evolgen | March 21, 2007SECOND ROUND PREVIEW | PRESS CENTER | PRINTABLE BRACKETS
Welcome back to our coverage of the second round of the Science Spring Showdown. We had two great games yesterday, and another one finished earlier today. The final game of the round, between HIV and Psychology, is just wrapping up now; we'll bring you the result as soon as that one goes final.
Tom Ribosome: Earlier today, Phylogenetics took on Unipotent in one of the more non-traditional match ups. Coming off of games against classic rivals, Taxonomy and Totipotent, no one was sure what to expect when the tree builders and fated cells…
evolgen | March 21, 2007SECOND ROUND PREVIEW | PRESS CENTER | PRINTABLE BRACKETS
Welcome, ladies and gentlemen, to our comprehensive coverage of the second round of the Science Spring Showdown. We had two great games yesterday, and we have two more match ups today. The game between Phylogenetics and Unipotent is just underway, and the final game of the round, between HIV and Psychology, is coming up this afternoon.
Jim Pipetman: Yesterday's first game, between the top seeded Invertebrates and the ninth seeded Surgeons, turned out like most of the experts predicted. The Surgeons came into the game bragging about…
evolgen | March 20, 2007Darwinian evolution means different things to different people. To me, and many other population geneticists, it refers to positive selection. To Jeffrey Schwartz, an anthropologist at the University of Pittsburgh, Darwinian evolution means gradual change. By the way, Schwartz also thinks humans are more closely related to orangutans than they are to chimps and gorillas.
I'm having a hard time making heads or tails of Schwartz. He seems hypercritical of all molecular evolution -- to the point where one wonders whether he even understands the field. He appears to not understand that evolution…
evolgen | March 19, 2007Both Carl Zimmer and Larry Moran have posts on the gene content in the human genome. Carl points out that the estimate of the total number of genes in the human genome is decreasing, but we still don't know what a whole bunch of those genes do (according to the one database he searched). Larry's post deals with what he considers a misconception regarding the historical estimates of gene content in humans. He argues that, while the estimates of the number of protein coding genes have decreased over the years, they haven't really decreased as much as some people seem to think (from about 40,000…
evolgen | March 19, 2007In the comments of my dinosaur genome size post, Shelley asked:
So do ALL birds have equally small genomes or is there variation among species?
I don't think she was looking for a trite response along the lines of: "Of course there's variation among species." What she was asking, I presume, is how much variation in genome size do we see in birds? As you can see in this phylogeny, all birds (and nearly all theropods) have small genomes. But that tree only presents data from a few species.
To get a better idea of genome size variation within birds, I downloaded C-values (amount of DNA in a…
evolgen | March 18, 2007Dr. Wayne Grody is a molecular biologist at UCLA. But his part-time job sounds like a lot more fun: "technical advisor on a number of motion picture and television productions". He's the guy responsible for giving Eddie Murphy's Professor Klump character a ginormous research lab despite the fact that he worked at a small liberal arts college. To Grody's credit, however, he did try to plant thermal cyclers, which the director found "visually boring". But, according to Grody, scientists account for such a small proportion of TV viewers and movie-goers that scientific accuracy isn't much of a…
evolgen | March 17, 20071st ROUND RESULTS | PRESS CENTER | PRINTABLE BRACKETS
After the excitement of the first round action in the Octopus region, we can only hope that the second round is half as dynamic. The big upset last round saw Unipotent knocking off Totipotent. There has also been an interesting twist, as Internal Medicine was disqualified for a positive steroid test. That means Surgery advances to play the Invertebrates. In the other matches this round, we will see Genomics take on Photosynthesis, Unipotent challenge Phylogenetics, and HIV play Psychology.
#1 Invertebrates vs. #9 Internal Medicine #8…
evolgen | March 17, 2007Genome size can be measured in a variety of ways. Classically, the haploid content of a genome was measured in picograms and represented as the C-value. People began to realize that the C-value was not correlated with any measures of organismal complexity and seemed to vary unpredictably between taxa. This was known as the C-value paradox, and it confused geneticists for quite a while. With an increased understanding of genome structure, however, came the resolution of the paradox: this measure of genome size does not correlate with gene content. The majority of many eukaryotic genomes…
evolgen | March 16, 20071st ROUND RESULTS | PRESS CENTER | PRINTABLE BRACKETS
The results are in from the first round in the Octopus Region of the Science Spring Showdown hosted at the World's Fair. By seed, there were three upsets, but the nine seed Internal Medicine knocking off eight seed Surgery was hardly a surprise (although the 107-76 score was a wider margin than many of the experts predicted). The win by 14 seeded Unipotent over the three seed, Totipotent, on the other hand, was quite a shocker, with many people attributing the victory to the definitive coaching style of the Unipotent's lead general,…
evolgen | March 16, 2007New Terms in Phylogenetics
I'm a cladist, and as a cladist I want all of my taxa monophyletic. That means anything given a name (animals, plants, vertebrates, insects, etc.) should include all the organisms that descend from the most recent common ancestor (MRCA) shared by the organisms you claim are in that group. Confused? Well, allow me to direct you to Wilkins's post on clades and this handy diagram:
In the tree above, grouping species A, B, C, and D into a single taxon results in a monophyletic clade. But if we exclude species A (calling species B, C, and D a single taxon), we create a…
evolgen | March 16, 2007If you happen to be a yeast population geneticist, then you probably already know about the Saccharomyces Genome Resequencing Project. They have resequenced 32 strains of S. cerevisiae and 27 strains of S. paradoxus at between 1x and 3x coverage. The nice thing about resequencing is that SNP discovery and genotyping occur simultaneously. That's in contrast to the human HapMap project which identified polymorphism in a few individuals, then searched for those polymorphisms in a larger panel. That means you can do some good population genetic analyses on the yeast data, which are not possible…
evolgen | March 15, 2007
The advertising department over at the Nature Publishing Group isn't filled with the sharpest knives in the drawer -- as I've pointed out previously. They are responsible for the long vertical banners that run along the right column of their webpages (see the example to the right). Each of these banners pushes some journal, webpage, or "portal" that Nature is trying to pimp. The example shown here links to a page for you to request that your library purchase a subscription to the Nature journal Leukemia.
