- January 7, 2010
- 05:14 PM
- 1,221 views
Ophthalmology Befuddler #001
by sandnsurf in Life in the Fast Lane
An medical student on your team asks you to review an 81 year-old female who speaks little English. She was BIBA to the ED following a fall. Her nursing home transfer sheet says that the fall was witnessed: she tripped and there was no loss of consciousness. The student is concerned that the patient's right pupil is fixed and slightly dilated in the presence of facial abrasions.... Read more »
Hunter, T., Yoshino, M., Dzioba, R., Light, R., & Berger, W. (2004) Medical Devices of the Head, Neck, and Spine. Radiographics, 24(1), 257-285. DOI: 10.1148/rg.241035185
- January 7, 2010
- 04:59 PM
- 724 views
XMRV not detected in UK chronic fatigue syndrome patients
by Vincent Racaniello in virology blog
A new retrovirus, xenotropic murine leukaemia virus-related virus (XMRV), first identified in tumor tissue of individuals with prostate cancer, was subsequently found in 68 of 101 US patients with chronic fatigue syndrome (CFS). This observation raised the possibility that XMRV is the etiologic agent of CFS. An important question is whether XMRV is associated with [...]... Read more »
Erlwein O, Kaye S, McClure MO, Weber J, Wills G, Collier D, Wessely S, & Cleare A. (2010) Failure to detect the novel retrovirus XMRV in chronic fatigue syndrome. PloS one, 5(1). PMID: 20066031
- January 7, 2010
- 03:22 PM
- 1,382 views
The outfielder problem: The psychology behind catching fly balls
by Dave Munger in Cognitive Daily
It's football season in America: The NFL playoffs are about to start, and tonight, the elected / computer-ranked top college team will be determined. What better time than now to think about ... baseball! Baseball players, unlike most football players, must solve one of the most complicated perceptual puzzles in sports: how to predict the path of a moving target obeying the laws of physics, and move to intercept it.
The question of how a baseball player knows where to run in order to catch a fly ball has baffled psychologists for decades. (You might argue that a football receiver faces a similar task, but generally in football, the distances involved are much shorter, and most football players aren't expected to catch passes at all.)
There are three primary possible explanations for how a baseball fielder catches a fly ball:
Trajectory Projection (TP): The fielder calculates the trajectory of a ball the moment it is hit and simply runs to the spot where it will fall (of course, taking into account wind speed and barometric pressure).
Optical acceleration cancellation (OAC): The fielder watches the flight of the ball; constantly adjusting her position in response to what she sees. If it appears to be accelerating upward, she moves back. If it seems to be accelerating downward, she moves forward.
Linear optical trajectory (LOT): The fielder pays attention to the apparent angle formed by the ball, the point on the ground beneath the ball, and home plate, moving to keep this angle constant until she reaches the ball. In other words, she tries to move so that the ball appears to be moving in a straight line rather than a parabola.
In principle, all three of these systems should work. However, TP is probably impossible; our visual system isn't accurate at determining distances beyond about 30 meters, and outfielders stand up to 100 meters away from home plate. The second system, OAC, might not work because the visual system isn't actually very sensitive to acceleration. And the third system, LOT, is problematic because it doesn't predict a unique path for the fielder to take to the ball. Further, the most likely paths a fielder would take to catch a ball wouldn't be much different under OAC and LOT.
But Philip Fink, Patrick Foo, and William Warren figured out a way to experimentally distinguish between all three models. They had 8 skilled male baseball players and 4 skilled female softball players don VR headsets and attempt to catch virtual balls in a large room. The room was big enough that they could freely move 6 meters in each direction. VR was necessary because the researchers made their virtual balls take paths that aren't possible in real life: Read the rest of this post... | Read the comments on this post...... Read more »
Fink, P.W., Foo, P.S., & Warren, W.H. (2009) Catching fly balls in virtual reality: A critical test of the outfielder problem. Journal of Vision, 9(13), 1-8. info:/10.1167/9.13.14
- January 7, 2010
- 01:10 PM
- 594 views
Even When Scientists are Wrong, Creationists Still Aren't Right
by Jon Voisey in Angry Astronomer
