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Prof. A.'s Science Fix- May 18 2012 Edition

Science at Atheist Universe


FEATURED IMAGE: The Tarantula Nebula

What a name for a nebula! Explanation: The Tarantula Nebula is located in our neighboring galaxy, in the Large Magellanic Cloud (LMC). The red and pink gas indicates a massive emission nebula.The images were obtained by the Hubble Space Telescope.  Visit our group The Daily Cosmos for many more beautiful nebula pictures posted by Doone in the comments section.

MICROBIOLOGY: 86 million year-old bacteria still alive in deep ocean mud. This is not the first time that living bacteria have been discovered many meters into marine sediments. But a new Science article this week, by Danish and German scientists, describe bacteria breathing oxygen at least 30 meters in deep red clay at the bottom of the Pacific ocean north of Hawaii. These bacteria have not had exposure to sunlight or organic matter for 86 million years! I will say it again: the last time these microbes saw fresh oxygen or sunlight, dinosaurs walked the Earth! So how are they still alive?  The bacteria living in these sediments are breathing oxygen at a much, much slower rate than other microbial communities. Scientists calculated that the respiration rate of these bacteria dropped ten thousand fold at 30 meters compared with at or near the surface of the sediment. Thus, aerobic metabolism can persist in deep marine sediments, although at an extremely low rate. It is amazing how little it takes to sustain life! The scientists measured the oxygen in the core with special sensors; because they know how much oxygen should have diffused down to each mud depth, any "missing" oxygen had to mean that microbes had consumed it. What is special about this North Pacific sediment is that the microbial community was too sparse to consume it all, which is why they detected oxygen all the way down to ~30 meters. In most places, bacteria consume all the oxygen within 10 cm of sediment. The very slow oxygen consumption by the microbes allow them to subsist on very small amounts of long-buried organic materials. This type of research may be useful in the search for life on other planets, given the extreme conditions in these deep clay sediments. Of course, to be absolutely sure these extreme microbes are alive, one would need to see them divide. But while E. coli divides every 1/3 hour, the calculated rate for these extremely slow microbes would be 1,000 years. We may need to wait a bit to see these microbes divide.


ANIMAL BEHAVIOR: Insect uses its victims’ carcasses as camouflageAcanthaspis petax, an assassin bug that lives in East Africa and Malaysia, hunts its prey by piercing it with its proboscis, dissolving the tissue with its potent saliva, and sucking it dry from the inside out.  But this is not novel. Other assassin bugs do this, too. What is special about A. petax is that it camouflages itself with the bodies of dead ants that it carries on its back, all bound together with a sticky substance. Although some scientists believed the dead ant exoskeletons were for olfactory camouflage when hunting, it turns out that the ghastly camouflage is for protection against their natural predators, jumping spiders. But New Zealand scientists showed experimentally that “naked” bugs were attacked 10 times more frequently than the ones carrying the dead ants on their backs. Jumping spiders hunt guided by vision, so the protection was not olfactory, but visual. For some reason, jumping spiders do not hunt ants, therefore they rejected the masked assassin bugs as prey.


GENETICS: Gene variant associated with better memory and higher risk for PTSD. Some researchers have hypothesized that the risk for post-traumatic stress disorder (PTSD)depends on the capacity a person has to form strong memories, especially emotional memories. Now a team of Swiss scientists has found that a variant of the gene PRKCA, that encodes an enzyme involved in the formation of emotional memories, correlates with PTSD in Rwandan refugees. The scientists tested 700 healthy volunteers by showing them photos with highly charged emotional content and quizzing them about details of the photos. Volunteers with two copies of the A allele of PRKCA remembered the most detail, those with two copies of the G variant the least amount of detail, and heterozygotes, with one copy of the A variant and one of the G variant, fell somewhere in the middle. The researchers also studied the distribution of the A allele in a group of 347 survivors of the 1994 Rwandan genocide; 134 of them had been diagnosed with PTSD, although all 347 refugees had experienced traumatic events. Carriers of the A allele had a 2-fold increase in risk for PTSD. The A allele is more frequent in Europeans than in African people. Larger studies will be needed to determine which other genes and variants are involved in PTSD; however, this finding is in itself very interesting because it confirms the hypothesis that increased emotional arousal can lead to the formation of stronger memories and to increased PTSD risk.


