Author: Mike White

Genomes, Books, and Science Fiction

Jerry Coyne reads Stanley Fish so we don’t have to

Why Evolution Is True: “Stanley Fish misunderstands science; makes it a faith equivalent to religion

Fish’s big mistake: the reasons undergirding that belief are not that we can engage in a lot of philosophical pilpul to justify using reason and evidence to find out stuff about the universe. Rather, the reasons are that it works: we actually can understand the universe using reason and evidence, and we know that because that method has helped us build computers and airplanes, go to the moon, cure diseases, improve crops, and so on. All of us agree on these results. We simply don’t need a philosophical justification, and I scorn philosophers who equate religion and science because we don’t produce one.

Continue reading “Jerry Coyne reads Stanley Fish so we don’t have to”

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”

Freeman Dyson on the rampage

Freeman Dyson muses on outsider science in the NYRB, “Science on the Rampage”:

In my career as a scientist, I twice had the good fortune to be a personal friend of a famous dissident. One dissident, Sir Arthur Eddington, was an insider like Thomson and Tait. The other, Immanuel Velikovsky, was an outsider like Carter. Both of them were tragic figures, intellectually brilliant and morally courageous, with the same fatal flaw as Carter. Both of them were possessed by fantasies that people with ordinary common sense could recognize as nonsense. I made it clear to both that I did not believe their fantasies, but I admired them as human beings and as imaginative artists. I admired them most of all for their stubborn refusal to remain silent. With the whole world against them, they remained true to their beliefs. I could not pretend to agree with them, but I could give them my moral support.

My main problem with Dyson’s view is that it doesn’t take into account those cranks and pseudoscientists who are actually acting in bad faith – peddlers of snake oil, front-men for deep-pocketed business interests threatened by research on tobacco, climate change, etc., and religious fundamentalists who can’t make peace between their faith and thoroughly established science. In fact, it’s likely that there are many, many more dishonest pseudoscientists than the deluded but honest amateurs that Dyson describes, and his knee-jerk sympathy for the scientific outsider makes him a potential sucker. Continue reading “Freeman Dyson on the rampage”

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.

Wikipedia fail #208 – on the origins of enthalpy

Admit it, we all have a love-hate relationship with Wikipedia, as we do with anything that is both useful and frustrating, which seems to include just about anything related to the internet.

Here is yet another instance where the weaknesses of Wikipedia’s crowd-sourcing comes to the fore: enthalpy. Under the subheading ‘Origins’, we first encounter two sentences explaining the Greek roots of the word, when one sentence would have been sufficient. Next, we read three sentences explaining that the origins of the concept are often misattributed Clapeyron and Clausius. Five sentences later, in the second paragraph, we finally read something about the origin of the concept of enthalpy (but the emphasis still inappropriately remains on the origin of the word and not the concept).

Wikipedia’s biggest weakness is not inaccuracy, but lack of a filter and a proper sense of emphasis, which is why the articles often read like they’ve been written by high school students. Of course that doesn’t stop me from reading Wikipedia 20 times a day.