evolgen | March 12, 2007
What a weekend! Professor Steve Steve and I returned from Philadelphia on Sunday after hanging out with the Drosophilists. Steve arrived in Philly on Thursday morning on a direct flight from Iowa City, but the staff at the Philadelphia Marriott couldn't understand his thick accent when he asked that they notify me of his arrival. The little guy wandered the lobby of the hotel until Saturday morning, when I found him nibbling on the flamboyant floral display. That wasn't the only thing the Marriott screwed up.
More stories and pictures can be found below the fold.
Why the Marriott sucks:…
evolgen | March 6, 2007Alex claims I do cowboy science because my protocol for DNA isolation requires cutting plastic with hot razor blades. But before we ever get to cut any plastic, we need to grind up the flies. I don't have any pretty pictures of this process, but I can capture the essence in words (picture may come later). It starts with "homogenizing" about two grams of flies in a few milliliters of buffer. We end up with a Drosophila shake -- kind of like a milk shake, only without milk and you probably don't want to drink it -- which has a bunch of particulate matter (pieces of exoskeleton, wings, legs,…
evolgen | March 5, 2007A discussion of open access data using bird flu and other disease data as examples.
The recent scares over bird flu have led many researchers to investigate the epidemiology, genetics, and disease risks of the virus. The researchers are focused on both preventing the transmission of the virus into human populations and preparing for a potential pandemic. By analyzing DNA sequences from different viral strains, researchers can understand how the virus spreads within and between populations, how it changes over seasons, and what (if anything) we can do to predict its next evolutionary jump.…
evolgen | March 4, 2007The word on the streets is that there used to be a blog at this URL (pronounced like the mountain range separating Europe from Asia). If this were a blog, however, it would be updated often and definitely not left dormant for over two weeks. All I can say is that meth is a hell of a drug. But fear not readers, I have reemerged from a research induced vanishing act, and I'll be blogging with some vigor for the near future (the specific amount of vigor cannot be guaranteed or measured with anything resembling an acceptable level of accuracy). In fact, I've got a long post -- filled with all the…
evolgen | February 15, 2007
Those kooky Canucks at the Science Creative Quarterly have started a new club: the Order of the Science Scouts of Exemplary Repute and Above Average Physique. Anyone is free to join, provided they're not a teetotaling, lying, world-dominating, badge-hater, 'cause they're really into badges. To profess their love of badges, the Science Scouts have produced quite a collection, some of which I feel qualified to wear on my Science Scout Sash. You see, these badges aren't handed out by some higher authority; you simply claim all the badges that apply to you and post them on your website, like so…
evolgen | February 15, 2007Some bio-bloggers are atwitter over an article by Wojciech Makalowski on Scientific American's website about Junk DNA. I'm a little late to the game because, well, I've been really busy looking at sequences to determine if they are junk DNA. Is it irony? Is it coincidence? Who cares? It's an opportunity to discuss semantics, and I love semantics.
Those of you who have hung around here for a while know this topic often comes up at evolgen (remember this, this, and this . . . hell, here's what a search for Junk DNA turns up). Long story short, I can't stand the term junk DNA, but I do agree…
evolgen | February 14, 2007In honor of all the snow being dropped on the Northeast US, I give you "Things that rock & things that suck." Cue the theme music...
Things that rock: Snowfall measured in feet.
Things that suck: Freezing rain.
Things that rock: Showing up to class/work on cross-country skis.
Things that suck: Cancelled classes.
Things that rock: Watching ill-prepared undergrads try to navigate an unplowed path or snow drift.
Things that suck: Navigating an unplowed path or snow drift.
Things that rock: Riding your bike in the snow.
Things that suck: Snow removal services that plow snow onto bike…
evolgen | February 13, 2007Duplicated genes can arise via various mechanisms -- polyploidization, chromosomal duplication, segmental duplication, and retroposition -- and we can usually distinguish the various mechanisms as each has distinct signatures. For example, retroposed duplicates arise when an RNA transcript is reverse transcribed back into DNA and re-inserted into the genome. This is how many transposable elements (TEs) and viruses propagate throughout genomes, but the reverse transcriptase encoded by TE and viral genomes can be used on endogenous transcripts as well. Because they arise via the reverse…
evolgen | February 12, 2007Does anyone know anything about NESCent (the National Evolutionary Synthesis Center in North Carolina)? They're affiliated with Duke, UNC, and NC State (the Research Triangle universities), and they offer postdoctoral fellowships. One of my committee members suggested it as a possible location for a postdoc, but I'm concerned that any potential project would be way heavy on computational work. I'm just trying to get a feeling for the center from anyone familiar with the research going on there.
evolgen | February 9, 2007Hsien at Genetics & Health has posted the newest edition of my favorite (just) science blog carnival: Mendel's Garden. There are oodles of reasons why you should love genetics (and only a couple why you should not).
