biology
sporte | October 15, 2007This morning Bora and I both gave talks in Second Life. Since this was a pretty new experience for me, I thought I'd share my thoughts on it.
Ever since the days when I watched cartoons on Saturday mornings, I thought it might be fun to be in one. But when I tried it this morning, truthfully, it was a bit scary. I haven't experienced stage fright like that for quite awhile. Perhaps it was the setting. I was really nervous and I hadn't practiced with Second Life enough to know what to do.
Watching a talk in Second Life
Moving around in my avatar felt awkward. It was strange not to be…
oracknows | October 12, 2007Although his taste in music is questionable at best, Snowball the Cockatoo definitely knows how to get down and get funky.
I can't say I've ever seen anything like this before. Now maybe if we introduced Snowball to some old Parliament-Funkadelic. Tear the roof off the sucker, Snowball, and give up the funk!
razib | October 12, 2007Eight Americas: Investigating Mortality Disparities across Races, Counties, and Race-Counties in the United States (Open Access). Here's the most interesting finding for me:
The 12.8-y gap in life expectancy between females in Americas 1 and 7 is approximately the same as the gap between Japan, with the highest national life expectancy for females in 2001 (84.7 y), and Fiji, Nicaragua, and Lebanon...Asian females in the US have a life expectancy that is 3 y higher than that of females in Japan...For males, the 15.4-y gap in life expectancy between Asians (America 1) and high-risk urban…
revere | October 12, 2007Interesting paper from McAuley et al. (St. Jude's) on the PB1-F2 protein produced by an alternative reading frame on the PB1 gene of the influenza A virus. Most of you know that genes encode proteins via a three letter code. If you read the sequence of three letters by starting one letter earlier or later you will get a different sequence (e.g., ABCDEF is two three letter sequences ABC and DEF, but if you start a letter later you get BCD EF+whatever would have started the next three letter sequence originally). You have shifted the three letter frame for reading, hence the designation as an…
terrasig | October 11, 2007[Aufmerksamkeit! Begrüßen Sie deutsche Freunde und Leser des Focus Wissenschafts-Community. Glückwünsche zu Profs Ertl und Grünberg auf dieser enormen Ehre!]
I'm intentionally being dramatic but an interesting discussion emerged in the comment thread of my post on the work of Germany's Gerhard Ertl being recognized with this year's Nobel Prize for Chemistry. One reader had a perception that the work of an American contributor to surface chemistry was being ignored. Dr Gerald Harbison followed up on this notion at his own blog, The Right Wing Professor.
Indeed, the three scientists that…
moleculeoftheday | October 11, 2007DCMU is a simple aromatic molecule, and a pretty specific electron acceptor for the photosystem II protein found in plants. What does this mean?
Electron transfer reactions are important in all of life; plants use it in photosynthesis. Some DCMU will kill your plants nicely, and it's a broad-spectrum insecticide. Similarly, all eukaryotes use proton transfer in their mitochondrion. This is why 2,4-dinitrophenol will help you lose weight like crazy (if it doesn't kill you, which isn't exactly unlikely). Different mechanism, but you're still collapsing a gradient and wreaking havoc on a vital…
revere | October 10, 2007It's taken longer than many of us wanted, but some new data on host susceptibility is now coming in. The influenza research group at St. Jude's has just published a paper in CDC's journal, Emerging Infectious Diseases, verifying that common land based birds can be infected with highly pathogenic avian influenza virus H5N1. The St. Jude's group inoculated house sparrows, European starlings and pigeons with four strains of H5N1 that were isolated in 2004 - 2006.
Hi path H5N1 was first found in poultry in southern China in 1996. It is lethal to chickens and other poultry. Ducks are usually…
razib | October 9, 2007Predicting Odor Pleasantness from Odorant Structure: Pleasantness as a Reflection of the Physical World:
Although it is agreed that physicochemical features of molecules determine their perceived odor, the rules governing this relationship remain unknown. A significant obstacle to such understanding is the high dimensionality of features describing both percepts and molecules. We applied a statistical method to reduce dimensionality in both odor percepts and physicochemical descriptors for a large set of molecules. We found that the primary axis of perception was odor pleasantness, and…
oracknows | October 8, 2007No IgNobels here, the 2007 Nobel Prize for Physiology or Medicine has been awarded to Mario R. Capecchi, Martin J. Evans, and Oliver Smithies for a technique that is so incredibly important to modern biomedical research that it's a wonder they didn't get the prize before:
This year's Nobel Laureates have made a series of ground-breaking discoveries concerning embryonic stem cells and DNA recombination in mammals. Their discoveries led to the creation of an immensely powerful technology referred to as gene targeting in mice. It is now being applied to virtually all areas of biomedicine - from…
omnibrain | October 8, 2007The Nobel Prize in Medicine has gone to Mario R. Capecchi, Oliver Smithies, and Sir Martin J. Evans for inventing a technique called Gene Targeting.
According to the NYTimes:
The three scientists were honored for a technique called gene targeting, which lets scientists inactivate or modify particular genes in mice. That in turn lets them study how those genes affect health and disease.
