“The limit of man’s knowledge in any subject possesses a high interest, which is perhaps increased by its close neighbourhood to the realms of imagination.” - Charles Darwin, The Voyage of the Beagle
“These experiments have not been published yet, but I shall assume the results.” - A.V. Hill, “The possible effects of the aggregation of the molecules of haemoglobin on its dissociation curves,” Proceedings of the Physiological Society, Jan. 22 1910, cited 1265 as of December 2011.
[Students of chemistry, computational biology, physics, and engineering] are increasingly finding themselves engages in research activities that cross traditional disciplinary lines. Successful outcomes for such projects often hinge on their ability to translate complex phenomena into simple models and develop approaches for solving these models. Because of its broad scope, statistical mechanics...
A model that is wrong in some details may nevertheless be useful in guiding and interpreting experiments. For computational modeling to be useful in incompletely understood systems, we must focus not on building the final, perfect, model with all parameters precisely determined, but on building incomplete, tentative, and falsifiable models in the most expressive and predictive fashion...
Quote of the day
The real world of evidence is often very irritating. - Ben Goldacre, “Will asking a question get your science paper cited more?”, The Guardian
Systems Biology Models are Sloppy - thankfully →
How to scientifically teach science
I’ve been a big fan of physics Nobel laureate Carl Wieman’s research on science education. He focuses on evidence-based methods for teaching science (and other subjects, but primarily science). Check out these teacher resources at the Carl Wieman Science Education Initiative at the U of British Columbia here.
Real climate scientists on the Berkeley study:
I’m also puzzled by the bizarre press coverage of Muller’s BEST group. Real Climate puts things in perspective: Anybody expecting earthshaking news from Berkeley, now that the Berkeley Earth Surface Temperature group being led by Richard Muller has released its results, had to be content with a barely perceptible quiver. As far as the basic science goes, the results could not have...
Harold Bloom makes Sophocles sound like H.P....
Oedipus, repeatedly stabbing his eyes with Jocasta’s brooches, passes judgment not so much upon the seen, as so upon the light by which we see. I interpret this as his protest against Apollo, who brings both light and the plague. The Freudian trope of blinding for castration seems to me less relevant here than the outcry against the god. To protest Apollo is necessarily dialectical, since...
In graphs: Eight human fingerprints on climate... →
As I contemplate presenting my research plans in job talks, I’m worried about clearly conveying what we get out of quantitative models. The vast majority of biologists don’t build or use quantitative models, which I recognize is a reasonable consequence of the history of the field, but I find it shocking nonetheless. What this means is that many of these researchers don’t share...
No attractors in equilibrium phase space
In statistical mechanics, at equilibrium every possible configuration of the system is just as probable as any other configuration. Rare states aren’t less probable than any other state; it’s just that they are only achieved by unique microscopic configurations - as any player of Settlers of Cataan intuitively knows. Any given roll of two six-sided dice is equally probable as any...
Richard Dawkins profile →
Dueling viewpoints on widespread transcription
PLoS Biology does point-counterpoint on whether our entire genomes are transcribed (and, by implication, whether the majority of our DNA is functional): The Reality of Pervasive Transcription - Clark, et al. Response - van Bakel, et al. Interestingly, these two viewpoints tend to split somewhat cleanly between those who came into biology as computational people, and those who came in as...
Predicting complex systems
Why we wouldn’t just calculate the future using the laws of physics and the positions and momenta of every particle, even if we could: - Most systems of interest exhibit chaotic motion, where the time evolution depends with ever increasing sensitivity on the initial conditions - you cannot know enough about the current state to predict the future. - Even if it were possible to evolve...
Does it matter that voters are stupid? Maybe not.... →
Let’s start on safe ground. We all agree, surely, that theory — the...– Denis Bray, Reasoning for Results, Nature 412, 863 (30 August 2001)
synthetic bio smorgasborg
From last week, but still good: Science magazine’s feature on synthetic biology.
I really wanted to like this book
Carlos Fuentes’ latest, Destiny and Desire sounds potentially amazing: a reflection on Mexico’s history and current troubles by looking at the parallel lives of two youths growing up in modern-day Mexico City. But the book fell flat. It just wasn’t compelling. The characters were boring. The prose, with some notable exceptions, was unremarkable, especially during sections of...