When I first read Dan Graur's paper, which heavily criticized the scientists involved in the ENCODE project and the media hype associated with the September 2012 ENCODE publications, I also thought that parts of the Graur paper with funny, but that its tone was too sarcastic. This sarcasm and snide comments ridiculing the ENCODE scientists were so distracting that it became difficult to focus on the actual scientific criticism in the paper. During a Twitter conversation, I noted how other scientists had experienced similar reactions.

The Guardian also ran an interview in which Dan Graur was quoted as saying "This is not the work of scientists. This is the work of a group of badly trained technicians." Jonathan Eisen correctly pointed out that this is completely wrong and unprofessional.

Dan Graur suggests that he was misquoted (and refers to how his name is spelled), but did not clarify what he had actually said about the ENCODE scientists. His reference to politeness not being noticed is quite ironic, because Graur's paper accuses the ENCODE project scientists of too much attention-seeking hype, but he himself falls into that same trap.

I think Mick Watson and Michael Eisen summed it up nicely, when they pointed out that one can disagree scientifically and be vocal, but one does not need to resort to name-calling. Asking for basic professional respect and courtesy is not the same as asking someone to be "nice and cuddly". 

We than discussed whether sarcasm should always be absent from scientific papers, even if they are written in an essay or commentary style.