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  • August 21, 2010
  • 05:39 AM
  • 703 views

Report from Alife XII: life's origin, and its evolution

by Bjørn Østman in Pleiotropy

When I say 'artificial life', what do you think of? I think of life-like systems in computers, mainly, but at the Alife 12 conference in Odense, Denmark that I am currently at, a large part of the presentation are really about chemistry. Many people might be surprise if they knew just how many people are working on the problem of getting chemicals to behave like life. That is, work on the origin of life is booming. ... Read more »

Costanzo, M., Baryshnikova, A., Bellay, J., Kim, Y., Spear, E., Sevier, C., Ding, H., Koh, J., Toufighi, K., Mostafavi, S.... (2010) The Genetic Landscape of a Cell. Science, 327(5964), 425-431. DOI: 10.1126/science.1180823  

  • August 21, 2010
  • 04:53 AM
  • 1,796 views

More (you know you wanted it) on fecal transplants and the microbiome

by Jonathan Eisen in The Tree of Life

Image fromI Heart Guts blogThere is an interesting mini review in the Journal of Clinical Gastroenterology's September issue that may be of interest to some out there. It is entitled "Fecal Bacteriotherapy, Fecal Transplant, and the Microbiome" by Martin Floch and well, the title is indicative of the article.Yes, the fecal transplant meme is here to stay. Sure, the cognoscenti already knew about fecal transplants. Perhaps they had read Tara Smith's discussion of it in her Aetiology blog in 2007. Perhaps they had pondered it when they read the article from my lab on intestinal transplants. Perhaps they had seen this discussion on MSNBC, or various other stories out there such as this or this post from Angry by Choice. Or, maybe you just learned about it from Bora's Carnival of Poop. But the meme on fecal transplants really spread and many may have first heard about fecal transplants from Carl Zimmer's New York Times article a month or so ago "How microbes defend and define us"In the article Zimmer discussed how Dr. Alexander Khoruts used a fecal transplant to treat a woman with a persistent and severe Clostridium infection. And Zimmer discusses how, thought such transplants had been done before, this was the first time that the microbial community was carefully surveyed before and after. (Note, my favorite part of the article is this part, where my friend Janet Jansson describes her reaction:Two weeks after the transplant, the scientists analyzed the microbes again. Her husband’s microbes had taken over. “That community was able to function and cure her disease in a matter of days,” said Janet Jansson, a microbial ecologist at Lawrence Berkeley National Laboratory and a co-author of the paper. “I didn’t expect it to work. The project blew me away.”Anyway Zimmer's article, as with many of his, garnered a lot of response and got many people discussing the poop on fecal transplants. Well, this issue of the Journal of Clinical Gastroenterology may now be the biggest pile of information about fecal transplants around. That is because, in addition to this little review mentioned above, there are in fact three articles in this issue relating to fecal transplant. Alas, most of you out there will probably only be able to read the review since the other articles are behind a pay wall. But the review is good. And I think this is not the last you will hear about this. (Though I note that, even though I think fecal transplants have some major potential, they seem to be being oversold a bit by many as some cure all -- fodder for a future "Overselling the Microbiome Award" I am sure). I will end with this line from the review which raises some other issues about fecal transplants:Probably one of the major problems is to define how this therapy can become socially accepted. (Can you imagine the Food & Drug Administration discussion?) Floch, M. (2010). Fecal Bacteriotherapy, Fecal Transplant, and the Microbiome Journal of Clinical Gastroenterology, 44 (8), 529-530 DOI: 10.1097/MCG.0b013e3181e1d6e2Grehan, M., Borody, T., Leis, S., Campbell, J., Mitchell, H., & Wettstein, A. (2010). Durable Alteration of the Colonic Microbiota by the Administration of Donor Fecal Flora Journal of Clinical Gastroenterology, 44 (8), 551-561 DOI: 10.1097/MCG.0b013e3181e5d06b... Read more »

  • August 21, 2010
  • 02:13 AM
  • 758 views

From the Literature: Tracking Dragonfly Migrations

by dragonflywoman in The Dragonfly Woman

It’s about the time of year for the dragonflies to start moving south!  I’ve already gotten several reports of big migratory swarms headed south from several locations across the eastern and midwestern U.S. and I expect many more – the … Continue reading →... Read more »

Wikelski M, Moskowitz D, Adelman JS, Cochran J, Wilcove DS, & May ML. (2006) Simple rules guide dragonfly migration. Biology letters, 2(3), 325-9. PMID: 17148394  

  • August 20, 2010
  • 11:25 PM
  • 1,394 views

Paleolithic whodunnit: Who made the Chatelperronian?

by Julien Riel-Salvatore in A Very Remote Period Indeed

The Chatelperronian is a lithic industry that springs up for several thousand years during the transition from Middle to Upper Paleolithic industries. Its precise age is debated, but it clearly is associated with this interval. One of the reasons the Chatelperronian is the subject of so much debate is because, since the discovery of a Neanderthal in a Chatelperronian level at the site of
St. ... Read more »

  • August 20, 2010
  • 10:30 PM
  • 556 views

Rubella – Discount babies! 50% off! Cataracts included!

by thomastu in Disease Prone

People shouting loudly and angrily against childhood vaccination seem to either evil or ignorant of what the world was like before vaccines were readily available. And Hanlon’s razor tells us “Never attribute to malice what can be blamed on ignorance”. So, as my civic duty, I am starting a series on vaccine preventatble diseases. First [...]... Read more »

