Showing posts with label gene expression. Show all posts
Showing posts with label gene expression. Show all posts

Thursday, May 29, 2014

Transcriptomic Evidence for Immaturity of the Prefrontal Cortex in Patients with Schizophrenia

 

This new research from Molecular Brain shows, for the first time, that the gene expression patterns in the schizophrenic prefrontal cortex (PFC) resemble those in the juvenile PFC. This can possibly open new avenues for therapeutic interventions (not with drugs), including some of the Mindsight techniques developed by Dan Siegel that target the medial prefrontal cortex.

Full Citation:
Hagihara, H, Ohira, K, Takao, K and Miyakawa, T. (2014, May 29). Transcriptomic evidence for immaturity of the prefrontal cortex in patients with schizophrenia. Molecular Brain; 7:41. doi:10.1186/1756-6606-7-41

Transcriptomic evidence for immaturity of the prefrontal cortex in patients with schizophrenia

Hideo Hagihara, Koji Ohira, Keizo Takao and Tsuyoshi Miyakawa
Author Affiliations

Abstract (provisional)


Background

Schizophrenia, a severe psychiatric disorder, has a lifetime prevalence of 1%. The exact mechanisms underlying this disorder remain unknown, though theories abound. Recent studies suggest that particular cell types and biological processes in the schizophrenic cortex have a pseudo-immature status in which the molecular properties partially resemble those in the normal immature brain. However, genome-wide gene expression patterns in the brains of patients with schizophrenia and those of normal infants have not been directly compared. Here, we show that the gene expression patterns in the schizophrenic prefrontal cortex (PFC) resemble those in the juvenile PFC.

Results

We conducted a gene expression meta-analysis in which, using microarray data derived from different studies, altered expression patterns in the dorsolateral PFC (DLFC) of patients with schizophrenia with those in the DLFC of developing normal human brains, revealing a striking similarity. The results were replicated in a second DLFC data set and a medial PFC (MFC) data set. We also found that about half of the genes representing the transcriptomic immaturity of the schizophrenic PFC were developmentally regulated in fast-spiking interneurons, astrocytes, and oligodendrocytes. Furthermore, to test whether medications, which often confound the results of postmortem analyses, affect on the juvenile-like gene expressions in the schizophrenic PFC, we compared the gene expression patterns showing transcriptomic immaturity in the schizophrenic PFC with those in the PFC of rodents treated with antipsychotic drugs. The results showed no apparent similarities between the two conditions, suggesting that the juvenile-like gene expression patterns observed in the schizophrenic PFC could not be accounted for by medication effects. Moreover, the developing human PFC showed a gene expression pattern similar to that of the PFC of naive Schnurri-2 knockout mice, an animal model of schizophrenia with good face and construct validity. This result also supports the idea that the transcriptomic immaturity of the schizophrenic PFC is not due to medication effects.

Conclusions

Collectively, our results provide evidence that pseudo-immaturity of the PFC resembling juvenile PFC may be an endophenotype of schizophrenia.

The complete article is available as a provisional PDF. The fully formatted PDF and HTML versions are in production.

Tuesday, January 14, 2014

The Top 10 Insights from the “Science of a Meaningful Life” in 2013 (Greater Good Science Center)

From UC Berkeley's Greater Good Science Center, here is a collection of 10 research summaries on topics related to having a meaningful life, for example the idea that a meaningful and healthy life is not the same as a happy life; or that mindfulness meditation can make people more altruistic (even when doing so has barriers) and that the emotional benefits of altruism are likely to be human universals.

There is some nice research summarized here - and for a nice change of pace, the news is good.

The Top 10 Insights from the “Science of a Meaningful Life” in 2013


Below are some of the most surprising, provocative, and inspiring findings published this past year.
By Jason Marsh, Devan Davison, Bianca Lorenz, Lauren Klein, Jeremy Adam Smith, Emiliana R. Simon-Thomas

January 2, 2014


The past few years have been marked by two major trends in the science of a meaningful life.

One is that researchers continued to add sophistication and depth to our understanding of positive feelings and behaviors. Happiness is good for you, but not all the time; empathy ties us together, and can overwhelm you; humans are born with an innate sense of fairness and morality, that changes in response to context. This has been especially true of the study of mindfulness and attention, which is producing more and more potentially life-changing discoveries.

The other factor involves intellectual diversity. The turn from the study of human dysfunction to human strengths and virtues may have started in psychology, with the positive psychology movement, but that perspective spread to adjacent disciplines like neuroscience and criminology, and from there to fields like sociology, economics, and medicine. Across all these fields, we’re seeing more and more support for the idea that empathy, compassion, and happiness are more than you-have-it-or-not capacities, but skills that can be cultivated by individuals and by groups of people through deliberate decisions.

In 2013, the UC Berkeley Greater Good Science Center is now part of a mature, multidisciplinary movement. Here are 10 scientific insights published in peer-reviewed journals from the past year that we anticipate will be cited in scientific studies, help shift public debate, and change individual behavior in the year to come.


A meaningful life is different—and healthier—than a happy one.



The research we cover here at the Greater Good Science Center is often referred to as “the science of happiness,” yet our tagline is “The Science of a Meaningful Life.” Meaning, happiness—is there a difference?

New research suggests that there is. When a study in the Journal of Positive Psychology tried to disentangle the concepts of “meaning” and “happiness” by surveying roughly 400 Americans, it found considerable overlap between the two—but also some key distinctions.

Based on those surveys, for instance, feeling good and having one’s needs met seem integral to happiness but unrelated to meaning. Happy people seem to dwell in the present moment, not the past or future, whereas meaning seems to involve linking past, present, and future. People derive meaningfulness (but not necessarily happiness) from helping others—being a “giver”—whereas people derive happiness (but not necessarily meaningfulness) from being a “taker.” And while social connections are important to meaning and happiness, the type of connection matters: Spending time with friends is important to happiness but not meaning, whereas the opposite is true for spending time with loved ones.

And other research published in the Proceedings of the National Academy of Sciences suggests that these differences might have important implications for our health. When Barbara Fredrickson and Steve Cole compared the immune cells of people who reported being “happy” with those of people who reported “a sense of direction and meaning,” the people leading meaningful lives seemed to have stronger immune systems.


The emotional benefits of altruism might be a human universal.



One of the most significant findings to have emerged from the sciences of happiness and altruism has been this: Altruism boosts happiness. Spending on others makes us happier than spending on ourselves—at least among the relatively affluent North Americans who have participated in this research.

But a paper published in the Journal of Personality and Social Psychology suggested that this finding holds up around the world, even in countries where sharing with others might threaten someone’s own subsistence.

