Molecular Biology
pharyngula | September 26, 2006
It’s April (not anymore—it's September as I repost this), it’s Minnesota, and it’s snowing here (not yet, but soon enough). On days like this (who am I fooling? Every day!), my thoughts turn to spicy, garlicky delicacies and warm, sunny days on a lovely tropical reef—it’s a squiddy day, in other words, and I’ve got a double-dose of squidblogging on this Friday afternoon, with one article on the vampire squid, Vampyroteuthis infernalis, and this one, on squid evolution and cephalopod Hox genes.
Hox genes are members of a family of genes with a number of common attributes:
They all contain a…
pharyngula | September 26, 2006
We need to appreciate beer more. Alcohol has a long history in human affairs, and has been important in purifying and preserving food and drink, and in making our parties livelier. We owe it all to a tiny little microorganism, Saccharomyces cerevisiae, which converts complex plant sugars into smaller, simpler, more socially potent molecules of ethanol. This is a remarkable process that seems to be entirely to our benefit (it has even been argued that beer is proof of the existence of God*), but recent research has shown that the little buggers do it all entirely for their own selfish reasons…
pharyngula | September 25, 2006
Here's a small taste of Roald Dahl's Charlie and the Chocolate Factory, a sweet story about a poor boy and his visit to an amazing candy factory…you've probably heard of it, since the new movie is getting a lot of press.
Only once a year, on his birthday, did Charlie Bucket ever get to taste a bit of chocolate. The whole family saved up their money for that special occasion, and when the great day arrived, Charlie was always presented with one small chocolate bar to eat all by himself. And each time he received it, on those marvelous birthday mornings, he would place it carefully in a small…
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…
pharyngula | September 25, 2006
Hox genes are metazoan pattern forming genes—genes that are universally associated with defining the identities of regions of the body. There are multiple Hox genes present, and one of their unusual properties is that they are clustered and expressed colinearly. That is, they are found in ordered groups on the chromosome, and that the gene on one end is typically turned on first and expressed at the head end of the embryo, the next gene in order is turned on slightly later and expressed further back, and so on in sequence. That the tidy sequential order on the chromosome is associated with…
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 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 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…
pharyngula | September 12, 2006I'm a little surprised at the convergence of interest in this news report of a conserved mechanism of organizing the nervous system—I've gotten a half-dozen requests to explain what it all means. Is there a rising consciousness about evo-devo issues? What's caused the sudden focus on this one paper?
It doesn't really matter, I suppose. It's an interesting observation about how both arthropods and vertebrates seem to partition regions along the dorso-ventral axis of the nervous system using exactly the same set of molecules, a remarkable degree of similarity that supports the idea of a common…
pharyngula | September 7, 2006I was reading a review paper that was frustrating because I wanted to know more—it's on the evolution of complex brains, and briefly summarizes some of the current confusion about what, exactly, is involved in building a brain with complex problem solving ability. It's not as simple as "size matters"—we have to jigger the formulae a fair bit to take into account brain:body size ratios, for instance, to get humans to come out on top, and maybe bulk is an inaccurate proxy for more significant matters, such as the number of synapses and nerve conduction velocities.
There's also a growing amount…
pharyngula | September 3, 2006
If you've ever wondered what the heck Behe was smoking when he claims there are literal trucks trundling about on literal highways with literal traffic signals inside of cells, well, I don't have an answer for you…but there is a wonderful Flash movie that will show you the Inner Life of a Cell so you can see what "molecular machines" look like, more or less. It's a spectacular show. What you'll see is the series of events that transpire when a lymphocyte encounters a cell surface signal that triggers emigration out of a capillary and into other tissues; it zooms rather abruptly from a…
evolgen | August 24, 2006In last week's edition of Phylogeny Fridays, I mentioned an essay that argued that biologists should refrain from using the term "prokaryote" because its definition is entirely negative. The author, Norman Pace, writes, "no one can define what is a prokaryote, only what it is not." Furthermore, I pointed out that prokaryotes are a paraphyletic taxon (a statement that drew some criticism in the comments), and that alone should lead to the disuse of the term.
