evolgen | May 17, 2007I'm working on a few graphs for a presentation. In a previous incarnation, I distinguished two partitions of my data using the colors red and green. This made sense intuitively (the red ones had something broken, and the green ones were a-ok), but I realized that people with red-green colorblindness would not be able to distinguish the different graphs. I switched the color scheme to white and gray, which should enable everyone to distinguish the two groups.
I also have a second way of partitioning the data, and I don't want to use the same color scheme for both. I initially used blue and…
evolgen | May 17, 2007Keith Robison, at Omics! Omics!, asks and answers the question, "What math courses should a biologist take in college?" His answer: a good statistics course is a must (one where you learn about experimental design and Bayesian statistics), and a survey course that covers topics like graph theory and matrix math would provide a nice introduction to important topics (that course probably doesn't exist at most colleges). He also advocates taking a programming class and turning math education into something more stimulating rather than rote drilling (easier said than done).
This being a blog, I,…
evolgen | May 16, 2007There's an interesting post over at Statistical Modeling, Causal Inference, and Social Science on calculating probabilities. Traditionally, if you observe a certain number of events (y) in some number of trials (n), you would estimate the probability (p) of the event as y/n. To calculate the variance around this estimate, you would use this equation: p(1-p)/n.
This leads to two problems. First, if you never observe the event, your estimate of the probability of the event is zero; if you observe the event in every trial, your estimate is one. This leads to a deterministic model even if the…
evolgen | May 14, 2007
The Canadian research organization Genome BC has unveiled a science education website, Genomics Education. One of the features of the website is Floyd the Fruit Fly, who, we can only presume, is some sort of cartoon drosophilid. Or maybe he's a tephritid, but I highly doubt it. When you hear "fruit fly" and "genetics", you think Drosophila, even if they really aren't fruit flies.
In the accompanying illustration, we see Floyd with smelly feet. Apparently, Floyd thinks that his foot stank is due to mitosis. He then learns, via a disembodied voice backed up by a soundtrack from an early Ron…
evolgen | May 14, 2007Paul Erdos was an extremely prolific and mobile mathematician who has left a legacy in academia in the form of the Erdos Number -- a count of your "academic distance" from Erdos. Anyone who published a paper with Erdos has an Erdos number of one (Erdos, himself, had a number of zero), people who published with anyone with an Erdos number of one have an Erdos number of two, and so on. It's a point of pride for a mathematician or other researcher to have a small Erdos number.
There is no widely recognized equivalent of the Erdos number for the life sciences. Given the diversity in the field, it…
evolgen | May 13, 2007Have you heard of the Encylopedia of Life? If not, get out from under the rock, dude. Seriously. The hype machine has been going at full steam. This is supposed to be a database of all known species of organisms on earth. It's the incarnation of E.O. Wilson's call for a database of all species. It's a database of all species! All species! Every species!! Hooray!!
Rod Page, the best biological databases blogger, isn't all that enthusiastic. He doesn't like the layout. He's seen similar ventures fail in the past. And then there's the whole issue that the EoL doesn't even exist yet. It's just a…
evolgen | May 10, 2007Rick at My Biotech Life is organizing all the genetics feeds into a single Feedburner feed. The DNA Network is a collection of feeds from sites that blog on genetics. You can subscribe to the DNA Network Feed to get the web's best genetics content delivered to your newsreader. If you would like to join the network, leave a comment on Rick's blog.
Via Neil Saunders I learned about Google's Image Labeler, in which you team up with another person to come up with labels for random pictures. I presume these labels will be used for smart searching in the future. Beware, this is an amazing time sink.
evolgen | May 10, 2007Nothing captures life in the academic sciences quite like Piled Higher and Deeper. In yesterday's comic, Jorge Cham shows us the disgusting innards of the lab/office fridge. Now, Jorge is a physicist engineer, so his fridge is the one where you're supposed to store your food and drinks. When a biologist thinks of a lab fridge, he pictures something quite different. With that in mind, here's my rendition of "The Lab Fridge":
Aside from the empty bottles that some lazy, inconsiderate lab mate (most likely me) failed to refill, what's missing from the fridge?
evolgen | May 9, 2007For the past decade, when a research community wanted to sequence the genome of their favorite species, they submitted a white paper to the National Human Genome Research Institute (NHGRI). Despite its name, the NHGRI funds genome sequencing projects of not only non-human mammals, but also non-mammalian animals and even non-animals (see here for a list). If a bunch of researchers want their species' genome sequenced, they would get together and explain why the genome should be sequenced. These should not be confused with typical research grant proposals that a principal investigator will…
evolgen | May 8, 2007Trevor has posted the newest edition of Mendel's Garden at Epigenetics News. Go check out the best genetics blogging of the past month.
