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Prof. A's Science Fix- September 28 2012 Edition



Evidence of past flowing water on Mars discovered by NASA’s Curiosi.... It’s not the first evidence of water on Mars’s past, but this one is impressive, because it shows an ancient streambed where water once flowed vigorously. The evidence consists of stones cemented into conglomerate rock, found at rocky outcrops inside Gale Crater, a few feet away from where the rover touched down last August. Damn, those scientists picked their landing place very well. The size of the gravel that was transported by the water suggests that it must have flowed very fast, similar to flash flood in desert areas here on Earth. The photographs of the area suggest that water flowed on the streambed for a long period of time, not just a flash flood. It happened several billion years ago, but a more precise timeframe still needs to be determined.  Because a long-ago flowing stream could be made habitable, Curiosity chief scientist John Grotzinger called this discovery “insurance” that Curiosity can find potentially habitable Martian environments. The rover’s ultimate destination is still the foothills of Mount Sharp; the base of this ~3 mile high mountain also shows signs of ancient exposure to water. NASA released the image I post here yesterday, September 27). We have followed the successes of the Curiosity mission on our site, here. Check the discussion for more photos and information.


Meanwhile, on planet Earth, we have a long way to go to solve an issue that should be a thing of the past already: equality of opportunity for qualified scientists of both sexes.




Science faculty’s gender bias is real. I highly recommend this excellent blog post in Scientific American by Janet Stemwedel. She dissects a very important finding, from an article published in the proceedings of the National Academy of Science USA this past week.   It’s very difficult to prove gender bias (or racial bias, or other biases), especially when the bias is unconscious. Most of what is measured is outcome, not opportunity, because it is easier, but many factors influence outcome and opportunity is only one of them, though a very important one. Many people for example, feel perfectly comfortable with fewer women than men in science, because they say it must be due to females being less interested in the sciences. They argue that equality of opportunity exists already. Not so fast. Many of us female scientists are not surprised by the findings of this new study, but it is nevertheless fantastic to have solid data to prove that gender bias does exist in the sciences. The data generated comes from a randomized controlled experiment: only one variable was changed, the gender of “scientist.” Researchers from Yale presented science faculty (n = 127) from research-intensive universities with identical application materials from a graduating college student applying for a lab manager position, who specified that he/she wanted to go to graduate school. Half the scientists were given the application with a male name attached, and half were given the same IDENTICAL application with a female name. Results found that the “female” applicants were rated significantly lower than the “males” in competence, hireability, and whether the scientist would be willing to mentor the applicant as a future graduate student. The ratings weren’t hugely different, but they were highly statistically significant. Even more startling, the professors also offered lower salaries to the “female” applicants: $26,500 compared to $30,200. Not unexpectedly, the bias was equally present in women faculty members, than in male faculty. Yes, women can be sexist too. These findings are VERY important. Sexism in the sciences exists, and much of it can be unconscious.  Educated people can behave in ways that are sexist, even if they do not realize this or do not think of themselves as sexist. I wonder how I would have rated the applicant myself. It is entirely possible I have this bias, unconsciously. It is very important for scientists especially to try to get rid of unconscious biases and to understand and examine why we have these biases. As the authors of the study suggest:  “Past studies indicate that people’s behavior is shaped by implicit or unintended biases, stemming from repeated exposure to pervasive cultural stereotypes that portray women as less competent.” And as Janet Stemwedel puts it: “These are the facts: equally competent women in science are viewed as less competent because of their gender. Remember them. Cite them. And if you want change, I would urge you to share them as widely as possible.” I’m sharing this with you guys. Pass it on. 