NEUROSCIENCE: Phineas Gage's connectome. Mo Costandi, from The Guardian (UK), one of my favorite science writers, who writes the blog Neurophilosophy, has a fantastic, informative, entertaining piece on the connectome of Phineas Gage's brain, after the famous accident he suffered in 1848 while working on the railroad. A 3-foot long metal rod, a "tamping iron", used to compact the powder, was shot through his skull after an accidental explosion (see video for the trajectory). He survived the horrific injuries, but his friends said his personality changed radically after the accident. So what is "connectome"? The Human Connectome Project, started in 2009, has the goal of mapping out all the connections in the human brain, down to the individual cells and their functions. Up to now, the brains mapped as those of healthy adult volunteers who undergo brain scans. But now, a paper has been published with the connectome of Phineas Gage brain. His brain is not preserved, so how was this done? Jack Van Horn and colleagues at UCLA used high-resolution CT scans of his skull, that digitally reconstructed the trajectory of the iron rod as it passed through his brain. Then they compared it with data from 110 healthy volunteers, all male, and approximately 25 years old (Gage's age at the time of the accident). The UCLA researchers estimate that the rod destroyed about 4% of his cerebral cortex, and ~ 11% of the white matter in the frontal lobe. Tracing the damage by building his connectome, it seems obvious that the damage was far more extensive than previously thought. Check out the two connectograms (the colorful circles below): that of 110 healthy adults, compared to his. It does not need a figure legend, I think. Gage's connectogram is consistent with damage to the frontal lobe and "limbic system", and with the behavioral changes that he apparently suffered. Gage died at age 36, after a series of severe convulsions. Here's the connectogram showing the major pathways in the healthy human brain, averaged from the 110 data sets.


MATHEMATICS/HUMAN PHYSIOLOGY: A mathematical model of obesity. The New York Times published today a fascinating interview with mathematician Carson Chow from the National Institute of Diabetes, Digestive and Kidney Diseases (NIDDK), who has developed an equation that describes the problem of obesity and how American became so overweight in such a short period of time. He explains that a mathematical model may give an answer to the question much faster than experimental work or fieldwork. He openly admits that the food industry lobby will not like his conclusions. According to Chow, it's the overproduction of food and the fact that it became so inexpensive that is causing this epidemics. Among the many surprising things his model predicts, is that if you're already obese, even an increase of 10 calories per day over long periods will cause you to gain more weight than if you are of normal weight and consume an extra 10 calories, every day. His model also predicts that humans are slow to respond to calorie intake changes, and that what counts is the # of calories consumed over the course of a year, not really daily variations in the food intake. I recommend reading the whole interview, is very interesting.


Science bits and news from other sites:


Paralyzed patients control robotic arms with their minds

Translating neuronal activity directly into control signals for devices to assist paralyzed people has been attempted for several decades now, with the latest successes being paralyzed people controlling the cursor on a computer screen, as well as able-bodied monkeys that were trained to control robotic arms. However, up until now, nobody knew if tetraplegic people could control robotic arms to perform fine tasks, such as moving in 3 dimensions, grasping objects, etc.  But in a new study published this week in Nature, two people with almost-complete body paralysis were able to reach and grasp small balls and a thermos of coffee with a robotic arm, using only their minds to direct the motion of the robotic arm. The way this works is as follows: the patients had a very small array of electrodes, called BrainGate, implanted in their motor cortex, which is the part of the brain that controls voluntary movements. BrainGate reads brain signals and sends them to an external computer that translates it into a command. Different brain patterns tell robotic arm to move right or left, go up or down, front and back, etc. The device was calibrated to the patients' thoughts. That took only about 30 minutes, and the patiens were not previously trained to use BrainGate.  After ~ 200 trials, both patients were able to use their thoughts to maneuver a robotic arm to grasp small foam balls, successfully, 95% of the time. One of the patients (in the video) who suffered a stroke 15 years ago, was able to control the robot arm to grab a thermos with coffee, direct it to her lips, so that she could actually get a sip of coffee by herself! Watch the video, her smile at the end is priceless.   This technology could help patients with brain or spinal injuries recover some of the freedom to perform everyday activities. This patient has had her implant for 5 years now, so it is safe to assume that BrainGate does not deteriorate easily with time.


