evolgen | November 23, 2006There's an old paradigm in human population genetics that we each differ from each other by less than one percent at the DNA sequence level. While that may be true for our DNA sequences, recent work indicates that there's also quite a bit of variation amongst individuals in the actual content of their genomes. Such variation is known as copy number variation (CNV) or copy number polymorphism (CNP). What it means is that some people may have one copy of a genomic region, other may have two, and even others may have none.
Nature thinks this research on CNV is quite important, as there are five…
evolgen | November 23, 2006Happy Turkey Day!! As a special gift, I give you yet another -ome to spread on your Thanksgiving bird. You see, I'm fascinated by -omics, the idea that you can affix "-ome" to your favorite biological system to prime the hype machine. And what I have for you this time makes me think of the juices of a turkey that's been cooked just right.
With that in mind, I give you the secretome. From what I can gather, these are the proteins secreted by an organism. The authors of the article linked above are interested in the evolution of the mollusk shell, but mice, humans, pufferfish, and pigs all have…
evolgen | November 22, 2006Colin Purrington, he of the great textbook disclaimer stickers (and whose website is a treasure trove of information), is looking for some prison statistics:
A common theme in anti-evolution writings is that teaching kids about Darwin will cause them to lose all touch with morality, and will end up committing crimes. It might follow that evolutionary biologists themselves would be especially overrepresented in the criminal justice system. Therefore, I'd like to make a bar graph that shows the number of individuals with PhDs in evolutionary biology who are currently in prison. A possible…
evolgen | November 22, 2006Who would you nominate for Scientist Laureate, if such a position existed?
That's the question they are asking us this week. And everyone is answering E.O. Wilson. This, of course, comes with the caveat that if Carl Sagan were alive today, he'd be the obvious choice.
If we can't get Carl Sagan, why not go after the guy Nick Matzke calls "the new Carl Sagan"? Nick's post is in response to this article in the NYTimes about the Beyond Belief meeting -- where science, religion, and atheism were discussed. Nick thinks Neil deGrasse Tyson stood out because, instead of attacking the religious or…
evolgen | November 22, 2006
The sixty seventh edition of the Tangled Bank has been posted at Newton's Binomium. It's a Thanksgiving edition, so go give thanks for some good science blogging.
evolgen | November 22, 2006I've got another pet-peeve-itch to scratch, so I'm picking up a tall glass of haterade.
I'm walking down the stairwell in my building, and I encounter someone heading upstairs carrying a styrofoam container (I can't tell what's in it, but it's probably filled with ice and something worth keeping cold). We approach the door to the floor we both work on. She gets there first and extends her hand to open the door -- a hand ensconced in a rubber glove.
When doing lab work, we wear gloves for two reasons:
To protect our samples from contamination from ourselves.
To protect ourselves from…
evolgen | November 21, 2006The new issue of Current Biology contains an interview with Drosophila geneticist Michael Ashburner. Here's a quote from the article:
Scientists should realize that if they submit to journals -- like those published by Elsevier, Springer, Kluwer, Wiley and the like -- then their work will be less accessible and not as widely read as it would be if it was published in an Open Access journal.
Current Biology is published by Elsevier (who are also involved in the arms trade), which means that Ashburner is pushing for Open Access publishing in a non-Open Access journal. Good stuff.
Ashburner's…
evolgen | November 21, 2006John Hawks reports that the gene that, when mutated, can turn male flies gay and females into lesbians can also make boy flies fight like girls and vice-versa. This research will be published in an upcoming edition of Nature Neuroscience. And be sure to check out the videos from the fruit fly Drosophila Fight Club.
evolgen | November 21, 2006Two years ago today (November 21, 2004 at 11:23 AM) I launched evolgen in its original incarnation. The first post, entitled "First Post", celebrated the occasion:
This is the first post to the evolgen blog. Not much to say other than there is more to come (hopefully).
The first evolutionary genetics post didn't happen until January 9, 2005. For two months evolgen existed in name only, plus four posts on topics ranging from restless legs syndrome to dinosaurs. I eventually got my act together, increased my posting frequency, submitted posts to blog carnivals (mostly Tangled Bank), and left…
evolgen | November 21, 2006When we were asked what the best science TV show is, a couple of people answered Mythbusters. It turns out it's not a science show. Here's how Jamie Hyneman, one of the shows creators, describes it:
Mr. Hyneman, however, insists that he and the "Mythbusters" team "don't have any pretense of teaching science . . . If we tried to teach science," he said, "the shows probably wouldn't be successful."