Brain slices in the lab can store temporary “memories”. Hat tip to Michel for posting this great science article by Mo Costandi at The Guardian. Memories form by the strengthening of connections between neurons within a network; memories are information that is stored and is retrievable by reactivation of the neural network. The mechanisms of memory formation and retrieval are as you can imagine, of tremendous interests to neuroscientists. Researchers at Case Western Reserve University in Cleveland, have just published in Nature Neuroscience that they can take thin slices of rat hippocampus (a brain area critical for long-term memory formation), put them on tissue culture dishes in the lab, and stimulate them with of rats, placed them into Petri dishes, and used electrodes to stimulate (input) and measure the activity (output) of four individual neurons in the slices. If the neurons were stimulated independently of each other, they each generated their own distinct pattern of output, which however was the same for each neuron and each specific input. The neurons were also stimulated in succession by a sequence of inputs. The outputs predicted the inputs accurately, both the individual inputs and the succession of inputs. The activity patterns stayed in the network for up to 15 seconds, after what the accuracy of prediction decreased. The activity patterns were similar those associated with working memory storage monkey experiments carried out in the 1940s. Also, fascinatingly, the activity demonstrated that contextual information was important, since in a sequence of inputs, the pattern generated by each input depended on the previous input, and it was different from the pattern generated by that particular input when applied on its own.  No, the researchers didn’t really create memories in brain tissue on a Petri dish (the information they stored is meaningless, memories are not), but their method of stimulation and recording of patterns of activities in individual neurons within a network are going to be very useful in future experiments to further our understanding of the cellular and molecular mechanisms of memory formation. The original article can be found here (paid subscription required). 


Human delayed nerve myelination is evolutionarily unique. Myelin is the fatty substance in the sheaths that insulate our nerve fibers. Myelin speeds up the transmission of information between fibers, but at the same time slow myelination permits the brain to be molded by the cultural environment. It is thought to be the key to our malleable, adaptable brains. Human babies are born with very little myelin, and myelination progresses slowly throughout childhood. The maturation of this process continues throughout adolescence even into the thirties. In contrast, rhesus macaques are born with a lot more myelin and the process of myelinization is completed by the time the monkeys reach sexual maturity. Up until now, we did not know if our closest living relatives, the chimpanzees, were more like macaques than like humans. And it was a difficult to study because there aren't many chimp brains available for research (and rightly so). But a team of scientists has managed to get a hold of enough young specimens that died from natural causes to answer the question: humans are unique, chimps are like macaques, by the time they get to puberty, their myelinization process is complete. The shift is cortical maturation is uniquely human. Psychiatric disorders that manifest themselves mostly in early adulthood, such as schizophrenia, have been linked to lower expression of myelinization factors. It is possible that the delayed myelinization that is key to our adaptability to cultural environments may have left us humans vulnerable to mental illnesses. In the photo: electron microscopy of a nerve fiber covered by myelin sheaths.


And while your brain was busy getting properly but slowly myelinated when you were in your teens, were you also killing off a few neurons with your binge drinking?


Why Does Alcohol Cause the Spins? I want to see a show of hands: how many of you have experienced that awful sensation of lying down in bed after drinking some alcohol and seeing the room spin around like crazy? It happened to me twice personally. The most unpleasant one happened a few years ago after a party to wish good luck to a colleague who was starting his own lab. I have no idea why I ended up getting so drunk, since I had drunk larger amounts before with no consequence. Go figure. I ended up in a cab from Manhattan to my home in Queens, on a beautifully balmy summer night, while the high-rises and street lights spun around me. As we crossed the Triboro Bridge, the entire Manhattan skyline, brilliantly lit, spun around and around. I managed to sleep it off safely at home, and I did not even have a hangover. But the experience was truly psychedelic. But what causes the “spinning”? I bet you don’t know. I didn’t know exactly, until I read this enlightening little post: it’s all in your ears. In your inner ear, there are 3 really small structures, filled with fluid (endolymph is the scientific name). In addition to the liquid, the canals have a jelly-like tiny structure called the cupula, which is filled with specialized cells with very fine cilia (hair-like cellular organelles that protrude from cells), called stereocilia. When you normally move, and the endolymph moves too, the cupula is distorted and the stereocilia get bent.  An electrical signal is sent to your brain from these structures, and it tells your brain how your head is rotating. When you have enough alcohol in your blood, the density of the blood is slightly different, and when it reaches your inner ears, it creates a density difference between the cupula and the fluid in the canals, distorts the cupula’s shape, and bending the cilia, as if you were moving. Your brain thinks you are rotating, when you are not, and this creates the visual illusion of spinning. When you lie down and close your eyes, the sensation of motion gets worse because your visual system cannot use any physical cues to counteract the false motion sensing. As with motion sickness, it helps to look at a fixed object. This lessens the effects, but there is nothing to do but wait till it goes away. 


