Post List

  • October 19, 2010
  • 08:00 AM

Banana domestication revisited

by Jeremy in The Vaviblog

Edible bananas have very few seeds. Wild bananas are packed with seeds; there’s almost nothing there to eat. So how did edible bananas come to be cultivated? The standard story is that some smart proto-farmer saw a spontaneous mutation and then propagated it vegetatively. Once the plant was growing, additional mutants would also be seen [...]... Read more »

  • October 19, 2010
  • 05:39 AM

Did cavemen eat bread?

by Razib Khan in Gene Expression

Food is a fraught topic. In How Pleasure Works Paul Bloom alludes to the thesis that while conservatives fixate on sexual purity, liberals fixate on culinary purity. For example, is it organic? What is the sourcing? Is it “authentic”? Obviously one can take issue with this characterization, especially its general class inflection (large swaths of [...]... Read more »

Anna Revedin, Biancamaria Aranguren, Roberto Becattini, Laura Longo, Emanuele Marconi, Marta Mariotti Lippi, Natalia Skakun, Andrey Sinitsyn, Elena Spiridonova, & Jiří Svoboda. (2010) Thirty thousand-year-old evidence of plant food processing. PNAS. info:/10.1073/pnas.1006993107

  • October 19, 2010
  • 05:33 AM

The role of media discourse framing attitudes towards the use of embryonic stem cells

by SAGE Insight in SAGE Insight

Beliefs about science and news frames in audience evaluations of embryonic and adult stem cell research From Science Communication There has been great global attention to the recent announcement that US doctors have begun the first official trial of using human embryonic stem cells in patients after getting the green light from regulators. The shift [...]... Read more »

  • October 19, 2010
  • 04:39 AM

The Impact of Supply Chain Strategy on Shareholder Value

by Daniel Dumke in SCRM Blog - Supply Chain Risk Management

I had this article marked for some time now and I finally got to read it. It describes the connection between Shareholder Value and the concept of Value Based Management (VBM) and Supply Chain Strategy.
Continue reading "The Impact of Supply Chain Strategy on Shareholder Value"
... Read more »

Christopher, M., & Ryals, L. (1999) Supply Chain Strategy: Its Impact on Shareholder Value. The International Journal of Logistics Management, 10(1), 1-10. DOI: 10.1108/09574099910805897  

  • October 19, 2010
  • 03:07 AM

Wired to be Social

by Glialdance in Glial Dance

Humans are a social species, we interact with other people – aided by language- and exchange information on daily basis. The effects of social isolation have been demonstrated and predicted to be very severe and “de-humanising” in many cases with a long list of adverse effects on cognitive abilities and emotional stability. The question often posed when [...]... Read more »

Umberto Castiello, Cristina Becchio, Stefania Zoia, Cristian Nelini, Luisa Sartori, Laura Blason, Giuseppina D’Ottavio, Maria Bulgheroni, & Vittorio Gallese. (2010) Wired to be Social: the ontogeny of human interaction. PLoS ONE. info:/

  • October 19, 2010
  • 02:20 AM

Patients Group Communication on Facebook a Good Idea?

by Dr Shock in Dr Shock MD PhD

Social networking sites such as Facebook are used for several disease specific information changes. They have become sources of knowledge, support and engagement especially for patients with chronic diseases such as diabetes.
One recent survey indicates patients search the Internet more frequently than they communicate with their doctors about health care questions
Recent research evaluated the [...]

Related posts:Med Schools lack of policies for facebook and twitter use
The Dangers of Facebook or Let’s Be Careful Out There
Facebook and Professionalism
... Read more »

  • October 19, 2010
  • 12:29 AM

Paging Dr. Monarch Mom

by Michael Gutbrod in A Scientific Nature

New research has shown that the ability to medicate exists outside of the realm of humanity.  There goes that God complex.  In the kingdom of life, there are few examples of behavior specifically directed at treating a disease or infection outside of the scribbling your doctor calls a prescription.  However, a new study out of [...]... Read more »

