August 1, 2008
Category: Biology • Science
About a month ago, we were told that theory is dead. That was the thesis of Chris Anderson's article in Wired. Rather than testing hypotheses using the scientific method, Anderson argues that scientists are merely generating loads of data and looking for correlations and stuff. The article was a bit muddled, but that's Anderson's main point . . . I think.
Well, now the Times Higher Education has published an article by Tim Birkhead in which he argues the opposite (In praise of fishing trips). Birkhead says that the scientific establishment is too attached to hypothesis testing. This means funding agencies are reluctant to approve projects that are designed to collect data without testing a priori hypotheses. Here's the brunt of his argument:
The scientific research councils seem to be obsessed by hypothesis testing. Many times I have heard it said by referees rejecting a proposal: "But there was no hypothesis." The research council modus operandi now seems to be the h-d method, but taken to an almost ludicrous extreme - researchers basically have to know what they are going to find before putting in a research application (in truth, they need to have done the research, even though they will not actually say so, to write a convincing account of what they intend to do). That's hardly the best way of doing science. The other problem, and it is a much more serious one, is that by knowing what you will find out, science becomes trivially confirmatory and inherently unlikely to discover anything truly novel.
So, which one is it? Have we abandoned hypothesis testing? Or are we so attached to hypothesis testing that we overlook novel projects that would explore underdeveloped areas of research?
Posted by RPM at 1:00 PM • 6 Comments • View blog reactions
July 28, 2008
Category: Conferences • Evolution • Molecular Evolution
The University of Iowa is hosting next year's meeting of the Society of Molecular Biology and Evolution, SMBE 2009. I usually go to the annual SMBE conference, and I was probably going to attend SMBE 2009. Now I'm definitely going. Why? Because John Logsdon just announced that they'll be hosting a pre-conference meeting on the Evolution of Sex and Recombination.
The Sex & Recombination meeting was supposed to happen this summer, and it was scheduled for the week prior to the Evolution 2008 conference in Minnesota. But mother nature interrupted, and the flooded campus was in no state to host the conference (coitus interruptis as John calls it). So it's really good to hear that they'll be able to have the meeting in 2009. Hopefully I'll have some sexy results to present.
Posted by RPM at 4:00 PM • 1 Comments • View blog reactions
July 26, 2008
Category: Biology • Conferences • Out 'n About
So, I'm just hanging out here by the side of the water waiting for my lunch. Sure, I could go in the water and get my lunch. But that's not how I roll. I wait patiently for my prey to get within striking distance, and then I attack. So, here I am just hanging out by the side of the water.
Click to enlarge.
There they are. Just a bunch of cichlids waiting to be eaten. By me. Lunch would be good right now. But they won't get close enough. So I'll just hang out here with my jaw agape.
Read on »
Posted by RPM at 1:30 PM • 0 Comments • View blog reactions
July 25, 2008
Category: Biology • Conferences • Out 'n About
Last month I mentioned that I had been in Barcelona at the Society for Molecular Biology and Evolution conference. I arrived in Spain early in the morning, and, after I got checked in to my hotel, I went with a couple friends to the Barcelona Zoo. This zoo is famous for housing Snowflake, the albino gorilla who lived at the zoo from the mid-1960s until he died in 2003. They still have an impressive collection of primates despite the loss of the zoo's icon.
Additionally, the zoo has a roaming band of peafowl. The peacocks and peahens have free reign of the grounds, and you'll often see them roosting in the trees. When we were there, the males were aggressively courting the females and letting out loud mating calls. I captured this photo of a peacock trying to impress a hen:
She would have none if it, though. Eventually, the peahen scurried into the bushes, and the peacock wandered off to find a hen that would be impressed by his massive train.
Posted by RPM at 6:15 PM • 2 Comments • View blog reactions
July 22, 2008
Category: Pop Culture • Science
Randy Olson left a career as a marine biologist (Titleist!) to become a film maker. His first feature project was Flock of Dodos, a movie I enjoyed. His second film is Sizzle, a movie reviewed by lots of ScienceBloggers a couple weeks ago. The gist: a lot of ScienceBloggers didn't like sizzle. Neither did a reviewer for Nature (doi:10.1038/454279a).
I did not request a review copy of the movie because I don't like to diverge much from the main themes of evolgen: evolutionary genetics, manatees, and the douchebag who writes this blog. But some of the recent discussion surrounding Sizzle has caught my attention, and I think it relates to the broader issue of science outreach (that is: communicating science to the general public).