  • August 20, 2010
  • 09:34 PM
  • 1,120 views

Evolving Pesticide Resistance

by Matthew DiLeo in The Scientist Gardener

It's been estimated that genetic resistance to every pesticide that will ever be invented already exists in some microbe in some field, somewhere in the world. If you invent an incredible new spray that kills, say, Phytophthora infestans, you'd know that somewhere in the world there is a little P. infestans mycelium or spore that is already resistant. If you start spraying thousands and thousands... Read more »

Zhu, Y., Chen, H., Fan, J., Wang, Y., Li, Y., Chen, J., Fan, J., Yang, S., Hu, L., Leung, H.... (2000) Genetic diversity and disease control in rice. Nature, 406(6797), 718-722. DOI: 10.1038/35021046  

  • August 20, 2010
  • 04:16 PM
  • 1,252 views

Conduction aphasia, speech repetition, and the left parietal lobe

by Greg Hickok in Talking Brains

Julius Fridriksson has been featured on this blog before and now his team has just published another noteworthy paper in J. Neuroscience. This paper sought to identify the neural correlate of repetition disorder in aphasia. Repetition deficits are characteristic of conduction aphasia although they are not exclusive to conduction aphasia nor is repetition the only deficit in conduction aphasia. Some historical background is useful, if for no other reason than most people get it wrong in one way or another. Here are two myths/misunderstandings about conduction aphasia.1. It is a disorder of repetition. 2. It was first discovered/reported by Lichtheim.As Fridricksson is careful to point out, the repetition disorder is only one symptom of conduction aphasia, the others being impaired word-finding and phonemic paraphasias in production. In fact, the first characterization of the symptoms of conduction aphasia (by Wernicke not Lichtheim) did not make reference to a repetition deficit; rather the hallmarks were impaired word-finding and speech errors, typically with many self-corrective attempts, in the face of otherwise fluent and grammatical speech and good comprehension. Describing the predicted theoretical consequences of a lesion to the connecting pathway between the sensory and motor speech centers, Wernicke (1874) writes,In this case... the patient understands everything. He can always express himself, but his ability to choose the correct word is disturbed in a manner similar to that in the form just described [sensory, aka Wernicke's aphasia]. p. 54Repetition was a clinical assessment invented by Lichtheim which essentially was a means to highlight the paraphasic deficit. In my view, conduction aphasia is a disorder of speech production affecting phonological/phonetic levels of processing and which manifests in paraphasic output on a range of tasks including naming, connected speech and repetition. Regarding the second point, Wernicke was the first to describe a case of conduction aphasia. Most people get this wrong as the Fridriksson et al. paper demonstrates, "Although Wernicke had never seen such a patient, one was later described by Lichtheim" (p. 11057). Not that it matters that much to the science, but it is nice to get the history straight, so here is a quote from Wernicke 1874 (p. 73-74), 11 year before Lichtheim's monograph appeared:The following is a clear case of conduction aphasia... He understands everything correctly and always answers questions correctly. ... He shows no trace of motor aphasia .... He cannot, however, find words for many objects he wishes to designate [word finding deficit]. He makes an effort to find them, becoming agitated in the process, and if one names them for him he repeats the name without hesitation. ... He can say many things fluently, especially familiar expressions. He then comes to a word on which he stumbles, remains caught on it, exerts himself and becomes irritated. After that every word that he utters, haltingly, is nonsensical [phonemic paraphasias]; he corrects himself over and over again [self-corrective attempts], and the harder he tries the worse the situation becomes...Classically, conduction aphasia is thought to result from a disconnection between sensory and motor speech areas caused by damage to the arcuate fasciculus (the idea of AF involvement came after Wernicke's 1874 monograph, but he bought into it). Recent work has provided a pretty strong case against the AF being the critical structure. Here's a previous entry on this topic based on the work of Nina Dronkers and colleagues.Ok, enough with the history. Now on to the paper. Friderksson et al. studied a series of 45 acute stroke patients behaviorally, including a test of repetition, and neuroradiologically. For the latter they acquired by structural MRI and perfusion weighted MRI. The use of perfusion weighted imaging in acute stroke is a method championed by Argye Hills at Johns Hopkins, and is, in my view, an excellent tool. What's interesting about the study is that they didn't select patients on the basis of aphasia type or even the presence of a repetition disorder. Instead they included a range of patients, measured their repetition ability and looked to see what correlated with deficits. This is a useful approach. The only problem in this case is that, as noted in the paper, repetition deficits can result from disruption anywhere along the pathway between perception and production (e.g., peripheral hearing loss will cause a repetition deficit), so in this sense the study is kind of a shotgun approach that will only capture central tendencies. Nonetheless, here is what they found.Structural damage to the white matter beneath the left supramarginal gyrus, which includes the arcuate fasciculus, was the most strongly correlated region with repetition impairment. HOWEVER, perfusion imaging told a different story, implicating a cortical zone that included the parietal operculum (inferior SMG) (see their Figure 2, bottom row) and a temporal-parietal junction region (which unfortunately they don't picture). This is the same general region implicated in conduction aphasia (Baldo et al. 2008) and where sensory-motor area Spt lives (Hickok et al. 2003, 2009).Fridriksson et al. are appropriately cautious in concluding that it is the cortical involvement that causes the deficit, instead concluding that speech repetition is "strongly associated with damage to the left arcuate fasciculus, supramarginal gryus, and TPJ" (p. 11060). I wouldn't disagree that the AF, as a connecting pathway plays an important role, but I would argue strongly that the deficit results, computationally speaking, from damage to cortex, area Spt in particular. In addition, Fridriksson et al. suggest that their findings do not address the other symptoms of conduction aphasia. It is true that they didn't explicitly examine these symptoms, but I believe the symptoms are connected, particularly the repetition and phonemic paraphasias.ReferencesBaldo JV, Klostermann EC, & Dronkers NF (2008). It's either a cook or a baker: patients with conduction aphasia get the gist but lose the trace. Brain and language, 105 (2), 134-40 PMID: 18243294Fridriksson J, Kjartansson O, Morgan PS, Hjaltason H, Magnusdottir S, Bonilha L, & Rorden C (2010). Impaired speech repetition and left parietal lobe damage. The Journal of neuroscience : the official journal of the Society for Neuroscience, 30 (33), 11057-61 PMID: 20720112Hickok, G., Buchsbaum, B., Humphries, C., & Muftuler, T. (2003). Auditory-Motor Interaction Revealed by fMRI: Speech, Music, and Working Memory in Area Spt Journal of Cognitive Neuroscience, 15 (5), 673-682 DOI: 10.1162/jocn.2003.15.5.673... Read more »

