DE Shaw & Company takes its very smartest people (and a non-trivial portion of their profits) and puts them to work at DE Shaw Research, where they work on protein folding and other computational biology that could help cure cancer and HIV. I think that's a pretty worthwhile use of talent :-D
From what I was told, David Shaw is spending most of his time on the research group these days.
They ostensibly don't consider themselves a finance firm - they consider themselves a tech firm that will use their skills wherever they can to increase efficiency and make money.
I doubt it is fair to say they are ignoring software improvements. I saw Shaw talk about the machine architecture and he had a lot to say about balancing programmability for later software improvements vs. specialized computational resources. Also, it was his algorithmic improvements, the "neutral territory" methods, that were inspiration for the machine. Are NT methods still state of the art for molecular simulation?