Lefèvre, T., Oliver, L., Hunter, M., & De Roode, J. (2010) Evidence for trans-generational medication in nature. Ecology Letters. DOI: 10.1111/j.1461-0248.2010.01537.x  

  • October 19, 2010
  • 12:19 AM

population genetics, evolution, and ocean ecosystems

by HeathO in We Beasties

I was trained as an Environmental Scientist long before I was at all interested in Microbes. So, I get excited when I come across microbial studies that are environmentally relevant. I get particularly nerd-cited when these studies take place in the ocean. A paper published in PNAS last week describes identifies what may be the [...]... Read more »

Coleman ML, & Chisholm SW. (2010) Ecosystem-specific selection pressures revealed through comparative population genomics. Proceedings of the National Academy of Sciences of the United States of America. PMID: 20937887  

  • October 19, 2010
  • 12:17 AM

Critiquing LaPlant et al, in Nature Neuroscience, Part 2: The sensitization

by Scicurious in Neurotic Physiology

Last week I began a breakdown of this paper. It’s a much more complicated paper than I usually cover round here, and I will also be covering it in more depth than usual, because I think there are a lot of things about it that are worth discussion, and I think that even this kind [...]... Read more »

LaPlant Q, Vialou V, Covington HE 3rd, Dumitriu D, Feng J, Warren BL, Maze I, Dietz DM, Watts EL, Iñiguez SD.... (2010) Dnmt3a regulates emotional behavior and spine plasticity in the nucleus accumbens. Nature neuroscience, 13(9), 1137-43. PMID: 20729844  

  • October 18, 2010
  • 08:21 PM

Smoking bans are good for barkeeps

by PalMD in White Coat Underground

Barkeep and blogger Scribbler has a piece up giving one bartender’s view of New York’s smoking ban.  Since I like Scribbler, I wondered what the data say about the effect of smoking bans on his health.  Cigarette smoke has many harmful physiologic effects, and the data are pretty clear that you don’t have to be [...]... Read more »

Eisner MD, Smith AK, & Blanc PD. (1998) Bartenders' respiratory health after establishment of smoke-free bars and taverns. JAMA : the journal of the American Medical Association, 280(22), 1909-14. PMID: 9851475  

Menzies D, Nair A, Williamson PA, Schembri S, Al-Khairalla MZ, Barnes M, Fardon TC, McFarlane L, Magee GJ, & Lipworth BJ. (2006) Respiratory symptoms, pulmonary function, and markers of inflammation among bar workers before and after a legislative ban on smoking in public places. JAMA : the journal of the American Medical Association, 296(14), 1742-8. PMID: 17032987  

  • October 18, 2010
  • 06:52 PM

The Curious Tale of a Far-Flung Whale

by Laelaps in Laelaps

When marine biologists first spotted the humpback whale AHWC no. 1363, there did not appear to be anything remarkable about her at all. Seen with another female on the Abrolhos Bank off the coast of Brazil on August 7th, 1999, the whale simply stuck around long enough for the scientists to snap a few photographs [...]... Read more »

  • October 18, 2010
  • 05:21 PM

New in PLoS ONE: Citation rates of self-selected vs. mandated Open Access

by Martin Fenner in Gobbledygook

PLoS ONE today published a paper very relevant to Open Access Week (which started today):
Gargouri Y, Hajjem C, Larivière V, Gingras Y, Carr L, Brody T, Harnad S. Self-Selected or Mandated, Open Access Increases Citation Impact for Higher Quality Research. PLoS ONE. 2010;5(10):e13636+. doi:10.1371/journal.pone.0013636.
The paper studied the citation rates of papers from four institutions with the longest-standing self-archiving mandate: Southampton University, CERN, Queensland University of Technology and Minho University. The mandates (instituted between 2002 and 2004) increased the rate of self-archiving in the respective institutional repositories from around 15% to 60%:

