Category Archives: RNA

Life


This is Carl Woese, he’s a biologist. Although I’ve been aware of several of the theories that he has espoused over the years, it wasn’t until recently that I attributed their authorship to this great thinker. Three of the “biggest” ideas that he’s responsible for are: the RNA world hypothesis, the current organization of the tree of life with three domains at the bottom, and the concept that there was a time, before species existed, when Darwinian evolution was not dominant because of the prevalence of horizontal gene transfer. Briefly, the RNA world hypothesis suggests that the most primitive version of life as we know it must have consisted entirely of RNA because RNA can act as both an enzyme (for which we mainly use proteins) and as an information storage molecule (for which we use DNA). The three domain system split the prokaryotes (simple cells having little to no internal membrane structure like bacteria) into two separate groups: bacteria & archaea. As to pre-Darwinian evolution and horizontal gene transfer, well the idea there is that before there were individual species, all the forms of life were so similar that there was massive intermixing of genetic information betwen living organisms such as we do with bits of electronic data today. This is incredible because it’s essentially akin to lizards appropriating wings from birds because they’re an effective way to avoid ground predators (excuse the hyperbole).

This is Gertrude (gerry) Brin and her grandson Colby, another great thinker. In reading Colby’s blog post from today, about his grandmother and life in general, I was reminded of what I think is Woese’s most powerful idea.

As an undergraduate student of Physics and Mathematics just starting to become interested in Neuroscience, and delighted by the fact that I could use my beloved equations to explain the behavior of biological systems, it none the less seemed to me that we would need an entirely new form of Mathematics, spurred by a paradigmatic shift in thinking, to really understand such complex systems as brains and indeed life in general. The best that I could do was to think of life as a temporary reduction in entropy. Perhaps you remember from some physics course that the universe is constantly tending towards an increasing state of disorder (entropy). This is true on a global (all-universe) scale, but smaller scale things such as life defy this. Life forms, temporarily, organize molecules. I’ve never been able to do much more with this idea, but I am fond of it and try to consider its ramifications once in a while.

One of the big problems we’ve had with understanding these very complex systems, is that all of our science has been reductionist for a very long time. We take something we don’t understand (a watch is one classic though not ideal example) and we open it up and look at all the pieces and how they fit and work together, and then we can understand in some way how the watch functions, but only in terms of the smaller pieces. I could say much much more about this, but I think Dr. Woese says it far better in the piece he wrote in Microbiology and Molecular Biology Reviews in 2004. I must also preface the following quote from that work by saying that I was turned on to ALL of this by Freeman Dyson’s fantastic article in the July 19th issue of the New York Review of Books (that link may expire fairly soon, I found it by googling the second paragraph of the text below), which also uses a substantial portion of the quote that follows.

“Let’s stop looking at the organism purely as a molecular machine. The machine metaphor certainly provides insights, but these come at the price of overlooking much of what biology is. Machines are not made of parts that continually turn over, renew. The organism is. Machines are stable and accurate because they are designed and built to be so. The stability of an organism lies in resilience, the homeostatic capacity to reestablish itself. While a machine is a mere collection of parts, some sort of “sense of the whole” inheres in the organism, a quality that becomes particularly apparent in phenomena such as regeneration in amphibians and certain invertebrates and in the homeorhesis exhibited by developing embryos.

If they are not machines, then what are organisms? A metaphor far more to my liking is this. Imagine a child playing in a woodland stream, poking a stick into an eddy in the flowing current, thereby disrupting it. But the eddy quickly reforms. The child disperses it again. Again it reforms, and the fascinating game goes on. There you have it! Organisms are resilient patterns in a turbulent flow—patterns in an energy flow. A simple flow metaphor, of course, fails to capture much of what the organism is. None of our representations of organism capture it in its entirety. But the flow metaphor does begin to show us the organism’s (and biology’s) essence. And it is becoming increasingly clear that to understand living systems in any deep sense, we must come to see them not materialistically, as machines, but as (stable) complex, dynamic organization.”

That last sentence just kills me, we must in some sense abandon our devotion to the material. For what is life about if not interaction.