Post List

  • August 19, 2010
  • 11:00 AM

Does caffeine help you drink?

by TwoYaks in Gene Flow

It was my brother who told me that drinking coffee while drinking alcohol was a good idea - it would lessen the effects of intoxication. I launched into an ethanol fuelled discussion of how physiologically implausible that sounded to me, but we were celebrating a great occasion, and so I don't think I got much beyond slurring something about cyclic AMP before we instead had some of Arizona's ... Read more »

Ferreira, S., de Mello, M., Pompeia, S., & de Souza-Formigoni, M. (2006) Effects of Energy Drink Ingestion on Alcohol Intoxication. Alcoholism: Clinical and Experimental Research, 30(4), 598-605. DOI: 10.1111/j.1530-0277.2006.00070.x  

  • August 19, 2010
  • 10:04 AM

Where did the oil go?

by Sarah Stephen in An ecological oratorio

The recent oil spill in the Gulf of Mexico released, as we have all seen on tv, a lot of oil. Quite how much is a "lot" is a bit of a guess, but roughly 4.9 million barrels, or 784 million litres*. What actually happened to this oil was reviewed recently in an article in Science (Kerr 2010). Only about 0.1% was recovered from beaches and marshes (that´s still an awful lot of oil!). About 17% was siphoned away at the well head, 5% burned off at the surface, and only 3% skimmed off by booms, despite a lot of effort and money spent. And the other 75%? It's, er, disappeared.So where did this oil go? Some evaporated, but with luck most of it was eaten.Oil is energy, that's why we use it in our cars and power stations. And energy means food. There are actually quite a few bacteria that digest and breakdown crude oil, and these are massively important in the recovery of the ocean from disasters like this. They work as a consortium, each concentrating on a particular fraction of the oil, and as one hydrocarbon is degraded to another, other bacteria take over. The first, and so in many ways the most important, are Alcanivorax species (Vila et al 2010). These are found in tiny quantities in unpolluted waters, but their numbers rocket when in the presence of linear and branched alkanes, common in crude oil. In fact they are so specialised for this type of hydrocarbon that without long chain alkenes they grow very poorly, but by then their job is done. Now other species such as Roseovarius and Marinobacter take over.This breakdown was helped by the massive release of chemical dispersants at the oil head, 1.1 million gallons (Kintisch 2010). These are similar to the detergent in your kitchen, breaking down lumps of oil into tiny droplets, which are "dispersed" and can be attacked much more efficiently by bacteria. This was very controversial, as dispersants are pretty toxic and an immense quantity was involved. Still, it seemed to work, and much of the oil was broken down into 1-10 micrometer droplets. In fact, it started to raise fears that it was working TOO well, a microbial explosion depriving the ocean floor of oxygen and creating a huge dead zone. But this seems not to have happened, and in fact so far the prognosis is good.We´re not out of the woods yet, the oil could yet turn up in unwanted places, and chemical damage by detergents might yet, for instance, devastate the local tuna population. But there have been lessons learnt for next time - and there will be a next time.Kerr RA (2010). Gulf Oil Spill. A lot of oil on the loose, not so much to be found. Science (New York, N.Y.), 329 (5993), 734-5 PMID: 20705818;329/5993/734?maxtoshow=&hits=10&RESULTFORMAT=&fulltext=oil biodegradation&searchid=1&FIRSTINDEX=0&sortspec=date&resourcetype=HWCITKintisch E (2010). Gulf Oil Spill. An audacious decision in crisis gets cautious praise. Science (New York, N.Y.), 329 (5993), 735-6 PMID: 20705819, J., Nieto, J., Mertens, J., Springael, D., & Grifoll, M. (2010). Microbial community structure of a heavy fuel oil-degrading marine consortium: linking microbial dynamics with polycyclic aromatic hydrocarbon utilization FEMS Microbiology Ecology DOI: 10.1111/j.1574-6941.2010.00902.x* the oil "barrel" is actually based on a type of old English wine barrel or "teirce" holding 35 gallons.... Read more »

  • August 19, 2010
  • 09:54 AM

If You’re Gonna Monitor Employee Vehicles, Do It Right

by Richard Landers in NeoAcademic

A new student by McNall and Stanton in the Journal of Business and Psychology examines electronic monitoring of employee vehicle location.... Read more »

