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Prof. A's Science Fix- October 19 2012 Edition

I’m trying something different for this blog. Normally I highlight a combination of science news or studies that I pick from within our site, and others that were not posted on our site, but that I find interesting. For this edition, I’m highlighting only news and studies from outside our site, and the blog will also be shorter. The reasons I’m doing this are: 1) it’s an experiment! And you are the study subjects, your opinions are the data. Do you like this format better? 2) I’ve been very, very busy lately and it may not get better any time soon, so I decided a shorter Science Fix is better than no Science Fix, at least for now. If you already follow our Science groups, if someone posts something interesting on our site, you most probably saw it already.




Medicine and Physiology: John Gurdon and Shinya Yamanaka, for reprogramming mature cells back into embryonic-like stem cells. What does “reprogramming” mean in this case? When you were an early embryo, just a tiny ball of undifferentiated cells, your cells had the capacity to develop into multiple cell types. These cells are called “pluripotent” because they are able to become many different tissue types. But once muscle becomes muscle, for example, muscle cells cannot go back to being other types of cells. However, it is possible to coax differentiated, mature cells into going back to being pluripotent, that is, embryo-like cells, called induced stem cells. This is an area of very active research given the potential to use this technology to generate tissue and organs, avoiding the use of harder to obtain actual embryonic cells. John B. Gurdon, a developmental biologist at the Wellcome Trust/Cancer Research was a true pioneer in this field. Believe it or not, as early as 1962, he showed reprogramming worked in the lab. He introduced the nucleus of a mature intestinal cell from the frog Xenopus laevis (a favorite lab animal model) into a frog egg that had been emptied of its own nucleus and shown that the intestine cell nucleus got reprogrammed and formed an entire new embryo, tadpole and adult frog!  Those were the first cloned animals ever. It took almost 40 years until Shinya Yamanaka showed that you could do the trick with cells other than eggs. In 2006, his lab reprogrammed mouse skin cells into pluripotent stem cells, by adding 4 key genes, Oct3/4, Sox2, c-Myc, and Klf4, to these cells, under special culture conditions. A few years ago, Yamanaka’s lab showed that this is possible with human cells as well. This opened the way to establishing stem cells from people suffering from various diseases, making it possible to study these diseases in an unprecedented way. We are still a way from utilizing this knowledge and translating it into therapies, but their discoveries were a gigantic step forward. In the photo: Human induced pluripotent stem cell colonies made from adult skin cells: DNA is stained blue, green and red stain specific proteins on the surface of the cells (taken by William Collins in the lab of Deepak Srivastava and Christopher Schlieve at the  Gladstone Institutes).


Chemistry: Robert Lefkowitz and Brian Kobilka, for G-protein coupled receptors. To me, this Nobel Prize belongs more in the category of Physiology and Medicine than in Chemistry, because it has to do with life. But of course, living organisms are made of chemicals, so as usual it is a bit of both. If “G-protein coupled receptor” or GPRC, sounds like soporific gibberish to you, I’m here to help. What is a receptor? A receptor is a protein that senses a stimulus and transmits that to the cell, which can then respond to the stimulus. Most functions you can think of necessitate receptors. The regulation of bodily parameters such as blood pressure happens through receptors; pain and pleasure, immune responses, touch, olfaction, all of these processes need receptors.  So what is a G-protein? It is short for guanine-binding protein. These proteins are switches: they receive the signal through the receptor and they transmit the information inside the cell. G-protein coupled receptors work by interacting with G-proteins, hence the name GPCR.  There is an entire huge family of GPCRs, with over 800 different members, with different functions. This astonishing protein family is necessary for the therapeutic effects of over one third of all drugs used in modern medicine! Robert Lefkowitz was a pioneer in this field. In the 60s, he was working on a hormone that stimulates the production of adrenaline, the adrenocorticotropic hormone, and by tracking where the hormone went inside the cell, he identified 9 types of adrenaline receptors, also called adrenergic receptors or AR). It took him two decades to identify the genes that coded for these proteins.  Brian Kobilka was then a student in his lab. They immediately noticed the similitudes with genes that encoded other known receptors, such as the light receptor in the retina. These proteins all had 7 regions that threaded back and forth through the cell membrane, and they all coupled to G-proteins inside the cell.  Other scientists then identified other receptors that coupled with G-proteins, and it turns out that they all had these seven transmembrane regions! That’s how the family was discovered. It is a molecular design that works so well, that evolution has used it over and over again, for varied processes from basic physiological responses to vision and pain perception! Kobilka then went on to establish the crystal structure of GPCRs. This was very difficult because GPCRs are huge proteins, and pretty “floppy. ” Last year they published the first full high-resolution structure of a GPCR.  When a stimulus binds to the portion of the receptor outside the cells, a conformational change occurs, the 7 transmembrane domains bunch up together, and fan out inside the cells, creating a structure that allows the G-protein to bind. Thus, a small change on the outside of the cell becomes a huge change inside the cell, triggering a cascade of event that allows the cell to respond to the external stimulus. Given all the GPCRs do for cell function and physiological processes, it is not surprising that it earned these two scientists a Nobel Prize. GPCRs remain a very hot area of research in medicine and pharmacology.


