Banner
Melville on Science vs. Creation Myth

From Melville's under-appreciated Mardi: On a quest for his missing love Yillah, an AWOL sailor...

Non-coding DNA Function... Surprising?

The existence of functional, non-protein-coding DNA is all too frequently portrayed as a great...

Yep, This Should Get You Fired

An Ohio 8th-grade creationist science teacher with a habit of branding crosses on his students'...

No, There Are No Alien Bar Codes In Our Genomes

Even for a physicist, this is bad: Larry Moran, in preparation for the appropriate dose of ridicule...

User picture.
picture for Hank Campbellpicture for Heidi Hendersonpicture for Bente Lilja Byepicture for Wes Sturdevantpicture for Ian Ramjohnpicture for Patrick Lockerby
Michael WhiteRSS Feed of this column.

Welcome to Adaptive Complexity, where I write about genomics, systems biology, evolution, and the connection between science and literature, government, and society.

I'm a biochemist

... Read More »

Blogroll

If you had to pick one organism with which to tell the story of the modern science of biology, you couldn't do better than to pick the tiny gut bacterium Escherichia coli, commonly called just E. coli. In his latest book Microcosm: E. coli and The New Science of Life, Carl Zimmer, uses E. coli as a decoder ring to open up the dense and diverse world of biological research, taking us on a panoramic tour of some of the most important conceptual advances and outstanding scientific questions in this important realm of science.

Biology, in contrast to a science like physics, is a science of particulars. In physics, if you understand one electron, you understand them all, but in biology every organism is unique. In biology it is more challenging to find universals, to pick an object of study that let's you ask big questions with the hope of finding general answers.

With E. coli we can come quite close: this tiny bacterium is the hydrogen atom of biology, a model simple enough to be experimentally tractable, but representative of general principles that apply to all life. As the pioneering molecular biologist Jacques Monod put it, "What is true for E. coli is true for the elephant," and also true for us. In Microcosm, we follow E. coli through a survey of some of the deep foundations and controversies of biology.

I just got my hands on a recent book by two influential biologists, Marc Kirschner, chair of Harvard's recently created Systems Biology Department, and John Gerhart, a professor at UC Berkeley. Their book, The Plausibility of Life, lays out some influential ideas about where biological research should be headed, and it has stimulated a lot of discussion in the systems biology community. I think this book will be a useful vehicle to go over some provocative ideas about what the most exciting questions in biology are right now. So starting this weekend, we'll walk through this book here, chapter by chapter.
Dividing is one of the trickiest things a cell has to do. The cell needs to faithfully copy its entire genome, with very few mistakes, and it needs to then divvy up those two genome copies equally among the two new cells that are created during division. Going through this process is a bit like going down a double black diamond ski run: once you set things in motion, there's no stopping until you get to the end. In the case of cell division, there are two critical points of no return: at the decision to start replicating DNA, and when it's time to equally split up the chromosomes. A cell that's going to copy its genetic material had better be ready, with all the necessary supplies in hand, because once the copying process initiates, it's a bad idea to stop: a cell can't really do much with a half-replicated genome, and it's in danger of permanently ruining its genome. And it doesn't do you any good to successfully finish that copying process, only to misallocate what you've copied among the two daughter cells. Without the right chromosomes in each cell, there is only a slim chance of survival. So how do cells make these critical decisions?
"Can scientists and journalists learn to beat the doubt industry before our most serious problems beat us all?" This is the question asked in an interesting piece at a news? site I've never heard of - "Miller-McCune: Turning Research Into Solutions." I'm not sure about the research and solutions thing, but they do have some interesting comments about the "Doubt Industy." "Doubt Industry" means organized interests with a strong motivation to get the public to question science: the link between smoking and cancer, the scientific status of evolution, the health hazards of beryllium (apparently a problem for workers in the atomic industry). Whenever scientific results cause problems for someone, especially someone with a strong financial incentive to not believe the science, the time-tested strategy is to question the certainty of the science. A well-known internal memo from one cigarette company in the 1960's famously claimed(PDF):
We like to talk about the amazingly complex machinery of the cell: flagella that resemble finely tuned outboard motors, or complex information processing circuits that help a cell process information about its environment. Biologists work hard at understanding how these systems work. They will take a wiring diagram like the following, and ask why is it set up this way?
A report in this week's issue of Science describes a set of genes that enable members of the bacterial species Proteus mirabilis to tell the difference between kin and strangers. The bacteria engage in a social behavior (common to teenagers and bacteria) called swarming: they like to get together in groups. If you spread these bacteria on a petri dish, they are able to move together to form a colony. The catch is this: like humans, bacteria of the same species can be divided up into smaller populations of more closely related individuals.