The Low Quality of Scientific Code

http://techblog.bozho.net/?p=1423

The general feeling is that scientific libraries have mostly bad code. I will not point fingers, but there are too many freshman mistakes – not considering thread-safety, cryptic, ugly and/or stringly-typed APIs, lack of type-safety, poorly named variables and methods, choosing bad/slow serialization formats, [b]writing debug messages to System.err (or out)[/b], lack of documentation, lack of tests.

Can someone tell me what's wrong with that? Implementing a -dflag and writing all the debug messages to stderr is not something a freshman would do.