  • August 19, 2010
  • 09:35 AM

Bicycles are Good For You--Really

by Paul Statt in Paul Statt Communications

Public health law research is necessary, even if so much is proving the obvious, but once you get the numbers, you can hopefully get policy changes. But now it can be told: your bicycle is good for your health, despite its dangers.... Read more »

Johan de Hartog, J., Boogaard, H., Nijland, H., & Hoek, G. (2010) Do the Health Benefits of Cycling Outweigh the Risks?. Environmental Health Perspectives, 118(8), 1109-1116. DOI: 10.1289/ehp.0901747  

  • August 19, 2010
  • 09:25 AM

Heroic Fungi

by Journal Watch Online in Journal Watch Online

Talk about your historic biodiversity. A polar hut built by famed Antarctic explorer Ernest Shackleton turns out to house an extraordinary array of fungi. The discovery could help conservators preserve the landmark structure, and offers new insights into life on a continent once viewed as barren.
Shackleton and his 15-member British Antarctic Expedition erected the […] Read More »... Read more »

Blanchette, R., Held, B., Arenz, B., Jurgens, J., Baltes, N., Duncan, S., & Farrell, R. (2010) An Antarctic Hot Spot for Fungi at Shackleton's Historic Hut on Cape Royds. Microbial Ecology, 60(1), 29-38. DOI: 10.1007/s00248-010-9664-z  

  • August 19, 2010
  • 09:14 AM

Improved survival with ipilimumab in metastatic melanoma

by Sally Church in Pharma Strategy Blog

The latest New England Journal of Medicine dropped in the mail yesterday afternoon, it has some interesting articles on how palliation plus chemotherapy offers improved survival over chemo alone and a small study on the positive impact of T'ai Chi...... Read more »

Hodi, F., O'Day, S., McDermott, D., Weber, R., Sosman, J., Haanen, J., Gonzalez, R., Robert, C., Schadendorf, D., Hassel, J.... (2010) Improved Survival with Ipilimumab in Patients with Metastatic Melanoma. New England Journal of Medicine. DOI: 10.1056/NEJMoa1003466  

Hwu, P. (2010) Treating Cancer by Targeting the Immune System. New England Journal of Medicine, 363(8), 779-781. DOI: 10.1056/NEJMe1006416  

