evolgen | April 26, 2007Ever wonder what biobloggers are blogging about on their blogs? Here's what:
Razib posts part of a paper by Jerry Coyne and others (which I can't seem to track down) which questions the role cis regulatory elements play in adaptive phenotypic evolution. This all part of Coyne's war on evo-devo.
Another post at GNXP (this one by p-ter) describes a polymorphic deletion that is associated with resistance to retroviral infection. P-ter tries to throw me a bone by mentioning the relevance of Drosophila research, but ends up shooting himself in the foot (how's that for mixed metaphors?).
Orac's got…
evolgen | April 26, 2007
The recent Scientific American article on junk DNA (discussed here) has instigated a quite a furor in the bioblogosphere. Here is a collection of links:
ERV linked with a tone of disgust.
I restated my frustration with the term junk DNA.
JR Minkel, the author of the Scientific American article, responded to my criticisms.
Ryan Gregory replied to Minkel's SciAm blog post, introducing the term "junctional DNA" to replace junk DNA describe sequences with unknown function. Gregory also tells us how a genome is like an onion (let me count the ways), or something of the sort wonders why onions…
evolgen | April 24, 2007Would I write about junk DNA? No. Never. Not me. Not even when Scientific American publishes sub par articles on junk DNA. Well, they're at it again.
The most recent junk DNA article describes a study by Gill Bejerano of Stanford University which I can't find published anywhere (neither can ERV). Is Scientific American describing unpublished research on their website? Either way, they're doing it poorly. The study described in the article identified non-coding sequences that were conserved across all sequenced mammalian genomes but missing from the chicken genome. Five percent of the…
evolgen | April 23, 2007Because my browser consists of a growing forest of tabs containing stuff waiting to be blogged, and there is no way I can write a complete entry on each one, and I want to at least link to the relevant sites so that I can close those tabs, I give you a link dump with maximal run-on sentences:
Remember my post on the evolution of zombie populations? If so, you've got a good memory. If not, who cares? Anyway, there's an article in arXiv about ghosts, vampires and zombies. (Via Ortholog).
The evolution of snake venom genes. They make up part of the venome.
Jonathan Eisen on the Human…
evolgen | April 23, 2007...that appears to do absolutely nothing (link). Usually they do something mundane in a really complex manner. But all this one does is open the curtains so that the credits can run. The device pictured below is different from the one linked above, but I figured this post needed something to fill up more space.
(Via The Disgruntled Chemist.)
evolgen | April 21, 2007Over at GNXP, Razib has posted a few links to papers concerning adaptive evolution (aka, positive selection or Darwinian selection) in humans and chimps. He's been following the coverage of this paper from George Zhang's group which provides evidence that more genes have been under positive selection along the chimpanzee lineage than the human lineage. The popular press are advertising this finding as "chimps more evolved than humans", and Razib's gotten a kick out of the phrasing (part 1, part 2, part 3). Zhang and colleagues interpret their finding the in framework of the nearly neutral…
evolgen | April 20, 2007
The boys at Deep Sea News are wrapping up their Megavertebrate Week in which they profile various charismatic animals with backbones that live in the sea (including seals). Go check out their site for other cool pictures and stories about swimming with sharks. For those of you who like spotting critters in the field, Jeremy at the Voltage Gate has the thing for you: the first ever Blogger Bioblitz. If you enjoy identifying organisms in the wild, sign up, observe, and report back what you see. And, if you live by the ocean, you may even spot a seal.
evolgen | April 20, 2007It seems like everything is coming in twos the past couple of days. Yesterday we mentioned two books on the evolution of genomes and two stories involving either Wolbachia or sex determination. Today, we have two stories involving criticisms of scientific papers. One deals with the evolution of the bacterial flagellum, and the other addresses natural selection on the brain expressed gene ASPM in humans.
The first story involves everyone's favorite irreducibly complex cellular apparatus: the bacterial flagellum. During the Kitzmiller v. Dover trial, Nick Matzke worked with the plaintiffs (the…
evolgen | April 19, 2007There are two cool articles on two related topics, but the articles themselves don't deal with the area in which these topic overlap. Confused? Here's a quick description of the two articles:
One article is on the change in fecundity cost of Wolbachia infections in a population of Drosophila simulans. Wolbachia are bacterial symbionts which can do all kinds of cool stuff to their hosts, including preventing infected males from mating with uninfected females (cytoplasmic incompatibility) and causing male zygotes to die before fully developing (male killing). Wolbachia can really do a number on…
evolgen | April 19, 2007Oxford University Press will be releasing a new book in June entitled Darwinian Detectives: Revealing the Natural History of Genes and Genomes. From the OUP description of the book:
Molecular scientists exploring newly sequenced genomes have stumbled upon quite a few surprises, including that only one to ten percent of the genetic material of animals actually codes for genes. What does the remaining 90-99% of the genome do? Why do some organisms have a much lower genome size than their close relatives? What were the genetic changes that were associated with us becoming human?