If you would like to host a future edition of Mendel's Garden, visit the carnival's blog and leave a comment or email Paul.
evolgen | February 8, 2007I have previously mentioned, in passing, a pet peeve of mine: when people conflate ecology with environmentalism (see here and here for examples). It's an odd pet peeve for an admitted non-ecologist, but it falls under the umbrella of distinguishing science from technology which is at the heart of the real pet peeve. It just happens that the ecology/environmentalism issue pops up more often than other science/technology issues in my daily life (I don't deal with stem researchers or people cloning whole organism).
Before I get too far ahead of myself, allow me to define what I mean by science…
evolgen | February 7, 2007Shotgun sequencing refers to the process whereby a genome is sequenced and assembled with no prior information regarding the genomic location of any of the DNA we sequence. There are quite a few steps that you have to go through before you have an assembled genome sequence. We're going to cover isolating DNA, putting the DNA in bacteria, sequencing the DNA, and assembling those sequencing into a complete genome.
Sandy has been running a series on sequencing genomes (parts 1, 2, 3, 4, 5, 6, 7). You should go check it out even if you read this post; while I'm going to deal with some of the…
evolgen | February 6, 2007Where the variation comes from.
Evolution proceeds by the action of many different evolutionary forces on heritable variation. Natural selection leads to the increase in frequency of variation that allows individuals to produce more offspring who, themselves, produce offspring. Genetic drift changes the frequency of variation through random sampling of individuals from one generation to the next. Population subdivision divides the variation into isolated groups where other forces (selection, drift, etc) act upon it. But where does all this variation come from?
Given the title of the post, the…
evolgen | February 5, 2007I've been chatting up Wilkins about the role of natural selection in speciation (and when I say "speciation" I mean "reproductive isolation"). Wilkins listed a few cases where speciation would occur independently of natural selection. Amongst the mechanisms in Wilkins's list was speciation via karyotypic changes (polyploidy, inversions, fusions or fissions). I cried shenanigans, and this is why.
The karyotype refers to the organization of an organism's genome -- chromosome number, fusions/fissions of chromosomes, and gene order within chromosomes. One way to change the karyotype is to…
evolgen | January 31, 2007Jeremy has posted the newest edition of the Circus of the Spineless -- the blog carnival dedicated to invertebrates -- at the Voltage Gate. We'll excuse the carnival organizers for creating a carnival organized around a paraphyletic taxon this one time because Jeremy included one of our posts on wasps. He's also got stuff on cephalopods, shrimp, snails, spiders, and a bunch of other spineless critters.
evolgen | January 30, 2007I straddle the line between being a population biologist and a molecular geneticist. That's a self-congratulatory way of saying that I am an expert in neither field. But existing in the state I do allows me to observe commonalities shared by both. For example, both fields have terminology (or what the uninitiated would call jargon) that lack sufficient definitions.
Amongst my minimal postings from last week were included a couple of riffs on species and speciation (the first, the second) getting at the lack of a coherent definition of species. My conclusion is that there is not, nor will…
evolgen | January 29, 2007The Week of Science Challenge (official website here) begins next Monday (5 February 2007). During the time of the challenge, all participating bloggers will post at least once per day on science and only science -- no anti science or non-science material.
If you would like to participate, you can sign up here by providing your blog name, email address, blog URL, and blog RSS feed. There will be an official Week of Science feed made up of all the participating blogs.
evolgen | January 25, 2007We've got Phil Skell, and we can't get rid of him. Both Michael Behe and William Harris have rolled through my parts in the past few years. Tonight we get disciples of Adnan Oktar (Harun Yahya), the muslim creationist described in this article on creationism in Turkey. He's also an alleged holocaust denier.
When I got my "Invitation to attend Evolution lecture tonight" (reproduced below the fold) from the president of the Muslim Student Association, I didn't know what to think. I'm not sure if I'll be attending the talk (I've got real work to do), and Oktar won't even be there; he's sending…
evolgen | January 24, 2007Wilkins has replied to my post on species concepts.
The gist: there are a bunch of species concepts, many of which are pretty darn good.
My reply: that's awesome as long as they guide future research. The BSC provides a framework for studying reproductive isolation. Ecological species concepts are useful when studying adaptation to niches. But I still see nothing interesting that can be garnered from purely phylogenetic- or divergence-based species concepts.
evolgen | January 23, 2007Because I haven't riled up Wilkins in a while.
I was chatting with a friend who has published a fairly high profile article on speciation about species concepts. We came to the conclusion that species concepts are useless unless they guide future research. Okay, we were just echoing Coyne 'n Orr.
As crappy as the biological species concept is, the BSC is really good for guiding research on the evolution of pre-zygotic, intrinsic reproductive isolation. I realize this is entirely circular (the BSC states that speciation has occurred when reproductive isolation is achieved). All of the research…