  • August 19, 2010
  • 09:06 AM

Scientist Urges "Four Culture" Partnerships on Climate Change Communication

by Matthew C. Nisbet in Age of Engagement

More than 50 years after the publication of CP Snow's seminal Two Cultures, interdisciplinary partnerships between science and other academic "cultures" are being urged once again. Today, urgency is not focused on the Cold War but rather the challenge of engaging society on climate change and other environmental problems.
In an open access article published this month at the journal Frontiers in Ecology and the Environment, I joined with several colleagues to describe the potential for partnerships that involve interdisciplinary "four culture" initiatives across universities and community-based institutions.
The essay is based on the insights, revelations, and conclusions from the 16 member Columbia River Quorum, which was composed of scientists, scholars, and professionals - four representatives from each of what we describe as the four academic "cultures" - who met in Oregon in 2009 for the first of what we hope will be many similar summits across the world (see photo below). The goal of that meeting was to identify and build synergies by which members of traditionally separate disciplinary cultures -- specifically the environmental sciences, philosophy and religion, the social sciences, and the creative arts and professions -- can accomplish collaboratively what none are capable of doing alone.
In the essay, we propose specific strategies for catalyzing these inter-disciplinary partnerships with the goal of creating a new communication infrastructure around the issue of climate change. These strategies include a bold proposal to pool "public impact" money from individual research grants at the university level to be re-invested by a "four culture" expert committee in local and regional public engagement initiatives. It also includes a call for a digital news community--a Chronicle of Higher Ed focused on climate change education and communication--that would serve as a catalyst for identifying and diffusing best practices and partnerships.
One of the organizers of the Four Cultures summit in Oregon was Mark Hixon, professor of Marine Conservation Biology at Oregon State University. In an interview I did with Hixon, he reflects on the origins of the summit and his outlook on the urgent need for Four Culture initiatives on climate change communication and education at universities across the country. Along with the interview, I have posted a photo and a list of the participants in the summit.
What motivated you to organize the Columbia River Quorum?
My Oregon State University (OSU) philosopher / writer colleague and friend, Kathy Moore, and I were sharing lunch, lamenting on the increasingly bad news regarding the state of the global environment and the lack of substantial remedial action by the United States regarding climate disruption.  We focused on the need for our society's response to accelerate past the exponentially increasing rate of environmental degradation if all the Earth's children and grandchildren are to enjoy healthy lives.
Where did the idea come from?
The need for an accelerated response by society to climate disruption and other pressing environmental issues stimulated the idea that we need new synergies.  Natural science has done a wonderful job documenting environmental threats, yet that knowledge alone has not stimulated an adequate response within our nation.  Needed are all four academic cultures -- natural sciences, social sciences, philosophy and religious studies, and communication and creative arts -- to fully engage with each other to create those synergies.  Once that need became clear to us, hosting a quorum with representatives from each of the four cultures was the logical next step.
Over the course of the weekend, what things did you come to realize?
In March 2009, Kathy's organization, OSU's Spring Creek Project, hosted 4 members of each of the 4 academic cultures at a beautiful retreat in the Columbia River Gorge (see photo below).  The energy of the weekend was exciting and truly palpable.  Ideas flowed like the great flood that carved the Gorge!  I realized then that the time was right for these new synergies to develop -- that together we in academia truly can help to bring about "the great turning" in new, more integrated, and more effective ways.
If you were to emphasize two take away conclusions from the experience for environmental scientists, what would they be?
First, let go of the entrenched worldview that our role as environmental scientists is ONLY to provide data to society regarding climate disruption and other environmental threats -- that providing data ALONE will stimulate society to respond to these threats.  That partial and isolated role has failed and will continue to do so.  
Second, engage with social scientists and non-scientist colleagues, indeed, with the public at large regarding these important issues that affect us all.  In short, do not abdicate your citizenship -- actively engage in changing the world!
Why do you think some scientists might have reservations about interdisciplinary partnerships focused on public engagement?
There are many reported reasons:  (1) the perceived lack of time and energy as we focus exclusively on teaching, research, and university administration, (2) the ineffective worldview that our role is only to provide information, (3) the false belief that our credibility as scientists will dissolve if we fully engage as citizens, etc.  I personally reject all these excuses, and I highly recommend that all scientists read Michael Nelson's recent papers on these issues [attached -- check with Michael to see if you can provide download links].
What do you think are steps that can be taken at the university and disciplinary level to encourage greater "Four Culture" partnerships?
Traditional university organizational structures are insufficiently integrated and often terribly isolating, especially between the sciences and the liberal arts.  At OSU, two recent efforts building on the Spring Creek Project are fostering new synergies among the four academic cultures.  First, the once fully separate colleges of science and liberal arts have been folded into a single division of arts and sciences.  Second, a new environmental humanities initiative, the interdisciplinary Three Rivers Institute, has been formed to foster integration among human values, science, and environmental leadership.
If colleagues at another university wanted to organize their own Four Culture quorum, what advice would you give them?
Go for it!  Start with a simple foursome of one member from each culture, then build from there.  I truly believe that people are ready for revolutionary integration.  All four cultures have been working for changing the world in positive ways, largely in parallel, isolated, and often (but certainly not always) ineffective.  The time is ripe for new synergies that will accelerate our society's response to pressing environmental threats.

Members of the Columbia River Quorum (March 2009): Back row: Bob Frodeman, Scott Sanders, Steve Vanderheiden, Andreas Schmittner, Hank Green, Fred Swanson, Charles Goodrich, Kathie Olsen, John Bliss, Mark Hixon. Front row: Kathy Moore, Carly Johnson, Michael Nelson, Pam Sturner, Alison Deming, Michaela Hammer. Missing: Eban Goodstein and Matt Nisbet.
Nisbet, M., Hixon, M., Moore, K., & Nelson, M. (2010). Four cultures: new synergies for engaging society on climate change Frontiers in Ecology and the Environment, 8 (6), 329-331 DOI: 10.1890/1540-9295-8.6.329
... Read more »

Nisbet, M., Hixon, M., Moore, K., & Nelson, M. (2010) Four cultures: new synergies for engaging society on climate change. Frontiers in Ecology and the Environment, 8(6), 329-331. DOI: 10.1890/1540-9295-8.6.329  

  • August 19, 2010
  • 09:00 AM

Another pointless "acupuncture" study misinterpreted

by Orac in Respectful Insolence

At the risk of once again irritating long time readers who've hear me say this before, I can't resist pointing out that, of all the various forms of "alternative medicine" other than herbal medicines (many of which are drugs, just adulterated, impure drugs), acupuncture was the one treatment that, or so I thought, might actually have a real therapeutic effect. Don't get me wrong; I never bought magical mystical mumbo-jumbo about "meridians" and "unblocking the flow of qi" (that magical mystical life energy that can't be detected by scientists but that practitioners of woo claim to be able to manipulate for therapeutic intent). The point is (sorry, couldn't resist) that acupuncture actually involves doing something physicial to the body, namely inserting thin needles into it. Shorn of its trappings of prescientific Eastern mysticism, acupuncture struck me as something that might have something to it.