Fig 1. Open Access Self-archiving percentages for institutions with self-archiving mandates compared to non-mandated, self-selected controls. doi:10.1371/journal.pone.00136363.g001
The authors then compared the citation rates of self-archived papers from the four institutions published in non-Open Access (OA) journals (mandated OA) to matched papers from the same non-OA journal, volume and year (non-OA). 15% of the latter papers were also available from repositories (self-selected OA). Overall the study examined the citations of 27,197 papers from 1,984 non-OA journals. The study also looked at the influence of other factors that affect citation rates, e.g. article age, journal impact factor or number of references.
The main results of the study are that OA articles are cited more frequently than non-OA articles and that there is no difference in citation rates between mandated and self-archived articles. The authors conclude that OA articles are cited more often not because of self-selection (articles with higher impact more likely become OA), but because of readers cite OA articles more often.
The study is an effort to better understand if and why OA papers are cited more often, the so-called OA Advantage. Unfortunately I feel that the paper comes a little short. Yes, they did a very detailed analysis of the citation behavior, and take into account important cofactors. But the reader is left with the impression that mandatory self-archiving of post-prints in institutional repositories is the only reasonable Open Access strategy, and the introduction and discussion accordingly leave out some important arguments.
The authors fail to mention that not all studies show a citation advantage for OA articles (e.g. the randomized controlled trial by Davis PM et al. 2008), and they only look at self-archiving in institutional repositories (green OA). Not only are there important disclipline-specific repositories such as PubMed Central and ArXiv, but of course also OA journals such as PLoS ONE that published the study (gold OA). And the study only discussed archiving of articles after peer review, even though archiving of preprints is a popular strategy in high-energy physics and related disciplines (and here the self-archiving rate is close to 100%). I also don’t see a discussion of why the self-archiving rate of post-prints in institutions with a mandate is 60% and not close to 100%. And what is wrong if archiving rates are only around 15% if it is left to the researchers to decide? Finally, there are many reasons other than citation rates that make OA worthwhile, including access to the literature for those not working in academic institutions (and maybe never citing a paper), and work that uses the OA literature in new and exciting ways that go beyond citations. For me personally, the OA advantage is much more in these two aspects than in the citation rates of papers.
For me Open Access week is an opportunity to celebrate what has been achieved over the years. But it is equally important to look at the road ahead. There is no “one size fits all” solution for Open Access, and we shouldn’t look away from the things that aren’t working, and the solutions that haven’t been found yet.
Gargouri, Y., Hajjem, C., Larivière, V., Gingras, Y., Carr, L., Brody, T., & Harnad, S. (2010). Self-Selected or Mandated, Open Access Increases Citation Impact for Higher Quality Research PLoS ONE, 5 (10) DOI: 10.1371/journal.pone.0013636
... Read more »

  • October 18, 2010
  • 04:53 PM

Spreading Salmonella—hyper-replicating bacteria act as a reservoir for dissemination

by geekheartsscience in geek!

New research reveals how Salmonella enterica spread in the gut and gallbladder—a subpopulation of Salmonella primed for invasion rapidly replicate in the host cell cytosol such that bacteria-laden cells are extruded out of the epithelial-cell layer releasing invasive Salmonella into the gastrointestinal and biliary lumen. Leigh Knodler and colleagues write that other mucosal-dwelling pathogens could [...]... Read more »

Knodler, L., Vallance, B., Celli, J., Winfree, S., Hansen, B., Montero, M., & Steele-Mortimer, O. (2010) Dissemination of invasive Salmonella via bacterial-induced extrusion of mucosal epithelia. Proceedings of the National Academy of Sciences, 107(41), 17733-17738. DOI: 10.1073/pnas.1006098107  

  • October 18, 2010
  • 02:45 PM

Crabs expose colliding continents

by Lucas in thoughtomics

Every high school student now learns that plate tectonics slowly drive our continents in different directions. Since only the most uncontroversial scientific knowledge finds its way to high school text books, it’s hard to imagine that when the theory of continental drift was proposed by Alfred Wegener in 1912, it was firmly rejected by [...]... Read more »

