biology
revere | September 29, 2006We've now had a chance to take a look at a new paper in Nature (advance online publication 27 September 2006 | doi:10.1038/nature05181) on increased host immune and cell death responses in mice infected with the reconstructed 1918 virus compared to other viruses with only some of the 1918 gene segments. It is a very interesting paper.
The authors (Kash et al.) infected mice intranasally (through the nose) with four viruses, one a currently circulating human H1N1 virus, A/Texas/36/91, dubbed Tx91 for short, and three others, two produced by replacing first two of the eight gene segments of…
razib | September 27, 2006Our old friend Brown Gaucho is hosting Tangled Bank #63. I enjoyed his post, The importance of evolution in medicine. BG is a primatologist-turned-med student, so he knows of what he speaks. But, I do have to take some issue with this contention:
Anatomically and genetically, humans haven't changed all that much in the past 100,000 years.
Yes, anatomically modern humans emerged over 100,000 years ago, but, that does not suffice to allow us to assume that genetically humans haven't changed "all that much." Of course, that depends on how you define "all that much," but a supercharged…
terrasig | September 26, 2006Dr Bruce Alberts, recently departed president of the US National Academy of Sciences and Professor of Biochemistry and Biophysics at UCSF, just spoke this morning at a symposium celebrating the 75th anniversary of the Duke University School of Medicine. The overall program is incredible, with four Nobel laureates in three days, plus a number of Lasker Award winners including one of this year's (Linda Grieder).
I'm compelled to put up this quick post on Dr Alberts' talk because of his ambitious plan for improving scientific literacy of the US and the scientific prospects for grad students and…
evolgen | September 25, 2006
As if we didn't have enough "-omes" in biology, I have come across yet another one: the methylome. It's beginning to sound like a Hindu temple up in here. My fascination with the -ome is well documented. I was made aware of the newest -ome in my collection by this preview of this article in Cell. The preview is entitled "The First High-Resolution DNA 'Methylome'" and describes a paper announcing a high resolution map of DNA methylation in the Arabidopsis genome.
We can thank Andrew Feinberg for introducing the term methylome, which he defines as "a neologism that describes the complete set…
tfk | September 24, 2006In order to protect their property values, landowners in North Carolina are clearcutting their land. If that seems silly to you, know that you aren't alone. Apparently, their plan is to make the land unsuitable for endangered red-cockaded woodpeckers. The town is considering instituting a moratorium on land-clearing permits, and the feds are pointing out that even if the land were designated as protected habitat, it would still be possible to build, and indeed trees with nests in them could still be cut down under some circumstances.
Personally, I'd rather buy land that I knew would be…
tfk | September 22, 2006
Finding a rat snake coiled up on a bit of shrubbery is a bit of a surprise. Rat snakes like this Elaphus obsoleta are among the most abundant snakes around, and are incredibly economically beneficial. As the name suggests, they are major predators on various pest species.
This one was just hanging out comfortably on a branch. I nearly walked right past it. The snake didn't seem to mind me going in for a close-up, which is unusual. These snakes are known to be a bit touchy.
Even though these snakes are quite common and can get up to 8 feet long, they still manage to hide right under…
evolgen | September 21, 2006Tara has been given the task of pointing out some of the flaws in Chapter 7 of Jonathan Wells's The Politically Incorrect Guide to Darwinism and Intelligent Design. From what I can gather, this is the chapter in which Wells claims that biology does not need evolution because evolution has no applications in medicine or agriculture. In doing so, Wells reveals he does not understand the difference between natural and artificial selection:
The clinical use of antibiotics creates a highly artificial situation. Antibiotic-producing microbes must be isolated from their natural surroundings and…
razib | September 19, 2006A spicy solution for colon cancer?:
Looking for a cancer cure? Try the spice rack.
In the last few years, that tactic has proved productive for researchers investigating turmeric, a curry spice used for centuries in Indian traditional medicine.
They've found that turmeric's active ingredient, curcumin, works in the lab to fight skin, breast and other tumor cells. In fact, human clinical trials employing curcumin have already been launched.
You gotz to know, my shit is medicinal! Sweetness in, and sweetness out.
Update: Abel says my shit isn't applicable.
revere | September 19, 2006[Warning: this post is fairly long and has a reasonable geek factor. It explores the question whether the virulence of H5N1 "must" moderate as the virus evolves.]
The high case fatality ratio of H5N1 (currently around 60%) is a reflection of how virulent this virus appears to be at the moment. Virulence is the ability to cause severe disease. The common cold virus and H5N1 both cause disease (both "pathogenic") but H5N1 is highly virulent, the common cold virus is not. The only thing a virus does is make copies of itself. It doesn't grow, it doesn't eat, it doesn't eliminate waste or move. It…
tfk | September 15, 2006Voles are among the most abundant mammals in North America, but most people have never actually seen one. There's a native vole species found pretty much anywhere from the Arctic into Mexico. There are a couple dozen species in North America, and about twice as many in the Old World.