There may be a link to alcohol consumption and losing your sexual inhibitions for some people, so it seems that the next post is not entirely out of place here.


Neuroscience and female sexual desire. Some of you may have seen that the internet is abuzz with pretty ferocious critiques of Naomi Wolf's new book: "Vagina: a New Biography". As an example you can read this review at The Guardian. I have not seen a single positive review so far, and most of the criticisms come from the many pseudoscientific or inaccurate statements that apparently she makes throughout her book, especially from a neuroscience point of view.  The criticism is not, of course that the vagina and the brain are not connected (I would argue the whole body is connected to our brain, one way or another!) but that she oversimplifies what is known about a very, very complex subject, and that many of the scientific statements in the book are even simply false. in other words, the book is not very well researched. I will have to read it to see why people are so irritated about this book, while Natalie Angier's "Woman, an intimate geography" was so well received ~a decade ago (it really is a good book). But I came across this very thorough article by Maia Szalavitz in Time magazine Healthland section, dissecting some facts about dopamine and sexual desire (hint: it is not "more dopamine = more sexual desire"), how she oversimplifies oxytocin by calling it a "female superpower", how she concludes that women are less able to control their desire than men because of their "brain chemistry", etc. Read the entire article, it's very, very informative. I love the conclusion: The brain and female sexuality are extremely complicated — and reducing them to simplistic formulations that deny women their humanity fails to do justice to either feminism or science. Properly contextualized, neuroscience can add to our knowledge of sexuality, but not if it’s twisted to support sexist ideas about women as “animals” who are so addicted to love that they become zombies.




African mouse species is first regenerating mammal discovered. Regenerating organs or limbs is no easy feat in nature, although there are a few vertebrates that are capable of doing it. The most famous are of course, lizards that can shed their tails and grow them back, and salamanders that can regenerate an entire limb, digits and all. Up until now, it was thought that mammals had totally lost this ability. Sure, mammals can repair wounds but scar tissue is formed, not the original tissue, unless it is the most superficial skin layer. But two species of African spiny mouse now has the honor of becoming the first mammal with regenerating abilities: it can shed its skin (all the layers) and regenerate it all: hair follicles, sweat glands and all! These little rodents can shed their brittle skin when bit by a predator, and they can effectively escape with their life by leaving behind a frustrated predator with a mouth full of hair and skin. The researchers are now focusing on determining the molecular mechanisms and gene networks that direct the regeneration process. It is likely that these are the same or similar to those in salamanders and have been somehow switched on in the African spiny mice. Uncovering these mechanisms will not only be intellectually fascinating, but in addition could lead to improved treatments for wound healing in humans.


Cats hunt mice the world over, and many cat species are spotted or striped, a camouflage that may give them an edge as stealthy stalkers.


Stripes or Spots? It’s in the cat genes. The same gene is responsible for dark spots or stripes in cheetahs and in domestic cats. And a mutation in this gene causes the cheetah spots or tabby stripes to become blotched, when both alleles of the gene are mutated. There is type of cheetah, called king cheetah (seen at right in the photo, that carries the mutation in the gene. In these cheetahs, the spots bleed into one another and coalesce into these remarkable stripes.  When the cat genome was published, researchers started looking for coat color genes; now, a multinational team of geneticists has identified the spot-stripe gene, called Taqpep (short for transmembrane aminopeptidase Q). The gene encodes a protease, an enzyme that chops proteins up, and it was totally off anyone’s radar as a coat color gene. In fact, Taqpep is not responsible for the dark color itself; another gene, Edn3, expressed at the roots of hair follicles, is responsible for the dark coloration. Taqpep appears responsible for the sharpness of the pattern. Because Taqpep belongs to a family of genes that are involved in immunity, a mutation in this gene have contributed to better survival from infection at some point in the cats’ evolution, and that could be the origin of the blotched pattern, nothing to do with the pattern of coloration in itself, in terms of survival advantage.


