Molecular Biology
pharyngula | August 20, 2007Here's some exciting news: Artificial life likely in 3 to 10 years. It is exciting but not surprising at all — but of course we're going to be able to assemble entirely artificial life forms soon. It's just a particularly complicated kind of chemistry, and it's more of a deep technical problem than anything else. I wouldn't be quite so specific about the date — there are also all kinds of surprises that could pop up — but I'm optimistic, and I think the overall assertion is supported by the increasing rate of accomplishment in the field.
But of course, in addition to the usual suggestions…
pharyngula | August 20, 2007If it existed, it might also be profoundly autistic and … diabetic? So science cannot disprove the existence of a soul, but one thing we're learning is how much valued human properties such as love and attachment and awareness of others are a product of our biology — emotions like love are an outcome of chemistry, and can't be separated from our meaty natures.
The latest issue of BioEssays has an excellent review of the role of the hormone oxytocin in regulating behaviors. It highlights how much biochemistry is a determinant of what we regard as virtues.
Anyone with a little familiarity with…
pharyngula | August 15, 2007Sandy is peeking at and playing with Jim Watson's most intimate bits. So can you!
neurophilosophy | August 8, 2007 Alzheimer's is a progressive neurodegenerative disorder characterised by the formation of senile plaques consisting of amyloid-beta protein. The molecular genetic basis of Alzheimer's is very complex. Amyloid-beta is a toxic protein fragment produced by abnormal processing of amyloid precursor protein (APP), which accumulates to form the insoluble plaques found within cells. (This occurs by a seeding mechanism similar to that of prion proteins.)
A new study, by researchers at UCL's Institute of Ophthalmology, in collaboration with French and Italian colleagues, now confirms the role of…
pharyngula | August 2, 2007Abbie of ERV has made her first guest post on the Panda's Thumb, and it's a good one. Go see how Behe was wrong and there are documented genetic and biochemical changes in the evolution of HIV, including the evolution of new molecular machinery.
pharyngula | August 1, 2007Since I was asked what a cnidarian "head" is in reference to this work on multi-headed cnidarians, I'll answer. In short, they don't have one.
Longer answer: the paper in PLoS describes a procedure for generating homeotic mutations in cnidarians by manipulating the expression of Cnox genes in hydrozoans. Knock outs of various cnidarian Hox-like genes and the medusae develop extra manubriae, or the tentacled part at the oral end of the animal, which the authors colloquially call "heads" (and they do usually put the word in quotes). These structures aren't homologous to the things we consider…
neurophilosophy | July 31, 2007
This one only has two, but Wolfgang Jacob and Bernd Schierwater, of Yale University and Hanover University of Veterinary Medicine, respectively, have created jellyfish with up to 12 heads.
The multiple-headed hydromedusa (Eleutheria dichotoma) specimens were created by using RNA inhibition or antisense oligonucleotides to silence various homeobox genes (Cnox-2 and Cnox-3) that are involved in head formation.
pharyngula | July 16, 2007One of the traditional ways to explain a scientific subject is the historical approach: start at the beginning of the endeavor and explain why people asked the questions they did, how they answered them, and how each answer blossomed into new potential. It's a popular way of teaching science, too, because it emphasizes the process that leads to new discovery. Middle World: The Restless Heart of Matter and Life(amzn/b&n/abe/pwll), by Mark Haw, exemplifies the technique. Not only is it effective, but this one slim book manages to begin with a simple, curious observation in 1827 and ends up…
pharyngula | July 10, 2007We now have a draft of the sea anemone genome, and it is revealing tantalizing details of metazoan evolution. The subject is the starlet anemone, Nematostella vectensis, a beautiful little animal that is also an up-and-coming star of developmental biology research.
(click for larger image)Nematostella development. a. unfertilized egg (~200 micron diameter) with sperm head; b. early cleavage stage; c. blastula; d. gastrula; e. planula; f. juvenile polyp; g. adult stained with DAPI to show nematocysts with a zoom in on the tentacle in the inset; h, i. confocal images of a tentacle bud stage and…
evolgen | July 1, 2007It's not entirely obvious at first, but this article in the New York Times is about the problems with gene patents in a world where one gene does not equal one protein. Now, we've known that this model isn't entirely correct, what with alternative splicing and all. Additionally, the human genome also contains many "genes" which are only transcribed into RNAs, but not translated into proteins. All of this has been pretty much accepted by geneticists for a few years.