These fuzzy beasts are one species I study (this Meadow Vole, Microtus pennsylvanicus, was at a rest stop in Massachusetts), and I wholeheartedly agree with the sentiment expressed in by the author of a recent review of vole genetics:
"Nobody has posters of voles on their wall," said J. Andrew DeWoody,…
evolgen | September 13, 2006My last post was rather negative, and I tried my damnedest to not come across as an asshole. I think it's important to realize, however, that as cool as evo-devo is, it won't revolutionize evolutionary biology until it can be extended beyond animal body plans. Carl Zimmer commented that studies on social microbes may just make that extension. Lo and behold, PLoS Biology has published an essay on cooperation among microorganisms. It's very accessible to a general audience and open access, so you have no excuse not to read it.
The article is so readable (without requiring expertise in…
terrasig | September 12, 2006I have to admit to feeling a bit unnerved by smelling fire all day yesterday, the anniversary of the US terrorist attacks.
Little did I know that we've got a little case of overzealous municipal composting gone awry:
A massive pile of leaves and wood at a city of Durham composting facility ignited over the weekend...Durham officials said in a media release issued Monday that the giant pile of rotting organic matter is thought to have spontaneously caught fire.
I was just reminded over the weekend that alligators make compost piles to generate the heat necessary to incubate their eggs.…
moleculeoftheday | September 11, 2006A diverse series of compounds, known as the phenethylamines, are created from the amino acid tyrosine (bold, at bottom, below). In vivo, things like adrenaline and dopamine are generated. Small amounts of tyramine are also generated. These are particularly concentrated in fermented foods like cheese, beer, wine, and pickles. Normally, the body can process these with facility; an enzyme called "monoamine oxidase" exists to do just this. If a food with a large amount of tyramine is ingested, though (mistletoe, apparently, fits this bill), or the MAO pathway is compromised (certain, older…
razib | September 9, 2006The current issue of Current Biology is about sex. I really dig David C. Queller's primer on sex ratios, Fisher in 'da house yo!
tfk | September 8, 2006On Fridays, we like to highlight some of the remarkable and beautiful things you find right under your nose.
This week, a reader sends in some photos of Lycoperdon pulcherrimum, Latin for "most beautiful wolf-fart."
What we see is the fruiting body of a fungus. Most of the biomass of fungi is below ground, thin threads called hyphae that reach out and absorb nutrients and break down dead material.
Some fungi grow into roots (forming what are called mycorrhizae) get sugar from trees and in exchange help extend their ability to gather water and nitrogen. There have even been studies showing…
tfk | September 5, 2006I've never seen a train wreck. At least not outside of news reports and movies like The Fugitive. So I can't be certain if reading the commentary at Billy Dembski's blog is exactly like watching a train wreck, or if the right analogy is less bloody and more entertaining.
Today, PaV asks How Random is Random Mutation?, because he came across a study in which four different strains of yeast evolved the same solution to a resource shortage. Somehow, he spends a thousand words pondering this problem without using the only word that matters: selection (though he does dismiss "selective…
evolgen | September 5, 2006As I was working on my computer (in my office) this afternoon, a small critter was flying around my head. Based on my current location (in a building housing at least 3 Drosophila labs) and my previous whereabouts (our lab's fly room), I surmised that this was most likely a member of genus Drosophila. My suspicions were confirmed when, at 7:45pm (about 3 hours after I first noticed the pest), she (I think it was a she from the quick glance I got) landed on my computer monitor. Upon closer inspection (although not long enough to adequately surmise the sex) I noticed the fly was too lightly…
evolgen | September 5, 2006I got all excited when I read the following article title in the week's issue of PNAS:
Abnormal sex ratios in human populations: Causes and consequences
I hoped the authors would discuss meiotic drive and segregation distortion. It turns out they're concerned with son preference and sex-selective abortion. I guess stuff like this doesn't really interest them.
tfk | September 4, 2006In Science, two biologists reported on the effects of fishing in South American rivers. Removing a large fish, Prochilodus mariae, from the river causes rapid changes in how carbon (stored energy) passes through the river, decreasing the cycling of carbon. In fact, they explain, "Impacts of removing Prochilodus on carbon flow equaled or exceeded effects of removing [in different studies] all fish, invertebrates, shrimps, and predatory fish in other streams and lakes."
The removal of one species from one side of a river reduced flow of organic material by 60%, and changed the sort of growth…
tfk | September 3, 2006
Saying "This compares with any treasure anywhere in the world,":
Gov. Kathleen Sebelius and the Nature Conservancy on Friday announced the donation of a conservation easement encompassing 10,000 acres [of tallgrass prairie in the Flint Hills].
The tallgrass prairie once stretched in a giant sea of grass from Alberta down to Texas, a continuous swath of grass across the continent. Pioneers describe having to stand in their stirrups to see over the grass. Giant herds of bison migrated across it, with native people and the prairie wolves trailing the herds.
A prairie lives in its roots, with…