Also, we need hosts for the upcoming editions. If you'd like to host the June, July, or August editions, please email me (see the contact tab at the evolgen webpage) or visit the Mendel's Garden page.
evolgen | May 3, 2007Here's some interesting science:
A commonly used medicinal leach may have been misidentified as the wrong species.
Here is a description of the Human Variome Project, which seems more focused on mapping disease genes than doing cool population genetics. That's too bad.
Science has an article on the benefits of undergraduate research. The most important one: to get into grad school.
You can use molecular markers to determine that a lonesome tortoise has no reason to feel alone.
The central nervous system is homologous across all animals.
What is the greatest innovation? I've tackled this…
evolgen | May 3, 2007Sorry, dude, but it has to be said. In a feature from the March issue of Seed Magazine (one that doesn't appear to be available online), Jonah Lehrer profiles six young scientists dubbed "The Truth Seekers". In his description of Pardis Sabeti, Jonah makes the common error of conflating evolution with natural selection.
Sabeti has helped develop algorithms that use linkage disequilibrium (LD) in DNA sequence polymorphism data to detect evidence for natural selection acting on those regions. She was also involved in a study that identified signatures of natural selection in the malaria…
evolgen | May 2, 2007The Savannah River Ecology Laboratory (SREL) is experiencing a financial crisis. They have received financial support from the Department of Energy (DOE) for over fifty years. The DOE has cut funding, which may force SREL to close down. SREL operates as a unit of the University of Georgia, but depends on money from the DOE maintain operations. Besides basic and applied research, SREL is also involved in teaching, outreach, and environmental monitoring.
I have reproduced information from SREL on how you can help encourage the government to continue funding this important research station.
The…
evolgen | May 2, 2007Spring is in the air. The obvious signs are everywhere: the temperature is rising, the flowers are blooming, and everyone's writing about boners. There's this post from Darren Naish on turtle gonads, and Carl Zimmer has an article on duck phalluses (don't call them penises, as Darren explains) in the NYTimes (and a blog post advertising it). Carl's article summarizes the findings of this study. The basic story is that some ducks have really big penis-like structures (penises are unique to mammals, so a bird schlong is called a phallus), and the females have crazy reproductive organs to match…
evolgen | April 30, 2007Dr. Doris Haggis-on-Whey and her husband Benny, as part of their H-O-W series of books, have produced an absolutely dispensable piece of misinformation, the third in a series of we can only hope not too many, ineloquently titled Animals of the Ocean: In Particular the Giant Squid. They claim that their World of Unbelievable Brilliance series, of which Animals of the Ocean is the third in a series of we can only hope . . . um, they claim that their series . . . well, I don't really know what they claim, because they never get around to it.
Dr. and Mr. Haggis-on-Whey are neither not biologists…
evolgen | April 29, 2007A few articles have come out recently dealing with sex chromosomes in a variety of taxa. Here are some links to those articles, in list form:
Given all we know about vertebrate sex chromosomes, it's surprising that we don't know how sex determination works in many fish, including the pufferfish Takifugu rubripes. That's especially surprising given that the fugu genome was sequenced. That is, we didn't know much until researchers mapped a sex determining locus and reported it in this paper. You see, fish use a wide range of mechanisms for sex determination, including environmental cues and…
evolgen | April 28, 2007In a round-up of some of the coverage of Shelley's run-in with Wiley, Scientific American's Nikhil Swaminathan wrote the following:
Anyway, on Tuesday, over at the ScienceBlog Retrospectacle, neuroscience PhD student Shelley Batts (who based on her pictures alone seems to be both attractive and avian-friendly) posted an analysis of a study appearing in the Journal of the Science of Food and Agriculture, which suggested that the antioxidants properties in fruits were boosted by alcohol.
So, Nik wants to hit that shit. This is, like, two steps away from passing Shelley a note in homeroom that…
evolgen | April 27, 2007The most recent issue of the Journal of Heredity contains a bunch of articles from a symposium on the "Genetics of Speciation" organized by Loren Rieseberg. Included in the collection is an article by Allen Orr and two of his students on speciation in Drosophila, which discusses mapping speciation genes, the role of meiotic drive in speciation, and Dobzhansky Muller incompatibilities via gene translocation (the latter two are the topics of recent papers from Orr's group -- here and here). Also in the special issue is an article from Mohamed Noor's lab on mapping inversion breakpoints between…
evolgen | April 27, 2007This week's phylogeny comes from this paper on molecular dating of speciation events. I won't be addressing molecular dating per se, but I will be dealing with what molecular clocks tell us. Like, do they actually reveal the speciation time of a pair of species?
The divergence date of a pair of species can refer to two things: when the two populations became two species (no longer exchanging alleles) or when the two genetic lineages split. The splitting of genetic lineages happens prior to the speciation event. That's because within a population there is variation throughout the genome. It's…