Molecular Biology
evolgen | May 2, 2006I'm trying to emerge from hibernation, and I'll hopefully have some good blogging material up in the next few days. In lieu of my own ideas, I'm going to link to what other people have written. Read them, because I ain't saying much right now. The list can be found below the fold.
Neil Saunders points us to this article from the BBC on a new function for "junk DNA". I hope Neil is right: "one day the term 'junk DNA' will fall into disuse."
John Hawks has a good discussion of a recent paper on inferring population size using mtDNA. Apparently cytoplasmic DNA is under selection, and that…
pharyngula | April 30, 2006
In previous articles about fly development, I'd gone from the maternal gradient to genes that are expressed in alternating stripes (pair-rule genes), and mentioned some genes (the segment polarity genes) that are expressed in every segment. The end result is the development of a segmented animal: one made up of a repeated series of morphological modules, all the same.
Building an animal with repeated elements like that is a wonderfully versatile strategy for making an organism larger without making it too much more complicated, but it's not the whole story. Just repeating the same bits over…
pharyngula | April 26, 2006Paul Nelson has been twittering about ORFans for some time now—he seems to precede his talks by threatening to make us evolutionists tremble in our boots by bringing them up, but he never seems to follow through. Ian Musgrave got tired of waiting for him to give us a coherent creationist argument about them, and has gone ahead and cut him off at the knees by explaining the place of ORFans in evolution.
In case you're baffled by the jargon, "ORF" is an Open Reading Frame, or a stretch of DNA bracketed by a start and stop codon; it's a kind of bare minimum criterion for recognizing an actual…
pharyngula | April 25, 2006This really is an excellent review of three books in the field of evo-devo—
From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design (amzn/b&n/abe/pwll),
Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom (amzn/b&n/abe/pwll), and
The Plausibility of Life:Resolving Darwin's Dilemma (amzn/b&n/abe/pwll)—all highly recommended by me and the NY Times. The nice thing about this review, too, is that it gives a short summary of the field and its growing importance.
evolgen | April 25, 2006Bora 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 jump.
Previous entries:
Part 1 - Introduction
The Backstory
The enzyme fructose-1,6-bisphosphate aldolase (hereafter referred to as aldolase) is responsible for splitting fructose-1,6-bisphosphate into glyceraldehyde-3-phosphate and dihydroxyacetone-phosphate during glycolysis.…
evolgen | April 21, 2006Pharyngula has a good summary of the new Sean Carroll Drosophila wing dot paper. Eventually Sean's gonna try to mess around with a hawaiin species and blow the roof off this mother.
pharyngula | April 21, 2006a–c, The wing spots on male flies of the Drosophila genus. Drosophila tristis (a) and D. elegans (b) have wing spots that have arisen during convergent evolution. Drosophila gunungcola (c) instead evolved from a spotted ancestor. d, Males wave their wings to display the spots during elaborate courtship dances.
It's all about style. When you're out and about looking for mates, what tends to draw the eye first are general signals—health and vigor, symmetry, absence of blemishes or injuries, that sort of thing—but then we also look for that special something, that je ne sais quoi, that dash of…
pharyngula | April 19, 2006
Here's what seems to be a relatively simple problem in evolution. Within the Drosophila genus (and in diverse insects in general), species have evolved patterned spots on their wings, which seem to be important in species-specific courtship. Gompel et al. have been exploring in depth one particular problem, illustrated below: how did a spot-free ancestral fly species acquire that distinctive dark patch near the front tip of the wing in Drosophila biarmipes? Their answer involves dissecting the molecular regulators of pattern in the fly wing, doing comparative sequence analyses and…
pharyngula | April 18, 2006The relative length of bat forelimb digits has not changed in 50
million years. (a) Icaronycteris index, which is a 50-million-year-old bat fossil. (b) Extant adult
bat skeleton. The metacarpals (red arrows) of the first fossil bats are already
elongated and closely resemble modern bats. This observation is confirmed by
morphometric analysis of bat forelimb skeletal elements.
or•gan•ic | ôr'ganik | adjective. denoting a relation between elements of something such that they fit together harmoniously as necessary parts of a whole; characterized by continuous or natural development.
