evolgen | September 28, 2006There is a general disconnect between the people I know from blogging and the people I know in real life. I've only met a couple of my fellow SciBlings (ScienceBlogs siblings): John Lynch, Mad Mike, and Carl. I have only once had a real world friend or colleague overtly mention to me in real life that they read or know of my blog. That's probably to be expected given that I blog pseudo-pseudonymously (quite an appropriate title given my study species).
But there are people in the bloggy world who have figured out who I am in the real world. I don't mind, I just ask that they not broadcast it…
evolgen | September 27, 2006
The sixty-third edition of Tangled Bank has been posted by the Indian Cowboy. Go read yourself some science.
evolgen | September 26, 2006If it weren't for coffee, much of the research that gets done today wouldn't get done. Or so I am led to believe based on the reverence people seem to have for the sacred bean. Frankly, I'd trade a cup of coffee for a good night's sleep. Hell, I'd trade a cup of coffee for pretty much anything. That's because I don't drink coffee. That sound you hear is from all the coffee drinkers (yourself included, probably) letting out a gasp as they wonder how someone can function without a chugging liquid caffeine.
I don't really have a secret. I just never got addicted -- to coffee or caffeine. I've…
evolgen | September 25, 2006Ever wanted a tattoo of your favorite invertebrate? I hear they're inking insects, molluscs, cnidarians, and all kinds of other spineless critters in Monterey. To get your tat, visit the newest edition of Circus of the Spineless at Deep-Sea News.
evolgen | September 25, 2006
As if we didn't have enough "-omes" in biology, I have come across yet another one: the methylome. It's beginning to sound like a Hindu temple up in here. My fascination with the -ome is well documented. I was made aware of the newest -ome in my collection by this preview of this article in Cell. The preview is entitled "The First High-Resolution DNA 'Methylome'" and describes a paper announcing a high resolution map of DNA methylation in the Arabidopsis genome.
We can thank Andrew Feinberg for introducing the term methylome, which he defines as "a neologism that describes the complete set…
evolgen | September 24, 2006I'm so vain I think I every single song is about me.
Dave wants us to "make a music mix that is a reflection of your informative years." I have no idea what he means by informative years, so I'm going to give you a list of a dozen or so songs (Dave's suggested amount) that I like, each by a different band. The order makes sense to me, but it probably won't make sense to you.
Faith No More - Falling to PiecesFaith No More's The Real Thing was the first album I ever bought with my own money. I would listen to the album over and over, singing along to the lyrics in the liner notes. Once I…
evolgen | September 23, 2006I saw him again at the supermarket today. This is the second time I've seen him at the supermarket -- and third time overall. But this is the first time I was stealth, without any identification of my alma mater.
In case you're late to the game, this guy is an emeritus professor at my current university, and he also graduated from my alma mater. I've run into him twice around town, both times I had something that gave away my former school (either a hat or a license plate holder). Like the last time I saw him in the supermarket, we were both in the produce section. However, today I was…
evolgen | September 22, 2006Five nurses and one doctor have been imprisoned in a Libyan jail since 1999, accused of infecting more than 400 children with HIV. They were condemned to death in 2004, but the verdict was overturned. Their retrial is due to wrap up very soon, and they await their new sentencing. The problem: the scientific evidence indicates that the medics were not responsible for the infections, but the Libyan courts threw out that evidence. For more information, please read the news item in Nature as well as this editorial.
The blogosphere has been quite active in the cause to free the Tripoli six (the…
evolgen | September 22, 2006The Scientist (we're not sure which one) reviews the palm tree sympatric speciation paper from February (doi here). Here's what Jerry Coyne has to say:
"Both these cases are most parsimoniously interpreted as sympatric speciation," said Jerry Coyne at the University of Chicago. Still, he questioned whether the species are truly sister taxa, and didn't reach the island or crater lake from separate invasions from a source population. "If there's a little bit of hybridization between the species, they're going to become genetically more similar to each other than either is to a mainland species…
evolgen | September 22, 2006
My previous claims of geekiness were in jest. And if that wasn't clear to you, do you understand anything? Anyway, I defined nerds as book smart, dweebs as socially awkward, and dorks as nerdy dweebs (or dweeby nerds). Geeks to me are sideshow acts (freaks) that bite the heads off of live chickens. Some people consider them nerds with a specialized type of knowledge.
Which brings us to this quiz that assesses your nerdiness, geekiness, and dorkiness (as defined below). Razib started it, and my results are below. I am pure nerd (book smart), with traces of geekiness and dorkiness. By the way…
evolgen | September 22, 2006We've been working our way across through the tree of life in the past few editions of Phylogeny Friday. Last week we took a look at the evolutionary relationships of the animals, and we realized that many of the branching orders are extremely difficult to resolve. Today we're going to zoom in on one of those branches: the vertebrates. Why? Because we're vertebrates and we want to know about ourselves. Also, we know more about this taxon than any other taxon. These are the same rules than have governed us throughout our journey.
