Tag: Biology

Dueling viewpoints on pervasive 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 experimentalists. (The split’s not perfect but the trend is there, and you can see it in the authorship of the two papers above.)  Computational people (or, at least those who came in as computational people – I’m not making judgments about anyone’s experimental skills) are more likely to believe in pervasive transcription, and while others are more likely see it as experimental and biological noise.

Following the trend, I fall into the latter camp.

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.

Happy Birthday, Gregor!

Gregor Mendel (1822-1884)
Image via Wikipedia

On this day in 1822, Gregor Mendel was born. Forty-three years later he would give birth to genetics when he reported his discovery of the laws of inheritance from pea hybridization experiments. It took about forty more years for his work to be rediscovered and applied.

 

The Finch and Pea is half-named in honor of Mendel’s pea hybridization experiments. The discovery of genetics combined with Darwin’s ideas about evolution form the foundation of modern biology (along with molecular methods from physics – but they do not have a model organism that makes a cool pub-y name).

Happy 189th Birthday, Gregor! You look great.