by John P. Thomas
Health Impact News

In 2013, President Obama established a 12 year research goal to find cures for brain related illnesses. Expenditures for this project from public and private sources are estimated to reach 4.5 billion dollars by its culmination in 2025. President Obama stated:

Last year [2013], I launched the BRAIN Initiative to help unlock the mysteries of the brain, to improve our treatment of conditions like Alzheimer’s and autism and to deepen our understanding of how we think, learn and remember. I’m pleased to announce new steps that my Administration is taking to support this critical research, and I’m heartened to see so many private, philanthropic, and academic institutions joining this effort. [1]

Concerns about the BRAIN Initiative

This article will look at the research priorities of the government agencies that are leading the BRAIN Initiative. Based on this information, and actual objectives of funded studies, it is clear that the BRAIN Initiative is ignoring the cutting edge science about multiple brain centers in the human body that comes to us through alternative medicine. Instead, it is focusing on a limited view of the brain that fits in with the agenda of conventional medicine and Big Pharma.

In later years of the BRAIN Initiative, there will be a high need for large numbers of human research subjects with impaired brain functioning. These people will be needed for clinical trials of new devices and drugs. This need opens the door to recruitment abuse in a group of people who may not be able to give true informed consent.

Even though the tools that will be developed by the Brain Initiative promise to help control a wide range of illnesses with emotional, memory, and cognitive symptoms, the new technology could be used for other purposes. A long list of benefits are being touted by researchers as they discuss their plans to freely activate and deactivate brain cells and multiple sets of cells. One must wonder whether these same tools could eventually be used for other purposes. Could they become tools for aggressive interrogation or mind control?


NIH Director Dr. Francis Collins and President Barack Obama announcing the BRAIN Initiative. Image source.

Let’s take a look at the Initiative.

Details of the B-R-A-I-N Initiative

The acronym in the title “BRAIN” Initiative stands for Brain Research through Advancing Innovative Neurotechnologies. The Administration is calling the BRAIN Initiative a “bold new Grand Challenge” that promises to revolutionize our understanding of the human brain. They are comparing the size and scope of the BRAIN Initiative to the Human Genome Project. They expect to see the development and application of innovative technologies that will create a dynamic understanding of brain function. According to the 2014 Administration report, this should help researchers uncover the mysteries of brain disorders, such as Alzheimer’s and Parkinson’s diseases, depression, and traumatic brain injury (TBI). [2]

The cast of players in the BRAIN Initiative, which, on the surface, has a medical/healthcare orientation, include the National Science Foundation (NSF) and the 9 agencies of the National Institutes of Health (NIH). Other government agencies that will be directly involved in the unfolding of this program over the next ten years are the Intelligence Advanced Research Projects Activity (IARPA), the Defense Advanced Research Projects Agency (DARPA), and the Food and Drug Administration (FDA).

The 2015 BRAIN Institute progress report states:

There has been an enthusiastic response to the President’s call for an “all hands on deck” effort. Major foundations and private research institutions, including the Howard Hughes Medical Institute, Allen Institute for Brain Science, and the Kavli Foundation, as well as patient advocacy organizations and universities have committed over $240 million to the BRAIN Initiative. In addition, members of the National Photonics Initiative and other companies such as GE, GlaxoSmithKline and Inscopix have joined this effort through commitments of more than $30 million in research and development investments. The President’s 2016 Budget proposes to increase the Federal investment in the BRAIN Initiative from about $200 million in FY (fiscal year) 2015 to more than $300 million in FY 2016. [3]

The proposed budgets of the government agencies and examples of the research that they are funding are shown below. Most of this information was taken from the President’s 2015 BRAIN Initiative report. [4]


Programs Funded by the National Institutes of Health (NIH)

In FY (fiscal year) 2016, the nine agencies of the NIH will provide an estimated $135 million in funding for the BRAIN Initiative. Projects include developing new devices to record and modulate activity in the human nervous system, revolutionizing human neuroimaging technologies to understand how individual cells and complex neural circuits interact in time and space, and modeling and analyzing the complex data that scientists obtain in their quest to understand how the brain works. They are trying to use new technologies to create a dynamic picture of the brain in action, which researchers can use to treat, cure, and even prevent brain disorders.

