evolgen | November 15, 2006Nature has published a correspondence from Maciej Giertych, a Polish biologist, defending his view that evolutionary biology is bullshit. He's actually striking back at Nature for this news item on creationism in Poland. Long story short, the League of Polish Families (LPR), a group led by Roman Giertych (Maciej Giertych's son), has been pushing for the inclusion of creationism in the science curriculum of Polish schools. Maciej Giertych did not like how he and his fellow creationists were portrayed in the Nature article. He decided to defend himself in a letter to Nature, despite the fact…
evolgen | November 15, 2006Dan Hartl just finished a two day whirlwind speaking tour at my university (three talks in under 24 hours). He discussed detecting weak selection in protein coding sequences, identifying the underlying genetic causes of phenotypic variation in yeast, and the genetics of malaria parasites. I won't get into the details of these talks, but I will point out one thing Hartl brought up in his first talk that goes well with our recent discussion of computational and wet lab biologists.
The topic is revolutionary developments, the field is population genetics, and the time frame is the past twenty…
evolgen | November 14, 2006As I've pointed out before, the big division in biology is currently between computational groups and wet labs. Michael White agrees with me. Here's his take on the current state of computational work in cell biology:
The result is that you get different groups coming up with all sorts of new analyses of the same genomic data . . . but never really making any serious progress towards improving our understanding of the biological process in question. The worst part is that, over time, the researchers doing this kind of work start talking as if we are making progress in our understanding, even…
evolgen | November 13, 2006They just act stoned.
As Dean Wormer would tell you, "Fat, drunk, and stupid is no way to go through life." We can rule out that manatees are drunk -- although alcohol run off from Panama City Beach may bump the Gulf of Mexico up to 10 proof, that's hardly enough liquor to get a half ton beast hammered. But they're definitely fat and appear quite stupid.
Research out of the Mote Marine Lab indicates that we shouldn't mistake the manatees' half-baked attitude for stupidity. These marine mammals aren't stupid; they're just happy. And lazy. And fat. But they ain't dumb:
Hugh, a manatee in a tank…
evolgen | November 10, 2006Neil Saunders goes searching for the MCPH1 gene in the Neanderthal sequences available in Genbank. You'll have to go over to his site to see what he found.
evolgen | November 10, 2006In case you didn't hear, a sea urchin genome has been sequenced, analyzed, and the results published (Science has a page dedicated to it here). I say a sea urchin genome because there are many species of sea urchins. This paper reports the sequence of one species, Strongylocentrotus purpuratus, a model organism in developmental biology.
Despite the fact they are quite common-place, genome sequencing projects still draw some attention in the popular science press (see the honeybee as an example). And, as usual, the articles written about this scientific study are fraught with errors and…
evolgen | November 10, 2006I stole this picture from the front page of my university's student newspaper:
The Dog Fucker looks pissed. His wife is forcing a smile. And his daughter looks like she's about to cry. I feel bad for his daughter. Imagine growing up in a house where the biggest concern is that you don't fuck the pet dog. On top of that, her parents dress her in clothes to match her doll's outfit. That's just sick.
evolgen | November 9, 2006In one of the most important papers in population genetics, Begun and Aquadro showed that levels of DNA sequence polymorphism are positively correlated with recombination rate. There are three ways of interpreting this result:
Recombination is mutagenic, and polymorphism is higher with increased mutation.
Positive selection on beneficial mutations decreases levels of linked neutral polymorphism. This effect is greater in regions of decreased recombination and is known as hitchhiking.
Selection against deleterious mutations also decreases linked neutral polymorphism. Like hitchhiking,…
evolgen | November 8, 2006They've finally done it. Bruce Lahn's lab has an article in PNAS (review here) showing evidence for introgression of a gene from an archaic Homo species into the modern human genome. They suggest the possibility that Neanderthals are that archaic species. That's right: there are Neanderthals among us (at least in small portions of our genome).
For those of you interested in the details, here's a brief summary. The gene in question, microcephalin (MCPH1) has an interesting pattern of polymorphism. The approximate coalescence time for all MCPH1 alleles in humans is approximately one million…
evolgen | November 7, 2006That's right: if you study human genetics, you suck. In relation to Drosophila geneticists, of course. You see, human geneticists are boring. Drosophila geneticists come up with clever names for genes. When the homologues are identified in humans, the names are deemed offensive and inappropriate. Apparently, patients don't like being told they have a mutation in the lunatic fringe gene. Or sonic hedgehog. Or mothers against decapentaplegia. This is according to an article in Nature.
Maybe I don't know jack about bedside manner, but I can appreciate the amount of thought that goes into naming…
evolgen | November 7, 2006
This morning, I walked into my local polling place, signed in, and voted. There were fewer than ten items on the ballot, and it only took a few minutes. I had to wait a moment for one of the booths to open up, but there was no one in line ahead of me. If people aren't voting at 8am before work, when are they voting?
