Biology and Physical Factors #3: Clocks

The circadian rhythm. It’s a natural oscillation within the bodies of living things with a periodicity of a day – 24 hours (It’s why we experience jet lag). What acts as this clock in living things? Raghuveer Parthasarathy explains the concept in So Simple a Beginning:

“The simplest possible oscillator is a gene that represses itself.”

This sounds crazy at first: once repressed, how would it activate itself again?

“The answer lies in the fact that both expression and repression take time.”

 

He elaborates. But first, a quick recap from an earlier blog: DNA has the gene to create the protein, and promoter and repressor sites before it. When read, the gene produces the protein (red blob) which attaches itself to the repressor site, thus physically blocking any RNA attempts to read the gene. 

Coming back to the oscillator. All the above steps (creating the protein, then for the protein to “meander and find the promoter region”) take time. Ok, so it took time. But isn’t the gene now permanently blocked? Where is the cyclical element in all this?

 

The answer is another physical characteristic: proteins degrade over time. Once the red blob degrades, there is nothing to block the gene from being read and for the cycle to repeat itself. Since every step takes time, you have a clock.

 

In real life though, no single gene mechanism like this will have a predictable exact frequency. It would be a very low quality/precision clock. But the basic concept is what we were expected to learn here. Extend this to involve a bunch of genes “connected by intertwined feedback loops”, and the resulting cycle time becomes predictable. Ta da, we have a good quality clock.

 

By similar principles, you could have a gene A that expresses itself only if (1) proteins B and C are present; (2) D but not E is present; (3) F or G is present. Notice the highlighted words above. Once and, or, not operators exist, you have a computer or a computing device!

 

Notice something? The computer and clock are entirely based on physical principles, the organism doesn’t need a brain for any of this. Which is why these are considered fundamental principles of all life forms.