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Prof. A. Weekly Science Fix- March 9 2012 Edition

Science at Atheist Universe


VIDEO OF THE WEEK: Time-lapse footage of the Earth as seen from the ISS


More great videos like this at our group The Daily Cosmos. Please join us!

ASTRONOMY: Two great discussions this week:


New SuperEarth Discovery Shows Signs of Water in Atmosphere. Harvard Smithsonian Center for Astrophysics astronomers used the Hubble Space Telescope (in the photo) to observe the atmosphere of a Super-Earth planet known as GJ1214b. This exoplanet is 6.5 heavier than Earth and it has a radius 2.7 bigger than that of our planet. It orbits a small M-dwarf star. The term Super-Earth refers to exoplanets whose mass is between 2-10 Earth-masses.  As  GJ1214b orbited its star, it absorbed light, thad that altered the spectra in its atmosphere.  Based on our current knowledge of the atmospheres of planets in our own solar system, this super-Earth shows signs of harboring water vapor. Unless the atmosphere has a thick top layer of clouds which obscure the measurements, the spectra detected by the Hubble telescope are best explained by the presence of abundant water vapor. Further observations will be needed to confirm these early results. Future observations of this and other transiting exoplanets will lead to a better understanding of how atmospheres form, evolve, and behave under a wide range of physical conditions.


Sand dunes of Mars and other places in our solar system. Do not miss this post containing many gorgeous photographs of Martian sand dunes and the explanation for their formation and their color. For example, here is the explanation for the strange looking brown streaks that appear to be trees in these Martian sand dunes.  The dark sand on the interior of Martian sand dunes became more and more visible as the spring Sun melted the lighter carbon dioxide ice. The dark sand appearing at the top of a dune cascaded down, leaving the brown streaks on the pinkish sand. The image was taken while the dark sand was sliding. It was photographed by the Mars Reconnaissance Orbiter in 2008 April near the North Pole of Mars.


PHYSICS: Nothingness. I would like to direct your attention to a fascinating discussion, initiated by one of our newest members, Mansour. We hear it all the time: something cannot come from nothing. But while this may be true for most practical everyday purposes, it is not true for our physical Universe. Mansour has recently read “A universe from nothing” by physicist Lawrence Krauss and he concluded that there is no such thing as nothingness in physics. So what is “nothing” from a scientific perspective? Several of our members weighed in, several great articles were posted. In our universe, “nothing” is hard to come by. Matter, radiation, and energy are everywhere we look. If we blocked it all, we would have only spacetime, and this “empty” spacetime will be flat instead of curved. But on the Planck scale (that of the tiniest particles, spacetime is not flat at all. In the words of Ethan Siegal, “empty space itself vibrates and curves, and there is a fundamental uncertainty in the energy content, at any given time, of nothingness. This quantum vacuum manifests this fundamental uncertainty by spontaneously creating pairs of particles-and-antiparticles for very brief amounts of time. Everywhere. All the time”. Come and join the discussion!


GENETICS: Are human races a biological reality or social constructs? Kenan Malik in his blog Pandemonium wrote possibly the best article on human race and the current controversy between "race realists" and biologists and geneticists who say that race is not a biological reality. The controversy flared up a bit recently due to a review, written Jan Sapp (a biologist) of two books that insist that race has no biological validity. Sapp agrees, and states that race as "type" or as "genetic population" is a misconception, and that human races are sociocultural constructs. According to Sapp, most biologists would agree on this. I think that Sapp is correct in stating that most biologists agree with this. But Jerry Coyne disagreed with Sapp and wrote that "human races exist in the sense that biologists apply the term to animals". Jonathan Marks (a biological anthropologist) got really aggravated because he says that Coyne is ignoring all that anthropology has to say about the subject. Marks writes: "Of course the discovery that people in different places are different is a trivial one.  At issue is the pattern of those differences and its relation to the classification of the human species.  To equate the existence of between-group variation to the existence of human races is to miss the point of race entirely.  Race is not difference; race is meaningful difference".  Malik's position is that both sides of the debate are wrong. And both are right. His article is long, but worth every word. He explains why most biologists or geneticists refuse to think of human races as being biologically valid, emphasizing that the more we know about human genomics and genetics, the fuzzier the picture becomes. His conclusion is that race is a social category but one which can have biological consequences. I'm in agreement with this. Read the entire article, you will not get bored or regret it.


