evolution
grrlscientist | September 12, 2007tags: Tangled Bank, blog carnivals
The 88th issue of Tangled Bank is now available for you to read. This blog carnival links to the best recent writing about nature, science and medicine in the blogosphere. Be sure to go there to explore the links they have!
sporte | September 11, 2007Two protein structures from an avian influenza virus are shown below. One form of the protein makes influenza virus resistant to Oseltamivir (Tamiflu®)
Don't worry, these proteins aren't from H5N1, but they do come from a related influenza virus that also infects birds.
technorati tags: molecular models, protein structures, influenza, bioinformatics, Cn3D
One protein structure is from a strain that is sensitive to an anti-viral drug called "Tamiflu®". The other structure is from the same virus, except there's a slight difference. A single base change in the viral RNA changed the codon that…
loom | September 10, 2007The bloggers here at Scienceblogs all have other professional lives--professors, doctors, software engineers, and so on. My own line of work as a science writer can make blogging a bit awkward every now and then. Take, for instance, an article I wrote for tomorrow's New York Times about moray eels. It turns out that they have bizarre jaws hidden in their throats that catapult forward into their mouth to grab prey.
If you read other blogs at Scienceblogs, this may sound like slightly old news. That's because the paper describing this research came out on Wednesday in the journal Nature, and…
loom | September 10, 2007What do human spit, baker's yeast, and fly sex have in common? Together, they illustrate a way in which new kinds of genes evolve.
Scientists published a paper in Nature Genetics Sunday in which they studied an enzyme called amylase that's produced in saliva and breaks down starch. Human amylase genes share a common ancestry with the amylase gene found in our close relative, the chimpanzee. But they are different in some important ways. Instead of one amylase gene, we have several. Human amylase genes range from 2 to 15 copies, averaging three times as many as chimpanzees. But our extra…
sporte | September 10, 2007One of the places that I've always wanted to visit in Portland, OR, is Powell's City of Books. Powell's is the kind of bookstore that people in Seattle discuss in the same reverent tones that they use when they're describing Cody's in Berkeley or City Light in San Francisco.
It's not just a bookstore. It's a destination.
I guess that's why I was soooo disappointed.
From the outside Powell's looks pretty low key and you're really relieved to have escaped the overpowering smell of patchouli and the feeling that maybe Jerry didn't die, he just moved to Portland and hangs out at the…
oracknows | September 9, 2007The Secular Outpost informs me of the existence of a brand new Jack Chick tract. I don't know if it truly is new or not, but it does have its copyright listed as 2007. This time around, Jack is explaining why the dinosaurs really died out. (Hint: It wasn't some big nasty meteor millions of years ago.) It starts out with humans hunting a dinosaur and degenerates from there.
(Click on the picture for the full tract.)
This was so silly that at first I thought it must be a parody. But then I remembered: This is Jack Chick we're talking about here. I will say one thing, though. The picture of…
pharyngula | September 9, 2007Whenever I spot some old thread suddenly getting a surge of new comments, I can guess what has happened: a creationist or two has come to visit. That's happening right now on this very short article that mentions the peppered moths; we're up above 200 comments now, and it seems to have very little to do with moths anymore. Instead, we've got a creationist complaining about the absence of transitional species and the Cambrian 'explosion', with a little quote-mining of Richard Dawkins. You commenters are taking care of him ably, but there are just a few things I want to mention, and a few…
pharyngula | September 8, 2007I got some email today with lots of constructive suggestions (See? Not all my email is evil!) for how we ought to change the education of biology students — such as by giving them a foundation in the history and philosophy of our science, using creationist arguments as bad examples so the students can see the errors for themselves, etc. — and it was absolutely brilliant, even the parts where he disagreed with some things I'd written before. Best email ever!
Of course, what helped is that I spent my summer "vacation" putting together a new freshman first semester course for biology majors that…
evolvingthoughts | September 7, 2007
Now we turn to the modern accounts of life.
In 1828, Friedrich Wöhler produced uric acid without using “kidney of man or dog”. Prior to that time, there was considered to be something different between organic chemistry and inorganic chemistry. Living things had some “vital fluid” that other things lacked. Most often this was expressed in Aristotelian terms even if, like Buffon, they were very anti-Aristotelian. But still life was not fully explicable in chemical terms.
Vitalism, as this idea was termed, did not die with Wöhler, though. In fact, we can find instances of it until the…
loom | September 6, 2007I want to give readers of the Loom a heads up about book that I've edited that's coming out in November. The author is a very interesting writer named Charles Darwin.
