evolgen

Archives for April, 2006

Phylogeny Friday – 28 April 2006

Over at my old site, I lamented the apparent death of distance based tree building algorithms. Just as all of life on earth can be divided into three domains, phylogenetic methods can be split into three groups: distance based, maximum parsimony, and maximum likelihood. Distance and parsimony based approaches have been around for a while…

Via Janet comes the ABC meme. To learn a bit about me, click through to below the fold.

From the Junk Rise the ORFans

Ian Musgrave has a good summary of genes appearing from non-coding DNA (ORFans) on the Panda’s Thumb. I have written about ORFans here and here (dude’s gotta link to himself sometimes). Ian’s post is targeted at some claims made by the creationist Paul Nelson, but he focuses more on the science that on the ignorant…

Kids Email the Darndest Things

If you know anything about bioinformatics, you know that programmers love to come up with clever names for their applications. NCBI’s BLAST (Basic Local Alignment Search Tool) programs are some of the most used tools, but behind every successful program is a stupid acronym or cute name. Do the people who name these programs realize…

What I Think You Should Know

Via BioCurious comes this article on ten “science question[s] every high school graduate should be able to answer.” Read the list — most of the questions are bullshit. Ok, they aren’t bullshit, but they are trivia. “What percentage of the earth is covered by water?” “What sorts of signals does the brain use to communicate…

Bora has been pushing the idea of publishing original research (hypotheses, data, etc) on science blogs. This post is part of a series exploring the evolution of a duplicated gene in the genus Drosophila. Links to the previous posts can be found below. Part 2 of this series (The Backstory) can be found after the…

Bora has been pushing 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 published anything we have been working on together. But what about small side projects or minor findings that I don’t expect to…

An Alignment Tree

Via nodalpoint comes this UPGMA tree of sequence alignment algorithms from this paper. The first thing that comes to mind is that there are way too many sequence alignment methods. The second, it’s kinda cool to see one method used to understand another. And Nucleic Acids Research gets mad props for being entirely open access…

Race or Whatever

If you read evolgen, you’ve probably been following the race riots that Wilkins started. It’s pretty much died down now, and it was more a debate about semantics rather than an actual scientific disagreement. This is usually the case in evolutionary biology — take, for example, the neutralist-selection debate or the recent junk DNA fun…

I am an endosymbiotic cyanobacterium

Otherwise known as a choloroplast: The Chloroplast You scored 46 Industriousness, 54 Centrality, and 23 Causticity! You’re the Chloroplast! Most of the Earth’s energy comes from the chloroplast’s ability to capture the energy of the sun and fix cabon dioxide for conversion to starch. Like the mitochondria, they have their own DNA and live somewhat…