Molecular Biology
pharyngula | June 8, 2006
Creationists are fond of the "it can't happen" argument: they like to point to things like the complexity of the eye or intricate cell lineages and invent bogus rules like "irreducible complexity" so they can claim evolution is impossible. In particular, it's easy for them to take any single organism in isolation and go oooh, aaah over its elaborate detail, and then segue into the argument from personal incredulity.
Two things, one natural and one artificial, help them do this. Organisms are incredibly complicated, there is no denying it. This should be no solace to the anti-evolutionists,…
grrlscientist | June 6, 2006
Although these fish look similar and have the same genetic makeup, they
produce very different electrical signals (right) and will only mate with fish that produce
the same signals. Cornell researchers believe that these different electrical signals are the
fishes' first step in diverging into separate species. [Image: Carl Hopkins.]
The fishes depicted in the picture above are several types of mormyrids that are endemic to some tributaries of the Ivindo River in Gabon, Africa. These fishes produce weak electrical signals from a battery-like organ at the base of the tail to communicate…
pharyngula | June 6, 2006Last night, I had to read this book RPM mentioned. It's not very long—about 100 pages, counting a preface, an epilogue, and an afterward, and it has lots of pictures—but be warned: it's very inside baseball.
The book is Won for All: How the Drosophila Genome Was Sequenced(amzn/b&n/abe/pwll) by Michael Ashburner, and its subject is the rush to sequence the Drosophila genome in 1998-1999. It's a rather strange twist on what I expected, though. While the subtitle says "How the Drosophila Genome Was Sequenced," there is almost no science at all in the body of the book; instead, it's all about…
pharyngula | June 3, 2006Since Evolgen recognizes the importance of evo-devo, I'll return the favor: bioinformatics is going to be critical to the evo-devo research program, which to date has emphasized the "devo" part with much work on model systems, but is going to put increasing demands on comparative molecular information from genomics and bioinformatics to fulfill the promise of the "evo" part. I'm sitting on a plane flying east, and to pass the time I've been reading a very nice review of the concept of modularity in evo-devo by Paula Mabee (also a fish developmental biologist, and also working in a small…
pharyngula | June 2, 2006The Art of Science exhibition has many lovely pictures in the galleries, but I think my favorite is this image of Nodal expression in zebrafish.
pharyngula | May 31, 2006Fellow scienceblogger Evolgen has seen the light—evo-devo is wonderful. He's attending a meeting and listening to some of the bigwigs in the field talk about their work, in particular some research on the evolution of gene regulation. While noting that this is clearly important stuff, he also mentions some of the bickering going on about the relative importance of changes in cis regulatory elements (CREs) vs. trans acting elements, transcription factors. I've got a longer write-up of the subject, but if you don't want to read all of that, the issue is about where the cool stuff in the…
evolgen | May 31, 2006...or how a learned to stop worrying and love evo-devo.
As my mind gets a chance to process some of the stuff I heard and talked about at the meeting I just returned from, I'll post some thoughts that will help me organize my ideas (hopefully better organized than that last sentence). This is the first (of perhaps few, perhaps many) of those (possibly incoherent) ramblings -- interrupted by as few paranthetical remarks as possible.
In this post, I'll try to tie together:
A talk by Sean Carrol on the evolution of wing pigmentation.
A talk by Peter Andolfatto on the evolution of Drosophila non…
pharyngula | May 26, 2006
One of the most evocative creatures of the Cambrian is Anomalocaris, an arthropod with a pair of prominent, articulated appendages at the front of its head. Those things are called great appendages, and they were thought to be unique to certain groups of arthropods that are now extinct. A while back, I reported on a study of pycnogonids, the sea spiders, that appeared to show that that might not be the case: on the basis of neural organization and innervation, that study showed that the way pycnogonid chelifores (a pair of large, fang-like structures at the front of the head) were innervated…
pharyngula | May 26, 2006
I'm going to introduce you to either a fascinating question or a throbbing headache in evolution, depending on how interested you are in peculiar details of arthropod anatomy (Mrs Tilton may have just perked up, but the rest of you may resume napping). The issue is tagmosis.
The evolutionary foundation for the organization of many animal body plans is segmental—we are made of rings of similar stuff, repeated over and over again along our body length. That's sufficient to make a creature like a tapeworm or a leech (well, almost—leeches have sophisticated specializations), but there are…
pharyngula | May 23, 2006
I just learned (via John Lynch) about a paper on cetacean limbs that combines developmental biology and paleontology, and makes a lovely argument about the mechanisms behind the evolution of whale morphology. It is an analysis of the molecular determinants of limb formation in modern dolphins, coupled to a comparison of fossil whale limbs, and a reasonable inference about the pattern of change that was responsible for their evolution.
One important point I'd like to make is that even though what we see in the morphology is a pattern of loss—whale hindlimbs show a historical progression over…
pharyngula | May 22, 2006
I'm going to briefly summarize an interesting new article on cnidarian Hox genes…unfortunately, it requires a bit of background to put it in context, so bear with me for a moment.
