Wednesday, August 28, 2013

The Anti-Virgin

When you have sex for the first time and "lose your virginity" it is a big deal and marks a transition point in your life. You are well aware of it. But the last time you have sex, when you become an anti-virgin,  probably occurs without you knowing it, without much fanfare. 

Wednesday, August 14, 2013

A bacteria scanner

A technology goal: to create a scanner capable of probing the bacterial population at a variable depth within tissue. How could you probe without damaging tissue? Maybe with a thin enough glass tube, you could sample many bacteria, while killing a only a few tissue cells. For example, a thin glass tube with small pores and an internal thread or "sponge". You insert the tube into tissue, pull back on the thread- to get a fresh sample,  then pull back a little more to isolate the sample, then remove the tube. Later, pull the thread more to expose the samples.

Wednesday, August 7, 2013

Monitoring Soil Volumes

With respect to the previous post "Handling bacterial and genomic diversity", I have devised an experiment: drill a hole in the soil; put sterile sand in the hole; wait a fixed length of time; do a spectral analysis of the sand before and after.This determines which chemicals have leached into the sand over that time frame - the byproducts of organisms living around the hole.
One person with a mass spectrometer and a microscope could do a lot. Or, instead of spectrum, you could culture the sand as a way of monitoring. They must do this somewhere.
Update: or some kind of probe could be used to take a core sample from living tissue.

Saturday, August 3, 2013

Handling bacterial and genomic diversity

I went to the MBL Friday Night Lecture last night. It was by Richard Roberts, entitled "Why I love bacteria". Essentially it was a review of the zoology of bacteria and contained little to no new science [my how the Friday Night Lectures have been dumb-ed down!]. But over and over it was reiterated that bacteria are present in most biological reactions; that their colonies are hugely diverse; that their genomes are more numerous and complex than the genomes of their hosts (us); and that little is known about these complex realities.

Listening in, it seemed to me that we are being limited by the concept of individual organisms and that we need new ways of thinking about these hugely complex biological processes in a way that bypasses the complexities. Let me make an analogy with physics: firstly there is an uncertainty principle that forces physicists to ignore the lowest level details; secondly they have the approach of statistical thermodynamics allowing macroscopic properties to be derived from aggregate behavior of the smaller parts. In other words, modern physics has ways to avoid losing the forest for the trees. Maybe biology needs something like that.

(Returning momentarily to the quality of recent Friday Night Lectures, one of the visible manifestations is of older scientists talking about old research and then segueing into extensive discussions of their laboratory protocols. The tools for studying the questions have replaced the questions themselves, as the focus of their research interest. Here we see from a more personal perspective the "lose forest for trees" phenomenon.)

So this lecture got me wondering how we could get away from thinking about individual organisms and their diversity, how we could break the combinatoric deadlock faced by biological sciences? Borrowing from Physics, what kind of statistical biodynamics might be possible? I propose that such a discipline could be based on biological tissue volumes and their macroscopic material properties - namely the chemical and genetic characteristics of what flows across the surface demarcating a given tissue volume; or perhaps a study of how the volume changes shape.
You might want to know how those fluxes change when the volume contains more or fewer of a given organism.  It might never happen that different organism mixtures would produce the same macroscopic characteristics but if it did, you might be glad to ignore details that, in the end, did not matter.
And so what? How would such "statistical" thinking change anything? I say it would change the type of experiments you might do with bacteria. Rather than isolate a tubercle bacillus you might instead compare two volumes of soil - one with and one without these creatures. OR you could look at a piece of lung tissue. Figure out how to monitor the flow across the (arbitrary) volume boundary. With bacteria tending to like living in a film, this makes the boundary geometry simpler. And while I am ranting away, what organisms cooperate with TB? You could experiment with the composition of these volumes (adding and subtracting different components) and with their geometries. New forests! New trees!
Update: Suppose two volumes of tissue with TB. In one volume the TB is quiescent, in the other the TB is happily reproducing.  The question is: what is the difference in the chemical or organism flux at the edges of such tissue volumes?