evolgen | January 10, 2007Mutations are the fuel that drives the engine of evolution. Without mutations there would be no variation upon which natural selection and other evolutionary forces could act. Furthermore, much of the theoretical results regarding evolutionary genetics depend on estimates of mutation rates. For example, Kimura showed that the rate of fixation of neutral mutations is equal to the neutral mutation rate. Additionally, many models to explain the evolution of sex and recombination depend on the amount of deleterious mutations per genome per generation (U).
A group led by Peter Keightly (DOI) have…
evolgen | January 10, 2007First of all, do you consider the terms "Caucasian" and "of European ancestry" synonyms? How about the use of those terms in the popular press? If the two terms are equivalent in the common vernacular, which one do you prefer?
What about the words "race" and "ethnicity"? Are they equivalent in the common vernacular? Should they be?
This one was about human races -- unlike the last one.
evolgen | January 9, 2007Imagine you have two races -- because calling them populations is just too damn PC -- that are fixed for different alleles. Additionally, at loci were there are no fixed differences, alleles are segregating at different frequencies between the two races. In order to keep each of the races pure we must prevent any interbreeding (hybridization) between the two races.
Why the hell would we want to keep the races pure? For conservation reasons, of course. You didn't think I was talking about human races, did you? Because I wasn't. Seriously.
The NYTimes is running an article on efforts to…
evolgen | January 9, 2007Via Snail's Tails comes this podcast (dated 05 January 2006 on this page) featuring E.O. Wilson. According to Aydin (I'm a blogger so I don't fact check my sources) Wilson lays out the two fundamental laws of biology:
All of the phenomena of biology are ultimately obedient to the laws of physics and chemistry.
All of the phenomena of biology have arisen by evolution thru natural selection.
Everything in biology is the product of evolution. Only some biological phenomena can be attributed to natural selection. The issue of neutral versus selected (and within selected we have constrained…
evolgen | January 8, 2007The NYTimes reports on the impending budget crunch at US science funding agencies. The last Congress only passed spending bills for the military and domestic security, leaving nine others at the same level as the previous year. If we take inflation into account, the stagnant budgets result in a decrease in funding of 3-4% for most federal science and engineering programs.
Congressional Democrats do not plant to update the unfinished spending bills, and will extend them in their current state through September. (To learn how to petition your congressional representatives to increase funding…
evolgen | January 8, 2007I'm become quite obsessive about the false dichotomy between humans and animals, but that's what blogs are for. Anyway, you can probably guess why this gets under my skin:
evolgen | January 8, 2007Phenotypic differences between populations, species, or any other taxonomic classification can be attributed to genetic and environmental causes. The genetic differences can be divided into sequence divergence of transcribed regions, copy number divergence, and expression divergence. These categories are hardly independent -- expression divergence results from the evolution of the protein coding sequences of transcription factors and cis regulatory regions of transcribed sequences.
An article in press in Nature Genetics (news item here) reports on differences in expression of 4,197 genes…
evolgen | January 7, 2007After beating a dead centaur yesterday, Dictionary.com's word of the day for today seems quite appropriate:
chimerical \ky-MER-ih-kuhl; -MIR-; kih-\, adjective:
1. Merely imaginary; produced by or as if by a wildly fanciful imagination; fantastic; improbable or unrealistic.
2. Given to or indulging in unrealistic fantasies or fantastic schemes.
I would have thought chimerical meant part one thing and part another -- you know, a chimera. I guess not.
evolgen | January 6, 2007
There is currently much debate over the ethics of chimeras -- organisms that are partially one species and partially another. This debate is especially heated when humans are one of the species involved. Nature has published an editorial on the controversy. I don't intend to comment on the position of the editorial, but rather on the sloppy use of language by the unattributed author.
I don't know enough about the research and clinical applications of chimeras involving humans to make any claims about the ethics of such creations, but I do know enough about biology to get all hot under the…
evolgen | January 5, 2007We still have a chance to increase the NIH budget for this year. Go here to contact your US Senators and Representatives to request that they increase the NIH budget -- the last congress failed to vote on a budget for the NIH, resulting in a FY2007 budget identical to that of FY2006. From the website with the petition:
The Congress reconvened today in order to finish the FY 2007 appropriations process. The Labor-Health and Human Services-Education appropriations bill (Labor-HHS) that funds the NIH is one of the nine bills that still need to be considered. Unless funds are added to the NIH…
evolgen | January 5, 2007In light of the recent post on translational selection, I give you this paper from PLoS Genetics on tissue specific differences in tRNA expression from humans. From the abstract:
We found tissue-specific differences in the expression of individual tRNA species, and tRNAs decoding amino acids with similar chemical properties exhibited coordinated expression in distinct tissue types. Relative tRNA abundance exhibits a statistically significant correlation to the codon usage of a collection of highly expressed, tissue-specific genes in a subset of tissues or tRNA isoacceptors. Our findings…
evolgen | January 4, 2007Jacob appears to be an enemy combatant in the War on ManateesTM. They are attacking the Northeast United States via our inland waterways. Jacob, who lives west of the continental divide, is safe from the attack. Many of us are not so lucky. Quit being such an enabler, Jacob.