New evidence has shown the most commonly given age of the solar system is wrong.The equations used to derive the age of it from radiometric dating of numerous isotopes was fundamentally flawed because it assumed that the ratio of certain isotopes was the same. Detailed new measurements have shown it's not.This "implies substantial uncertainties in the ages previously determined by Pb-Pb dating". So astronomers have had to recalculate the age of the solar system given this new information.The old age: 4.6 billion years.The new age: 4.6 billion years.Oh wait.... let me zoom in a bit and add a few more significant digits.Old: 4.567 billion years.New: 4.566 billion years.See! See! Scientists got it wrong!But wait.... how it that "substantial"? It still doesn't mean that the Earth is 6,000 years old and Jesus rode around on a dinosaur.In the full geological history of the Earth, that ~1 million years isn't that important. But on the timescales in which solar system formation takes place, it's a decent chunk of time and we need a good understanding of timescales to put into models to make them as accurate as possible.This won't mean a rewrite of any high school textbooks since the significant digits are rounded off before this change is even noticed, but this is yet another example of how science is self correcting and is constantly challenging its own assumptions.Brennecka, G., Weyer, S., Wadhwa, M., Janney, P., Zipfel, J., & Anbar, A. (2009). 238U/235U Variations in Meteorites: Extant 247Cm and Implications for Pb-Pb Dating Science DOI: 10.1126/science.1180871... Read more »
Brennecka, G., Weyer, S., Wadhwa, M., Janney, P., Zipfel, J., & Anbar, A. (2009) 238U/235U Variations in Meteorites: Extant 247Cm and Implications for Pb-Pb Dating. Science. DOI: 10.1126/science.1180871
- January 7, 2010
- 12:49 PM
- 518 views
Omega-3 Fatty Acids - A Promising Novel Therapy For Non-Alcoholic Fatty Liver Disease
by Michael Ash in Nutri-Link Ltd - Clinical Education
Compared with our ancestors, Western societies today lead a lifestyle that is much more sedentary, probably as a result of cultural changes stemming from modern socio-economic morays. Taking into account differences in body size, our energy expenditure per kilogram of body weight has been estimated to be ... Read more »
Hambrecht R, & Gielen S. (2005) Essay: Hunter-gatherer to sedentary lifestyle. Lancet. PMID: 16360760
Manson JE, Skerrett PJ, Greenland P, & VanItallie TB. (2004) The escalating pandemics of obesity and sedentary lifestyle. A call to action for clinicians. Archives of internal medicine, 164(3), 249-58. PMID: 14769621
Harrison SA, & Day CP. (2007) Benefits of lifestyle modification in NAFLD. Gut, 56(12), 1760-9. PMID: 17911352
- January 7, 2010
- 11:22 AM
- 711 views
One Puff Forward, Two Pounds Back
by Shaheen Lakhan in Brain Blogger
Considerable improvements have been made in the health of the population of the United States in the last three decades owing to healthy living interventions, specifically a reduction in smoking. However, during the same period, substantial increases in the incidence of overweight and obesity have adversely impacted the health of the same population. A new [...]... Read more »
Lubetkin, E., & Jia, H. (2009) Health-Related Quality of Life, Quality-Adjusted Life Years, and Quality-Adjusted Life Expectancy in New York City from 1995 to 2006. Journal of Urban Health, 86(4), 551-561. DOI: 10.1007/s11524-009-9344-9
Stewart, S., Cutler, D., & Rosen, A. (2009) Forecasting the Effects of Obesity and Smoking on U.S. Life Expectancy. New England Journal of Medicine, 361(23), 2252-2260. DOI: 10.1056/NEJMsa0900459
Reuser, M., Bonneux, L., & Willekens, F. (2009) Smoking Kills, Obesity Disables: A Multistate Approach of the US Health and Retirement Survey. Obesity, 17(4), 783-789. DOI: 10.1038/oby.2008.640
Wang, Y., Colditz, G., & Kuntz, K. (2007) Forecasting the Obesity Epidemic in the Aging U.S. Population**. Obesity, 15(11), 2855-2865. DOI: 10.1038/oby.2007.339
van Baal, P., Hoogenveen, R., de Wit, G., & Boshuizen, H. (2006) Estimating health-adjusted life expectancy conditional on risk factors: results for smoking and obesity. Population Health Metrics, 4(1), 14. DOI: 10.1186/1478-7954-4-14
- January 7, 2010
- 11:13 AM
- 844 views
Is the Earth even more sensitive to CO2 levels than we thought?
by James Hrynyshyn in Class M
One of the more common arguments from skeptics of anthropogenic climate change is that the Earth has experienced periods during which atmospheric carbon dioxide levels were much much higher than they are today -- as much as 10 times higher. Why worry about a mere 30% increase over pre-industrial levels?
There are several answers to that challenge. The most obvious is that while it may be true that CO2 levels have been several times higher that today's 387 parts per million, the Earth was also a very different place back then. The sea level was much higher, the temperature was much warmer and it bears noting that the biodiversity at such times was quite different. But the assumption that the atmospheric CO2 levels might have been 3,000 ppm did pose some challenges to climatologists trying to figure out how the rest of the planetary ecosystem responded to dramatic changes in CO2. Some of the things that were apparently happening during high CO2 periods didn't quite make sense.
