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Catholic Charities counselor Deb Collett, right, hugs Tommie Coleman at the former residence of murder victim John Wilson Jones Jr. on Linden Street and 30th Street in Oakland, Calif. on Wednesday, Jan. 26, 2010. Coleman was friends with Jones, who was shot across the street from his home on March 5, 2010. Collett has been providing therapy to the Jones family and handling their case. (Jane Tyska/Staff)

OAKLAND -- The experiment was designed to track what happens when human brains take in new information. The lead scientist, Bessel van der Kolk, president of the International Society for Traumatic Stress Studies, wanted to track differences between chronically traumatized and otherwise normal brains.

The brain, he surmised, held the key to both the roots and the treatment for severe trauma.

What he and dozens of other scientists around the world are continuing to discover could have far-reaching consequences for millions of Americans, especially in Oakland, where thousands of people, many of them children, are regularly exposed to chronic levels of stress and trauma.

This trauma-informed science is pushing boundaries in fields as diverse as neuroscience, brain imaging, meditation and psychotherapy. Scientific value aside, the results could go a long way toward understanding, and ultimately treating, families and communities affected by murder and violence, communities like the one John Jones left behind when he was killed a year ago outside his West Oakland home.

Van der Kolk knew that a normal brain does two things with new data. It generates a filter-like impulse called an N½'200, an "inhibitory wave" that allows the brain to focus on the most important things. Then it creates a P½'300 impulse that allows the brain to learn from the experience.

He soon discovered that traumatized people do not generate the N½'200 inhibitory wave, nor do they generate a good quality P½'300.

"This study changed my whole understanding of what trauma is about," van der Kolk said. "Trauma was no longer about something that happened a long time ago, it was about being unable to fully engage with the present. Nothing new was coming into the brain."

The science around chronic trauma is evolving quickly and in exciting new ways. Even as scientists discover new evidence about what is happening in the brains of chronically traumatized people, intriguing new techniques are emerging for coping with the effects.

Researchers are focusing their energies most intensely on children, for whom early trauma can often become a debilitating, lifelong hurdle; early treatment offers the best chance for full and effective recovery.

"Trauma is at the root of it all in these kids," said Debra Wesselmann, co-founder of the Attachment and Trauma Center of Nebraska. "Their neural networks are full of trauma, they have very little adaptive information in their brains."

Severe challenges

Scientists and therapists now believe the long-term effects of childhood trauma are more far-reaching and worrisome than previously thought.

"One consistent finding has been traumatized children have smaller brains after you control for body size and head size compared to kids who've not been traumatized," said Frank Putnam, director of the Trauma Treatment Replication Center at Cincinnati Children's Hospital.

White matter, the tissue in the brain that makes connections within the neuron-rich gray matter, is diminished in traumatized children, several studies have found.

That means fewer neurons making fewer connections -- and making connections is what creates higher IQs.

That's just the beginning.

One 2010 study Putnam helped direct found that sexually abused children had higher-than-normal levels of cortisol, a hormone that can be lifesaving in emergencies, but which is thought to destroy brain tissue in higher amounts. Repeated trauma caused over-secretions of cortisol, and a subsequent failure of the brain and body to drain the hormone away.

Trauma can even affect the brain's ability to know where it is in physical space. One Canadian study found that the posterior singulate -- a part of the brain that confirms your physical existence -- wasn't active in traumatized people. "Trauma is the residue of what those experiences leave in your body," van der Kolk said. "People's brains change because of trauma."

The effects of this are well-known: anti-social behavior, emotional numbness, aggression, violence and physical and mental dissociation -- the hallmarks, in other words, of the emotional states of many traumatized youth in cities like Oakland and Richmond.

What the science is helping to decipher now, however, is how this works in the brain. Traumatic experiences like shootings, rapes, robberies or emotional abuse leave an imprint in the central part of the brain called the medial prefrontal cortex, which helps regulate our relationship to ourselves -- to self-reflect and self-observe, and to establish social relationships with others.

Trauma also muddies the connections between the left and right sides of the brain, affecting speech and cognitive abilities. "These things change the brain to become chronically fearful, or to not fear at all, or think the best thing to do before someone hurts you is to hurt them," van der Kolk said. "It's bad news."

Chances to heal

One big problem that scientists are only beginning to grapple with is how often victims of chronic trauma are unable to escape the traumatic environments around them. But recent studies suggest there may be hope.

Techniques like eye movement desensitization and reprocessing, or EMDR, neuro-feedback and even mindfulness and meditation are proving effective as therapeutic tools for people trapped in traumatic environments. EMDR has been around for about a decade, but is only now gaining serious traction for treatment of complex post-traumatic stress disorder. Recent studies of drug court attendees who received EMDR showed a 91 percent graduation rate.

The therapy works by accessing memories through bilateral stimulation of the brain's two hemispheres, and then reprocessing them to strip them of the emotional charge of the trauma. Francine Shapiro, who pioneered the use of EMDR, said there is evidence that trauma victims build "resiliency" through treatment.

In one study, traumatized Palestinian refugees receiving EMDR therapy were interrupted by another trauma. "The expectation was that they would have to start over," Shapiro said. "But what happened instead was resiliency." The same resiliency effect occurred in a 2009 study of German bank-tellers who had been repeatedly robbed at gunpoint.

Other tools have also excited neuroscientists lately. van der Kolk has had positive results among traumatized people using neuro-feedback, in which patients are "fed back" images of their brain activity that correspond to their mental states. With training, they can learn how to access the deep theta brain waves that correspond to states of emotional calmness and rational thinking.

van der Kolk is working with about 50 children at the Trauma Research Center in Boston. He said he believes that treating one traumatized person in a traumatic environment is akin to creating "an island of stability" around which others can congregate and from whom they may learn to cope better. "I think the 50 kids we have are no longer the future rapists and killers of America," he said at a symposium in Los Angeles earlier this month on healing trauma.

Why it matters

The newest area of serious study may also be one of the most promising. Neuroscientists, clinicians and Ph.D. researchers are increasingly turning their attention to an area Buddhists and philosophers have been studying for more than two millennia: mindfulness. The number of serious scientific case studies of how mindfulness can help trauma victims has grown exponentially in the past few years.

One reason is that mindfulness is increasingly being associated with the kinds of positive social and emotional experiences that trauma victims often no longer feel, what clinicians describe as emotional numbness.

Ruth Lanius, an associate professor in the Department of Psychiatry at the University of Western Ontario, has been studying emotional awareness and mindfulness in complex PTSD for several years, and has found direct correlations between mindfulness and brain activity. Using MRI scans, she found that the more mindful her subjects were, the more activation showed up in an area of the brain called the dorsomedial prefrontal cortex -- a brain region involved in reflective awareness.

There is good reason for all the interest in brain science and its affect on traumatized youth. For one, it's relatively cheap. "For small expenditures, we know more about how trauma hurts kids than we do about schizophrenia, or even ADHD, or even bipolar disorder," Putnam said. "It's an area where payoff of minor sums has been quite dramatic."

Secondly, a consensus is emerging among many therapists that far too many traumatized kids are being overmedicated. Last year alone, American children consumed $16.3 billion in anti-psychotic medication. Researchers like van der Kolk and others say these medications are destroying children's capacity to engage in the world.

"I bet half the kids on these medications will never be functional members of society," he said. "It's a national catastrophe."

Contact Scott Johnson at 510-208-6429. Follow him at Twitter.com/scott_c_johnson and Twitter.com/oaklandeffect.