Post List

  • October 12, 2010
  • 05:30 AM

Pakistan’s nuclear weapons program and implications for US national security

by SAGE Insight in SAGE Insight

From International Relations Pakistan’s nuclear weapons program causes concern for a variety of reasons and in particular generates threats to US national security. This article outlines how the deep animosity between Pakistan and India has been a key driving force behind the nuclear program. They have fought three major wars against each other: India is [...]... Read more »

  • October 12, 2010
  • 02:21 AM

Video podcasts not ready to replace lectures

by Dr Shock in Dr Shock MD PhD

This disappointing result is recently published online at BMC medical education. Teachers are eager to use new information technology to teach. When I’m doing a lecture at our Med School, these lectures are made to podcasts and posted on Blackboard. Together with the slides students can rehears or listen to the lecture after worths when [...]

Related posts:iTunes can Replace Professors
Book review: Blogs, wikis, podcasts and other powerful web tools for classrooms
Twitter during Lectures part 2
... Read more »

  • October 12, 2010
  • 02:00 AM

Research Blogging: The Postpartum Brain

by Dr Becca in Fumbling Towards Tenure Track

I describe a new paper that looks at spine density and cognitive function in the brains of postpartum female rats.... Read more »

  • October 11, 2010
  • 08:52 PM

Substantial equivalence

by Anastasia Bodnar in Biofortified

One important concept that is used in most countries to regulate products of genetic engineering is substantial equivalence. The way to determine substantial equivalence is comparative assessment. What do substantial equivalence and comparative assessment mean? Depending on the source we use, we might find different definitions and different opinions of how useful they are in determining the safety of products of genetic engineering. The USDA provides information on Food Safety Assessment and Considerations as part Continue reading...... Read more »

Kogel KH, Voll LM, Schäfer P, Jansen C, Wu Y, Langen G, Imani J, Hofmann J, Schmiedl A, Sonnewald S.... (2010) Transcriptome and metabolome profiling of field-grown transgenic barley lack induced differences but show cultivar-specific variances. Proceedings of the National Academy of Sciences of the United States of America, 107(14), 6198-203. PMID: 20308540  

Baker JM, Hawkins ND, Ward JL, Lovegrove A, Napier JA, Shewry PR, & Beale MH. (2006) A metabolomic study of substantial equivalence of field-grown genetically modified wheat. Plant biotechnology journal, 4(4), 381-92. PMID: 17177804  

  • October 11, 2010
  • 07:53 PM

Costridium virulence: What's essential?

by Michael Clarkson in Conformational Flux

Clostridium difficile is an intestinal pathogen that causes diarrhea in hospitals and other healthcare settings (including nursing homes). Present as a commensal bacterium in a significant fraction of the population, C. difficile is usually rather harmless, its numbers suppressed by competition with the intestinal flora. When its competitors are decimated by antibiotics, however, C. difficile flourishes, releasing toxins that cause inflammation and diarrhea, which can be dangerous because the individuals suffering these effects are often already ill. There has been conflicting information, however, as to which of C. difficile's toxins are necessary to cause disease. A paper in the recent Nature (1) aims to resolve the question.
The two best-characterized C. difficile toxins (TcdA and TcdB) have the same general arrangement and function (and ~45% identical AA sequence). An N-terminal glucosylating domain attacks the cytoskeleton of host cells by inactivating Rho GTPases, a C-terminal domain mediates binding and uptake by the host cells, and a protease domain in the middle releases the glucosylating domain to do its work. Since these proteins appear to serve redundant functions, one might expect that both would support virulence. However, preceding work in the field has variously identified TcdA or TcdB as a key virulence factor (2,3). Differences in methodology and materials have contributed to the confusion, in part because different kinds of cells seem to be more or less susceptible to particular toxins, and different strains of C. difficile might have different behaviors.

Kuehne et al. aim to relieve some of the confusion by removing a subset of these confounding factors. In a single strain of C. difficile they inactivated the genes for either TcdA, TcdB, or both by inserting introns into them. An intron would be no problem for a eukaryote, but bacteria can't handle them, so this has the effect of eliminating the expression of the gene. They then tested the toxin mixtures shed by the bacteria against cultured human and monkey cells. As expected, A-B- bacteria (with both toxins knocked out) showed no toxicity towards the cells, but A-B+ and B+A- variants were toxic towards both kinds of cells to roughly the same degree. This suggests that both toxins are sufficient for virulence.