Physics: Serge Haroche and David Wineland, for manipulating the quantum states of single particles. I’m way out of my comfort zone with quantum physics, but here is a summary of why this Nobel Prize is so relevant. Quantum physics has traditionally been mostly theory, necessary to explain seemingly strange behavior at the level of subatomic particles.  But now physicists can actually run experiments by studying the interactions of individual particles in specific quantum states. Serge Haroche’s field is called "cavity quantum electrodynamics." Photons are trapped in an “optical cavity” formed by two mirrors, and researchers can then probe the interaction of the light particles with a single atom sent into the cavity. Wineland’s contribution has been developing techniques of trapping ions. These techniques may be used in the future to develop a quantum computer that could solve computations that would overwhelm a “regular” computer.  What I loved from this Nobel Prize is that serge Haroche wrote a wonderful piece in Nature, called The secrets of my prizewinning research, in which he warns us of the dangers of “short-termism” in science funding. I suggest reading it all. I leave you here with a quote from his opinion piece: “Scarcity of resources due to the economic crisis, combined with the requirement to find scientific solutions to practical problems of health, energy and the environment, tend to favor short-term, goal-oriented projects over long-term basic research. Scientists have to describe in advance all their research steps, to detail milestones and to account for all changes in direction. This approach, if extended too far, is not only detrimental to curiosity-driven research. It is also counterproductive for applied research, as most practical devices come from breakthroughs in basic research and would never have been developed out of the blue.”  Needless to say, I fully agree with Haroche.




A scientific explanation for “palate cleansing”. Why is it that most cultures pair the consumption of certain foods with astringent foods or drinks? Astringent substances shrink tissues or constrict them. Think “unripe banana in your mouth”: it’s the rough-mouth, dry feeling that we experience when tannins in certain fruits or drinks cause the aggregation of saliva in our mouth. Tea and wine are beverages containing tannins. Typically, high tannin wines are paired with fatty foods, such as steak or meat stews, and it is believed that tea, wine, pickles, tart sorbets “cleanse the palate.” But how do mild astringents like wine and tea achieve the cleansing effect? A recent publication in Current Biology revealed the “secret” (obviously not a secret to chefs around the world): it’s the alternation of a portion of an over-lubricating food (any greasy food will cause over-salivation), with an astringent drink (over-drying), which does the trick. The over-salivating produced by the fatty food and the drying effect produced by the tea or wine, basically cancel each other out, leaving a pleasant sensation in the mouth. The experiment was the following: volunteers ate greasy salami and took little sips of either water or tea. While the sips of water did nothing to counteract the greasy feel in the mouth, little sips of even mild tea did the trick. The tea was very weakly astringent but the repeated exposures (sips) resulted a build up of astringency sensation, and if you want to be super-technical, the sensation builds “to an asymptotic level determined by the structure and concentration of the compound.” No alternation, no “palate cleansing.” Keep sipping the wine, my friends, don’t just gulp it down; little sips do the job better.




A virus inside a virus inside a parasite. The most remarkable discoveries can come out of pretty commonplace events. Scientists came upon a “Russian-doll” set of new parasites, nested within each other, in the contact lens liquid of a French lady who had irritated eyes. The liquid contained an amoeba (a protozoan), which was in turn infected with a totally novel gigantic virus, which the French scientists called “Lentille virus” (contact lens in French), a new member of a family of giant viruses called Mimiviridae. And inside the Lentille virus, there was a virophage, which is a virus that infects other viruses. They called the virophage “Sputnik 2”. Sputnik 2 is only the fourth virophage ever described. And the French scientists found even more wholesome viral weirdness: there were bits of DNA termed transpovirons (bits of DNA that jump from one site to another) that shuttled between Lentille and Sputnik 2.  These observations are so novel, they ended up getting published in the prestigious journal PNAS (Proceedings of the National Academy of Sciences).  The world of viruses is incredibly genetically diverse. Imagine the future discoveries awaiting the attentive virologist, if all of this was newly found in a bit of contact lens fluid from someone’s inflamed eye! (Electronmicrograph: giant viruses assembling inside a cell)