These advertisements cycle without any apparent rhyme or reason; I came across the…
evolgen | March 15, 2007I'm really digging the interviews with high profile scientists that Current Biology has been publishing. Last November I quoted their interview with Michael Ashburner (ie, he who will not pose with Prof. Steve Steve) on his thoughts on open access publishing and pointed out that they were being published in a non-open access journal. In the most recent issue, they interview Stephen O'Brien, head of the Laboratory of Genomic Diversity at the National Cancer Institute. O'Brien was trained as a Drosophila geneticist, and now works on topics as diverse as cheetah population genetics and HIV…
evolgen | March 15, 2007This post is part of a series documenting Professor Steve Steve's recent visit to Philadelphia for the Drosophila Research Conference (aka, the Fly Meeting).
Professor Steve Steve had a wild Saturday night. He was quite happy to have met leaders in the fields of evo-devo, population genetics, and genomics. Of course, Steve Steve is a pioneer in popula-devo-geno-metrics, so everything that came up in discussion was old-hat to him. That said, it was definitely a night to remember. And a morning to forget.
Pictures of Steve Steve at the Sunday plenary session and on the drive home can be found…
evolgen | March 14, 2007It's March, and you know what that means: brackets. There are two ScienceBlogs brackets to keep your eye on:
The barkers at the World's Fair have put together a Science Showdown -- bracket style -- broken into four regions: Octopus (life sciences), Mortar and Pestle (chemistry), Chair (philosophy and science studies), and Orbit (physics). Showdowns between competing disciplines will be decided, in part, by reader participation, and the winners will advance to face off with other disciplines. Go here to share your opinion on the opening round.
A more traditional March bracket contest is…
evolgen | March 14, 2007It seems like only yesterday (okay, less than two years ago) that I learned about 454 sequencing. It's the new technology that many folks think will replace dye termination Sanger sequencing using capillary arrays (the method used to sequence the human genome and many other genomes). A new technology is coming on the scene which may make 454 obsolete before it ever gets a foot-hold in the market (making it the laser disk of DNA sequencing).
454 sequencing works by copying small stretches of DNA sequence that have been attached to tiny beads. As each nucleotide is added to the growing sequence…
evolgen | March 14, 2007This post is part of a series documenting Professor Steve Steve's recent visit to Philadelphia for the Drosophila Research Conference (aka, the Fly Meeting).
In the previous two installments of Steve Steve in Philly, we finally managed to meet up despite the best efforts of the staff at the Marriott to prevent our rendezvous, and we got Steve Steve up to date on the newest developments in fly pushing and Drosophila genetics. It had been quite a tiring day, so we ventured down to the hotel bar for a few drinks. Some of us were ready to hit the sack, but Steve Steve would have none if it; he…
evolgen | March 13, 2007The New York Times has published an article in their Science section on the evolution of human parasites, and it's not by Carl Zimmer. In the article, Nicholas Wade (another good science writer at the NYTimes) presents a few vignettes of human-parasite co-evolution, including a bacterium that causes tooth decay, the ulcer causing Heliobacter, and a tapeworm we share with pigs. I guess Carl called dibs on the pubic lice. Anyway, Wade made me smile when he presented the phylogeography of one human parasite:
The latest organism to be identified as a longtime member of the human biota club is…
evolgen | March 13, 2007This post is part of a series documenting Professor Steve Steve's recent visit to Philadelphia for the Drosophila Research Conference (aka, the Fly Meeting).
After tracking down Steve Steve in the lobby of the hotel on Saturday, we picked up some food at the Reading Terminal Market -- a permanent sort-of-farmers-market next to the Philly Convention Center. The place was pretty packed, due in part to the Flower Show going on next door. Steve Steve was a little bummed that he didn't have time to check out any of the garden displays -- being an amateur horticulturalist and developer of the…