Molecular Evolution
evolgen | December 18, 2008A couple of years ago, there was talk in the bioblogosphere about getting the general public interested in bioinformatics and molecular evolution:
Amateur bioinformatics?
Lowering the Ivory Tower with Molecular Evolution
Molecular Evolution for the Masses
The idea was inspired by the findings of armchair astronomers -- people who have no professional training, but make contributions to astronomy via their stargazing hobbies. With so much data available in publicly accessible databases, there's no reason we can't motivate armchair biologists to start mining for interesting results.
But how…
sb admin | December 17, 2008Larry Moran points to a couple of posts critical of microarrays (The Problem with Microarrays):
Why microarray study conclusions are so often wrong
Three reasons to distrust microarray results
Microarrays are small chips that are covered with short stretches of single stranded DNA. People hybridize DNA from some source to the microarray, which lights up if the DNA hybridizes to the probes on the array.
Most biologists are familiar with microarrays being used to measure gene expression. In this case, transcribed DNA is hybridized to the array, and the intensity of the signal is used as a…
sb admin | November 16, 2008
Population biologists often want to infer the demographic history of the species they study. This includes identifying population subdivision, expansion, and bottlenecks. Genetic data sampled from multiple individuals can often be applied to study population structure. When phylogenetic methods are used to link evolutionary relationships to geography, the approaches fall under the guise of phylogeography.
The past decade has seen the rise in popularity of a particular phylogeographical approach for intra-specific data: nested clade analysis (Templeton et al. 1995; Templeton 2004). Many of…
evolgen | October 9, 2008The Penn State Alumni Association has produced trading cards featuring the best and the brightest of the university's faculty (Pa. trading cards highlight brains, not brawn). The cards are only available at University President Graham Spanier's tailgate parties on home football weekends. The biologists featured include entomologist Jim Tumlinson and molecular evolution pioneer Masatoshi Nei.
I haven't been able to find a complete list of all ten faculty members featured, and I don't think that individual images of the ten cards are available online. If anyone can track them down, post a link…
evolgen | October 7, 2008One of the hot topics in evolutionary biology concerns the relative contributions of protein coding sequence changes and non-coding changes that lead to differences in the expression of protein coding genes. A subset of this debate can be summarized as cis versus trans. Non-coding sequences that regulate gene expression are known as cis regulatory elements (CREs). The protein coding genes that bind to CREs and control the expression of genes act in trans.
That's the background,and here are some more details. The poster boy for the importance of CREs is Sean Carroll, who argues that the…
evolgen | July 28, 2008
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…
evolgen | July 21, 2008We 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.…
evolgen | April 23, 2008Brian Charlesworth wrote a review of Mike Lynch's The Origins of Genome Architecture, in which Charlesworth argues that sexual reproduction can explain many of the features Lynch claims evolved under nearly neutral processes (doi:10.1016/j.cub.2008.01.008). Not to be left out of the party, Deborah Charlesworth has chimed in with her opinion, and it's much more critical of Lynch than her husband's (doi:10.1017/S0016672308009282). The main thesis that Lynch has been presenting in both this book and some of his recent papers is that many features of eukaryotic genomes (introns, complicated cis…
evolgen | April 14, 2008I think I'm cursed. Or I have bad luck. Or conference organizers think I'm a morning person. Alright, so maybe I really am a morning person. But that's besides the point. Because it sucks to give a talk on a Saturday morning. Saturday mornings should be reserved for things like Belgian waffles, homemade hash browns, made to order omelets, and mimosas. Not for 12 minute talks about my research. How much can you fit into a 12 minute talk? Not much. And you end up speeding up at the end when you realize you've got about 1 minute to make it through four slides. It's either that or go over 12…
evolgen | April 8, 2008Us dudes are always accused of thinking with our dicks. Perhaps it's because the genes expressed in our brains are similar to those expressed in our 'nads:
Among the 17 tissues, the highest similarity in gene expression patterns was between human brain and testis, based on DDD and clustering analysis. Genes contributing to the similarity include ribosomal protein (RP) genes as well as genes involved in transcription, translation and cell division.
The authors of the paper allege that their result has something to do with speciation. They even claim, "Brain is the most important tissue in…
evolgen | March 6, 2008Olivia Judson (aka, Dr. Tatiana) has a blog at the NYTimes website. It's usually a good read, but she has been known to go off the deep end. In this week's entry, Judson posts on how bones are not the only fossils. What other fossils does Judson write about? Genomes.