After last week's disappointingly unresolved tree, I have a…
evolgen | September 22, 2006Alex has been pondering the nature of non-protein-coding RNAs. So have the boys at Gene Expression (how appropriate). Coffee Mug and JP have pointed out that a large portion of the human genome is transcribed, and much of it has an unknown function. Now JP describes a paper that takes an evolutionary approach towards studying the function of intergenic transcripts. By comparing human and chimp transcription profiles, the authors "that intergenic transcripts show patterns of tissue-specific conservation of their expression which are comparable to exonic transcripts of known genes." This…
evolgen | September 21, 2006Tara has been given the task of pointing out some of the flaws in Chapter 7 of Jonathan Wells's The Politically Incorrect Guide to Darwinism and Intelligent Design. From what I can gather, this is the chapter in which Wells claims that biology does not need evolution because evolution has no applications in medicine or agriculture. In doing so, Wells reveals he does not understand the difference between natural and artificial selection:
The clinical use of antibiotics creates a highly artificial situation. Antibiotic-producing microbes must be isolated from their natural surroundings and…
evolgen | September 20, 2006If you enjoyed my post on the evolution of sex chromosomes in tetrapods, you should check out Darwin Central for even more. It starts with the story of the vole, and goes into how mammalian sex chromosomes have evolved and what we can expect in the future.
evolgen | September 20, 2006Over a year and half ago (~1 eon in internet time) I wrote this blog entry in which I turned around the title of Dobzhansky's famous essay "Nothing in Biology Makes Sense Except in the Light of Evolution". I didn't think I was being all that clever when I came up with the following:
NOTHING IN EVOLUTION MAKES SENSE EXCEPT IN THE LIGHT OF GENETICS
I pointed out that evolution requires heritable variation first and foremost, hence genetics lies at the center of all of evolution. I then took the opportunity to explain why Hardy and Weinberg's derivation that random mating does not change allele…
evolgen | September 19, 2006I'm slowly working my way1 through my complementary copy of What We Believe but Cannot Prove. I'm almost done -- at page 214 out of 252 -- and I can say that it is very diverse. The essays range from very thoughtful and interesting to way too specific to a particular discipline . . . to off the mark. Thankfully essays in the last category are few and far between. But when someone gets it so very wrong (or not even wrong), and they're writing about something you know about . . . well, it warrants a blog entry. This is that blog entry (with a maximal number of ellipses).
The someone in this…
evolgen | September 19, 2006So I'm back doing lab work again. That means I'm stumbling across weird stuff that Dylan might get a kick out of. Before I could start isolating any DNA, I had to make sure all my reagents and buffer solutions were ready to go. I was digging through our chemicals cabinet when I found this buffer:
In case you can't read the label (the camera wouldn't focus on the text) it says "Buffer". For those of you not in the know, that isn't very informative. The rest of the label doesn't provide much more information. It tells you into which solvent it should be dissolved and store at room temperature…
evolgen | September 19, 2006Scientific American has an online review of four books: God's Universe by Owen Gingerich, The Language of God by Francis Collins, The God Delusion by Richard Dawkins, and The Varieties of Scientific Experience by Carl Sagan. Here's a choice quote:
"In my view," [evolgen's least favorite NIH director, Francis] Collins goes on to say, "DNA sequence alone, even if accompanied by a vast trove of data on biological function, will never explain certain special human attributes, such as the knowledge of the Moral Law and the universal search for God." Evolutionary explanations have been proffered…
evolgen | September 18, 2006Adam Eyre-Walker has published a review of adaptive evolution in a few well studied systems: Drosophila, humans, viruses, Arabidopsis, etc. These organisms have been the subject of many studies that used DNA polymorphism, DNA divergence, or a combination of the two to detect natural selection in both protein coding and non-coding regions of the genomes. Now that we have whole genome sequences for multiple closely related species from a few different taxa, many researchers are interested in determining the role of natural selection in the evolution of DNA sequences.
Eyre-Walker claims that the…
evolgen | September 18, 2006After spending the last couple of years in front of a computer or in the fly room, I finally returned to the wet lab last week. The occasion: DNA isolation. Now, this isn't any ole' DNA isolation protocol. That would be too easy. Instead, I need some high molecular weight DNA, which means it takes a few days from start to finish with lots of centrifugation throughout.
Because I need lots of high quality DNA, I need a fair bit of tissue. This wouldn't be much of a problem if I were working with an organism with a substantial body mass. Alas, I work with Drosophila, and they're tiny. That means…