Five years ago.

Since I started actually studying acupuncture and acupuncture studies, I've become acutely aware that my previous assessment was incorrect, and my pointing that out from time to time sometimes results in comments along the lines of, "We don't need to hear this again." Tough. For the benefit of new readers and readers who might not have read some of my previous posts on acupuncture before, I consider it important to reinforce that I have, in fact, undergone a bit of a change of heart. I have reviewed studies that showed that sham acupuncture works as well or even better than "true" acupuncture, with the needles placed right where those fancy acupuncture charts say they should be placed and that you don't even need needles. Toothpicks with their points twirled against the skin will do. I've also come to realize that many of the explanations postulated by acupuncturists and doctors who believe in acupuncture are actually far less interesting than actual scientific results that they produce in their search for "proof" that "acupuncture works." Sometimes, acupuncturists substitute active sorts of treatment for acupuncture and call it something else, like "electroacupuncture, which involves hooking up a weak electrical current to acupuncture needles. Electroacupuncture is in essence nothing more than transcutaneous electrical nerve stimulation (TENS), an accepted modality to treat pain.

Add to the evidence pile yet another study demonstrating that acupuncture is placebo medicine, reported in Arthritis Care & Research by a team of investigators based primarily at the M.D. Anderson Cancer Center that I heard about via the TIME Magazine Wellness Blog. The study, entitled A Randomized controlled trial of acupuncture for osteoarthritis of the knee: Effects of patient-provider communication, demonstrates about as unequivocally as one can imagine that one form of so-called "acupuncture" is, as far as can be detected, virtually all placebo. What is surprising about this study is not so much that it shows that acupuncture doesn't work. In fact, it doesn't actually show that, because what is being used is not acupuncture. What is being used is "electroacupuncture, which is in essence nothing more than TENS! More amazingly, no one whom I've yet seen seems to be mentioning this. In essence, the results of this study are entirely consistent with the hypothesis that it doesn't matter whether you place TENS needles on acupuncture points or not. Will wonders never cease? Actually, that's not quite the right interpretation, as we shall soon see. Read the rest of this post... | Read the comments on this post...... Read more »

  • August 19, 2010
  • 08:17 AM

Jumping Spiders Prefer Vegetated Corridors

by Kevin Zelnio in The Online Laboratory of Kevin Zelnio

Barriers to dispersal come in all shapes and sizes and not all are obvious. Baker conducted experiments with jumping spiders, Phidippus princeps (Salticidae) in which he manipulated corridors connecting patches of old growth fields (clover and alfalfa). Patches were either not connected (bare corridors), all connected, or partly connected by vegetated corridors (see schema [...]... Read more »

  • August 19, 2010
  • 08:01 AM

Misinformed Consent? What not to tell a patient with back pain

by Lorimer Moseley in BodyInMind

We just came across a fancy patient information form that was given to a patient after an assessment by a clinician. The form just blew our minds (but not in a good way) because it seemed to be the perfect clinical tool for generating ongoing pain and disability, and all by the simple process of [...]... Read more »

Borenstein DG, O'Mara JW Jr, Boden SD, Lauerman WC, Jacobson A, Platenberg C, Schellinger D, & Wiesel SW. (2001) The value of magnetic resonance imaging of the lumbar spine to predict low-back pain in asymptomatic subjects : a seven-year follow-up study. The Journal of bone and joint surgery. American volume, 83-A(9), 1306-11. PMID: 11568190  

Kalichman L, Li L, Kim DH, Guermazi A, Berkin V, O'Donnell CJ, Hoffmann U, Cole R, & Hunter DJ. (2008) Facet joint osteoarthritis and low back pain in the community-based population. Spine, 33(23), 2560-5. PMID: 18923337  

  • August 19, 2010
  • 08:00 AM

Should Obesity Prevention Efforts Focus Less On Individuals?

