evolgen | December 28, 2006
Barbaro, the 2006 Kentucky Derby winner who broke his leg during the Preakness Stakes, is almost healthy enough to be released from his ICU stall at University of Pennsylvania's New Bolton Center. He has been the focus of hopes and prayers of many horse racing fans -- and little kids who are fans of horsies in general. The chief surgeon at the center has this to say about Barbaro's recovery:
"It's not a miracle. It's anything but that," he said, sitting next to a Christmas tree topped with a stuffed Barbaro.
"Some of the Barbaro fans aren't going to like that, perhaps. I'm a scientist, I'm a…
evolgen | December 28, 2006The editors at Scientific American are afraid of PLoS ONE, but they're more than happy to publish articles about Nature papers. Their coverage of the Komodo dragon virgin births contains the following lead in:
The "immaculate conception" of Komodo dragons at two English zoos might provide one explanation why Jesus was not a clone of Mary
And now a freakin' Jew will explain why this is wrong. You see, the Immaculate Conception refers to the conception of Mary, free from original sin. This allowed her to be inseminated by God and give birth to the baby Jesus -- God wouldn't boink any ol'…
evolgen | December 26, 2006John Wilkins has replied to Larry Moran on the role of "chance" in evolution (incidentally, Moran replies to Wilkins on the same topic, but a different post by Wilkins). Here's what Larry wrote:
Nobody denies the power of natural selection and nobody claims that natural selection is random or accidental. However, the idea that everything is due to natural selection is the peculiar belief of a relatively small number of people, of whom Richard Dawkins is the most outspoken.
A great deal of evolution is the result of chance or accident, as is a great deal of the rest of the universe. It's…
evolgen | December 25, 2006
James Brown, the Godfather of Soul, has passed away at the age of 73 in Atlanta, Georgia. The world is a slightly less funky place today. I've posted some videos -- in honor of the hardest working man in show business -- below the fold.
The early years:
Eddie Murphy as James Brown in "Celebrity dHot Tub Party":
James Brown -- along with Clive Owen, Gary Oldman, and Marilyn Manson -- in BMW Films' "Beat the Devil". Brown plays a Robert Johnson character looking to renege on his deal with the devil:
evolgen | December 25, 2006
The University of California, Berkeley and Texas A&M University will square off in this year's Holiday Bowl football game on Thursday, December 28. While not quite as complex as last year's national championship game pairing, there is a nice dichotomy when one considers the stereotypes of Cal and Texas A&M. In general, Cal is home to a bunch of liberal, tree hugging, pinko hippies, whereas the Texas A&M student body is made up of gun wielding, warmongering good ol' boys (and Nick). The tale of the tape is laid out in this article from the San Diego Union-Tribune -- San Diego is…
evolgen | December 25, 2006Carl Zimmer has an article in the upcoming edition of Scientific American that looks at cancer from the perspective of evolutionary biology. The most obvious parallel is that of cancer cells within an individual modeled as an evolving population:
Rare mutations, for instance, may cause a cell to lose restraint and begin to multiply uncontrollably. Other mutations can add to the problem: They may allow deranged cells to invade surrounding tissues and spread through the body. Or they may allow tumor cells to evade the immune system or attract blood vessels that can supply fresh oxygen.
Cancer,…
evolgen | December 24, 2006As Lynn Margulis elegantly explained, some eukaryotic organelles -- such as mitochondria and chloroplasts -- are the product of an ancient endosymbiosis event. Free living prokaryotes were absorbed by primitive eukaryotes and, over many generations, become entangled in an obligate host-symbiont interaction. There are other examples of such interactions between eukaryotes and intracellular symbionts, such as those found within deep sea tubeworms, sponges, and plant roots.
The structures we currently call organelles were, at one point, merely endosymbionts. Where do we draw the line between…
evolgen | December 23, 2006Molecular markers are becoming more and more popular for species identification -- a practice known as DNA barcoding. Researchers sequence a region of the genome from an organism of interest and search that sequence against a DNA database using BLAST. Such an analysis is contingent on a comprehensive database containing sequences from representatives of many diverse taxa.
We do not possess such a database for fungal species. Researchers have estimated that less than 5% of all fungal species have been identified, which means the chances are good that you may be the first person to sequence…
evolgen | December 22, 2006The editors at Scientific American are taking note that the review process at PLoS ONE differs from that of traditional journals:
With the burden of proof off of the reviewers, we in the science press will have to be more vigilant than ever. We can't rush to put stories out until we've focus-grouped findings with a number of experts in a study's particular field. It will force us to become better reporters and to resist the urge to sensationalize and invoke hyperbole--which, while it may not move magazine units or generate hits, will make our service more noble.
The technical quality of the…
evolgen | December 22, 2006Via the error prone cosmologists I learned about this challenge:
Physicist Richard Feynman once said that if all knowledge about physics was about to expire the one sentence he would tell the future is that "Everything is made of atoms". What one sentence would you tell the future about your own area, whether it's entrepreneurship, hedge funds, venture capital, or something else?
