I don't disagree that badly-written scientific code exists (both in academia and in the industry), but I want to point out a couple of things for people who have only a software engineering background.

1. Keep in mind that most scientific code for numerical analysis, being based in mathematics, follows the convention for using algebraic symbols, e.g. even in physics, we write

F=m*a

instead of the wordy version, which we overcame a couple of centuries ago. So using shortened variable names [1] comes from that background, and using longer names as in Java-world seems like a regression.

2. Writing code like [2]

    Ax_1 += Bx_1 + Cx_1 # Add Bx_1 to Cx_1
    Ax_2 += Bx_2 + Cx_2 # Same thing, but for Ax_2
    Ax_3 += Bx_3 + Cx_3 # "
    Ay_1 += By_1 + Cy_1 # "

is known as loop unrolling [3,4] and is used for optimization.

[1] https://news.ycombinator.com/item?id=10539078

[2] https://news.ycombinator.com/item?id=10540446

[3] https://en.wikipedia.org/wiki/Loop_unrolling

[4] http://stackoverflow.com/questions/2349211/when-if-ever-is-l...