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How does the brain work? Using real and fictional characters to setup a story framework, I write about the science of the human (and sometimes animal) mind. I am a journalist rather than a neuroscientist so my approach is exploratory.

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“Why a map, Mom?”

“Well, how do people normally use a map?”

“To get oriented to a place and to use that to find their way around.” Brian thinks for a minute. “So, it’s to understand where neurons are located inside the brain and how they are connected?” He pauses. “But don’t neuroscientists and neurosurgeons already know the locations and the connections?”

“They do but the brain has more than one billion neurons–” his mom says.

“–and several trillion neural connections or roads, you can say. Wait, are the neurotransmitters like roads or like cars? I guess they are like cars.”

His mom smiles. “That’s a close analogy. How do you think they will use the map?”

Brian scratches his chin.

“There are many diseases like Alzheimer’s or Parkinsons that we don’t fully understand,” his mom says. “ Obama’s BRAIN (Brain Research through Advancing Innovative Neurotechnologies) initiative will help them develop tools that can be used to not only map the brain but to understand how the neurons behave. So, it’s not just about creating a more detailed map but it’s also about getting a dynamic view of the stuff that happens in the brain.”

“But, how, how exactly? How will they capture the messages, the path traversed by the neurotransmitters, the messengers of the brain? I mean, that’s not a static thing…”

“Good point. The current studies use fMRI technologies to measure blood flow in specific parts of the brain. This helps them locate the place where neurotransmitters are active.”

“Yes, I know that!”

“Well, the idea of BRAIN is to provide funding to create more sophisticated tools than the fMRI, to see both high-level view of the neurons and their activities and to get a more close-up view—“

“—yeah, I get it.” He says impatiently. “But how is it different than the research already happening?”

“It’s not necessarily different. It’ll build on the existing work and provide additional resources.”

“Ah, so we can learn about the brain faster.”


“Mom, maybe I can get involved with the BRAIN initiative.”

“Yes, it’s a new thing. So, there will be all types of opportunities if the funding continues. But, first if you have to get qualified by studying neuroscience.”

“Maybe I can become a brain surgeon!”

“Sure, but that means you will learn and use what is already known about the brain. You won’t be making new discoveries. So you won’t be part of BRAIN.”

“So, a neuroscientist then?”

“Yes, or both,” his mom says.

“I can be like Oliver Sacks and be a brain-surgeon and a neuroscientist and a neuroscience writer.”

“Yes, you can be. But first, start exercising your brain on the math homework that’s due tomorrow.”

“Yes  Mom.”

Leena Prasad has a writing portfolio at Links to earlier stories in her monthly column can be found at

Josh Buchanan, a UC Berkeley graduate, edits this column with an eye on grammar and scientific approach.


  1. Flatow,  Ira, host of President Obama Calls for a BRAIN Initiative, NPR>Science>Research News, April 5, 2013,
  2. Neuroscientists Weigh In on Obama’s BRAIN Initiative, Scientific American, May 2, 2013,

Phil’s Trip


topic Psilocybin (“magic mushroom”)
region hippocampus, posterior cingulate. medial prefrontal cortex


Phil is moving slowly through the jungle. Is it a jungle or a banana plantation? All he sees are the tall and thick banana leaves. And why is he moving so slowly. He looks down. He is riding an animal. A bright orange animal.  Orange? That is strange. It lifts its long trunk and makes a sound.

An elephant! He is riding an elephant. What the fuck? Where is he? He must have said something out loud because a voice answers back.

Relax Phil. Enjoy the ride.

He recognizes the voice. It is his friend Lucy. Her voice calms him down. Everything must be okay.

He starts to do as she suggests and concentrates on enjoying the ride. It is pleasant really, so smooth. Elephants are gentle animals, he recalls from the Nature show he saw with Lucy a few weeks ago.

He feels a desire to lie down.

Is it okay to lie down, he says to Lucy.

Yes, you are in the backseat of car, she says. Albert is driving. He is taking us to Dolores Park.

Oh, he is in a car. Not on an elephant. The “banana” leaves are actually the palm trees along Dolores Street. The orange elephant is Lucy’s shawl sprawled on the seat near him. He was hallucinating.