This implication was largely backed up by a subsequent experiment in hamsters. The animals were dosed with an antibiotic and then infected with C. difficile spores of a single strain. Colonization occurred (in every case but one) within three days. The hamsters infected with A-B- C. difficile remained asymptomatic until the end of the experiment, but the recipients of the other strains all perished within a week. The A+B- group survived somewhat longer, but not dramatically so; again, this supports the interpretation that both proteins are sufficient for virulence.

This contrasts with an earlier study published in Nature (2) where it was shown that deletion of the B toxin protected hamsters from C. difficile-associated disease, using very similar protocols. Kuehne et al. attribute the differences in their results to the hamsters or genetic variation in the C. difficile strains used. While the virulence of the B- strain in this experiment was slightly attenuated, all colonized hamsters still died in relatively short order, and in human beings the situation might well be reversed, since cultured human cells are more vulnerable to toxin A.

The results of Kuehne et al. largely agree with earlier experiments (3) and with what one would naturally expect of two very similar toxins being released by the same organism. While susceptibility to a particular toxin may vary with characteristics of the host species or cell type, it seems likely that both toxins are capable of supporting virulence. While it is to be hoped that additional research will clarify the reasons for the discrepancy between these two experiments, efforts to treat C. difficile-associated disease by attacking the toxins should proceed with the assumption that both must inactivated. Thanks to their functional and sequence similarity this will hopefully not be too much of a complication.

1. Kuehne, S., Cartman, S., Heap, J., Kelly, M., Cockayne, A., & Minton, N. (2010). The role of toxin A and toxin B in Clostridium difficile infection Nature, 467 (7316), 711-713 DOI: 10.1038/nature09397

2. Lyras, D., O’Connor, J., Howarth, P., Sambol, S., Carter, G., Phumoonna, T., Poon, R., Adams, V., Vedantam, G., Johnson, S., Gerding, D., & Rood, J. (2009). Toxin B is essential for virulence of Clostridium difficile Nature, 458 (7242), 1176-1179 PMCID: PMC2679968 OPEN ACCESS

3. Voth, D., & Ballard, J. (2005). Clostridium difficile Toxins: Mechanism of Action and Role in Disease Clinical Microbiology Reviews, 18 (2), 247-263 PMCID: PMC1082799 OPEN ACCESS... Read more »

Kuehne, S., Cartman, S., Heap, J., Kelly, M., Cockayne, A., & Minton, N. (2010) The role of toxin A and toxin B in Clostridium difficile infection. Nature, 467(7316), 711-713. DOI: 10.1038/nature09397  