Examples of projects funded in 2015 by the NIH are shown below. They are typical of the grants given to the 67 institutions. [5]

Time-Reversal Optical Focusing for Noninvasive Optogenetics

(California Institute of Technology)

Goal: to develop a light and sound system that will noninvasively shine lasers on individual cells deep within the brain and activate light-sensitive molecules to precisely guide neuronal firing.

Dissecting human brain circuits in vivo using ultrasonic neuromodulation in rodents, monkeys and eventually humans

(California Institute of Technology)

Goal: to use non-invasive, high resolution ultrasound to impact neural activity deep in the brain and modify behavior.

High-resolution noninvasive neuronal current tomography

(Children’s Hospital Corporation)

Goal: to “tag” specific locations in the brain using sound waves. This approach would leverage the millisecond temporal resolution of conventional scalp electroencephalography (EEG) with millimeter spatial resolution of ultrasound. This information could be used noninvasively to construct a tomographic image of neuronal currents not only in the neocortex, but in deep brain structures as well. This technology will open the door for whole-brain mapping with high temporal and spatial resolution in the human brain, not only to map the functions of brain circuits in healthy individuals, but also for understanding and potentially diagnosing complex neuropsychiatric disorders.

Computational and circuit mechanisms for information transmission in the brain

(Cold Spring Harbor Laboratory)

Goal: to investigate how information is integrated into decision making, and then further transformed into behavior. By performing parallel, large-scale, simultaneous electrical recordings of neural activity in different brain regions of trained rats while they are performing two different decision-making tasks, these researchers hope to observe how activity in one area influences activity in a downstream area. In addition, there are plans to identify and manipulate the activity of neurons that connect these brain areas to understand the causal relationships governing information flow among these regions. Gaining such mechanistic insights into how the brain processes information will provide insights into how both the normal and disordered brain operates.

High-Bandwidth Wireless Interfaces for Continuous Human Intracortical Recording

(Massachusetts General Hospital)

Goal: to develop an implantable system designed to allow physically disabled users to control an external device, such as a prosthetic arm, by thought alone. In this project, researchers intend to make a fully implanted medical treatment system, freeing patients from externally tethered components, and giving them greater control over their home environments and daily lives.

Neurophysiologically Based Brain State Tracking and Modulation in Focal Epilepsy

(Mayo Clinic Rochester)

Goal: to use neuro engineering devices to manage epilepsy for people who cannot be treated successfully with drugs or surgery. Wireless devices will be used to measure brain activity, predict seizure onset, and deliver therapeutic stimulation to limit seizure activity. Researchers will test their device on dogs with naturally occurring epilepsy. If this is successful, then they will conduct a pilot clinical trial in human epilepsy patients.

Funding from the National Science Foundation (NSF)

In FY 2016, NSF plans to spend $72 million to support the BRAIN Initiative. NSF investments in the BRAIN Initiative are focused on generating an array of physical and conceptual tools needed to determine how healthy brains function over the lifespan of an organism, including humans. NSF will also focus on the development and use of these tools to understand how thoughts, memories, and actions emerge from brain activity.

NSF has funded the building of a new $25 million Science and Technology Center on “Brains, Minds and Machines” at the Massachusetts Institute of Technology. NSF will begin to discuss and coordinate plans for the potential creation of a National Brain Observatory with other agencies and the National Laboratory Network.

Funding from the Defense Advanced Research Projects Agency (DARPA)

In FY 2016, DARPA plans to allocate an estimated $95 million in the BRAIN Initiative. DARPA’s mission is to develop projects that focus on military application of new technology. In the case of the BRAIN Initiative, DARPA’s projects are designed to alleviate the burden of illness and injury. In addition, researchers will seek greater understanding of the brain by fostering advancements in data handling, imaging, and advanced analytics.

