evolgen

May 4, 2008

Dichotomous Inverts

Category: Blog Carnivals

Kevin has posted the newest Circus of the Spineless at Deep See Nudes News. Go get your monthly fix of inverts.

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April 25, 2008

Phylogeny Friday -- 25 April 2008

Category: Phylogenetics

Duh! That's Obvious, Edition

Take a look at this mastodon skeleton:

Does it look like anything you recognize? Perhaps a large terrestrial mammal with big tusks. If you said "elephant" you win. The prize: nothing.

That is half of the conclusion from a recent paper in Science (doi:10.1126/science.1154284). Really. The other half: birds and dinosaurs are pretty closely related. Or, more specifically, birds and Tyrannosaurus rex -- THE COOLEST MOST AWESOMEST OF ALL DINOSAURS EVER!! -- are closely related. And, for this, they get a Science paper.

Now, the way they did this is pretty damn cool: they sequenced proteins from T. rex bones. But that was reported last year (doi:10.1126/science.1137614) in the paper where they screwed up the species name in the title (they got it right this time around). Anyway, some of the same people took those sequences and, along with some other sequences that they mined from various databases, constructed a phylogenetic tree of vertebrates.

Read on »

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April 23, 2008

Deborah Charlesworth on Lynch's Origin of Genome Architecture

Category: Book Reviews • Molecular Evolution • Population Genetics

Brian Charlesworth wrote a review of Mike Lynch's The Origins of Genome Architecture, in which Charlesworth argues that sexual reproduction can explain many of the features Lynch claims evolved under nearly neutral processes (doi:10.1016/j.cub.2008.01.008). Not to be left out of the party, Deborah Charlesworth has chimed in with her opinion, and it's much more critical of Lynch than her husband's (doi:10.1017/S0016672308009282). The main thesis that Lynch has been presenting in both this book and some of his recent papers is that many features of eukaryotic genomes (introns, complicated cis regulatory regions, lots of non-coding DNA) arose via relaxed constraint due to small population sizes, not adaptation.

In her review, Deborah Charlesworth takes Lynch to task for not devoting enough of his discussion to within species polymorphism. Additionally, she argues that comparisons between distantly related taxa are limited by confounding variables. By ignoring recent studies that have identified evidence for selection on large portions of some genomes (and by excluding some important tests for selection, e.g., the McDonald-Kreiman test), Lynch paints a biased picture of what we know about adaptive evolution at the molecular level. However, Charlesworth does make the point that Lynch's book is not the be all and end all of genome evolution; rather, it is designed to get the reader to consider other explanations besides adaptive evolution when explaining genomic features.

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April 22, 2008

Saving the Name of Drosophila melanogaster

Category: Drosophila • Phylogenetics

The Drosophila genus is paraphyletic. That means there are species nested within the phylogeny of the genus that belong to other genera. Or, in other words, there are species descended from the most recent common ancestor (MRCA) of all Drosophila species that belong to different genera. If that doesn't make sense, just look at the tree.

A paraphyletic genus is a no-no in taxonomy. There are two ways to deal with the problem. First, the genera nested within the Drosophila phylogeny can be redesignated into the Drosophila genus. That's not going to happen because the genus is too freakin' big to begin with. The second option is to split the Drosophila genus into multiple genera. The genus is already split into two subgenera, Drosophila and Sophophora. D. melanogaster, the best known Drosophila species, is in the Sophophora subgenus. D. funebris, the type species of the genus (or the one that holds the rights to the name "Drosophila"), is in the Drosophila subgenus. So, if the genus gets split, D. funebris gets to keep the genus name Drosophila, while D. melanogaster will probably be renamed Sophophora melanogaster. That doesn't sit well with some people.

Read on »

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April 21, 2008

Who said this?

Category: Academia • Science Policy

Someone was asked something along these lines by a member of some legislative body:

How will your research help protect this country?

That someone replied with something like this:

It won't, but it will keep this country worth protecting.

The exact wording in those quotes probably differ from what was actually said.

This isn't a rhetorical question, nor is it an exercise in trivia. I don't know who said it, what the exact context of the quote was, or whether this was actually said by anyone, anytime, anywhere. So, if you know of the exact quote, who said it, and where it was said, please leave a note in the comments. Thanks!

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Expelled Exaggerated?

Category: Anti-Science • Pop Culture

The creationist movie that everyone* is talking about came out was released this weekend. Early reports have Expelled coming in 9th nationally in weekend gross, with about $3 million. That's a lot of money, and you can color Randy Olson freakin' impressed. However, put in the context of what the producers were expecting, it's not so good.

