I didn't think the speaker was very sharp, but I didn't challenge him on the Perl since the audience was (ugh) lacking in Perl experience and laughed at his Perl jokes. Well, he was missing other questions too (he couldn't answer my question about how fiting a model to data in a biased way might violate the scientific method of hypothesis testing through data collection). This java talk was mostly in regard to the "caBIG" (cancer bioinformatics grid -- essentially web services and not technically a distributed computing system) and he was discussing how they were replacing a bunch of random things with Java. The part that didn't drive is that good grids are language agnostic. He also stated there bascially was no room for more Comp. Sci folks in the field now, which I also didn't believe. In fact, I left a little early to get some food -- he was just infuriating me with his language bias :)

This would be another meditation, I guess, but is bioinformatics actually open to new programmers (compared with "pure software"), particularly in Perl? And how much emphasis is actually placed on biology experience? I was expecting tremendous love of Perl in that room, and what I saw instead was a tremendous love of Java for the wrong reasons.

Ex: Java w/ matlab. Now there is a cast-heavy bloated syntax I don't want to have to deal with when doing math!

I don't think times are changing, it's just that some folks have this bad taste in their mouths about Perl, and well...some people are just stupid!