First you need to understand what Hox genes are. They are transcription factors that use a particular DNA binding motif (called a homeobox), and they are found in clusters and expressed colinearly. What that means is that you find the Hox genes that are essential for specifying positional information along the length of the body in a group on a chromosome, and they are organized in order on the chromosome in the…
pharyngula | May 19, 2006
Four of my favorite things are development, evolution, and breasts, and now I have an article that ties them all together in one pretty package. It's a speculative story at this point, but the weight of the evidence marshaled in support of the premise is impressive: the mammalian breast first evolved as an immunoprotective gland that produced bacteriocidal secretions to protect the skin and secondarily eggs and infants, and that lactation is a highly derived kind of inflammation response. That mammary glands may have had their origin as inflamed glands suppurating mucus may not be the most…
evolgen | May 19, 2006My advisor once told me that the best way to get your paper into a high profile journal like Science or Nature is to find the biggest of something, the smallest of something, or something that fucks funny. It turns out doing research on drugs doesn't get you in. No, not those drugs. These drugs.
Researchers in Japan have identified a molecular marker that distinguishes strains of Cannabis sativa with high Δ-9-tetrahydrocannainolic acid (THCA) content from those without. For those of you not hip with the lingo, they have developed an easy test to tell the difference between the weed that gets…
grrlscientist | May 18, 2006A vaccine that triggers immunity against those viruses that cause most cervical cancers was found to be safe and effective and should be approved soon, a federal panel recommended today. The pharmaceutical company that developed this vaccine, Merck, said the vaccine could reduce global deaths from the second leading cause of cancer in young women by more than two-thirds.
The Food and Drug Administration (FDA) advisory committee voted 13-0 on five separate occasions to endorse the Merck vaccine, Gardasil. The FDA rarely ignores its panels' recommendations when making its final decisions. The…
grrlscientist | May 17, 2006tags: human genome project, chromosome 1, medicine, molecular biology
Scientists have reached a landmark point in one of the world's most important scientific projects by sequencing the last chromosome in the human genome, the so-called "book of life". [Image: False-color photograph showing human chromosomes, with the Chromosome 1 pair highlighted in blue. Indigo Instruments / Wellcome Trust Sanger Center]
Packed with 3,141 genes and linked to 350 illnesses including cancer, Alzheimer's and Parkinson's diseases, the important but mysterious chromosome number 1 comprises eight percent of the…
evolgen | May 16, 2006I remember watching this movie (WARNING: link to a large file) during my sophomore year of college. It now appears that some folks at Kenyon College plan to do a remake. For those of you too lazy to follow the links, the movie depicts protein synthesis using people acting out the roles of mRNA, tRNA, amino acids, ribosomes, and other assorted players. And it was made in 1971. And it involved interpretive dance. And hippies. Good shit, yo.
(Via Neil Saunders.)
pharyngula | May 8, 2006
The Wnt genes produce signalling proteins that play important roles in early development, regulating cell proliferation, differentiation and migration. It's hugely important, used in everything from early axis specification in the embryo to fine-tuning axon pathfinding in the nervous system. The way they work is that the Wnt proteins are secreted by cells, and they then bind to receptors on other cells (one receptor is named Frizzled, and others are LRP-5 and 6), which then, by a chain of cytoplasmic signalling events, removes β-catenin from a degradation pathway and promotes its import into…
pharyngula | May 8, 2006
One of the hallmark characters of animals is the presence of a specific cluster of genes that are responsible for staking out the spatial domains of the body plan along the longitudinal axis. These are the Hox genes; they are recognizable by virtue of the presence of a 60 amino acid long DNA binding region called the homeodomain, by similarities in sequence, by their role as regulatory genes expressed early in development, by the restriction of their expression to bands of tissue, by their clustering in the genome to a single location, and by the remarkable collinearity of their organization…
pharyngula | May 8, 2006
There are quite a few genes that are known to be highly conserved in both sequence and function in animals. Among these are the various Hox genes, which are expressed in an ordered pattern along the length of the organism and which define positional information along the anterior-posterior axis; and another is decapentaplegic (dpp) which is one of several conserved genes that define the dorsal-ventral axis. Together, these sets of genes establish the front-back and top-bottom axes of the animal, which in turn establishes bilaterality—this specifically laid out three-dimensional organization…
evolgen | May 4, 2006Via EurekAlert comes this news release on research into error checking during DNA polymerization. I'm not judging the science; I'm judging the reporting, which includes the following statement:
Everyone knows mutations - genetic mistakes in DNA, the material of heredity - are bad: The more mutations in the cell's DNA, the higher the risk of cancer developing.
In case the syntax in the title is unfamiliar to you, lemme spell it out for you: MUTATIONS ARE NOT NECESSARILY BAD. Sure, genetic mutations are responsible for diseases such as cancers, but they are also the raw material upon with all…