  • October 11, 2010
  • 06:59 PM

This Week in the Universe: October 5th – October 11th

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

Astrophysics and Gravitation:
Early Universe was Overheated, says NASA
Michael Shull, Kevin France, Charles Danforth, Britton Smith, & Jason Tumlinson (2010). Hubble/COS Observations of the Quasar HE 2347-4342: Probing the Epoch of He II Patchy Reionization at Redshifts z = 2.4-2.9 arXiv arXiv: 1008.2957v1
Credit: NASA/Michael Shull, University of Colorado
From the Press Release:
During a period of universal warming 11 billion years ago, quasars — the brilliant core of active galaxies — produced fierce radiation blasts that stunted the growth of some dwarf galaxies for approximately 500 million years.  This important conclusion comes from a team of astronomers that used the new capabilities of NASA’s Hubble Space Telescope to probe the invisible, remote universe. The team’s results will be published in… The Astrophysical Journal.
For more, see Hubble Astronomers Uncover an Overheated Early Universe.
Dark Matter, Neutron Stars, and Strange Quark Matter, Oh My!
Perez-Garcia, M., Silk, J., & Stone, J. (2010). Dark Matter, Neutron Stars, and Strange Quark Matter Physical Review Letters, 105 (14) DOI: 10.1103/PhysRevLett.105.141101
The abstract:
We show that self-annihilating weakly interacting massive particle (WIMP) dark matter accreted onto neutron stars may provide a mechanism to seed compact objects with long-lived lumps of strange quark matter, or strangelets, for WIMP masses above a few GeV. This effect may trigger a conversion of most of the star into a strange star. We use an energy estimate for the long-lived strangelet based on the Fermi-gas model combined with the MIT bag model to set a new limit on the possible values of the WIMP mass that can be especially relevant for subdominant species of massive neutralinos.
For more, see Does dark matter trigger strange stars?.
High Energy Physics and Particles:
Hey, this isn’t research news!
Yeah, it’s not… But, for anyone who will be in Manchester from October 23rd – 27th, 2010 should make sure they check out Super K Sonic Booooum!
This large installation consists of a 22 meter long ‘river’ of water running through a tunnel lined with thousands of silver balloons (photomultiplier tubes). Members of the public embark on a boat, pulled through the tunnel on a submerged track using a pulley system, with sound and lighting effects, and with an expert particle physicist navigator as a guide. On the journey they learn of neutrinos, their role in the Universe and how scientists detect them. All crew members must first don white Tyvek suits, wellies and hard hats or else face the wrath of Nelly the security chief, at the entrance of the tunnel. This installation is designed to deliver physically thrilling experiences; emerging the audience on a journey through the physics of the Universe.
Workshop on Sunday 24 October – 2pm – 4pm
Capture the Invisible: Craft and Science in particle physics.
In this workshop you will get the chance to make your own photomultiplier tube to capture the invisible in your own bedroom! Designed by Nelly Ben Hayoun in collaboration with Dr Jonathan Perkin, physicist and glassblower Jochen Holz
For more, see Super K Sonic Booooum.
SuperB Project Preparing for Construction!
SuperB Collaboration, E. Grauges et al., Francesco Forti, Blair N. Ratcliff, & David Aston (2010). SuperB Progress Reports — Detector arXiv arXiv: 1007.4241v1
It looks like funding for the SuperB Collaboration will come through and see the new experiment built in Frascati.  I hope the Italians take this great opportunity to make many “flavour country” jokes.
From the press release:
The most elementary components of matter, quarks and leptons, have been found, as the result of 100 years of research, to be organized into three replicating “families”. The reason for this specific number or organization remains a full mystery. Flavor physics, the detailed understanding of the relationship between these families and the comparison between properties of matter and antimatter, is one of the most promising ways to explore new physics, quite complementary to the energy frontier research most notably pursued at the CERN LHC collider. Different kinds of new physics have different effects on rare decays of bottom and charmed quarks and of heavy tau leptons. These particles are all produced at SuperB in unparalleled abundance, making possible for the first time measurements of the precision required to be sensitive to the details of new physics uncovered at CERN.
For more, see SuperB project moves forward, preparing for construction.
Bonner Nuclear Lab to Study Quark-Gluon Plasma
Credit: Frank Geurts/Rice University
It was a good week to get funding for high-energy experiments.
From the Press Release:
Rice University’s Bonner Nuclear Lab has won a $1.175 million grant that will support its research on high-density and hot nuclear matter.  Rice physicist Frank Geurts, who has spent his career looking for clues to the basic elements of the universe by smashing the nuclear contents of gold, lead and other heavy atoms, said the Department of Energy grant will facilitate his group’s transition from constructing and commissioning a highly complex detector system to using that machinery to do basic research.
Video: Quark gluon plasma (QGP)
For more, see Grant advances quark-gluon ... Read more »

Michael Shull, Kevin France, Charles Danforth, Britton Smith, & Jason Tumlinson. (2010) Hubble/COS Observations of the Quasar HE 2347-4342: Probing the Epoch of He II Patchy Reionization at Redshifts z . arXiv. arXiv: 1008.2957v1

Perez-Garcia, M., Silk, J., & Stone, J. (2010) Dark Matter, Neutron Stars, and Strange Quark Matter. Physical Review Letters, 105(14). DOI: 10.1103/PhysRevLett.105.141101  

SuperB Collaboration, E. Grauges et al., Francesco Forti, Blair N. Ratcliff, & David Aston. (2010) SuperB Progress Reports -- Detector. arXiv. arXiv: 1007.4241v1

Gary Felder, & Stephanie Erickson. (2010) CurvedLand: An Applet for Illustrating Curved Geometry without Embedding. arXiv. arXiv: 1010.1426v1

  • October 11, 2010
  • 06:34 PM

Pipefish: Battle of the Sexes Reversed

by Joris van Alphen in Joris van Alphen Photography Blog

Male pipefish may have lost the battle over parental care, but they haven’t lost the war.... Read more »

