OK, I'll bite. Why the hell would anyone want to go back to Perl? That is one disgusting mashup of a language.
I'm horrified by it daily when I have to use scripts written by older bioinformaticians. The best benefits I've heard are string processing speed (<3 you Ruby) and package management (hello Python, Ruby, R).
Sometimes Perl works really well. For example, just the other day I wrote a tokenizer in Perl after attempting to do the same in other languages, doesn't it look pretty?
What position? The position I see it in is a legacy language that used to run the internet and was the first language that really worked for bioinformatics. Is it different outside science?
Yes--people who have practical experience writing and maintaining code that has to be maintained tend to write maintainable code.
Scientists (and, in my experience, especially bioinformaticians) tend to make horrible, awful messes no matter how maintainable you think a language is. (You can hand them Inform 7 and it'll still end up looking like Fortran ate the csh manual and vomited all over an APL keyboard.)
Perl has always been designed from a get-things-done point of view, rather than adhering to a particular philosophy. It also has a huge number of well-maintained libraries available. These are both big plusses in some contexts.
(Not speaking for myself here, BTW. A decade ago I tried Python & never looked back.)
In your case, part of the problem may not be due so much to the language, as to the authors of those scripts you mention. People who have not studied software development as their primary discipline have typically not been exposed to ideas about good design, writing maintainable code, etc.
Yeah I agree the programmers whose code I'm reading are likely skewing the sample. But, as anecdata, when I moved to my current lab I requested that we not code in perl because people were writing unreadable, unmaintainable code. When we stiched to Ruby en masse, people really pulled it out of the bag and we now have really quite a nice codebase. I think the very strong community focus on standards in Ruby helped that along, as did the basic aesthetic of the language.
Yes, I know quite a few. In computational genomics in the south-east UK there's us (University of Cambridge Plant Sciences), Queen Mary University (Yannick Wurm's group), and The Sainsbury Lab at the John Innes Centre in Norwich (Dan Maclean's lab).
I'm horrified by it daily when I have to use scripts written by older bioinformaticians. The best benefits I've heard are string processing speed (<3 you Ruby) and package management (hello Python, Ruby, R).