Molecular Biology
pharyngula | December 22, 2006The rest of you might be totally lost. Here's a soon-to-be-classic paper on the characterization of the Hoho2 gene (292K pdf)—the Santa phenotype seems to represent an optimization for an arctic niche. They suggest the allele might have had an origin in Neandertal populations, but then they also show its effect in reindeer and E. coli (yes, they have beardy bacteria). It's a very confused paper.
In this paper we unequivocally identify and characterize the genetic determinant of the famous white beard of Santa Claus to be the ortholog of human KRT6B. The newly discovered gene is named Hoho2…
evolgen | December 21, 2006As we all know, the genetic code is redundant. Within protein coding regions, substitutions at silent sites do not affect the amino acid sequence of the encoded protein. Because of this property, these synonymous substitutions (so-called because they result in the same amino acid) are often used to estimate the neutral rate of evolution -- they should not be under selection. But there is evidence for natural selection operating on silent sites. That's because, even though different codons encode the same amino acid, the tRNAs for the synonymous codons are found at different frequencies within…
pharyngula | December 21, 2006
What are the key ingredients for making a multicellular animal, or metazoan? A couple of the fundamental elements are:
A mechanism to allow informative interactions between cells. You don't want all the cells to be the same, you want them to communicate with one another and set up different fates. This is a process called cell signaling and the underlying process of turning a signal into a different pattern of gene or metabolic activity is called signal transduction.
Patterns of differing cell adhesion. But of course! The cells of your multicellular animal better stick together, or the…
pharyngula | December 19, 2006Once upon a time, in Paris in 1830, Etienne Geoffroy St. Hilaire debated Georges Léopole Chrétien Frédéric Dagobert,
Baron Cuvier on the subject of the unity of organismal form. Geoffroy favored the idea of a deep homology, that all animals shared a common archetype: invertebrates with their ventral nerve cord and dorsal hearts were inverted vertebrates, which have a dorsal nerve cord and ventral hearts, and that both were built around or within an idealized vertebra. While a thought-provoking idea, Geoffroy lacked the substantial evidence to make a persuasive case—he had to rely on fairly…
pharyngula | December 4, 2006
One of my favorite signal transduction pathways (what? You didn't know that true nerds had favorite molecular pathways?) is the one mediated by the receptor Notch. Notch is one of those genes in the metazoan toolkit that keeps popping up in all kinds of different contexts—it's the adjustable wrench of the toolbox, something that handles a general problem very well and therefore gets reused over and over again, and the list of places where it is expressed in Drosophila is impressive.
The general problem that Notch solves is the resolution of a binary decision in cell fate, one where a few…
grrlscientist | November 27, 2006
This is a really interesting video that I found more than a month ago but never published it here because I could not view it on the hospital's crappy Dell computer. However, I can't resist the suspense any longer since I have shared it with other people, all of whom tell me to post it anyway! So you, amigos bonitos, will have to be my eyes and ears on this one, just until I get out of here (fingers crossed) and back to my own computer.
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tags: streaming video, Nobel Prize, RNAi
pharyngula | November 20, 2006
I've been writing a fair amount about early pattern formation in animals lately, so to do penance for my zoocentric bias, I thought I'd say a little bit about homeotic genes in plants. Homeotic genes are genes that, when mutated, can transform one body part into another—probably the best known example is antennapedia in Drosophila, which turns the fly's antenna into a leg.
Plants also have homeotic genes, and here is a little review of flower anatomy to remind everyone of what 'body parts' we're going to be talking about. The problem I'll be pursuing is how four different, broadly defined…
pharyngula | November 15, 2006
Ian Musgrave has just posted an excellent article on the poor design of the vertebrate eye compared to the cephalopod eye; it's very thorough, and explains how the clumsy organization of the eye clearly indicates that it is the product of an evolutionary process rather than of any kind of intelligent design. A while back, Russ Fernald of Stanford University published a fine review of eye evolution that summarizes another part of the evolution argument: it's not just that the eye has awkward 'design' features that are best explained by contingent and developmental processes, but that the…
pharyngula | November 13, 2006
Oh happy day, the Sea Urchin Genome Project has reached fruition with the publication of the full sequence in last week's issue of Science. This news has been all over the web, I know, so I'm late in getting my two cents in, but hey, I had a busy weekend, and and I had to spend a fair amount of time actually reading the papers. They didn't just publish one mega-paper, but they had a whole section on Strongylocentrotus purpuratus, with a genomics mega-paper and articles on ecology and paleogenomics and the immune system and the transcriptome, and even a big poster of highlights of sea urchin…
pharyngula | November 8, 2006Fascinating stuff…read this paper in PNAS, Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage, or this short summary, or John Hawks' excellent explanation of the concepts, it's all good. It's strong evidence for selection in human ancestry for a gene, and just to make it especially provocative, it's all about a gene known to be involved in brain growth, and it's also showing evidence for interbreeding between Homo sapiens and Neandertal man.
The short short explanation: a population genetics study of a gene called…
pharyngula | November 7, 2006Here's an annoying case of political correctness run amuck.
…the Human Genome Organisation (HUGO) Gene Nomenclature Committee…is renaming a number of genes that have potentially offensive or embarrassing names.