But rather than putting all of this in the appropriate context, Denise Caruso muddies the waters by overemphasizing the…
pharyngula | June 28, 2007Albert Mohler might be freaking out at some of the new biotechnologies, but he missed a big one, one that might give him nightmares: synthetic biology. This week's Nature has a very fine editorial on a subject that's probably going to be more troubling to the religious than evolution, in a few years. We're on the verge of being able to create life in the laboratory.*
Synthetic biology provides a welcome antidote to chronic vitalism.Many a technology has at some time or another been deemed an affront to God, but perhaps none invites the accusation as directly as synthetic biology. Only a deity…
pharyngula | June 23, 2007
The general pattern of developing positional information in Drosophila starts out relatively simply and gets increasingly complicated as time goes by. Initially, there is a very broad distribution of a gradient of a maternal morphogen. That morphogen then triggers the expression of narrower (but still fairly broad) bands of aperiodic gap genes. The next step in this process is to turn on sets of genes in narrow, periodic bands that correspond to body segments. This next set of genes are called the pair-rule genes, because they do something surprising and rather neat: they are turned on in…
grrlscientist | June 17, 2007tags: Junkin's warbler, birds, ornithology, DNA technology
An ornithologist prepares to band a mysterious Junkin's warbler.
Image: Sandy Junkin.
With all the skilled birders and ornithologists in North America, it is truly remarkable to find a bird that cannot be identified, especially when that bird was captured in a mist net. After all, when you have a bird in your hand, you have the opportunity to examine its field marks closely.
Enter Dave Junkin. Junkin was the director of Buffalo Audubon's Beaver Meadow Wildlife Sanctuary in Java, and even after his retirement, he is an expert bird…
evolgen | June 16, 2007
Last year, Katie Pollard and colleagues published a couple of papers in which they identified regions of the human genome that had recently undergone an acceleration in their rate of evolution and characterized the expression pattern of an RNA gene located in one of those regions. The RNA gene is expressed in the developing brain, which lead people to speculate that it played some important role in making humans smarter than chimps (my round-up and stab at speculation can be seen here). Their approach toward identifying those regions is quite simple, but the cause of accelerated evolution in…
pharyngula | June 7, 2007No, actually they don't — but they do have some proteins that are essential components of synapses, and it tells us something important about the evolution of the nervous system. A new paper by Sakarya et al. really isn't particularly revolutionary, but it is very interesting, and it does confirm something many of us suspected.
First, in case you don't know what I'm talking about, here's a synapse:
A synapse is a kind of gateway for the transmission of electrical impulses in the nervous system. What's portrayed above is the terminal of a generic neuron; electrical signals travel down from…
evolgen | June 3, 2007Let's go through the basics again. Cracking the genetic code refers to figuring out how DNA encodes the information to make proteins -- that was done decades ago. Sequencing a genome does not mean that you have decoded the genome; presumably, decoding a genome would mean you've figured out the function of every part of a sequenced genome, but there really isn't a proper definition. In genetics, mapping refers to determining the location of genetic elements, which is different than sequencing. And deciphering has no real meaning.
With that said, check out the newest New York Times article on…
evolgen | May 31, 2007Late last week, my PCRs stopped working. One day I was able to amplify DNA from multiple different templates using different primers, and the next day I couldn't. This is a major setback for me -- a huge chunk of the remaining work I need to complete for my PhD involves doing PCR. If I can't get my PCRs to work, I'm royally screwed.
As soon as I couldn't get any PCR products, I went into troubleshooting mode. I had just made a new batch of dNTPs, so those were the first thing to get replaced. No dice. I thought there might be something wrong with my water, so I grabbed a new bottle and made…
pharyngula | May 30, 2007The Newsweek cover story is on recent efforts to create life in the laboratory, and of course they call this "playing God". Haven't they got the message yet? "Playing God" is where you do absolutely nothing, take credit for other entities' work, and don't even exist — scientists don't aspire to such a useless status. Besides, creating life is mundane chemistry, no supernatural powers required.
It's a curious article. There's some solid discussion of ongoing work on synthetic biology, with Craig Venter and George Church as the stars. These fellows and others are confident (and rightfully so, I…
pharyngula | May 22, 2007Here are three animals. If you had to classify them on the basis of this superficial glimpse, which two would you guess were most closely related to each other, and which one would be most distant from the others?
On the left is a urochordate, an ascidian, a sessile, filter-feeding blob that is anchored to rocks or pilings and sucks in sea water to extract microorganismal meals. In the middle is a cephalochordate, Amphioxus, also a filter feeder, but capable of free swimming. On the right are some fish larvae. All are members of the chordata, the deuterostomes with notochords. If you'd…
grrlscientist | May 18, 2007tags: cell, molecular biology, cell biology, streaming video
This streaming video shows a small number of the millions of amazing things that are happening within cells and also between cells millions of times every day [3:09].