Sea lions are not really cats, or related to lions, but these playful marine mammals are astonishing in their own right. Have you ever considered how marine mammals avoid “the bends”?


How sea lions dive deep and avoid the bends. Hat tip to Davy for this really fun story. Decompression sickness, or “the bends”, is caused by nitrogen gas, which gets compressed when diving down, gets expanded when an animal or person resurfaces, causing excruciating pain or even death. Some marine mammals have to dive deep to hunt their prey. How do they avoid the bends? Researchers at the Scripps Institution of Oceanography fitted the main artery of a female adult California sea lion (Zalophus californianus), with tiny instruments to record oxygen pressure, as well as depth, and time. They released the animal and logged the data that was sent through radio transmitter. They gathered data for 48 dives.  I was not aware that sea lions dove so deep! In one dive, at a depth of around 225 meters (~740 feet), the oxygen pressure took a dive too, indicating that the sea lions’ lungs had collapsed. This cuts off the air (and consequently, nitrogen) supply to the blood. Marine mammals are known to be able to collapse their lungs when they dive. The elastic air sacs (alveoli) are depleted of air and they collapse. The sea lion went down to ~ 300 meters (almost 1,000 feet!), then started ascending. At ~247 meters (~800 feet), the oxygen pressure rose again, indicating that the lungs had reinflated. But wait a minute, if it collapsed its lungs, where did our sea lion keep the air to inflate its lungs again. The air was stored as a “pocket” in the upper airways: the trachea and the bronchi, both lined with tissue that exchange air and therefore cannot dissolve gases into the bloodstream. Isn’t nature simply amazing? I was happy to learn that at the end of the experiment, the scientists removed the measuring devices from the sea lions before releasing back into the wild. The original publication can be found here.




Murder victim identified by maggots on body. Burning a body does not only make it very difficult to recognize, but it makes it impossible for investigators to get a decent DNA sample. When a badly burned body was found in the woods in Mexico, police suspected it was that of a woman who had disappeared a few weeks earlier, since her ring was found in the area. But they needed certainty to close the case. Resourceful forensic scientists at the Autonomous University of Nuevo León in San Nicolás, Mexico, had the idea to use three maggots that were feeding in the charred body, to see if any of the victim’s DNA could be found in their digestive system. Human DNA was found in the maggots’ guts, and it was unmistakably female DNA. Then they asked the father of the disappeared woman to donate some DNA and they compared his DNA to the human DNA found in the maggots. They determined that there was a 99.7% chance that the DNA was from his daughter. This is the first time that human DNA from a maggot gut has been used to successfully identify a victim in a legal case. Although it is rare that a body would be so badly damaged to not yield any DNA, the technique could be used in other cases; for example, a maggot found in the trunk of a car can be used as evidence that a particular corpse had been in that trunk. Murderers beware: scientists have a new weapon to solve crimes: insects.


And after such a gruesome, grim post, we could all use a little humor.




The 2012 Ig Noble Prizes. As the organizers put it: “The Ig Nobel Prizes honor achievements that first make people laugh, and then make them think. The prizes are intended to celebrate the unusual, honor the imaginative, and spur people's interest in science, medicine, and technology.” Actual Nobel prize winners hand out prizes at an annual ceremony at Harvard, and everyone has a lot of fun. Go to the web site for a complete listing of this year’s winners. My two favorites for this year are:

NEUROSCIENCE PRIZE: Craig Bennett, Abigail Baird, Michael Miller, and George Wolford (USA), for demonstrating that brain researchers, by using complicated instruments and simple statistics, can see meaningful brain activity anywhere, even in a dead salmon. REFERENCE: "Neural correlates of interspecies perspective taking in the post-mortem Atlantic Salmon: An argument for multiple comparisons correction," Craig M. Bennett, Abigail A. Baird, Michael B. Miller, and George L. Wolford, 2009. Journal of Serendipitous and Unexpected Results, vol. 1, no. 1, 2010, pp. 1-5.