Now, however, comes a paper in PNAS (access priviledges req'd) that reports a strong possibility that CO2 levels during one of those curious periods -- the Mesozoic, which was between 251 and 65 million years ago -- were much lower that previous estimates. If the authors are right, we may have to reconsider our predictions of what might happen over the next century if CO2 levels don't stabilize soon.
Read the rest of this post... | Read the comments on this post...... Read more »
Breecker, D., Sharp, Z., & McFadden, L. (2009) Atmospheric CO2 concentrations during ancient greenhouse climates were similar to those predicted for A.D. 2100. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.0902323106
- January 7, 2010
- 11:11 AM
- 713 views
Social filtering of scientific information - a view beyond Twitter
by Björn Brembs in bjoern.brembs.blog
It's not information overload, it's filter failure (Clay Shirky)Bonetta (2009) gave an excellent introduction to the micro-blogging service Twitter and its uses and limitations for scientific communication. We believe that other social networking tools merit a similar introduction, especially those that provide more effective filtering of scientifically relevant information than Twitter. We find that FriendFeed (already mentioned in the first online comment on the article, by Jo Badge) shares all of the features of Twitter but few of its limitations and provides many additional features valuable for scientists. Bonetta quotes Jonathan Weissman, a Howard Hughes Medical Institute investigator at the University of California, San Francisco: "I could see something similar to Twitter might be useful as a way for a group of scientists to share information. To ask questions like 'Does anyone have a good antibody?' 'How much does everyone pay for oligos?' 'Does anyone have experience with this technique?'" It is precisely for such and many more purposes that scientists use FriendFeed, which allows the collection of many kinds of contributions, not just short text messages. Also in contrast to Twitter, comments to each contribution are archived in that context (and without a time limit), providing a solid base for fruitful, threaded discussions. In your user profile, you can choose to aggregate any number of individual RSS or Atom 'feeds', including scientific publications you bookmark in your online reference manager (e.g. CiteULike or Connotea), your blog entries, social bookmarks (Google Reader, del.icio.us, etc.), and Tweets; and any other items you wish to post directly to your feed. You then look for other users whose profile is relevant to your work and subscribe to them. Every individual item posted in your subscriptions will then appear on your personalized FriendFeed homepage, plus optionally a configurable subset of the feeds you subscribed to. You can choose to bookmark ('like') any of these items (Facebook copied this 'like' functionality just before it bought FriendFeed), comment on them, and share discussion threads in various ways. At first, this aggregation of information and threaded discussions might seem daunting. However, the stream of information can be channeled by organizing it into separate sub-channels ('lists'; similar to but more versatile than 'folders' in email), according to your personal preferences (e.g. one for search alerts). In addition to individual users, you can also subscribe to 'rooms' that revolve around particular topics. For example, the "The Life Scientists" room currently has 1,267 members and imports one feed. The feature that makes FriendFeed truly useful is its social filtering system. Active discussions move to the top of your FriendFeed homepage with each new addition, which automatically brings them to the attention of you and everyone else who reads those feeds. In a sense, the most current and the most popular entries compete for attention at the top, making notifications unnecessary. This means that your choice of both rooms and subscriptions affects and filters the content you see. In that way, for instance, you could set your preferences such that you would only see papers with a certain minimum number of 'likes' among your colleagues. Alternatively, you can opt to hide items with zero likes or comments, ensuring that only those that someone found interesting will reach you. Thanks to a very fine-grained search functionality, threads also remain easily retrievable. Some of the synergistic effects of the many scientists interacting on FriendFeed are already apparent at this early stage of adoption. FriendFeed provides a convenient way to microblog from conferences by means of dedicated threads or discussion rooms created for the event, thus allowing to share comments within and across sessions, or even with people not physically present at the meeting. Such conference coverage has even received direct (e.g. ISMB09, BioSysBio09) or indirect (e.g. ISMB08) support from the conference organizers. Above and beyond conference coverage, scientists use FriendFeed to share papers, experiences on laboratory equipment, resources for teaching, or anything else commonly asked at mailing lists. A number of real-world scientific collaborations have already been sparked from such interactions. Collaborative grant proposals have been initiated, submitted and some of them approved after the idea was passed around and discussed on FriendFeed. Several bioinformatics problems have been solved by code-sharing and advice. Articles in scientific journals have been published by FriendFeed users after meeting and discussing on the platform [1-5]. Of course, since FriendFeed was not designed for scientists, there is room for improvement