DNA has a 521-year half-life. I hate to break the news to you, my friends, but there will be no “Jurassic Park.” No cloned dinosaurs. This is because DNA from dinosaurs could have never survived to today. New Zealand scientists have been studying fossil moa bones that made possible to calculate the half life of DNA. Half life is a technical term that means the is time it takes for half the amount of X compound or material to decay and decrease to half the original amount. Calculating the half life of DNA was hard because it required fossil samples in similar preservation states, but from different points back in time. Fortunately a team of paleogeneticists from New Zealand and Denmark found 158 moa leg bones ranging in age from 600 to 8,000 years old. They all come from sites in close proximity and they were all in identical state of preservation. They measured the degradation of DNA and correlated it with age, coming to the conclusion that the half life of DNA is 521 years: after 521 year, half the bonds in the DNA molecule would have broken, then in the following 521 years, half of the remaining half would be gone, etc. The prediction is that even in perfect temperature, humidity, etc. preservation conditions, effectively all bonds in a DNA molecule would have broken down 6.8 million years after the death of the animal. But you need more than a few bonds to read a DNA sequence, you need a certain fragment length, and those calculations are even grimmer. After only 1.5 million years, all the DNA left would be totally unreadable. The last dinosaurs disappeared around 65 million years ago.  Sorry, T. rex, we will not be able to bring you back to life.


A 16 million year old hitchhiker. A tiny creature the size of a grain of salt was caught n the act of hitching a ride on a mayfly, holding on to the bigger insect with its minuscule antennae. The fantastic discovery comes from a piece of 16 million year old amber found in 2008 in the Dominican Republic. The hitchhiker belongs to the springtail group of arthropods. They look a bit like insects, they have six legs like insects, but they are not considered insects and are more ancient in origin; they are found today in soil, and are one of the most abundant groups of animals on the planet. Scientists had found springtail fossils in amber before, getting a ride on spiders or daddy longlegs. This second discovery is prompting scientists to investigate if modern day springtails are hitchhikers, too.  It has not been reported so far. The remarkable amber discovery has been published just two days ago in the journal PLoS ONE. You can read the while article for free, here.




How the deadly blue-ring octopus flashes its warning. Octopuses are fascinating animals, they are chockfull of interesting adaptations and they are very smart. Among their outstanding abilities is color changing and mimetics. The blue-ringed octopus (Hapalochlaena lunulata) is a small, beautiful octopus. It is brightly colored with blue rings all over its body, which the cephalopod flashes within a fraction of a second if threatened. Its attractiveness is unfortunately a deadly warning: a bite from this creature injects a neurotoxin that can rapidly kill an adult human being. To us, the flashing blue rings look beautiful, but to other sea denizens, its message is clear: I’m venomous, stay away from me. But how does this octopus flash its warning so quickly? To answer that question, marine biologist Lydia Mäthger, (Marine Biological Laboratory in Woods Hole, Massachusetts) filmed captive blue-ringed octopuses at super slow speed, to observed the behavior of its color-producing skin structures. H. lunulata has three types of structures: 1) chromatophores, which are sacs full of pigment, surrounded by muscles, that contract or expand the sacs, changing their appearance in a fraction of a second; 2) iridophores, are firmer, slower-acting structures that produce iridescence by shifting proteins inside the cells, that reflect different light wavelengths; 3) leucophores which are basically reflectors that add contrast and luminosity. In other octopuses, iridophores are located beneath the chromatophores in the skin, but in the blue-ringed octopus, the iridophores are unobstructed by chromatophores, and are located in muscular skin areas so they can quickly “flash”. To produce more contrast, the chromatophores surrounding the blue rings turn a darker color when the animal flashes, creating high contrast for the blue rings. Why does blue work well as a warning signal? In the sea, the blue and green part of the spectrum is very well perceived by predators such as fish, whales, birds, and other octopuses.


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Comment by Doone on October 24, 2012 at 11:36pm


Scientists have mapped a tiny roundworm's entire nervous system. Did it teach them anything about its behavior?