EVOLUTION: There is a little bit of gorilla in our DNA. I'm sure you're saying, "well, of course there is a little bit of gorilla in our DNA, we are related!" In fact, we are, and perhaps more closely than previously thought. The genome of Kamillah (in the photo), a western lowland female gorilla living at the San Diego Zoo was just sequenced to completion and will be published in this week's issue of Nature; it was the last great ape genome to be sequenced, following that of the chimpanzee and the orangutan. Taking into account this new data, the chimpanzee remains our closest relative, but the gorilla turned out to be closer than we previously thought. Around 70% of the human genome is closer to chimpanzees, on average, but 15 % percent is in fact closer to gorillas, and a few of the same genes previously to be part of our unique evolution are a key part of their genome, and their evolution, too. Genes involved in hearing underwent rapid evolution in humans, and they were thought to be perhaps key to the development of language. But gorillas also show accelerated evolution in these genes, so perhaps the role of these hearing genes in language needs to be revisited.  There was also evidence of parallel acceleration in the evolution of brain development genes in both species. Interestingly, some genes tied to the development of dementia and heart failure in humans are pretty much identical to those in the gorilla. Since these genes do not appear harmful for gorillas, they ay help understand why they are harmful for our species. Among the genes clearly unique to gorillas vs humans, there is a gene related to the formation of very tough keratin, that allows for extremely tough skin, useful for knuckle walking.  Gorillas also have inactivated a specific gene that allows for sperm to compete with that of other males inside the female body. It makes sense, since gorillas live in groups with only one male, therefore there is no opportunity for sperm competition. Both humans and genes have the gene variant that allows for sperm competition, since both these species live in groups with multiple males around.


Science bits and news from other sites:


Seeing science with an artist's eye. Many people associate scientific research with boring lab work, best-case scenario, performed utilizing really fancy instruments. And while like with all human activities, a certain level of drudge is unavoidable, science ultimately is about storytelling, in the sense that the scientist needs to convince other scientists, and people in general, that their hypothesis makes sense or their explanation of the data is the closest to a representation of reality. And here is where art comes into place. Drawing models, or taking beautiful and detailed photos, whether they are electron microscopy or photos of fossils, or astonishing photographs of far away nebulas, is a crucial part of science. These visuals help the scientist further their research, and they also enchant the public and contribute to the spread of scientific knowledge to the general public. Science and art go very well together. And sometimes they both coexist within one person. Meet Heather Bimonte-Nelson, a neuroscientist at Arizona State University. She produces intensely detailed paintings represent findings in her area of research: learning, memory and the aging brain. Her paintings depict neurons, cell death, and what happens to the brain during seizures, for example. In the painting in the photo, titled “GABA,” the colors represent neurotransmitters in the brain: blues and greens are for the inhibitory gamma-aminobutyric acid, or GABA, and the red is glutamate, an excitatory neurotransmitter.  Dr. Bimonte-Nelson claims that painting helps her find the right words to describe her proposed work in a grant application, for example. “Artistic expression drives my understanding of science,” she says. “I think it’s made me more of an intellect, because it’s carried my science to a new level. I am not doing anything when I’m painting. I’m thinking about the science I’m doing, but not so much consciously.” Go to the link for more great paintings, and cool bits about neuroscience.


The lethal 2500-year-old mutation that emerged in ancient Palestine. Discover magazine has posted a free article online, beautifully written, informative, a real gem of scientific journalism in my opinion. The article is about BRCA1, one of the most studied genes in the human genome. Carriers of BRCA1 mutations are at high risk of breast cancer. BRCA1 is a tumor-suppressor gene: disabling mutations abolish its protective function. The article starts with the story of Shonnie Medina (in the photo), a beautiful, vibrant young woman from the San Luis Valley in Colorado who died at age 28 from breast cancer, after foregoing treatment. She was a Hispano, a population with a mix of Spanish and Indian people, who have lived in northern New Mexico and southern Colorado for the past 400 years. Shonnie inherited a BRCA1 mutation known as185delAG, a 2500-year old mutation that arose in ancient Palestine and is present in 1% of Ashkenazi Jews. Some Hispano people suspected they may have descended from Marranos, Sephardic Jews who lived in Spain and were forced to convert to Catholicism, but they did not know if it was a rumor or if it was truly part of their history. The discovery of the mutation in Shonnie (and subsequently in other members of the Hispano community) confirmed the “rumors”. Since the discovery of this ancestral mutation, in the late 1990s, over 2,000 BRCA1 mutations have been recorded, affecting all ethnic groups, but the 185delAG mutation is especially lethal because it is a dominant mutation, in other words, just one copy of the defective gene is capable of causing cancer. However, carrying the mutation is not a guarantee that the carrier will get cancer, since its penetrance is incomplete. Penetrance in genetics is the proportion of individuals carrying a particular variant of a gene that also express an associated trait, in this case breast cancer. Estimates of penetrance for this particular mutation is 80%, meaning 80% of carries will develop the disease, 20% will not. Because in Shonnie’s family there were several healthy carriers as well as women who died of breast cancer, it was not immediately obvious that the family was at high risk. The article is long, but I trust you will be gripped and fascinated by the account of the history and dissemination of the BRCA1 mutations.


