In President Obama's most recent State of the Union address, he mentioned neuroscience three times. One was a stated commitment to ensure top-quality mental healthcare for returning soldiers. One was the reference to the effect of early education on child learning and performance (I know it's a stretch, but I'm counting it. They aren't learning with their livers.) And third was a reference to brain mapping that could "unlock the answers to Alzheimer’s". A short time later, the President proposed a new, ambitious federal Brain Activity Map project. You may question many of the President's positions, but he's clearly pro-brain, and that's good.
The Brain Activity Map would be unique among brain mapping projects already underway. The idea came from a 2012 paper published in the journal Neuron by Alivisatos et. al. (including recent Science2.0 interviewee George Church). The paper suggests that technologies are theoretically possible that could examine the activity of hundreds of thousands of active neurons at a time. We don't have those technologies now, which means that our ability to resolve the activity of large-scale brain circuits is really puny. Their paper wasn't as much about neuroscience then it was about physics and bioengineering. They called for new tools, and the President would like to buy them. (For more info, see here, here and here)

Now, putting aside the fact that whether or not such a program gets off the ground in the near future is dubious, since sequestration just slammed federal science funding (and by the way, if you ever hear someone saying that sequestration was "just" a few percent of our budget that got cut, it's OK to yell at them) one might wonder if there are any downsides to this proposal. After all, new ways of examining the brain should be good, right? The sick brain is still the most costly of our sick organs (heart problems kills more people, but brain problems kill more slowly). We won't ever come close to being able to really treat disorders like autism or schizophrenia unless we can do some serious science at the microcircuit level. So, let's do it! Let's map the brain!

But wait. Embedded into the Alivisatos article, there's a paragraph about ethics which states: 

"There are also potential ethical ramifications of the BAM Project that will arise if this technology moves as swiftly as genomics has in the last years. These include mind-control, discrimination, health disparities, unintended short-and long-term toxicities, and other consequences. Well in advance, the scientific community must be proactive, engaging diverse sets of stakeholders and the lay public early and thoughtfully."

The "if it moves as swiftly" line gives us some comfort. But let's take the issues one at a time:

1. "mind control..."  I know that sounds bad. I'll come back to this.

2. "discrimination..." What I think they mean by this is that there may be beneficial brain technologies that could be made selectively available to certain (rich) parties. That's nothing new.

3.  "health disparities..." This means that not everything in an experimental technology program with the most complicated biological network on Earth will work well. Noted.

4. "unintended short- and long-term toxicities..." See #3.

5. "other..." The most interesting one. We don't know what we don't know. That's what people say to cover their bases when taking a risk. And make no mistake, decoding the brain at an ever finer level has risks. I'm not saying that we shouldn't try to cure or treat all brain disorders, but the question arises, should there be limits to how much we hack our own brain circuitry? Are there neural schematics that are best left uncharted? Maybe. To an extent, we used to worry about something similar with our genome, but there's a big difference between the genome and the brain: the brain is much easier to alter.

Are these novel concerns? Hardly. We've been dealing with issues of brain access technology for a long time now. What this is is refinement. Instead treating epilepsy, Parkinson's or depression by having a single-shank deep brain stimulation probe jammed like a tree into the middle of a critical brain region, perhaps we'll have numerous fine electrodes, or some conductive, interactive material layered onto our cortices. Having a better brain activity map means more precision and accuracy, more biomedical finesse.
Here's the thing. There are no ethical situations in which a person can have a foreign object embedded in the brain unless something inside is truly broken and needs fixing. For non-sick people, the skull should stay closed. If that's the rule that we accept, then a fine brain activity map shouldn't be a big deal ethically. That should, in part, take care of the "mind control..." issue. Although, it would be nice to have an "Anti-Mind Control Law" preemptively on the books.

But that "other..." category is a doozy. 

The fear in all of this comes from the idea that more we know about how the brain is wired, the more hackable it becomes. That's the way we think in the Device Age. The argument has merit. Knowing more about the brain has led to more deep brain stimulation and pharmacology targets, and activating those targets can and do change people.  Add to that the assumption that the ability to record from large scale brain circuits will lead to the ability to translate the functional meanings of the neural firing of populations. By "functional meanings", I mean thoughts.

Now things are getting legitimately dicey.

There is a parable in the New Testament about wheat and tares. Tares are grasses that look like young wheat, but they're no good. In the parable, the farmers want to just rip everything out, but their boss tells them not to. Instead, he lets the wheat and the tares grow together until their maturity lets them sift one from the other. What the brain mapping project could do is help us to identify "normal" and "disordered" in the brain on a level never seen before, and that should theoretically allow us to go in and extract "disordered" from brains in ways that we never could before. But while doing this, someone is bound to say, "what should we do with all this wheat?"

On the other hand, it will probably be fine.