evolution
evolgen | January 17, 2006Chad at Uncertain Principles, one of my ScienceBlogs siblings, is requesting his co-bloggers suggest the most important experiment or discovery in their field. There are a disproportionate amount of "bio-bloggers" -- though we each have our own niche -- and he's asking us to nominate "the most important experiment or observation in biology". I'm expecting that because of our diverse interests, you'll see some differences in how we interpret "important". This leads me to wonder why we have so many life-sciences types at ScienceBlogs and so few math/physics/chemistry types, but that's a…
evolgen | January 17, 2006PZ Myers is reposting some of his greatest hits from the old Pharyngula website to his new digs at ScienceBlogs. In one post he gets into the deficiencies of modern evolutionary theory using West-Eberhard's book as a guide. I agree with most of the thing he says (and I'll get into how I agree with him below), but first I need to scratch a pet-peeve itch:
"You can see this in any textbook of population genetics: the effect of selection is to impose a gradual shift in the mode of a pattern of continuous variation. Stabilizing selection chops off both tails of the distribution, directional…
pharyngula | January 16, 2006This is a post originally made on the old Pharyngula website; I'll be reposting some of these now and then to bring them aboard the new site.
There are a number of reasons why the current theory of evolution should be regarded as incomplete. The central one is that while "nothing in biology makes sense except in the light of evolution", some important disciplines within biology, development and physiology, have only been weakly integrated into the theory.
Raff (1996) in his book The Shape of Life(amzn/b&n/abe/pwll) gives some of the historical reasons for the divorce of evolution and…
cmooney | January 16, 2006I was watching CNN the other day, and saw a segment they had on the latest "intelligent design" case out of California (no link available). My impression? Whew: We're going to win this one easily if it goes to trial, because once again, the creationists aren't smart enough to cover their tracks. It was like Bill Buckingham and Alan Bonsell all over again.
I went to Lexis-Nexis this morning to get the CNN segment transcript. In particular, CNN interviewed, on the air, a kid who had taken the notorious "philosophy" class that is at the center of the dispute. Wisely, CNN asked the twirp what he…
jlynch | January 15, 2006Over at Evolgen, RPM has posted the seventh installment of his series on detecting natural selection, a piece on nucleotide polymorphism and selection. As always, it is worth checking out. For those that missed the earlier pieces, here is RPM's summary with links:
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…
grrlscientist | January 15, 2006
Dodos, rabbit poop, Mt. Rushmore and poker .. what more could you ask for than to make sense of the controversy regarding the teaching of so-called "intelligent design" versus evolution in science classrooms. To this end, the artistic community has teamed up with scientists to produce a film that explores strategies used by proponents of so-called "Intellegent Design" to confuse and mislead the general public about evolution.
Advance screenings;
February 2 - KANSAS 730pm, Glenwood Arts Theater, call 913.642.4404 for tickets.
February 6 - HARVARD 700pm Geology Lecture Hall
February 10 -…
evolgen | January 14, 2006Nucleotide Polymorphism and Selection
This is the seventh 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…
jlynch | January 14, 2006Last night's talk on the Cambrian explosion went really well - managed to nicely weave a narrative of fossils, genetic analysis, and evo-devo over the two hours (questions were spread throughout the talk). Over at Pharyngula, PZ has linked to some nice scanning electron micrographs of Cambrian arthropods. Check 'em out, they're quite cool.
pharyngula | January 14, 2006Bredocaris admirabilis
Ooooh, there's a gorgeous gallery of Orsten fossils online. These are some very pretty SEMs of tiny Cambrian animals, preserved in a kind of rock called Orsten, or stinkstone (apparently, the high sulfur content of the rock makes it smell awful). What are Orsten fossils?
Orsten fossils in the strict sense are spectacular minute secondarily phosphatised (apatitic) fossils, among them many Crustacea of different evolutionary levels, but also other arthropods and nemathelminths. The largest fragments we have do not exceed two mm. Orsten-type fossils, on the other hand,…
evolgen | January 13, 2006Paul Nurse, president of Rockefeller University, has a commentary (I believe it requires a subscription) in this week's issue of Cell. Within his essay he lays out some of the impediments to biomedical research in America. He starts by explaining current funding problems and suggests that smaller research groups may be able to deal with budget cuts. Larger groups could be form through collaborations between the smaller groups when projects demand such interdisciplinary approaches. He also discusses problems with science education and the reluctance of researchers to communicate with the…
evolgen | January 12, 2006I have been describing some recently published worked on polymorphic deletions (see here and here for the previous two posts) on the old site. I will conclude that series here at ScienceBlogs with a discussion of linkage disequilibrium and deletions.
