I am making the same decision for my daughter, who is also planning to major in either biology or chemistry. I am a science/engineering faculty at a major research university and use a 15" rMBP (Core i7, 768 GB SSD, 16 GB memory) as my computer for everything (I do have access to a cluster at work for larger computational jobs). I previously had two generations of 13" MBP that I used in the same way. I carry the computer to work every day and typically used it plugged into large (24" and 30" monitors). I also carry it when I travel to conferences and vacations. I really like having all my stuff with me all the time. I absolutely love the 15" rMBP. It is without reservation the best computer I have every had. The large memory is very nice if I have to run Windows in a VM, but I don't think it is otherwise necessary for normal scientific/academic tasks. I checked the memory usage and there is currently 10.5 GB used, but 2.75 GB is Inactive, 5.34 GB is Active, and 2.8 GB is Wired. It has been up 4 days and I am currently running Word, Excel, PowerPoint, Outlook, Calendar, and Terminal. I had 8 GB in my previous MBP and that was fine too. I had 4 GB in the one before that, which didn't work well for VMs or even when I had a lot of stuff running that I was switching back and forth between. I bought the 15" before the 13" came out. If I had to do it again I think I would get the 13" as I like that size better for portability and the ability to use it on airplanes (a 15" display is a bit crunched when the person in front tilts their seat back). I frankly don't think I would miss the discrete graphics or quad core, though the 16 GB is nice for occasions where I run a VM and switch back and forth between apps.
In terms of the form factor, I will almost certainly get either a 13" rMBP or 13" MBA. I eliminated the 15" largely because of cost and because I simply don't think she would need the extra cores or screen size. I am pretty sure we won't go with the 13" MBP because SSDs are really nice, optical disks are not that necessary, it weights more, and it doesn't really cost that much less than an rMBP once you add the SSD. Another reason for not considerin the 15" is that I have found you have to be careful that it isn't running on the discrete graphics when on battery, or the battery life is not very good. (Some programs, like XQuartz, automatically turn on the discrete graphics). My daughter has had a 13" unibody MB for high school and is quite happy with that form factor and screen size. I have also found that the Retina display makes things feel a lot bigger since you can use smaller fonts and still see things very well. I have an old 19" display that I will let her take to college if she wants it. However, she says she doesn't need it. I think the screen on the 11" MBA is way too small.
So, the decision comes down to the 13" rMBP or 13" MBA. Ultimately I will probably let her make the decision after a trip to the Apple Store. The MBA is a bit lighter, but I don't think it is enough to make a noticeable difference, especially given the immense backpack she was used to carrying around in high school. The extra battery life on the new MBA would be nice, but I think the life on the 13" rMBP is plenty long enough for college use. I think I would miss the extra performance on the Air, but am not sure that she would. I frankly think the Retina display is so nice that it trumps portability and battery life, but will let her decide. My only reluctance about buying the 13" rMBP is timing: I really wish the Haswell based ones were out.
I will definitely get her 8 GB of memory and a 256 GB SSD on either.
), I still have all of my important files backed up. Dropbox makes it effortless and is worth it.