It will be easier in Dolores Park, Lucy says. Since Albert lives nearby you can use his restroom or we can go to his place if you need to lie down or something.

Yes, it would be nice to be in nature. How long has it been now? He and Lucy had started the “journey” in the morning, at Lucy’s apartment in Bernal Heights. Dolores Park is not that far away from Lucy’s house. Why is it taking so long to get there?

He and Lucy are holding Albert’s hands. No. It’s Albert who is holding their hands. Unlike them, Albert is sober and is their guide. It’s his job to make sure that they are safe both physically and emotionally.

Phil stops to look at a purplish blue flower. He knows the street and the neighborhood fairly well and remembers seeing this flower before. But now he feels compelled to observe it more intimately. It’s so beautiful. He wants to gaze at every intricate detail.

Come on Phil. You have been staring at the flower for more than ten minutes now. We should head down to the park. It’s Albert, urging them on.

But look how beautiful it is, how perfect. Phil doesn’t want to move.  Albert puts a firm hand on his shoulder and starts to guide him down the steep hill to the park.

Phil stops at the corner of Church and 20th to admire the cityscape. He has seen this view countless times yet he feels as if he is seeing it for the first time.  The three of them sit down near the corner, at the crest of a hill.

Phil hears a jazz band playing not too far from where they are sitting. He looks at the band and can see the music coming towards him in beautiful improvised notes. He can see the music. How strange, he thinks.

Phil is not dreaming. He is fully conscious and will remember all the details of his experiences later when the effect of the Magic Mushrooms wears off from his system.  Magic Mushroom is a popular term for a wide variety of mushrooms that contain psilocybin, a chemical that is known to produce hallucinations and other effects.

Psilocybin is not addictive. Probably because the effects last for several hours and the experience is not all thrills and games and there is potential for dangerous side effects. Products that contain psilocybin, including the “magic” mushroom family and the synthetic drug LSD, are Schedule I illegal drugs in the United States because of the possibility of dangerous side effects.

On the other hand, psilocybin has potential benefits which researchers around the world have been studying. In 2010, scientists at Johns Hopkins conducted an experiment to examine the affect of psilocybin on cancer patients. Many patients reported relief from depression and long-term improvements in their lifestyle. One patient, Dr. Martin, rated the experience as “among the most meaningful events of his life.”

“Under the influences of hallucinogens, individuals transcend their primary identification with their bodies and experience ego-free states before the time of their actual physical demise, and return with a new perspective and profound acceptance of the life constant: change.” This statement was made by Dr. Charles S. Grob who conducted an identical study at UCLA on cancer patients. He noted that psilocybin helps lessen the intensity of fear, panic, and depression in terminally ill patients.

Phil is not terminally ill and does not have any mental disorders. Psilocybin or any other hallucinogens are also not recommended for people with mental illness because the impact on a disturbed mind cannot be measured or controlled and could lead to serious consequences. The formal studies are conducted in regulated lab environments within the supervision of medical professionals. Phil is being guided by his friends Albert and Lucy who are experienced users of the drug. They are ensuring that his experiences stay within a “safe” zone.

But what’s going on in Phil’s mind? A lot of what’s happening is a mystery but scientists have some clue. While people often speak of psychedelic experiences as something that expands their consciousness, the fact is that psilocybin reduces blood flow in the brain. Another common experience is that of feeling more connected with nature and other people. Ironically, during the hallucinations, critical areas of perception and cognition actually show a decreased level of connectivity. This explains, however, as to why depression can be lowered by this drug. People in the throes of depression also suffer from an overactive mind. Thus, slowing down the brain can slow down this increased activity and produce a calmer frame of mind. Extrapolating from this, it makes sense for people who are not depressed to also feel happier under the influence.

This explanation of lower activity in the brain due to reduction in blood flow and connectivity was discovered in an experiment by lead researcher Robin Carhart-Harris of Imperial College London. His team used functional MRI brain scans to observe the brain activity of thirty volunteer participants while they were under the influence of psilocybin. The researchers measured the blood flow in half the patients and in the in the other half, they measured the connectivity among different brain regions. In both cases, the posterior cingulate and the medial prefrontal cortex of the brain were affected. There was less blood flow in these areas and the connectivity between these regions and the hippocampus was reduced. In addition, the thalamus had less blood flow also.