Nanotechnology: Viral electronics! Who would have thought such a thing could be possible? UC Berkeley scientists have built a proof-of-principle generator that used viruses to create electricity! The generator consists of a postage stamp-sized electrode on a small film of viruses. The virus used in the research was an M13 bacteriophage. Bacteriophages attack bacteria but are harmless to humans.  The scientists added four negatively charged molecules to one end of the corkscrew-shaped proteins that form the virus coat, using standard genetic engineering techniques; these molecules boost the voltage of the virus because they increase the charge difference between the positive and negative ends of the coat proteins. The viruses naturally self assemble into an orderly film, and this structure is much sought after in nanotechnology.  The researchers found that a stack about 20 layers of viruses exhibited the strongest piezoelectric effect (conversion of mechanical energy into electricity). The generator works as follows: a finger was used to apply pressure on the viral layers, which then converted this mechanical energy into ¼ of the voltage of a AAA battery. Of course this is not much, but it is an encouraging first step toward the development of personal power generators or actuators for use in nanodevices. This generator is a precursor to tiny devices that could harvest electrical energy from the vibrations of everyday tasks, such as shutting a door or climbing stairs.


A high fructose diet is bad for memory and learning. If you are a rat, six weeks of drinking water with a high fructose solution as drinking water, will make your brain slow.  UCLA scientists gave two groups of lab rats the fructose-containing solution instead of drinking water, but they gave a supplement of omega-3 fatty acids to one of the groups (flaxseed oil and DHA, or docosahexaenoic acid). Omega-3 fatty acids are known to protect neuronal synapses from damage. Needless to say, healthy synapses are key to memory and learning. Prior to the 6-week diet, the rats were trained on a maze for 5 days; the maze contained visual landmarks to help rats remember the way out.  After the 6-week diet, the rats were tested to see how well they remembered the way out of the maze. The animals that were given the omega-3 fatty acids navigated the maze much faster than the rats that did not receive the supplements. The DHA-deprived animals were slower, and they did not recall the escape route that they had learned 6 weeks earlier as well as the other group. Their brains showed a decline in synaptic activity. The DHA-deprived rats developed signs of insulin resistance, meaning that insulin had lost much of its power to influence the brain cells. The researchers are not too concerned with the normal consumption of fruit, since fructose is not concentrated in the fruit, and fruits have other nutrients and fiber as well. The principal investigator, Dr. Fernando Gómez-Pinilla, advises people to keep the intake of sugary treats to a minimum and also eat foods rich in omega-3 fatty acids. For vegetarians, good sources are walnuts and flaxseed; for fish eaters, salmon is an excellent source of DHA.


Why manta rays need trees to survive. Carl Zimmer wrote a very fine piece on new research from the Palymra Pacific atoll that reveals how intimately interconnected sea and land ecosystems are. Scientists tracking manta rays that live around the atoll noticed that the manta rays seems to swim off the coast where there were native forests, and not off the coast were coconut trees were planted as a crop. The data showed that for every 4 manta rays they found off the coast of the native forest areas, they found none by the coconut groves. To find out why native forests help manta rays thrive, the researchers studied both the terrestrial and the marine ecosystems. They found that the native forests had five times more birds, such as red-footed boobies, than the coconut forests. While nesting in the trees, the birds’ droppings (guano) fall to the ground. Guano is very rich in nitrogen; it fertilizes the trees, more leaves are produced and the leaf litter creates a very rich soil. When it rains, the guano-rich soil; is washed into the ocean. The nitrogen and other nutrients flowing out from the native forests fertilize the phytoplankton; thus zooplankton, which feeds off the phytoplankton, was found to be three times more abundant off the coast of native Palmyra forests than off the coasts of palm forests. More zooplankton, more food for manta rays, that are filter eaters. When people in the Pacific cut down native trees to plant coconut palms, they of course had no idea that they are affecting manta ray populations. The link between terrestrial and marine ecosystems is very string, and very important, but also very vulnerable to human intervention. The “dead zones” in places like the mouth of the Mississippi River, for example, are created by pumping too much nitrogen from fertilizers used for crops in a very short time into a marine ecosystem.