We evolutionary biology bloggers are a bit ahead of the game on this one, presenting our definition of evolution in 10 words or less:
Differential inheritance of genetic variation via stochastic and deterministic…
evolgen | December 22, 2006
Eugenie Scott and Glenn Branch are two of the leaders in the movement to keep the science in science classrooms in American public schools. Both Scott and Branch hold administrative position at the National Center for Science Education (NCSE), and they've displayed great commitment to maintaining the scientific integrity of American primary and secondary education. Of recent note is their new book Not in Our Classrooms, which offers an introduction to modern creationism and science education in the United States.
Barry Lynn, executive director of Americans United for the Separation of Church…
evolgen | December 21, 2006There's an interesting discussion going on at Pharyngula regarding virgin birth in Bethlehem Komodo dragons. Two captive females in Europe recently gave birth to clutches of eggs despite no to minimal contact with males. The progeny are all homozygous at the each of the seven loci surveyed, with alleles matching those of the mothers. The logical conclusion to be drawn is that the eggs arose via parthenogenesis -- either by reabsorption of the second polar body or suppression of the second meiotic division.
Take note that this is not clonal reproduction -- the progeny contain two copies of…
evolgen | December 21, 2006As we all know, the genetic code is redundant. Within protein coding regions, substitutions at silent sites do not affect the amino acid sequence of the encoded protein. Because of this property, these synonymous substitutions (so-called because they result in the same amino acid) are often used to estimate the neutral rate of evolution -- they should not be under selection. But there is evidence for natural selection operating on silent sites. That's because, even though different codons encode the same amino acid, the tRNAs for the synonymous codons are found at different frequencies within…
evolgen | December 21, 2006
The Public Library of Science (PLoS), an open access, web-based publisher, has launched its newest venture, PLoS ONE. PLoS ONE aims to bring scientific publishing into the Web 2.0 era, with a simple interface for commenting on published research articles. This feature is not unique to PLoS ONE, as the Nature blogs and BioMed Central both allow commenting on articles. What makes the site unique are the annotation features, personalize alerts, and rating of journal articles. Whereas the previous implementations of commenting on journal articles were an accessory to the publishing process, PLoS…
evolgen | December 20, 2006It's evolgen. E-V-O-L-G-E-N. Think "evil jen".
One thing our blog is not is "evolvgen". Notice the extra "v". We do, and we don't like it. You may like calendars with nekkid people or studying some insignificant primate. But, whatever you fancy, whatever floats your boat, whatever tickles your noodly appendage, please leave off the second V.
We've been known to change our name in the past. Don't make us do it again.
evolgen | December 20, 2006This past summer, Matt Hahn presented a talk at the Society for Molecular Biology Evolution meeting and Evolution 2006 entitled "The 17% Solution: Gene Family Divergence Between Human And Chimpanzee". The basic premise was that, even though humans and chimps are ~99% identical at the DNA sequence level, they differ substantially in copy number variants. That is, the two species have different amounts of genes from certain gene families, which Hahn estimated as a 17% difference in genes between them. Given the amount of copy number polymorphism within humans, it should come as no surprise that…
evolgen | December 19, 2006
Via this press release I learned about this book: The Top Ten Myths About Evolution. The book deconstructs ten myths that creationists propagate while spreading misinformation. It also gives me an excuse to post cute pictures of furry primates.
The official website lists the ten myths:
1) Survival of the Fittest; 2) It's Just a Theory; 3) The Ladder of Progress; 4) The Missing Link; 5) Evolution is Random; 6) People Come from Monkeys; 7) Nature's Perfect Balance; 8) Creationism Disproves Evolution; 9) Intelligent Design is Science; 10) Evolution is Immoral
It sounds like a good treatment of…
evolgen | December 19, 2006John Hawks, along with Gene Expression regular Greg Cochran, has published a paper (PDF) on adaptive introgression in human evolution. In case the jargon is too much, we're talking about the caveman gene. Both Greg and John have blogged the paper. Check out what John says about mtDNA:
However, there have been a growing number of examples of adaptive introgression between different natural populations as well. The use of more nuclear markers has begun to uncover many, but importantly many species have adaptive introgression of mitochondrial DNA.[emphasis from original]
Adaptive introgression…
evolgen | December 18, 2006Since my last report on Nature's copy number polymorphism (CNP) papers, a couple other journals have published studies of human structural polymorphisms:
Genome Research has two papers on detecting CNPs using oligonucleotide microarrays. The strategy here is to develop a microarray that contains all the unique regions of the genome (divided into ~20 nucleotide pieces). You can quantify the amount of DNA hybridized to the array. So, when you test genomic DNA, regions of single copy DNA will have a certain intensity, whereas regions that are present at multiple copies will have higher…
evolgen | December 12, 2006My call for ecology blogs went better than expected. I expected next to nothing, but I got more than nothing -- at least enough to consider it further away from nothing than next to it. Anyhow, I have compiled a list of blogs below the fold. They are grouped into those that deal with the science of ecology and those that deal with conservation, environmentalism, bird watching, etc. Some of the blogs were on the boarder between science and other, and I can't give a great explanation for how I decided where to put them. The order is somewhat arbitrary; it's the order in which I put toghether…