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

Obesity is now increasingly recognised as the “natural” consequence of societal changes that have occurred over the past decades to foster an increasingly obesogenic environment.
Yet, rather than focus on the root causes of these societal drivers of obesity, governments apparently prefer to make obesity prevention a personal matter, with a strong emphasis on trying to [...]... Read more »

  • August 19, 2010
  • 08:00 AM

Ageing per se increases susceptibility to lipid induced insulin resistance in rats

by Colby in

I am constantly on the lookout for studies on how biochemical mechanisms shift with age, the significance of these changes and how nutrition and lifestyle interact with them to potentially affect health.  Ageing itself is clearly an immensely complex process, and teasing … Continue reading →... Read more »

Einstein FH, Huffman DM, Fishman S, Jerschow E, Heo HJ, Atzmon G, Schechter C, Barzilai N, & Muzumdar RH. (2010) Aging per se increases the susceptibility to free fatty acid-induced insulin resistance. The journals of gerontology. Series A, Biological sciences and medical sciences, 65(8), 800-8. PMID: 20504893  

  • August 19, 2010
  • 08:00 AM

Why is a spider like a Derringer?

by Zen Faulkes in NeuroDojo

The Derringer pistol:

Pros: Easy concealment. Stylish.

Con: You’ve only got one shot.

Argiope bruennichi of the male variety are rather like Derringer pistols. Because, you see, their sex organs tend to break during mating.

Yes. Break off.

You almost can’t help but wonder if being eaten by the female – which is the fate for a large percentage of them – isn’t almost a relief to the poor boys at that point.

When you only one shot at genetic glory, you would expect to aim at the target carefully. You might expect the males to be incredibly selective about what females they mate with. In many invertebrates, there’s an easy measure of female quality: size. Bigger bodies mean more eggs.

Shulte and colleagues tested this by experiments in the field and the lab. The males had a choice between two females that differed in size. They didn’t just measure which female was mated with, but the level of the male’s interest, from “Just looking” (male comes to female’s web) to “Sure I’ll come in to see your etchings” (male enters web) to fake yawn (male courts female) to squeaking bedsprings (copulation).

The prediction is that as the differences in the two females get bigger, so too should the differences in the males’ behaviours.

The reality was... not much difference in the males’ behaviour. The males tended to go to one female very quickly and stay with that female regardless of the size, particularly in the lab. In the field, there’s more evidence for choosiness: half the males

What’s going on here? It’s not terribly clear. Maybe the cost of searching for females is so high (predation, maybe?) that the pressure is on for males to mate with the first female they meet. Maybe the male of this species doesn’t have the sensory ability to discriminate sizes, but it would be darned unusual, because lots of arthropods can do such tasks.

The males aren’t complete oblivious to the females, though. Males select quite strongly for unmated females. Because, you see, if there had been a previous male... well, let’s just say that working around the broken sex organs of a previous suitor can really cramp your style. The likelihood of siring any little spiderlets goes way down for previously mated females. But even then, some males would reject unmated females, and it’s not clear why.


Schulte, K., Uhl, G., & Schneider, J. (2010). Mate choice in males with one-shot genitalia: limited importance of female fecundity Animal Behaviour DOI: 10.1016/j.anbehav.2010.07.005

Derringer photo by remixoverdrive on Flickr. Spider photo by Joachim S. Müller on Flickr. Both used under a Creative Commons license.

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Life and death and sex choices in mantids... Read more »

  • August 19, 2010
  • 07:30 AM

Numbers on the Brain: Neurobiology of Mathematics

by Jason Goldman in Child's Play

Nearly everyone has heard of developmental dyslexia – a learning disorder characterized by poor reading skills despite otherwise sufficient schooling – but have you heard of developmental dyscalculia? Many people have not. Here is part 4 in a week-long series on this lesser-known learning disorder. Case-studies of patients with various brain lesions have demonstrated the [...]... Read more »

Ardila A, & Rosselli M. (2002) Acalculia and dyscalculia. Neuropsychology review, 12(4), 179-231. PMID: 12539968  

Dehaene, S. (2004) Arithmetic and the brain. Current Opinion in Neurobiology, 14(2), 218-224. DOI: 10.1016/j.conb.2004.03.008  

Isaacs EB, Edmonds CJ, Lucas A, & Gadian DG. (2001) Calculation difficulties in children of very low birthweight: a neural correlate. Brain : a journal of neurology, 124(Pt 9), 1701-7. PMID: 11522573  