Sagebakken, G., Ahnesjo, I., Mobley, K., Goncalves, I., & Kvarnemo, C. (2009) Brooding fathers, not siblings, take up nutrients from embryos. Proceedings of the Royal Society B: Biological Sciences, 277(1683), 971-977. DOI: 10.1098/rspb.2009.1767  

  • October 11, 2010
  • 04:50 PM

Will Global Warming Continue Even After Greenhouse Gas Removal?

by Michael Long in Phased

Computer simulations by Susan Solomon (National Oceanic and Atmospheric Administration, United States) and coworkers suggest that heat trapped deep with the ocean, and only slowly released, will enable a continuation of global warming long after greenhouse gases have been removed from the atmosphere; longer warming will result the longer we wait to stop greenhouse gas emissions. This news feature was written on October 11, 2010.... Read more »

Susan Solomon,, John S. Daniel,, Todd J. Sanford,, Daniel M. Murphy,, Gian-Kasper Plattner,, Reto Knutti,, & Pierre Friedlingstein. (2010) Persistence of climate changes due to a range of greenhouse gases. Proceedings of the National Academy of Sciences. info:/10.1073/pnas.1006282107

  • October 11, 2010
  • 04:40 PM

My IVF story: conclusions

by Kate Clancy in Context & Variation

I discuss aging and reproductive health, reproductive choice, and the naturalistic fallacy in my concluding post on IVF.... Read more »

  • October 11, 2010
  • 03:30 PM

Location Location Location. Acupuncture and chronic shoulder pain – CAM or Sham?

by Lorimer Moseley in BodyInMind

Having written a number of posts on acupuncture (see here, here, and here) I guess my particular biases are reasonably apparent. So imagine my surprise when a large RCT published in the journal “Pain” reports a significant and substantial effect of Chinese acupuncture in comparison with sham acupuncture or conventional orthopaedic therapy for chronic shoulder [...]... Read more »

  • October 11, 2010
  • 02:40 PM

Where are you from? Where have you been?

by Dan in The Endolymph

In my opinion one of the most interesting questions asked about fish is where are you from?  Or where have you been?  Unfortunately, fish don’t carry around birth certificates that make answering these questions easy and uncomplicated…or do they?Enter otolith microchemistry.  In a sense the elemental makeup of the core of an otolith can act as a “birth certificate” for a fish.  The idea is that the elemental composition at the core of the otolith will reflect the chemistry of the water it was born in.  If there is enough differentiation between different habitats you should be able to see clear separation between fish born in different areas.  The clearest examples of this technique have been in looking at fish from different rivers, and estuaries. An example of this technique put to use is Thorrold et al. (1998).  In this study elemental and isotopic ratios in otoliths were used to classify juvenile weakfish to natal estuaries along the east coast of the United States.  Fish from different estuaries showed pretty clear differences in elemental and isotopic ratios, which allowed accurate classification of these fish to their natal estuaries. Me with weakfishOther examples of classifying juvenile fish to their natal area include Brazner et al. (2004), which classified juvenile yellow perch to natal areas of Lake Superior and Walther et al. (2008), which classified juvenile American shad to natal rivers along the east coast. So why is any of this important?   Well, believe it or not investigating and understanding the life history of a fish is really hard.  Traditional mark and recapture studies, which usually involve sticking a tag into a fish, releasing and then hoping to recapture it at some point are often ineffective and typically wind up relying on pretty low recapture rates.  Also, tagging young juvenile fish can be tedious and unfortunately usually has fairly high mortality.  However, if you are able to identify a reliable elemental signature for a river that is reflected in fish otoliths it acts as a “natural tag”.  Therefore, if in the future you capture an adult fish you can examine the elemental signature at the core of that otolith to determine where that fish was born.  This is what Thorold et al. (2001) did as a follow up to Thorrold et al. (1998). This information is useful in looking at natal homing; straying rates between spawning locations, stock discrimination, movements and migrations, and by catch rates.  This technique forms the basis for my project.  I am attempting to classify juvenile river herring to natal watersheds within the Albemarle Sound NC.  While this area isn’t on the same scale as some of the studies mentioned previously, I think I should be able to find some differences in the elemental composition of fish otoliths from these waters.  Brazner, J., Campana, S., Tanner, D., & Schram, S. (2004). Reconstructing Habitat Use and Wetland Nursery Origin of Yellow Perch from Lake Superior using Otolith Elemental Analysis Journal of Great Lakes Research, 30 (4), 492-507 DOI: 10.1016/S0380-1330(04)70365-2Thorrold, S., Jones, C., Swart, P., & Targett, T. (1998). Accurate classification of juvenile weakfish Cynoscion regalis to estuarine nursery areas based on chemical signatures in otoliths Marine Ecology Progress Series, 173, 253-265 DOI: 10.3354/meps173253Thorrold, S. (2001). Natal Homing in a Marine Fish Metapopulation Science, 291 (5502), 297-299 DOI: 10.1126/science.291.5502.297Walther, B., Thorrold, S., & Olney, J. (2008). Geochemical Signatures in Otoliths Record Natal Origins of American Shad Transactions of the American Fisheries Society, 137 (1), 57-69 DOI: 10.1577/T07-029.1... Read more »

