Great Topic!!
1. Well, honestly I'm a little insecure that I haven't committed to a particular question yet. I've applied to a lot of umbrella programs to allow for some rotations to figure my interests out a little better. That said, there are definitely questions and topics that I'm interested in. Here's a couple:
Exploring the ways that bacterial populations with identical genotypes can demonstrate phenotypic diversity through stochastic switching really intrigues me, since it challenges the clockwork view of biology where genes have a very specific expression A->B, and instead suggests a fuzzier reality where genes code for a 'cloud' of phenotypes, mediated by epigenetics, the environment, and randomness itself.
Figuring out an in vitro protocol for efficient directed evolution of proteins is another question I think is really cool. If we could figure this out, you could essentially have an automated drug-design machine. Other advantages would be that you could design protocols for multi-parametric optimization and select against unwanted interactions/pH/temp/etc.
In addition to these I have broad interests in exploring protein structure-function relationships and cell signaling cascades
2.) What do you think is the biggest challenge facing researchers today (i.e. open publication vs. journals like Nature; securing funding, lack of scientific literacy, etc.)
I think the the journal pay-wall is a huge issue. How can we kindle the imaginations of the next generation of scientists if they can't learn about the research being done today? I can't say how frustrating it was trying to research potential PI's and programs and constantly running into dead ends trying to look up papers. If science continues to cloister itself inside these prestigious academic clearinghouses it risks calcifying itself and further separating itself from the public at large.
In this country how can we hope to have strong government support for research if scientists don't make their case to the greater public for the value of the research they do? Currently it seems like the scientific community has let the ideologues on the right define science, and the recent headline showing declining Republican confidence in evolution should be an another alarm bell that we have to take action, or risk watching a slow, gradual decline of funding and research productivity.