What does this mean?

“Changes in function in the posterior cingulate in particular are associated with changes in consciousness,” per Robin Carhart-Harris.  Both the posterior cingulate and medial prefrontal cortex are thought to be involved in functions related to self-awareness.

The thalamus regulates many functions of the brain so less blood flow to this region means less processing across the different regions.

The hippocampus plays a central role in consolidating short term memory to long-term storage. More studies will be needed to determine the implication of reduced connectivity between the hippocampus, the posterior cingulate and the medial prefrontal cortex.

While more experiments are required to fully document the details of what happens to a brain on psilocybin, scientists have discovered that the molecular structure of psilocybin is similar to the neurotransmitter serotonin which regulates mood. Thus psilocybin binds to the some of the same neuron receptors as serotonin and produces similar results. They are many legal prescription drugs that regulate serotonin. As per Franz Vollenweider of the Psychiatric University Hospital Zurich, it’s the long-term effects of psilocybin that are important not just the temporary altered states of participants. Even though brain connectivity is reduced in the short term, the long-term effect of the drug is to affect neural growth and connectivity, according to Vollenweider.

Other brain changes that are influenced by psilocybin are still under study and the Schedule I status of this drug complicates the research. It would be helpful to develop a more comprehensive understanding of how the brain is physiologically affected by this chemical but scientists are also studying other benefits. For example, a study by Harvard researchers Dr. R. Andrew Sewell and Dr. John H. Halpern, concluded that psilocybin is useful in reducing cluster headaches. “Our observations suggest that psilocybin and LSD may be effective in treating cluster attacks, possibly by a mechanism that is unrelated to their hallucinogenic properties. This report should not be misinterpreted as an endorsement of the use of illegal substances for self-treatment of cluster headaches.”

Phil is taking a risk in experimenting with something that is illegal and potentially dangerous. But, on the other hand, many patients in the Johns Hopkins and the UCLA studies said that their psilocybin experience was one of the most memorable and valuable events of their lives. It will probably be a while before psilocybin is used in a legal, guided, and safe environment to help people experience the levity that is often the affect of this drug. Perhaps it might become possible to safely “tune out” and feel happier and more connected to the universe. After all, there are many legal drugs like Prozac and Zoloft that have similar characteristics as psilocybin and help improve people’s lives.



Charles S. Grob, MD, et. all. “Pilot Study of Psilocybin Treatment for Anxiety in Patients With Advanced-Stage Cancer.”Arch Gen Psychiatry. 2011;68(1):71-78. doi:10.1001/archgenpsychiatry.2010.116

Tierney, John. “Hallucinogens Have Doctors Tuning In Again.” New York Times 11 April 2010. <>

Sewell, Dr. R. Andrew MD, Halpern, Dr. John H. MD. “Response of cluster headache to psilocybin and LSD.” Neurology. June 27, 2006 66:1920-1922

Brauser, Deborah, “Psychedelic Drugs May Reduce Symptoms of Depression, Anxiety, and OCD”, 25 August 2010.  <>

Mental Movies


topic memory
region Amygdala, hippocampus


She turns on the CD player in her car and “When I’m 64” streams out over the speakers. Mona starts to cry. She is on Highway 280, driving down to Palo Alto to see her brother Michael. She’s flooded by memories of her childhood with Michael. She can hear his voice and visualize him singing the song when he was 9 or 10 years old. Michael has been in a car accident and has been in a coma for several weeks. It all seems hard to believe. He’s only 24. How can this be happening?

Mel is walking around in the grocery store. He sees a ripe yellow mango with red spots on the top. He picks it up and sniffs it. “Singaporean,” he can hear his ex-girlfriend’s voice say. He can visualize her eating the mango, the juices running down her mouth as she bites into the skin. He wonders what she is doing now. Perhaps she is eating one of these; he thinks and puts it in his grocery cart.