Ferris Jabr in Scientific American:

ScreenHunter_11 Oct. 24 17.04In the 1970s biologist Sydney Brenner and his colleagues began preserving tiny hermaphroditic roundworms known asCaenorhabditis elegans in agar and osmium fixative, slicing up their bodies like pepperoni and photographing their cells through a powerful electron microscope. The goal was to create a wiring diagram—a map of all 302 neurons in the C. elegans nervous system as well as all the 7,000 connections, or synapses, between those neurons. In 1986 the scientists published a near complete draft of the diagram. More than 20 years later, Dmitri Chklovskii of Janelia Farm Research Campus and his collaborators published an even more comprehensive version. Today, scientists call such diagrams "connectomes."

So far, C. elegans is the only organism that boasts a complete connectome. Researchers are also working on connectomes for the fruit fly nervous system and the mouse brain. In recent years some neuroscientists have proposed creating a connectome for the entire human brain—or at least big chunks of it. Perhaps the most famous proponent of connectomics is Sebastian Seung of the Massachusetts Institute of Technology, whose impressive credentials, TED talkpopular book, charisma and distinctive fashion sense (he is known to wear gold sneakers) have made him a veritable neuroscience rock star.
Other neuroscientists think that connectomics at such a large scale—the human brain contains around 86 billion neurons and 100 trillion synapses—is not the best use of limited resources. It would take far too long to produce such a massive map, they argue, and, even if we had one, we would not really know how to interpret it. To bolster their argument, some critics point out that the C. elegans connectome has not provided many insights into the worm's behavior.

More here.

Posted by S. Abbas Raza at 11:04 AM | Permalink

Comment by Doone on October 24, 2012 at 9:30pm

Ozone Layer Hole Second Smallest It Has Been In 20Years (PHOTOS)

Ozone Layer Hole Second Smallest It Has Been In 20 Years (PHOTOS)The average annual size of the hole in Earth’s ozone layer over Antarctica, caused mainly by chlorine released by human-produced chemicals, is the second smallest it’s been of any year in the past 20, NASA and the National Oceanic and Atmospheric Administration (NOAA) announced Wednesday. The hole this year had an average size of 6.9 million square miles (17.9 million square kilometers), the agencies reported, compared to the smallest average annual size during the past 20 years of …Read More →

Comment by archaeopteryx on October 24, 2012 at 8:51pm

The history of life on Earth has been marked by the evolution of new genes—humans clearly have more genes with more diverse functions than do amoebas. So where do these additional genes, with their new roles, come from? Analysis of genomes shows that the duplication and modification of existing genes seems to be a major avenue for such innovation.

Conventional wisdom had it that duplicate genes provide raw material for evolution. The original gene continues to do its job, whereas the other copy is free to evolve in a different direction.

For example, the venomous cocktail delivered by a platypus's spurs includes three peptides remarkably similar to an antimicrobial compound used in the critter's immune system. The venom molecules evolved from duplications of the gene that codes for an immune comp.... Scientists refer to groups of similar genes with different functions as families. Humans carry duplications, too—a group of molecules in the back of the eye that react to incoming photons of light hail from the family of opsin genes. Duplicate genes in the human genome were likely key during divergence from our common ancestry with chimps.

The idea that gene duplication could result in genes with new functions has been around for awhile. Geneticist Susumu Ohno explained the theory in detail in 1970. He argued that duplication is the most important evolutionary force—more powerful than genetic drift, for example. Scientists are still working out the specifics because the vast majority of mutations eventually arising in the duplicates are harmful, meaning they result in function loss; the duplicates would need to stick around for generations before acquiring helpful mutations. But the model required that natural selection should spare the extra gene copies until they had a chance to change for the better.

This problem bothered Dan Andersson, a microbiologist at Uppsala University in Sweden, and John Roth, a geneticist at the University of California, Davis. To better explain how new genes could evolve they suggested a modification of the old model: instead of waiting around for a beneficial mutation, perhaps the beneficial mutation comes first.

This model takes note of the fact that many genes do their primary job of coding for a particular protein very well, but also have a weak secondary function that may become important under certain environmental stressors. For example, one gene might code for a protein that helps bacteria gobble glucose, but also allows the bacteria to snack on starchy cellulose. If all sugar disappears from its environment and only cellulose remains, the bacteria that have this gene will have the capacity to eat more cellulose and therefore be selected for over time and endure. Andersson and Roth's model posited that beneficial mutations already present by chance would be favored by natural selection and stick around in the genome. When the gene is amplified through the duplication, the extra copies give rise to new genes that are better at performing the secondary function, thereby making it prime. "The key is that it never goes off selection," Roth says.