in terms of usability for scientific purposes. For instance, files can only be uploaded upon starting a thread, not while commenting on it, and there is currently no functionality which infers a measure of reputation to a user from his/her contributions (though the wide-spread use of real names somewhat allows that to be imported). As with all online contributions, citability and long-term archiving are unresolved issues, as is the permanence of services whose source code is not public. Fortunately, the development of social networks tailored to the needs of scientists is actively being pursued from various angles. The Polymath projects, in which researchers collaborate online to solve mathematical problems, provide a number of examples. The recent award of two NIH grants of over $US10M each for exactly such purposes is another. Ultimately, the continued enthusiastic adoption of the sophisticated variants of social filtering tools by a broad community of researchers interested in sharing their science will only increase the usefulness for and thus the capabilities of the online scientific community.References: Lister, A., Charoensawan, V., De, S., James, K., Janga, S. C. C., Huppert, J., 2009. Interfacing systems biology and synthetic biology. Genome biology. 10 (6), 309+. http://genomebiology.com/2009/10/6/309Saunders N, Beltr‹o P, Jensen L, Jurczak D, Krause R, et al. (2009) Microblogging the ISMB: A New Approach to Conference Reporting. PLoS Comput Biol 5(1): e1000263. http://dx.doi.org/10.1371/journal.pcbi.1000263 Neylon C, Wu S (2009) Article-Level Metrics and the Evolution of Scientific Impact. PLoS Biol 7(11): e1000242. http://dx.doi.org/10.1371/journal.pbio.1000242Daub J, Gardner PP, Tate J, Ramskšld D, Manske M, Scott WG, Weinberg Z, Griffiths-Jones S, Bateman A. (2008): The RNA WikiProject: community annotation of RNA families. RNA. 14(12):2462-4 http://dx.doi.org/10.1261/rna.1200508 Huss & al. The Gene Wiki: community intelligence applied to human gene annotation. http://dx.doi.org/10.1093/nar/gkp760 Acknowledgment: This comment has received input from a number of FriendFeed users, as detailed in this thread, and was jointly blogged today by Björn Brembs (Friendfeed, this blog post), Allyson Lister (FriendFeed, blog post) and Daniel Mietchen (FriendFeed, blog post).... Read more »
Bonetta, L. (2009) Should You Be Tweeting?. Cell, 139(3), 452-453. DOI: 10.1016/j.cell.2009.10.017
- January 7, 2010
- 10:39 AM
- 973 views
Circumcision: A Response to Amy Tuteur
by Martin Robbins in The Lay Scientist
This is a response to a controversial piece in Science Based Medicine by Amy Tuteur, M.D. on circumcision: "The case for neonatal circumcision," which cites a recent journal paper of the same title [1]. Beyond calling for the American medical establishment to put pressure on parents to circumcise their infant children, the article implicitly compares those who don't circumcise or who are opposed to circumcising infants to anti-vaccination activists.
read more... Read more »
Tobian, A., Gray, R., & Quinn, T. (2010) Male Circumcision for the Prevention of Acquisition and Transmission of Sexually Transmitted Infections: The Case for Neonatal Circumcision. Archives of Pediatrics and Adolescent Medicine, 164(1), 78-84. DOI: 10.1001/archpediatrics.2009.232
Kim, D., & Pang, M. (2007) The effect of male circumcision on sexuality. BJU International, 99(3), 619-622. DOI: 10.1111/j.1464-410X.2006.06646.x
Krieger, J., Mehta, S., Bailey, R., Agot, K., Ndinya-Achola, J., Parker, C., & Moses, S. (2008) Adult Male Circumcision: Effects on Sexual Function and Sexual Satisfaction in Kisumu, Kenya. Journal of Sexual Medicine, 5(11), 2610-2622. DOI: 10.1111/j.1743-6109.2008.00979.x
- January 7, 2010
- 10:05 AM
- 989 views
Masquerading caterpillars hide in plain sight
by Jeremy Yoder in Denim and Tweed
Insects that have evolved elaborate mimicry of inanimate objects – leaves, twigs, even bird droppings – to hide from predators are a staple of nature documentaries. But do these masquerades work because they help insects blend into the background, or because predators actually see the insects and then dismiss them as inedible leaves, twigs, or bird droppings? It's a tricky question to answer, but a brief paper in this week's Science presents an experiment that tries to do just that [$a].
The paper's authors reasoned that if mimicry-based camouflage works through disguise rather than invisibility, a predator's experience might determine their response to mimic camouflage. They trained three experimental groups of young domestic chicks by introducing them into trial arenas containing either natural hawthorn branches, empty arenas, or hawthorn branches wrapped in purple thread. The wrapped branches were used to test whether the chicks would be more or less likely to attack something twig-like but differently colored (though this is only clear from the supplementary online material).
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Larva of the brimstone moth Opisthograptis luteolata, looking distinctly twig-like. Photo by Michael E. Talbot.
The authors then presented chicks from each "training" group with either one of two species of hawthorn-twig-mimicking moth larvae (the brimstone moth, or the early thorn moth), or a hawthorn twig about the size of a caterpillar. Chicks that had previously encountered natural twigs waited longer to attack the caterpillars than chicks that hadn't previously seen twigs, or that saw the colored hawthorn branches. So, apparently, the chicks were reasoning (inasmuch as chicks reason) that the twig-like object in front of them was the same as the inedible twigs they had tried before.
