# AlphaFold: A New Kind of Science

Last night I was watching an interesting video on AlphaFold, which is basically using modern deep learning techniques to solve a longstanding problem in molecular biology, determining how a protein folds based on its sequence.

One part that is interesting is that they develop an intermediate structure which looks very “vectory” - a matrix of how close each part of the molecule is to each other part. In some sense this is redundant; you are storing a position for each pair instead of a single position per component. But it means if you screw up one part of the output you don’t automatically screw up all the other parts. It is more “local” in a sense.

The other part that is interesting to me is that it is an approach towards solving the “middle size of problem” that I mentioned in my previous post on the “theory of everything”. How should we interpret this?

## The Lottery Ticket Hypothesis

One way of understanding modern machine learning is the Lottery Ticket Hypothesis. Roughly, the lottery ticket hypothesis says that for problems that deep learning works well on, there exists an algorithm that solves the problem, and you know how to make a large deep network that is shaped in a way that is similar to this solution, so probably there is some subset of the randomly initialized deep network that happens to be close to the solution. The process of training a deep learner can then be thought of as searching for this subnetwork that happens to contain the answer.

The lottery ticket hypothesis is not necessarily true. For example, the training process might get closer and closer to a decent answer by assembling the algorithm bit by bit, rather than discovering an algorithm that already is mostly there at initialization time. It’s probably different for different problems. But it’s a useful approximate way of thinking about it. Deep learning is a search through the space of possible formulas, looking for one that solves the problem.

## A New Kind Of Science

Here I’m talking about the generally-poorly-regarded book that Stephen Wolfram quasi-self-published 20 years ago. One way of interpreting the thesis here is that we could discover the laws of physics by searching through the space of all small computer programs.

In a sense, this is exactly what AlphaFold is doing! It isn’t using Mathematica, and it isn’t using any of Wolfram’s preferred algorithms like a linear search over cellular automata rules, and it isn’t aiming at sub-quantum-mechanics laws of physics. Okay, that’s a lot of things that are different. But the fundamental idea of discovering laws of science by doing an exhaustive computer search, that part is what AlphaFold is doing.

## The “Real” Laws of Physics

You might say that AlphaFold isn’t looking for the *real* laws of
physics. It isn’t even pretending to model every electron and use those
low-level laws of physics to calculate protein structure. It’s just
looking for an approximation that works at the level we want to
calculate at.

But is any science actually looking for the *real* laws? Or just laws
that are close enough for any practical use?
Differential calculus is great for physics because it is a great
approximation tool. Any function that is “continuous enough” can be
approximated locally by a matrix, you can approximate this matrix with
calculus, and then you can get pretty good answers. That’s why we like
using it to solve problems. We have never observed a true “real
number” in nature (because real numbers, rigorously defined, are based
on infinite sets).

We have spent a long time lamenting that we cannot get quantum mechanics and gravity to line up. Well, that doesn’t really matter. What we should be lamenting is that neither quantum mechanics nor gravity provides a useful approximation for these intermediate-size problems like how to construct a useful machine out of 1000 atoms. Tools like AlphaFold seem like they could get us there.