Specific programs include:

Electrical Prescriptions (ElectRx)

ElectRx seeks to understand and leverage the function of peripheral nerve and spinal cord neural circuits to advance neuromodulation therapies for immunological and mental health disorders.

Neuro-Function, Activity, Structure, and Technology (Neuro-FAST)

Neuro-FAST will be testing how new imaging discovery tools using optical and photonic techniques are capable of sensing the structure and activity of thousands of neurons simultaneously in the active brain.

Systems-Based Neurotechnology for Emerging Therapies (SUBNETS)

SUBNETS aims to demonstrate the first set of prototype closed-loop medical devices able to measure and modulate networks of neurons in research participants with intractable psychiatric illness and alleviate severe symptoms of diseases such as post-traumatic stress disorder and major depression.

Funding from Intelligence Advanced Research Projects Activity (IARPA)

“The Intelligence Advanced Research Projects Activity (IARPA) invests in high-risk, high-payoff research programs to tackle some of the most difficult challenges of the agencies and disciplines in the Intelligence Community.” [6]

IARPA does not have an operational mission and does not deploy technologies directly to the field. Instead, IARPA facilitates the transition of research results to intelligence community customers for operational application. In FY 2016, IARPA plans to invest in at least three research programs in applied neuroscience to advance understanding of cognition and computation in the brain. These are its three research areas:

Strengthening Human Adaptive Reasoning and Problem-solving (SHARP)

The SHARP program will test and validate non-invasive neural interventions that have the potential to significantly improve adaptive reasoning and problem-solving, ultimately leading to improvements in human performance in information-rich environments.

Knowledge Representation in Neural Systems (KRNS)

The KRNS program will seek insights into the brain’s representation of conceptual knowledge as a step toward building new analysis tools that acquire, organize, and wield knowledge with unprecedented proficiency.

Machine Intelligence from Cortical Networks (MICRONS)

The MICRONS program will begin to reverse-engineer the algorithms of the brain to motivate the design of novel, neurally-derived machine learning algorithms that can perform complex information processing tasks.

Activity of the Food and Drug Administration (FDA)

In FY 2016, FDA plants to assist developers and innovators of medical devices by establishing a voluntary program for certain medical devices, including devices applicable to the BRAIN Initiative, that demonstrate the potential to address unmet medical needs for life threatening or irreversibly debilitating diseases or conditions. This new program would provide an expedited pathway to market for qualified devices.


Click for full infographic.

Reflections and Considerations on the BRAIN Initiative

On the surface, the BRAIN Initiative promises to break ground into many new areas of brain related research. As shown by the representative sample of NIH grants, research is still quite basic. Scientists are focusing mostly on developing tools for doing the next generation of brain research. They are trying to see into the brain at the cellular level. They believe that if they can watch and record brain activity inside the skull while it is happening and trigger brain cells, then they can understand how human memory, human emotions, human thought, and human expression of intelligence normally operate. They can then look at people with certain conditions and find where the brain has become dysfunctional. The next step would be to use technology and drugs to target the dysfunctional activity in the brain and make the brain behave “normally.”

This approach to research and illness is not new. It is the standard research and treatment method that has been used by conventional medicine and Big Pharma over the past hundred years or so. The fruit of using the same old system for analyzing and treating illness will inevitably lead to more high cost interventions and high cost drugs. It will perpetuate the current American medical care system, which is the most expensive and least effective medical system among developed countries. [7]

A Serious Flaw of the BRAIN Initiative

The first flaw is found in the mechanistic model of brain functioning. In other words, the brain is characterized as a machine. They treat it like a box containing millions of switches that are rapidly being turned on and off. Researchers think of the human brain as if it is a highly evolved and extremely fast computer, which they believe they can learn to decode, control, and even reproduce. Yes, they are even looking forward to the day when they can establish a new super computer based on the architecture of the human brain, which will be capable of self-directed learning and self-development. [8]

What if there is more to the brain than a series of rapidly moving switches that control cognition, memory, emotions, motivation, and behavior? What if the conventional medical model of conceptualizing the functioning of the human brain as a machine is missing key components, because scientists are only looking at the three pounds of tissue in the skull? Will they make false and misleading assumptions about human functioning while they are doing their “all hands on deck” rush to visualize single neurons, visualize thousands of neurons interacting with one another in the head, and developing sophisticated technology and drugs? What if the seat of emotions, perception, cognition, memory, motivation, learning, and some brain-related illnesses are not exclusively located in the skull? What if the cause of so-called mental illnesses are not actually centered in the head? Will BRAIN Initiative scientists dare to look beyond the head to other brain centers?