Dehaene, S, Piazza, M, Pinel, P, & Cohen, L. (2003) Three Parietal Circuits for Number Processing. Cognitive Neuropsychology, 487-506. info:/

  • August 19, 2010
  • 07:15 AM

A voyage from molecular genetics to microbial ecology -- includes a fish tank and some cartoons

by Cesar Sanchez in Twisted Bacteria

The March issue of International Microbiology included a very nice article by Roberto Kolter, professor of Microbiology and Molecular Genetics at Harvard Medical School. The title is Biofilms in lab and nature: a molecular geneticist’s voyage to microbial ecology (freely available as PDF).In the article, the author gives an entertaining account of the path that lead him to the study of biofilms -- that is, aggregations of microbes growing on solid substrates. He also highlights some of his recent research on the ecology of microbial islands.There is also a fish tank anecdote. And I added a couple of microbial cartoons, just for fun!Microbes are excellent model organisms... at least for studies on basic cellular processes. As Jacques Monod put it: Ce qui est vrai pour le colibacille est vrai pour l’éléphant ("what is true for the colibacillus is true for the elephant"). That is why Roberto Kolter (and many other researchers) soon fell under the spell of bacteria and, in particular, the colibacillus Escherichia coli.For some time, Kolter studied the regulation of cell growth in E. coli. Under the right conditions, cells divide to yield daughter cells, which grow and divide quickly again, and so on -- and the bacterial population undergoes exponential growth. This exponential phase of growth (a.k.a. log phase) is typically followed by a stationary phase, when the growth rate slows down due to a scarcity of nutrients and accumulation of toxic products. Eventually, the bacterial population shrinks, in what is known as death phase (you can visit Cells alive! or Wikipedia for basic information on bacterial growth). These processes are typically studied in the laboratory using shaken cultures. The shaking of flasks and test tubes keeps the broth composition uniform throughout the flask, and provides a continuous supply of fresh air that helps microbes grow fast. As a result, the cells are in a planktonic state; that is, they grow in suspension in the broth. From these shaker-sick cultures, Kolter and coworkers learnt a few interesting things about what happens during the stationary and death phases. In the International Microbiology article, he summarizes their findings as follows: "And what we found through genetic analyses was rather extraordinary. Death allowed new life; we were witnessing evolution in real time [...]. Underlying the usually observed death phase was a dynamic world of dying and growing bacteria. There were constant population takeovers such that pre-existing fitter bacterial mutants grew as the original population met its demise. Evolutionary cheating we would call it later on [...]"In other words, the adverse conditions occurring in the E. coli cultures during the death phase (toxic products, little food) appeared to have two contrasting effects. It was obvious that many cells were dying -- but, at the same time, successive waves of different spontaneous mutants were able to thrive and outgrow their dying siblings in this less-than-optimal environment. These findings were reviewed in two papers with memorable titles: Life after log and GASPing for life in stationary phase. Isn't that a fascinating microcosms? The little creatures in the test tube were not just dying; they were evolving! And now, the fish tank anecdote. Or, in Kolter's own words, the epiphany of the fish tank: "The years that followed represented for me a dramatic turn of direction in my research. One might ascribe the change to some sort of “post-tenure depression”; I refer to it as the “epiphany of the fish tank” now. [...]Microbial life on surfaces, for decades studied by Bill Costerton and other intrepid pioneers of the biofilm field, had been long ignored by most microbial physiologists and molecular geneticists, myself included. However, things changed for me in 1994 when, noticing my depressed state, members of my laboratory gave me a fish tank in a effort to draw me out of the blues. As I sat locked-up in the office staring at the tank, I realized that by studying shaken cultures of E. coli I had been barking up the wrong tree. The water in the fish tank remained crystal clear, it was on the surfaces where most microbial activity was occurring."That observation applies well beyond fish tanks. It is possible that the majority of microbes on Earth spend most of their lives in aggregates attached to surfaces, and therefore not in a free-floating or swimming, planktonic state. Obviously, they are not solitary guys: we could view biofilms in nature as quite complex 'societies' or 'cities' where different types of microorganisms inhabit buildings made out of sticky macromolecules (polysaccharides, proteins, DNA). Importantly, microbes in biofilms are sometimes resistant to the action of antibiotics, to which the same organisms are sensitive when in planktonic state. So, have microbiologists been "barking up the wrong tree" all this time? Well, not exactly. Experiments using shaken cultures have been, and will continue to be, extremely useful. They are, without doubt, highly valuable to learn about the biochemistry, genetics and many other aspects of the biology of microbes. And they have been instrumental in providing us with antibiotics and vaccines to fight infectious disease.But it is true that shaken cultures are sometimes not the best research models, especially if we try to understand 'the real life' of a microbe in its natural environment.The 'fish tank epiphany' lead Kolter into biofilm research. A first approach he and his collaborators took was to study the biofilms formed by certain Bacillus subtilis strain. The accompanying image shows --on the left-- a beaker with a floating film that the microbe for... Read more »