Fridriksson J, Kjartansson O, Morgan PS, Hjaltason H, Magnusdottir S, Bonilha L, & Rorden C. (2010) Impaired speech repetition and left parietal lobe damage. The Journal of neuroscience : the official journal of the Society for Neuroscience, 30(33), 11057-61. PMID: 20720112  

  • August 20, 2010
  • 04:10 PM
  • 890 views

Genome-Scale Epigenetic Marker Detection Across Populations

by Michael Long in Phased

Lior Pachter (University of California at Berkeley, United States) and coworkers have developed MetMap software for uncovering epigenetic data hidden by standard MethylSeq analysis, which will advance our understanding of the role of epigenetics in human health and medicine. This news feature was written on August 20, 2010.... Read more »

Singer, M., Boffelli, D., Dhahbi, J., Schoenhuth, A., Schroth, G. P., Martin, D. I. K., & Pachter, L. (2010) MetMap Enables Genome-Scale Methyltyping for Determining Methylation States in Populations. PLoS Computational Biology, 6(8). DOI: 10.1371/journal.pcbi.1000888  

  • August 20, 2010
  • 03:00 PM
  • 512 views

Spindles are Important for a Good Night's Sleep

by Allison in Dormivigilia

Harvardian researchers have uncovered the secret to a sound night's sleep in a busy city. Sleep spindles. These spontaneous brain waves over protection from nighttime arousals induced by traffic and miscellaneous environmental noise... Read more »

Dang-Vu TT, McKinney SM, Buxton OM, Solet JM, & Ellenbogen JM. (2010) Spontaneous brain rhythms predict sleep stability in the face of noise. Current biology : CB, 20(15). PMID: 20692606  

  • August 20, 2010
  • 02:38 PM
  • 805 views

The Scientist and the Anarchist - Part III

by Eric Michael Johnson in The Primate Diaries

The latest stop in the #PDEx tour is being hosted by Deborah Blum at her website Speakeasy Science.When an estimated 1,400 match-girls went on strike in July, 1888 to protest for better working conditions, it started a fire that became known as New Unionism. Soon after came the London dock workers’ strike, and within twelve months the UK’s Trade Union Congress had increased its membership from 670,000 to 1,593,000. [1]For Thomas Henry Huxley and Peter Kropotkin these labor developments were interpreted very differently, and yet both saw in them important connections with their work in evolutionary biology. Huxley, who had pulled himself out of East London poverty through a combination of sheer brilliance and stubborn determination, was greatly concerned about what the workers democracy movement meant for social stability. Now the President of the Royal Academy of Sciences and a living legend in the recently established field of evolutionary biology, Huxley had come to identify with the aristocracy he’d worked so hard to be accepted by. Kropotkin, however, had rejected the silver spoon he had once been fed with as a Russian prince after coming face to face with the exploitation that made such ostentatious luxury possible. For him, the growing workers movement was the only path by which the poor could achieve any justice in a world that was undergoing radical change. Both saw in these developments a force of nature — one ominous, the other hopeful — and these conflicting visions would ultimately collide on the pages of the Nineteenth Century.Read the rest of the post here (also Part I and Part II) and stay tuned for next week's post at Anthropology in Practice.Peter Kropotkin (1902). Mutual Aide: A Factor of Evolution New York: McClure, Philips & Co.... Read more »

Peter Kropotkin. (1902) Mutual Aide: A Factor of Evolution. New York: McClure, Philips . info:/

  • August 20, 2010
  • 02:38 PM
  • 668 views

The Scientist and the Anarchist - Part III

by Eric Michael Johnson in The Primate Diaries in Exile

The latest stop in the #PDEx tour is being hosted by Deborah Blum at her website Speakeasy Science.When an estimated 1,400 match-girls went on strike in July, 1888 to protest for better working conditions, it started a fire that became known as New Unionism. Soon after came the London dock workers’ strike, and within twelve months the UK’s Trade Union Congress had increased its membership from 670,000 to 1,593,000. [1]For Thomas Henry Huxley and Peter Kropotkin these labor developments were interpreted very differently, and yet both saw in them important connections with their work in evolutionary biology. Huxley, who had pulled himself out of East London poverty through a combination of sheer brilliance and stubborn determination, was greatly concerned about what the workers democracy movement meant for social stability. Now the President of the Royal Academy of Sciences and a living legend in the recently established field of evolutionary biology, Huxley had come to identify with the aristocracy he’d worked so hard to be accepted by. Kropotkin, however, had rejected the silver spoon he had once been fed with as a Russian prince after coming face to face with the exploitation that made such ostentatious luxury possible. For him, the growing workers movement was the only path by which the poor could achieve any justice in a world that was undergoing radical change. Both saw in these developments a force of nature — one ominous, the other hopeful — and these conflicting visions would ultimately collide on the pages of the Nineteenth Century.Read the rest of the post here (also Part I and Part II) and stay tuned for next week's post at Anthropology in Practice.Peter Kropotkin (1902). Mutual Aide: A Factor of Evolution New York: McClure, Philips & Co.... Read more »