Humans have Multiple Brains in One Body

Is the whole human brain really in the head? Cutting edge research from scientists and physicians involved with alternative medical care answers this question with a definitive NO! I will provide two views of brain function that extend far from the confines of the human skull. There are many others that describe the gut-brain axis.

Dr. Andreas Kalcker, PhD, is a bio-physicist, known around the world by doctors and scientists as a man who asks questions that make scientists and doctors uncomfortable. He asks the questions that no one else dares to ask and he is willing to do the research to find simple answers to complicated problems. In his research, he describes three human brain centers. Beyond the brain in the head, which is known as the first brain, he describes two other brains. The second brain is known as the emotional or enteric brain, and the third brain is called the intentional brain. (Dr. Kalcker’s first language is not English. I have inserted bracketed words to add clarity to the remarks he spoke during a 2014 lecture.) He stated:

We have several types of brains. The second brain [enteric brain in the gut] is full of neurotransmitters, and we have hundreds of millions of neurons in this brain. When somebody is jealous, where do we feel it? We feel it in the enteric system [the gut] — this is where all the emotions are. All the emotions are in the enteric system, because 90% of the serotonin comes from there and 50% of the dopamine. There are more than 32 neurotransmitters transmitting in the emotional brain. So, our emotional brain is here [in the gut].

Our rational brain is here [in the head], and we can even add another brain. The heart has neurotransmitters too. It has less neurotransmitters. This is a scientific fact, but it is a very high magnetic force field. This [heart] is the intentional brain. We have the rational brain, intentional brain, and the emotional brain. This [intentional brain] is something we can feel. As a person we can connect directly [to other people] if the intention is a true one and [we do not connect] if it is not a true one. You can feel the intentions of other people if all these brains are synchronistic. [9]

I wonder if the BRAIN Initiative researchers who are trying to cure depression and other illnesses with intense emotional symptoms will find true cures by looking in the brain located in the head, when numerous researchers have established that the seat of emotional functioning is not the brain in the head, but the brain in the gut. It is not just that we have more than one brain, but more importantly, they are all designed to work in harmony. Thus, if one is impaired, then they all will be impaired to some degree. Researchers might see some level of impairment in the head, but treatments might be best directed to the gut.

Dr. Marco Ruggiero, PhD, M.D., adds to the topic of multiple human brains. Dr. Ruggiero holds a PhD in Molecular Biology, is a Medical Doctor who specialized in Clinical Radiology, and has been professor of Molecular Biology at the Department of Experimental and Clinical Biomedical Sciences of the University of Firenze, Italy for more than 20 years. (Dr. Ruggiero’s first language is not English. I have inserted bracketed words to add clarity to the remarks he spoke during a 2014 lecture.) He stated:

Let me spend a few seconds on the so called second and third brain. We all know that we have one brain inside our skull. We all know, and it has been known for ten years that [the second brain consists of a] complex array of neurons in our GI tract from our mouth down to the bottom. The number of neurons in the GI tract equals the number of neurons in the brain. They are all interconnected. Those in the gut are connected to those in the skull up to the point where many psychiatrists have changed their focus from what they thought were brain-based disorders to gut-based disorders. There are hundreds of papers published on this [in major scientific journals], which describe how the [second brain in] the gut influences mood and wellbeing.