One of the…
evolgen | April 7, 2006This week's evolgen Double Entendre Friday is brief. It's also not my own idea, and I can't seem to remember where I stole it from (if I stole it from you, drop a note in the comments). Sorry. Here it is:
Two glutamines bump into each other waiting to aminoacylate a tRNA. One says to the other, "I saw you hanging out near that ribosome with your last tRNA. Did you go all the way?" The other replies, "Well, my tRNA got me into the A site, but we were caught pretending to be a histidine. After that, there was no way the ribosome was going to let me get through her exit tunnel."…
evolgen | March 27, 2006My little screed on junk DNA elicited some good feedback, including a comment from Dan Graur. In a somewhat ill-thought out rant, I implied that anyone who uses the term 'junk DNA' should be ostracized from the scientific community (or something along those lines). I restated my opinion in a far more diplomatic manner in the discussion that followed in the comments: junk DNA is an appropriate term for DNA that serves no function (non-transcribed, non-regulatory, and non-structural), but we should refrain from using that term for all non-coding DNA. I elaborate my opinion and reference a…
evolgen | March 23, 2006The term "Junk DNA" is bullshit. There, I said it. The moment I hear someone utter that phrase, I immediately lose respect for him or her. No one whose opinion is worth anything will refer to non-coding DNA as junk. That's why this article bothers me. The title, "Junk DNA may not be so junky after all" has nothing to do with the content of the article. The research being described is not about showing that non-coding DNA has a function. The function has already been determined. The researchers have used zebrafish to identify enhancers for human genes. The subtitle to the article (…
pharyngula | March 20, 2006
What has always attracted me to developmental biology is the ability to see the unfolding of pattern—simplicity becomes complexity in a process made up of small steps, comprehensible physical and chemical interactions that build a series of states leading to a mostly robust conclusion. It's a bit like Conway's Game of Life in reverse, where we see the patterns and can manipulate them to some degree, but we don't know the underlying rules, and that's our job—to puzzle out how it all works.
Another fascinating aspect of development is that all the intricate, precise steps are carried out…
evolgen | March 19, 2006The human Y, that is. The Science Creative Quarterly has a very thorough (ie, make sure you have some time to spare) review of the mammalian Y chromosome (focusing on the human Y). The article covers the origin and evolution of the mammalian Y and what the degeneration of the Y means for the future of human male fertility and sex determination. I should point out that the mammalian Y chromosome is an anomaly in origin and sex determination. In fact, every single sex determination system and sex chromosome system that I know of differs from all of the others in some manner. It looks like…
evolgen | March 17, 2006Today marks the anniversary of the death of St. Patrick -- the dude who ridded Ireland of its non-existent snakes (some folks claim it was a metaphor for pagans). In honor of this great feat, people around the world drink green beer and pretend to be Irish. What does that have to do with double entendres? Absolutely nothing, but it's my excuse for the following lame joke:
Two transcription factors are hanging out. One says to the other, "Did you end up scoring with that cis regulatory region you were macking on last night?" The other replies, "Yeah, I gave her the old zinc finger."
evolgen | March 16, 2006Do you want a quick and dirty guide to DNA replication without any of the fancy pictures or cumbersome terminology commonly found in text books? David Ng has published such a guide at The Science Creative Quarterly. It's a good read even if you already know that stuff.
evolgen | March 15, 2006Hey, Myers, two can play at this game. An article in the Journal of Molecular Evolution presents structural and sequence analysis of hemocyanin (an oxygen carrying protein) from the cephalopod, Nautilus pomilius (shown at the left). They also compared the sequence to another cephalopod, Octopus dofleini, and found that the two species diverged approximately 415 million years ago.
Bergmann, S, B Lieb, P Ruth, and J Markl. 2006. The Hemocyanin from a Living Fossil, the Cephalopod Nautilus pompilius: Protein Structure, Gene Organization, and Evolution. J Mol Evol 62: 362-374.
evolgen | March 10, 2006I commented a couple of days ago on a news item about a journal article on the evolution of gene expression in primates that had yet to be published. Well, the article has been published, and I've read it (Nature has also published a news and views piece on the study by Rasmus Nielsen). I have a few comments on why this research is unique, what the researchers found, and the implications of this research below the fold.
WHY THIS STUDY IS UNIQUE: This is the first large scale study to examine gene expression in primates using species specific probes. Gene expression can be measured by…
evolgen | March 8, 2006Kevin White (aka, Mr. Drosophila microarray data) has a paper coming out in tomorrow's issue of Nature. The paper (which is not available on the Nature website yet) compares the expression of over 1,000 genes from humans, chimpanzees, orangutans and rhesus monkeys. From a news write up of the findings:
When they also looked for human genes with significantly higher or lower expression levels, they found 14 genes with increased expression and five with decreased expression. While only ten percent of the genes in the total array were transcription factors, 42 percent of those with increased…
evolgen | February 27, 2006I have a little bit of an infatuation with copy number polymorphism (CNP), which describes the fact that individuals within a population can differ from each other in gene content. Some genes, such as olfactory receptors (ORs), have many different related variants in any animal genome. New copies spring up via duplication events (a type of mutation), so one could imagine that individuals from a single population differ in the number of copies of these genes. In fact, this is the case with any gene or gene family (a group of related genes) in the genome -- there may be duplications…