Read on »
Posted by RPM at 6:30 PM • 5 Comments • View blog reactions
Category: Academia • Evolution
All good medicine is evidence based -- that is, diagnoses and treatments are developed via the scientific method. Oftentimes, evolutionary biology is employed to understand human health and diseases. This is known as evolutionary medicine.
Evolutionary medicine is a growing field that takes an interdisciplinary approach toward studying human disease. Tools from population ecology, molecular evolution, comparative anatomy, and many other fields are all integrated with clinical medicine to improve our understanding of human disease and develop new treatments. This approach can be applied to infectious diseases, congenital diseases, and acquired diseases.
Despite the rapid growth of this field, there is no central society or journal that deals with these topics. Additionally, because relevant research is often spread across otherwise disparate subdisciplines, people looking for literature on evolutionary medicine must search many different journals. To remedy this problem, a group of researchers working in evolutionary medicine have started an on-line review journal, or Web Based ReView (WeView), called The Evolution & Medicine Review. The creators view it as a sort-of cross between a blog and a review journal, although I'd categorize it as a single topic blog written by experts.
The Evolution & Medicine Review does not publish original research. Instead, the list of contributors produce short reviews on topics that interest them (very bloggy, not that it's a bad thing). You can read more about the EMR on their website.
(Via EvolDir.)
Posted by RPM at 9:00 AM • 0 Comments • View blog reactions
July 21, 2008
Category: Biology • Drosophila • Genetics • Molecular Evolution
We all know that Drosophila are the gayest bunch of gays that ever gayed up genetics. This is especially true when you create mutations in fruitless (nee fruity), "the gay gene". Male flies with mutations in fruitless will try to get it on with other males (e.g., doi:10.1016/S0092-8674(00)81802-4). That's gay!
But fruitless is an old school gene that needs to be fucked up to turn the flies gay (doi:10.1093/molbev/msj070; the first author on that paper is, I shit you not, named Gailey). Drosophila really aren't as gay as they are made to appear in the articles describing fruitless mutants. But the males are still kind of in to dudes, as is shown by a new paper from Manyuan Long's group (doi:10.1073/pnas.0800693105).
Read on »
Posted by RPM at 10:00 AM • 4 Comments • View blog reactions
July 18, 2008
Category: Phylogenetics • Science News
Phylogeny Friday -- 18 July 2008
When they published the initial analysis of the complete platypus genome (doi:10.1038/nature06936), Nature, as they're wont to do, also put out a news item announcing the major findings (doi:10.1038/453138a). That news article included a phylogeny illustrating the evolutionary relationships of various animal species in various stages of having their complete genomes sequenced.
The problem with the illustration: they got some of the relationships wrong. This sparked a letter from Peter Ducey of SUNY Cortland (doi:10.1038/454027d), in which he wrote the following:
In your News story 'Top billing for platypus at end of evolution tree', the graphic depicting genome status presents a shocking new phylogeny of the Vertebrates -- with Archosaurs (birds and crocodilians) and Mammals forming a monophyletic group.
In all honesty, the tree is so craptacularly drawn that it's hard to say that Archosaurs and Mammals are monophyletic based on the illustration. It looks more like the branching order of most vertebrates (and most animals) is unresolved, but I can definitely understand how Ducey interprets the tree. Either way, Nature did a bad job with this illustration. Why did they suck so bad? Here's what Ducey thinks:
The bad news is that this dramatic new 'proposal' is completely adrift from the research Article by Wesley C. Warren and colleagues that the figurative tree is intended to illustrate, and it continues a persistent tendency in popular literature to portray all evolution as leading towards humans.
Totally! The idea of a great chain of being, starting with bacteria and progressing through animals to humans, permeates much of the popular discussion of evolution. And it's just not true. It's a phylogenetic fallacy.
Coincidentally, Ducey points out, Science repeated the same error Nature made. In their coverage of the platypus genome paper (doi:10.1126/science.320.5877.730), Science included this image:
Ouch! At least the tree accompanying the Nature article was ambiguous enough that it could be interpreted to represent the true phylogeny. While the cladogram from Science does not perpetuate the great chain of being myth, it does represent a completely resolved phylogeny that also happens to be incorrect.
Posted by RPM at 12:00 PM • 6 Comments • View blog reactions
Category: Vanity
Until yesterday, there was a span of about two weeks in which this blog laid dormant. I did that on purpose because I didn't want to give you all the blogging you crave. All three of you who may crave my blogging. And I'm guessing not one of those three even noticed the silence. Ah, the joys of insignificance.