Pterosaur versus fish. A battle of titans was immortalized in Jurassic limestone in Solnhofen (Bavaria, Germany), but was it mortal combat or unfortunate accident? On the left you can see a pterosaur, a Jurassic fish-eating flying reptile, Rhamphorhynchus, who skimmed the water to catch its prey. You can clearly see the skull on top of the image, the arm bones, which supported its leathery wings, to the left, and the long tail, pointing downwards. On the right you can see a large predatory fish, Aspidorhynchus, that had a long, pointed snout. Was the fish trying to skewer and eat the pterosaur? Two German paleontologists studied the fossil pair in great detail, and they think the death of both animals was accidental. This specimen of Rhamphorhynchus has a small fish lodged in its throat, so it had just caught its prey and had started to swallow it when the huge fish caught it. The pterosaur was likely pulled underwater and drowned. But the predator died as well, because it did not have a flexible skull and it could not swallow such large prey. The fish could not get rid of the unfortunate pterosaur: its skeleton shows distorted arms but was otherwise intact. The paleontologists speculate that the pterosaur’s wing got snagged in the fish’s teeth, which were tightly packed.  Even more amazingly, the scientists found three other limestone slabs with a Rhamphorhynchus entangled with an Aspidorhynchus, always with one of the pterosaur’s wing bones within the jaws of the fish. Since not a single one of these occurrences shows pterosaur bones actually inside the fish’s stomach, the scientists think that these were unlucky but common accidents.  They speculate that a school of fish was being targeted from above by Rhamphorhynchus and by Aspidorhynchus from below, in a similar fashion to sardines being targeted by dolphins or big fish from below, and by seagulls from the sky. The collisions and snaggings could have occurred when both animals zeroed at the same spot and became entangled.


What’s wrong with fossil dinosaurs’ necks? Why do so many dinosaur fossils have their necks contorted into the painful-looking backwards position? This position is called “opisthotonus” from the Greek “tonos,” meaning tightening, and “opistho,” behind. Did the dinosaurs die in pain? Or does the position derive from rigor mortis? Many of the dinosaurs found in opisthotonic posture were land animals that fossilized because they fell into sediment at the bottom of bodies of water. One hypothesis is that this is the position floppy long necks adopt in water. Scientists studied the carcasses of an extant relative of dinosaurs: the humble chicken. They plunged the carcasses under water and let them rot. The ligaments in chicken necks are bendable, but when the animal is alive, they are contracted to hold the head upright.  When a chicken dies, the ligaments try to return to their normally tense position, but gravity fights against it, and the chicken carcass behaves like a rag doll. But in water, buoyancy allows the ligaments to contract into their natural shape, and this results in a cranking backwards of the neck. When first plunged in water, the scientists were amazed to see that the necks bent backwards immediately at 90 degrees. After 3 months of decay, the necks bend back even further to 140 degrees. This may the cases of opisthotonus in fossils found in or near what was a body of water. But it does not explain the rest of the cases. The observations were replicated in other bird species, in saltwater and fresh water, and at various depths. But not every paleontologist is convinced, because similar contortions of the spine and neck occur when modern animals experience trauma, and died of suffocation, starvation, and poisoning or brain injuries. Another objection is that mammal fossils also opisthotonus and they have a different ligament anatomy than the birds.  And so the debate will continue.