This is an elegant experimental test of the effect of mimicry as mimicry – what the authors propose to call camouflage by "masquerade." However, it doesn't actually show that what the authors term camouflage by crypsis – blending into the background – isn't also contributing to the benefits that these caterpillars receive from their unique shape and coloration. There's no reason to think that twig-shaped caterpillars can't benefit in both ways, by being less visible in the first place, and then easily mistaken for a twig if they are seen.
In conclusion, here's some video footage of another natural mimic, the leaf insect.
Reference
Skelhorn, J., Rowland, H., Speed, M., & Ruxton, G. (2010). Masquerade: Camouflage without crypsis Science, 327 (5961), 51 DOI: 10.1126/science.1181931
... Read more »
Skelhorn, J., Rowland, H., Speed, M., & Ruxton, G. (2010) Masquerade: Camouflage without crypsis. Science_id, 327(5961), 51-51. http://www.sciencemag.org/cgi/doi/10.1126/science.1181931
- January 7, 2010
- 09:30 AM
- 623 views
Cycling Cells - The circadian rhythm
Circadian rhythm is the cyclic control of cellular processes over a period of roughly twenty-four hours. There are many processes within the body that are held under circadian control; the need to eat and sleep, blood pressure and some hormone production to name a few. Circadian control is an important development in evolution, as it allows behaviour to adapt to appropriate times in the day. Humans have not adapted to function particularly well at night, so using that time for sleeping means they can be more alert during the day and in the hour or so before you wake up (on weekdays at least), the body gets busy increasing the blood-pressure, preparing you to need the bathroom and, slightly bizarrely, increasing testosterone levels.I wasn't planning on doing a post on circadian rhythms, but Alejandro mentioned it in one of the comments, so it was in the back of my head when I was looking for a paper to review this week. And it's about time I started getting back into more general molecular biochemistry (less than five months left till exams!) rather than concentrating exclusively on bacteria.From a cellular point of view circadian rhythms are controlled by careful feedback loops between interacting proteins. In this paper, the main positively regulating proteins they were looking at were proteins named CLOCK and BMAL1, which bind to promoter sequences of circadian rhythm genes and switch them on. They also turn on the negative regulators PER and CRY which, when they get to high enough levels, bind to CLOCK and BMAL1 and stop them from functioning, turning the circadian rhythm genes off again.Many clock proteins undergo post-translational modifications in order to give a further level of control. In particular they can be phosphorylated (a phosphate group is added onto the protein) by proteins known as protein kinases. The main work of the paper I decided to look at (reference below) was identifying GSK3β, a protein kinase which phosphorylates BMAL1. Like most kinases, GSK3β is not just involved in circadian rhythm control, but takes part in many other cellular functions such as control of glucose homeostasis, cell fate determination, and cell survival. It's not surprising, therefore, that is can be involved in a number of pathological conditions, including diabetes, Alzheimer's disease, cancer and bipolar disorder.The first study done for the paper was to show that GSK3β will bind to BMAL1 and phosphorylate it. This was done by adding pure samples of the proteins together, along with radiolabelled ATP as a source of phosphate. The result is shown below (all diagrams taken from the reference at the bottom) wiith GST used as a control to check what the GSK3β does when there's nothing for it to phosphorylate (it phosphorylates itself):As only radiolabelled material shows up on the autoradiogram, this shows that the GSK3β has transferred the radiolabelled phosphate onto the BMAL1.For further proof that the GSK3β was carrying out the phosphorylation under physiologically relevant conditions, cell lines were used which contained no GSK3β (-/- mutants). Comparing the levels of BMAL1 in these cells with wild type cells showed higher levels of BMAL1 in the mutant strain. This is expected as the addition of the phosphate is thought to lead to the addition of another group, ubiquitin. Ubiquitin is (as far as I am aware) an almost universal signal for 'Degrade This Protein'.The next stage was to look for the actual sites of phosphorylation; the places on the BMAL1 where the GSK3β sticks the additional phosphate group. As with most kinases, GSK3β recognises a specific pattern of protein residues (T/SXXXS/T for anyone who's