You reference Gingko, but that company is (in my opinion) uniquely viable in terms of YC biotech investments.
Of course, my perspective is based on media reports (famously unreliable), by public information, and by my own experience in biotech. I would love to be completely wrong, and I could easily be completely wrong since I don't have access to the information that you do. Also, maybe an outside perspective is what is needed in biotech—good things happen when smart people from other disciplines cross-pollenate. Also, my own startup is not yet successful, so I criticize from within a lovely glass house surrounded by stones. That said, based on what is public, I don't have confidence in YC's biotech investments. I am hesitant to even consider applying, given with what is publicly available.
I don't think this is an appropriate forum to be specific with criticisms, nor do I wish to be a "negative Nancy" with YC's new push—if YC could do a fraction of what it did in software in the biotech area, it'd be amazing. I would however like to offer one particular outsider's perspective.