evolution
pharyngula | July 12, 2006(click for larger image)
A new report in this week's Nature clears up a mystery about an enigmatic fossil from the Cambrian. This small creature has been pegged as everything from a chordate to a polychaete, but a detailed analysis has determined that it has a key feature, a radula, that places it firmly in the molluscan lineage. It was a kind of small Cambrian slug that crawled over matted sheets of algae and bacteria, scraping away a meal.
Here it is, a most unprepossessing creature. It was small (less than a 5 inches long), a flattened oval with few striking features, with a small mouth…
pharyngula | July 12, 2006
Neck anatomy has long terrified me. Way back when I was a grad student, my lab studied the organization and development of the hindbrain, which was relatively tidy and segmental; my research was studying the organization and development of the spinal cord, which was also tidy and segmental. The cervical region, though, was complicated territory. It's a kind of transitional zone between two simple patterns, and all kinds of elaborate nuclei and new cell types and structural organizations flowered there. I drew a line at the fifth spinal segment and said I'm not even going to look further…
loom | July 12, 2006It was eight years ago that some computer programmers got together and issued a manifesto for something they called open source software. Conventional software development--kept hidden behind walls of intellectual property, copyright, and secrecy--was clumsy and slow. It would be far better, the open source advocates declared, to make software open to all. It would foster the growth of a vast decentralized community of developers and consumers who could work together to create better software together. Individuals would grab software created by others, tinker with it, and then make it…
stcynic | July 12, 2006One of the tried and true tactics of creationists of all stripes has long been to equate evolution with atheism, and thus those who accept evolution become atheists. In a society where surveys show that atheists are, for some bizarre reason, among the most distrusted people, this is good political strategy; it's also false. It is simply a scare tactic, designed (intelligently, perhaps, but also unethically) to exploit the public's fear and distrust of atheists. Such fears are utterly irrational, of course, but that is precisely why they can be exploited so effectively by demagogues. Those…
loom | July 11, 2006A good article on the importances of big animals helps put the new dodo fossil discoveries in some ecological context. If you can't bring dodos back, at least bring in the giant tortoises!
mikethemadbiologist | July 10, 2006
Tara and Revere are both confronting the creationist anti-mutation 'argument.' I've faced this before regarding antibiotic resistance. I find it ironic that Mike Martin argues against evolution by mutation, when other creationists argue that small mutations happen, but 'kinds' are immutable. I wish these guys would figure out which idiocy they plan to adopt.
cmooney | July 10, 2006As Matt Nisbet has already noted, the flagship journal of the American Institute of Biological Sciences has a very important editorial in its latest issue about the importance of scientists learning framing devices. The piece appears to have been inspired by a joint presentation that Nisbet and I did before the AIBS a few months back. Here's a snippet:
The frames concept recognizes that facts are not enough to win popularity; emotional responses need to be excited as well. Scientists may find that notion alarming, because scholarly communications must be forthright about the uncertainties of…
clock | July 10, 2006This post, originally published on January 16, 2005, was modified from one of my written prelims questions from early 2000.
EVOLUTIONARY PHYSIOLOGY OF BIOLOGICAL CLOCKS
"Circadian clocks allow organisms to predict, instead of merely react to, cyclic (predictable) changes in the environment". A sentence similar to this one is the opening phrase of many a paper in the field of chronobiology. Besides becoming a truth by virtue of frequent repetition, such a statement appeals to common sense. It is difficult to imagine a universe in which it was not true. Yet, the data supporting the above…
pharyngula | July 10, 2006
I've written about this fascinating Drosophila gene, bicoid, several times before. It's a maternal effect gene, a gene that is produced by the mother and packaged into her eggs to drive important early events in development, in this case, establishing polarity, or which end of the egg is anterior (bicoid specifies which end of the egg will form the fly's head). Bicoid is also a transcription factor, or gene that regulates the activity of other genes. We also see evidence that it is a relatively new gene, one that is taking over a morphogenetic function that may have been carried out by…
loom | July 10, 2006I just want to make one thing clear. When Ann Coulter talks about her Giant Raccoon Flatulence Theory, she's talking about me. Don't let anyone else tell you that they are a giant flatulent raccoon. They're all just a bunch of wannabes. For I am the One True Giant Flatulent Raccoon.
Allow me to explain...
Coulter dedicates the last four chapers of her new book Godless to evolution. She claims that it is nothing more than the religion of liberalism (as opposed to the foundation of modern biology, as 92 national scientific academies and dozens of scientific societies attest.)
When I first…
razib | July 9, 2006Update: Hawks responds.