  • October 11, 2010
  • 02:36 PM

Counting your blessings? or looking on the bright side of life [whistles]

by Bronwyn Thompson in Healthskills: Skills for Healthy Living

My family were big on the Andrews Sisters. One of my strong memories as a child is listening to the song ‘count your blessings, name them one by one…’ [no, I will not sing it ok?!]. And I remember the book Pollyanna (you can read it for free here!) and the ‘Glad game’ where she … Read more... Read more »

Wood, A., Froh, J., & Geraghty, A. (2010) Gratitude and well-being: A review and theoretical integration. Clinical Psychology Review, 30(7), 890-905. DOI: 10.1016/j.cpr.2010.03.005  

  • October 11, 2010
  • 01:00 PM

Cheap Exports

by Daniel Smith in Small Things Considered

by Daniel Smith

Evolution is often thought of in functional terms. Mutations that improve or diversify a protein’s function are selected for, whereas disruptive mutations are selected against. However, economy can also play a role in protein evolution.

Amino acids used in proteins vary in size, complexity and chemical characteristics, which makes some cheaper to synthesize than others. Consequently, some proteins are more economical to produce than others. by Daniel Smith

Evolution is often thought of in functional terms. Mutations that improve or diversify a protein’s function are selected for, whereas disruptive mutations are selected against. However, economy can also play a role in protein evolution.

Amino acids used in proteins vary in size, complexity and chemical characteristics, which makes some cheaper to synthesize than others. Consequently, some proteins are more economical to produce than others. Previous studies have shown that abundant proteins are often less expensive to make, thus reducing their cellular cost. However, the connection between a protein's location and its expense has not been appreciated. ... Read more »

  • October 11, 2010
  • 12:58 PM

169 years of sauropod research in 26 pages

by Michael Taylor in Sauropod Vertebra Picture of the Week

You may remember that when I wrote about Amphicoelias diplobrontobarowassea the other day, I rather ungraciously complained that “I don’t want to talk about that.  There are other things I do want to talk about”.  Well, with A. suuwatorneriosaurodocus now firmly dealt with, I can talk about what I wanted to — which is Taylor (2010), a [...]... Read more »

Taylor, M. (2010) Sauropod dinosaur research: a historical review. Geological Society, London, Special Publications, 343(1), 361-386. DOI: 10.1144/SP343.22  

  • October 11, 2010
  • 12:57 PM

How did our nitrogen cycle evolve?

by Akshat Rathi in The Allotrope

In trying to feed our growing population, we now add twice as much nitrogen to the soil (after chemically ‘fixing’ it to make fertilisers) as microbes fix from the atmosphere. Human activity has skewed the balance in the earth’s nitrogen cycle. But how did the modern nitrogen cycle evolve? A recent review published in Science tries to answer that question and make suggestions about the future. more.

Canfield, D., Glazer, A., & Falkowski, P. (2010). The Evolution and Future of Earth's Nitrogen Cycle Science, 330 (6001), 192-196 DOI: 10.1126/science.1186120... Read more »

Canfield, D., Glazer, A., & Falkowski, P. (2010) The Evolution and Future of Earth's Nitrogen Cycle. Science, 330(6001), 192-196. DOI: 10.1126/science.1186120  

  • October 11, 2010
  • 12:52 PM

What Are Those Darned Neanderthals Up to Now?