Mina passes by Dosa on Valencia Street. She remembers the time she went in there with her aunt, who was visiting from India. She remembers that day and how much fun it was to have dosa in her own neighborhood with her favorite aunt from India.

It’s not difficult to guess that the music, the scent, the visual cues produce emotional reactions in the brain of these people. But, what exactly happens in the brain when we store and retrieve a memory?

“What seems to happen is that a piece of familiar music serves as a soundtrack for a mental movie that starts playing in our head,” according to Petr Janata, a cognitive neuroscientist at University of California, Davis. “It calls back memories of a particular person or place, and you might all of a sudden see that person’s face in your mind’s eye.”

Familiar with studies of brain areas activated during recall of autobiographical stories, Janata theorized that the brain area behind the forehead is responsible for recalling memories associated with music. This area is called the medial pre-frontal cortex. He conducted a study in which he had college students listen to top-40 music when the students would have been between the ages of 8-18. Using fMRI brain scan, he noted the music was associated with mental activity spikes in the medial pre-frontal cortex of the subjects’ brain. The subjects later wrote down the memories recalled by the music.The vividness of the memory recalled was proportional to the intensity of activity in the medial pre-frontal cortex.

This area of the brain is just one of the many areas involved in long-term memory and one of the areas associated with Mona’s recall of her childhood memories of her brother.

The hippocampus, a tiny structure that resembles a sea horse and curls near the center of the brain, is one of the primary regions involved in orchestrating the storage of information from short-term memory to long-term memory. As Mona and her brother listen to “The Beatles” and their eyes and ears register the event, the hippocampus harmonizes the visual and auditory sensations into one “event”. The event is stored as a pattern of biochemical changes in nerve cell networks. Later the hippocampus will manage the retrieval and re-play of the event.

Over time and with repetitions of the stored events in the brain, other parts of the brain eventually do not need the hippocampus to manage them and can recall the information on their own. In Mona’s case and in the case of the college students in the experiment, the memory has been in the brain for so long that the hippocampus is probably no longer required to manage the recall. Depending on how long ago it was that Mel’s ex-girlfriend told him about the Singaporean mango and how often he has replayed that memory in his head, his hippocampus might or might not still be involved in recalling this memory. Same applies to Mina’s memories of her aunt.

All the memories presented here (Mona’s of her brother, Mel’s of his ex-girlfriend, and Mina’s of her aunt) have emotional context. This suggests the involvement of a region of the brain called the limbic system and one particular organ called the amygdala. Often referred to as amygdala, there are actually two of them in the brain. They are almond shaped with a diameter of about an inch but the size can vary from person to person. The amygdala assists in deciding as to whether an experience has emotional significance and prioritizes the event in terms of importance for storing in long-term memory.

The memories discussed here are all associated with storage of emotionally significant events. In each of these three examples the memory can be triggered by sensual clues: the sound of the music, the feel and smell of a mango, the taste of Indian dosa. Mona and her brother listen to music as he sings the lyrics and they both activate their auditory senses. Mel’s girlfriend picks out a mango and tells him about it. He smells it. Later, she eats it in a way that’s unfamiliar to him, without peeling and cutting it. His auditory and olfactory senses are activated. Mina has an enjoyable dinner with her aunt. Her olfactory senses are activated and so are her taste buds. In all these case, the visual senses are also activated. The combination of activities creates an event that is prioritized by the amygdala and managed by the hippocampus for storage in long-term memory. Later, the network of brain cells in various locations in the brain will synchronize to retrieve the memory.

Although there have been tremendous advances in the biochemistry and anatomy of long-term memory, much remains unknown. There is a strong indication, however, that it’s the result of team-work amongst complex networks of nerve cells and organs that provides human beings with the ability to replay events from their life based on retrieval cues that are picked up by the senses.

Dr. Nicola Wolfe is the neuroscience consultant for this column. She earned her Ph.D. in Clinical Psychopharmacology from Harvard University and has taught neuroscience courses for over 20 years at various universities.

References for this article:,, Dr. Wolfe’s Behavioral Psychology class at Berkeley extension.