In a letter to Nature, Bill Martin and Eugene Koonin point out that there is a positive definition of prokaryotes:
Prokaryotes are cells…
pharyngula | August 8, 2006
I've been getting swamped with links to this hot article, "Evolution reversed in mice," including one from my brother (hi, Mike!). It really is excellent and provocative and interesting work from Tvrdik and Capecchi, but the news slant is simply weird—they didn't take "a mouse back in time," nor did they "reverse evolution." They restored the regulatory state of one of the Hox genes to a condition like that found half a billion years ago, and got a viable mouse; it gives us information about the specializations that occurred in these genes after their duplication early in chordate history. I…
pharyngula | August 7, 2006Over at the Panda's Thumb, there is a sharp rebuttal of the creationists' complaint about junk DNA. Read it, it's useful. It leads to a bothersome and more general point, though.
Despite its connotations, the phrase “junk DNA” (originated by Susumu Ohno in 1972) does not intend to convey an absolute and irreversible lack of function. Indeed, as it is often noted, had that been the case “garbage DNA” would have been a better term. In fact, “junk” is what accumulates in people’s basements and attics, not immediately useful but not nasty or burdensome enough to be quickly discarded – indeed,…
pharyngula | August 3, 2006Often, as I've looked at my embryonic zebrafish, I've noticed their prominent median fins. You can see them in this image, although it really doesn't do them justice—they're thin, membranous folds that make the tail paddle-shaped.
These midline fins are everywhere in fish—lampreys have them, sharks have them, teleosts have them, and we've got traces of them in the fossil record. Midline fins are more common and more primitive, yet usually its the paired fins, the pelvic and pectoral fins, that get all the attention, because they are cousins to our paired limbs…and of course, we completely…
pharyngula | August 2, 2006If you're at work, I hope you have headphones; if you don't, check in once you get home. Here are a couple of audio recordings of good science.
John Rennie speaks out on stem cells on an Australian program, the Science Show.
I reviewed her new book a while ago, and now you can hear Christiane Nüsslein-Volhard lecture on basic developmental biology. She has a very nice light German accent that makes it especially pleasant to listen to, I think.
evolgen | August 1, 2006According to this press release, cancer cells can be kept from dividing by preventing them from making cell walls. Cell walls? Yeah, cell walls. Like plants or bacteria. Last time I checked, animal cells ain't got no walls. Ordinarily, I'd attribute this to a stoopid reported getting the information screwed up, but here's a quote from the lead author of the paper:
"Last year we discovered that a protein called SREBP1 that regulates the synthesis of lipids needed for new cell walls was regulated during the cell cycle."
Cell membranes are made of lipids. Membranes! MEMBRANES!! Not walls. I'd…
pharyngula | July 30, 2006
Assuming that none of my readers are perfectly spherical, you all possess notable asymmetries—your top half is different from your bottom half, and your front or ventral half is different from you back or dorsal half. You left and right halves are probably superficially somewhat similar, but internally your organs are arranged in lopsided ways. Even so, the asymmetries are relatively specific: you aren't quite like that Volvox to the right, a ball of cells with specializations scattered randomly within. People predictably have heads on top, eyes in front, arms and legs in useful locations…
pharyngula | July 27, 2006
I am going mildly nuts right now—somehow, I managed to arrange things so multiple deadlines hit me on one day: tomorrow. I've got a new lecture to polish up for our introductory biology course, a small grant proposal due, and of course, tomorrow evening is our second Café Scientifique. Let's not forget that I also have a neurobiology lecture to give this afternoon, and I owe them a stack of grading which is not finished yet. I'm really looking forward to Wednesday.
Anyway, so my new lecture for our introductory biology course is on…creationism, yuck. What I'm planning to do is to describe…
pharyngula | July 26, 2006
People, scientists included, are always looking for simple, comprehensible explanations for complex phenomena. It's so satisfying to be able to easily explain something in a sound bite, and sound bites are so much more easily accepted by an audience than some elaborate, difficult collection of details. For example, we often hear homosexual behavior reduced to being a "choice," the product of a "gay gene," a "sin," or something similarly absolute and irreducible…suggesting that it is part of a diverse spectrum of sexual behaviors with multiple causes and that different individuals are…