Decompression sickness in Jurassic reptiles. Rising too quickly to the surface when diving causes decompression sickness or “the bends”. The changing pressure causes dissolved gases in the blood to form tiny bubbles (the same phenomenon happens when we open a bottle of fizzy water).  The bubbles can be fatal, depending on which tissues they end up. Experienced divers know to avoid the bends by rising slowly to the surface. Incredibly, air-breathing diving vertebrates such as dolphins, and extinct marine reptiles can suffer from the bends also. The evidence is in their bones: when the bubbles form in bone, they cut the circulation of blood in that bone area causing the tissue to die and weakening the bone, eventually causing fractures or collapse. Bruce Rothschild has studied bone diseases in prehistoric animals for many decades. He found evidence of decompression sickness in ~15% of fossils of prehistoric turtles, ichthyosaurs, mosasaurs, and sauropterygians. But why would animals adapted to live in the sea make such a mistake? The explanation seems to be that they were swimming to the surface as fast as they could to avoid being eaten by gigantic prehistoric shark. Rothschild figured this out because he found traces of the bend in Jurassic and Cretaceous marine reptiles, but not in ichthyosaurs from Triassic. But wait a minute. The Triassic is BEFORE the Jurassic and Cretaceous. One would expect more decompression sickness in earlier times. But there were no big, fast-swimming predators in Triassic waters that could have preyed on ichthyosaurs!  When new predators such as gigantic sharks appeared in the Jurassic, marine reptiles sometimes could not avoid surfacing very quickly to escape the predator! It was either the sharks’ jaws, or the bends.

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Comment by Adriana on May 21, 2012 at 12:20pm

Thanks, Hope! i'm glad you liked it :-) It is a very interesting fact. 

Comment by Hope on May 21, 2012 at 11:24am

MICROBIOLOGY: So how are they still alive?  The bacteria living in these sediments are breathing oxygen at a much, much slower rate than other microbial communities. Scientists calculated that the respiration rate of these bacteria dropped ten thousand fold at 30 meters compared with at or near the surface of the sediment. Thus, aerobic metabolism can persist in deep marine sediments, although at an extremely low rate. It is amazing how little it takes to sustain life!

  Another great proof of EVOLUTION..

Thanks Adriana I like it.

Comment by Adriana on May 18, 2012 at 8:15pm

@doone: is it a subtype of this snub-nosed monkey?

Comment by Adriana on May 18, 2012 at 8:04pm

Well, I was making the comment half in jest, actually :-)

Thanks for the tip about flax meal, I will try it!

Adding butter to PBJ? WTF??

Comment by Neal on May 18, 2012 at 5:44pm

You make that saturated fat and conservative cognitive abilities in jest, but the hardest to the right conservatives that I have in my circle revel in eating the fat off of flesh. Even when I was eating meat I could never stand how they prepared the cuts, horrible. 

They have had obesity problems - and still do - yet even when making something simple like peanut butter and jelly sandwiches for the young ones they will add a layer of butter. I'm like, WTF? They don't notice the taste yet you added another 100 or more calories of fat. 

Freedom again.

Comment by Neal on May 18, 2012 at 5:35pm

That NYT article is excellent. How well balanced is life in its natural state. Then we come and screw it up.

