REUTERS U.S. President Barack Obama delivers his State of the Union speech on Capitol Hill in Washington D.C. on Feb. 12, 2013.

To navigate something as complex and dynamic as the brain, a map would help.

Researchers have learned an enormous amount about how we think, what drives our behaviors, and why we feel the way we do since President George H.W. Bush proclaimed the 1990s the “decade of the brain,” but many fundamental questions about the three-pound universe remain unanswered. So President Obama has proposed a Brain Activity Map (BAM) project to reveal some of these remaining secrets, using the Human Genome Project as a model. Not all scientists, however, are on board.

In his state of the union speech, the President noted that every dollar invested in the human genome project “returned $140 to our economy.” With some $3.8 billion spent over 13 years, the resulting gene-based boon turned out to be $796 billion in new jobs, medical treatments, increased salaries and other benefits, according to a 2011 analysis conducted for the federal government. Although medical care has not advanced as much as initially expected because — surprise — the science of genetics is more complex than scientists had anticipated, the data is continuing to yield fruit and promises to provide more value in years to come.

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The BAM project hopes to offer returns of equal or greater value, although the amount of funding has not yet been determined. The New York Times reports that scientists hope for at least as much money as was devoted to the genome project— $300 million a year for at least ten years— but what the administration will seek as part of the proposed budget and where the money will come from is not yet clear.

The goal is to produce the first map of brain function to explore every signal sent by every cell and track how the resulting data flows through neural networks and is ultimately translated into thoughts, feelings and actions. While work is already underway to understand the wiring diagram of the whole brain— known as the connectome— this project would go beyond that to try to understand what this circuitry actually does.

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“I have been interested throughout my entire career in one burning question: how do we turn thought into action?” says John Donaghue, professor of neuroscience at Brown University, who is one of the core scientists involved in the project. Although current brain imaging techniques and cell-based studies offer some insight into how the brain works, they don’t provide a deep enough look at the brain’s inner workings.

“It’s like looking at a page of TIME from six feet away,” he says of imaging methods like functional MRI (fMRI), “You can get a general idea of what’s going on and maybe read the headline but you can’t [understand] the text.” Meanwhile, simply dissecting or manipulating single cells or studying several of them interacting at a time, is “like looking through a microscope and seeing every ink imperfection in a ‘T.’ Maybe you don’t want to do that if you want to understand what a paragraph says.”

What’s missing, says Donoghue, is “that middle level of analysis. How does the brain transform, ‘I want my coffee cup,’ into reaching out with my hand grabbing the cup, bringing it to my mouth and taking a sip, effortlessly, naturally, fluidly.”

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Donoghue says that the project’s lofty goal is to provide that level of analysis, in part by developing new tools needed to study neural networks to such a detailed extent. Some of the research will be done on animal models and some will require the development of nanotechnology specifically designed for the task.

In 2006, Microsoft co-founder Paul Allen funded, with an initial investment of $100 million, the first complete mapping of the mouse brain, and the Allen Brain Atlas is well on its way to doing the same for the human brain.

“There are already [neuroscientists] working on many aspects of this, so the first thing is to bring them together,” says Donoghue. “The second thing is to bring together physical scientists like nanotechnology engineers and computational people with neuroscientists so they can exchange ideas and develop technologies to revolutionize the study of the brain.”

Ultimately, researchers believe that by understanding the brain at a circuit level, diseases like Alzheimer’s, schizophrenia, depression and other brain disorders could be better treated and perhaps even cured.

But some scientists are skeptical that current science is up to the task and are even more wary about whether funding a single project like BAM is the best way to gain this understanding. “I favor diversity in science, by funding lots of scientists pursuing their own research agendas, rather than funding one large project or initiative,” says Ed Vul, assistant professor of psychology at the University of California San Diego, who has published research on flaws in data analysis of fMRI research. Rather than channeling funding into one, potentially misguided pathway, the individual approach “allows funding agencies to adapt nimbly to results, and to what seems to be more or less promising,” Vul says.

Other researchers are concerned that the project might take resources away from trying to cure specific diseases in favor of a basic science approach that might take decades to yield treatments or cures. As Bloomberg reported, Maria Carillo, vice president for medical and scientific relations at the Alzheimer’s Association said that the project should be conducted in concert with approaches like the National Alzheimer’s Plan, instead of separate from them.

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Brain mapping is an exciting new area of research, as evidenced by the fact that overseas, European officials recently announced that they will spend 1 billion euro on their own major neuroscience effort, the Human Brain Project. That initiative will attempt to simulate the brain in a computer, based on existing data, rather than map its actions in finer detail. While Donoghue has reservations about the European project because he doesn’t think there is enough data to build a decent model yet, he thinks that BAM might ultimately be able to provide such information.

“I predict the spinoffs will be unbelievable and amazing,” he says of BAM. As long as the President can find a way to pay for it.