John Hawks has not commented on this feature in Wired titled Code of the Caveman. But I'm sure he will, and when he does, I will point you to it because what he says on this topic is worth listening to. But, until then, here are a few points.
1) This extraction of ancient autosomal DNA, not just the copious mtDNA, from Neandertals by the Paabo group and its associates has been talked about for a year or so now. So within the scientific community this isn't a big surprise.
2) The new bioinformatically flavored techniques offer up the possibility to "learn more about…
pharyngula | July 9, 2006
Intelligent Design creationists are extremely fond of diagrams like those on the left. Textbook illustrators like them because they simplify and make the general organization of the components clear—reducing proteins to smooth ovoids removes distractions from the main points—but creationists like them for the wrong reasons. "Look at that—it's engineered! It's as if God uses a CAD program to design complex biological systems!" They like the implication that everything is done with laser-guided precision, and most importantly, that every piece was designed with intent, to fill a specific role…
pharyngula | July 9, 2006
Last week, I wrote a bit about maternal genes, specifically bicoid, and described how this gene was expressed in a gradient in the egg. Bicoid is both a transcription factor and a morphogen. The gene product regulates the activity of other genes, controlling their pattern of expression in the embryo. Today I thought I'd get more specific about the downstream targets of bicoid, the gap genes.
Expression domains of the gap genes. The pink bars chart the strength of gene expression as a function of position along the lengths of the embryo for hunchback (hb), huckebein (hkb), tailless (tll),…
purepedantry | July 9, 2006This paper in Proceedings of Royal Society Biology purports to show that there is an investment trade-off between immunocompetence and animal growth. In cases where parasitism is high, the trade-off tends to tilt towards investment in immunocompetence.
I love this article for two reasons.
1) It was conducted on a species that -- I &%^@ you not -- is called the Great Tit:
The study was performed in 2004 in a population of great tits breeding in nest boxes in a mixed forest near Bern, Switzerland. The great tit is a small (16-20 g) hole-nesting passerine that produces one or two broods…
pharyngula | July 9, 2006
In my previous comments about maternal effect genes, I was talking specifically about one Drosophila gene, bicoid, which we happen to understand fairly well. We know its sequence, we know how it is controlled, and we know what it does; we know where it falls in the upstream and downstream flow of developmental information in the cell. So today I'm going to babble a bit more about what bicoid is and does, and how it works.
Bicoid is a transcription factor.
The diagram above illustrates what a transcription factor (in this case, called "gene X") is. Gene X is transcribed to form a strand of…
pharyngula | July 9, 2006
In developmental biology, and increasingly in evolutionary biology, one of the most important fields of study is deciphering the nature of regulatory networks of genes. Most people are familiar with the idea of a gene as stretch of DNA that encodes a protein in a sequence of As, Ts, Gs, and Cs, and that's still an important part of the story. Most people may also be comfortable with the idea that mutations are events that change the sequence of As, Ts, Gs, and Cs, which can lead to changes in the encoded protein, which then causes changes in the function of the protein. These are essential…
mikethemadbiologist | July 7, 2006Sounds dirty, don't it? It's always nice to see sites that usually deal with politics discuss science. Or in this case, the opposite, also known as Ann Coulter. Robert Savillo, of Media Matters, demolishes the creationist arguments found in Ann Coulter's latest book Why I Think All Liberals Should Be Brutally Murdered Godless: The Church of Liberalism. Before I get to Savillo's summary, he discusses a part of the book where Coulter refers to the 'Flatulent Racoon.' Now, a farting racoon is sort of funny in a five year-old kind of way, but we all know that this just means she is…
mikethemadbiologist | July 6, 2006Matt Stoller at MyDD.com comments on Andrew Sullivan's and Robert Samuelson's apologetics for global warming:
This is rich. The rush to war was premised on the assumption that the judgment of the Bush administration (and Sullivan) was superior to that of professional weapons inspectors like Hans Blix. This turned out to be false. Now, the foot-dragging on global warming is premised on the assumption that the judgment of the Bush administration (and Sullivan) is superior to that of the global scientific community.
As usual, this is an issue of judgment and trust. Put Sullivan and Samuelson…
grrlscientist | July 6, 2006The new BMC Evolutionary Biology open access journal just received its first Journal Impact Factor rating. This Impact Factor of 4.45 places it 6th out of 33 journals in the Evolutionary Biology category. Impact Factors are a standardized measure of the frequency that the "average article" in a particular journal has been cited within a year or other specified period of time. The higher the Impact Factor, the greater number of citations the "average article" receives and thus, the more "important" the journal itself is.
BMC Evolutionary Biology is open access and publishes original peer-…