Besides being a lazy dick, I actually have a valid excuse for my silence: I was moving. Or, rather, I am moving (my move is not yet complete). Where am I moving? From grad-school to post-doc. It also happens to be a move from one city in the middle of nowhere to another city in the middle of nowhere. But I'm even more in the middle of nowhere in my new locale that I was previously. So much so, that when I looked out my window on the first day in my new home, this is what I saw:
And I think I saw at least one of those each day I was there. That's not to say that there aren't deers in the middle of nowhere town I lived in during grad school (there are plenty); but my new house is in the middle of nowhere within the middle of nowhere. It's isolate, which is not necessarily a bad thing.
In closing, two things: First, hopefully blogging will resemble yesterday's activity more that the previous two weeks' worth. Second, it's not that I don't like living in the small towns (I do), it's just that I was surprised to be living so close to what can pass as "nature" in this modern age. I'm sure PZ Myers can top me by showing off how small his town is, how many woodland creatures he has prancing through his yard each day, and how many fucked up people he has sending him death threats every day.
Posted by RPM at 8:00 AM • 6 Comments • View blog reactions
July 17, 2008
Category: Anti-Science • Sports
The Creation Museum is located in northern Kentucky, just across the Ohio border from Cincinnati. Answers in Genesis, the folks behind the so-called "museum", claim that their "museum" is within a 6 hour drive of 2/3 of the US population. This is not true -- Kentucky is in the middle of bumfuck nowhere (I'm an expert on cities in the middle of bumfuck nowhere), and most people in the US can't get there in 6 hours.
But the museum is damn close to Cincinnati -- it's in what people would call the "greater Cincinnati area", and it's closer to the so-called Cincinnati airport (which is actually in Kentucky) than the airport is to Cincinatti. Anyway, it's so close to Cincinnati (how close is it?) that Answers in Genesis is advertising their "museum" on during what can be considered the most important event in all of Cincinnati: the broadcast of their beloved Reds' games (Reds think evolution is for suckers). If you listen to the local baseball team on the radio, you're going to hear about the Creation Museum.
Now, here's where it all comes full circle. You see, one the greatest Reds of all time, Joe Morgan, also happens to be an absolute ignoramus when it comes to baseball (Hey, Bob. You remember the other day, you asked me what the definition of "irony" was...). I've previously dubbed him the baseball creationist. Well, it appears that the Reds are going back to their roots by advertising the Creation Museum on their broadcast -- reaching out to Little Joe in the way a bunch of ignorant fucktards only know how.
Posted by RPM at 7:15 PM • 0 Comments • View blog reactions
Category: Evolution • Science News
Olivia Judson says Darwinism is dead. She's right. Anyone who talks about "Darwinism" or "evolutionists" gets my attention. That's not to say that any use of those terms is incorrect. But they are often used as framing devices by creationists, and those frames get carried over into the lay discussion of biology. You should read her discussion of why we should get rid of Darwinism.
On a somewhat unrelated note, Judson also writes the following:
We'd want to discuss evolution beyond natural selection -- the other forces that can sometimes cause (or prevent) evolutionary change. For although natural selection is the only creative force in evolution -- the only one that can produce complex structures such as wings and eyes -- it is not the only force that affects which genes will spread, and which will vanish.
Natural selection is not creative. It acts on variation that is created by mutation. That makes mutation the only creative force. Natural selection, like all other forces besides mutation, can produce complex structures (yes, complexity can be produce by entirely neutral processes). But, without mutation, there is no new variation upon which those forces can act.
Posted by RPM at 8:00 AM • 6 Comments • View blog reactions
July 1, 2008
Category: Biology • Science News
Wired Magazine has published an article by Chris Anderson arguing that theory is dead (The End of Theory: The Data Deluge Makes the Scientific Method Obsolete). The argument: with our ability to generate vast amounts of data, there is no need for theory. Now, it's hard to parse what Anderson means by "theory" from the article. But he seems to be arguing that scientists are merely looking for correlations between various parameters, and claiming that's a sufficient analysis. Is it? Well, sometimes, yes, if it's based on a sound theoretical framework.
Deepak Singh has already called out Anderson (Chris Anderson, you are wrong), and Andrew at the Social Statistics blog has commented (The End of Theory: The Data Deluge Makes the Scientific Method Obsolete). I would like to weigh in with my perspective as an evolutionary biologist. Is theory dead in this subfield of biology?
