What does our understanding of consciousness entail, exactly? On the surface it is simply scientific progress, a better understanding of our place in the world. But are these questions ones we want to answer? There seems to be something different about these questions compared to our inquiries about the universe.
Take, for example, free will: if we can map out the brain, perhaps we'll be able to understand whether free will is simply a romantic fiction. Do we want to know the answer to this, or is it better to leave this area unexplored? If it turns out that all our decisions can be reproduced by a sufficiently complex, deterministic model of the brain, can we go on blaming thieves and murderers for their wrongdoing?
And what about the sort of artificial intelligence that will arise from this project? If we can map the brain, will we be able to simulate it as well? If we can, the mind-body problem will take on a much more real edge: will this brain have desires, hopes, dreams? Will it have the ability to gain self-awareness? Would it have rights like you or I do? – it doesn't seem that having a body is an ethically important distinction.
Uncharted territory in science has always been unsettling: we are unsure of what we might find, but we press on into the unknown. But what happens when science changes our perception of ourselves, when it gains the ability to create suffering? Could it be that some questions about the brain are best left unexplored?
Sources
NYT (http://www.nytimes.com/2013/02/18/science/project-seeks-to-build-map-of-human-brain.html?pagewanted=all)
Economist (http://www.economist.com/news/science-and-technology/21573089-ambitious-project-map-brain-works-possibly-too-ambitious-hard)