Seeing the brain hear reveals surprises about how sound is processed

Seeing the brain hear reveals surprises about how sound is processed

Bandyopadhyay et al. Dichotomy of functional organization in the mouse auditory cortex. Nature Neuroscience, 2010; DOI: 10.1038/nn.2490

We discovered that the organization of the cortex does not look as pretty as it does in the textbooks, which surprised us," explains Kanold. "Things are a lot messier than expected." And we don't see evidence of the maps previously proposed using less precise techniques." But the disorder they found could indicate that the brain is far more adaptable than previously thought. "These results may rewrite our classical views of how cortical circuits are organized and what functions they serve," suggests Dr. Shihab Shamma, whose previous research has involved mapping responses in the auditory cortex using traditional microelectrodes.

Recent very moving email from Partners in Health about Haiti: "Responding to Anguish"

From

Cate Oswald
Program Manager for Psychosocial Support
and Mental Health, Haiti

"In the midst of all of the distress the earthquake brought in its initial days, the immediate response of many in the countryside was to rush to Port-au-Prince to look for family and friends—a very natural response given the circumstances. With cell phone communication down, this was the only way to verify they were ok, or in need of help.

For our patients receiving treatment for multi-drug resistant tuberculosis (MDR TB) at one of two treatment centers in the Central Plateau, this was not an option. Their illness requires a two-year treatment regimen, the first of which is administered as an inpatient. For them, leaving in search of their families was out of the question. Without communication capabilities and only listening to radio reports explaining the extent of the destruction, one can only imagine how distressing these first few days were for them.

In the days since, as cell phone service improved and patients were able to reach their families, many learned of the sudden and untimely death of their family and friends. One of our patients, Benjamin, who has been battling tuberculosis off and on for 18 years, learned that he lost 10 family members. Others lost siblings, aunts, uncles, mothers, fathers, cousins, friends. In their grief, they immediately started asking themselves why were they saved from this tragedy and not others? How would they continue to live? Why did some people have to die in an instant while they have been able to receive life-saving treatment for their deadly illness? Should they abandon treatment and give up on life?

The Zanmi Lasante staff at the Monseigneur Decoste Infectious Disease Pavilion at the St. Therese Hospital in Hinche immediately recognized their patients' anguish and called on the support of Zanmi Lasante's head psychologist and Director of Psychosocial Support Services, Father Eddy Eustache, to help work with their patients.

Drawing on a technique he has used at PIH's Rwanda project working with genocide survivors, Father Eddy led us in a memorial service remembering the lives of all those we had lost in this unthinkable disaster. Patients and staff alike sang songs, read scripture, shared stories of their memories of their loved ones, and in arguably the most moving part of the service, lit candles for each of the people we had lost while reading their names out loud. To conclude, staff provided words of encouragement and advice for patients on continuing to adhere to treatment and find support in each other.

Efforts such as these are part of a more comprehensive psychosocial support plan for Zanmi Lasante staff, patients, and their families as we work together to address the psychological impact that the earthquake has had on everyone in Haiti.

Kenbe Fem,

Cate Oswald"

Misunderstanding what brain scans can tell us

PTSD in the press--a MEG study distinguishes between PTSD and normal controls....The press misinterprets the results.

NEJM study finds post-event morphine cuts combat PTSD rates in half

From Neuron Culture Blog
NEJM study finds post-event morphine cuts combat PTSD rates in half

This is a pretty big deal if it holds up in future trials. One caveat I've not had time to check out is whether the morphine was often applied as part of an more robust medical response in general, which itself might reduce later PTSD symptoms. I hope the DOD soon follows up with another, larger study, for as Ben Carey notes, the has some substantial implications if indeed it holds up.

via nytimes.com:

In the new study, researchers at the Naval Health Research Center in San Diego reviewed detailed medical records of 696 troops who had been wounded in Iraq between 2004 and 2006, determining whether and when morphine was used in treatment. Military doctors used the drug for most serious injuries -- generally in the first two hours after the injury -- but sometimes administered others, like anti-anxiety medications

The study found that 243 of the servicemen and women were given a diagnosis of post-traumatic stress within two years of their injury. When the severity of the wounds was taken into account, researchers calculated that the diagnosis was half as common in those who had received morphine as in those who had not.

Age, sex and the cause of injury did not significantly alter the findings, said Troy Lisa Holbrook, the study's lead author.

"This is just one paper, one analysis, but it's exciting because of the strength of the finding," Dr. Holbrook said. "A lot of people have been looking for a secondary preventive to interrupt the formation of traumatic memories."

