Programmers want to embed domain terms everywhere. They look at scientific code and expect to see variables names containing "gravity," "velocity," etc.

Scientists need code to conform to the way they examine, solve, and communicate problems. I asked for an explanation of a particular function and was sent a PDF and was told to look at a certain page, where I found a sequence of formulas. All of the notation matched up, with the exception that superscripts and subscripts could not be distinguished in the code. To a programmer, the code looked like gibberish. To the scientists working on the code, it looked like a standard solution to a problem, or at least the best approximation that could be given in code.

You see the inverse problem when it comes to structuring code and projects: programmers see standard structures, expected and therefore transparent; scientists see gibberish. Scientists look at a directory called "tests" and think of a variety of possible meanings of the word, none of them what the programmer intended.