biology
revere | August 16, 2006A helpful reader (hat tip to easy hiker) sent along a story from New Scientist concerning a new report in The New England Journal of Medicine. The NEJM paper is a case series of six subjects who almost died as a result of a clinical trial of a monoclonal antibody being tested as a drug for rheumatoid arthritis. Within an hour of receiving the drug, TGN1412, all six suddenly developed a cytokine storm syndrome, with severe pain rapidly developing to multiorgan failure and respiratory distress. This result was unexpected as nothing like it had occurred in the animal trials and the dose given…
evolgen | August 15, 2006Given the expected frequency of a certain outcome of a replicate in an experiment, we can estimate the expected variance around that mean (either by deriving it or performing simulations). I have heard that laboratory experiments tend to have greater variances than expected due to conditions not included in the model (ie, we can't control for every variable in an experiment) when determining the expected variance. I am looking for a citation that addresses the issue of variance in laboratory experiments. Specifically, I am interested in an article that deals with higher than expected variance…
evolgen | August 14, 2006I can't speak for each and every one of the other biologist types in the house here at ScienceBlogs, but one comment on Chad's post on highfalutin particle physicists struck a chord with me. It all starts with this quote getting back at people who think their research is the be all and end all of all science:
One thing that bugs the heck out of me, is when I hear particle physicists talk about their field as if it is all of physics. I have a great love of particle physics, so I'm not dissing the field at all, nor arguing that it isn't more fundamental, but it rubs me the wrong way to…
oracknows | August 12, 2006After my experience with using (or, as at least one of my readers has suggested, misusing) my blog to get an article to which my university does not provide online access, it occurred to me just how much our means of accessing the scientific literature has changed in the last decade and just how radical those changes have been. Again, those who are old farts with me may remember that a little more than 10 years ago at the institution where I did my residency, we could do electronic searches of the Medline database, but it wasn't over the Internet. Basically, the library bought access to…
razib | August 11, 2006The headline says, Evolution Less Accepted in U.S. Than Other Western Countries, Study Finds, but here is the money shot: "The only country included in the study where adults were more likely than Americans to reject evolution was Turkey." My liberal friends often make fun of the "inbred" Creationist yokels who inhabit the hinterlands of this great nation, and contrast them with the sophisticated secularity over the waters. On the other hand, many Americans, especially culturally sensitive progressives declare that the EU should let Turkey in to show that it is "open minded" and not a "…
jlynch | August 9, 2006
This MSNBC article highlights research which has used synchroton-radiation X-ray tomographic microscopy to study the three-dimensional structure of embryos from the mid-Cambrian annelid, Markuelia. The research is being lead by Phil Donoghue at the University of Bristol, whose website also includes an impressive video. Donoghue provided the title for this post.
The paper is Donoghue, P. C. J., Bengtson, S., Dong, X., Gostling, N. J., Huldtgren, T. M., Cunningham, J. E., Yin, C., Yue, Z., Peng, F. and Stampanoni, M. 2006. "Synchrotron X-ray tomographic microscopy of fossil embryos" and has…
revere | August 9, 2006The Indonesian government has given permission to release the sequences of some 40 or so H5N1 viruses isolated from human cases in that country to publicly accessible gene databases. The US CDC has now removed any password protection preventing general access at the Influenza Sequence Database at Los Alamos National Laboratory and has indicated the sequences will also be deposited in the US National Library of Medicine's database, GenBank.
The move to put the data in the public domain, giving scientists from around the world free access, came after the Indonesian government told the World…
moleculeoftheday | August 8, 2006Methylene blue is a well-known dye. It is useful as a biological stain, binds to DNA, and can turn your urine blue.. Incredibly, I'm opting to talk about how it's used in time-sensitive DVDs.
Awhile back, a DVD format called Flexplay was introduced. The idea here is that since DVDs are so relatively cheap to produce, there's no real reason to have the customer return them (except to avoid diluting the value of purchased DVDs). One ill-fated format, DIVX, came about a few years back, but it was unwieldy and essentially a pay-per-view system - special players had to be hooked up to a phone line…
scientificactivist | August 8, 2006From the archives:
(13 January 2006) What do global warming and epidemic diseases have in common? Apparently they have a lot, at least when it comes to amphibians.
Microorganisms have a knack for showing up in unexpected places. In the 1980s, two scientists discovered a bacterium called Helicobacter pylori that causes over 80% of stomach ulcers, once thought to be primarily caused by stress. This turned medical dogma upside-down and earned them the 2005 Nobel Prize in Physiology or Medicine . Even microorganisms aren't safe from other microorganisms, with bacteria, for example under constant…
revere | August 5, 2006Indonesia is making its sequences available to the world scientific community, at long last. We aren't going to ask how or why or continue to chide them for keeping the sequences until now. We applaud their decision to do so and urge others to follow their example.