That doesn't stop Randy from pulling at Matt Nisbet and touting how awesome the creationists are and how shitty the "evolutionists" are. Fucking "evolutionists"! I'm gonna go off on a rant here, but, before I do, allow me to point out the beautiful irony that is Randy Olson. The guy comes out and criticizes "evolutionists" for being really bad at getting their message out to the general public. He even goes so far as making a movie about how shitty the "evolutionists" are at getting their message out to the general public. The entire point of the movie is about how "evolutionists" can't communicate with the general public. Randy Olson is trained to communicate with the general public, and loves telling you about how good the creationists are at communicating with the general public. You'd think that would make Randy Olson the perfect person to communicate with the general public about evolution. Only he doesn't; instead, he bitches about how bad the "evolutionists" are at communicating with the general public. Randy Olson can join Matt Nisbet as the official backseat drivers of science communication.

And that brings me to my rant. For a guy who's an advocate of science, as well as a trained biologist, Randy Olson sure likes to use the creationist frames. Like "evolutionist". Fuck it, Randy, why not just call ourselves baby eating satanists. When you use the label "evolutionist", you're playing right into the creationists' game. You've fallen for their frame. This isn't an issue between creationists and evolutionists -- it's between anti-science and science. That's our frame, and that's the truth. The wedge and all that shit are an attack on not only evolution, but all of science. If you don't get that, you don't understand any of this shit.

*Everyone = hard-core creationists, people who read science blogs, and 38 year olds who live in their mom's basement.

Read on »

Posted by RPM at 9:00 AM • 9 Comments • View blog reactions

April 20, 2008

Watson's Genome

Category: Genomics

Last year, Craig Venter became the first single person to have his genome sequence published (doi:10.1371/journal.pbio.0050254). That genome was sequenced using the old-school Sanger technique. It marked the second time the complete human genome had been published (which led to some discussion as to whether the publication deserved to be published in a high profile journal like PLoS Biology), and the first time all of the sequence came from a single individual.

This past week, Nature published the second complete genome sequence of a single individual (doi:10.1038/nature06884). Like Venter, this individual is also a famous scientists, known both within his field and to non-experts. His name is Jim Watson, he helped discover the structure of DNA, and he's been eviscerated in the past few months because of some comments he made about racial differences. So, we can expect the publication of his genome to be received with conflicted emotions.

What makes the sequencing of Watson's genome different from that of Venter's? It's the technology. Watson's genome was sequenced using one of the next generation sequencing technologies (454), which allows much more sequencing bang for the buck. This isn't a $1000 genome, but it's a step in that direction.

Read on »

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April 19, 2008

The Natural Selection of Ideas

Category: Anti-Science • Evolution

It's funny because some people think both groups are wrong:

Originally from Tom the Dancing Bug.

Posted by RPM at 4:15 PM • 1 Comments • View blog reactions

April 14, 2008

El Chupacabra de Barcelona

Category: Conferences • Molecular Evolution • Vanity

I think I'm cursed. Or I have bad luck. Or conference organizers think I'm a morning person. Alright, so maybe I really am a morning person. But that's besides the point. Because it sucks to give a talk on a Saturday morning. Saturday mornings should be reserved for things like Belgian waffles, homemade hash browns, made to order omelets, and mimosas. Not for 12 minute talks about my research. How much can you fit into a 12 minute talk? Not much. And you end up speeding up at the end when you realize you've got about 1 minute to make it through four slides. It's either that or go over 12 minutes, cutting into the three minutes allocated for questions at the end of your talk. I'm not even going to get into the ordeal that are questions at the end of 12 minute talks.

I gave one of those 12 minute talks at the Fly Meeting a week-or-so ago. All signs indicate that it went well. We'll see how the manuscript is treated in review. The biggest problem was that the talk was at 9:15 on a Saturday morning. Not only did I have to deal with all the regular issues that come with a 12 minute talk a big conference (yes, the Fly Meeting is a pretty big conference, with over 1000 participants), but I had to speak to a room full of tired and hung-over scientists. I think half of the evolutionary geneticists had spent the night before partying. The only thing worse is giving a talk on Sunday morning, the morning after everyone spent the night before hanging out in a tree drinking beer (or so I've heard). Thankfully, they only give invited speakers the Sunday morning talks at the Fly Meeting, so insecure grad students don't have to deal with half-empty rooms and a disinterested audience.

