Criticizing ENCODE -- who is your target audience?

First, a few links to commentaries on the latest article criticzing the ENCODE hype:

Biomickwatson’s Ridiculous Criticism of ENCODE Critics « Homologus

Spanking #ENCODE | The OpenHelix Blog

So I take it you aren’t happy with ENCODE… | The Finch and Pea

Scientists attacked over claim that 'junk DNA' is vital to life | Science | The Observer @ The Guardian

ENCODE, Apple Maps and function: Why definitions matter | The Curious Wavefunction, Scientific American Blog Network

Dear ENCODE…. | opiniomics

ENCODE gets a public reaming » Pharyngula

Graur et al. to ENCODE: Zing! « Genomicron

The ENCODE Controversy And Professionalism In Science | Scilogs

To me, one aspect of the ENCODE project that has been neglected is the moral hazard it enforces on the publication process. The concerted publication of 30 papers in practice prevents an objective peer review: 1) the publication is guaranteed; 2) the reviewer will feel responsible for the delay in case of honest concerns; 3) it is hard to find good reviewers if 'everybody' in the field is a coauthor (therefore you might have endogamic or non-expert reviewing). It also weakens the interpretation (value) of an academic article, shifting the importance of a discovery from the article itself to the number of articles. We should be struggling to create better measures of 'impact', and not stimulating the abuse of the current ones.

But another aspect of this discussion that is particularly relevant to me is the problem of the tone.

Lior Pachter on FB points out he deposited paper on 12/2012 critiquing ENCODE arxiv.org/abs/1212.3076 but got little response w/o snark
— Jonathan Eisen (@phylogenomics) February 24, 2013

It seems that other polite people have trashed ENCODE: ncbi.nlm.nih.gov/pubmed/23268340. Politeness is not always noticed.— Dan Graur (@DanGraur) February 24, 2013

Critical analyses of high-profile works never receive the same attention -- they are seldomly published in the same venues and are not always easy to follow. Grand conclusions are easier to grasp than more boring details and conditions. I have no answer to that -- while I do prefer a calm and objective response, I have first-hand experience that cordial arguments are more easily dismissed. And some times what is perceived as a personal attack by some is simply an objective statement that happens to put the criticized researchers in a less-than-comfortable position. In the end it is a matter of choice between convincing the opponent or the audience.

Oh, and there's also another element that we should take into account when criticizing other people's work: how well we have our backs covered. I cannot pretend that there are not vindictive professors out there that will not hesitate in painting us with the scarlet letter at the smallest sign of threat. Many scientists are miserably gregarious.

 

Update 2013.04.11: There's a longer comment from Dan Graur that expands on some of my observations.