I'm not a professor, but I started my career as an industrial engineering grad (MS, not PhD) who was writing code to build and solve a linear program for a supp

I'm not a professor, but I started my career as an industrial engineering grad (MS, not PhD) who was writing code to build and solve a linear program for a supply chain application. It was definitely one of those programs that does this, than that, the sometimes the other thing, and it went on forever. I had trouble understanding it myself. I didn't end up rewriting it because, well, startups. The whole thing went kaput, and nah, didn't have much to do with the code. I would agree with you that these programs are more understandable to someone with expertise, and that can be why it's so hard to refactor them. It's difficult to become this expert in a branch of science and also take the time to learn good software design and programming practices. But overall, I'd say that these programs could become vastly more manageable and easier to understand through better programming practices.