Category Archive: Molecular biology

Jul 22 2014

Biology is a hard problem

New genetic disorders pop up all the time — each one represents a child who may face incredible challenges, or even be doomed to death. A child named Bertrand exhibited some serious symptoms — profound developmental disabilities — shortly after he was born, and no one could figure out what was wrong with him. So …

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Jul 15 2014

The Lyon hypothesis, nicely illustrated

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 …

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Apr 22 2014

How kinesin actually moves

Horizontal grid lines (dotted lines) are spaced 8 nm apart. Data were median-filtered with a window width of 60 ms. b, Normalized histogram of pairwise distances between all pairs of data points in this record, showing a clear 8-nm periodicity. c, Normalized power spectrum of the data in b, displaying a single prominent peak at the reciprocal of 8 nm (arrow). d, Variance in position, averaged over 28 runs at 2 microM ATP (dots), and line fit over the interval 3.5 ms to 1.1 s. The y-intercept of the fit is determined by equipartition,  left fencex2right fence = kT/alpha, where alpha is the combined stiffness of the optical trap and bead–microtubule linkage. The rapid rise in variance at short times reflects the brownian correlation time for bead position.

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 …

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Feb 14 2014

The state of modern evolutionary theory may not be what you think it is

Selectionist, neutral and nearly neutral theories. a | Selectionist theory: early neo-Darwinian theories assumed that all mutations would affect fitness and, therefore, would be advantageous or deleterious, but not neutral. b | Neutral theory: the neutral theory considered that, for most proteins, neutral mutations exceeded those that were advantageous, but that differences in the relative proportions of neutral sites would influence the rate of molecular evolution (that is, more neutral sites would produce a faster overall rate of change). c | Nearly neutral theory: the fate of mutations with only slight positive or negative effect on fitness will depend on how population size affects the outcome.

I was rather surprised yesterday to see so much negative reaction to my statement that there’s more to evolution than selection, and that random, not selective, changes dominate our history. It was in the context of what should be taught in our public schools, and I almost bought the line that we can only teach …

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Dec 07 2013

The reification of the gene

Razib Khan poked me on twitter yesterday on the topic of David Dobbs’ controversial article, which I’ve already discussed (I liked it). I’m in the minority here; Jerry Coyne has two rebuttals, and Richard Dawkins himself has replied. There has also been a lot of pushback in the comments here. I think they all miss …

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Nov 22 2013

A rather remarkable deficiency

There’s a much ballyhooed article from Science going around that promotes the surprising conclusion that dogs were first domesticated in Europe. Dan Graur points out that there is one little problem with the data: The take home message of the Thalmann et al. paper is simple: Dogs were not domesticated in the Middle East or …

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Nov 22 2013

Sexy T-rex meets lecherous creationist

Charlie Stross has written a story, A Bird in Hand, which rather pushes a few boundaries. It’s about dinosaurs and sodomy, as the author’s backstory explains. And as everyone knows, every story is improved by adding one or the other of dinosaurs and sodomy, so it can’t help but be even better if you add …

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Nov 12 2013

Remedial reading for big-time scienticians

I don’t understand how this happens. You’ve got a good academic position. You’re bringing in reasonable amounts of grant money. You’re publishing in Nature Genetics and Nature Structural and Molecular Biology. And you don’t even understand the basic concepts in your field of study. For instance, here’s a press release titled “Cause of genetic disorder …

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Nov 07 2013

Ill-informed science making a case for a liberal arts education

Last month, I wrote about the terrible botch journalists had made of an interesting paper in which tweaking regulatory sequences called enhancers transgenically caused subtle shifts in the facial morphology of mice. The problem in the reporting was that the journalists insisted on calling this a discovery of a function for junk DNA — the …

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Oct 12 2013

microRNAs and cancer

I’m trying to raise money for the The Leukemia & Lymphoma Society, and I promised to do a few things if we reached certain goals. I said I’d write a post microRNAs and cancer if you raised $7500. And you did, so I did. I kept my clothes on this time, though, so here’s a …

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