theoretical light absorber is part of what would make the device unique, just as an important part of what separates a laser from a flashlight is the precision of the light a laser emits.

Instead of amplifying light into coherent pulses, as a laser does, an antilaser absorbs light beams zapped into it. It can be “tuned” to work at specific wavelengths of light, allowing researchers to turn a dial and cause the device to start and then stop absorbing light. “By just tinkering with the phases of the beams, magically it turns ‘black’ in this narrow wavelength range,” says team member A. Douglas Stone, a physicist at Yale University. “It’s an amazing trick.” [Science News]

The Yale University team has gone through the numbers for such a choosy absorber, which works partly by switching the material that reflects light in a laser with material that instead absorbs it. The paper describes a theoretical device using silicon.

A paper-thin slice of silicon would normally absorb about 20 per cent of the incoming light, but the team showed that in this set-up it would cancel nearly all of the light at 945 nanometres, in the near infrared…. So far the effect exists only on paper, but team member Douglas Stone says “ongoing experiments are extremely promising, and I have total confidence it can be realised”. [New Scientist]

Given the specificity of the light that this absorber requires it is unlikely, a Physics review says, to find future employment as part of a solar panel or stealth cloak (shielding a ship for example from radar). Instead, such a device could likely appear in pairs with lasers forming “optical switches” in circuits–and perhaps as the weapon of choice for science fiction foes.

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Image: Wikimedia / Jeff Keyzer

Hounds, pointers, and other dogs bred for their excellent abilities to pick up a scent tend to have longer snouts—but it’s not just that a bigger nose is a better one. Researchers have found that human domestication of dogs has shifted the structure and alignment of some dogs’ brains. And in those varieties with shorter snouts—which humans bred for other reasons, like appearance—the olfactory brain region rotated to a different part of their skull, leaving scientists to question whether we’ve crossed up their smelling abilities (and perhaps more).

Since the first wolf was domesticated an estimated 12,000 years ago, “selective breeding has produced a lot of [anatomical] variation, but probably the most dramatic is in terms of skull shape,” said study co-author Michael Valenzuela [National Geographic].

For this study, which appears in the open-access journal PLoS One, Valenzuela and colleagues examined the brains of 11 dog breeds and found great variation in the size and shape of their skulls. The breeds with shorter snouts had brains that rotated forward by as much as 15 degrees over the generations, the scientists say. That means that the olfactory lobe, as well as other parts of these dogs‘ brains, has shifted position and shape because humans guided their evolution through domestication.

Valenzuela says that in particular humans might have altered the dogs’ rostral migratory stream, or RMS, a connection in the brain that’s important for the sense of smell.

“The RMS starts very deep in the middle of the brain and traces a very predictable path to the olfactory bulb…. Since the olfactory bulb has moved in brachycephalic [short-snouted] dogs, you’d expect to see a change in the course of the RMS, or it may be disregulated” [National Geographic].

The researchers don’t know yet how much the brain changes affect the dogs and their world of smell. But they say the differences in brain size are another surprise showing how diverse dogs can be.

As Dr. Valanzuela explains, the most astounding thing is that dogs’ brains can actually handle such huge differences in the shapes of the skulls that house them. Dogs have already shown unprecedented levels of variety in their different physical breeds, but the variation in brain organization is an even more fundamental and thus more incredible form of diversity across the species [io9].

Related Content:
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Image: Wikimedia Commons

Meryl Dorey, head of the flailing Australian Vaccination Network — an organization dedicated to twisting the truth about vaccines and saying anything at all to scare people into an antivax stance — has once again put fingers to keyboard, and as usual the truth eludes her.

She wrote a lengthy essay about her dealings with Toni and David McCaffery, who lost their four week old infant Dana to pertussis two years ago.

I hardly need to point out that her interpretation of reality doesn’t come within a glancing blow of it; you can read what Dorey wrote, and then compare it to Toni McCaffery’s response detailing what really happened, and why Dorey is so wrong.

I also received a note from David McCaffery about a terrific site that helps educate people about vaccines: Chain of Protection. They have really good videos describing benefits of vaccinations. Here’s the one about herd immunity which shows just why it’s important:

Herd Immunity – How it works from Chain of Protection on Vimeo.

Check out the site. It’s what Meryl Dorey wouldn’t want you to do.

Though I don’t blog about the topic with the breadth and depth of individuals such as Brian Switek or Darren Naish I do take some interest in natural history. This is the domain which was my original focus as a child when it came to science, and I continue to observe it from afar with great fondness. General questions, such as the role of contingency and necessity in the arc of evolution, are obviously the sort of issue which natural history can be brought to bear upon. But I also have a fascination with specific, often anomalous details. For example, the Monito del Monte of Chile is generally held to be more closely related to the marsupials of Australia than those of the New World. It is the only extant member of the order Microbiotheria, and its connection to Australian marsupials is one of those surprises which go to show you why science is done in the field, and not just theorized from your a priori beliefs. It’s why you play the game, and don’t simply allow the handicapping professionals to decide wins and losses.

A new paper in PLoS Biology explores the phylogenetic relationship of Australian and New World marsupials through a more robust genomically focused technique. Though the method has a “in silico” spin, the basics seem to be grounded in cladistics. Look for derived characters which can indicate monophyly. Monophyly simply means that all of a set of organisms descend from one common ancestor. So, famously, the class of reptiles is not monophyletic. Some of the descendants of the common ancestors of all reptiles are not included within the class, birds. Earlier generations of taxonomists tended to classify organisms based on their characters, and the set of characters which they chose for reptiles included groups, such as crocodiles and tortoises, which were genetically very distant (when compared to crocodiles and birds). Though anatomically informative, these sorts of taxonomic classifications misled one as to evolutionary history. Not a minor matter. Ergo, the rise of cladistic techniques which replaced intuition with a more formal hypothetico-deductive framework. Because of its generality as a method naturally you can substitute genetic loci for morphological character traits, and so you get papers such as the one below.