interested) and fifteen of these sequences were found in BMAL1. The exact residues were found by point mutation; certain amino-acids were changed and the resulting change in phosphorylation measured:The wild type protein is shown on the left and the mutant, with the significant T residue converted to an alanine(A) on the left (the change is notated as T21A; the T in position 21 has been changed to an A). This change in one amino acid has decreased the phosphorylation by 40%, although it would be nice to see some actual values rather than relative ones.The final test to confirm that GSK3β is involved in circadian rhythm control of BMAL1 was to show some actual cyclic behaviour of the protein. For this two cell lines were used, the wild type and the GSK3β -/- mutant. α-tubulin was used as a control; this protein is expressed at constant levels over time and therefore shows that the decreasing and increasing levels of BMAL1 is actually due to changing levels in the cell, rather than just a smaller cell sample containing fewer proteins overall:That's quite a beautiful gel; in the wild type cells the BMAL1 cycles nicely over the time period (they don't run the experiment for terribly long, but BMAL1 cycling has been proved adequately elsewhere, and the wild type cells are more of a control than the actual experiment). When you knock out the GSK3β, however, the cycling pretty much stops. The paper is careful to point out that is doesn't completely stop, some evidence of differing levels is still seen, but this is to be expected. It's very rare that important cellular processes in mammals are placed entirely under the control of one protein, and there are likely to be other pathways involved in the circadian control of BMAL1.---Sahar, S., Zocchi, L., Kinoshita, C., Borrelli, E., & Sassone-Corsi, P. (2010). Regulation of BMAL1 Protein Stability and Circadian Function by GSK3β-Mediated Phosphorylation PLoS ONE, 5 (1) DOI: 10.1371/journal.pone.0008561---For those interested in such things, I now have a twitter. Like the blog, it will be strictly sciency, rather than personal and will be updated far more often.... Read more »
Sahar, S., Zocchi, L., Kinoshita, C., Borrelli, E., & Sassone-Corsi, P. (2010) Regulation of BMAL1 Protein Stability and Circadian Function by GSK3β-Mediated Phosphorylation. PLoS ONE, 5(1). DOI: 10.1371/journal.pone.0008561
- January 7, 2010
- 09:13 AM
- 669 views
Social filtering of scientific information - a view beyond Twitter
by Daniel Mietchen in Daniel Mietchen's blog
(Co-blogged with Björn Brembs and Allyson Lister.)
"It's not information overload, it's filter failure." (Clay Shirky)
Bonetta (2009) gave an excellent introduction to the micro-blogging service Twitter and its uses and limitations for scientific communication. We believe that other social networking tools merit a similar introduction, especially those that provide more effective filtering of scientifically relevant information than Twitter. We find that FriendFeed (already mentioned in the first online comment on the article, by Jo Badge) shares all of the features of Twitter but few of its limitations and provides many additional features valuable for scientists. Bonetta quotes Jonathan Weissman, a Howard Hughes Medical Institute investigator at the University of California, San Francisco: “I could see something similar to Twitter might be useful as a way for a group of scientists to share information. To ask questions like ‘Does anyone have a good antibody?’ ‘How much does everyone pay for oligos?’ ‘Does anyone have experience with this technique?’” It is precisely for such and many more purposes that scientists use FriendFeed, which allows the collection of many kinds of contributions, not just short text messages.
Also in contrast to Twitter, comments to each contribution are archived in that context (and without a time limit), providing a solid base for fruitful, threaded discussions. In your user profile, you can choose to aggregate any number of individual RSS or Atom 'feeds', including scientific publications you bookmark in your online reference manager (e.g. CiteULike or Connotea), your blog entries, social bookmarks (Google Reader, del.icio.us, etc.), and Tweets; and any other items you wish to post directly to your feed. You then look for other users whose profile is relevant to your work and subscribe to them. Every individual item posted in your subscriptions will then appear on your personalized FriendFeed homepage, plus optionally a configurable subset of the feeds you subscribed to. You can choose to bookmark ('like') any of these items (Facebook copied this 'like' functionality just before it bought FriendFeed), comment on them, and share discussion threads in various ways.