Peter Kropotkin. (1902) Mutual Aide: A Factor of Evolution. New York: McClure, Philips . info:/

  • August 20, 2010
  • 01:40 PM
  • 2,448 views

Cylons and Smelloscopes: False Positives and False Negatives in the Search for Extraterrestrial Life

by The Astronomist in The Astronomist.

Are there planets outside of our solar system? Is there life on other planets? Is life on other planets like life on Earth? These are questions that astronomers, astrobiologists, chemists, and geologists are trying to answer with current experiments. In order to answer these questions we must observe distant planets and we must determine what life on those planets may be like. Detecting extrasolar planets is tricky enough, but imaging what alien life is like may well be stranger than science fiction. Yesterday evening I attended a lecture sponsored by the Seattle Astronomical Society given by Shawn Domagal-Goldman titled Cylons and Smelloscopes: False Positives and False Negatives in the Search for Extraterrestrial Life. It was an excellent lecture and filled with interesting topics. Shawn touched on the philosophical problem of defining life in the broadest of senses (is Number Six alive?) and he pointed out that the verification of life on distant planets faces technical challenges and basic scientific limitations (a smelloscope sure would help!).Dimitar Sasselov set off minor shock waves of gossip and rumors in the media and astronomy communities when claimed that the NASA Kepler mission had found 140 Earth-like planets a few weeks ago during a talk he gave at the TED Global 2010 meeting in Oxford. The media thought we had found earth's twin, but astronomers knew that Sasselov had exaggerated the situation. Sasselov had to post a redaction of sorts on the Kepler blog in order to clarify what he said. What he should have said is that the Kepler mission will find and verify the presence of potentially habitable planets and that Kepler currently had 140 candidate extrasolar planets. The candidates are not confirmed and so a pessimistic outcome could be that half of the candidates will be false. The difficulty in finding extrasolar planets or life is fraught with false positive and false negatives. A false positive is a detection that seems like exactly what you were looking for, and maybe it is, but the detection was either bad data or you were looking for the wrong thing. A false negative is a detection which you conclude is not what you were looking for, but either your data was fouled or your detection threshold was too constrictive.How do we find planets outside of our solar system? There are at least five methods to find planets: Doppler shift, astrometric measurement, transit method, gravitational microlensing, and direct detection. Shawn discussed in depth the Kepler mission that is currently monitoring more than 150,000 stars in the direction of the Cygnus constellation for any signs of extrasolar planets that may be orbiting those stars. So, what method does Kepler use to find  planets? It watches for eclipses! When a planet orbiting a distant star crosses in front of the star some of the light from the host star is blocked. The planet will transit (astronomers often use the world transit not eclipse for exoplanets) in front of the the star once an orbit and thus the period of orbit can be determined. A secondary eclipse also occurs when the day side of the planet is blocked by the star. The video below illustrates the whole process.Yes, there are planets outside of our solar system. The current exoplanet detection count is 473 and counting; you can watch that count go up over at Planet Quest. Kepler may double that number, but more importantly it has the ability to find earth size planets. Most of the planets found to date have been large, hot, and inhospitable to most kinds of life anyone can fathom. How do we detect signs of life on other planets? Astronomers look for bio-markers in the planet's atmosphere. Bio-markers are molecular signatures of certain compounds that could not be produced by non-biological process; bio-markers indicate that dynamic non-equilibrium chemistry is present on the surface of that planet. Astronomers can measure the light emitted as a function of wavelength, the spectra, that a planet emits to determine the molecular species present in the atmosphere. For example the Earth's atmosphere has the spectral signature of water which means it has conditions in which life as we know it can thrive. If we found an earth size planet that had water in its atmosphere which wasn't too hot we would say we had found a habitable planet. If we found oxygen or ozone (03) in an atmosphere it would almost certainly mean life was present on the planet because 03 is quickly removed from atmospheres through standard geological processes such as oxidation of iron, but it may remain present in an atmosphere if it is continually replenished by the photosynthesis mechanism of algae and plants. One of the topics Shawn talked about in his talk and a focus of his research was the problem of being certain that non-biological processes are not creating the oxygen rich atmospheres. The runaway greenhouse effect combined with the photo-disassociation of carbon dioxide can produce oxygen in a similar way to biological life. This is where the smelloscope would be useful: ozone along with other non-equilibrium species such as nitrous oxide and methane in specific ratios would be the scent we are looking for. Bio-signatures were not present on the early Earth. In fact the Earth probably looked a lot more like Venus. The diagram above shows that Venus, Earth, and Mars all have distinct spectral features that tell us about their atmospheres. The hardest part of looking for bio-signatures is that we do not have a telescope that is sensitive enough. Trying to take the spectra of a planet orbiting a bright star is like trying to tell the color of the wings on a gnat hovering around a spotlight on the moon. Like a baseball player holding up one hand to block the sun from his eyes as he focuses on the ball an occulter or star shade working with an existing telescope in space would do the trick. The current funding situation in astronomy is dire, but there is hope that a mission called New Worlds will one day work with the James Webb Space Telescope to allow us to take a closer look at planets which Kepler is finding.Is there life on other planets? We don't know and it may be a more complicated question than is suspected. There is a bias towards looking for life that is similar to what life on Earth is like. There is a bias towards looking for life that alters its host planet's atmosphere significantly enough to detect it with telescopes on earth. There is a bias towards looking for life that is alive as we define it. These biases may lead to false negatives in the search for life, but as Shawn pointed out the possibilities for life to exist are much grander than our imaginations so we do the best we can. Also, despite the difficulties for finding life on other planets and the gulf between the public's perception of aliens and reality scientists are taking this as a serious venture. Scientists from diverse fields are coming together to forge a path forward. One such project is the Virtual Planet Laboratory which employs scientists in fields such as geology, chemistry, biology, and astronomy. The Virtual Planet Laboratory is a team of scientists who are building computer simulated planets to discover the likely range of planetary environments for planets around other stars so we can better look for habitable planets and distinguish between planets with and without life. However, we can't even discern with certainty the presence of life on Mars or Europa at this point, what hope do we have for finding life on distant planets?I think there is a lot of hope and I am not alone in that sentiment. I don't search for planets or life in my research, but I think that the search for life, pa... Read more »