In one study, the researchers examined data of more than 200,000 people from 136 countries; they determined that donating to charity in the past month boosts happiness “in most individual countries and all major regions of the world,” cutting across cultures and levels of economic well-being. It was even true regardless of whether someone said they’d had trouble securing food for their family in the past year.

When the researchers zeroed in on three countries with vastly different levels of wealth—Canada, Uganda, and India—they found that people reported greater happiness recalling a time when they’d spent money on others than when they’d spent on themselves. And in a study comparing Canada and South Africa, people reported feeling happier after donating to charity than after buying themselves a treat, even though they would never meet the beneficiary of their largess. This suggests to the researchers that their happiness didn’t result from feeling like they were strengthening social connections or improving their reputation but from a deeply ingrained human instinct.

In fact, they argue, the nearly universal emotional benefits of altruism suggest it is a product of evolution, perpetuating behavior that “may have carried short-term costs but long-term benefits for survival over human evolutionary history.”


Mindfulness meditation makes people more altruistic—even when confronted with barriers to compassionate action.



In March, the GGSC hosted a conference called “Practicing Mindfulness & Compassion,” where speakers made the case that the practice of mindfulness—the moment-by-moment awareness of our thoughts, feelings, and surrounding—doesn’t just improve our individual health but also makes us more compassionate toward others. Coincidentally, just weeks after the conference, two new studies bolstered this claim.

The first study, published in Psychological Science, found that people who took an eight-week mindfulness meditation course were significantly more likely than a control group to give up their waiting-room seat for a person on crutches. This was true despite the fact that other people in the waiting room (who were secretly working with the researchers) didn’t acknowledge the person in need or make any gesture to give up their own seats; prior research suggests that this kind of inaction strongly deters bystanders from helping out, but that wasn’t the case when the bystanders had received training in mindfulness.

A few weeks later, another study published in Psychological Science echoed that finding. In this second study, which was unrelated to the first, people who had practiced a mindfulness-based “compassion meditation” for a total of just seven hours over two weeks were significantly more likely than people who hadn’t received the training to give money to a stranger in need. What’s more, after completing their training, the meditation group showed noticeable changes in brain activity, including in networks linked to understanding the suffering of others.

“Our findings,” write the authors of the second study, “support the possibility that compassion and altruism can be viewed as trainable skills rather than as stable traits.”




Meditation changes gene expression.


Are genes destiny? They certainly influence our behavior and health outcomes—for example, one study published in 2013 found that genes make some people more inclined to focus on the negative. But more and more research is revealing how it’s a two-way street: Our choices can also influence how our genes behave.

In 2013, a collaborative project between researchers in Spain and France and at the University of Wisconsin found that when experienced meditators meditate, they quiet down the genes that express bodily inflammation in response to stress.

How did they figure this out? Before and after two different retreat days, the researchers drew blood samples from 19 long-term meditators (averaging more than 6000 lifetime hours) and 21 inexperienced people. During the retreat, the meditators meditated and discussed the benefits and advantages of meditation; the non-meditators read, played games, and walked around.

After this experience, the meditators’ inflammation genes—measured by blood concentrations of enzymes that catalyze or are a byproduct of gene expression—were less active. Blood samples from the people in the leisure-day condition did not show these changes.

Why does this matter? The researchers also looked at their study participants’ ability to recover from a stressful event. Long-term meditators’ ability to turn down inflammatory genes, it turns out, predicted how quickly stress hormones in their saliva diminished after a stressful experience—a sign of healthy coping and resilience that can potentially lead to a longer life.

This is good news to people who come from a family of stress cases who are stress-prone themselves: There are steps you can take to mitigate the impact of stressful events. Hard as it may be to find time or get excited about meditating, mounting evidence suggests that it can offer more concrete advantages to a healthy life than the leisurely activities we more readily seek.




Mindfulness training improves teachers’ performance in the classroom.


For educators grappling with students’ behavioral problems and other sources of stress, new research suggested an effective response: mindfulness.

Although mindfulness-based programs are not uncommon in schools these days, they’ve mainly been deployed to enhance students’ social, emotional, and cognitive skills; only a handful of programs and studies have examined the benefits of mindfulness for teachers, and in those cases, the research has focused largely on the general benefits for teachers’ mental health.

But in 2013, researchers at the University of Wisconsin’s Center for Investigating Healthy Minds broke new ground when they studied the impact of an eight-week mindfulness course developed specifically for teachers, looking not only at its effects on the teachers’ emotional well-being and levels of stress but also on their performance in the classroom.

They found that teachers randomly assigned to take the course felt less anxious, depressed, and burned out afterward, and felt more compassionate toward themselves. What’s more, according to experts who watched the teachers in action, these teachers ran more productive classrooms after completing the course and improved at managing their students’ behavior as well. The results, published in Mind, Brain, and Education, show that stress and burnout levels actually increased among teachers who didn’t take the course.

The researchers speculate that mindfulness may carry these benefits for teachers because it helps them cope with classroom stress and stay focused on their work. “Mindfulness-based practices offer promise as a tool for enhancing teaching quality,” write the researchers, “which may, in turn, promote positive student outcomes and school success.”




There’s nothing simple about happiness.


Who doesn’t want to be happy? Happy is always good, right?

Sure. Just don’t be too happy, OK? Because June Gruber and her colleagues analyzed health data and found that it’s much better to be a little bit happy over a long period of time than to experience wild spikes in happiness. Another study, published in the journal Emotion, showed how seeking happiness at the right time may be more important than seeking happiness all the time. Instead, allowing yourself to feel emotions appropriate to a situation—whether or not they are pleasant in the moment—is a key to long-lasting happiness.

In a study published earlier in the year in the journal Psychological Science, Sonja Lyubomirsky and Kristin Layous found that not all research-approved happiness practices work for everyone all the time. “Let’s say you publish a study that shows being grateful makes you happy—which it does,” Lyubomirsky recently told us. “But, actually, it’s much harder than that. It’s actually very hard to be grateful, and to be grateful on a regular basis, and at the right time, and for the right things.” She continued:
So, for example, some people have a lot of social support, some people have little social support, some people are extroverted, some people are introverted—you have to take into account the happiness seeker before you give them advice about what should make them happy. And then there are factors relevant to the activity that you do. How is it that you’re trying to become happier? How is it that you’re trying to stave off adaptation? Are you trying to appreciate more? Are you trying to do more acts of kindness? Are you trying to savor the moment? The kind of person you are, the different kinds of activities, and how often you do them, and where you do them—these are all going to matter.
The bottom line might be that if happiness were really that simple, we’d all be happy all the time. But we’re not, and that appears to be because there is no rigid formula for happiness. It’s a state that comes and goes in response to how we’re changing and how our world is changing.




Gratitude can save your life.


Or at least help lessen suicidal thoughts, says a study published in the Journal of Research in Personality.