by Krystal D'Costa in Anthropology in Practice

Scene from the Neanderthal diorama at the American Museum of Natural History.
Not shown: Male Neanderthal figure holding tool.
The Neanderthal story is quickly becoming a favorite serial—who knows what new drama the day will bring! Once regarded as brutish and stupid, it was accepted that they could not compete technologically and socially with early modern human (EMH) populations and were eradicated as the latter spread throughout the globe. But in the last few years, the reputation of our Neaderthal cousins has changed. In fact, we've learned that they were surprisingly like us in many ways: they painted shells for jewelry, provided care for those in need, and had a sophisticated tool industry (see more here). Their diorama at the American Museum of Natural History shows them in a family unit. Their genome has revealed few conspicuous differences, instead demonstrating that Neanderthals may have in fact left a trace of themselves in our own genes.
The Neanderthal story stimulates the imagination because for all the similarities and newly credited skills the fact remains that they disappeared completely (in geological terms), leaving the earth to Homo sapiens. And I think part of the reason we're so intrigued is that on one level we wonder as a species whether we could disappear in the same way—gone but for a few instances in the fossil record. The Discovery Channel has done an excellent job of presenting the disaster possibilities: an asteroid could strike, global warming could do us in, the sun will eventually die, and so on. All the scenarios present events with immense environmental impact that would threaten our ability to find sustenance and cripple our overall well-being. A recent paper in Current Anthropology proposes that Neanderthals fell victim to one such devastating environmental event—volcanic activity—and illustrates the ways the fallout from the event would have made their environment inhospitable.

The skeleton called the "Ring Lady"
unearthed in Herculaneum.
Credit: Wikipedia
Neanderthals lived in Europe from about 400,000 to about 40,000 years ago. And they were used to adverse conditions: their environment was a very cold one, and may have included a severe ice age known as glacial period OIS 4. Like EMHs, they were accustomed to and could manage the climatic variables of the northern European landscape they frequented. For example, they clothed themselves against the elements. However, we know from Vesuvius that volcanic activity can present an insurmountable challenge. The charred remains of Pompeii are a testament to the speed and finality with which ash can cover the surrounding area. And ash is a troublesome thing: it spreads easily, carrying its effects far and wide. When the Eyjafjallajökull Volcano erupted earlier this year, NASA documented the spread of the ash over the Atlantic. Ash can have a cooling effect, causing crop failures and widespread famine. If it reaches the stratosphere (upper atmosphere), these effects can be prolonged as sulfur lingers in a reflective layer above the earth keeping much needed sunlight from the planet's surface (and eventually falling as acid rain as an added bonus).
Researchers Golovanova et. al. (2010) believe that Neanderthals may have been overcome by the combined effects of three successive volcanic explosions, the largest of which would have been the Campanian Ignimbrite (CI) eruption from the Phlegraean Fields in Italy:We offer the hypothesis that the Neanderthal demise occurred abruptly (on a geological timescale) at around 40,000 BP after the most powerful volcanic activity in western Eurasia during the period of Neanderthal evolutionary history. We further hypothesize that this catastrophe not only drastically destroyed the ecological niches of Neanderthal populations but also caused their mass physical depopulation in most of their habitation areas across Europe and the Near East. This loss of viable source populations may have significantly contributed to the eventual extinction of Neanderthals throughout their range (673).Using soil samples from Mezmaiskaya Cave, a well-preserved site of occupation for both Neanderthals and EMHs in the Northern Caucasus, Golovanova et. al. were able to trace periods of occupation in the area, noting significantly that activity dropped in correlation to volcanic soil layers. This information not only demonstrates when the site was being used, but also provides us with a foundation with which to understand the apparent transition from Neanderthal occupation to EMH occupation of the region.
Soil samples from Mezmaiskaya Cave have revealed two distinct layers of volcanic ash, suggesting that the ash accumulated as a result of two different eruptions—neither of which are the CI eruption:Geochemical analysis suggests that eruptions in the Elbrus volcanic province between 45,000 and 40,000 years ago are the most likely sources of the ash in later 2B-1 at Mezmaiskaya Cave ... The basaltic chemical composition of the ash in layer 1D is closer to that of volcanic rocks of Mt. Kazbek in the Central Caucasus. The explosive volcanoes of Mt. Kazbek in the Terek River upper valley are the most likely sources of the ash in layer 1D at Mezmaiskaya (660).Soil analysis also suggests climatic shifts following the volcanic events as well, with low levels of pollen concentration and little arboreal spores (660). This would have made the area unsuitable for foraging and inhospitable for any animals that frequented the area as well, which in turn resulted in diminished activity in and around Mezmaiskaya. What is interesting, however, is that activity seems to have resumed at Mezmaiskaya following the Elbrus eruption:The first volcanic eruption produced ash in the later MP [Middle Paleolithic] layer 2B-1 and essentially resulted in the deterioration of ecological conditions in the region ... The intensity of site use increased, however, during the accumulation of the upper MP layers 2A and 2 when the climate became cool and wet. Although the lithic industry changed slightly after the environmental crisis of layer 2B-1, it still remained typically MP Eastern Micoquian. Skeletal and mtDNA evidence indicates that Neanderthals produced both the earlier and the later MP industries at Mezmaiskaya (667).The Kazbek eruption proved to have been more serious. The ash layer is about 0.7 m thick, and following the eruption signs of habitation are sparse. The CI eruption fits into this puzzle because it had a widespread ... Read more »

