It is interesting to consider this issue from the vantage point of human social behavior. We people are basically flock animals, most of us tend to do what others in our tribe do since we fear be left alone.

If some software, tool or whatever is what prevails in your university/workplace/community then it is very likely that you will end up doing/using just the same as others do/use. If there are better or cooler alternatives it is really a secondary issue, as peer pressure is a very important factor in humans and changing behavior requires a crisis or a long term open mindedness and commitment not usually seen in humans. Have you heard any of these?: Why change? Perl? What? Python/R/Matlab are what we use here and they are perfectly OK for our work!

Most scientists like me either have no idea of what Perl is, or think it is just a text parser. There is nothing wrong with Perl or with these people, it is just that things became this way because the way we humans are. There is nothing that R or Python can do that Perl Data Language (PDL) cannot do. It is just that PDL did not catch on a large scale in the science community. The system is now locked in a different mode.

In my opinion, there is nothing sad here, just a consequence of how we humans are. As for me, I love Perl and I think it is very useful. I do use R when I have to talk to others, but do a lot of my work in PDL, and I am more than fine with it!