Quite recently, about two or three years ago, it was discovered that we probably have a third brain, which is the so-called human microbiome. The human microbiome is the complex array of microbes – bacteria, yeast, fungi, viruses, as well as parasites – that constitute sort of a vital organ of about two kilos of weight, heavier than our liver. The microbiome in our gut produces neurotransmitters like dopamine and serotonin that contribute to the well-functioning of the neurons in the gut as well as the neurons in the first brain. [10]

Alternative Treatments for Brain Disorders

What if post-traumatic stress disorder and depression were actually not diseases of the first brain, but symptoms of a seriously unbalanced gut microbiome? What if dietary changes could actually heal the physical functioning of the gut and reverse so-called brain illnesses such as autism? What if healing the gut of Alzheimer’s patients could change the actual pathology in their first brain? What if fecal transplants or the removal of intestinal parasites could cure diseases that conventional medicine calls mental illness and have the secondary effect of restoring normal neuron activity in the first brain? Will this type of healing reach the awareness of BRAIN Initiative scientists if they exclusively focus on the brain in the head? Will they be able to imagine healing without the use of high cost devices and drugs?

Ethical Considerations for Brain Research: Experimenting on Human Subjects including Children

Human brain illustrated with millions of small nerves - Conceptu

The Presidential Commission for the Study of Bioethical Issues was charged to examine ethical considerations related to brain experimentation that might be carried out during the BRAIN Initiative. The Commission issued two lengthy reports called “Gray Matters.” In the second report, a number of ethical topics were targeted for careful consideration by BRAIN Institute researchers.

The first topic, and I believe most important, has to do with conducting research on people who cannot consent to participate in experimentation. This would include people with serious strokes effecting communication and cognitive functioning, people with late stage Alzheimer’s and other neurodegenerative conditions, and children under the legal jurisdiction of state Child Protective Services.

The concern is that there are not always clear systems in place for gaining consent. How much do people need to understand before they are considered able to make their own decision? Who can legally speak for people if they are not able to speak for themselves or have not reached a stage of mental development to make a well-reasoned decision? What forms of interaction are reasonable and appropriate for avoiding coercion and involuntary participation?

When the BRAIN Initiative reaches the final years of their research, and they need to experiment on human subjects, where will they get them? Will they gather them from nursing homes, mental hospitals, Alzheimer’s facilities, homeless veteran’s shelters, and the registry of Child Protective Services? Who will protect potential subjects with impairments from abuse or from simply being used to advance science without true informed consent?

Dr. Amy Guttman, PhD, chair of the Presidential Commission for the Study of Bioethical Issues, raised concerns about the capacity for gaining consent. She stated:

The bioethics commission recommends that research should include persons with impaired capacity but only with appropriate ethical protections in place. Federal regulations require permission from a legally authorized representative if research participants cannot provide their voluntary informed consent. However, laws are very unclear about who can serve as such a representative, and this leaves a gap in patient protection that impedes vitally important science. Laws need to provide more clarity. In addition, we recommend more research on the factors that play a role in decision-making capacity to better assess when and whether that capacity is present. [11]

Brain Control can Become Mind Control

Whenever I read about the planned use of technology to control brain functioning for the benefit of helping people alleviate their illnesses and suffering, I also wonder about the misuse of that same technology. Technology that could change our feelings, our perceptions, our thinking, our choices, and our behavior when we are ill could also be used to control people when we are well. I realize that these statements are the stuff of futuristic fantasy novels, but the technology is no longer a distant possibility. It will likely be in the hands of real people within ten years. The battle for maintaining the free mind is not just a concern of people with a paranoid disposition, but should be seriously considered by anyone who values the freedom for independent thinking.

Could technology that is designed to restore normal order in the human mind be used to create disorder for the sake of forcing people to divulge information that they wish to remain secret? Could the Intelligence Advanced Research Projects Activity (IARPA), sell new technology to the intelligence community? Could the Defense Advanced Research Projects Agency (DARPA) transform this new technology into tools of interrogation? Could they be used to reprogram the thinking processes of people who stand in firm opposition to governmental encroachment into the realm of constitutional freedoms and rights?

