Category: Curiosities of Nature

Stochastic gene expression and Prussian cavalry kicked by horses

Now this is morbidly entertaining. Apparently our understanding of Poisson processes, such as many of the events involved in gene expression, are derived from a study of fatal encounters with horses in the Prussian cavalry:

“Effects of Molecular Memory and Bursting on Fluctuations in Gene Expression”, Juan M. Pedraza and Johan Paulsson:

Similar Poisson statistics have been observed in a wide range of physical systems, starting with Bortkewitsch’s classic study on the number of Prussian cavalry officers kicked to death by horses (12).

Continue reading “Stochastic gene expression and Prussian cavalry kicked by horses”

No, we don’t assume that evolution must increase complexity

Ryan Gregory at Genomicron mocks an inane press release about a supposedly new evolutionary theory – the idea that endosymbionts will lose genes when their hosts or other microbes in their community can provide the functions of those genes. This is an old and widely established idea, so why anyone with any knowledge of recent evolutionary biology would play up this idea as novel is beyond me.

Sadly, the ignorance isn’t limited to whatever flack wrote the press release – at least one of the scientists involved is portrayed as the same misunderstanding of evolution that many creationists have:

“A common assumption about evolution is that it is directed toward increasing complexity,” said Erik Zinser, associate professor of microbiology. “But we know from analysis of microbial genomes that some lineages trend toward decreasing complexity, exhibiting a net loss of genes relative to their ancestor.”

Okay kids, repeat after me: evolution is not based on an assumption of increasing complexity. Increasing complexity (leaving aside the fact that the word complexity is terribly vague and non-quantitative) often happens in evolution, but we don’t assume that this is what should happen.

UPDATE: It could be that I’m being unfair to Dr. Zinser, that he’s being selectively quoted in a bad way by the same person who wrote the rest of the misguided press release. If that’s true, then all of my disdain is reserved for the anonymous press release writer.

I don’t understand my CD player or my genome

There is something dissatisfying about our current explanations of how the genome exerts its effects on the cell. This is particularly true of the non-protein-coding regulatory regions of the genome, which, as we all know, make up a substantially larger fraction of the genome than those DNA sequences that encode proteins.

So what is that we don’t understand? Rather than give a wordy and abstract explanation, let’s go with an analogy: our poor understanding of how the genome operates is like my poor understanding of how a CD player works.

Let’s start with what I do know about CD players (with a little help from Wikipedia, which I hate but still refer to dozens of times per day.) The data in a CD is encoded as little pits in a polycarbonate surface. Behind the polycarbonate surface is the shiny layer of the CD, and so the pattern of pits can be scanned by using a photodiode to detect laser light that is reflected off the CD. The pits change how the light is reflected, which changes the electrical signal that is emitted by the photodiode. Those output electrical signals are amplified, passed to a loudspeaker and finally to my ears and slightly buzzed brain. (Obviously I’m talking about listening to music after work.) Continue reading “I don’t understand my CD player or my genome”

Maxwell’s Demon, Boltzmann’s H theorem, Ergodicity and other awesome stuff

I just discovered this treasure trove on the foundations and history of statistical mechanics:

Compendium of the foundations of classical statistical physics, by Jos Uffink (PDF)

The abstract:

Roughly speaking, classical statistical physics is the branch of theoretical physics that aims to account for the thermal behaviour of macroscopic bodies in terms of a classical mechanical model of their microscopic constituents, with the help of probabilistic assumptions. In the last century and a half, a fair number of approaches have been developed to meet this aim. This study of their foundations assesses their coherence and analyzes the motivations for their basic assumptions, and the interpretations of their central concepts. The most outstanding foundational problems are the explanation of time-asymmetry in thermal behaviour, the relative autonomy of thermal phenomena from their microscopic underpinning, and the meaning of probability.

A more or less historic survey is given of the work of Maxwell, Boltzmann and Gibbs in statis- tical physics, and the problems and objections to which their work gave rise. Next, we review some modern approaches to (i) equilibrium statistical mechanics, such as ergodic theory and the theory of the thermodynamic limit; and to (ii) non-equilibrium statistical mechanics as provided by Lanford’s work on the Boltzmann equation, the so-called Bogolyubov-Born-Green-Kirkwood-Yvon approach, and stochastic approaches such as ‘coarse-graining’ and the ‘open systems’ approach. In all cases, we focus on the subtle interplay between probabilistic assumptions, dynamical assumptions, initial conditions and other ingredients used in these approaches.

This will keep me busy.

The Walking Dead’s Bloody Mess

There are spoilers below. You’ve been warned. If you are even further behind watching The Walking Dead – Season 2 than me and can’t bear the thought of being spared the waste of those hours of your life, this is not for you.

I have recently started catching up on The Walking Dead – Season 2. At the end of Episode 1, Carl Grimes, son of our hero, Rick Grimes, is wounded in a hunting accident. Episode 2 is then devoted to keeping Carl from bleeding out. This means surgery and blood transfusions. Unfortunately, you can’t just stick blood from one person into someone else1. The immune system will attack a blood transfusion as a foreign invader if the donated blood is not compatible with the recipient. These reactions can be fatal. Keeping blood banks stocked is difficult in our modern world. Trying to find appropriate blood donors for a kid with internal bleeding in a zombie-filled, post-apocalyptic wasteland poses a particular challenge. Continue reading “The Walking Dead’s Bloody Mess”