...The drugs appear to blunt the emotional charge of traumatic memories in several ways. Most obviously, they kill the pain when it is most excruciating; often, they scramble the ability to recall what exactly happened. Opiates also inhibit the production of a chemical messenger called norepinephrine, which is thought to enhance fear signals in the brain.

Tai Chi, Harvard Magazine and me

I am quoted on Tai Chi research in Harvard Magazine, alongside a nifty photo.

New paradigm in Cancer: focus on the context around the cell

New paradigm. In Cancer, the "context" around the cell (the extracellular "neighborhood") matters. Targeted therapies are needed to address (and not destroy) the neighborhood and social environment in which cells live.

Not surprisingly, a woman made this discovery (goes against the old warfare model --that focused only on massive cancer cell death and kill rates).

Atul Gawande, "Doctors are human"

Atul Gawande: New Yorker

"Our great struggle in medicine these days is not just with ignorance and uncertainty...It's also with complexity:how much you have to make sure you have in your head and think about. There are a thousand ways things can go wrong."

Too much information... drowning in a sea of data... swamped by "false positives"

When too much information is collected and when there is no rationale or organizing purpose for collecting the data, bad things can happen. This is the problem of "false positives' that you encounter in elementary statistics that is fundamentally misunderstood by the broader public.

Examples include: mammography in 40-50 year old women with no relevant history. So much counter-terrorism data, including drone data (see article in NYT), is collected that no one can connect the dots. Fmri brain scans collect zillions of bits in data in fishing expeditions with no clear hypotheses

What do all of these examples have in common? Computerized imaging and other systems "overcollect" data and imperil our ability to sort and process MEANINGFUL information. We are drowning in a flood of data....The alternative, as Matt Yglesias puts it, is that we will be "swamped with false positives."

Jim Arkedis did an excellent post last week based on his work as an intelligence analyst walking you through how difficult it is is actually “connect the dots” and find a bad guy. The mathematical fact underlying the problem is, as I’ve emphasized, that since only a tiny number of people are al-Qaeda operatives, anything you do is going to be swamped with false positives.

Standing Meditation in the Chinese Martial Arts

A post on kinaesthetic memory in Tai Chi and the qigong based internal meditative arts. One of the most prominent practices is called Zhan Zhuang. Many many Tai Chi players use this stance to enhance.

There are many descriptions of the benefits of Zhan Zhuang. But none of these descriptions offer a scientific account of why Zhan Zhuang might be beneficial. So, if you practice Zhan Zhuang, or anything like it, I am curious, how would you explain this practice to a scientist who was completely unfamiliar with it, what would you say?

Physicians' moods affect quality of care, according new study

Physicians' moods affect quality of care, according new study

This isn't too surprising.

I'm ambivalent about the neuroscience craze

I'm ambivalent about the neuroscience craze. The brain is a vast territory with new, fascinating discoveries being made every day. But, at the same time, it sometimes feels like, as John Lennon put it, impishly, a fad that is (inappropriately) "bigger than jesus."

Here are some recently published books:

Norman Doidge, The Brain that Changes itself

Andrew Newberg, Why God Won't Go Away

David Rock, Coaching with the Brain in Mind

Rick Hansen, Buddha's Brain

Madeline Van Hecke, The Brain Advantage: Becoming a More Effective Business Leader

New meditation studies

New meditation studies.....

Cahn Delorme and Polich, Occipital gamma activation during Vipassana meditation.
Cognitive Processing, 2009

Long-term Vipassana meditators sat in meditation vs. a control rest (mind-wandering) state for 21 min in a counterbalanced design with spontaneous EEG recorded. Meditation state dynamics were measured with spectral decomposition of the last 6 min of the eyes-closed silent meditation compared to control state. Meditation was associated with a decrease in frontal delta (1–4 Hz) power, especially pronounced in those participants not reporting drowsiness during meditation. Relative increase in frontal theta (4–8 Hz) power was observed during meditation, as well as significantly increased parieto-occipital gamma (35–45 Hz) power, but no other state effects were found for the theta (4–8 Hz), alpha (8–12 Hz), or beta (12–25 Hz) bands. Alpha power was sensitive to condition order, and more experienced meditators exhibited no tendency toward enhanced alpha during meditation relative to the control task. All participants tended to exhibit decreased alpha in association with reported drowsiness. Cross-experimental session occipital gamma power was the greatest in meditators with a daily practice of 10+ years, and the meditation-related gamma power increase was similarly the strongest in such advanced practitioners. The findings suggest that long-term Vipassana meditation contributes to increased occipital gamma power related to long-term meditational expertise and enhanced sensory awareness.
longterm meditators show enhanced occipital gamma (not alpha).

van den Hurk et al, Greater efficiency in attentional processing related to mindfulness meditation. Quarterly Journal of Experimental Psychology, 2009.