In 1871 Charles Darwin published pretty much his first and last word about human evolution: The Descent of Man. It's a marvelous, but sometimes maddening book. Darwin did a remarkably good job of hypothesizing how humans evolved, especially when you consider that barely any hominid fossils had yet been found. But Darwin packed the book with detail, a lot of it having to do with all sorts of animals other than Homo sapiens. I've…
pharyngula | September 6, 2007
When we look at the face of another person, we can recognize specific features that have familial resemblances. In my family, for instance, I can recognize a "Myers nose" that my grandmother and my father and some of my siblings and kids have, and it's different than my wife's or my mother's nose. These are subtle differences in shape—a bit of a curve, a knob, a seam—and their inheritance suggests that these differences are specified somehow in the DNA. If you think about it, though…how can whether the profile of a nose is straight or curved be encoded in a linear stretch of nucleotides? The…
loom | September 6, 2007At about a pound and a half, Mahakala omnogovae was certainly a cute dinosaur. But cuteness is not why paleontologists traveled to the remote ends of Mongolia to find it. It's part of a much bigger story.
Paleontologists have known for a while now that birds evolved from one group of dinosaurs called theropods--the two-legged beasts that include the likes of Tyrannosaurus rex and Velociraptor. But precisely which lineage of theropods birds belong to has been the subject of a lot of debate. These debates, like all debates in science, are fueled by uncertainty. Paleontologists can base their…
pharyngula | September 6, 2007Scott Lanyon, director of the Bell Museum, has an article on two disease we should worry about, VHSv and EAS.
Personally, I think VHSv is the worst. It's a virus that causes hemorrhagic septicemia in fish; just from the name you know it's bad, involving blood and sepsis. My most horrible experience raising zebrafish was the time hemorrhagic septicemia swept through my colony and I had to euthanize every animal and bleach every last bit of plumbing to eradicate it. This disease has been detected in waters of Wisconsin, and it's definitely not good.
EAS may not be as dramatically gory and…
evolvingthoughts | September 5, 2007
Carl Zimmer has one of his usually clear and precise articles on recent work on the nature of life, focussing on the work of Carol Cleland, who is at the National Astrobiology Institute, despite reduced funding for actual science by the present administration. I met Carol last year when we both spoke at the Egenis conference on the philosophy of microbiology.
Carol argues that we do not have a theory of what life is. She may be right. One of her arguments is that if there were multiple "origins of life" events that used different chemistry, we may not even be able to "see" the others…
neurotopia | September 5, 2007Ha ha, fooled you!
The Discovery Institute has just issued this on their blog, the inaccurately named Evolution News and Views:
According to CSC senior fellow and leading ID theorist William Dembski, what follows is:
"[A] big story, perhaps the biggest story yet of academic suppression relating to ID. Robert Marks is a world-class expert in the field of evolutionary computing, and yet the Baylor administration, without any consideration of the actual content of Marks's work at the Evolutionary Informatics Lab, decided to shut it down simply because there were anonymous complaints linking…
loom | September 5, 2007Earlier this summer my cover story on the meaning of life (or, at least, "life") came out in the July/August issue of Seed. Now, at long last, the Seedsters have posted the story online. Read it here.
mikethemadbiologist | September 5, 2007125 taxa. This analysis is never going to end (stupid GTR models):
I'm getting annoyed....
Update: It took five days to run this thing. And, yes, that was after using ModelTest.
By the way, if you have no idea what I'm talking about, here's a post (without technical jargon) on likelihood and phylogenetics to introduce you to the basics.
pharyngula | September 5, 2007Want to see Freeman Dyson and Richard Dawkins butt heads? It begins with a talk Dyson gave to an Edge conference in which Dyson (watch the whole talk) made these comments:
"By Darwinian evolution he [Woese] means evolution as Darwin understood it, based on the competition for survival of noninterbreeding species."
"With rare exceptions, Darwinian evolution requires established species to become extinct so that new species can replace them."
Dawkins rightly objects. Those are weird claims: the first is, I think, a misreading of Darwin. Darwin says something very different.
In the survival of…
loom | September 4, 2007Driving home at the end of the long weekend, I was amazed to see a tree here and there along the road with a touch of orange in its leaves. Fall already. And with fall comes another team of scientists to puzzle over why leaves change color.
I've been following this story for four autumns now, both in the New York Times, and in a series of blog posts (one, two, three, and four). It began with a simple question from one of the great evolutionary biologists since Darwin. William Hamilton argued that it takes a lot of energy for autumn leaves to produce the brilliant pigments that make fall so…
purepedantry | September 4, 2007The issue of sympatric speciation -- or how to separate species emerge from a single species without geographic isolation -- is a contentious issue in evolutionary biology. How can two species emerge without reproductive isolation of two separate groups? Wouldn't they all just breed together, hiding any new genes in heterozygotes?
Bomblies et al. publishing in PLoS Bio have something interesting to say about that. The use a plant called Arabidopsis thaliana or thale grass to show that the answer might be in genes that regulate the immune response.
Just to get some background, the genes…