Liubov Vitaliena Golovanova,, & Vladimir Borisovich Doronichev, Naomi Elansia Cleghorn, Marianna Alekseevna Koulkova, Tatiana Valentinovna Sapelko, M. Steven Shackley. (2010) Significance of Ecological Factors in the Middle to Upper Paleolithic Transition. Current Anthropology, 655-691. info:/10.1086/656185

  • October 11, 2010
  • 11:49 AM

Throat bacteria that destroy invaders

by Lab Rat in Lab Rat

I did a post about a week ago, talking about the relationship between the bodies natural (commensal) bacteria and the immune system. I was quite excited therefore to find a paper (reference below) which found a specific protease enzyme that is used by commensal throat bacteria to prevent harmful biofilm formation by Staphylococcus aureus, the bacteria responsible for MRSA.The helpful bacteria in question is Staphylococcus epidermidis which lives naturally in the throat and nasal cavity of humans. When culturing these bacteria along with the Staph aureus it was found that some epidermidis cultures were capable of destroying biofilm formation, by using the protease Esp. The diagram below shows the effects of extracted Esp on colonies of Staphylococcus aureus:Figures g and j show Gram stains of the colonies, the blue dye has just stained where bacteria are present. The remaining figures show scanning electron micrographs of the colonies taken at two different levels of magnification. For those interested, the scale bar for g,h,j and k is 10um and for i and l is 1um.To double check that this protein was having an effect within the bacteria knockout mutants were made which removed the gene from Esp from the epidermidis. These bacteria were incapable of destroying Staph aureus growth. Adding a plasmid containing the Esp gene back into the bacteria restored their ability to fight off the Staph aureus which seems fairly conclusive. Furthermore this affect also works with VRSA and MRSA; Staph aureus which are resistant to antibiotics.Below is a diagram of the effect of actual epidermidis bacteria on Staph aureus colonies.These are nasal swabs taken from volunteers who had Staph aureus infections and were given the commensal epidermidis strains to try and clear them. It can be seen that the number of staph aureus is decreasing, although some bacteria are still present after five days of treatment. That might not necessarily be a bad thing as it allows the immune system to kick in with a response, and make antibodies ready for the next potential attack.There are several exciting things that come out of this. Firstly the use of purified Esp as a defence against MRSA biofilms has the potential to be of major importance, although there may be clinical reasons why it's not such a good idea to spray proteases all over the inside of someones nose! From a less medically-useful perspective it's a wonderful example of bacterial-colony interaction. The kind of struggle for survival that happens inside your nose is occurring for bacteria everywhere; in soil, in the water, in the air, and even in humans.From the Staph epidermidis point of view your nasal cavity is just a great place to live (warm, safe, lots of nutrients) and it's not going to give up that kind of living environment without a fight!---Iwase, T., Uehara, Y., Shinji, H., Tajima, A., Seo, H., Takada, K., Agata, T., & Mizunoe, Y. (2010). Staphylococcus epidermidis Esp inhibits Staphylococcus aureus biofilm formation and nasal colonization Nature, 465 (7296), 346-349 DOI: 10.1038/nature09074---Follow me on Twitter!... Read more »