Judson's focus is on genome size. She's clear that differences in genome size are the result of stuff other than genes, but she doesn't want to call that extra stuff "junk". Here's why:
I don't like "junk," which suggests the DNA is useless: even if it doesn't hold the instructions for making proteins, it may still serve a…
evolgen | January 16, 2008Alex is pissed about science writers neglecting important discoveries in cell biology:
Why are cell biology, molecular biology, biochemistry, microbiology never covered in the media? I've spoken to so many science journalists - most of whom have no science training. I've come to the conclusion that the barrier is too high - as a result when it comes time to write about these topics, most science journalists end up writing about "genomes" and "junk DNA". These are easy subjects - sometimes they're discussed within the framework of evolution, but never within the context of "how a cell or an…
evolgen | December 4, 2007
I previously described where in a genome we would expect to find sexually antagonistic genes. Briefly, depending on whether a gene is male-biased or female-biased and whether beneficial mutations are dominant or recessive, we can predict whether these sexually antagonistic genes will be on X chromosomes or autosomes. As I mentioned in that post, the theoretical results can only be translated into realistic predictions if we have reliable estimates of the relevant parameters. We do not have such estimates, but we can study the distribution of sex-biased genes throughout genomes. The results…
evolgen | November 7, 2007What happens when I mention a paper describing two more Drosophila genomes? Well, I get a comment telling me that the 12 Genomes Papers have gone live over at Nature. They have provided a nifty 12 Genomes Portal for us to navigate the articles published by Nature based on data from the 12 Genomes Project. Now, these aren't the only papers published from the 12 Genomes Project -- look for 12 Genomes Papers in the November issues of Genetics (currently not web-available), PLoS Genetics (also not up on the website), and the December issue of Genome Research.
The 12 Genomes Papers include two…
evolgen | October 16, 2007Previous entries:
Part 1 - Introduction
Part 2 - The Backstory
Part 3 - Obtaining Sequences
Part 4 - Obtaining More Sequences
Part 5 - Examining the Outgroups
This post is part of a series exploring the evolution of a duplicated gene in the genus Drosophila. Links to the previous posts are above. Part 6 of this series (Evolutionary Relationships) can be found below.
Evolutionary Relationships
While we were probing the outgroup genomes for copies of aldolase genes using TBLASTX (Examining the Outgroups), we discovered that there are two excellent matches to aldolase genes in the honeybee,…
evolgen | October 1, 2007This is a repost (with some edits) of an introduction to publishing original research on blogs -- a series I am reintroducing. The original entry can be found here.
Previous entries:
Part 1 - Introduction
This post is part of a series exploring the evolution of a duplicated gene in the genus Drosophila. Links to the previous posts are above. Part 2 of this series (The Backstory) can be found below.
The Backstory
The reason you and I and all other animals (and most other forms of life) can do things (like live) is because we combine oxygen with sugars to make energy. Eventually, the oxygen…
evolgen | September 28, 2007This is a repost (with some edits) of an introduction to publishing original research on blogs -- a series I am reintroducing. The original entry can be found here.
In April of last year, Bora pushed the idea of publishing original research (hypotheses, data, etc) on science blogs. As a responsible researcher, I would need to obtain permission from any collaborators (including my advisor) before publishing anything we have been working on together. But what about small side projects or minor findings that I don't expect to publish elsewhere? As it turns out, such a project has been laying…
evolgen | September 26, 2007The human genome is one big, bloated motherfucker. It's almost all non-protein-coding DNA. The same is true for many other eukaryotic genomes. Sure, some of it has a function. But a whole lot of it (and maybe most of it) is just junk.
There are some who point to a relationship between genome size and organismal completexity and argue that those large genomes are necessary to explain the compelexity they observe. There are other that disagree -- T.R. Gregory at Genomicron being one of the more vocal objectors in the geno-blogosphere. First off, how do you measure complexity? Second of all,…
evolgen | September 26, 2007Over a year ago I threatened to perform some original research and publish it on my blog. I got as far as writing an introduction to the project, but I never actually posted any data. I know, I suck.I had hoped to make the project simple enough that people could follow along. The problem was the available data were not in a form that would be accessible for most readers. So, I've held off until now. But the appropriate data have now been deposited in Genbank, so I can continue the series.
Over the next couple of days I'll post the previously published entries, and they will be followed by the…
evolgen | September 16, 2007Carl Zimmer has a post covering three recent papers on gene duplication: one on amylase variation in humans, one on whole genome duplication in yeast, and one on duplications of genes in the Drosophila arizonae reproductive tract. In all three papers, results are presented showing the importance of duplicated genes in adapting to the environment.
Now, gene duplication isn't anything new around these parts. Those who know me know that I have a bit of an interest in gene duplication. Those who don't, well, consider yourself informed that I have a bit of an interest in gene duplication.
Given…