In this study, attentional processing in relation to mindfulness meditation was investigated. Since recent studies have suggested that mindfulness meditation may induce improvements in attentional processing, we have tested 20 expert mindfulness meditators in the attention network test. Their performance was compared to that of 20 age- and gender-matched controls. In addition to attentional network analyses, overall attentional processing was analysed by means of efficiency scores (i.e., accuracy controlled for reaction time). Better orienting and executive attention (reflected by smaller differences in either reaction time or error score, respectively) were observed in the mindfulness meditation group. Furthermore, extensive mindfulness meditation appeared to be related to a reduction of the fraction of errors for responses with the same reaction time. These results provide new insights into differences in attentional processing related to mindfulness meditation and suggest the possibility of increasing the efficiency in attentional processing by extensive mental training.

Evan Thompson, Contemplative Neuroscience as an Approach to Volitional Consciousness

This chapter presents a methodological approach to volitional consciousness for cognitive neuroscience based on studying the voluntary self-generation and self-regulation of mental states in meditation. Called contemplative neuroscience, this approach views attention, awareness, and emotion regulation as flexible and trainable skills, and works with experimental participants who have undergone training in contemplative practices designed to hone these skills. Drawing from research on the dynamical neural correlates of contemplative mental states and theories of large-scale neural coordination dynamics, I argue for the importance of global system causation in brain activity and present an “interventionist” approach to intentional causation.


Andrew J. Waters et al,
Associations Between Mindfulness and Implicit Cognition and Self-Reported Affect
Substance Abuse, 2009

Theory suggests that mindful individuals exhibit enhanced attentional processing (e.g., attentional control) and that they maintain a detached perspective to problematic stimuli. For smokers, smoking and affective stimuli are problematic stimuli when they try to quit. In this cross-sectional study, smokers (n = 158) completed 3 modified Stroop tasks (to assess attentional control), 3 Implicit Association Tests (IATs; to assess detached perspective), and a battery of self-report assessments. Degree of mindfulness was negatively associated (P < .05) with self-reported negative affect, perceived stress, and depressive symptom severity, and positively associated (P < .05) with positive affect. Degree of mindfulness was not associated with the ability to disengage attention from smoking or affective stimuli. On the depression IAT, more mindful participants exhibited a more negative IAT effect, suggesting that they may have developed a detached perspective to depression-related stimuli. Theoretical and clinical implications of the data are discussed.

How are scientists, in the deepest corners of their personality, motivated to carry out the research they do?

Just read a terrific interview with Lee Nadler, the Harvard oncologist who pioneered the discovery of monoclonal antibodies and their use in treatment of blood cancers. In the interview, he was touchingly personal and candid about his own upbringing. And he also described, in a full bodied way, what motivated him as a scientist. Not least was his desire to escape his family, especially his difficult, embarrassing father in Queens.

The personal stuff was quite moving and unusually revealing for a Harvard medical scientist.

What also struck me was his story of his own personal trajectory in science, how events as random as an afternoon conversation with a friend developed into a lifelong monoclonal research agenda.

I also just read the story of Eugene Braunwald's career at UCSD and Brigham and Womens as an investigator of heart attack -- he was the first to develop treatments for people undergoing active heart attacks. He has probably saved thousands/millions of lives. His story is interesting in the way that he is one of the first to bring together in a geniunely translational way molecular biology with treatments of disease.

The father of all of this research was Jacques Loeb, the early 1900s biologist who famously rejected vitalism. His dogma was: All biology can be reduced to biochemical cellular phenomena.

So, having considered all of this, the thing that came to mind was the question of whether "information" or "coordination" based cellular hypotheses (how do cells coordinate activity, share information etc) might be pushing back, however slightly, on the anti-vitalist, reductionist idea somewhat. Certainly the cortical dynamics hypotheses, which sanction action at a distance (through synchrony) and subtle "informational" interactions across many different cortical areas (related to many different subtle behaviors such as observing the pain or action of another, imagining music or sound or touch, undergoing an illusion that a rubber arm really belongs to you). And, then there is my idea that beta and piper/gamma rhythms suggest that brain rhythms extend into (and may possibly helpt to coordinate) a broad range of peripheral physical/sensorimotor processes: pain, balance, movement, blood flow.

The main point 1: how does my intellectual agenda work? Do my ideas, hypotheses and proposed experiments challenge some of these "big ideas"?
If these brain dynamic processes, in which motor cortex neurons are entrained and organized into cortical assemblies that exert influence on embodied physiological processes, then this would suggest a slight modifcation of Jacques Loeb's dogma. I'm sure I will have more to say about this at a later time.

