The publication of ENCODE data raised substantial discussions. Clear, open, rational debate with access to data is the cornerstone of science. For the scientific details the ENCODE papers are totally open, and we have aimed for a high level of transparency e.g. a virtual machine to provide complete access to data and code.
There is an important discussion – which no doubt will continue throughout this decade – about the correspondence between reproducible biochemical events on the genomes, their downstream cellular and organismal functions, their selection patterns in evolution and their roles in disease. ENCODE provides a substantial new dataset for this discussion, not some definitive answer, and is part of a longer arc of science in this general area. I touch on this on my blog
There are also "meta" questions concerning the balance of "big" and "small" science, and how "big" science projects should be conducted. The Nature commentary I wrote focuses on this.
ENCODE also had the chance of making our results comprehensible to the general public: those who fund the work (the taxpayers) and those who may benefit from these discoveries in the future. To do this we needed to reach out to journalists and help them create engaging stories for their readers and viewers, not for the readers of Nature or Science. For me, the driving concern was to avoid over-hyping the medical applications, and to emphasize that ENCODE is providing a foundational resource akin to the human genome.
With hindsight, we could have used different terminology to convey the concepts, consequence and massive extent of genomic events we observed. (Note to self: one can be precise about definitions in paper or a scientific talk to scientists, but it’s far harder via the medium of everyday press, even to the same audience). I do think we got our point to the general public: that there is a staggering amount of activity in the genome, and that this opens up a lot of sophisticated and highly relevant scientific questions. There was a considerable amount of positive mainstream press, sometimes quite nuanced. Hindsight is a cruel and wonderful thing, and probably we could have achieved the same thing without generating this unneeded, confusing discussion on what we meant and how we said it.
I am tremendously proud of the way that the consortium worked together and created the resources that it did. The real measure of a foundational resource such as ENCODE is not the press reaction, nor the papers, but the use of its data by many scientists in the future.