Across a four-week period, 209 college students answered questions to measure depression, suicidal thoughts, grit, gratitude, and meaning in life. The idea was to see if the positive traits—grit and gratitude—mitigated the negative ones. Since depression is a large contributing factor to suicide, they controlled for that variable throughout the study.

Grit, said the authors, is “characterized by the long-term interests and passions, and willingness to persevere through obstacles and setbacks to make progress toward goals aligned or separate from these passionate pursuits.” It stands to reason that someone with lots of grit wouldn’t waste much time on suicidal thoughts.

But what about gratitude? That entails noticing the benefits and gifts received from others, and it gives an individual a sense of belonging. That should make life living—and, indeed, the researchers found that gratitude and grit worked synergistically together to make life more meaningful and to reduce suicidal thoughts, independent of depression symptoms.

As the authors note, their study has huge clinical implications: If therapists can specifically foster gratitude in suicidal people, they should be able to increase their sense that life is worth living. This new finding adds to a pile of new research on the benefits of gratitude. Saying “thanks” can make you happier, sustain your marriage through tough times, reduce envy, and even improve physical health.




Employees are motivated by giving as well as getting.


Over the past two decades, work satisfaction has declined, while time spent at work has significantly increased. Not a good combination!

Would paying people more money help? Some studies have shown that rewarding employees for their hard work and late nights at the office with a bonus will make things a little better and quiet dissatisfaction. But in September, through the collaborative research of Lalin Anik, Lara B. Aknin, Michael I. Norton, Elizabeth W. Dunn, and Jordi Quoidbach, we learned that employee bonuses might have the most positive effects when they’re spent on others. The researchers suggested an alternative bonus offer that has the potential to provide some of the same benefits as team-based compensation—increased social support, cohesion, and performance—while carrying fewer drawbacks.

Their first experiment focused on broad, self-reported measures of the impact of prosocial bonuses on an employee’s job satisfaction. They were either given a bonus to spend on charity or were not given a bonus at all. Those who gave to charities reported increased happiness and job satisfaction. The second experiment was conducted in two parts—both focused on “sports team orientation” by looking at the difference between donating to a charity or a fellow employee—and attempted to see if these improved actual performance. In the first part of the experiment, these participants were given $20 and told to spend it on a teammate or on themselves over the course of the week. In the second part of this experiment, they were instructed to spend $22 on themselves or on a specified teammate over the course of the week. Both of these experiments found more positive effects for givers than those who spent the $22 on themselves.

This collaborative research indicates that prosocial bonuses can benefit both individuals and teams, on both psychological and “bottom line” indicators, in both the short and long-term. So when you receive your bonus this year, you might want to think twice before buying those pair of shoes you’ve been dying for, instead consider spending it on someone else—because, according to this research, you’ll probably be much happier and more satisfied with your job.


Subtle contextual factors influence our sense of right and wrong.



An out-of-control train will kill five people. You can switch the train onto another track and save them—but doing so will kill one person. What should you do?

A series of experiments published in the journal Psychological Science suggests that on one day you’ll divert the train and save those five lives—but on another you might not. It all depends on how the dilemma is framed and how we’ve been thinking about ourselves.

Through the train dilemma and other experiments, the study revealed two factors that can influence our moral decisions. The first involves how morality has been defined for you, in this case around consequences or rules. For example, when researchers asked participants to think in terms of consequences, some readily diverted the train, thus saving four lives. On the other hand, those who prompted to think in terms of rules (e.g., “thou shalt not kill”) let the five die. But that factor was influenced by another that depends on memory and whether your past ethical or unethical behavior is on your mind—a memory of a good deed might make you more likely to cheat, for example, if urged to think of consequences. It’s the complex interaction between those two factors that shapes your decision.

That wasn’t the only study published during the past year that revealed how susceptible we are to context. One study found that people are more moral in the morning than in the afternoon. Another study, cleverly titled “Hunger Games,” found that when people are hungry, they express more support for charitable giving. Yet another experiment discovered that thinking about money makes you more inclined to cheat at a game—but thinking about time keeps you honest.

The bottom line is that our sense of right and wrong is heavily influenced by seemingly trivial variables in memory, in our bodies, and in changes within our environment. This doesn’t necessarily lead us to pessimistic conclusions about humanity—in fact, knowing how our minds work might help us to make better moral decisions.


Anyone can cultivate empathic skills—even psychopaths.



In daily life, calling someone a “psychopath” or a “sociopath” is a way of saying that the person is beyond redemption. Are they?

When neuroscientist James Fallon accidentally discovered that his brain resembled that of a psychopath—showing less activity in areas of the frontal lobe linked to empathy—he was confused. After all, Fallon was a happily married man, with a career and good relationships with colleagues. How could he be beyond redemption?

Additional genetic tests revealed “high-risk alleles for aggression, violence and low empathy.” What was going on? Fallon decided he was a “pro-social psychopath,” someone whose genetic and neurological inheritance makes it hard for him to feel empathy, but who was gifted with a good upbringing and environment—good enough to overcome latent psychopathic tendencies.

This self-description found support in a study published this year by Swiss and German researchers, which showed education levels and “social desirability” seemed to improve empathy in diagnosed psychopaths. Another new study found that empathy deficits don’t necessarily lead to aggression.

It seems that psychopaths can be taught to feel empathy and compassion, though they have a disability that makes developing those skills difficult. When a team of researchers looked at the brain activity of psychopathic criminals in the Netherlands, for example, they discovered the predictable empathic deficits. But they also found that it made a difference in their brains to simply ask the criminals to empathize with others—hinting that empathy may be repressed rather than missing entirely in people classified as psychopaths. For some, at least, it may help a great deal to lift that repression.

Psychopathy remains an intractable mental illness and social problem—this year’s studies of treatment did not reveal a magic bullet that would turn psychopaths into angels. But we can take heart in the fact that if they can develop empathic skills, anyone can.

Monday, January 06, 2014

David Dobbs - The Social Life of Genes (on Epigenetics)

This article came out in Pacific Standard back in September of last year, and I likely posted it then. But it turned up in tabs again recently and it still feels like an excellent and important article.

The Social Life of Genes

By David Dobbs • September 03, 2013

gene-expression

Your DNA is not a blueprint. Day by day, week by week, your genes are in a conversation with your surroundings. Your neighbors, your family, your feelings of loneliness: They don’t just get under your skin, they get into the control rooms of your cells. Inside the new social science of genetics.