  • October 18, 2010
  • 02:37 PM

Working and chronic pain

by Bronwyn Thompson in Healthskills: Skills for Healthy Living

If there is one aspect of chronic pain management that has received more attention than returning to work, I don’t know it! In 1995 when I started working at my current workplace, work was almost a dirty word. I was accused at one time of being a ‘Siberian workcamp’ Commandante because some people thought it … Read more... Read more »

Costa-Black, K., Loisel, P., Anema, J., & Pransky, G. (2010) Back pain and work. Best Practice , 24(2), 227-240. DOI: 10.1016/j.berh.2009.11.007  

  • October 18, 2010
  • 02:34 PM

There are more things in heaven and earth, cobber, than are dreamt of in your philosophy

by Alun in AlunSalt

Studying astronomy in culture should be simple. There’s only so much that is visible by the naked eye, and it follows predictable patterns. Modern astronomy means that we can reconstruct what was visible anywhere in the world in human history, within certain boundaries for errors. If we know what happens when, then studying a culture... Read more »

Clarke, P.A. (2007) An Overview of Australian Aboriginal Ethnoastronomy. Archaeoastronomy: The Journal of Astronomy in Culture, 39-58. info:/

  • October 18, 2010
  • 01:19 PM

Chopping bits out of the genome

by Lab Rat in Lab Rat

Generally bacteria genomes tend to be fairly minimal in the amount you can remove from them. Unlike eukaryotes, which can have whole swathes of genome that codes for very little, bacteria, with their limited space for a chromosome, need every gene they can get. They just don't have the space for unnecessary genes.Streptomyces bacteria, however, have bigger genomes and the luxary to invest in genes which are not strictly necessary for bacterial survival. These are called Secondary metabolite genes (as opposed to the necessary primary metabolites) and they code for genes that aren't strictly needed for survival, but instead form an arsenal of weapons for the Streptomyces to deploy. Most Strep are soil-based, and they need the ability to produce secondary metabolites (such as antibiotics) to fight off invading bacteria, and clear terratory to expand their growth into.What has recently been done (very ingeniously) is to remove the secondary metabolism genes from the bacterial species Streptomyces avermitilis creating essentially an 'empty' strep bacteria, that can grow and divide but not produce any of the secretory substances that strep are known for. The researchers managed to cut an entire 1.5Mb of DNA right out of the genome - helped by the fact that all the secondary metabolite genes cluster together on one side of the chromosome.They did this using a common molbio technique, the cre-lox system. "Lox" is an area of DNA and "cre" is the protein that very specifically cuts DNA at the Lox site - it acts like a pair of scissors. They put a Lox site on either end of the DNA that codes for secondary metabolites (using a techinque called recombination in order to attach the lox into the chromosome) along with the DNA for the Cre protein under an inducible promoter. Once the bacteria had grown, they activated Cre production, which then cut the unwanted DNA out of the bacteria. This technique was amazingly successful and is shown diagramatically below (picture from the reference):The avimitilis now contains no secondary metabolites at all, which makes a wonderful 'empty' system to use for studying how secondary metabolites are made. Genes from other bacteria, or even some of the removed genes, can be added back in, piece at a time, to see how much of the gene is necessary for metabolite production, and which regulatory pathways are the most important. Creating an empty cell also has potential implications for biotechnology, after all when trying to produce antibiotics you want the cell working as hard as possible just to produce your product, not wasting time and resources on other metabolites!I'm really impressed at this kind of large scale synthetic-biology. It may be an area I end up going into in the near future...---Komatsu M, Uchiyama T, Omura S, Cane DE, & Ikeda H (2010). Genome-minimized Streptomyces host for the heterologous expression of secondary metabolism. Proceedings of the National Academy of Sciences of the United States of America, 107 (6), 2646-51 PMID: 20133795... Read more »

Komatsu M, Uchiyama T, Omura S, Cane DE, & Ikeda H. (2010) Genome-minimized Streptomyces host for the heterologous expression of secondary metabolism. Proceedings of the National Academy of Sciences of the United States of America, 107(6), 2646-51. PMID: 20133795  

  • October 18, 2010
  • 01:00 PM

Riding the Spore Wind

by Moselio Schaechter in Small Things Considered

Sooner or later, but usually sooner, anyone dealing with fungi will have to deal with the issue of spore dispersal. Many fungi, mushrooms included, are a spore’s way of spreading spores through the environment. They do this in varied and universally ingenious ways. Spores, like mammalian sperm, are made in excess, which enhances the chances of some “making it.” Anybody who has made the spore print from a mushroom can attest to the large number of spores produced. This is true not only for the Basidiomycetes, to which most mushrooms belong, but also for the larger Ascomycetes, (the group that includes not only yeast but also most molds, as well as larger organisms such as the cup fungi).