evolgen special feature: We have obtained an exclusive photograph from a manatee training camp located near Sarasota, Florida. The picture can be found below the fold.
Click to enlarge.
evolgen | January 3, 2007New Scientist reports on research to identify DNA sequences that cannot be found in any nucleotide database. These sequences are short -- so as to decrease the probability that they are missing due to chance alone -- and the researchers from the Boise State University have identified over 60,000 15 nucleotide stretches of DNA that are not present in any known sequenced region from all species. They also found 746 sequences of 5 amino acids that are not present in any known polypeptide. The article does not indicate whether the scientists utilized any hook and ladder or Statue of Liberty…
evolgen | January 3, 2007But where is halfway?
The Scientist has published an article by Mary Woolley, president of Research!America, on communicating science to the general public. The basic premise is that scientific literacy must increase, and scientists must perform the outreach in order to increase the science literacy of the average American. But what is the basal level of understanding that scientists can expect from the general public? To where are we expected to increase the scientific literacy? In other words, how much ground must we cover?
From the example Woolley gives, the prospects look bleak:
Consider…
evolgen | January 3, 2007Pim van Meurs has a blog post at The Panda's Thumb about the recent paper on translational selection on a synonymous polymorphic site in a eukaryotic gene (DOI link). He points out that this was predicted in a paper from 1987. In short, the rate of translation depends on the tRNA pool -- amino acids encoded by more abundant tRNA anti-codons will be incorporated more quickly than amino acids with rare tRNAs. Because protein folding begins during translation, codon usage can influence protein secondary structure. That's because rare codons could stall translation, allowing for protein…
evolgen | January 2, 2007It doesn't make up for the UCLA game, but the overrated, over hyped, team in the highlighter pants fell to the mighty Trojans. Fight on!
The USC bashers are pissed, and the sad Wolverines are moping. But this is par for the course at the school that has perfected losing in Pasadena.
evolgen | December 31, 2006Biologists often wear rubber gloves when doing their research to protect them from the nasty chemicals they're working with and to protect their samples from contamination. I've been known to bitch about people not removing those gloves prior to entering common areas -- touching things they shouldn't be touching with gloves. This could lead to mutagens, carcinogens, and simply abrasive reagents on doorknobs and elevator buttons that other people touch with their bare hands. Or it could lead to environmental particles on the gloves which could contaminate and ruin some experiment. The chances…
evolgen | December 30, 2006Endangered Ugly Things has a post on the eleven Drosophila species listed as endangered and the one listed as threatened in 2006. These flies are known as picture winged for the patterns found on their wings. (The obligatory pictures can be found below the fold.) I'm especially happy that these flies are listed as "pomace flies" on the NatureServe website (search for "Drosophila"), and I bet Mel Green is as well. But what are these beautiful creatures doing on a blog called Endangered Ugly Things?
I found this website with more information on Hawaiian Drosophila.
Drosophila heteronuera, one…
evolgen | December 29, 2006The rift in the biological sciences may lie between computational biologists and wet labs, but when we look at individual fields, we see other divisions. In an essay in PLoS Computational Biology Carl Zimmer describes the divide amongst evolutionary biologists. On one side are researchers who like to get their hands dirty -- ecologists, paleontologists, and others that fall under the label 'naturalist'. And on the other side we have the people that prefer to work with molecular tools; Zimmer calls these guys computational biologists, but they also generate their own data, so that label isn't…
evolgen | December 28, 2006Why, it seems like just last week that we were kvetching about the ad nominum attacks upon our character -- or, at least, the spelling of our blog's name. The people who add an extra "V" (turning evolgen into evolvgen) are lightweights compared to those who confuse us with Evolution Blog. As of today, we can add Page 6.0221415 Ã 1023 3.14 to the list:
From Evolgen, A Boom in Bible Publishing.
Jason Rosenhouse comments on an article in The New Yorker that casts Bible printing as a booming business.
I am not, nor have I ever claimed to be, named Jason Rosenhouse. I am an evolutionary…