The Secret Side of the BRAIN Initiative

We might think that the use of new technology for mind control would be stopped through public objection, however, there are parts of the BRAIN Initiative that will not become public knowledge. Information about the existence of some projects will not see the light of day because of secrecy agreements. A general purpose confidential disclosure agreement (CDA), also called a non-disclosure agreement (NDA) has been created for the BRAIN Initiative. It prevents institutions from sharing information about Modulating/Recording Devices for Human Clinical Studies that they obtained from corporation partners. Thus, if corporations such as GlaxoSmithKline or GE work with a university on a certain project, then the products they develop basically become secret unless the corporation wants to divulge the information to the public. [12]

We also know that there is great secrecy maintained by the U.S. FDA regarding approval for new products. The FDA’s commitment to “fast-track” new products created by the BRAIN Initiative makes it even more likely that we will never hear about certain projects until there are serious injuries, deaths, or ethical abuses. By the way, based on what I have read about the BRAIN Initiative, I interpret the words “modulating device” in the context of the BRAIN Initiative’s confidential disclosure agreement to mean a device that controls (modulates) brain activity.

Conclusion: BRAIN Initiative = Huge Profits for Expensive Drugs that Do not Cure?

As we watch the BRAIN Initiative unfold over the next 9 years we will likely see some stunning advances in knowledge. We should, however, not assume that this leap forward in knowledge will lead to the solving of all problems related to brain toxicity and brain degeneration. These problems will not be single handedly addressed by the BRAIN Initiative, while we keep ignoring the causes of brain related illness.

Unless we are willing to stop eating chemicalized, denatured, and genetically modified food, stop using vaccines, stop exposing ourselves to environmental chemicals, discontinue the over-prescribing of pharmaceutical drugs, limit our exposure to electro-magnetic smog, address our addiction to sugar and carbohydrates, and stop allowing the political and regulatory process to be controlled by mega-corporations, very little will change. As long as the plan of corporations to dominate all aspects of healthcare and agriculture is not stopped, we shouldn’t expect to see a great change in the pattern of brain related illness.

Conventional medicine has lost the war on cancer. Its human biome project has not revolutionized anything, and there is no reason to assume that the BRAIN Initiative will make a grand change in the landscape of brain related problems. The BRAIN Initiative is just another example of throwing money at a problem that Big Pharma and conventional medicine don’t really want to cure. They don’t want a cure for problems of the brain any more than they want a cure for cancer. They simply want to continue the endless treatment of illness with minimal benefit so that they can keep fighting the war and keep earning huge profits.


[1] “Obama Administration Proposes Over $300 Million in Funding for the BRAIN Initiative in 2016,” White House Office of Science and Technology Policy, February 2015, Page 1.

[2] “Fact Sheet: Over $300 Million in Support of the President’s BRAIN Initiative,” 9/30/2014.

[3] “Obama Administration Proposes Over $300 Million in Funding for the BRAIN Initiative in 2016,” White House Office of Science and Technology Policy, February 2015.

[4] IBID.

[5] “Grant Awards 2015 – BRAIN Initiative,” National Institutes of Health (NIH).

[6] “About IARPA.”

[7] “U.S. Ranks First in Healthcare Spending – Last in Life Expectancy,” Health Impact News.

[8] “Scientific collaboration needed to solve grand challenges,”   Jack Karsten, Center Coordinator, Governance Studies, Center for Technology Innovation, Brookings Institution.

[9] “Successful Treatment of Autism,” (The link between Intestinal Parasites and Autism), Dr. Andreas Kalcker, PhD, Autism 1 Conference 2014.

[10] (Keynote presentation), “The Autism Nexus, New Discoveries of links among the gut microbiome, the immune system, and brain Dysfunction,” Dr Marco Ruggiero, PhD MD, AutismOne 2014.

[11] “We Need to Unlock the Brain’s Secrets—Ethically,” Dr. Amy Gutmann, PhD, Scientific American, March 26, 2015.

[12] “CONFIDENTIAL DISCLOSURE AGREEMENT,” BRAIN_NDA-CDA_091715_508C.pdf, (This document is no longer available on the internet.).