Keep some space for ads if you want; I don't give a shit and I realize you've got bills to pay. I have the option of turning them off, but I don't because I like the site.
That said, information density is important. If you bump the font size and line spacing or significantly drop the comments column width, we can't read the comments or their surrounding comments' context. There'd better be a lot of lines before I have to "click for more", and I never want to have to "click for more" on the front page. This might mean reducing the size of those terrible banner images.
We need to be able to easily see the information on posts and navigate the discussion. Links to parent posts are absolutely necessary, current score, subject, and at least a preview of the post content if it's collapsed. Other useful information provided that I'd like to see stay prominent includes the username and UID number of poster. It was tough for me to get used to the collapsed/non-collapsed system with the last redesign, but it actually ended up giving a lot of information in a tight space and generally reserved more for better comments.
As it currently stands, the two problems cited above alone will kill the discussion oriented nature of Slashdot, users will desert, and revenue will tank.
Slashdot has never been a paragon of beauty OR usability, but this redesign really kills the discussion; I even gave it a shot.
Question for Mr. Mims: what was it like getting a completely handwritten book published? Did you approach RadioShack with the idea? Given all the modern publication options (self-pub, iBooks, etc.) and software to help, how would you go about it today? (I know, that's three questions...)
As I was browsing it, I realized that a single comment like the parent in the current format, that takes up less than a third of my browser viewport (so I can see the flow of conversation around it), takes up over two thirds in the beta format. I feel like "the medium is the message" applies here, or at least, the medium influences the message -- multi-paragraph comments are more common on slashdot than other sites, but if they want to discourage that kind of dialogue, this is a great way to do it.
That mechanism has already failed. Modern scientific research is so expensive that even tenured professors have to carter to the whims of funding agencies (NSF, NIH, etc.) in order to continue working. Intellectually autonomy doesn't keep the rat colony alive, pay the electric bill for servers or purchase chemical reagents.
I'm glad somebody said this. Though I'm sure it's always served both roles, another thought about modern tenure (in my opinion as a young academic) is that it's much less about guaranteeing academic freedom, and much more about managing hiring in the face of an ever growing crowd of PhDs. A department might hire a few adjuncts to teach and put 4 or 5 good researchers on the the tenure track, with what seems like a full expectation of granting tenure to one (or zero, if they feel like rolling the dice again) and firing the rest. Tenure is a beautiful ideal, but functionally it's a back-breaking 5-year interview, with a lot of benefit gained for the university in the meantime. And in the end, those that make it through have been selected based on funding ability weighted over any other metric.
I don't blame them for this really, there are many more PhDs than tenure slots and a maddening culture of anything-but-tenure as failure. I'll admit that I've only been in this game for a few years so I might be completely naive (I'm also lucky, being non-tenure track and on hard money), and I don't know how it works in the humanities. Nevertheless, I have a feeling that the concept of tenure is serving university endowments more and more and research and education less and less.
On the positive side, there are many good "teaching" universities and community colleges out there picking up the slack on the education side at least.
I'm actually really looking forward to a vast reduction in dataset size and cost in the life sciences, so we can make use of and design better algorithmic methods and get back to answering questions. That's up to the engineers designing the sequencing machines though..
One thing I can suggest as you prepare is to get your personal life together. I went through a divorce during my phd, and it definitely didn't help the process: be aware that doing a PhD can stress your personal relationships and take some time to work that out with your significant other or others you're close with, if you can. It's a time when you will be stressing hard without a whole lot to show for it, monetarily or otherwise. Build a support network with friends and family, and via counseling services at your university if necessary (my "grad student support group" helped tremendously with my own difficulties, both personally and professionally).
Oh, and since you're going into biological sciences, a great way to prepare for an awesome career is to learn programming, motherfucker. (I suggest python.) The job market is tough for life sciences in general these days, but curiously not if they can program and work the command line...