The main point 2: Noting the questions that matter for me, right now.

For right, now I think it's enough to note the questions that I am interested in: why are people really, in the deepest corners of their personality, motivated to carry out the research they do? How are lifelong research agendas launched by brief encounters with a subject or conversations with a person or fleeting personal experiences with illness or healing? How do abstract intellectual dogmas (Loeb's sustained effort to destroy theories of vitalism and promote reductionistic biology, for example) relate to a one's personal situation?

For me these questions feel especially charged.

Comparing Forest Masters’ Techniques and Implications for International Meditators

Comparing Forest Masters’ Techniques and Implications for International Meditators


Comparing the styles of two prominent Thai Vipassana monks.

January 5, 2010 by wanderingdhamma
Ajahn Chah and Luangda Mahabua are two of the most well-known teachers of the forest tradition for Thais and English-speakers alike. They both come from the lineage of

Ajahn Man and yet their styles and teachings differ enough to affect lay international meditators who come to their monasteries.

In a recording of a Dhamma Talk on 27/9/09, Ajahn Martin of Wat Pa Baan That says that Mahabua focuses on formal practice. At this wat it is recommended that one does the small tasks needed to keep the monastery functioning quickly and quietly. After this is done one returns to formal practice. This formal practice consists of much walking meditation on one’s individual jongrom path, practicing sitting meditation, and being mindful when doing everything else. Because of this stress on formal meditation practice, Luangda Mahabua’s monastery does not have communal activities such as daily chanting....

Ajahn Chah, in contrast, wanted to develop community in his monasteries and found this was especially important for his Western disciples. Ajahn Pasanno (Co-Abbot of Abhayagiri Monastery), who I spoke with at Wat Pah Nanachat, has also stated that Ajahn Chah felt that face to face communication was very important. The Western sangha continues this through their World Abbots Meeting held every two years...

Ajahn Chah also stresses meditation and mindfulness in daily life, rather than formal practice, in contrast to Mahabua. My previous post about the ‘style’ of Ajahn Chah describes his chiding of those who think that meditation can only happen on a cushion or on the walking path. For Chah every aspect of monastic life was to be a part of one’s practice......


These emphases in each master’s teachings and the way each has established their monasteries affects the experiences of international meditators. Because of Mahabua’s focus on formal practice, a retreat for foreigners at Wat Pah Baan That consists of much solitary meditation in one’s kuti. There are no group activities to attend and no chores assigned except to clean inside and the surrounding areas of one’s kuti. Because Mahabua’s teaching style includes this battle against the kilesas and the defiled citta, the dhamma talks in English by Ajahn Martin contain these same ideas. Meditators are taught about these concepts and how they relate to one’s daily practice.

For Ajahn Chah’s monasteries, however, this tradition of communal activities and mindfulness in daily life, certainly continue at Wat Pah Nanachat. Foreign meditators participate in group chanting, before-meal ceremonies, meditation, question and answer sessions, as well as assist with assigned chores. These organized chores and other activities are part of the meditation practice, as Chah intended. As well, since Chah did not have a meditation ‘method’ but more of a ‘style,’ this is not a formal meditation retreat as one would receive at Wat Pa Baan That. There is no monk assigned to teach the foreigners and there isn’t a predominance of the goal to reach the pure citta that is so prevalent in Mahabua’s and Ajahn Martin’s teachings.

Thus the personalities, backgrounds, and styles of each forest meditation master affect how meditation instruction is presented to lay foreign meditators. The styles of Mahabua and Chah affect the setup of each monastery, the amount of instruction received, the hours available for formal practice and other activities, and one’s integration into daily life at the monastery.

The main point: the meditative styles of two teachers from closely related (or the same?) lineages appear to be radically different (are they?).

Desire influences visual perception

Desire influences visual perception

Mind hacks links this experiment showing that motivation affects our perceptual judgments (specifically, thirsty people see a water bottle as being physically closer to them than do satiated, non-thirsty people) to an earlier generation of experiments carried out by Bruner and Goodman and others in the late 1940s and 1950s called the "New Look."

The main point: motivation and affect can have an impact on basic perceptual judgments, probably also effecting changes in primary sensory cortices. Seeing, hearing and touching are completely intertwined with wanting and feeling. My question: can changing the processes underlying seeing, hearing, touching through practices like meditation and tai chi lead to upstream clinically relevant changes in our awareness of motivation and of emotion?

