evolution
razib | March 7, 2006Nick Wade in The New York Times has a piece out titled Still Evolving, Human Genes Tell New Story, based on a paper published today in PLOS, A Map of Recent Positive Selection in the Human Genome. This paper is an extension of the research project that emerges out of the International HapMap Project. In short the HapMap is an assay of ~300 individuals from 3 populations, European Americans from Utah, ethnic Yorubas from Nigeria, and a collection of Japanese and Chinese. What can a few hundred individuals tell you? A lot.
Wade's piece is a soft landing survey of the major points. His…
evolgen | March 6, 2006I have to say, it's kinda cool to have my opinion acknowledged and used to correct an error. It looks like I pull some weight around here (not as much as some folks, but the 100 or so page views a day mean something).
But I ain't done yet. In honor of my dedication to correcting errors in the popular press, I have added a new category called "Science News" to this blog. In this installment, I will point out another error published by Seed. Not all of my posts will be devoted to copy-editing my bosses, it just so happens that they're now one hit away from a trifecta for the day.
This one…
evolgen | March 6, 2006If anyone thinks I have sold out to the Seed Gods, let this be my exhibit A against such opinions. Seed has published a review of Funk et al's ecological divergence and speciation PNAS paper. The scientific content is not all that bad, but it blows the implications of the study way out of proportion. My thoughts are below the fold.
The Seed article uses to the Funk paper to look at the role natural selection plays in speciation. The focus is put on whether allopatric speciation is a neutral process or if it depends on divergent selection in the two different environments. The article…
evolgen | March 6, 2006A very pretty picture (click on the image to make it larger):
Go read what Carl Zimmer and Rhosgobel have to say. For more on the Tree of Life, go here.
evolgen | March 6, 2006Dan Ely sounds a lot like Phil Skell. They both go to the evolutionary biologists at their respective universities and ask them ill-informed questions. They then misinterpret the answers and spread their misnomers throughout the anti-evolution community.
evolgen | March 5, 2006Polymorphism and Divergence
This is the eighth of multiple postings I plan to write about detecting natural selection using molecular data (ie, DNA sequences). The introduction can be found here. The first post described the organization of the genome, and the second described the organization of genes. The third post described codon based models for detecting selection, and the fourth detailed how relative rates can be used to detect changes in selective pressure. The fifth post dealt with classical population genetics methods for detecting selection using allele and genotype frequencies…
razib | March 4, 2006Dan Jones has a very thorough review of the recent paper in Nature which argues that negative epistasis will emerge out of sexual reproduction and so perpetuate itself. The only thing I'll add is what W.D. Hamilton noted in Narrow Roads of Gene Land, questions of fitness need to be evaluated over the long term, rather than just across a few generations. Also check out the lead author's blog.
Related: Through the rugged roads of gene land.
loom | March 3, 2006
Scientists are probably centuries away from drawing the full tree of life. For one thing, they have only discovered a small fraction of the species on Earth--perhaps only ten percent. They are also grappling with the relationships between the species they have discovered. Systematists (scientists who study the tree of life) rely mainly on DNA these days to figure out how species are related to one another. They compare the similarities and differences in a given gene in several different species to figure out which ones share the closest kinship. But they have actually sequenced DNA from…
evolgen | March 2, 2006I have posted on microbial diversity in the soil previously. Tara pointed out that even though we are just now learning about what ecological factors determine soil microbial diversity, we also have a lot to learn about microbial diversity within the human digestive tract. She asked:
I wonder what a meta-analysis of the diversity of human-associated bacteria would find? For example, we already know that diversity can vary even by location within the colon; we also know that the pH of different areas in the body can vary (due not only to bodily secretions but also other bacterial flora that…
razib | March 2, 2006Life is about choices made in the context of scarcity and constraint. In an ideal world (OK, my ideal world) I would be dictator, and all would do my bidding and satisify most proximate desires. Alas, it doesn't work that way. We all have to jump through hoops to get where we want. Whatever our core, or ultimate, values, most people have to compromise to fulfill them. If you are a religious soul for whom God and family are the summum bonum of your existence, well, by the nature of your two ultimate ends you can't go into the cloister or spend all your waking hours with your family. You…
grrlscientist | March 1, 2006
Click image for a slightly larger view in its own window.
I found a really interesting animation that demonstrates evolution of "Darwin's Finches" (Flash required, 515kb).
