As an academic your currency is your reputation, and how often your papers get cited (well assuming they aren't citing you for making up data). The inevitable result of this are battles of ideas being fought out at conferences, in special issues of journals and in review articles. If you discover something interesting and the mechanisms are not clearly visible (as they usually are not - especially in something like psychology!) other scientists begin to attack you - especially if your new idea challenges theirs!
In the science of the brain there are a few debates that immediately come to mind. The first is the debate on neurogenesis. It was originally believed that once all the neurons were formed in the brain that was it. All they could do was slowly die off. In the late 90s Elizabeth Gould discovered that this was untrue, and in fact the hippocampus showed the growth of new neurons. This angered established researchers, especially Rakic. In the last few years the debate has dwindled off as most people have come to accept the results of Gould.
Another debate closer to some of my own research is the debate between a modular view of the brain and a distributed representation. This has primarily been played out between Nancy Kanwisher and James Haxby in their papers on the representation of objects, faces and scenes in the brain. There are some very compelling reasons to believe either one of these opinions (and of course -like always- it's probably a mix of the two).
When I look outside my field I only really see the obvious debates played out in the media, like the hobbit and pluto debates. I would love to know what the other debates are that don't quite make it to the pages of USA Today.
What are the big nasty debates in your field?
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Back in the 1960, the bloody debate was between the 'endogenous' and 'exogenous' school: i.e., if the circadian rhythms are generated by the organims or responding to some mysterious Factor X. Frank Brown, the leader of the exogenous school finally lost, but not without putting up a huge fight.
In the late 1990s and early 2000s, there were two groups trying to figure out which molecule was the non-visual pigment used by the retinal ganglion in light entrainment of the clock. The 'melanopsin' mafia ultimately won over the 'cryptochrome' mafia, but the leader of the losing side, Aziz Sankar, wrote a big review in which he accepted the defeat and is continuing to work within the new paradigm. The whole fight really sped up the work and produced some exciting research.
The up-and-coming fight (brewing at the edges right now) is for the exact role of core clock genes in generation of circadian rhythms, i.e., what is the role of the rest of the cell.
An oldie but a goodie in taxonomy is the use of identity (apomorphies) versus similarity (niches and the like) in classifying organisms - are birds Aves because they all resemble each other in some manner, or because they share homologies that are not found in other groups? In short, Gradism versus Cladism. Even now, 30 yars after these debates began, it is still a hot button topic, because people tend to fall back on similarity-based classification by default.
Solar Physics was never very vicious. There was/is a bit of tension over whether the corona is heated by waves or reconnection. Personally I doubt that you can really distinguish between the two - take a really inhomogeneous magnetic field, shake it around with some turbulence, some magic happens, and magnetic-field energy gets turned into kinetic energy and radiation. What's the problem?
The only time things ever got really nasty was when my solar colleagues tried to muscle in on climate science with ideas about long-term solar effects on climate. Big stakes. Big turf wars.
vi vs. emacs?
One of the big debates in behavioral neuroscience is over whether hippocampal encoding is explicitly spatial or whether there are a lot of other things that get thrown in.
It's a similar old guard vs. new youngsters conflict. The canonical view is represented by O'Keefe and Nadel in their work "The Hippocampus as a Cognitive Map," 1978. Several problems with this theory have emerged though, and the old guard keeps trying to resolve them in terms of the spatial map.
Anyway, I doubt there are shouting matches at scientific meetings about it, but it is something we all like to argue about.
The genetics of donkey colors. HAH--beat that. The American Donkey and Mule Society has been doing research on this for years now--and a couple of morons who don't know from crap about genetics keep publishing articles giving wrong information and calling us all sorts of names---how's that for an odd flap of the scientific kind?
One big honking debate that's been going for years, and is still pretty relevant: is Long-Term Potentiation the mechanism to explain behavioural learning and memory?
There has been so much research on LTP that it's easy to just assume it's *the* mechanism - but how do you explain papers that show AMPA receptor (GluR1) knock-out mice, who can't show LTP, can perform fine in spatial memory tasks?
Very interesting stuff - also a recent Science 2006 which shows learning in fact induces LTP.