I will probably have a great deal more to say about this in the coming days/month/years, but here are a few very quick points I want to make:
1. I am broadly in favor of big public investments in basic science, and not only because my livelihood depends on them. I think it is good policy. Unforeseen benefits tend to accrue from asking fundamental questions that don't have immediately obvious application. Examples include the device on which you read these words and most cancer drugs. There are many, many others.
2. That being said, I am less of a fan of congress or the president setting strategic priorities for research, for precisely the same reason. Most of the publicly-funded science done in this country in the last half-century has been investigator-initiated. It's a "bottom-up" model and I think that on balance it has worked exceedingly well. Science funding is largely zero-sum, both in terms of the money itself, and the time and creative energy that individual scientists put into developing their projects. A "top-down" approach diverts monetary and intellectual resources into what the politicians decide is important and away from the scientists themselves think is worth pursuing.
3. The comparisons to the Human Genome Project are tenuous. The HGP had a well-defined endpoint. We knew what the data would be, and we knew when we would be "done". Getting there was simply a matter of brute force. The brain is infinitely more complex than "ATACGGATTACG ATTACCGATAG CGGCTAGCCTAG, etc."
4. $100 million isn't as much as you probably think it is.
5. Much of what the BRAIN Initiative purports to accomplish is the subject of research already underway by very capable investigators. A cynic might be tempted to point out that this smacks of politicians (and particularly the President) trying to swoop in and take some credit for whatever happens next (and was going to happen anyway.)