"I've learned that scientists across the world have complained that they could not access the data and made statements as if we had hidden it," Health Minister Siti Fadilah Supari told a press conference here Thursday.
"For the sake of basic human interests, the Indonesian government declares that genomic data on bird flu viruses…
evolgen | August 3, 2006I am housed in a biology department. Wow, that came out a lot more impersonal than I intended. Let me try that again: My advisor's appointment is to the Biology Department at my university (not much better...eh). Being in a biology department means the faculty interests are very diverse (compared to, say, a biochemistry department, ecology and evolution department, or a neurobiology and behavior department), and so are the departmental seminars. This may seem like a bonus at first, but, in reality, it means that any given seminar will be fairly inaccessible to most people in the department.…
razib | August 2, 2006I have talked about the problems that may occur because of long term societal inbreeding in the past. In short, in a society that is predominantly outbred isolated cases of cousin marriage are not particularly deleterious, but in many cultures systemic inbreeding results in tunneling and narrowing of lineages into discrete effective population pools where stochastic effects start to loom large. In plain English, the number of unique ancestors in inbred clans starts drop in relation to what one would predict in a panmictic context. Deleterious recessives masked in the ancestors are then…
revere | August 2, 2006I have now had a chance to read the PNAS paper by Maines et al. and it is surprising in two respects. The first is it isn't that interesting. The second is related to the first. Why did they bother to hold a press conference about it? Even more, why did the press conference focus on the reassortment question when that didn't establish much. Anyway, that's how I read it. Here are my reasons.
The most important part of this paper is methodological, testing a ferret infection model for transmissibility. Ferrets have been used as a reasonably good biological model for infectivity and virulence in…
grrlscientist | August 1, 2006I just received this emergency email from the American Bird Conservancy.
The U.S. Environmental Protection Agency (EPA) is poised to make a decision on whether to ban the bird-killing pesticide, carbofuran. This is the most deadly pesticide to birds currently being used in the United States. It is more toxic than DDT. A single drop is enough to kill a bird.
The ABC just learned that because of pressure from the manufacturer, FMC corporation, the EPA may make act like a bunch of governmental whores by making the wrong decision to elect to keep this pesticide on the market. We have 24 hours…
revere | August 1, 2006The long awaited reassortment experiment where the 1997 H5N1 virus was combined with a seasonal strain of human H3N2 virus is being reported today in the Proceedings of the National Academy of Sciences (PNAS, known colloquially amongst scientists as "penis"). As of this writing I was not able to get a .pdf so all I know is what is being reported on the newswires as a result of a press conference held by CDC Director Gerberding and a co-author of the study, Dr. Jacquiline Katz of CDC. It's hard to know the real significance of this work until we see the actual paper but here is the synopsis as…
evolgen | July 31, 2006I have mentioned before that at one point in my life I wanted to study conservation genetics. This field can be thought of a subdiscipline of molecular ecology -- wherein researchers use molecular markers to test hypotheses regarding demography in their population of interest. Jacob at Salamander Candy has a post on the usefulness of neutral markers in conservation. Here's a taste:
The problem is, a growing body of evidence suggests that patterns of variation and divergence in adaptive traits are not well reflected by neutral markers (refs 1-8). In the hypothetical species mentioned above, a…
evolgen | July 27, 2006I'm in the process of exhuming myself from under a mountain of work, that's why the posting's been ultra-light. My last link to cool pictures of bugs went over well, so I'm giving you a few more pictures. These come from a friend's website -- be sure to check out the bee and its hitchhiker.
revere | July 27, 2006Influenza/A viruses naturally infect aquatic wildfowl like ducks and there are a lot of influenza/A subtypes besides the H5N1 that has been in the news. Some people are heavily exposed to wild ducks, namely serious duck hunters and game handlers. Why don't they get infected with some of the other influenza virus subtypes? It turns out nobody has looked to see if they do until now. In a paper just published in CDC's journal, Emerging Infectious Diseases scientists from the University of Iowa and St. Jude's Children's Hospital report that on occasion it is possible to see evidence of infection…
evolgen | July 23, 2006Check out these pictures of tiny little critters up close. Wow! Thanks to Neil for pointing this out.
evolgen | July 20, 2006A few months ago I promised that I would publish some original research on this blog. I managed to churn out some background, but I still haven't gotten around to presenting any results. Even though I wasn't able to get my original research out, it doesn't mean that no one is publishing research on Drosophila on blogs. MissPrism has performed a somewhat scientific study of condiment preference in Drosophilids. Her conclusion: they prefer vinegar to sweet things. I guess that's why they call them vinegar flies.