A few years ago, Gene Robinson, of Urbana, Illinois, asked some associates in southern Mexico to help him kidnap some 1,000 newborns. For their victims they chose bees. Half were European honeybees, Apis mellifera ligustica, the sweet-tempered kind most beekeepers raise. The other half were ligustica’s genetically close cousins, Apis mellifera scutellata, the African strain better known as killer bees. Though the two subspecies are nearly indistinguishable, the latter defend territory far more aggressively. Kick a European honeybee hive and perhaps a hundred bees will attack you. Kick a killer bee hive and you may suffer a thousand stings or more. Two thousand will kill you.

Working carefully, Robinson’s conspirators—researchers at Mexico’s National Center for Research in Animal Physiology, in the high resort town of Ixtapan de la Sal—jiggled loose the lids from two African hives and two European hives, pulled free a few honeycomb racks, plucked off about 250 of the youngest bees from each hive, and painted marks on the bees’ tiny backs. Then they switched each set of newborns into the hive of the other subspecies.

Robinson, back in his office at the University of Illinois at Urbana-Champaign’s Department of Entomology, did not fret about the bees’ safety. He knew that if you move bees to a new colony in their first day, the colony accepts them as its own. Nevertheless, Robinson did expect the bees would be changed by their adoptive homes: He expected the killer bees to take on the European bees’ moderate ways and the European bees to assume the killer bees’ more violent temperament. Robinson had discovered this in prior experiments. But he hadn’t yet figured out how it happened.

He suspected the answer lay in the bees’ genes. He didn’t expect the bees’ actual DNA to change: Random mutations aside, genes generally don’t change during an organism’s lifetime. Rather, he suspected the bees’ genes would behave differently in their new homes—wildly differently.

This notion was both reasonable and radical. Scientists have known for decades that genes can vary their level of activity, as if controlled by dimmer switches. Most cells in your body contain every one of your 22,000 or so genes. But in any given cell at any given time, only a tiny percentage of those genes is active, sending out chemical messages that affect the activity of the cell. This variable gene activity, called gene expression, is how your body does most of its work.

Sometimes these turns of the dimmer switch correspond to basic biological events, as when you develop tissues in the womb, enter puberty, or stop growing. At other times gene activity cranks up or spins down in response to changes in your environment. Thus certain genes switch on to fight infection or heal your wounds—or, running amok, give you cancer or burn your brain with fever. Changes in gene expression can make you thin, fat, or strikingly different from your supposedly identical twin. When it comes down to it, really, genes don’t make you who you are. Gene expression does. And gene expression varies depending on the life you live.

Every biologist accepts this. That was the safe, reasonable part of Robinson’s notion. Where he went out on a limb was in questioning the conventional wisdom that environment usually causes fairly limited changes in gene expression. It might sharply alter the activity of some genes, as happens in cancer or digestion. But in all but a few special cases, the thinking went, environment generally brightens or dims the activity of only a few genes at a time.

Robinson, however, suspected that environment could spin the dials on “big sectors of genes, right across the genome”—and that an individual’s social environment might exert a particularly powerful effect. Who you hung out with and how they behaved, in short, could dramatically affect which of your genes spoke up and which stayed quiet—and thus change who you were.

Robinson was already seeing this in his bees. The winter before, he had asked a new post-doc, Cédric Alaux, to look at the gene-expression patterns of honeybees that had been repeatedly exposed to a pheromone that signals alarm. (Any honeybee that detects a threat emits this pheromone. It happens to smell like bananas. Thus “it’s not a good idea,” says Alaux, “to eat a banana next to a bee hive.”)

To a bee, the pheromone makes a social statement: Friends, you are in danger. Robinson had long known that bees react to this cry by undergoing behavioral and neural changes: Their brains fire up and they literally fly into action. He also knew that repeated alarms make African bees more and more hostile. When Alaux looked at the gene-expression profiles of the bees exposed again and again to alarm pheromone, he and Robinson saw why: With repeated alarms, hundreds of genes—genes that previous studies had associated with aggression—grew progressively busier. The rise in gene expression neatly matched the rise in the aggressiveness of the bees’ response to threats.

Robinson had not expected that. “The pheromone just lit up the gene expression, and it kept leaving it higher.” The reason soon became apparent: Some of the genes affected were transcription factors—genes that regulate other genes. This created a cascading gene-expression response, with scores of genes responding.

This finding inspired Robinson’s kidnapping-and-cross-fostering study. Would moving baby bees to wildly different social environments reshape the curves of their gene-expression responses? Down in Ixtapan, Robinson’s collaborators suited up every five to 10 days, opened the hives, found about a dozen foster bees in each one, and sucked them up with a special vacuum. The vacuum shot them into a chamber chilled with liquid nitrogen. The intense cold instantly froze the bees’ every cell, preserving the state of their gene activity at that moment. At the end of six weeks, when the researchers had collected about 250 bees representing every stage of bee life, the team packed up the frozen bees and shipped them to Illinois.

There, Robinson’s staff removed the bees’ sesame-seed-size brains, ground them up, and ran them through a DNA microarray machine. This identified which genes were busy in a bee’s brain at the moment it met the bee-vac. When Robinson sorted his data by group—European bees raised in African hives, for instance, or African bees raised normally among their African kin—he could see how each group’s genes reacted to their lives.

Robinson organized the data for each group onto a grid of red and green color-coded squares: Each square represented a different gene, and its color represented the group’s average rate of gene expression. Red squares represented genes that were especially active in most of the bees in that group; the brighter the red, the more bees in which that gene had been busy. Green squares represented genes that were silent or underactive in most of the group. The printout of each group’s results looked like a sort of cubist Christmas card.

When he got the cards, says Robinson, “the results were stunning.” For the bees that had been kidnapped, life in a new home had indeed altered the activity of “whole sectors” of genes. When their gene expression data was viewed on the cards alongside the data for groups of bees raised among their own kin, a mere glance showed the dramatic change. Hundreds of genes had flipped colors. The move between hives didn’t just make the bees act differently. It made their genes work differently, and on a broad scale.

What’s more, the cards for the adopted bees of both species came to ever more resemble, as they moved through life, the cards of the bees they moved in with. With every passing day their genes acted more like those of their new hive mates (and less like those of their genetic siblings back home). Many of the genes that switched on or off are known to affect behavior; several are associated with aggression. The bees also acted differently. Their dispositions changed to match that of their hive mates. It seemed the genome, without changing its code, could transform an animal into something very like a different subspecies.

These bees didn’t just act like different bees. They’d pretty much become different bees. To Robinson, this spoke of a genome far more fluid—far more socially fluid—than previously conceived. 

Gene Robinson, an entomologist at the University of Illinois, found that when European honeybees are raised among more aggressive African killer bees, they not only start to become as belligerent as their new hive mates—they come to genetically resemble them. (PHOTO: COURTESY OF GENE ROBINSON)

ROBINSON SOON REALIZED HE was not alone in seeing this. At conferences and in the literature, he kept bumping into other researchers who saw gene networks responding fast and wide to social life. David Clayton, a neurobiologist also on the University of Illinois campus, found that if a male zebra finch heard another male zebra finch singing nearby, a particular gene in the bird’s forebrain would “re up—and it would do so differently depending on whether the other finch was strange and threatening, or familiar and safe.