Duck Rabbit ... How Anticipatory Structures in Science Shape Scientists' Perception

Ian Hacking Holborg Prize Symposium. Professor Dagfinn Fossedall speaks about Hacking's ideas about social construction of science. Husserl, Frege, Wittgenstein. Duck Rabbit and the Gestalt of Science (in relation to Husserl). Our experience is shaped and contrained by pre-existing, anticipatory patterns.

This Image Is Not Moving § SEEDMAGAZINE.COM

This Image Is Not Moving § SEEDMAGAZINE.COM

An interesting description of perceptual illusions

Finding disease mutations in a sea of noise

Why massive DNA sequencing in search of cancer-related mutations is unlikely to improve cancer treatment in the real world anytime soon (from the Genetic Future blog)

Finding disease mutations in a sea of noise

Review of Jones et al. (2009). Exomic Sequencing Identifies PALB2 as a Pancreatic Cancer Susceptibility Gene. Science DOI: 10.1126/science.1171202

"A paper published online today in Science illustrates both the potential and the challenges of using large-scale DNA sequencing to identify rare genetic variants underlying disease risk.....

First, the good news: as you might have guessed from the fact that the study is published in Science, the authors did in fact find the likely disease-susceptibility mutation. They were able to distinguish this mutation from the many other variants in the patient's exome (more on those in a second) by a particular quirk of cancer susceptibility variants: they are often found in only a single copy (along with a healthy version of the gene) in normal tissue from a patient, whereas in cancer cells from the same patient the normal copy is disrupted.

Now, the bad news: the researchers also found a whole stack of red herrings. In total, the authors looked at sequence from 20,661 genes, and identified 15,461 genetic variants not found in the reference human genome. Of these, 7,721 changed the sequence of the encoded protein, 64 resulted in abnormal stop codons, 108 were predicted to alter RNA splicing of the gene, and 250 were small deletions or insertions (115 of which would be predicted to dramatically alter the encoded protein through a frameshift). The stop codons, splicing mutations and frameshift insertion/deletions, and many of the protein sequence-altering variants, would all have to be regarded as plausible candidates for a disease-causing mutation.

Although it would probably be possible to exclude many of these variants using other sources of information (e.g. functional information about the genes, presence in healthy controls, patterns of evolutionary conservation), this is an enormous number of potential disease-causing variants to filter. The success of the authors in identifying PALB2 as the disease-causing gene relied heavily on the "one bad copy in normal tissue, two bad copies in cancer" rule, but most other severe diseases do not provide such convenient sign-posts.

The sheer scale of the noise variation in the human genome has only really become apparent in the last two years, following the publication of the Watson and Venter genomes. Both of these genomes contained a huge number of variants that could easily be interpreted as disease-causing, often with no clear way of distinguishing the villains from the innocent bystanders.

As such, researchers hunting for disease-causing mutations using genome-scale data will find their traditional problem is now turned on its head: instead of being unable to find plausible mutations, they will be faced with far too many possible candidates.

That problem will only get worse as we move from exome sequences - which at least comprise segments of protein-coding DNA for which we mostly understand the basic biological rules - to the vast, swampy, uncharted morass of non-coding DNA that makes up the other 98% of our genomes. It's clear from recent genome-wide association studies that the majority of disease risk variants are lurking in these regions, but we're currently almost entirely unable to filter out the functional disruptors from the millions of other polymorphisms littering non-coding DNA.

So the message from this paper is mixed. On the one hand, this is a genuine triumph for brute-force genomics, a case where generating staggering amounts of sequence data produced results with very clear clinical relevance. On the other hand, filtering out the true disease mutation from the background noise owed a hefty amount to the special properties of tumour suppressor genes, and more than a little luck; this approach will not be so easy in all cancer patients, and certainly not in patients suffering from other genetic diseases.

There's a dire warning here, as the age of clinical genomics approaches with blinding speed: if we want to be able to convert masses of sequence data into useful clinical information we need to get much better at assigning function to new sequence variants, and we need to learn how to do it fast. "

"I suffer from a motor neuron disorder, in my case a variant of amyotrophic lateral sclerosis (ALS): Lou Gehrig's disease. Motor neuron disorders are far from rare: Parkinson's disease, multiple sclerosis, and a variety of lesser diseases all come under that heading. What is distinctive about ALS—the least common of this family of neuro-muscular illnesses—is firstly that there is no loss of sensation (a mixed blessing) and secondly that there is no pain. In contrast to almost every other serious or deadly disease, one is thus left free to contemplate at leisure and in minimal discomfort the catastrophic progress of one's own deterioration."

Moving, troubling, matter-of-fact description by Tony Judt in the NYR of his experiences trapped inside a body with ALS.