In the previous two posts I outlined two different approaches for identifying polymorphic deletions using single nucleotide polymorphisms (SNPs). I also described some of the analysis performed on that data set, which revealed that many of the deletions resulted in the elimination of at least a portion of a gene (some removed complete genes,…
pharyngula | January 12, 2006Every biology student gets introduced to the chordates with a list of their distinctive characteristics: they have a notochord, a dorsal hollow nerve cord, gill slits, and a post-anal tail. The embryonic stage in which we express all of these features is called the pharyngula stage—it's often also the only stage at which we have them. We terrestrial vertebrates seal off those pharyngeal openings as we develop, while sea squirts throw away their brains as an adult.
The chordate phylum has all four of those traits, but there is another extremely interesting phylum that has some of them, the…
jlynch | January 11, 2006While finishing up graduate school, I worked for the Irish government on on a project to study fish stocks in the Irish Sea - this involved modelling biological and economic aspects with a view to the long term survival of the stocks. This, therefore, caught my eye:
Why does it take so long for fish stocks to recover from over-fishing? This problem has been worrying both scientists and fishery managers who expect stocks to quickly rebound when fishing stops. Now a research team from Stony Brook University [SUNY Stony Brook?] believes they have an answer: continually harvesting the largest and…
loom | January 11, 2006Last year was the hottest on record, or the second hottest, depending on the records climatologists look at. The planet has warmed .8 degrees C over the past 150 years, and scientists are generally agreed that greenhouse gases have played a major part in that warming. They also agree that the warming will continue in the decades to come. Many experts are concerned that warming may make two unpleasant things more common: extinctions and diseases. In tomorrow's issue of Nature (link to come here), a team of scientists report on a case that ties these two dangers together: frogs have become…
loom | January 10, 2006Governor Ernie Fletcher of Kentucky uses his State of the Commonwealth speech last night to plug intelligent design:
As I close, let me recognize Kentucky's veterans. You have served to protect our liberty and the freedom that spurs our quality of life in this nation. Please know that this administration is committed to supporting you.
And where does this freedom come from that many have died to protect?
Our founding fathers recognized that we were endowed with this right by our creator.
So I ask, what is wrong with teaching "intelligent design" in our schools. Under KERA, our school…
sb admin | January 10, 2006So what do you see? A groove and some lines? Truth be told, this is possibly the oldest recorded chordate fossil (or, should I say, one of a number of seventeen specimens of same). It dates from the pre-Cambrian - i.e. before 543 million years ago - during a period known as the Ediacarian. Found by Ross Faraghar seven years ago in the Flinders Range of Australia, the specimens represent our earliest view of chordate evolution, that is, the evolution of the group that we belong to (along with a few squishy things, and the more familiar fish, amphibians, reptiles, and mammals). Unfortunately,…
jlynch | January 10, 2006So what do you see? A groove and some lines? Truth be told, this is possibly the oldest recorded chordate fossil (or, should I say, one of a number of seventeen specimens of same). It dates from the pre-Cambrian - i.e. before 543 million years ago - during a period known as the Ediacarian. Found by Ross Faraghar seven years ago in the Flinders Range of Australia, the specimens represent our earliest view of chordate evolution, that is, the evolution of the group that we belong to (along with a few squishy things, and the more familiar fish, amphibians, reptiles, and mammals). Unfortunately,…
cmooney | January 9, 2006I have already confessed to you about a serious, debilitating weakness of mine: I like to watch crap action movies to let my mind rejuvenate itself after I've been working for a while. I don't care how bad they are, as long as they're well produced, and as long as they allow me to escape. Some people do drugs. I do DVDs.
And so it was that I recently found myself watching a recently released movie called The Cave. Here's the film's website. And now allow me to spoil the plot: It's about experienced cave divers who take on a gig in Romania that winds up being more dangerous than even they…
loom | January 6, 2006I've updated yesterday's cat evolution post with some tough comments from an expert on cat fossils. Check it out.
loom | January 6, 2006Rick Perry's on board! And no postmodern vagueness for him. He's here to tell us that intelligent design is a "valid scientific theory." That's right, governor. Just check out all the work on intelligent design going on in the biology department at your state's fine university. Um...wait...it's there somewhere. Just let me figure out how to work this search function...
(Hat tip to Panda's Thumb.)