For dispersal to be efficient, the spores must travel a certain distance from their place of origin. They are ejected with great force, sometimes challenging our belief.... Read more »

Roper M, Seminara A, Bandi MM, Cobb A, Dillard HR, & Pringle A. (2010) Dispersal of fungal spores on a cooperatively generated wind. Proceedings of the National Academy of Sciences of the United States of America. PMID: 20880834  

  • October 18, 2010
  • 12:23 PM

Internal coarse-graining of molecular systems

by evopapers in evopapers

Feret J, Danos V, Krivine J, Harmer R, & Fontana W (2009). Internal coarse-graining of molecular systems. Proceedings of the National Academy of Sciences of the United States of America, 106 (16), 6453-8 PMID: 19346467, PNAS page, Supporting Information.   Models of molecular dynamics suffer from combinatorial explosion: the phenomenon of an exponential number of [...]... Read more »

Feret J, Danos V, Krivine J, Harmer R, & Fontana W. (2009) Internal coarse-graining of molecular systems. Proceedings of the National Academy of Sciences of the United States of America, 106(16), 6453-8. PMID: 19346467  

  • October 18, 2010
  • 12:00 PM

Guest Post: The fine-structure constant is probably constant by Sean Carroll

by S.C. Kavassalis in The Language of Bad Physics

This is the first guest post on The Language of Bad Physics by Cosmic Variance‘s Sean Carroll.  This post is cross-posted on Cosmic Variance.
A few weeks ago there was a bit of media excitement about a somewhat surprising experimental result. Observations of quasar spectra indicated that the fine structure constant, the parameter in physics that describes the strength of electromagnetism, seems to be slightly different on one side of the universe than on the other. The preprint is here.
Remarkable, if true. The fine structure constant, usually denoted α, is one of the most basic parameters in all of physics, and it’s a big deal if it’s not really constant. But how likely is it to be true? This is the right place to trot out the old “extraordinary claims require extraordinary evidence” chestnut. It’s certainly an extraordinary claim, but the evidence doesn’t really live up to that standard. Maybe further observations will reveal truly extraordinary evidence, but there’s no reason to get excited quite yet.
Chad Orzel does a great job of explaining why an experimentalist should be skeptical of this result. It comes down to the figure below: a map of the observed quasars on the sky, where red indicates that the inferred value of α is slightly lower than expected, and blue indicates that it’s slightly higher. As Chad points out, the big red points are mostly circles, while the big blue points are mostly squares. That’s rather significant, because the two shapes represent different telescopes: circles are Keck data, while squares are from the VLT (“Very Large Telescope”). Slightly suspicious that most of the difference comes from data collected by different instruments.