Okay, I'm probably making too big of a deal out of giving a talk on a Saturday morning at one meeting. But I haven't told you when I'm scheduled to speak at the next meeting I'm going to. That said, I bet you can guess. No, it's not 9:15 on a Saturday morning. It's 9:30, which I guess is a slight improvement over 9:15. The talk will be given at the Society for Molecular Biology and Evolution conference (SMBE 2008) in Barcelona. Being in Barcelona should make up for the fact that I need to give a talk on a Saturday morning.

Last year, we had a blogger meet-up at SMBE in Halifax (picture here). I've set up another Nature Network Group, SMBE 2008, where we can coordinate a meet-up of bloggerly folks. Basically, if you're reading this post, you're invited. If you have a blog, even better. Logsdon, I'm looking at you.

Posted by RPM at 10:00 AM • 5 Comments • View blog reactions

April 13, 2008

Varmus Screws the Pooch

Category: Biology • Open Access • Science Policy

Harold Varmus is one of the most high profile advocates of open access to biomedical research. As one of the cofounders of the Public Library of Science (PLoS), he has played an important role in making published results freely available to all. And he's a Nobel Laureate, which ain't too shaby either.

Varmus was interviewed by Ira Flatow for NPR's Science Friday program about the NIH's new policy requiring that research publications presenting results funded by the NIH be deposited in PubMed Central (the NIH's free online archive of biomedical journal articles) within a year of publication. Before I get into the problems with Varmus' interview, I'd like to highlight one important point Varmus made: the current NIH policy is a comprimise between the ideal open access solution and what pay-access publishers want. In the ideal situation, all papers published about publicly funded research would be made freely available at the moment of publication. There would be no moving wall before they can be freely obtained. But that would ruin the business model of the pay-access journals, who make a fair bit of their profit from both individual and institutional (i.e., university) subscriptions. If a big chunk of the articles in those journals were freely available, the journals would stand to lose many of their subscribers.

Despite making that point, Varmus struggled to point out the big differences between open access and pay-access journals. He was clear that the differences lie in the business models, but he did not present the details of those differences with the clarity required when speaking to the general public. First, he made it seem as if open access journals are the only ones that require a payment from the author in order to publish in those journals. Second, he failed to clearly point out that open access and peer review are orthogonal issues, despite a perfect opportunity to do so.

Read on »

Posted by RPM at 1:00 PM • 9 Comments • View blog reactions

April 11, 2008

Phylogeny Friday -- 11 April 2008

Category: Drosophila • Phylogenetics

Drosophila Are Not Fruit Flies Edition

As I have mentioned before, Drosophila are not fruit flies. Tephritids are fruit flies. Drosophila feed on rotting fruit, while true fruit flies feed on fresh fruit. That makes true fruit flies agricultural pests. Drosophila, on the other hand, are connoisseurs of the finer things in life -- wine, beer, cheese, and the like.

In addition to rotting fruit, Drosophila also feed on mushrooms and crabs. Yes, crabs. Well, they don't actually feed on the crabs, just like they don't actually feed on the fruit. The flies and their larva are more interested in the yeast that ferment fruit or the microbes found on crabs.

Drosophilids that live on crabs can be found in two locations: the Caribbean and Christmas Island. One species of Caribbean Drosophila, D. endobranchia, was last observed in the mid-1960s. It's placement in phylogeny of Drosophila was not well resolved, and it was thought that it may be extinct. A new paper in PLoS ONE reports the rediscovery of that species, as well as the evolutionary relationship of the crabby flies (doi:10.1371/journal.pone.0001942.g001)

Read on »

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April 9, 2008

Press Releases are Written by Stupid People

Category: Evolution • Science Education • Science News

PLoS Biology's press releases have taken another step toward being dismissed as "crap" by people who know jack shit about evolution, thanks to a new press release published last week.

It starts off like so:

Evolution has taken another step away from being dismissed as "a theory" in the classroom, thanks to a new paper published this week in the online open-access journal PLoS Biology.

And goes on like this:

As all students of Darwin know, evolution occurs when there is variation in a population; where some variants confer a survival or reproductive advantage to the individual, and where the basis for this advantage can be inherited. Finally, there must be a selection pressure -- a reason that not all animals can survive or reproduce -- such as a limited supply of food or a predator that must be avoided.

As any biologist worth shit knows, natural selection occurs when some heritable variants confer a survival or reproductive advantage. That differential survival is the result of a selection pressure. But evolution can occur without natural selection -- it only requires differential survival/reproduction. How can there be differential survival without natural selection? Easy, there are factors independent of your genotype that influence your survival and reproductive success. For example, you'd be hard pressed to argue that your propensity to be struck by lightning is genetically encoded.