Read on »
Posted by RPM at 8:00 AM • 14 Comments • View blog reactions
June 30, 2008
Category: Genomics
There's a post up at Pharyngula describing the concept of synteny in comparative genomics (Basics: Synteny). The definition given by PZ Myers will sound pretty familiar to those of you who have read some of the genomics literature. The problem: it's not quite correct. It's actually the definition that I think most comparative genomics folks would give if they were asked to define synteny. But they keep using that word, and I don't think it means what they think it means. What's the definition? Here it is in PZ's own words:
Synteny is the conservation of blocks of order within two sets of chromosomes that are being compared.
I disagree. While this is what many genomicists mean when they write or talk about synteny, they are wrong. Instead, I would argue that synteny merely means that genes are found on the same chromosome. Synteny says nothing about the order of genes. What give me the right to say this?
Read on »
Posted by RPM at 9:00 AM • 5 Comments • View blog reactions
June 27, 2008
Category: Phylogenetics
Phylogeny Friday -- 27 June 2008
I haven't done a Phylogeny Friday in about a month, but a recent paper reporting a "phylogenomic study of birds" was worth mentioning (doi:10.1126/science.1157704). Now, this isn't phylogenomics as Jonathan Eisen defined it. The bird evolution paper describes building a tree using lots of molecular markers.
I don't have much to say about the new bird phylogeny (I'll let the expert handle the details), but I wanted to post one of the trees for Phylogeny Friday. Here is one of the phylogenies they present, attempting to reconcile their results with those that had been previously published:
Click to enlarge.
The three columns at the tips indicate three previously published taxonomic classifications. Those with black text are monophyletic taxa in this new study, while those with white text are paraphyletic. The different colored lineages indicate various clades that are supported by this new study (e.g., green indicates land birds, blue are water birds, etc.).
Eisen. 1998. Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary Analysis. Genome Res. 8: 163-167 [link]
Hackett et al. 2008. A Phylogenomic Study of Birds Reveals Their Evolutionary History. Science 320:1763-1768 doi:10.1126/science.1157704
Posted by RPM at 5:30 PM • 2 Comments • View blog reactions
Category: Academia • Genetics • Science Education
PLoS Genetics has published an interview with Jenny Graves. Graves is one of the leaders in monotreme and marsupial genetics, and has been involved in some of the recent mammalian genome projects, including the platypus genome project (doi:10.1038/nature06936). She is also an expert in the evolution of mammalian sex chromosomes and sex determining genes. However, I'd like to point to a quote in PLoS Genetics' interview of Graves that deals with science education:
So I'm becoming very interested in education, particularly of young children, which is where I think the rot sets in. Science is not taught well even at high school level, and at primary school level it is taught by people who are generally scared of science! Anybody who has anything to do with kids this age knows they are incredibly observant and incredibly clever at working out how what they observe relates to other things. Somehow that just gets lost. I'd love to see more attention on encouraging young kids to make their own hypotheses--crazy though they may be.
The entire interview is interesting, and it touches on many of the highlights (and lowlights) of Graves' career.
Posted by RPM at 2:00 PM • 1 Comments • View blog reactions
June 23, 2008
Category: Sports • Statistics
Dak at Fire Joe Morgan asks:
I've been watching a fair amount of SportsCenter / BBTN today, and every two minutes someone mentions that there are "seven teams going for a sweep in an interleague series!", as if this is some sort of big deal. There are fourteen interleague series this weekend. If every match were a coin-flip, wouldn't we expect exactly seven teams to be going for sweeps in the third game of a series?
We'll start by assuming each team has an equal probability of winning each game, and the results of each game are independent. After one game, you're guaranteed that one team will have a 1-0 advantage. There is a 50% chance that the team that won the first game will win the second, meaning that there is a 50% chance the series will be 2-0 after two games. Therefore, dak is correct, you would expect half of the series to be on the verge of a sweep.
Why did the media make a big deal out of this -- and, I can confirm dak's observation: this was a big deal on SportsCenter and Baseball Tonight -- if it's actually expected? Because they don't understand basic probability. In fact, they are overtly antagonistic toward understanding simple logic and math. That's why websites like Fire Joe Morgan are so much fun to read. Media stupidity is such an easy target, and, even when their stupidity is pointed out them, they show no interest in correcting their errors or remedying the problem. It's like dealing with creationists.
Posted by RPM at 9:00 AM • 4 Comments • View blog reactions
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