People love to feel right, and geeks in particular like to feel intelligent. Unfortunately, one popular way of feeling intelligent is to take a complex system which you don't understand, and paint it with a broad brush describing how inferior it is. Many people, on seeing or working with Perl code, become bewildered and frustrated. This occurs in every language. But somehow, for Perl, a strong meme has developed that blames the language rather than ignorance of it. This makes it easy for people to feel intelligent despite their earlier feelings of bewilderment, by simply blaming the language. It's worth noting that pretty much everyone but the most enlightened of humans engages in this behavior to some extent, with whatever our favorite whipping-boy language happens to be (e.g. Visual Basic, COBOL, APL).

In my view, it's important to try to rise above the bickering and not become upset. After all, they're making snarky comments to feel superior, so by becoming defensive you show weakness, making them think you've got something that needs defending, and reinforces their snarkiness. Perl does not need defending. You can just say "haters gonna hate" and let it be. Chances are they will doggedly defend their opinion no matter what you bring to the argument, because to concede their point is to reveal their own ignorance.

However, on the off chance they are actually willing to learn something, or can accept that the facts as they understand them are inaccurate, it does help to have correct information on hand:

• Readability, organization, ease of articulation are things that are both based on experience and taste. It's hard to argue these other than by saying that Perl is flexible enough to adapt to whatever style you personally find beautiful (unless you're allergic to sigils). One telling fact is that Ruby should receive roughly the same treatment, but doesn't. I think Ruby is quite beautiful, but it can be made opaque and terse just like Perl. Even so, people love to hate Perl more, so it's not just a matter of syntax.
• On the matter of Perl being kept alive only by bio data in text files, just ask for data. It's hard to measure things like how popular a language is, and every measure has some flaw, but just about any site you can find that attempts to measure this will rank Perl in the top 10, and consider it a mainstream language. For example, tiobe, langpop, or even GitHub's Top Languages. It would be hard to imagine that all those Perl jobs and projects are supported by the bio information market.