Even if they aren't teaching science, they are approaching problems using experimentation. So, they're doing science (minus the whole 'replication' thing), even if they aren't calling it that.
evolgen | November 20, 2006Massimo Pigliucci and Jonathan Kaplan have written a book on evolutionary theory. Check out Massimo's description on his blog. But it's not all masturbatory philosophy -- these guys understand the science. Here's Massimo describing their treatment of adaptive landscapes:
To make the story short (for the longer version you'll have to read the book), Jonathan and I claim that the idea was fraught with problems and inconsistencies from the beginning, and that it has now been radically modified by the work of a mathematical biologist named Sergey Gavrilets. Sergey actually showed that the…
evolgen | November 20, 2006The Discovery Institute's Evolution News and Views blog neither reports news on evolution nor offers interesting views. One of their bloggers, Casey Luskin, is notorious for misunderstanding and misrepresenting science -- which is par for the course at the Disco. Casey recently decided to attack a piece published in National Geographic on the evolution of complex structures written by Carl Zimmer. Carl just so happens to be among the best science journalists writing today; his work is both accurate and easy to understand.
Carl wasn't going to take Luskin's inanity lying down; he's responded…
evolgen | November 20, 2006One of the potentially most interesting, yet untapped, area of study in population biology is that of intra-individual variation. One thing we do know, however, is that this variation can contribute to cancers. When cells accumulate mutations, some of these cell lines become cancer cells due to changes to genes involved in regulating the cell cycle. It would be especially interesting to apply the theory from population biology to this somatic variation within individuals.
If any of that stuff sounds interesting, you should check out this paper from Nature Reviews Cancer. The authors summarize…
evolgen | November 19, 2006Like a lot of evolutionary biologists not studying the root of the tree of life, I assumed the three domain hypothesis was fairly well supported by the research community. This model posits that the tree of life can be broken up into three taxa at its most basal level: eukaryotes, bacteria, and archaea. It's the hypothesized evolutionary relationships of these taxa that caused researchers to break the tree of life into three domains.
It turns out the three domain model isn't as supported as many of us assume. Larry Moran put me in my place, pointing out arguments against the three domain…
evolgen | November 18, 2006Most of the DNA sequenced from the Neanderthal genome projects came from the microbes that decomposed the dead fella'. This poses a problem for the human geneticists who are only interested in the Neanderthal DNA. But you could probably do some interesting things with the non-Neanderthal DNA. John Hawks says:
I suppose if you were interested in the long-term microbial decomposition of fossil bone, you could do your dissertation on those. For the rest of us, the final step is to let the computer spit out the humanlike sequences, which are assumed to be the Neandertal DNA plus some proportion…
evolgen | November 18, 2006After a month-long hiatus, a new edition of Animalicules is available at Baumhaus (I think the name means tree house). Animalicules has posts from around the blogosphere about microscopic living things. Check it out.
evolgen | November 17, 2006 . . . and so does the current grant review system. And manuscript review sucks, too. And your argument is based on flawed data.
A couple of months ago I posted on an article in Cell that drew parallels between the NIH grant review process and the TV show American Idol. As someone new to the grant writing game (and who has never seen what happens when they get reviewed), I wasn't sure if the metaphor was appropriate or not. Michele Pagano's article also advocated prescreening proposals, switching to an electronic system, and holding review panels over teleconference. These suggestions are…
evolgen | November 16, 2006Yesterday, I mentioned that one of the greatest technological developments that contributed to the evolution of population genetics was the automation of DNA sequencing. I was unaware, however, that the automated DNA sequencing method that most people use was patented by a group from Caltech (including Leroy Hood) in 1998. The actual invention was conceived in the early 1980s, but a competing group claims they came up with the idea first according to this article in the NYTimes.
If Enzo Biochem, the group suing Caltech over the patent, were to win their lawsuit, companies such as Applied…
evolgen | November 16, 2006The editors are asking us for the best pickup lines for scientists and science-savvy folks. How's about this:
Hey baby, that's a nice cleavage furrow, how about we introgress? I promise, no incomplete penetrance.
evolgen | November 15, 2006Razib and John Hawks have been all over the Neanderthal introgression story, but they hinted that there was more. And they thought that more would come from Svante Paabo. And it has, in the form of one million base pairs of Neanderthal DNA sequence published in this week's issue of Nature (here is Nature's Neanderthal page).
Not to be outdone, Science has published a paper described 65,250 base pairs of Neanderthal DNA (here is a link to the pdf and here is some coverage from Science). It looks like Science got the short end of the stick, with over an order of magnitude less DNA than the…