This animation is interactive, and is based on the only figure (above) that appeared in the first edition of Darwin's groundbreaking book, On The Origin of Species by Natural Selection. This diagram, a family tree or phylogeny, was printed on an oversized page that had to be folded out of the book to be seen, which was a difficult and expensive task for the printers of the day. This diagram appeared as some of the…
razib | February 28, 2006I'm calling out for evolution & genetics raps on my other weblog. A few players have represented, but not nearly enough. I mean, if the Assemblies of God could produce Scott Stapp, surely the evolution & genetics community has some freestylin' thugs lurking in the shadows?
razib | February 28, 2006I have a friend who is a graduate student in evolutionary biology at an elite university...and she told me that when she went to a seminar on adaptive landscapes...everyone was making hand movements and gesturing wildly. She pantomimed it out for me, it was pretty funny.
jlynch | February 28, 2006The University of Pittsburgh School of Medicine is partnering with Carnegie Museum of Natural History in a first-of-its-kind program that will educate medical students on the evolutionary history of humans and animals. By learning the origins of human disease, such as back pain and cancer - which existed in Jurassic Age dinosaurs - students should better understand contemporary public health concerns and think about treatment and prevention approaches that modern society may have overlooked. More here.
razib | February 28, 2006Here is a popular press piece on Geert Vermaij's paper in PNAS where he argues that evolution is not highly contingent process on particular historical events, in other words, if you rewound the clock and let it flow the rivers would occupy the same channels. These ideas seem rather similar to those of Simon Conway Morris. In the end, I think this might be a "hillist vs. mountainist" issue, draw a conceptual line somewhere, give it a label and defend your position like hell. All the while characterize your position as reasonable and moderate and caricature your "opponents" so that they…
cmooney | February 28, 2006Talk about a perfect combination of topics that are of interest to Science Blogs readers. I just came across this starred review in Publisher's Weekly:
January 30, 2006
Pilgrim on the Great Bird Continent: The Importance of Everything and Other Lessons from Darwin's Lost Notebooks Lyanda Lynn Haupt. Little, Brown, $24.95 (288p) ISBN 0-316-83664-8
When Charles Darwin set out on his voyage of discovery aboard the Beagle in 1831, he was a naive naturalist. Upon his return to England five years later, as nature writer Haupt (Rare Encounters with Ordinary Birds ) capably demonstrates, he was a…
evolgen | February 27, 2006You, me, your pet dog, and any other animal with a backbone are deuterostomes. So are sea stars, sea urchins, and sea cucumbers. During early development you, me, and echinoderms (sea stars et al) are a round ball of cells. The ball of cells invaginates and that opening becomes our anus. This differs from other animals like flies, worms, and snails whose first opening becomes a mouth. A second opening forms later in development, and it becomes our mouth (hence the name "deuterostome", or mouth second). The deuterostomes can be broken into two groups: the chordates and the echinoderms.…
grrlscientist | February 27, 2006
How important it is to walk along, not in haste, but slowly,
looking at everything and calling out
Yes! No!
-- Mary Oliver
Almost everyone has heard about "Darwin's Finches" -- those dark little birds that live on the Galapagos Islands. But most people don't realize that Darwin didn't set eyes upon those birds until nearly the end of his five year journey. Additionally, when Darwin first stepped aboard the HMS Beagle in 1831, he was neither an ornithologist nor a professional scientist; instead, he was a 22-year-old beetle collector and an amateur naturalist with only a smattering of…
evolgen | February 27, 2006I have a little bit of an infatuation with copy number polymorphism (CNP), which describes the fact that individuals within a population can differ from each other in gene content. Some genes, such as olfactory receptors (ORs), have many different related variants in any animal genome. New copies spring up via duplication events (a type of mutation), so one could imagine that individuals from a single population differ in the number of copies of these genes. In fact, this is the case with any gene or gene family (a group of related genes) in the genome -- there may be duplications…
oracknows | February 27, 2006
I love blog carnivals.
In fact, I love 'em so much that I hosted four of them took one over when its creator decided to retire from blogging.
But here's one that PZ, RPM, Afarensis, and all of the other ScienceBloggers inclined to defend evolution will want to wander over to see just how inane some creationist arguments can be. Indeed, the Pooflinger has already targeted them for some particularly ripe debunkings:
Yesterday marked the launch of an entirely new carnival over at Radaractive called, amusingly, the "Darwin Is Dead" carnival. Oh yeah: and it began with a whopping five (count…