Archive for the 'Molecular biology'

Researchers have taken a photo of a DNA strand, which is kind of cool, but also confused me a bit. Here it is: Wait. The link says that this photo reveals the familiar “spiralling corkscrew” of the DNA double helix, but that can’t be right. The familiar B-DNA form has a diameter of 2nm and the helices ought to show a 3.3nm repeat — this photo shows something way too thick and far too tightly wound to be a single strand. Also, every source I’ve found so far reproduces the photo with the scale bar but doesn’t tell us the size of that bar, which is really annoying. I looked a little further elsewhere (I don’t have access to the journal it was published in, unfortunately) and found a slightly different story: …at present, the method only works with “cords” of DNA made up of six molecules wrapped around an seventh acting as a core. That’s because the electron energies are high enough to break up a single DNA molecule. Oops, yeah. That makes more sense. So sorry, you still haven’t seen a photograph of a single double-helical strand of DNA. But at least now you’ve seen many strands of DNA wrapped around a filament. Here’s a much more detailed critique of the reporting on that paper.

A while back, two physicists, Paul Davies and Charles Lineweaver, announced their explanation for cancer with a novel theory, which is theirs, that cancers are atavisms recapitulating in a Haeckelian reverse double backflip their premetazoan ancestry. They seemed very proud of their idea. I was aghast, as you might guess. They even claimed that human embryos go through a fish/amphibian stage with gills, webbed feet, and tails in a pattern of Haeckelian development. They do not understand evolution, development, or cancer, facts that were apparent even in the absence of their admission that they had no prior knowledge, and it was freaking embarrassing to see two smart guys with a measure of legitimate prestige in their own specialties charging off into another discipline with such crackpot notions. Now they’ve done it again, repeating the same claims all over again. And worse, they’ve now published it in the journal Physical Biology, under the title “Cancer tumors as Metazoa 1.0: tapping genes of ancient ancestors”. Read more

In about 20 minutes, Atheist Talk radio will be interviewing George Church, the molecular geneticist who has been working to make genetic sequencing affordable, and preparing us for the day high school students are building designer organisms in their garage. Listen to it, or be unprepared for the sneaky stuff the kids will be up to.

I approve this plan. A number of researchers have gotten together and worked out a grand strategy for sequencing the genomes of a collection of cephalopods. This involves surveying the phylogeny of cephalopods and trying to pick species to sample that adequately cover the diversity of the group, while also selecting model species that have found utility in a number of research areas — two criteria that are often in conflict with one another. Fortunately, the authors seemed to have found a set that satisfies both (although it would have been nice to see the Spirulida and Vampyromorpha make the cut — next round!). Here’s the initial group, table taken directly from the text with the addition of a few pretty pictures for those of you unfamiliar with the Latin names. Table 1: Cephalopod species proposed for initial sequencing efforts. Species Estimated genome size Current sequencing coverage Geographic distribution Lifestyle juvenile/adult Research importance O. vulgaris 2.5-5 Gb 46× world-wide planktonic/ benthic classic model for brain and behavior, fisheries science O. bimaculoides 3.2 Gb 50× California, Mexico benthic emerging model for development and behavior, fisheries science H. maculosa 4.5 Gb 10× Indo-Pacific benthic toxicity S. officinalis 4.5 Gb - East Atlantic- Mediterranean nectobenthic classic model for behavior and development, fisheries science L. pealeii 2.7 Gb - Northwest Atlantic nectonic cellular neurobiology, fisheries science E. scolopes 3.7 Gb - Hawaii nectobenthic animal-bacterial symbiosis, model for development I. paradoxus 2.1 Gb 80× Japan nectobenthic model for development, small genome size I. notoides - 50× Australia nectobenthic model for development, small genome size A. dux 4.5 Gb ...
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Evolution News & Views, the DI’s Pravda, did something good for a change: they alerted me to the availability of BBC 2′s show, Secret Universe: The Hidden Life of the Cell. Here it is! Secret Universe – The Hidden Life Of the Cell by David_Tennnant_Spain Of course, you can see why the DI would like this video, since it uses all their favorite buzzwords like “complexity” and “machines” to describe processes in the cell. And it’s true that the cell is complex and contains complex machinery, but that, as I’ve been trying to get through to them for years, does not imply that they did not evolve, because evolution routinely generates complex machines. The evolutionary explanations given are not “spin”, as the DI explains, but good answers for the origin of these processes. One major caveat: the star of this show is the CGI animation of the molecular activity of the cell, and as usual, it portrays everything as excessively linear and deterministic, and the necessary omission of water from the animation grossly skews the chemistry. One of the scientist narrators, Bonnie Bassler, does briefly explain that everything is stochastic, with molecules bouncing about randomly rather than zooming through empty space directly to their destination. But otherwise, it is a nice basic and rather cartoony overview of what goes on in a cell.