Roberto Kolter. (2010) Biofilms in lab and nature: a molecular geneticist’s voyage to microbial ecology. Int. Microbiol., 1-7. info:/10.2436/20.1501.01.105

  • August 19, 2010
  • 06:14 AM

And so on, ad infinitum

by iayork in Mystery Rays from Outer Space

Rosy Apple Aphid (Whalon lab, MSU) Normally I don’t talk about research that’s well covered elsewhere, but I like this one so much (and it links back to so many of my earlier posts; check the footnotes for those links) that I’ll make an exception here.  I’d seen bits and pieces of this story, but [...]... Read more »

  • August 19, 2010
  • 06:00 AM

Evolution of Colour Terms: 3 Perceptual Constraints

by Sean Roberts in A Replicated Typo 2.0

Continuing my series on the Evolution of Colour terms, this post reviews evidence for perceptual constraints on colour terms. For the full dissertation and for references, go here.

The perceptual space that results from the processing of opponent colours is non-uniform (see Figure below), meaning that there are optimal ways to describe it (Jameson & D’Andrade, . . . → Read More: Evolution of Colour Terms: 3 Perceptual Constraints... Read more »

  • August 19, 2010
  • 05:04 AM

The final (?) word on those handaxes from Crete

by Julien Riel-Salvatore in A Very Remote Period Indeed

While everybody was busy talking about unexpectedly old cutmarks and other Pleistocene goings-on last week, the paper by Strasser et al. (2010) describing the discovery of quartz handaxe assemblages on Crete quietly came out in Hesperia. This is a topic that was discussed at length on this blog, in several posts that generated a large amount of comments a few months back. The sticking point of ... Read more »

  • August 19, 2010
  • 04:40 AM

What is being taught in the operating room?

by Dr Shock in Dr Shock MD PhD

You can think of a lot such as technical procedures or washing your hands. For residents it’s obvious. Mostly learning the technical procedure of an operation. During long operations I used to count the number of stitches. Once during a vascular operation the chief surgeon out of the blue asked what vessel it was they’re [...]

Related posts:Bedside teaching, Computer Based Learning and Wiki in Medical Education
Personalized Medical Education
Empathy for the Mentally Ill in Medical Education
... Read more »

Irani, J., Greenberg, J., Blanco, M., Greenberg, C., Ashley, S., Lipsitz, S., Hafler, J., & Breen, E. (2010) Educational value of the operating room experience during a core surgical clerkship. The American Journal of Surgery, 200(1), 167-172. DOI: 10.1016/j.amjsurg.2009.06.023  

  • August 19, 2010
  • 12:00 AM

Ultracold atoms as model systems

by Joerg Heber in All That Matters

One of the fundamental concepts of quantum mechanics is that objects can be described as waves, whether they are electrons, atoms, light, anything really, even your cat (or that of Erwin Schrödinger). And of course, if the equations that describe their wavefunctions are identical, objects will behave in the same way. Even if they are fundamentally different physical entities.

Two papers published this week highlight just how far this analogy can go. In one study a gas of ultracold atoms behaves like electrons in a crystal, whereas in the other study the ultracold atoms show quantum effects known from laser physics. [...]... Read more »

Sherson, J., Weitenberg, C., Endres, M., Cheneau, M., Bloch, I., & Kuhr, S. (2010) Single-atom-resolved fluorescence imaging of an atomic Mott insulator. Nature. DOI: 10.1038/nature09378  

Manning, A., Hodgman, S., Dall, R., Johnsson, M., & Truscott, A. (2010) The Hanbury Brown-Twiss effect in a pulsed atom laser. Optics Express, 18(18), 18712. DOI: 10.1364/OE.18.018712  

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