At first, this aggregation of information and threaded discussions might seem daunting. However, the stream of information can be channeled by organizing it into separate sub-channels ('lists'; similar to but more versatile than 'folders' in email), according to your personal pr... Read more »
Bonetta, L. (2009) Should You Be Tweeting?. Cell, 139(3), 452-453. DOI: 10.1016/j.cell.2009.10.017
- January 7, 2010
- 09:00 AM
- 1,517 views
Evaluating State Endangered Species Lists
by John Beetham in A DC Birding Blog
Long-billed Curlew / Photo by Mike BairdAt a time when federal listings have been delayed and international standards are difficult to implement, state endangered species lists can play an important role in protecting at-risk species. That is, they can protect globally threatened species, especially ones for which their region bears high responsibility. Jeffrey Wells of the Boreal Songbird Initiative set out to assess how well state lists are identifying and protecting globally threatened species and the results were published this week as an article in PLoS ONE, "Global versus Local Conservation Focus of U.S. State Agency Endangered Bird Species Lists."In the United States, 48 states maintain their own lists of species that are endangered, threatened, or of special concern. Wells uses 47 of these lists (excluding Hawaii) and divides the species into four categories based on their global risk of extinction and the degree to which a state bears responsibility for its global population. Global risk is based on assessments produced by Partners in Flight.Percent of each state's E-T-SC bird species in each of four risk-responsibility categories. doi:10.1371/journal.pone.0008608.g002The results show that states are effective at protecting those species that are at risk globally and for which states bear high responsibility. States also give protections to some species that are not at risk globally but are concentrated in their region. However, they also put a lot of effort into protecting secure but locally uncommon species that may not need help as much as the others. For example, state lists include such species as Double-crested Cormorant (2 states), Great Egret (12 states), Laughing Gull (2 states), Bank Swallow (3 states), Magnolia Warbler (2 states), and Dark-eyed Junco (3 states). Meanwhile, some globally threatened species are getting ignored, even when states bear some responsibility for maintaining that global population. Lesser Prairie-Chicken, Long-billed Curlew, Bendire's Thrasher, and Golden-winged Warbler are all listed in half or less of the states that comprise their ranges. Since none of them are federally listed either, those four receive no legal protections in the U.S. apart from what the Migratory Bird Treaty Act offers. My state, New Jersey, lists Savannah Sparrow (locally uncommon) but not Saltmarsh Sparrow (globally at-risk).To a certain extent, it is not really the job of state wildlife agencies to assess and protect based on global risk. That is a task that should belong to the federal government, which has greater resources and more connections to international wildlife agencies for cooperation. However, many globally at-risk species fail to reach even the federal endangered list, let alone benefit from conservation actions. (According to Wells, 16 bird species listed on the IUCN Redlist are not present on the U.S. federal list.) In that context, perhaps states should take a greater role in protecting species based on their global risk of extinction, rather than local criteria. Wells, J., Robertson, B., Rosenberg, K., & Mehlman, D. (2010). Global versus Local Conservation Focus of U.S. State Agency Endangered Bird Species Lists PLoS ONE, 5 (1) DOI: 10.1371/journal.pone.0008608Posted on A DC Birding Blog under a Creative Commons 3.0 License.... Read more »
Wells, J., Robertson, B., Rosenberg, K., & Mehlman, D. (2010) Global versus Local Conservation Focus of U.S. State Agency Endangered Bird Species Lists. PLoS ONE, 5(1). DOI: 10.1371/journal.pone.0008608
- January 7, 2010
- 08:28 AM
- 583 views
Science News: Week of January 3, 2009
by Susan Steinhardt in BioData Blogs
Our weekly compilation of science news for the week of January 3, 2009.... Read more »
Zhang, K., Sha, J., & Harter, M. (2010) Activation of Cdc6 by MyoD is associated with the expansion of quiescent myogenic satellite cells. The Journal of Cell Biology. DOI: 10.1083/jcb.200904144
Meacham, L., Chow, E., Ness, K., Kamdar, K., Chen, Y., Yasui, Y., Oeffinger, K., Sklar, C., Robison, L., & Mertens, A. (2010) Cardiovascular Risk Factors in Adult Survivors of Pediatric Cancer--A Report from the Childhood Cancer Survivor Study. Cancer Epidemiology Biomarkers , 19(1), 170-181. DOI: 10.1158/1055-9965.EPI-09-0555
- January 7, 2010
- 08:00 AM
- 638 views
Scientists torn between cash and kudos
by sciencebase in Sciencebase Science Blog
With ailing banks propped up by billions in taxpayers’ money and nations rolling through the mud of economic recession is it any surprise that we get mightily frustrated to hear of their enormous bonuses and golden pension pots? Of course not… But, here’s a thought…
As the lines drawn between commercial and academic research become increasingly [...]Scientists torn between cash and kudos is a post from: Sciencebase Science Blog
... Read more »
Rose H.C. Wong, & Robert Westwood. (2010) The public good vs. commercial interest: research scientists in search of an accommodation. Int. J. Learning and Change , 4(1), 77-97. info:/
- January 7, 2010
- 08:00 AM
- 762 views
How far can a bee fly, and why should we care?
by Rob Goldstein in Conservation Maven
Entomologists from Switzerland have published a study that measures how far three different species of bees can fly to forage for food. Their study is innovative because it uses a new, direct experimental approach in which patches of host plants were moved progressively farther back from the nest over time. Antonia Zurbuchen and fellow authors measured the number of female bees that were able to forage at the patch at each distance. This research question is crucial for addressing the widespread decline in bee species. ... Read more »
A. Zurbuchen, L. Landert, J. Klaiber, A. Müller, S. Hein, and S. Dorn. (2010) Maximum foraging ranges in solitary bees: only few individuals have the capability to cover long foraging distances. Biological Conservation. info:/10.1016/j.biocon.2009.12.003
- January 7, 2010
- 08:00 AM
- 605 views
Cuttlefish camouflage split decision
by Zen Faulkes in NeuroDojo
As I've written about before, cephalopods are the masters of camouflage. But what happens if they have to try to match two different backgrounds? Allen and colleague (containing several members who worked on the paper I wrote about earlier) tackle this problem with cuttlefish (Sepia officinalis).