Tracking Marsupial Evolution Using Archaic Genomic Retroposon Insertions:

Ever since the first Europeans reached the Australian shores and were fascinated by the curious marsupials they found, the evolutionary relationships between the living Australian and South American marsupial orders have been intensively investigated. However, neither the morphological nor the more recent molecular methods produced an evolutionary consensus. Most problematic of the seven marsupial groups is the South American species Dromiciops gliroides, the only survivor of the order Microbiotheria. Several studies suggest that Dromiciops, although living in South America, is more closely related to Australian than to South American marsupials. This relationship would have required a complex migration scenario whereby several groups of ancestral South American marsupials migrated across Antarctica to Australia. We screened the genomes of the South American opossum and the Australian tammar wallaby for retroposons, unambiguous phylogenetic markers that occupy more than half of the marsupial genome. From analyses of nearly 217,000 retroposon-containing loci, we identified 53 retroposons that resolve most branches of the marsupial evolutionary tree. Dromiciops is clearly only distantly related to Australian marsupials, supporting a single Gondwanan migration of marsupials from South America to Australia. The new phylogeny offers a novel perspective in understanding the morphological and molecular transitions between the South American and Australian marsupials.

Retroposons are genetic elements which insert randomly throughout the genome, and rarely in the same location in across lineages. This avoids “false positives” where you observe genetic features across taxa which you incorrectly infer to indicate a phylogenetic relationship. The pattern of variation of randomly distributed distinctive retroposons can theoretically be used to map the sequence of relatedness of the same genes (orthologous) across species. Retroposon insertions copious within the marsupial genome, so naturally they’re a good candidate for markers which might exhibit the distinctiveness necessary to explore deep time evolutionary relationships. Additionally retroposons can nest within each other, within newer insertion events overlain over older ones, so that they create a sort of genetic palimpsest. These researchers filtered the loci harboring retroposons down to 53 which were particularly informative for relationships across the marsupial species for which they had genomic data, two species per order excluding orders without more than one species. The two species within each order were selected from lineages which were presumed to exhibit the deepest evolutionary split within the clade.

Granted, it isn’t as if taxonomists haven’t been interested in the relationships of marsupial mammals. As noted in the paper the nature of the phylogenetic tree frames plausible hypotheses which explain the current biogeographic pattern we see. Where there are two sets of marsupial mammals separated by the Pacific, but where the spatial pattern does not perfectly correspondent to the phylogenetic relationship. Here is a figure from a 2004 paper:

Australian and South American marsupials are color coded. As you can see, Dromiciops, Monito del Monte, is nested within the monophyletic clade which includes all the Australian mammals. But, the aforementioned paper was based on mitochondrial DNA. The DNA passed along the maternal lineage, easy to extract and amplify, as well as analyze (because of the lack of recombination). But for the purposes of exposing such deep time relationships mtDNA may not be optimal, and should not be the last word.

Much of the “guts” of the paper was obviously computational, and wasn’t explored in detail within the text. So let’s jump to the outcome, the new branch of the tree of life for marsupials:

Ah, now you see that Australian marsupials are a monophyletic clade! The Monito del Monte is no longer nested within their own lineage, but is now an outgroup. It would be peculiar if it was not the closest of the outgroups, so its positioning is reasonable in terms of what we’d expect. From the discussion:

Given the limitations just mentioned, the retroposon marker system identified a clear separation between the South American and Australasian marsupials. Thus, the current findings support a simple paleobiogeographic hypothesis, indicating only a single effective migration from South America to Australia, which is remarkable given that South America, Antarctica, and Australia were connected in the South Gondwanan continent for a considerable time.

The search for diagnostic South American or Australidelphian marsupial morphological characters has been so far confounded by the lack of a resolved marsupial phylogeny…The newly established marsupial tree can now be applied not only to morphological and paleontological studies but also to clearly distinguish genomic changes.

Life is not always parsimonious, but when more powerful techniques which can resolve issues to a greater degree of precision produce more parsimony, then the world is as it should be in science. The main curiosity I have is to wonder if the outcome isn’t a little too convenient for the generation of more elegant paleontological models. I’m not casting doubt on the integrity of the researchers, but with methods which require such heavy cognitive lifting, and operationally are a touch opaque because of the technical component, one would be assuaged by replication. I believe we will be in the future. If we have $1,000 genomes for human beings in a few years, NSF grants for taxonomists who lean on genomics may go a lot further in 2020.

Image Credit: José Luis Bartheld from Valdivia, Chile

Citation: Nilsson MA, Churakov G, Sommer M, Tran NV, Zemann A, Brosius J, & Schmitz J (2010). Tracking marsupial evolution using archaic genomic retroposon insertions. PLoS biology, 8 (7) PMID: 20668664

Click here to view the embedded video.

There’s a Spirit update, still no Marian update.

Update on the update:   Well, I managed to do this post quite a while earlier and hit the wrong button, I managed to find it.  Whew…

I have reason to believe Marian is computerless, but trying very hard not to be.

I need everybody to send her good vibes – we need to change her computer karma.  Ready?   Send. . . . . . .

Video Source

As I hoped, Marlene Zuk, a biologist at UC Riverside, has chimed in with her own thoughts on Friday’s post on the meaning(lessness) of sexual displays. Check it out!