Comment by Neal on May 18, 2012 at 5:30pm

Vegan/vegetarian way to get omega 3's is flax seed as an egg substitute in baking. I mix 1 tablespoon flax meal to 3 tablespoons water as an egg substitute. If you mix, wait a bit, mix, wait; you will get a gelatinous mixture. I use in pancakes and quick breads, works well.

Comment by Adriana on May 18, 2012 at 5:16pm

And it seems that not only high fructose can impair cognition and learning, animal fats as well. Could this explain why so many people in America have turned anti-science? Could this explain why still so many will vote Republican? Time to ditch junk food, people :-)

Ditching Saturated Fats Could Improve Memory and Cognition

Saturated fats don't just clog your arteries -- they hinder your brain's effectiveness, too.


Eating foods that are high in saturated fat -- red meat, butter, and other animal products -- clog your arteries and increase your risk for heart disease and stroke. Until now, that's all we thought they did. Now it seems that saturated fats may also be linked to how efficiently our brains work.

In a paper published today in Annals of Neurology, a team of scientists analyzed dietary data from 6,000 women over age 65. Over the course of a four-year monitoring period, women who consumed more saturated fat scored worse on cognitive function tests than those who ate less of the stuff.

What's more, women who ate healthier types of fat, such as the monounsaturated fats found in olive oil, actually showed improvements in their test results. The findings suggest that swapping one kind of fat for another may not only improve your cardiovascular health, but may also enhance your brain function. That's particularly important for middle-aged adults who may be at risk for Alzheimer's, dementia or other degenerative brain disorders.

"The total amount of fat intake did not really matter, but the type of fat did," said Olivia Okereke, the study's lead researcher. "Substituting in the good fat in place of the bad fat is a fairly simple dietary modification that could help prevent decline in memory."

The study drew data from the Women's Health Study, a 10-year clinical trial of 40,000 women aged 45 and up -- so it looks like the jury's still out for men.

Comment by Doone on May 18, 2012 at 4:09pm

Good news about monkey preservation

New golden monkey variety found in SW China

Updated: 2012-05-16 19:39


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KUNMING - Chinese scientists have identified a variety of snub-nosed monkey living in southwestern Yunnan Province, making China home to four of five varieties of the endangered primates.

The species, identified as Rhinopithecus strykeri, was first discovered in Myanmar in 2010, and is known as the Nujiang Golden Monkey in Chinese, said Long Yongcheng, chief scientist for China program of the Nature Conservancy.

"The newly-discovered snub-nosed monkeys are covered in black fur, weigh 20-30 kg, measure 1.2 meters long and bear significant differences from the Yunnan Golden Monkey," Long said.

Long, who is also the director of the China Primate Specialist Group, said researchers located 50 to 100 such monkeys in March, but more studies are needed to reveal the exact population and habitat of the animal.

Snub-nosed monkeys, or golden monkeys, are a critically-endangered species. Among the estimated 25,000 currently living, three varieties are endemic to China and the fourth inhabits Vietnam.

In 2010, a new variety of snub-nosed monkey was found in Myanmar. Local villagers said the monkeys bury their faces between their knees when it rains as rainwater flows into their uncovered nostrils, causing them to sneeze.

Believing that such monkeys also existed near China's border region with Myanmar, scientists combed the mountains of Yunnan and managed to photograph a snub-nosed monkey in the Gaoligong Mountain Natural Reserve in Nujiang Lisu Autonomous Prefecture in October 2011, and videotaped another in March 2012.

Researchers then conducted DNA tests on fur and excrement samples left by the monkeys, which showed a 98.2-percent similarity between their DNA sequences and those of their peers in Myanmar.

Researchers are calling for urgent government measures to enhance protection and put an end to hunting activities by residents unaware of the animal's endangered status.

"We've put 'Nujiang' in their Chinese name, as we hope it will boost local people's awareness of, and enthusiasm for, protecting the animal," Long said.

Forestry authorities in Nujiang said they have dispatched more forces to monitor and protect the golden monkeys, as well as to educate local residents on the monkey's endangered status.