The shortlist of 10 genes -Â including radical fringe, lunatic fringe and, bizarrely, Indian hedgehog -Â was compiled in response to physicians’ worries about “inappropriate, demeaning and pejorative” names.
The problem arose because most of the genes were initially discovered in fruitflies, and their names were then transferred to the human versions of the genes, which were discovered…
pharyngula | November 4, 2006
This odd marine worm, Xenoturbella bocki, is in the news right now, and I had to look it up in Pechenik's Biology of the Invertebrates(amzn/b&n/abe/pwll) to remind myself of what it was. Here's the complete entry:
Xenoturbella bocki
This marine worm, first described in 1949 as an acoel flatworm and later claimed as either an early metazoan offshoot or a primitive deuterostome, has recently been affiliated with primitive bivalve molluscs, based upon a study of gamete development (oogenesis) and an analysis of sequence data from both 18S rRNA and mitochondrial genes. Little is known about…
pharyngula | October 18, 2006Human X (left) and Y (right) chromosomes
Did the internet get stupider while I was away this past week? I mean, it's gratifying to my ego to imagine the average IQ of the virtual collective plummeting when I take some time off, but I really can't believe I personally have this much influence. Maybe the kooks crept out in my absence, or maybe it was just the accumulation of a week's worth of insanity that I saw in one painful blort when I was catching up.
What triggers such cynicism is the combination of Deepak Chopra, Oliver Curry, and now,William Tucker. Tucker wrote a remarkably silly piece…
evolgen | October 17, 2006Science has published THE genome of breast and colorectal cancers. Not the whole genome, mind you, but just 13,023 protein coding genes. The researchers identified mutations associated with cancers, but I'm not sure if they looked outside of the protein coding sequences (I have yet to read the paper, and I'm not sure when I'll get around to it). Nobel Intent has a review of the paper.
When I first heard about this project I wondered what exactly they'd be doing. The fact that this study only looked at 11 cancers for each tissue is somewhat surprising. What I'd really like to see is a study…
evolgen | October 12, 2006One of the greatest developments of the post-genomic era has been the refinement of the concept of the 'gene'. The central dogma states that genes encode RNA transcripts which are translated into the amino acid sequence that makes up a protein. But protein coding genes make up a small fraction of many genomes, so what does the rest of the genome do? Some say it's junk. Others say that it's involved in regulating the transcription of the other regions. And even others say that it's transcribed, but not translated. (Note: most think it's some combination of the three.)
We're now discovering…
evolgen | October 9, 2006I'm looking for a good recent review of DNA double-strand break repair. The review should focus on more than just humans and mammals, but it shouldn't be on just yeast either. Ideally, it would show schematics of different ways to repair and resolve double-strand (and, possibly, single-strand) breaks. I don't want something that just lists the known gene products involved in different repair mechanisms. And it should be from the last couple of years.
If anyone reading this blog knows about this area of research, please lend a hand. To provide some incentive, the person who suggests the best…
pharyngula | October 3, 2006
How we sense the world has, ultimately, a cellular and molecular basis. We have these big brains that do amazingly sophisticated processing to interpret the flood of sensory information pouring in through our eyes, our skin, our ears, our noses…but when it gets right down to it, the proximate cause is the arrival of some chemical or mechanical or energetic stimulus at a cell, which then transforms the impact of the external world into ionic and electrical and chemical changes. This is a process called sensory signaling, or sensory signal transduction.
While we have multiple sensory…
pharyngula | October 2, 2006Andrew Fire and Craig Mello, for the discovery of RNAi. Read Pure Pedantry for an explanation for why this is important.
I'll also mention that Carl Zimmer presents his take on this award…and wouldn't you know it, evolution has its greasy fingerprints all over it.
I must also promote an excellent comment from Andy Groves:
I've said it before, and I'll say it again for the benefit of ID supporters out there - this is what a real scientific revolution looks like. Fire and Mello published their paper in 1998 (two years after "Darwin's Black Box" came out, for those who are interested). Since…
pharyngula | September 30, 2006Here's a prediction for you: the image below is going to appear in a lot of textbooks in the near future.
(click for larger image)Confocal image of septuple in situ hybridization exhibiting the spatial expression of Hox gene transcripts in a developing Drosophila embryo. Stage 11 germband extended embryo (anterior to the left) is stained for labial (lab), Deformed (Dfd), Sex combs reduced (Scr), Antennapedia (Antp), Ultrabithorax (Ubx), abdominal-A (abd-A), Abdominal-B (Abd-B). Their orthologous relationships to vertebrate Hox homology groups are indicated below each gene.
That's a technical…
pharyngula | September 27, 2006There are days when I simply cannot believe how dishonest the scoundrels at the Discovery Institute can be. This is one of them. I just read an essay by Jonathan Wells that is an appalling piece of anti-scientific propaganda, an extremely squirrely twisting of some science news. It's called "Why Darwinism is doomed", and trust me, if you read it, your opinion of Wells will drop another notch. And here you thought it was already in the gutter!
First, here's the science news that was published in Nature back in August, and which has set Wells off. The research is the result of the ability to…