Molecular Biology
pharyngula | February 14, 2007I may have to find an excuse to use this in my genetics class—I'll definitely be showing it in my intro biology course in the fall. Very groovy.
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 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 | 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…
pharyngula | January 25, 2007Yesterday, I pointed out that Jonathan Wells was grossly ignorant of basic ideas in evo-devo. This isn't too surprising; he's a creationist, he has an agenda to destroy evolutionary biology, and he's going to rail against evolution…same ol', same ol'. That's nothing, though. Wells and his fellows at the Discovery Institute have an even more radical goal of fighting natural, material explanations of many other phenomena, and his latest screed at the DI house organ is against natural explanations of development. Not evolution, not evo-devo, just plain basic developmental biology—apparently, he…
pharyngula | January 18, 2007
The vulva is one of my favorite organs. Not only is it pretty and fun to manipulate, but how it responds tells us so much about its owner. And it is just amazing how much we're learning about it now.
Don't worry about clicking to read more…this article is full of pictures, but it is entirely work safe because it's all about science.
It also helps that all I'm going to talk about is worm vulvas. Anybody who has taken a developmental biology class in the last ten years knew exactly what to expect: when a developmental biologist starts getting all enthusiastic about vulvas, you know he's…
pharyngula | January 17, 2007This is cool: a team using distributed computing to solve the protein folding problem has put out a promotional video asking for your unused computing cycles…and along the way they explain exactly what it is they are doing.
evolgen | January 16, 2007Gregg Easterbrook -- good sportswriter, crappy at pretty much everything else he does -- likes to take pot-shots at scientific research in his ESPN column "Tuesday Morning Quarterback" (TMQ). In this week's edition he tells us how he doesn't think scientific papers should have multiple authors and how he doesn't like the advertisements in the journal Science.
TMQ dislikes the modern convention of listing multiple people as "authors" of a work written by a single person; this is part of the overall cheapening of the written word. Several previous items have concerned the absurd number of…
pharyngula | January 16, 2007I mulled over some of the suggestions in my request for basic topics to cover, and I realized that there is no such thing as a simple concept in biology. Some of the ideas required a lot of background in molecular biology, others demand understanding of the philosophy of science, and what I am interested in is teetering way out at the edge of what we know, where definitions often start to break down. Sorry, I have to give up.
Seriously, though, I think that what does exist are simple treatments of complex subjects, so that is what I'm aiming for here: I talk a lot about genes, so let's just…
evolgen | January 16, 2007To the uninitiated, chromosome number may appear to reflect genome size -- more chromosomes would mean a larger genome. This is not necessarily the case if we measure genome size by the number of base pairs in a genome. There are two primary ways to change chromosome number: chromosomal duplications and chromosomal fusions/fissions. Chromosomal duplications (either through polyploidization or aneuploidy) do change the size of the genome, either by creating a second copy of a single chromosome or duplicating an entire genome. Fusions and fissions, on the other hand, merely rearrange the…
evolgen | January 15, 2007There are a lot of different ways for animals to determine which individuals develop into boys and which ones become girls. You're probably most familiar with the form of chromosomal sex determination that utilizes X and Y chromosomes -- males are XY and females are XX. There are others, including ZW (males are ZZ, females are ZW) and environmental sex determination (e.g., sex can be determined by egg rearing temperature).
One of the most interesting sex determination systems -- from an evolutionary perspective -- involves differences in ploidy between males and females. Hymenoptera (ants,…
pharyngula | January 14, 2007
Q: What unique organ is found only in mammals, but not in fish, amphibians, reptiles, or birds?
The title and that little picture to the left ought to be hint enough, but if not, read on.
A: The vagina. Aren't we lucky?
There's an old joke going around about poor design: what kind of designer would route the sewer pipes right through the center of the entertainment center? It's a good point. It doesn't make sense from a design standpoint to have our reproductive and excretory systems so intimately intermingled, but it does make a heck of a lot of sense from a purely historical point of view…
evolgen | January 10, 2007Mutations are the fuel that drives the engine of evolution. Without mutations there would be no variation upon which natural selection and other evolutionary forces could act. Furthermore, much of the theoretical results regarding evolutionary genetics depend on estimates of mutation rates. For example, Kimura showed that the rate of fixation of neutral mutations is equal to the neutral mutation rate. Additionally, many models to explain the evolution of sex and recombination depend on the amount of deleterious mutations per genome per generation (U).
A group led by Peter Keightly (DOI) have…
pharyngula | January 9, 2007
If you've seen BladeRunner, you know the short soliloquy at the end by one of the android replicants, Roy, as he's about to expire from a genetically programmed early death.
"I've seen things you people wouldn't believe. Attack ships on fire off the shoulder of Orion. I watched c-beams…glitter in the dark near Tanhauser Gate. All those…moments will be lost…in time, like tears…in rain. Time…to die."
There's an interesting idea here, that death can be an intrinsic property of our existence, a kind of internal mortality clock that is always ticking away, and eventually our time will run out…
evolgen | January 8, 2007Phenotypic differences between populations, species, or any other taxonomic classification can be attributed to genetic and environmental causes. The genetic differences can be divided into sequence divergence of transcribed regions, copy number divergence, and expression divergence. These categories are hardly independent -- expression divergence results from the evolution of the protein coding sequences of transcription factors and cis regulatory regions of transcribed sequences.
An article in press in Nature Genetics (news item here) reports on differences in expression of 4,197 genes…
pharyngula | January 8, 2007
As we are so often reminded by proponents of Intelligent Design creationism, we contain molecular "machines" and "motors". They don't really explain how these motors came to be other than to foist the problem off on some invisible unspecified Designer, which is a poor way to do science—it's more of a way to make excuses to not do science.
Evolution, on the other hand, provides a useful framework for trying to address the problem of the origin of molecular motors. We have a theory—common descent—that makes specific predictions—that there will be a nested hierarchy of differences between…
evolgen | January 5, 2007In light of the recent post on translational selection, I give you this paper from PLoS Genetics on tissue specific differences in tRNA expression from humans. From the abstract:
We found tissue-specific differences in the expression of individual tRNA species, and tRNAs decoding amino acids with similar chemical properties exhibited coordinated expression in distinct tissue types. Relative tRNA abundance exhibits a statistically significant correlation to the codon usage of a collection of highly expressed, tissue-specific genes in a subset of tissues or tRNA isoacceptors. Our findings…
evolgen | January 3, 2007New Scientist reports on research to identify DNA sequences that cannot be found in any nucleotide database. These sequences are short -- so as to decrease the probability that they are missing due to chance alone -- and the researchers from the Boise State University have identified over 60,000 15 nucleotide stretches of DNA that are not present in any known sequenced region from all species. They also found 746 sequences of 5 amino acids that are not present in any known polypeptide. The article does not indicate whether the scientists utilized any hook and ladder or Statue of Liberty…
evolgen | January 3, 2007Pim van Meurs has a blog post at The Panda's Thumb about the recent paper on translational selection on a synonymous polymorphic site in a eukaryotic gene (DOI link). He points out that this was predicted in a paper from 1987. In short, the rate of translation depends on the tRNA pool -- amino acids encoded by more abundant tRNA anti-codons will be incorporated more quickly than amino acids with rare tRNAs. Because protein folding begins during translation, codon usage can influence protein secondary structure. That's because rare codons could stall translation, allowing for protein…