  • October 11, 2010
  • 10:18 AM

Paleo Diet for Heart Patients With Diabetes and Prediabetes

by Steve Parker, M.D. in Diabetic Mediterranean Diet Blog

A Paleolithic diet lowered blood sugar levels better than a control diet in coronary heart disease patients with elevated blood sugars, according to Swedish researchers reporting in 2007. About half of patients with coronary heart disease have abnormal glucose (blood sugar) metabolism.  Lindeberg and associates wondered if a Paleolithic diet (aka “Old Stone Age,” “caveman,” or ancestral human diet) [...]... Read more »

  • October 11, 2010
  • 09:31 AM

The 20th Anniversary of Steven Pinker & Paul Bloom: Natural Language and Natural Selection (1990)

by Michael in A Replicated Typo 2.0

The day before yesterday Wintz mentioned two important birthdays in the field of language evolution (see here): First, Babel’s Dawn turned four, and second, as both Edmund Blair Bolles and Wintz pointed out, Steven Pinker‘s and Paul Bloom‘s seminal paper “Natural Language and Natural Selection” (preprint can be found here) has its 20th anniversary.
Wintz wrote that he . . . → Read More: The 20th Anniversary of Steven Pinker & Paul Bloom: Natural Language and Natural Selection (1990)... Read more »

Pinker, Steven, & Bloom, Paul. (1990) Natural Language and Natural Selection. Behavioral and Brain Sciences, 13(4), 707-726. info:/

  • October 11, 2010
  • 09:05 AM

Why I'm out online

by Jeremy Yoder in Denim and Tweed

Exactly a year ago today, I came out of the online closet. Now it's another National Coming Out Day, and it seems like as good a time as any to think out loud about why I made that decision.
.flickr-photo { }.flickr-frameright { float: right; text-align: left; margin-left: 15px; margin-bottom: 15px; width:40%;}.flickr-caption { font-size: 0.8em; margin-top: 0px; } Image borrowed from Wikipedia under fair use rationale.My reasons aren't going to surprise anyone who has even a passing familiarity with gay rights history:Familiarity breeds acceptance. This is mainly a political argument. It's widely accepted (and supported by ongoing public opinion surveying) that people who personally know GLBT folks are overwhelmingly more likely to support treating GLBT people like full citizens. The psychology isn't hard to understand—it's easy to hate the nebulous, faceless, unknown Gays; it's rather harder to hate your son, or your niece, the nice neighbors who let you borrow their lawnmower, or (I hope) the guy who writes that one not-entirely-terrible science blog you check every so often.
Gotta give'em hope. And an example. This is more personal. I grew up without knowing any out gay people, which was, to put it mildly, not helpful. I was, to paraphrase the Onion headline, The Only Homosexual in the World; I didn't have any of the support, or visible examples, that would've helped me think critically about my sexual orientation or imagine a future in which I was out, and happy about it. (Which I very much am, these days.) By being open about my orientation, maybe I can help someone else figure out his (or hers) in a way I couldn't, and even show that, as confusing and frequently miserable as growing up gay is, it gets better.
And if there's one impression I hope to give a confused, lonely (and presumably nerdy) gay kid reading D&T, it's that it did get better for this formerly confused, lonely (and unquestionably nerdy) gay kid. And a large part of how it got better, for me, has to do with going into science.

Evolutionary biology has turned out to be a good field for me, in this personal respect. When I started my first genuine biology-related internship, I was surrounded for the first time by people who didn't talk about gays in the hushed, scandalized tones I'd heard through a lot of my childhood and schooling. Biologists are as human as the next ape descendent, but they're also a generally open-minded bunch who tend to be more interested in the quality of your work than what you do after you leave the lab. And, for what are probably obvious reasons, evolutionary biology doesn't attract the sort of people who hold doctrinaire conservative religious positions on any subject.

Evolutionary biology is also a pretty good academic discipline for me because evolutionary biology has something to say about sexual minorities, just as it has something to say about humans in general. Humans are biological beings, and we're part of an animal kingdom that exhibits a wide array of sexual behaviors, as elaborately documented by the evolutionary biologist Joan Roughgarden in her book Evolution's Rainbow. Exactly how to explain this diversity, particularly in the case of humans, is still quite controversial [$a]—but it's a question for which I have some expertise, and one I'd like to weave into the writing I do for D&T in the future.


Futuyma, D. (2005). Celebrating diversity in sexuality and gender. Evolution, 59 (5), 1156-9 DOI: 10.1111/j.0014-3820.2005.tb01052.x

Roughgarden, J. (2004). Evolution's Rainbow. Berkeley: University of California Press. Preview on Google Books.

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