In a study in the journal Science, Andersson, Roth and their colleagues demonstrate the process in lab-grown Salmonella enterica. They grew one strain missing a gene key for expressing the essential amino acid tryptophan. The strain needed to rely on another gene, which had a primary job but also a weak ability to take on the missing gene's work. The researchers encouraged the bacteria to duplicate the overworked gene, and its copies gathered mutations—some of which enhanced tryptophan production. At the end of a year's time (3,000 generations later) the bacteria had one gene that did the original job and a second that had evolved a new primary function—manufacturing tryptophan.

Prior to this study, scientists have relied on more theoretical approaches such as bioinformatics to infer how new genes arise. Now they have demonstrated the evolution of a new gene experimentally. The team published their results on October 19.

Comment by archaeopteryx on October 23, 2012 at 2:17pm

"Fa loves Pa --"

Comment by Doone on October 23, 2012 at 10:15am


Ben Ambridge at the blog of the Welcome Trust:

Disappointed-and-sulkyPreviously it was thought that the magical ability which non-human species lack is the understanding that words can be put together in different orders to express different meanings. There’s a saying in journalism: Dog Bites Man isn’t news, but Man Bites Dog is. It makes sense only because we understand that the order of the words tells us who’s doing the biting and who’s getting bitten.

However, a few species have actually passed this test. On the comprehension front, we have Phoenix and Akeakamai, two dolphins studied at the University of Hawaii, who were taught a language in which the ‘words’ were different whistle sounds played by the trainer (and chosen to approximate dolphins’ own calls). The dolphins understood that, for example, “put the pipe on the hoop” and “put the hoop on the pipe” meant different things and were able to respond accordingly, even when the exact sentence hadn’t been presented before. Some apes, such as Kanzi, a bonobo raised in Atlanta, have passed a similar test although debate continues as to whether or not they can combine words – in this case hand signs – in their own communication (watch the 2011 film Project Nim to see this controversy played out).

The finding that some species do seem to appreciate the powerful combinatorial properties of language serves only to deepen the mystery. If these animals are so smart, why aren’t they explaining what it’s like to be a chimpanzee, or at least politely asking to be let out of the cage? Tomasello’s answer is that what they just don’t seem to get is that language is fundamentally cooperative, almost altruistic, in nature. You understand that, if I say something to you (“Look, there’s your boss”), I’m doing so because I believe you will find it useful or interesting. Tomasello’s big idea is that this idea of doing something for the benefit of someone else is completely alien to other species.

More here.

Posted by S. Abbas Raza at 04:10 AM | Permalink

Comment by Chris on October 23, 2012 at 12:35am

Imagine what the Beluga human voice mimic sounded like to sailors (of long ago) who've been at sea for months. I'll have to ask a squid I know if he's noticed that in his sonar before.

Comment by archaeopteryx on October 22, 2012 at 11:23pm

Rare wildlife photos highlight winning entries in worldwide contest



Worth a further read, as with each photo is an explanation of how the shot was acquired!

Comment by archaeopteryx on October 22, 2012 at 3:04pm

Blue Iguana Slithers Back from Extinction

Just a decade ago, the Grand Cayman blue iguana was on the brink of extinction, with only 10 to 25 individuals left in the wild. But the reptile has made a major comeback and is no longer listed as a critically endangered species.

The blue iguana, which is only found on the Caribbean island Grand Cayman, now has a population of about 750, thanks to a recovery program. And over the weekend, the International Union for Conservation of Nature (IUCN) updated its listing of the species from critically endangered to endangered.

An endangered status is probably the best conservationists could ever hope for as far as the reptile is concerned, said Fred Burton, director of the Blue Iguana Recovery Program.

"Human impacts on Grand Cayman are now so extensive that there just isn't scope for these iguanas to regain numbers in the tens of thousands," Burton explained in a statement. "However, we are confident that we will achieve our lon-term goal of restoring at least 1,000 Grand Cayman blue iguanas to the wild."

The blue iguana is the largest native species on Grand Cayman. The reptiles often grow to more than 5 feet (1.5 meters) in length and weighs more than 25 pounds (11 kilograms). They once ranged over most of the island's coastal areas and interior dry shrub lands before habitat destruction, car-related deaths and free-roaming dogs and cats pushed them toward extinction.

Comment by archaeopteryx on October 22, 2012 at 1:20pm

You know what they say about great minds --

Comment by Adriana on October 22, 2012 at 1:16pm

Ha! Our posts have crossed, I just posted this as full discussion, here

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