The press release describes an article on the automation of a laboratory evolution protocol (doi:10.1371/journal.pbio.0060085). The sad part is, the experiment incorporates a stochastic element -- mutation. There is also selection, but the press release even describes a "random" component of evolution.

Paegel BM, Joyce GF. 2008. Darwinian Evolution on a Chip. PLoS Biol 6: e85 doi:10.1371/journal.pbio.0060085

Posted by RPM at 10:00 AM • 11 Comments • View blog reactions

April 8, 2008

Evidence that Men Think With Their Junk

Category: Evolution • Genomics • Molecular Biology • Molecular Evolution • Speciation

Us dudes are always accused of thinking with our dicks. Perhaps it's because the genes expressed in our brains are similar to those expressed in our 'nads:

Among the 17 tissues, the highest similarity in gene expression patterns was between human brain and testis, based on DDD and clustering analysis. Genes contributing to the similarity include ribosomal protein (RP) genes as well as genes involved in transcription, translation and cell division.

The authors of the paper allege that their result has something to do with speciation. They even claim, "Brain is the most important tissue in human speciation." Given their data, it may be balls, not brains.

J. Guo, P. Zhu, C. Wu, L. Yu, S. Zhao, X. Gu. 2003. In silico analysis indicates a similar gene expression pattern between human brain and testis. Cytogenet Genome Res 103: 58-62 doi:10.1159/000076290

Read on »

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March 31, 2008

This is the Future of Eukaryotic Genome Sequencing

Category: Genomics

As I have mentioned before, de novo sequencing of whole eukaryotic genomes may be a thing of the past (or, at least, these whole genome projects won't be getting very much more common). Instead, I proposed that people would use the new high-throughput technologies to sequence parts of the genome they found interesting. What did I propose they'd sequence (based on discussion I'd had with various folks)? The transcriptome, or, essentially, a whole genome cDNA library. This allows for a much higher coverage of the genes in the genome, but sacrifices information regarding non-transcribed sequences and gene order.

It turns out that sacrifice is one worth making. In the April issue of Molecular Ecology, Vera et al. report that they used 454 to sequence the genome of the Glanville fritillary butterfly (doi:10.1111/j.1365-294X.2008.03666.x). This organism is a popular model in population biology, but had no genetic resources. That's changed thanks to this project. Here's the punchline from the abstract:

We conclude that 454 sequencing, when performed to provide sufficient coverage depth, allows de novo transcriptome assembly and a fast, cost-effective, and reliable method for development of functional genomic tools for nonmodel species. This development narrows the gap between approaches based on model organisms with rich genetic resources vs. species that are most tractable for ecological and evolutionary studies.

Molecular Ecology also has a review of the paper (doi:10.1111/j.1365-294X.2008.03699.x).

Posted by RPM at 2:00 PM • 1 Comments • View blog reactions

March 18, 2008

Sleep, Sex, and Drosophila

Category: Biology • Drosophila • Science News

60 Minutes ran a special on the science of sleep this week. The special included an interview with Scott McRobert about sleep deprivation and mating in Drosophila.

So if lack of sleep impacts our appetite, our metabolism, our memory, and how we age, is there anything it doesn't affect? How about sex? Scientist Scott McRobert at St. Joseph's University in Philadelphia is asking that very question, studying fruit flies.

McRobert could be seen showing Lesley Stahl a fly in a vial, which he then sucked up in a pooter. He then placed that male, along with a female, in a small dish.

Stahl watched as McRobert used a bizarre contraption to suck a male drosophila (fruit fly) out of a vial and put him into a little dish with a female.

McRobert does the play by play as the male courts the female.

McRobert gave Stahl a play-by-play of the action. "Okay. So now, the female's walking around the outside of the chamber," McRobert explains. "And the male's in the center. And you see he's orienting toward her, everywhere she goes."

"He's following her. If you watch closely, he'll touch her with his front legs. It's hard to see, but he will. And he'll sing. Here comes the song," McRobert says.

That's right, Drosophila can sing.

Flies sing, he tells Stahl, by lifting one wing to the side and vibrating it up and down.

And then: they do it! That's right, CBS showed footage of S-E-X on the TeeVee. Really. It was HAWHT!!!

Read on »

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March 13, 2008

Try this line in a bar this weekend:

Category: Genetics

It's not very funny, but it's about a topic that comes up around here often (groans...). That said, this is something you'd expect to see over at Genomicron, not evolgen. In fact, the guy looks a bit like a young TR Gregory.

For the full strip, go here.

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