To use this technique, researchers introduce a genetic change into mouse embryonic stem cells. These cells are then injected into mouse embryos. The mice born from these embryos are bred with others, to produce…
scientificactivist | October 8, 2007The winners of the 2007 Nobel Prize in Physiology or Medicine were announced this morning. The prize went to Mario R. Capecchi (University of Utah), Martin J. Evans (Cardiff University), and Oliver Smithies (UNC), all for their work contributing to knockout (and knock-in) mice becoming one of the most powerful scientific tools available to biologists today. Or, in the less inspiring Nobel-speak, "for their discoveries of principles for introducing specific gene modifications in mice by the use of embryonic stem cells."
From the official press release:
This year's Nobel Laureates have made a…
evolgen | October 7, 2007My series on using computational tools to study molecular evolution [Publishing Original Research on Blogs] has focused on the evolution of the aldolase gene family in Drosophila. When I described the Backstory, I left out a lot of details regarding the biochemistry of glycolysis. Well, Larry Moran happens to be a biochemist -- he's even written a book about biochemistyr -- and he's posted a more comprehensive look at aldolase. I focused my introduction on animals, which use aldolase in glycolysis -- the breakdown of glucose into smaller molecules. Larry points out that the opposite pathway (…
oracknows | October 6, 2007I know I've said before that I don't really "get" the whole cephalopod thing that P. Z. has, but I wonder if he's heard of this little thing:
Monday, October 8 is Unofficial International Cephalopod Awareness Day.
Certainly, I hadn't.
revere | October 6, 2007The headline was worrisome: "Bird flu becoming riskier for humans." The story was about a new paper in PLoS Pathogens from Kawaoka's lab that was said to identify "a specific change that could make bird flu grow in the upper respiratory tract of humans," according to the lab leader.
Birds usually have a body temperature of 41 degrees Celsius, and humans are 37 degrees Celsius. The human nose and throat, where flu viruses usually enter, is usually around 33 degrees Celsius.
"So usually the bird flu doesn't grow well in the nose or throat of humans," Kawaoka said. This particular mutation…
tqa | October 5, 2007
Last week, I had a picture of a live spider for you to identify. Most of the guesses came quickly, and were absolutely correct - the spider in the picture was a Spiny-Backed Orbweaver. This week's arthropod might be a little more challenging.
The picture below features a pinned museum specimen, and was taken through a light microscope at about 40x magnification. The edge of a quarter appears in the photo for scale. The species in question is unique to the island of Hawaii, and is found on the wetter slopes of the younger volcanoes.
Good luck. I'll post either the answer (if someone…
grrlscientist | October 3, 2007tags: researchblogging.org, H-index, impact numbers, scientific journals
A friend, Ian, emailed an opinion paper that lamented the state of scientific research and the effect this has had on science itself. In this paper, by Peter A. Lawrence, a Professor of Zoology at University of Cambridge, the main point is that modern science, particularly biomedicine, is being damaged by attempts to measure the quality and quantity of research being produced by individual scientists. Worse, as this system careened out of control, it gave rise to a new and more damaging trend: ranking scientists…
tfk | October 1, 2007Last year (just before I joined the fold) the Scienceblogs gang teamed up with a company called DonorsChoose to help out teachers with good ideas about how to make science education better.
DonorsChoose is a website that lets teachers post proposals for funding, and lets potential donors search through those projects for ideas that seem to match their own sense of what's needed.
This year, we're doing the Blogger Challenge again. If you click through the little thermometer link in the sidebar, or this link right here, you can pick one of the projects I've chosen and help fund any of the…
evolgen | September 29, 2007Most of us are so used to the male+female=baby system of reproduction that we practice that it doesn't even occur to us that there are other options. Sure, there's the occasional instance of parthenogenesis in some megafaunal species, but that seems like the exception rather than the norm. And we do recognize that a lot of the microbes that make up the majority of life on Earth reproduce asexual. But, when it comes to sex, we're stuck on male+female=baby.
Kurt Vonnegut thought otherwise. In his classic novel Slaughterhouse Five, he introduced the Tralfamadorians and their understanding of…
purepedantry | September 28, 2007The Scientist has a wonderful article about complimentarity in biology. Complimentarity is the application of two or more different theoretical approaches to a single problem:
"Light and Life" is perhaps best known for its focus on Bohr's concept of complementarity. According to this concept, some natural phenomena can only be completely understood by combining two or more experimental approaches that cannot be simultaneously implemented. More generally, complementarity asserts that apparently incompatible ideas or perspectives can both be necessary to achieve a fuller understanding of an…
evolgen | September 27, 2007Or is he micro-phobe?
Nature Genetics has published a mostly positive review of the new Evolution textbook by Nick Barton and others (the others include blogger Jonathan Eisen) The review is penned by Francisco Ayala. Among the things Ayala brings up is the coverage various taxa receive:
Surprisingly, however, five of the nine chapters of Part II are dedicated to the history of microbial evolution, and only one chapter deals with the diversification of plants and animals.
So, of the nine chapters in Part II, six deal with particular groups of organisms. Of those six, five focus on microbial…