Beichman, C. A., Woolf, N. J., & Lindensmith, C. A. (1999) The Terrestrial Planet Finder (TPF) : a NASA Origins Program to search for habitable planets. JPL publication. info:/

  • August 20, 2010
  • 12:53 PM
  • 677 views

Frogs, Big Mountains, and Speciation

by Michael Windelspecht in RicochetScience

The formation of new species is always a great way to discuss evolutionary change over time. Most textbooks do an adequate job of providing examples of how geographic isolation contributes to the the process of speciation. However, where many books are lacking is showing how the resulting species then adapt to their new environment following the establishment of the geographic barrier. If you are looking for an interesting way to show the relationship between geographic isolation, adaptation, and speciation, then you need to visit a very special group of frogs in southeast Asia.
 
A study coming out of UC Berkeley demonstrates how a really big mountain range, the Himalayas, has influenced the speciation of frogs in Southeast Asia.  the study focuses on a group of amphibians commonly called the spiny frogs. According to the article , the ancestors of the spiny frogs first occupied the area that is now western China around 27 mya. When the Indian subcontinent collided with south Asia, the uplifting created the Himalayan mountains, and created the Tibetan plateau. Right in the middle of these events were the spiny frogs. And as their environment changed, the spring frogs diverged into several very different species - the Nanorana subgenus, which occupies elevations up to 4,700 meters, and the lowland Quasipaa group.


PNAS cover image (Yu Zeng - University of California, Berkeley, CA)


But what is interesting about this study is not that it is just another example of allopatric speciation. Rather, a closer look at the species of frogs in the report reveals some really interesting adaptations that have occurred in these spiny  frogs, most notably the Nanorana species. These frogs are well adapted to life at high-elevation. As frogs, their life cycle is tied to the water environment. However, unlike the rivers and lakes of the lowlands, the waters of high elevation mountains moves fast, which can create some real problems for holding onto a mate. But the Nanorana have evolved some interesting adaptations. The most notable one is that the male frogs have large forearms (see photo) and spines on their chests, allowing them to establish a firm grip on the females despite the rapid rush of water. These features are largely absent in theQuasipaa group.  Other adaptations to a cold, oxygen-deprived environment, include evidence of organ degeneration, although the authors of the paper are careful to note that additional studies of these adaptations are needed. Overall, however, the research does provide an interesting look at how new species form due to geographic isolation. 

Additional resources

UC Berekely News Release (August 2010)
Understanding Evolution entry on patterns of speciation 
PNAS article on spiny frog evolution  (full-text available):Che,
J., Zhou, W., Hu, J., Yan, F., Papenfuss, T., Wake, D., & Zhang, Y.
(2010). From the Cover: Spiny frogs (Paini) illuminate the history of
the Himalayan region and Southeast Asia Proceedings of the National Academy of Sciences, 107 (31), 13765-13770 DOI: 10.1073/pnas.1008415107
McGraw-Hill material on allopatric speciation .


... Read more »

Che, J., Zhou, W., Hu, J., Yan, F., Papenfuss, T., Wake, D., & Zhang, Y. (2010) From the Cover: Spiny frogs (Paini) illuminate the history of the Himalayan region and Southeast Asia. Proceedings of the National Academy of Sciences, 107(31), 13765-13770. DOI: 10.1073/pnas.1008415107  

  • August 20, 2010
  • 12:32 PM
  • 1,031 views

Study: In Communicating about Nano and GMOs, Do the Frames or the Facts Matter?