Others found this same gene, dubbed ZENK ramping up in other species. In each case, the change in ZENK’s activity corresponded to some change in behavior: a bird might relax in response to a song, or become vigilant and tense. Duke researchers, for instance, found that when female zebra finches listened to male zebra finches’ songs, the females’ ZENK gene triggered massive gene-expression changes in their forebrains—a socially sensitive brain area in birds as well as humans. The changes differed depending on whether the song was a mating call or a territorial claim. And perhaps most remarkably, all of these changes happened incredibly fast—within a half hour, sometimes within just five minutes.

ZENK, it appeared, was a so-called “immediate early gene,” a type of regulatory gene that can cause whole networks of other genes to change activity. These sorts of regulatory gene-expression response had already been identified in physiological systems such as digestion and immunity. Now they also seemed to drive quick responses to social conditions.

One of the most startling early demonstrations of such a response occurred in 2005 in the lab of Stanford biologist Russell Fernald. For years, Fernald had studied the African cichlid Astatotilapia burtoni, a freshwater fish about two inches long and dull pewter in color. By 2005 he had shown that among burtoni, the top male in any small population lives like some fishy pharaoh, getting far more food, territory, and sex than even the No. 2 male. This No. 1 male cichlid also sports a bigger and brighter body. And there is always only one No. 1.

I wonder, Fernald thought, what would happen if we just removed him?

So one day Fernald turned out the lights over one of his cichlid tanks, scooped out big flashy No. 1, and then, 12 hours later, flipped the lights back on. When the No. 2 cichlid saw that he was now No. 1, he responded quickly. He underwent massive surges in gene expression that immediately blinged up his pewter coloring with lurid red and blue streaks and, in a matter of hours, caused him to grow some 20 percent. It was as if Jason Schwartzman, coming to work one day to learn the big office stud had quit, morphed into Arnold Schwarzenegger by close of business.

These studies, says Greg Wray, an evolutionary biologist at Duke who has focused on gene expression for over a decade, caused quite a stir. “You suddenly realize birds are hearing a song and having massive, widespread changes in gene expression in just 15 minutes? Something big is going on.”

This big something, this startlingly quick gene-expression response to the social world, is a phenomenon we are just beginning to understand. The recent explosion of interest in “epigenetics”—a term literally meaning “around the gene,” and referring to anything that changes a gene’s effect without changing the actual DNA sequence—has tended to focus on the long game of gene-environment interactions: how famine among expectant mothers in the Netherlands during World War II, for instance, affected gene expression and behavior in their children; or how mother rats, by licking and grooming their pups more or less assiduously, can alter the wrappings around their offspring’s DNA in ways that influence how anxious the pups will be for the rest of their lives. The idea that experience can echo in our genes across generations is certainly a powerful one. But to focus only on these narrow, long-reaching effects is to miss much of the action where epigenetic influence and gene activity is concerned. This fresh work by Robinson, Fernald, Clayton, and others—encompassing studies of multiple organisms, from bees and birds to monkeys and humans—suggests something more exciting: that our social lives can change our gene expression with a rapidity, breadth, and depth previously overlooked.

Why would we have evolved this way? The most probable answer is that an organism that responds quickly to fast-changing social environments will more likely survive them. That organism won’t have to wait around, as it were, for better genes to evolve on the species level. Immunologists discovered something similar 25 years ago: Adapting to new pathogens the old-fashioned way—waiting for natural selection to favor genes that create resistance to specific pathogens—would happen too slowly to counter the rapidly changing pathogen environment. Instead, the immune system uses networks of genes that can respond quickly and flexibly to new threats.

We appear to respond in the same way to our social environment. Faced with an unpredictable, complex, ever-changing population to whom we must respond successfully, our genes behave accordingly—as if a fast, fluid response is a matter of life or death.

ABOUT THE TIME ROBINSON was seeing fast gene expression changes in bees, in the early 2000s, he and many of his colleagues were taking notice of an up-and-coming UCLA researcher named Steve Cole.

Cole, a Californian then in his early 40s, had trained in psychology at the University of California-Santa Barbara and Stanford; then in social psychology, epidemiology, virology, cancer, and genetics at UCLA. Even as an undergrad, Cole had “this astute, fine-grained approach,” says Susan Andersen, a professor of psychology now at NYU who was one of his teachers at UC Santa Barbara in the late 1980s. “He thinks about things in very precise detail.”

In his post-doctoral work at UCLA, Cole focused on the genetics of immunology and cancer because those fields had pioneered hard-nosed gene-expression research. After that, he became one of the earliest researchers to bring the study of whole-genome gene-expression to social psychology. The gene’s ongoing, real-time response to incoming information, he realized, is where life works many of its changes on us. The idea is both reductive and expansive. We are but cells. At each cell’s center, a tight tangle of DNA writes and hands out the cell’s marching orders. Between that center and the world stand only a series of membranes.

“Porous membranes,” notes Cole.

“We think of our bodies as stable biological structures that live in the world but are fundamentally separate from it. That we are unitary organisms in the world but passing through it. But what we’re learning from the molecular processes that actually keep our bodies running is that we’re far more fluid than we realize, and the world passes through us.”

Cole told me this over dinner. We had met on the UCLA campus and walked south a few blocks, through bright April sun, to an almost empty sushi restaurant. Now, waving his chopsticks over a platter of urchin, squid, and amberjack, he said, “Every day, as our cells die off, we have to replace one to two percent of our molecular being. We’re constantly building and re-engineering new cells. And that regeneration is driven by the contingent nature of gene expression.

“This is what a cell is about. A cell,” he said, clasping some amberjack, “is a machine for turning experience into biology.”

When Cole started his social psychology research in the early 1990s, the microarray technology that spots changes in gene expression was still in its expensive infancy, and saw use primarily in immunology and cancer. So he began by using the tools of epidemiology—essentially the study of how people live their lives. Some of his early papers looked at how social experience affected men with HIV. In a 1996 study of 80 gay men, all of whom had been HIV-positive but healthy nine years earlier, Cole and his colleagues found that closeted men succumbed to the virus much more readily.

He then found that HIV-positive men who were lonely also got sicker sooner, regardless of whether they were closeted. Then he showed that closeted men without HIV got cancer and various infectious diseases at higher rates than openly gay men did. At about the same time, psychologists at Carnegie Mellon finished a well-controlled study showing that people with richer social ties got fewer common colds.

Something about feeling stressed or alone was gumming up the immune system—sometimes fatally.