There's a couple of possibilities. Because octopus and squid and such can control colour on each half of their body independently, they'll try to match both sides. Another possibility is that they will opt to match only one pattern, and the third option is that they'll opt for something half-way between both.
Cuttlefish match their colour patterns using vision, so the authors created a tank where each half had a different pattern on the bottom. The cuttlefish chose the compromise solution. When against a large checkered pattern and a uniform background, the animals picked something that could be described as a small checkered pattern.
This paper does some other experiments with substrate choices. When they tested more than one substrate at a time, the animals didn't have strong preferences. When given just two choices, cuttlefish like gray bottoms over white ones. But the key finding in substrate choices was that cuttlefish strongly prefer anything that lets them bury themselves.
Why bother trying to look inconspicuous out in the open if you can just hide?
Reference
Allen, J., Mathger, L., Barbosa, A., Buresch, K., Sogin, E., Schwartz, J., Chubb, C., & Hanlon, R. (2009). Cuttlefish dynamic camouflage: responses to substrate choice and integration of multiple visual cues Proceedings of the Royal Society B: Biological Sciences DOI: 10.1098/rspb.2009.1694... Read more »
Allen, J., Mathger, L., Barbosa, A., Buresch, K., Sogin, E., Schwartz, J., Chubb, C., & Hanlon, R. (2009) Cuttlefish dynamic camouflage: responses to substrate choice and integration of multiple visual cues. Proceedings of the Royal Society B: Biological Sciences. DOI: 10.1098/rspb.2009.1694
- January 7, 2010
- 07:59 AM
- 1,455 views
Darwin's Finches Develop Immunity to Alien Parasites
by GrrlScientist in Living the Scientific Life (Scientist, Interrupted)
tags: evolutionary biology, immunology, immune response, antibodies, parasite, avian pox virus, Poxvirus avium, nest fly, Philornis downsi, birds, ornithology, Darwin's Finches, Medium Ground Finch, Geospiza fortis, Ecuador, Galapagos Islands, bpr3.org/?p=52,peer-reviewed research, peer-reviewed paper
A male Medium Ground Finch, Geospiza fortis, sits on a tree branch in Ecuador's Galapagos Islands.
Image: Jen Koop.
People often view the Hawaiian islands as a tropical paradise, the ideal vacation site, but you wouldn't agree with this assessment if you happen to be a bird. According to a federal report published last year in the United States, nearly all of Hawaii's birds are in danger of becoming extinct due to habitat destruction, competition from imported species and of course, infections by alien disease organisms. In short, this tropical paradise is an ecological disaster area.
Read the rest of this post... | Read the comments on this post...... Read more »
Huber, S., Owen, J., Koop, J., King, M., Grant, P., Grant, B., & Clayton, D. (2010) Ecoimmunity in Darwin's Finches: Invasive Parasites Trigger Acquired Immunity in the Medium Ground Finch (Geospiza fortis). PLoS ONE, 5(1). DOI: 10.1371/journal.pone.0008605
- January 7, 2010
- 07:00 AM
- 467 views
At Your Service….. Part II
by Elements Team in Elements
By: Rosemary Stephen PMed, (cert) EOH, IPM, Elements: Environmental Health Intelligence
In Part I of our three part series, we looked at the contributions animals offer to Public health. Cats and dogs played an important a role in both World Wars, controlling mice and rats in the trenches, and today they are central in numerous beneficial [...]... Read more »
Rosemary Stephen PMed, (cert) EOH, IPM. (2010) At Your Service.. Part II. Elements: Environmental Health Intelligence. info:/
- January 7, 2010
- 06:48 AM
- 551 views
Devil’s Facial Tumor: Tracing Origins with Next-Gen Seuqencing
by Rick Scavetta in DNA Dude
Since the mid 90s everyones favourite carnivorous marsupial, the Tasmanian Devil, has been suffering from an unusual from of cancer called Devil Facial Tumor Disease. What’s so unusual about this cancer is that it’s transmissible. That means it can be passed onto another, unrelated animal. This occurs through biting during mating and feeding when the [...]... Read more »
Murchison, E., Tovar, C., Hsu, A., Bender, H., Kheradpour, P., Rebbeck, C., Obendorf, D., Conlan, C., Bahlo, M., Blizzard, C.... (2009) The Tasmanian Devil Transcriptome Reveals Schwann Cell Origins of a Clonally Transmissible Cancer. Science, 327(5961), 84-87. DOI: 10.1126/science.1180616
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