On 2015 Nov 12, Leonid Teytelman commented:

I think there are harder questions underneath this discussion. Is funding ENCODE-like projects a good idea? If so, which ones?

I agree with Sean Eddy that the misleading hype in the presentation of the ENCODE results was deplorable. I also agree that it is critical to develop common resources, datasets, and infrastructure. I would be crazy to argue that the enormous effort to sequence the human genome wasn't worth the money.

However, just because the human genome sequencing was a great idea, that doesn't necessarily mean all Big Science efforts are good ideas. The difficult question here is whether ENCODE itself was in fact a good idea. Was it a good use of the already over-stretched NIH budget? What else could we have done with that $200m? Were the resulting datasets enabling in a transformative way? If not, could funding for dedicated method and technology development on a fraction of the cost, have served the community better?

Michael Eisen asked these questions in Blinded by Big Science: The lesson I learned from ENCODE is that projects like ENCODE are not a good idea. Very hard to answer this, but if we don't, we may end up wasting a lot of money in the years to come.

On 2015 Nov 11, Nikolai Slavov commented:

This is a very insightful essay that presents the different sides in a balanced and reasonable framework. I agree that much of the controversy and tension arise from misrepresentation and not recognizing large-scale projects for what they really are. Such dissonance, I believe, is rooted in the politics of credit attribution and budget justification. The incentives for exaggeration are strong. Until these incentives are counterbalanced, we will continue to have problems with exaggeration, misrepresentation, and failure to recognize and credit large-scale projects for what they really are.

On 2015 Nov 11, Nikolai Slavov commented:

This is a very insightful essay that presents the different sides in a balanced and reasonable framework. I agree that much of the controversy and tension arise from misrepresentation and not recognizing large-scale projects for what they really are. Such dissonance, I believe, is rooted in the politics of credit attribution and budget justification. The incentives for exaggeration are strong. Until these incentives are counterbalanced, we will continue to have problems with exaggeration, misrepresentation, and failure to recognize and credit large-scale projects for what they really are.