As an addendum to Jason’s earlier post, here’s a story of scientific discourse gone horribly wrong. It would be funny if it wasn’t so.. somehow really not funny.
How to Publish a Scientific Comment in 123 Easy Steps http://d.scribd.com/ScribdViewer.swf?document_id=18773744&access_key=key-1md5zdvu8wpysalhsmqg&page=1&version=1&viewMode=
Via björn.brembs.blog.
Mendeley Blog 
Fantastic post. I laughed, I cried, it was better than Cats- and it was painfully true.
I agree with all of your suggestions for improving the system, although I’m more on the side of going away from so-called “peer” review entirely.
And I disagree with potential improvement suggestion #2.
#2 makes sense from your point of view, as the person who has precedent. However, the person who has precedence is not always correct. Nor are they always scrupulous. The person who has precedent is often powerful, which makes this scenario very dangerous for younger scientists.
So the equation might look something like this:
predecent + lack of scruples + power = my paper is consigned to oblivion, just because it came after yours
Does that seem fair to you?
I agree that the way the journal handled this situation is deplorable. But I’d propose a more drastic solution: we should boycott these journals, and ridicule them as you have done so well here.
Editors have too much power, and as yours openly admitted, not enough expertise. Why we agree to put our careers and the fate of science in the hands of these people is beyond logic, so far as I can see.
Thank you, Sam!
But I’m afraid I can’t take the credit for this incredible story – it was lived and suffered through by Rick Trebino (http://www.physics.gatech.edu/people/faculty/rtrebino.html).
The weirdest thing I can claim to have experienced is this: After my very first paper was published in Media, Culture & Society (a Sage Publications journal), I asked the journal if I could get a PDF copy of the proofed & layouted final version. They refused, so I had to buy a copy of my own article.
As for the suggestions: Though I find #2 very intriguing, I would disagree with it for the very same reason as you. It’s unfortunate, but as was so impressively described in Lee Smolin’s The Trouble with Physics (http://www.thetroublewithphysics.com), you just can’t ignore the sociological aspects and power dynamics in any community – scientific or other.
Oh, jesus…
I too think the publication process is badly broken. Also money-wise: First, public money is spent on financing the research, then, sometimes, public money is spent for publishing the research, and third, public money is again spent to access that research via the libraries…
Why not publishing everything on a free webserver and then public money is used to finance an “Institute for Reproduction of Scientific Results” that independently verifies the most important articles published on the free webserver and attributes an “these results have been independently reproduced” tag on the article?
This would also urge the scientists to add a very detailed methods chapter, something that more and more journals consider less important but in fact is extremely useful for scientists.