“You’re besieged by a virus that’s going to kill you,” says Cole, “but the fact that you’re socially stressed and isolated seems to shut down your viral defenses. What’s going on there?”

He was determined to find out. But the research methods on hand at the time could take him only so far: “Epidemiology won’t exactly lie to you. But it’s hard to get it to tell you the whole story.” For a while he tried to figure things out at the bench, with pipettes and slides and assays. “I’d take norepinephrine [a key stress hormone] and squirt it on some infected T-cells and watch the virus grow faster. The norepinephrine was knocking down the antiviral response. That’s great. Virologists love that. But it’s not satisfying as a complete answer, because it doesn’t fully explain what’s happening in the real world.

“You can make almost anything happen in a test tube. I needed something else. I had set up all this theory. I needed a place to test it.”

His next step was to turn to rhesus monkeys, a lab species that allows controlled study. In 2007, he joined John Capitanio, a primatologist at the University of California-Davis, in looking at how social stress affected rhesus monkeys with SIV, or simian immunodeficiency virus, the monkey version of HIV. Capitanio had found that monkeys with SIV fell ill and died faster if they were stressed out by constantly being moved into new groups among strangers—a simian parallel to Cole’s 1996 study on lonely gay men.

Capitanio had run a rough immune analysis that showed the stressed monkeys mounted weak antiviral responses. Cole offered to look deeper. First he tore apart the lymph nodes—“ground central for infection”—and found that in the socially stressed monkeys, the virus bloomed around the sympathetic nerve trunks, which carry stress signals into the lymph node.

“This was a hint,” says Cole: The virus was running amok precisely where the immune response should have been strongest. The stress signals in the nerve trunks, it seemed, were getting either muted en route or ignored on arrival. As Cole looked closer, he found it was the latter: The monkeys’ bodies were generating the appropriate stress signals, but the immune system didn’t seem to be responding to them properly. Why not? He couldn’t find out with the tools he had. He was still looking at cells. He needed to look inside them.

Finally Cole got his chance. At UCLA, where he had been made a professor in 2001, he had been working hard to master gene-expression analysis across an entire genome. Microarray machines—the kind Gene Robinson was using on his bees—were getting cheaper. Cole got access to one and put it to work.

Thus commenced what we might call the lonely people studies.

First, in collaboration with University of Chicago social psychologist John Cacioppo, Cole mined a questionnaire about social connections that Cacioppo had given to 153 healthy Chicagoans in their 50s and 60s. Cacioppo and Cole identified the eight most socially secure people and the six loneliest and drew blood samples from them. (The socially insecure half-dozen were lonely indeed; they reported having felt distant from others for the previous four years.) Then Cole extracted genetic material from the blood’s leukocytes (a key immune-system player) and looked at what their DNA was up to.

He found a broad, weird, strongly patterned gene-expression response that would become mighty familiar over the next few years. Of roughly 22,000 genes in the human genome, the lonely and not-lonely groups showed sharply different gene-expression responses in 209. That meant that about one percent of the genome—a considerable portion—was responding differently depending on whether a person felt alone or connected. Printouts of the subjects’ gene-expression patterns looked much like Robinson’s red-and-green readouts of the changes in his cross-fostered bees: Whole sectors of genes looked markedly different in the lonely and the socially secure. And many of these genes played roles in inflammatory immune responses.

Now Cole was getting somewhere.

Normally, a healthy immune system works by deploying what amounts to a leashed attack dog. It detects a pathogen, then sends inflammatory and other responses to destroy the invader while also activating an anti-inflammatory response—the leash—to keep the inflammation in check. The lonely Chicagoans’ immune systems, however, suggested an attack dog off leash—even though they weren’t sick. Some 78 genes that normally work together to drive inflammation were busier than usual, as if these healthy people were fighting infection. Meanwhile, 131 genes that usually cooperate to control inflammation were underactive. The underactive genes also included key antiviral genes.

This opened a whole new avenue of insight. If social stress reliably created this gene-expression profile, it might explain a lot about why, for instance, the lonely HIV carriers in Cole’s earlier studies fell so much faster to the disease.

But this was a study of just 14 people. Cole needed more.

Over the next several years, he got them. He found similarly unbalanced gene-expression or immune-response profiles in groups including poor children, depressed people with cancer, and people caring for spouses dying of cancer. He topped his efforts off with a study in which social stress levels in young women predicted changes in their gene activity six months later. Cole and his collaborators on that study, psychologists Gregory Miller and Nicolas Rohleder of the University of British Columbia, interviewed 103 healthy Vancouver-area women aged 15 to 19 about their social lives, drew blood, and ran gene-expression profiles, and after half a year drew blood and ran profiles again. Some of the women reported at the time of the initial interview that they were having trouble with their love lives, their families, or their friends. Over the next six months, these socially troubled subjects took on the sort of imbalanced gene-expression profile Cole found in his other isolation studies: busy attack dogs and broken leashes. Except here, in a prospective study, he saw the attack dog breaking free of its restraints: Social stress changed these young women’s gene-expression patterns before his eyes. 

Gene-expression microarray printouts (this one comes from a study of autistic versus non-autistic people) depict snapshots of activity across a genome. Red squares represent genes that are more active, green squares represent genes that are less active. (PHOTO: PUBLIC DOMAIN)

IN EARLY 2009, COLE sat down to make sense of all this in a review paper that he would publish later that year in Current Directions in Psychological Science. Two years later we sat in his spare, rather small office at UCLA and discussed what he’d found. Cole, trimly built but close to six feet tall, speaks in a reedy voice that is slightly higher than his frame might lead you to expect. Sometimes, when he’s grabbing for a new thought or trying to emphasize a point, it jumps a register. He is often asked to give talks about his work, and it’s easy to see why: Relaxed but animated, he speaks in such an organized manner that you can almost see the paragraphs form in the air between you. He spends much of his time on the road. Thus the half-unpacked office, he said, gesturing around him. His lab, down the hall, “is essentially one really good lab manager”—Jesusa M. Arevalo, whom he frequently lists on his papers—“and a bunch of robots,” the machines that run the assays.

“We typically think of stress as being a risk factor for disease,” said Cole. “And it is, somewhat. But if you actually measure stress, using our best available instruments, it can’t hold a candle to social isolation. Social isolation is the best-established, most robust social or psychological risk factor for disease out there. Nothing can compete.”

This helps explain, for instance, why many people who work in high-stress but rewarding jobs don’t seem to suffer ill effects, while others, particularly those isolated and in poverty, wind up accruing lists of stress-related diagnoses—obesity, Type 2 diabetes, hypertension, atherosclerosis, heart failure, stroke.

Despite these well-known effects, Cole said he was amazed when he started finding that social connectivity wrought such powerful effects on gene expression.