Spider silk spun into violin strings. Shigeyoshi Osaki of Japan's Nara Medical University has studied the mechanical properties of spider silk for many years. His field of expertise is what is called the “dragline”, the thin strand of silk that spiders dangle from, when they’re not on the web. He has figured out a way to produce large quantities of dragline silk from 300 female Nephila maculata spiders that he keeps in his lab.  His latest research, to be published in Physical Review Letters, involves violin strings.  Osaki spun a set of violin strings from 3,000 to 5,000 silk strands, twisting them in a packed structure that leaves virtually no space between the strands. Each string is made from 3 bundles of these fibers, twisted together in opposite directions. The spider silk strings produce a soft and profound timbre, when compared to traditional steel strings. Check out the sound they produce (YouTube video below), it is beautiful. Some musicians are saying they can produce totally new sounds with these strings.

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Comment by Adriana on March 10, 2012 at 5:52pm

What a cool animated gif, doone!

Comment by Doone on March 10, 2012 at 5:48pm

funny science news experiments memes - It changed our understanding of our universe 

Comment by Adriana on March 10, 2012 at 1:40pm

Christopher, you just made me VERY HAPPY! I love to hear about kids who love science and I love to be able to help! Get him to read "Thinking Fast, Thinking Slow" by Daniel Khaneman. Also "Who's in Charge" by Michael Gazzaniga.

Comment by Christopher DiBattista on March 10, 2012 at 11:31am

I love that there are articles on neuroscience here. I have a student in my Algebra 2 class that loves neuroscience and I email him the articles. He has already read my copy of Consciousness: An INtroduction by Blackmore. He just finished Incognito. I wish I had more students like him, as opposed to the self-centered kids who live with a sense of entitlement.


Comment by Michel on March 9, 2012 at 7:05pm

Between that and the Matrix, I prefer the Matrix.

Comment by James M. Martin on March 9, 2012 at 6:44pm

Listen, this stuff is really offensive to me.  Don't you know that the universe was created about five or six centuries before the Lord and that Eve came from a rib, Adam rode dinonsaurs, and fossils are things God left in the earth to fool Darwinists.

Comment by Michel on March 9, 2012 at 2:48pm

Very interesting book indeed!

Comment by Adriana on March 9, 2012 at 2:19pm

Thanks, Doone :-)

And that book looks interesting!

Comment by Doone on March 9, 2012 at 2:14pm

Your blog is an example of the Pareto Principal at work


From Edge:

BookAs you march through or dance around in this book, you'll see that some of the entries describe the patterns of the world. Nicholas Christakis is one of several of scholars to emphasize that many things in the world have properties not present in their parts. They cannot be understood simply by taking them apart; you have to observe the interactions of the whole. Stephon Alexander is one of two writers (appropriately) to emphasize the dualities found in the world. Just as an electron has both wave-like and particle-like properties, so many things can have two sets of characteristics simultaneously. Clay Shirky emphasizes that while we often imagine bell curves everywhere, in fact the phenomena of the world are often best described by the Pareto Principle. Things are often skewed radically toward the top of any distribution. Twenty percent of the employees in any company do most of the work, and the top 20 percent within that 20 percent do most of that group's work. As you read through the entries that seek to understand patterns in the world, you'll run across a few amazing facts. For example, I didn't know that twice as many people in India have access to cell phones as latrines. But most of the essays in the book are about metacognition. They consist of thinking about how we think. I was struck by Daniel Kahneman's essay on the Focusing Illusion, by Paul Saffo's essay on the Time Span Illusion, by John McWhorter's essay on Path Dependence, and Evgeny Morozov's essay on the Einstellung Effect, among many others. If you lead an organization, or have the sort of job that demands that you think about the world, these tools are like magic hammers. They will help you, now and through life, to see the world better, and to see your own biases more accurately.

But I do want to emphasize one final thing. These researchers are giving us tools for thinking. It sounds utilitarian and it is. But tucked in the nooks and crannies of this book there are insights about the intimate world, about the realms of emotion and spirit. There are insights about what sort of creatures we are. Some of these are not all that uplifting. Gloria Origgi writes about Kakonomics, our preference for low-quality outcomes. But Roger Highfield, Jonathan Haidt, and others write about the "snuggle for existence": the fact that evolution is not only about competition, but profoundly about cooperation and even altruism. Haidt says wittily that we are the giraffes of altruism. There is something for the poetic side of your nature, as well as the prosaic.

More here.

Posted by Azra Raza at 06:57 AM | Permalink

Comment by Adriana on March 9, 2012 at 2:04pm

Thanks for stopping by, Davy! I had the same thought when reading the pterosaur-fish entanglement: nothing really changes, the animals are slightly different, but the same scenes are played near the surface of the water when schools of fish are being preyed upon. 

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