by Matthew C. Nisbet in Age of Engagement

When attempting to communicate effectively with the public about a science-related debate, which is more important, framing the message or conveying science-based facts about the topic?  A forthcoming study (Word) at the Journal of Communication by Northwestern University researchers James Druckman and Toby Bolsen sheds new light on this long standing question.
As I will be highlighting at this blog, previous research consistently finds that the public typically form opinions in the absence of factual information, instead relying on mental short-cuts based on personal experience, values, and the selective presentation—or “framing”--of an issue. 
Frames influence perceptions and decisions because they focus on just one dimension of a complex topic over another, in the process communicating why an issue matters, why it might be personally relevant, and why a related action might lead to specific benefits or risks. 
Understanding and applying research on framing is particularly relevant to engaging the public on emerging issues such as nanotechnology and genetic engineering, but it also applies to communicating about entrenched policy debates such as climate change.  For example, in a recent study I conducted with Ed Maibach and colleagues, we find that when climate change is re-framed as a health problem rather than an environmental one, this re-interpretation is evaluated favorably and positively by a broad cross-section of Americans.  A frame in essence switches the train of thought for an audience, leading to a different set of attributions and conclusions.
Framing is an unavoidable aspect of human communication.  There is no such thing as unframed information.  On science-related issues, this idea is difficult to grasp for some advocates and scientists who still view communication through the lens of what scholars call the “deficit model” which assumes that opinion formation is a direct consequence of knowledge (or alternatively ignorance).  If the public only better understood the facts of a scientific topic they would more likely view the issue as scientists do and controversy would go away.
There is no question that deliberate decisions to selectively frame an issue can be used to deceive, but they can also be used to more effectively explain and engage audiences, boosting interest, attention, and learning.  As an example, in a recently published book chapter, I discussed the audience research approach that the National Academies used in framing the structure of a report on the teaching of evolution in schools (PDF). 
A second example is our recent research on the potential to re-frame climate as a health problem.  Not only does this new focus likely increase personal significance and relevance among Americans but it also communicates about objectively real and scientifically well-documented health risks that the public should know about.   It also starts to promote greater attention to adaptation policies and strategies--such as evacuation procedures, water and agricultural sanitation policies, improved housing, cooling stations during heat waves, and new transportation infrastructures-- that are needed to protect people and communities and that also result in healthier and higher quality lives.
Frames vs. Facts on Nano and GMOs
The forthcoming study by James Druckman and Toby Bolsen provides new understanding and data on how frames influence public perceptions and decisions about emerging areas of science.  Later today, I will post an interview with Druckman about his research (read it here).  In the rest of this post, I discuss and provide background on the study.
Druckman and Bolsen were interested in understanding whether the inclusion of facts--specifically reference to the findings of a scientific study---added additional power and influence to the framing of nanotechnology and genetically modified food. 
These issues--like many science debates--are often debated and talked about in terms of benefits and risks, typically in very general terms without much reference to actual scientific research.  Does providing more precise information about scientific findings relative to benefits and risks matter to public judgments or are more general assertions what really drive perceptions?
Importantly, Druckman and Bolsen also wanted to know whether after a frame was set on an issue, how did subjects then interpret information about scientific studies on the topic?  Were subjects open to re-considering their views or did they interpret the studies as fitting with their pre-conceived opinion?
On election day in 2008, Druckman and Bolsen assembled 20 teams of students to conduct exit polls of 621 voters in the Chicago region, querying voters on their perceptions of carbon nanotubes (CNTs) and genetically-modified foods (GMOs).  For the interviews, voters were randomly assigned to separate frame and issue conditions. 
For different groups of voters, CNTs or GMOS were defined using either a “fact” free frame or fact-based frame, with an emphasis on either benefits or risks.  In the case of CNTs, respondents were read the following introduction followed by one of the following frames, depending on their assigned experimental condition.  A similar method was used on GMOs (see the paper for more details):

One of the most pressing issues facing the nation—as has been clear from the election—concerns the limitations to our energy supply (e.g., with regard to coal, oil and natural gas).  One approach to addressing this issue is to rely more on carbon nanotubes or CNTs. CNTs are tiny graphite with distinct chemical properties. They efficiently convert sunlight into electricity, and thus, serve as an alternative to coal, oil, and natural gas. The uncertain long-term effects of CNTs are the subject of continued study and debate.

Fact Free Benefits of Nanotechnology

Most agree that the most important implication of CNTs concerns how they will affect energy cost and availability. A recent study on cost and availability showed that CNTs will double the efficiency of solar cells in the coming years.

Fact Free Risks of Nanotechnology

Most agree that the most important implication of CNTs concerns their unknown long-run implications for human health. A recent study on health showed that mice injected with large quantities of CNTs reacted in the same way as they do when injected with asbestos.

Fact-based Benefits of Nanotechnology

A recent study on cost and availability showed that CNTs will double the efficiency of solar cells in the coming years.

Fact-based Risks of Nanotechnology

A recent study on health showed that mice injected with large quantities of CNTs reacted in the same way as they do when injected with asbestos.

Subjects were asked on a 7 point scale to express their level of support or opposition for either CNTs or GMOs depending on the frame condition.  Other questions measuring pre-existing levels of scientific knowledge, demographic background, and generalized views about science were asked and used as controls in their analysis.
After completing the interviews on Election Day, participants were re-contacted 10 days later.  At this time, depending on their frame condition, they were presented with reminder information about CNTs and GM foods.  Then, for each technology, respondents evaluated the “effectiveness” of three distinct factually based scientific studies “in providing information or making an argument” (on 7-point scales with higher scores indicating increased effectiveness). Respondents also rated the extent to which each study opposed or supported the technology (on 7-point scales with higher scores indicating increased effectiveness), and re-reported their overall support for each technology.
In their analysis Druckman and Bolsen find that on both issues, frames that emphasize general statements about either the benefits or the risks of the technology influenced perceptions, with slightly stronger effects for the risk conditions.  Yet importantly, when frames included “facts” that reference specific findings from scientific studies, the inclusion did not significantly enhance the power of the frames. 
As they conclude, contrary to the strong emphasis of the deficit model on promoting scientific literacy as the key to communication, referencing facts adds little to how framing influences individuals’ opinions about new technologies.
Finally, when they analyzed the results of the follow-up interviews, they found that how subjects evaluated information presented about research on the technologies was strongly influenced by their pre-existing views.  In other words, much like a strong Democrat or Republican tends to view even favorable news coverage as reinforcing their pre-existing opinion of an opposing party's cand... Read more »