But from a completely separate angle, there is also good reason for theorists to be skeptical, which is what I wanted to talk about. Theoretical considerations will always be trumped by rock-solid data, but when the data are less firm, it makes sense to take account of what we already think we know about how physics works.
The crucial idea here is the notion of a scalar field. That’s just fancy physics-speak for a quantity which takes on a unique numerical value at every point in spacetime. In quantum field theory, scalar fields lead to spinless particles; the Higgs field is a standard example. (Other particles, such as electrons and photons, arise from more complicated geometric objects — spinors and vectors, respectively.)
The fine structure constant is a scalar field. We don’t usually think of it that way, since we usually reserve the term “field” for something that actually varies from place to place rather than remaining constant, but strictly speaking it’s absolutely true. So, while it would be an amazing and Nobel-worthy result to show that the fine structure constant were varying, it wouldn’t be hard to fit it into the known structure of quantum field theory; you just take a scalar field that is traditionally thought of as constant and allow it to vary from place to place and time to time.
That’s not the whole story, of course, When a field varies from point to point, those variations carry energy. Think of pulling a spring, or twisting a piece of metal. For a scalar field, there are three important contributions to the energy: kinetic energy from the field varying in time, gradient energy from the field varying in space, and potential energy associated with the value of the field at every point, unrelated to how it is changing.
For the fine structure constant, the observations imply that it changes by only a very tiny bit from one end of the universe to the other. So we really wouldn’t expect the gradient energy to be very large, and there’s correspondingly no reason to expect the kinetic energy to matter much.
The potential energy is a different matter. The potential is similar to the familiar example of a ball rolling in a hill; how steep the potential is near its minimum is related to the mass of the field. For most scalar fields, like the Higgs field, the potential is extremely steep; this means that if you displace the field from the minimum of its potential by just a bit, it will tend to immediately roll back down.

A priori, we don’t know ahead of time what the potential should look like; specifying it is part of defining the theory. But quantum field theory gives us clues. At heart, the world is quantum, not classical; the “value” of the scalar field is actually the expectation value of a quantum operator. And such an operator gets contributions from the intrinsic vibrations of all the other fields that it couples to — in this case, every kind of charged particle in the universe. What we actually observe is not the “bare” form of the potential, but the renormalized value, which takes into account the accumulated effects of various forms of virtual particles popping in and out of the quantum vacuum.
The basic effect of renormalization on a scalar field potential is easy to summarize: it makes the mass large. So, if you didn’t know any better, you would expect the potential to be as steep as it could possibly be — probably up near the Planck scale. The Higgs boson probably has a mass of order a hundred times the mass of a proton, which sounds large — but it’s actually a big mystery why it isn’t enormously larger. That’s the hierarchy problem of particle physics.
So what about our friend the fine structure constant? Well, if these observations are correct, the field would have to have an extremely tiny mass — otherwise it wouldn’t vary smoothly over the universe, it would just slosh harmlessly around the bottom of its potential. Plugging in numbers, we find that the mass has to be something like 10-42 GeV or less, where 1 GeV is the mass of the proton. In other words: extremely, mind-bogglingly small.
But there’s no known reason for the mass of the scalar field underlying the fine structure constant to be anywhere near that small. This was established in some detail by Banks, Dine, and Douglas. They affirmed our intuition, that a tiny change in the fine structure constant should be associated with a huge change in potential energy.
Now, there are loopholes — there are always loopholes. In this case, you could possibly prevent those quantum fluctuations from renormalizing your scalar-field potential simply by shielding the field from interactions with other fields. That is, you can impose a symmetry that forbids the field from coupling to other forms of matter, or only lets it couple in certain very precise ways; then you could at least imagine keeping the mass small. That’s essentially the strategy behind the supersymmetric solution to the hierarchy problem.
Problem is, that route is a complete failure when we turn to the fine structure constant, for a very basic reason: we can’t prevent it from coupling to other fields, it’s the parameter that governs the strength of electromagnetism! So like it or not, it will couple to the electromagnetic field and all charged particles in nature. I talked about this in one of my own papers from a few years ago. I was thinking about time-dependent scalars, not spatially-varying ones, but the principles are precisely the same.
That’s why theorists are skeptical of this claimed result. Not that it’s impossible; if the data stand up, it will present a serious challenge to our theoretical prejudices, but that will doubtless goad theorists into being more clever than usual in trying to explain it. Rather, the point is that we have good reasons to suspect that the fine structure constant really is constant; it’s not just a fifty-fifty kind of choice. And given those good reasons, we need really good data to change our minds. That’s not what we have yet — but what we have is certainly more than enough motivation to keep searching.

... Read more »

J. K. Webb, J. A. King, M. T. Murphy, V. V. Flambaum, R. F. Carswell, & M. B. Bainbridge. (2010) Evidence for spatial varia. arXiv. arXiv: 1008.3907v1

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