“Or not that we found it,” he corrected, “but that we’re seeing it with such consistency. Science is noisy. I would’ve bet my eyeteeth that we’d get a lot of noisy results that are inconsistent from one realm to another. And at the level of individual genes that’s kind of true—there is some noise there.” But the kinds of genes that get dialed up or down in response to social experience, he said, and the gene networks and gene-expression cascades that they set off, “are surprisingly consistent—from monkeys to people, from five-year-old kids to adults, from Vancouver teenagers to 60-year-olds living in Chicago.”

COLE’S WORK CARRIES ALL kinds of implications—some weighty and practical, some heady and philosophical. It may, for instance, help explain the health problems that so often haunt the poor. Poverty savages the body. Hundreds of studies over the past few decades have tied low income to higher rates of asthma, flu, heart attacks, cancer, and everything in between. Poverty itself starts to look like a disease. Yet an empty wallet can’t make you sick. And we all know people who escape poverty’s dangers. So what is it about a life of poverty that makes us ill?

Cole asked essentially this question in a 2008 study he conducted with Miller and Edith Chen, another social psychologist then at the University of British Columbia. The paper appeared in an odd forum: Thorax, a journal about medical problems in the chest. The researchers gathered and ran gene-expression profiles on 31 kids, ranging from nine to 18 years old, who had asthma; 16 were poor, 15 well-off. As Cole expected, the group of well-off kids showed a healthy immune response, with elevated activity among genes that control pulmonary inflammation. The poorer kids showed busier inflammatory genes, sluggishness in the gene networks that control inflammation, and—in their health histories—more asthma attacks and other health problems. Poverty seemed to be mucking up their immune systems.

Cole, Chen, and Miller, however, suspected something else was at work—something that often came with poverty but was not the same thing. So along with drawing the kids’ blood and gathering their socioeconomic information, they showed them films of ambiguous or awkward social situations, then asked them how threatening they found them.

The poorer kids perceived more threat; the well-off perceived less. This difference in what psychologists call “cognitive framing” surprised no one. Many prior studies had shown that poverty and poor neighborhoods, understandably, tend to make people more sensitive to threats in ambiguous social situations. Chen in particular had spent years studying this sort of effect.

But in this study, Chen, Cole, and Miller wanted to see if they could tease apart the effect of cognitive framing from the effects of income disparity. It turned out they could, because some of the kids in each income group broke type. A few of the poor kids saw very little menace in the ambiguous situations, and a few well-off kids saw a lot. When the researchers separated those perceptions from the socioeconomic scores and laid them over the gene-expression scores, they found that it was really the kids’ framing, not their income levels, that accounted for most of the difference in gene expression. To put it another way: When the researchers controlled for variations in threat perception, poverty’s influence almost vanished. The main thing driving screwy immune responses appeared to be not poverty, but whether the child saw the social world as scary.

But where did that come from? Did the kids see the world as frightening because they had been taught to, or because they felt alone in facing it? The study design couldn’t answer that. But Cole believes isolation plays a key role. This notion gets startling support from a 2004 study of 57 school-age children who were so badly abused that state social workers had removed them from their homes. The study, often just called “the Kaufman study,” after its author, Yale psychiatrist Joan Kaufman, challenges a number of assumptions about what shapes responses to trauma or stress.

The Kaufman study at first looks like a classic investigation into the so-called depression risk gene—the serotonin transporter gene, or SERT—which comes in both long and short forms. Any single gene’s impact on mood or behavior is limited, of course, and these single-gene, or “candidate gene,” studies must be viewed with that in mind. Yet many studies have found that SERT’s short form seems to render many people (and rhesus monkeys) more sensitive to environment; according to those studies, people who carry the short SERT are more likely to become depressed or anxious if faced with stress or trauma.

Kaufman looked first to see whether the kids’ mental health tracked their SERT variants. It did: The kids with the short variant suffered twice as many mental-health problems as those with the long variant. The double whammy of abuse plus short SERT seemed to be too much.

Then Kaufman laid both the kids’ depression scores and their SERT variants across the kids’ levels of “social support.” In this case, Kaufman narrowly defined social support as contact at least monthly with a trusted adult figure outside the home. Extraordinarily, for the kids who had it, this single, modest, closely defined social connection erased about 80 percent of the combined risk of the short SERT variant and the abuse. It came close to inoculating kids against both an established genetic vulnerability and horrid abuse.

Or, to phrase it as Cole might, the lack of a reliable connection harmed the kids almost as much as abuse did. Their isolation wielded enough power to raise the question of what’s really most toxic in such situations. Most of the psychiatric literature essentially views bad experiences—extreme stress, abuse, violence—as toxins, and “risk genes” as quasi-immunological weaknesses that let the toxins poison us. And abuse is clearly toxic. Yet if social connection can almost completely protect us against the well-known effects of severe abuse, isn’t the isolation almost as toxic as the beatings and neglect?

The Kaufman study also challenges much conventional Western thinking about the state of the individual. To use the language of the study, we sometimes conceive of “social support” as a sort of add-on, something extra that might somehow fortify us. Yet this view assumes that humanity’s default state is solitude. It’s not. Our default state is connection. We are social creatures, and have been for eons. As Cole’s colleague John Cacioppo puts it in his book Loneliness, Hobbes had it wrong when he wrote that human life without civilization was “solitary, poor, nasty, brutish, and short.” It may be poor, nasty, brutish, and short. But seldom has it been solitary.

TOWARD THE END OF the dinner I shared with Cole, after the waiter took away the empty platters and we sat talking over green tea, I asked him if there was anything I should have asked but had not. He’d been talking most of three hours. Some people run dry. Cole does not. He spoke about how we are permeable fluid beings instead of stable unitary isolates; about recursive reconstruction of the self; about an engagement with the world that constantly creates a new you, only you don’t know it, because you’re not the person you would have been otherwise—you’re a one-person experiment that has lost its control.

He wanted to add one more thing: He didn’t see any of this as deterministic.

We were obviously moving away from what he could prove at this point, perhaps from what is testable. We were in fact skirting the rabbit hole that is the free-will debate. Yet he wanted to make it clear he does not see us as slaves to either environment or genes.

“You can’t change your genes. But if we’re even half right about all this, you can change the way your genes behave—which is almost the same thing. By adjusting your environment you can adjust your gene activity. That’s what we’re doing as we move through life. We’re constantly trying to hunt down that sweet spot between too much challenge and too little.

“That’s a really important part of this: To an extent that immunologists and psychologists rarely appreciate, we are architects of our own experience. Your subjective experience carries more power than your objective situation. If you feel like you’re alone even when you’re in a room filled with the people closest to you, you’re going to have problems. If you feel like you’re well supported even though there’s nobody else in sight; if you carry relationships in your head; if you come at the world with a sense that people care about you, that you’re valuable, that you’re okay; then your body is going to act as if you’re okay—even if you’re wrong about all that.”