Ignoring the…
evolgen | April 19, 2007On yesterday's episode of Mythbusters they tested the myth that birds in a trailer decrease the weight of the trailer when the birds take flight. The 'busters put a bunch of birds into a trailer, weighed the trailer + birds, and then allowed the birds to fly in the trailer, measuring the weight every fraction of a second. The myth was rejected because, while the weight fluctuated a fair bit, the mean weight remained the same before and after the birds took flight.
When a bird (or anything else that flies) gets airborne, it must exert a downward force equal to its weight. The weight of the…
evolgen | April 18, 2007Dan Hartl was inducted into the National Academy of Sciences of the USA in 2005 for his contributions to the field of evolutionary genetics. His inaugural article as an Academy member was published this week in the Proceedings of the National Academy of Sciences (PNAS, pronounce pee-nas, hehe). Hartl and colleagues compared levels of polymorphism in 91 genes from Drosophila melanogaster with divergence from D. simulans. They were interested in determining the effect of natural selection on nonsynonymous mutations, kind of like what was done in this paper (reviewed here).
Hartl and colleagues…
evolgen | April 18, 2007
Two unemployed stem cell researchers have performed a pilot study indicating that the chief researcher's dog likes beer (reported here). They noticed that erratic behavior tended to increase with beer consumption, but his tolerance did increase over the course of the experiment. The dog also preferred certain beers over others, although the researchers did not have sufficient funds to test the dog's preference for anything better than Presidente. And they didn't see if he enjoyed salt in his beer either.
This research was partially funded by a New Jersey state research subsidy of $2.55 from…
evolgen | April 17, 2007A lot of interesting evolutionary genetics research gets published, and I don't have time to write an insightful commentary on all of it (some may argue that I have never written an insightful commentary on anything). Here's a brief overview of the stuff I have missed in the past few weeks:
A population of sheep was started with the introduction of two individuals on a remote island in the southern region of the Indian Ocean. Surprisingly, genetic diversity has increased over time in this population (reported here). This increase in heterozygosity (measured by the amount of microsatellite…
evolgen | April 17, 2007Two recent papers have been published that both deal with chromosomal aberrations and autism. One paper reports de novo copy number mutations associated with some cases of autism. These are copy number polymorphisms not present in either parent; the mutation arises in the parental germ line, although, I believe it is also possible the mutation happens after fertilization. The other paper presents data using SNPs and copy number variants to map regions of the genome associated with autism risk. I'm not all that interested in the autism component of this research, but the prevalence of…
evolgen | April 14, 2007
As you've probably already heard, George Allen's favorite primate has had its genome sequenced. I promised to blog on the article, but this is not the post. Instead, this post is to kvetch about the coverage of this story in the popular press. It's another adventure in bad science reporting!
Here are two examples of people misreporting the sequencing of a macaque genome:
The Los Angeles Times reports that the "Macaque genome is decoded". They also report, "A team of researchers has deciphered the genome of the rhesus macaque". Decoded and deciphered, but not sequenced. Thomas H. Maugh II,…
evolgen | April 13, 2007Science has published two papers on Tyrannosaurus rex proteins (are we in the golden age of dino molecular biology?). In one paper, the authors report that they extracted proteins from T. rex soft tissue that was preserved for millions of years. In the other paper, some of the same researchers write about how they used mass spectrometry to determine the sequences of proteins obtained from a 68 million year old T. rex fossil and a mastodon that died hundreds of thousands of years ago. But the title of the paper is:
Protein Sequences from Mastodon and Tyrannosaurus Rex Revealed by Mass…
evolgen | April 13, 2007Today's password is coevolution.
First of all, here is a pair of phylogenies. The one on the left shows the relationships of a bunch of dove species, and the one on the right shows a bunch of lice that parasitize the doves. The lines connecting doves and lice indicate lice that parasitize each dove species..
Notice that parts of the tree mirror each other. We see that closely related dove species are infected by closely related lice. But that tree is nowhere as clean as this one:
On the left is an aphid phylogeny, and the tree on the right is from their obligate symbionts (speaking of…
evolgen | April 13, 2007According to Physorg.com, this study on epigenetic inheritance in chickens "shake[s] Darwin's foundation". Who knew inheritance in a flightless bird could induce an earthquake in northern Australia? That's not what they're referring to? They're not claiming that a neo-Lamarckian process could produce seismic activity?
For everyone running around like a chicken with its head cut off (where's my damn rim-shot?), this result is more of a shot at Mendel than Darwin. And it's not all that surprising. Don't get me wrong, it's cool to see the inheritance of acquired characteristics (unless Reed…
evolgen | April 12, 2007In addition to the paper on adaptive evolution in the Drosophila melanogaster genome (reviewed here yesterday), Chung-I Wu is also senior author on a sort-of companion paper studying adaptive evolution in the human genome. Yeah, I know, who really cares about the human genome, human evolution, or humans? The real interest is in Drosophila. But, believe it or not, there are some people who find human population genetics totally engrossing.
The paper using sequences from the human genome, which Wu co-authored with Jun Gojobori (who is not this Gojobori), Hua Tang and Josh Akey, looks at…