I remember seeing a talk by a synthetic biologist, almost a decade ago. The biologist used a genetic algorithm to evolve an electronic circuit, something like this:

(source)

He then printed out the evolved circuit, brought it to his colleague in the electrical engineering department, and asked the engineer to analyze the circuit and figure out what it did.

“I refuse to analyze this circuit,” the colleague replied, “because it was not designed to be understandable by humans.” He has a point - that circuit is a big, opaque mess.

This, the biologist argued, is the root problem of biology: evolution builds things from random mutation, connecting things up without rhyme or reason, into one giant spaghetti tower. We can take it apart and look at all the pieces, we can simulate the whole thing and see what happens, but there’s no reason to expect any deeper understanding. Organisms did not evolve to be understandable by humans.

I used to agree with this position. I used to argue that there was no reason to expect human-intelligible structure inside biological organisms, or deep neural networks, or other systems not designed to be understandable. But over the next few years after that biologist’s talk, I changed my mind, and one major reason for the change is Uri Alon’s book An Introduction to Systems Biology: Design Principles of Biological Circuits.

Alon’s book is the ideal counterargument to the idea that organisms are inherently human-opaque: it directly demonstrates the human-understandable structures which comprise real biological systems. Right from the first page of the introduction:

… one can, in fact, formulate general laws that apply to biological networks. Because it has evolved to perform functions, biological circuitry is far from random or haphazard. ... Although evolution works by random tinkering, it converges again and again onto a defined set of circuit elements that obey general design principles.

The goal of this book is to highlight some of the design principles of biological systems... The main message is that biological systems contain an inherent simplicity. Although cells evolved to function and did not evolve to be comprehensible, simplifying principles make biological design understandable to us.

It’s hard to update one’s gut-level instinct that biology is a giant mess of spaghetti without seeing the structure first hand, so the goal of this post ...