I got to use one of those new fangled touch screen voting machines. It wasn't Diebold, but I still felt a bit uncomfortable when I cast my ballot to dumprick. Was my vote actually going for the other guy or was the dog fucker stealing it somehow? Was a being paranoid?
As I was…
evolgen | November 7, 2006A few months ago, JP posted at GNXP that random mating is not necessary for Hardy-Weinberg Equilibrium (HWE). One round of random mating is still sufficient to achieve HWE genotype frequencies, but there are some non-random mating strategies that will also allow for HWE.
HWE is quite robust to violations of the assumptions. That makes it a poor test for things like natural selection, but it is commonly used to detect population structure. If you sample allele and genotype frequencies from a single population, the genotype frequencies should be in HWE. If, however, you sample from two separate…
evolgen | November 5, 2006The Seed editorial staff want to know how we're voting in the upcoming election. I try to avoid politics on this blog -- not because I don't have an opinion, but because I'd rather write about science. Here's what they want to know:
What's the most important local political race to you this year (as a citizen, as a scientist)?
As much as I would love to wax eloquently on issues of local politics, I've got a statewide race on my mind.
You see, Rick "Man on Dog1" Santorum is one of my US Senators. Zuska is also suffering from this same condition. Hopefully, come Tuesday, the Dog Fucker won't…
evolgen | November 4, 2006For all you runners and cyclists out there, I give you a toy you're sure to enjoy: Gmaps Pedometer.
Ever had a ride or run you wanted to do, but weren't sure how long it was or the elevation change? Enter Gmaps Pedometer. It works with the Google Maps interface, by far the best online maps application. You tell it where you want to start, enter checkpoints by double clicking, and that's it. It tells you mileage, elevation change, and you can save your routes.
There is a website that has good information on local rides in my area, but it gets boring doing the same routes every time. I started…
evolgen | November 3, 2006When Phylogeny Friday last made an appearance on this blog, we were exploring the vertebrates. This was part of a larger series in which we were working our way through the eukaryotes, focusing on animals. I've come to realize that weekly phylogenies are too much, so we're scaling Phylogeny Friday back to appear on the first Friday of the month.
Today, we will take a look at another group of eukaryotes: the fungi. (We'll return to the animals in a future edition.) Both fungi and animals are unikonts, and the clade containing fungi is sister to the clade containing the animals:
This is one…
evolgen | November 2, 2006A couple of days ago I showed you pictures of where we can find Drosophila in the Southwestern United States. Today, I'll show you some pictures of those flies. Below the fold are flies with racing stripes and others with fancy colored testicles. That's right: fly balls only a click away. You know you want it.
Before we get to the red and yellow testicles, I've got some striped flies to show you. Now, these guys aren't Drosophila, but they are members of a closely related genus. Well, closely related as far as insects go. The two genera diverged at least 50 million years ago. Here is a dorsal…
evolgen | November 1, 2006You are all the products of retard fish having sex with squirrels. And monkeys are involved somehow. Anyway, someone needs to post Mr. Mrs. Garrison's lesson on evolution from tonight's South Park. All I've got is this:
All hail the retarded fish frogs!!
But Dawkins having the hots for Garrison is a bit too much. Isn't he married to a sex symbol?
evolgen | November 1, 2006Sorry to beat a long-dead horse, but I thought I saw a leg twitch:
Atlantic Books have begun to publish this year a series of texts titled 'Books that shook the world', which, rightly, includes a new biography of Charles Darwin's Origin of Species by Janet Browne. And some new shaking definitely seems to be in order. Darwinism appears under increasing challenge as 'creationism' and 'intelligent design' continue to creep into curricula, particularly in the US and the UK.
That quote comes from Nigel Williams's review of Brown's book. Williams writes for Current Biology, a widely read journal…
evolgen | November 1, 2006Nature Reviews Genetics has published a review (go figure) of speciation genetics penned by Mohamed Noor and Jeff Feder. Here is the purpose of the review, from the horses' mouths:
Here, we review how recent advances in molecular and genomic techniques are helping to achieve a greater understanding of the genetics of speciation. For the purpose of this review, we focus on technical advances rather than theoretical concepts, which are discussed extensively elsewhere. We define speciation for sexually reproducing organisms as the transformation of within-population variation into taxonomic…
evolgen | October 31, 2006As promised, I'll be posting some pictures of flies we caught in and around Tucson, Arizona. But before we can talk about the flies, we need to talk about the local flora. The host plants for these flies serve as a restaurant, discotheque, bedroom, and nursery. In Arizona, those plants tend to be cacti. Below the fold I have posted a picture of a cactus that met a sad fate: it was struck by a bold of lightning. But from the ashes of the dead saguaro came a diverse collection of Drosophilids.
Drosophila are NOT true fruit flies (see here), and they prefer rotting plants to fresh fruit. For…