I don't quite understand what you try to say. What kind of lenses are they going to supply for the course? Are you planning on buying your own lens or are you going to borrow the lenses for the course and then decide what you want to buy?
The Nikon D5000 and D60 don't have an autofocus motor built into the body, so cannot autofocus on some Nikon lenses. You should find out what lenses they are going to supply you and see if they are compatible. If you only do manual focus for the course, then this will not be an issue. The Nikon D90 does not have this autofocus compatibility problem but costs more.
Canon entry level D-SLRs do not have this autofocus compatibility issue either. Canon and Nikons are both very good, cannot honestly say that one is clearly superior to the other. Nikon is now actually slightly better in high ISO than Canon, it was the other way around several years ago. But the difference now is very small and not a practical issue to the photography.
If you are going to buy your own lens, then why can't you buy the Sony lenses? The Sony (formerly Minolta) lenses are very good, and the Carl Zeiss series have exceptional quality. There is usually little reason to switch the entire D-SLR system, except for those who always wonder whether the grass is really greener in the other lawn. And there is always the honeymoon or placebo effect, new is always much better.
Your biological photography course is taking photos of wildlife, right? I suppose you are not doing microscope photography on microscopic biological life forms. But if you are, then Nikon is actually excellent for microscope photography. Years ago I used Nikon microscope and SLR to take photos for scientific publications, and they are excellent. The Nikon system can capture brilliant vivid fluorescent photos of the mysterious looking microscopic world. There is actually an annual Nikon Small World photomicrography competition.
Hey, I already have a Sony A200 but unfortunately the course I want to do in Biological Photography in Nottingham cannot supply lenses etc for Sony, only Nikon or Canon.
I know there has always been a debate between Nikon and Canon SLRs and that some say Nikon are better for landscape and Canon better for portrait. I would be using the DSLR for taking photos of birds and animals out and about, so will have to look into getting my own 200 or 300mm lens before I start this course and for personal enjoyment, but I also was thinking about making taking photos at gigs and similar places. I have read that Canon are better at handling higher iso and so would be better in these kind of situations.
So I was wondering if anyone had any advice? The models I have been looking at are Nikon D5000 and D60 (if i can get my hands on one as they dont seem to be stocked in that many places) I could maybe stretch to the D90 but if I want to get a half decent lens then would rather spend the money on that rather than the body.
Canon EOS 450D and 500D, which is again a trade off between getting a cheaper model and a better lens etc, or geting a better body and getting a lens later.
If a similar thread is about let me know 
Thank you!!
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