  • August 20, 2010
  • 10:43 AM
  • 1,114 views

Healthy Lifestyle and Mortality Risk in Men

by William Yates, M.D. in Brain Posts

In 2001 I went to the Cooper Clinic in Dallas, Texas for an executive physical examination.  Although not for everyone, I had good experience and I’m a strong supporter of their research program.  I have participated in mail survey research studies since my physical examination.  One recent publication from the their Aerobics Center Longitudinal Study caught my eye.Epidemiological studies typically look for risk factors for a disease or death.  Fewer studies try to identify protective factors or the contribution of healthy lifestyle behaviors to morbidity and mortality.   This study examined five healthy lifestyle/fitness variables:Body mass index (BMI) between 18.5 and 25Not a current smokerModerate alcohol intake (1 to 14 drinks per week)Top 2/3rd in test of cardiorespiratory fitness (corrected for age)Moderate to high daily physical activity Physical exams at the Cooper Clinic typically includes a treadmill exercise test.   Participants were ranked based on treadmill time with those in the top two thirds were assigned the protective fitness factor.   Moderate physical activity was relatively easy to meet.  Subjects reporting no aerobic activities in the last 3 months were classified as low physical activity.  Any activity above this classified as moderate or high.Mortality was ascertained through the use of the National Death Index.  The study uses a regular query of the National Death Index to follow mortality for those who have been through the Cooper Clinic.  During the follow-up period of the study, 2642 deaths occurred in a sample of 38, 110.Final estimates of mortality risk corrected for age,  presence of hypertension, diabetes and hypercholesterolemia.  The study found an additive effect so it was better to have more healthy lifestyle variables.  The risk for death by number of healthy lifestyle factors was compared to those with no protective factors set at 1.0.No positive health factors            1.0One positive health factor           .78         Two positive health factors         .61Three positive health factors      .54Four positive health factors        .43Five positive health factors         .39 The data show that having all five positive health factors reduced mortality by 61%, having 3 reduced mortality by 46% and having one reduced mortality by 22%.  This study is helpful in getting an estimation of the size of the effect of these types of healthy lifestyle behaviors.  The study design does not allow concluding that increasing healthy lifestyle behavior in midlife actually reduces mortality risk.  But a previous study by King et al, found that U.S. men switching to a healthy lifestyle of 5 fruits and vegetables daily, getting BMI between 18.5 and 25, not smoking and exercising at least 2.5 hours per week reduced all-cause mortality by 40% in a 4-year follow-up.So the epidemiological data is becoming more clear.  Healthy lifestyle factors do matter and making a change towards a more healthy lifestyle appears to have a significant effect on reducing risk of premature death.Photo of Triathlete on Bicycle Courtesy of Yates PhotographyByun W, Sieverdes JC, Sui X, Hooker SP, Lee CD, Church TS, & Blair SN (2010). Effect of Positive Health Factors and All-Cause Mortality in Men. Medicine and science in sports and exercise PMID: 20142782King DE, Mainous AG 3rd, & Geesey ME (2007). Turning back the clock: adopting a healthy lifestyle in middle age. The American journal of medicine, 120 (7), 598-603 PMID: 17602933... Read more »

Byun W, Sieverdes JC, Sui X, Hooker SP, Lee CD, Church TS, & Blair SN. (2010) Effect of Positive Health Factors and All-Cause Mortality in Men. Medicine and science in sports and exercise. PMID: 20142782  

King DE, Mainous AG 3rd, & Geesey ME. (2007) Turning back the clock: adopting a healthy lifestyle in middle age. The American journal of medicine, 120(7), 598-603. PMID: 17602933  

  • August 20, 2010
  • 10:33 AM
  • 1,232 views

Cocoa drink reduces DOMS. Really? Well, Maybe...

by mc in begin to dig (b2d)

What if cocoa in a drink of protein and carbs could mitigate DOMS - delayed onset muscle soreness? This is what researchers in a newly published Aug 2010 study have explored. And thank goodness, since most of us have struggled with DOMS at one time or another - new routine and next day or next few days our muscles pay for it. We walk like cowboys coming off a long jaunt in the saddle. Could ... Read more »

Karp JR, Johnston JD, Tecklenburg S, Mickleborough TD, Fly AD, & Stager JM. (2006) Chocolate milk as a post-exercise recovery aid. International journal of sport nutrition and exercise metabolism, 16(1), 78-91. PMID: 16676705  

Wiswedel, I., Hirsch, D., Kropf, S., Gruening, M., Pfister, E., Schewe, T., & Sies, H. (2004) Flavanol-rich cocoa drink lowers plasma F2-isoprostane concentrations in humans. Free Radical Biology and Medicine, 37(3), 411-421. DOI: 10.1016/j.freeradbiomed.2004.05.013  

Green MS, Corona BT, Doyle JA, & Ingalls CP. (2008) Carbohydrate-protein drinks do not enhance recovery from exercise-induced muscle injury. International journal of sport nutrition and exercise metabolism, 18(1), 1-18. PMID: 18272930  

  • August 20, 2010
  • 10:21 AM
  • 600 views

Prehistoric Poo Linked Dinosaurs to Snails

by Brian Switek in Dinosaur Tracking

One of the many reasons I love paleontology is that every now and then I stumble across a paper on some aspect of ancient life I had never considered before. There is much more to the science than descriptions of new species, and one of the studies that most recently caught my eye carried the [...]... Read more »