ANATOMY PRIZE: Frans de Waal (The Netherlands and USA) and Jennifer Pokorny (USA) for discovering that chimpanzees can identify female chimpanzees individually from seeing photographs of their rear ends. REFERENCE: "Faces and Behinds: Chimpanzee Sex Perception" Frans B.M. de Waal and Jennifer J. Pokorny, Advanced Science Letters, vol. 1, 99–103, 2008.

Other fun prizes were: a chemistry prize for solving the puzzle of why, in certain houses in the town of Anderslöv, Sweden, people's hair turned green, and fluid dynamics prize given to a multinational team for studying the dynamics of liquid-sloshing, to learn why and how coffee spills when a person walks while carrying a cup of coffee.


And to see if you are still awake (if you are not, this video WILL wake you up), do not miss this 1958 footage from two underwater nuclear tests, termed Wahoo and umbrella. See this sequence and more in the new HD version of Atomic Filmmakers - Hollywood's Top Secret Film Studio available for viewing on the GoDigital channel on Youtube.

Hat tip to Phil Plait.



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Comment by archaeopteryx on September 29, 2012 at 5:46pm

Last one, I promise - there's been slow rain falling all day, and I have nothing else to do --

Giant Viruses Are Ancient Living Organisms, Study Suggests

Researchers have debated whether viruses, which have genes but no cellular structure, should be considered forms of life. A new study suggests they should, showing that giant viruses have some of the most ancient protein structures found in all organisms on the planet.

The researchers conducted a census of all the protein folds occurring in more than 1,000 organisms in the three traditional branches on the tree of life — bacteria, microbes known as archaea and eukaryotes. Giant viruses, which are considered "giant" based on the size of their genomes, also were included in the study because they are large and complex, with genomes rivaling some bacteria, University of Illinois researcher Gustavo Caetano-Anollés said in a statement.

For instance, the ocean's largest virus, a giant virus called CroV, has genes that let it repair its genome, make sugars and gain more control over the very machinery the virus hijacks in host cells to replicate itself. (Since viruses are essentially DNA wrapped in a protein coat, they need the goods of a host to replicate themselves.)

Caetano-Anollés said his team looked at protein folds instead of genetic sequences because these structural features are like molecular fossils that are more stable over time. They assumed the folds that appear more often and in more groups are the most ancient structures.

"Just like paleontologists, we look at the parts of the system and how they change over time," Caetano-Anollés said.

Giant viruses should be included in reconstructions of the tree of life, researchers report in a new study. The mimivirus, shown here (small black hexagons) infecting an amoeba, is as big as some bacterial cells and shares some ancient protein strands.

They found that many of the most ancient protein folds in living organisms were present in the giant viruses, which "offers more evidence that viruses are embedded in the fabric of life," Caetano-Anollés said. The tree his team created had four clear branches, each representing a distinct "supergroup" — bacteria, archaea, eukaryotes and giant viruses.

The researchers said the study, which was published in the journal BMC Evolutionary Biology, also bolsters claims that giant viruses were once much more complex than they are now. A dramatic decline in their genomes over time likely reduced them to their current parasitic lifestyle, Caetano-Anollés said.

"giant viruses have some of the most ancient protein structures found in all organisms on the planet" -- Hmmm, Adam?

Comment by Adriana on September 29, 2012 at 5:44pm

And regarding starfish, yes, some species can generate an entire animal from an arm; it is a form of asexual reproduction. The form that reproduces this way is called a comet.

Comment by Adriana on September 29, 2012 at 5:39pm

Archaeo, I love that fish circles story! I forgot to add it! Sorry, I've been kinda doimng too many things at the same time! I'm glad you posted it here.

