Tag: Systems Biology

How to reference a rejected paper on your CV

From Rob Phillips’ list of publications on his lab website:

A First Exposure to Statistical Mechanics for Life Scientists. (with Hernan G. Garcia, Jane’ Kondev, Nigel Orme and Julie A. Theriot), Rejected by Am. J. Phys., 2007. [online full text]

The paper itself is a great read, with some important ideas for anyone who thinks about how to incorporate more quantitative/physical concepts into our program of biology education. It also tells you that stat mech is almost effortless once you understand the Boltzmann distribution: Continue reading “How to reference a rejected paper on your CV”

Life versus the molecular storm

lifes-ratchetRichard Feynman put it best: “Things on a very small scale behave like nothing that you have any direct experience about. They do not behave like waves, they do not behave like particles, they do not behave like clouds, or billiard balls, or weights on springs, or like anything that you have ever seen… Because atomic behavior is so unlike ordinary experience, it is very difficult to get used to, and it appears peculiar and mysterious to everyone.”

The same could be said about things on a very large scale, such as planets and galaxies. It could also be said about extremes of time and temperature – we have no direct experience with microseconds and millions of years, or with what happens at thousands of degrees or near absolute zero. Scientific concepts that deal with such extremes defy our meso-scale common sense.

We respond to these assaults on our intuition sometimes with gee-whiz fascination, and at other times, when cherished beliefs are on the line, with resistance. Can our mundane actions really change the climate of something so large as the earth? How could we possibly have descended from small, furry dinosaur prey? And if a tornado whipping through a junkyard can’t spontaneously create a Boeing 747, can it really be true that complex, living, self-directing beings are formed out of molecules that merely follow the laws of physics and chemistry, without the guiding influence of vital spirits? Continue reading “Life versus the molecular storm”

“Lectures on Chemical Reaction Networks”

A classic set of lectures by Martin Feinberg:

The occasion was a semester-long in-gathering of people interested in the behavior of complex chemical systems. At the end of that period there was a large meeting, the proceedings of which were published by Academic Press in a book, “Dynamics and Modeling of Reactive Systems,” edited by W. Stewart, W. H. Ray and C. Conley. My chapter amounted to a summary of some of the things I talk about during the course of the nine lectures.

It was an exciting time, which began when Charles Conley called me at the University of Rochester. He explained the MRC plans for 1979 and asked if I could spend a semester in Wisconsin. He said that they would pay my salary, provided that my salary wasn’t too high. I told him my salary. Conley asked if I could come for a year.

These seem useful, at least based on what I see in this paper: “A Linear Framework for Time-Scale Separation in Nonlinear Biochemical Systems,” Jeremy Gunawardena.

How to find your way in E. coli without stopping for directions

One of the keys to success in life is to regulate your genes properly. Genes are regulated by transcription factor proteins, which have to navigate their way around the genome and bind particular DNA targets. The problem is that there are only a few correct targets and the genome is large. So an obvious question is, why don’t transcription factors get lost? Do they stop and ask for directions? Where is the information for genome navigation coming from?

The answer to this question is still being worked out for eukaryotes, but it has been solved for E. coli. Peter von Hippel and Otto Berg largely figured out the answer in their classic 1986 paper “On the specificity of DNA protein interactions.” E. coli’s solution for making gene regulation manageable is simple and elegant, because this bacterium has the virtue of possessing a small genome. Let’s take a look at how genome navigation works in a bacterium: Continue reading “How to find your way in E. coli without stopping for directions”

Turing asked the most interesting questions in science

Turing biographer Andrew Hodges writes in today’s issue of Science:

But more deeply, anything that brings together the fundamentals of logical and physical description is part of Turing’s legacy. He was most unusual in disregarding lines between mathematics, physics, biology, technology, and philosophy. In 1945, it was of immediate practical concern to him that physical media could be found to embody the 0-or-1 logical states needed for the practical construction of a computer. But his work always pointed to the more abstract problem of how those discrete states are embodied in the continuous world. The problem remains: Does computation with discrete symbols give a complete account of the physical world? If it does, how can we make this connection manifest? If it does not, where does computation fail, and what would this tell us about fundamental science?

Personally I find this the most interesting question in science. It’s what drew me to biology, and it is what drives my current research in gene regulation. The problem of gene regulation is a problem of computation, and what is remarkable is the fact that genetic information is stored digitally as a string of discrete, two-bit chemical units. It didn’t have to be that way, and people* didn’t think that way until Schrödinger’s speculations on aperiodic crystals and the discoveries of molecular biologists in the 50’s and 60’s.

*To be fair, geneticists were thinking digitally, beginning with Mendel, and continuing, after a hiatus, with the early 20th century pioneers. But these geneticists didn’t really didn’t care about the physical implementation of genetic information. Those who did think about it weren’t thinking in terms of digits.