  • August 20, 2010
  • 10:02 AM
  • 862 views

Schizophrenia, Genes and Environment

by Neuroskeptic in Neuroskeptic

Schizophrenia is generally thought of as the "most genetic" of all psychiatric disorders and in the past 10 years there have been heroic efforts to find the genes responsible for it, with not much success so far.A new study reminds us that there's more to it than genes alone: Social Risk or Genetic Liability for Psychosis? The authors decided to look at adopted children, because this is one of the best ways of disentangling genes and environment.If you find that the children of people with schizophrenia are at an increased risk of schizophrenia (they are), that doesn't tell you whether the risk is due to genetics, or environment, because we share both with our parents. Only in adoption is the link between genes and environment broken.Wicks et al looked at all of the kids born in Sweden and then adopted by another Swedish family, over several decades (births 1955-1984). To make sure genes and environment were independent, they excluded those who were adopted by their own relatives (i.e. grandparents), and those lived with their biological parents between the ages of 1 and 15. This is the kind of study you can only do in Scandinavia, because only those countries have accessible national records of adoptions and mental illness...What happened? Here's a little graph I whipped up:Brighter colors are adoptees at "genetic risk", defined as those with at least one biological parent who was hospitalized for a psychotic illness (including schizophrenia but also bipolar disorder.) The outcome measure was being hospitalized for a non-affective psychosis, meaning schizophrenia or similar conditions but not bipolar.As you can see, rates are much higher in those with a genetic risk, but were also higher in those adopted into a less favorable environment. Parental unemployment was worst, followed by single parenthood, which was also quite bad. Living in an apartment as opposed to a house, however, had only a tiny effect.Genetic and environmental risk also interacted. If a biological parent was mentally ill and your adopted parents were unemployed, that was really bad news.But hang on. Adoption studies have been criticized because children don't get adopted at random (there's a story behind every adoption, and it's rarely a happy one), and also adopting families are not picked at random - you're only allowed to adopt if you can convince the authorities that you're going to be good parents.So they also looked at the non-adopted population, i.e. everyone else in Sweden, over the same time period. The results were surprisingly similar. The hazard ratio (increased risk) in those with parental mental illness, but no adverse circumstances, was 4.5, the same as in the adoption study, 4.7.For environment, the ratio was 1.5 for unemployment, and slightly lower for the other two. This is a bit less than in the adoption study (2.0 for unemployment). And the two risks interacted, but much less than they did in the adoption sample.However, one big difference was that the total lifetime rate of illness was 1.8% in the adoptees and just 0.8% in the nonadoptees, despite much higher rates of unemployment etc. in the latter. Unfortunately, the authors don't discuss this odd result. It could be that adopted children have a higher risk of psychosis for whatever reason. But it could also be an artefact: rates of adoption massively declined between 1955 and 1984, so most of the adoptees were born earlier, i.e. they're older on average. That gives them more time in which to become ill.A few more random thoughts:This was Sweden. Sweden is very rich and compared to most other rich countries also very egalitarian with extremely high taxes and welfare spending. In other words, no-one in Sweden is really poor. So the effects of environment might be bigger in other countries.On the other hand this study may overestimate the risk due to environment, because it looked at hospitalizations, not illness per se. Supposing that poorer people are more likely to get hospitalized, this could mean that the true effect of environment on illness is lower than it appears.The outcome measure was hospitalization for "non-affective psychosis". Only 40% of this was diagnosed as "schizophrenia". The rest will have been some kind of similar illness which didn't meet the full criteria for schizophrenia (which are quite narrow, in particular, they require 6 months of symptoms).Parental bipolar disorder was counted as a family history. This does make sense because we know that bipolar disorder and schizophrenia often occur in the same families (and indeed they can be hard to tell apart, many people are diagnosed with both at different times.)Overall, though, this is a solid study and confirms that genes and environment are both relevant to psychosis. Unfortunately, almost all of the research money at the moment goes on genes, with studying environmental factors being unfashionable.Wicks S, Hjern A, & Dalman C (2010). Social Risk or Genetic Liability for Psychosis? A Study of Children Born in Sweden and Reared by Adoptive Parents. The American journal of psychiatry PMID: 20686186... Read more »

  • August 20, 2010
  • 10:00 AM
  • 759 views

Exploring Information Interaction ‘Context’ with Tefko Saracevic at #IIIX2010

by Anatoliy Gruzd in Social Media Lab

I am writing from the ‘Information Interaction in Context Symposium‘ in New Brunswick (the one in New Jersey, not the one in Canada), the home of Rutgers University. Usually I would wait until a conference is over and the dust is settled before blogging about an event, but in this case I’ll make an exception. Specifically, I would like to share some of the highlights from the keynote speaker while it’s still fresh in my mind.... Read more »

Saracevic, T. (2010) The Notion of Context in "Information Interaction in Context.". Inivited keynote at the conference Information Interaction in Context. info:/

  • August 20, 2010
  • 08:00 AM
  • 1,638 views

Do Environmental Toxins Promote Obesity?

by Arya M. Sharma in Dr. Sharma's Obesity Notes

Our environment is full of man-made chemicals, the biological actions of which we rarely fully understand.
There is now considerable data showing that some of these chemicals may well have biological effects that can potentially change metabolism. These compounds are, therefore, sometimes referred to as “endocrine disrupting chemicals” (EDC) and can potentially promote weight gain and [...]... Read more »

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