Tag: Systems Biology

Model angst

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 my fundamental outlook, and, as good skeptical scientists, they won’t take it for granted that models are useful. In fact they’ve probably seen plenty of examples of bad models.

So here is how I justify my mathematical modeling work: Continue reading “Model angst”

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.

Gene Logic: Finding your (micro)Identity

The secret to success in life is to find your identity, particularly if you are a cell. Achieving and holding an identity is the prime concern of life at its most fundamental, cellular level; it is the key to engaging in behavior which best meets the challenges and demands of the molecular thicket that is the environment of the cell. Life can downright bewildering on the micron level. An identity makes this world navigable. Identity determines how a cell looks, what it eats, and the company it keeps. It specifies what environmental signals can be received, and what responses those signals elicit. An E. coli bacterium metabolizing a favorite monosaccharide in your gut, a yeast cell looking to hook up with one of the opposite gender, a nerve cell in your brain primed for an electric response, that light-detecting rod cell in your retina, the myocyte harboring a molecular power train in your bicep, and a cancer cell gone rogue: each of these has at its core an identity that dictates its behavior.
Continue reading “Gene Logic: Finding your (micro)Identity”