Author: Mike White

Genomes, Books, and Science Fiction

Winning science by attrition is boring

Nature has an interesting piece on the 24/7 lab:

It’s just about midnight on a hot Friday night in July, Enrique Iglesias’ ‘ Dirty Dancer ‘ is on the radio, and 26-year-old graduate student Sagar Shah is starting to look winded. The problem, he says, is not how late it is, or even that he has spent the past three hours working in a cramped sterile cell-culture hood. The problem is that the routine cell-culture maintenance he is doing, bathing his collection of rare human tumour cells with fresh medium, produces no data. And a lack of data, says Sagar, makes him “hungry” for it.

The piece goes on to talk about one of those high-intensity, work all weekends and holidays labs. That lab, and many like it, certainly crank out papers, but they are basically factories. Continue reading “Winning science by attrition is boring”

Science musings

What biologists need to do more of:

A major goal in all sciences is to be able to explain large-scale phenomena as consequences of the interactions of small-scale components. This is what drives me to study what I’m studying – in my case, the large scale-phenomena are patterns of gene expression, and the small-scale components are transcription factors and DNA binding sites.

Biologists do a lot of measuring of large-scale phenomena, via genomics or classical genetic phenotying. Biologists also spend a lot of time discovering what the small-scale components and interactions are. But they don’t really spend enough effort trying to understand how it is that large-scale phenomena are consequences of the interactions of small-scale components.

Just to be clear: your typical blob-and-arrow pathway diagram featured in Figure 7 of nearly every Cell paper (Fred Cross calls these ‘Figure 7 models’) is not the answer to this question, because it is essentially impossible, in nearly all cases, to predict the large-scale behavior just by looking over one of those diagrams.

Wetware

Just added to the stack: Wetware, by Dennis Bray. Bray has been a systems biologists at the University of Cambridge, since way back before they were calling people like him systems biologists. His papers have long inspired me, and I recently had the pleasure of conversing with him over lobster dinner at the Cold Spring Harbor Computational Cell Biology meeting earlier this year. (Yes, I lead a glamorous life.)

The blurb on the back of the book is exactly the question in biology that fascinates me more than any other:

How is a single-cell creature able to hunt living prey, respond to external stimuli, and display complex sequences of movements without the benefit of a nervous system?

Of course, this question does not just pertain to single-celled organisms. Think of the prey-hunting macrophages in your own body, or really any cell, whether it hunts or not – all cells sense and respond to their environments without nervous systems.

Stay tuned for updates on the book.

John Baez does network theory

I love John Baez’s blog that was a blog before we called things blogs, This Week’s Finds. (He also writes the Azimuth blog, linked in our blogroll below. And I tip my hat to my father-in-law, who first introduced me to Baez’s blog.)

Baez is now writing on network theory. Baez typically focuses on math and physics, but this series is great for biologists:

I wish there were a branch of mathematics—in my dreams I call it green mathematics—that would interact with biology and ecology just as fruitfully as traditional mathematics interacts with physics. If the 20th century was the century of physics, while the 21st is the century of biology, shouldn’t mathematics change too? As we struggle to understand and improve humanity’s interaction with the biosphere, shouldn’t mathematicians have some role to play?

And while you’re over there, check out his section on how to learn math and physics, and his advice to young scientists.

Teachers can slam creationism in school

I can understand the frustration, but I would probably find a different way to respond to the challenge of a fundamentalist student. Nonetheless, if students are aggressively challenging teachers with fundamentalist, anti-science claims, then teachers need room to respond. The NCSE reports:

The case originated when Corbett, a twenty-year history teacher at Capistrano Valley High School in Mission Viejo, California, was accused by a student, Chad Farnan, of “repeatedly promoting hostility toward Christians in class and advocating ‘irreligion over religion’ in violation of the First Amendment’s establishment clause,” according to the Orange County Register (May 1, 2009). Farnan cited more than twenty offending statements of Corbett’s in his complaint.

The federal Appeals Court ruled in Corbett’s favor:

In broaching controversial issues like religion, teachers must be sensitive to students’ personal beliefs and take care not to abuse their positions of authority. … But teachers must also be given leeway to challenge students to foster critical thinking skills and develop their analytical abilities. This balance is hard to achieve, and we must be careful not to curb intellectual freedom by imposing dogmatic restrictions that chill teachers from adopting the pedagogical methods they believe are most effective. … At some point a teacher’s comments on religion might cross the line and rise to the level of unconstitutional hostility. But without any cases illuminating the “‘dimly perceive[d] . . . line[ ] of demarcation'” between permissible and impermissible discussion of religion in a college level history class [Corbett was teaching Advanced Placement European history], we cannot conclude that a reasonable teacher standing in Corbett’s shoes would have been on notice that his actions might be unconstitutional.