Comment by archaeopteryx on September 29, 2012 at 5:01pm

Most of the world's Vegans, i.e., herbivores, don't have to chase their dinners, but some do --

Tiny Sea Plant Swims from Predators

"It has been well observed that phytoplankton can control their movements in the water and move toward light and nutrients," marine scientist Susanne Menden-Deuer, of the University of Rhode Island, said in a statement. "What hasn't been known is that they respond to predators by swimming away from them. We don't know of any other plants that do this."

In lab experiments, Menden-Deuer and her team observed that groups of the phytoplankton Heterosigma akashiwo flee when in the presence of predatory zooplankton. What's more, the tiny plants swim away from areas that previously contained the predators even if the immediate threat is gone. (memory?)

"The phytoplankton can clearly sense the predator is there," Menden-Deuer said. "They flee even from the chemical scent of the predator but are most agitated when sensing a feeding predator."

The algae do this to stay alive. If the phytoplankton have no place to hide, they'll get eaten up by their zooplankton predators within a day. But the algae double in population every two days if they have a refuge, the researchers said.


Comment by archaeopteryx on September 29, 2012 at 3:24pm


All "rear end" jokes aside --

The planet Uranusreaches opposition on Saturday (Sept. 29). This means that Uranus is directly opposite the sun in the sky.

Uranus will rise as the sun sets, and set as the sun rises. It will be highest in the sky at local midnight, roughly 1 a.m. if you are on Daylight Saving Time.

Uranus was discovered accidentally by William Herschelon the night of March 13, 1781. All the other planets had been known since prehistoric times, so this was a major discovery in its time, and made Herschel famous.


The reason Uranus had remained undiscovered for so long is that, although it is quite large, the third largest planet after Jupiter and Saturn, it is very far away from the sun, so is very dimly lit. If you know exactly where to look, it is just possible to see Uranus with the naked eye, but most of us need binoculars and a good chart to spot it among the thousands of stars of similar brightness.

When Herschel first observed it, he was unsure what he had seen: a nebula, a comet, or a planet. After a night or two, he saw that it had moved, so it couldn’t be a nebula. It didn’t change size or shape, so he knew it wasn’t a comet.

Once the object's orbit was determined, Herschel knew he had found the sun’s seventh planet: 31,763 miles (51,118 km.) in diameter, four times larger than the Earth. It orbits at 19 times the distance from Earth to the sun, twice as far from the sun as Saturn. [Amazing Photos of Uranus]

Comment by archaeopteryx on September 29, 2012 at 1:59pm

Alien underwater "crop" circles? Can anyone here draw a circle this nearly perfect? One little guy can --

Earlier this year, off the southern coast of Japan, Yoji Ookata, a deep-sea photographer and diver who has been documenting the deep sea for more than 50 years, saw something he had never observed before. A circular pattern of rippling sand about 80 feet below sea level and 6 feet in diameter was on the ocean floor. Ookata returned to the same spot with a TV camera crew in tow to capture the discovery and figure out who or what had created its intricate design.

Ookata dubbed his new find the "mystery circle" and was shocked to find out that a single puffer fish, no more than a few inches long, had created the circles using just one fin. The tiny fish works tirelessly day and night to complete the design. While the circled sculpture is beautiful to look at, Ookata and his crew learned that the fish's creation maintained a dual purpose. Female fish are attracted to the ridges and valleys left in the sand, and they deposit their eggs in the center. The eggs are then shielded from the ocean currents, as the higher points of the sculpture create a barrier to protect them. The more ridges a sculpture contains, the more likely it will attract the females of the species.



Just goes to show you to what lengths some guys will go, to get chicks --

Comment by Neal on September 29, 2012 at 1:56pm

Oh man, awesome ad. Shows how long corporations have been practicing deception. Health does not matter, only consumption.

Comment by doone on September 29, 2012 at 1:33pm

Soda!  Good for Scientists and Good for You!

Get to Them Before They Have Teeth
Submitted by: Unknown
Comment by Susan Stanko on September 29, 2012 at 12:24pm

I feel the same way way about leg and arm pit hair.

Comment by Michel on September 29, 2012 at 12:22pm

I wish I'd stop regenerating facial hair.

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