The Futile Cycle

PLoS ONE is out, and it has a cool systems biology paper.

One of most interesting things about biology is how organisms live in different environments. Bacteria, for example, can survive the most remarkable situations, from the high heat conditions of Yellowstone’s sulphur springs to radiation doses that can shred their genome to pieces. Mostly, these abilities to survive have been evolved specifically; there are genes and parts of the genome arranged in very specific ways to cope with the lack of, say, sunlight and oxygen at the bottom of the ocean, or even just the lack of nutrients. Often, these abilities of the cells are invoked by a relay of molecular signals. The presence of lactose causes a switch to be triggered in a bacterium, leading to the production of lactase, which digests lactose. Sophisticated molecular switches and circuits in cells allow for such responses to the environment, the same way you start shivering when you’re cold. Your circuits are designed so that you don’t shiver when it’s warm, only when it’s cold.

But evolution can’t anticipate everything that could possibly happen; all organisms can do is change in retrospect. There might, however, be a mechanism that allows for organisms to “cope” with the new environment by simply adapting to the situation as best as can be allowed by their genome. This ensures that the species has the chance to evolve to the new environment; after all, if organisms were wiped out by the first unanticipated situation, it would be pretty hard to have evolution.

Some researchers from Japan tried to see if, absent any specific set of detectors and signals, cells might not somehow be able to change the way they behave to act optimally in different circumstances. Thus, for example, cells might code enzymes to make glutamine when they aren’t provided any, or to make folate when they don’t have that. They engineered bacteria with new, synthetic genes that were isolated from the rest of the molecular signaling circuitry, so that there wouldn’t be any specific way a bacterium could “know” that there wasn’t any glutamine or folate. Yet, they found that even without a specific logical circuit that said, “no glutamine, make glutamine” or “no folate, make folate”, that’s what the cells did! Somehow, the cells were able to make a decision to choose the optimal thing to do even in the absence of a specific signal to do so.

The explanation is that cells making the wrong decision stop growing as fast, and then become subject to fluctuations in their gene expression patterns. Eventually, the noise would just become so overwhelming dominant in the cell that cells will spontaneously switch over to the other, “better” phenotype. On the other hand, cells that make the right decision don’t have such fluctuations, and will grow fast and have a prosperous existence. This is a pretty neat thing to highlight. Makes a lot of sense in retrospect, but the insight is very neat. It means that we might not need to always have specifically evolved mechanisms to deal with all circumstances. Crude decision-making machinery is built into the way we work via chemistry and physics, giving us the bare means to survive and eventually evolve more efficient ways of dealing with those harsh circumstances, if we need to. In addition, our evolution might involve a new pathway simply being snapped onto this existing framework, preselecting us to, say, make lactase or have dark skin, instead of waiting for our environmental stresses to force our cells to start making that decision under duress.