According to official data, there are about 20,000 Sichuan Golden Monkeys, 3,000 Yunnan Golden Monkeys and 1,000 Guizhou Golden Monkeys living in high-altitude mountains in central and Southwest China.

Like the giant panda, the monkeys are counted among China's "national treasures" and placed under top state protection. Conservationists have said the species is threatened by shrinking habitats and hunters who crave their shiny furs.

Comment by Adriana on May 18, 2012 at 4:07pm

The manta ray and the land ecosystem caught the eye of the NYT too. It's an important story:


The Ray and the Coconut: Tracing Life on an Atoll

Kydd Pollock

Palmyra Atoll is part of the Northern Line Islands in the Pacific.

The idea that all life is interdependent is familiar to anyone who has seen “The Lion King,” but this “circle of life” is rarely displayed in such a long chain of connections as it is on Palmyra Atoll.

Scott Hamilton

Palmyra, part of the Northern Line Islands in the Pacific, was brieflyoccupied by the United States. in World War II and is now a nationa... with no permanent residents but a changing cast of scientists for whom it is a rich site for ecological research. It is also the site of a linked chain of birds, trees, soil, plankton and manta rays so nicely forged that it deserves its own song.

The chain is an example of natural intricacy and balance so easy to miss that it should make us consider what unknown processes human activity could be disrupting, according to Douglas J. McCauley, an ecologist at Stanford University who is one of the authors of a study on Palmyra just published online in Scientific Reports.

Birds make a good place to start. Red-footed boobies and other seabirds roost and nest in the high trees of the native forest on Palmyra, as they do on other atolls. They feed on sea life — predominantly flying fish and squid, in the case of the boobies — and their guano is rich in the nutrients they have harvested from the sea.

That guano falls from the trees in abundance and “is being used by everything in that native forest,” said Dr. McCauley. All that life in the forest contributes to the richness of the soil. Rains and tides wash nutrients from the forest floor into the coastal waters in a “rich organic slurry,” as Dr. McCauley described it.

The nutrients in the water feed plankton. And all the fish in the sea are part of a food system that starts with plankton. And the fish, some of them, provide nutrients for the seabirds, which fly home to roost at night and deposit guano, completing the circle.

Other ecological chains that cross from one ecosystem to another have been reported, like the relation of fish to flowers around ponds in Florida. The fish eat dragonfly larvae, which are aquatic, thus cutting down the number of adult dragonflies, which eat bees and other insects that pollinate flowers. When the fish kept down the dragonfly numbers, the pollinators, and the flowers, flourished. Fish-free ponds had fewer flowers. The movement of salmon, which migrate and die in freshwater rivers, has also been shown to affect land vegetation.

Another author of the new paper, Hillary S. Young, from Harvard, had earlier publishedresearch on the effect of coconut palms on Palmyra. They are not native to the atoll, and seabirds don’t like to nest or roost in them. So palm forests lack guano and have poorer soil than native forests.

What Dr. Young, Dr. McCauley and several other Stanford researchers found in the new study is how giant manta rays fit into the system. Dr. McCauley said he started out following the rays. “That’s how we got into this story,” he said. “We were actually tracking the movements of manta rays.”

He and other researches found the rays were going back to the same spots on the coast, where the native forests predominated. Where palms were dense, the manta rays were not.

The researchers tracked the nutrients coming from the seabird guano to the coastal waters and documented an abundance of the rays in the waters by the native forests. Dr. McCauley emphasized that the manta rays, which can travel long distances and have many choices of where to feed, are not in trouble. What he found most significant was the length of this ecological chain, and the many points at which it could be interrupted by breaking one link.

James Estes of the University of California, Santa Cruz, who was not part of the research, but read drafts of the work along the way, said that such long interactive chains might be more common than we realize, and that the research ought to “open our minds to the length and complexity of ecological processes.”

These chains might also inspire some new Disney movies. “The Tale of the Coconut and the Manta Ray” has a nice ring to it.

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