Molecular Biology

Pharyngula

Category archives for Molecular Biology

Scientists behaving deviously

There are some scientific technologies that rapidly become ubiquitious and indispensible, and they become the engine that drives tremendous amounts of research, win Nobel prizes, and are eventually taken for granted. Polymerase chain reaction (PCR) is one example: PCR is routine in molecular biology now, but I remember when PCR machines were magical objects of…

This could get interesting. I’ve seen a lot of stories about this recent paper on the tardigrade genome: Horizontal gene transfer (HGT), or the transfer of genes between species, has been recognized recently as more pervasive than previously suspected. Here, we report evidence for an unprecedented degree of HGT into an animal genome, based on…

A defense of ENCODE?

Dan Graur has snarled at the authors of a paper defending ENCODE. How could I then resist? I read the offending paper, and I have to say something that will weaken my own reputation as a snarling attack dog myself: it does make a few good points. But it’s mostly using some valid criticisms to…

Dan Graur has suggested some changes to the classification of DNA. It’s one more pile of terminology to keep straight, but the distinctions are conceptually useful — I particularly appreciate literal vs. indifferent DNA as subdivisions of functional DNA. The pronouncements of the ENCODE Project Consortium regarding “junk DNA” exposed the need for an evolutionary…

On the importance of luck

That paper that proposed that most cancers were due to bad luck, that is, that they were a consequence of biological factors that could not be controlled, has been surprisingly controversial. I thought it was a fairly unsurprising paper that confirmed what we already suspected, but wow, the furious pushback has been something to behold.…

Let’s slap ENCODE around some more

Since we still have someone arguing poorly for the virtues of the ENCODE project, I thought it might be worthwhile to go straight to the source and and cite an ENCODE project paper, Defining functional DNA elements in the human genome. It is a bizarre thing that actually makes the case for rejecting the idea…

Ophelia has summarized a series of science questions Richard Dawkins asked on Twitter. Hey, I thought, I have answers to lots of these — he probably does, too — so I thought I’d address one of them. Maybe I can take a stab at some of the others another time. I like this one, anyway:…

Dang, I teach all this stuff about genes and chromosomes and epigenetics, but I don’t have the advantage of giant floating holographic molecules floating around me. Maybe I’ll have to steal this for my classes. Although it could use some discussion of Blaschko’s lines, to explain why you get a stripey pattern rather than just…

Deconstructing metaphors

Oh, that’s right — that’s what philosophers are good for. They’re really good at questioning models. John Wilkins has been busily dismantling the cheap and easy metaphors we use to describe molecular biological concepts in a series of posts, taking on genes as language, other popular gene myths and metaphors, and explaining why genes aren’t…

How kinesin actually moves

Recently, Carl Zimmer made a criticism of the computer animations of molecular events (it’s the same criticism I made 8 years ago): they’re beautiful and they’re informative, but they leave out the critical aspect of stochastic behavior that is important in understanding the biochemistry. He’s talking specifically about kinesin, a transport protein which the animators…