Cole was channeling John Milton: “The mind is its own place, and in itself can make a heaven of hell, a hell of heaven.”

Of course I did not realize that at the moment. My reaction was more prosaic.

“So environment and experience aren’t the same,” I offered.

“Exactly. Two people may share the same environment but not the same experience. The experience is what you make of the environment. It appears you and I are both enjoying ourselves here, for instance, and I think we are. But if one of us didn’t like being one-on-one at a table for three hours, that person could get quite stressed out. We might have much different experiences. And you can shape all this by how you frame things. You can shape both your environment and yourself by how you act. It’s really an opportunity.”

Cole often puts it differently at the end of his talks about this line of work. “Your experiences today will influence the molecular composition of your body for the next two to three months,” he tells his audience, “or, perhaps, for the rest of your life. Plan your day accordingly.”

Thursday, December 12, 2013

Gene Expression Changes With Meditation


New research from Richard Davidson's team at the U of Wisconsin has identified gene expression changes in meditation. After eight hours of mindfulness practice, the meditators showed a range of genetic and molecular differences, including altered levels of gene-regulating machinery and reduced levels of pro-inflammatory genes, which in turn correlated with faster physical recovery from a stressful situation.

The full article is available online (the link is below the summary). Here is a summary of the findings followed by the abstract from the full article.

Gene Expression Changes With Meditation


Dec. 8, 2013 — With evidence growing that meditation can have beneficial health effects, scientists have sought to understand how these practices physically affect the body.

A new study by researchers in Wisconsin, Spain, and France reports the first evidence of specific molecular changes in the body following a period of mindfulness meditation.

The study investigated the effects of a day of intensive mindfulness practice in a group of experienced meditators, compared to a group of untrained control subjects who engaged in quiet non-meditative activities. After eight hours of mindfulness practice, the meditators showed a range of genetic and molecular differences, including altered levels of gene-regulating machinery and reduced levels of pro-inflammatory genes, which in turn correlated with faster physical recovery from a stressful situation.

"To the best of our knowledge, this is the first paper that shows rapid alterations in gene expression within subjects associated with mindfulness meditation practice," says study author Richard J. Davidson, founder of the Center for Investigating Healthy Minds and the William James and Vilas Professor of Psychology and Psychiatry at the University of Wisconsin-Madison.

"Most interestingly, the changes were observed in genes that are the current targets of anti-inflammatory and analgesic drugs," says Perla Kaliman, first author of the article and a researcher at the Institute of Biomedical Research of Barcelona, Spain (IIBB-CSIC-IDIBAPS), where the molecular analyses were conducted.

The study was published in the journal Psychoneuroendocrinology.

Mindfulness-based trainings have shown beneficial effects on inflammatory disorders in prior clinical studies and are endorsed by the American Heart Association as a preventative intervention. The new results provide a possible biological mechanism for therapeutic effects.

The results show a down-regulation of genes that have been implicated in inflammation. The affected genes include the pro-inflammatory genes RIPK2 and COX2 as well as several histone deacetylase (HDAC) genes, which regulate the activity of other genes epigenetically by removing a type of chemical tag. What's more, the extent to which some of those genes were downregulated was associated with faster cortisol recovery to a social stress test involving an impromptu speech and tasks requiring mental calculations performed in front of an audience and video camera.

Perhaps surprisingly, the researchers say, there was no difference in the tested genes between the two groups of people at the start of the study. The observed effects were seen only in the meditators following mindfulness practice. In addition, several other DNA-modifying genes showed no differences between groups, suggesting that the mindfulness practice specifically affected certain regulatory pathways.

However, it is important to note that the study was not designed to distinguish any effects of long-term meditation training from those of a single day of practice. Instead, the key result is that meditators experienced genetic changes following mindfulness practice that were not seen in the non-meditating group after other quiet activities -- an outcome providing proof of principle that mindfulness practice can lead to epigenetic alterations of the genome.

Previous studies in rodents and in people have shown dynamic epigenetic responses to physical stimuli such as stress, diet, or exercise within just a few hours.

"Our genes are quite dynamic in their expression and these results suggest that the calmness of our mind can actually have a potential influence on their expression," Davidson says.

"The regulation of HDACs and inflammatory pathways may represent some of the mechanisms underlying the therapeutic potential of mindfulness-based interventions," Kaliman says. "Our findings set the foundation for future studies to further assess meditation strategies for the treatment of chronic inflammatory conditions."

Study funding came from National Center for Complementary and Alternative Medicine (grant number P01-AT004952) and grants from the Fetzer Institute, the John Templeton Foundation, and an anonymous donor to Davidson. The study was conducted at the Center for Investigating Healthy Minds at the UW-Madison Waisman Center.

* * * * *

Rapid changes in histone deacetylases and inflammatory gene expression in expert meditators

Perla Kaliman, Marıa Jesus Alvarez-Lopez, Marta Cosın-Tomas, Melissa A. Rosenkranz, Antoine Lutz, Richard J. Davidson

Full Citation:
Kaliman, P, Alvarez-Lopez, MJ, Cosın-Tomas, M, Rosenkranz, MA, Lutz, A, Davidson, RJ. (2014). Rapid changes in histone deacetylases and inflammatory gene expression in expert meditators. Psychoneuroendocrinology; 40, 96—107. DOI: 10.1016/j.psyneuen.2013.11.004

Summary

Background: A growing body of research shows that mindfulness meditation can alter neural, behavioral and biochemical processes. However, the mechanisms responsible for such clinically relevant effects remain elusive.

Methods: Here we explored the impact of a day of intensive practice of mindfulness meditation in experienced subjects (n = 19) on the expression of circadian, chromatin modulatory and inflammatory genes in peripheral blood mononuclear cells (PBMC). In parallel, we analyzed a control group of subjects with no meditation experience who engaged in leisure activities in the same environment (n = 21). PBMC from all participants were obtained before (t1) and after (t2) the intervention (t2 t1 = 8 h) and gene expression was analyzed using custom pathway focused quantitative-real time PCR assays. Both groups were also presented with the Trier Social Stress Test (TSST).

Results: Core clock gene expression at baseline (t1) was similar between groups and their rhythmicity was not influenced in meditators by the intensive day of practice. Similarly, we found that all the epigenetic regulatory enzymes and inflammatory genes analyzed exhibited similar basal expression levels in the two groups. In contrast, after the brief intervention we detected reduced expression of histone deacetylase genes (HDAC 2, 3 and 9), alterations in global modification of histones (H4ac; H3K4me3) and decreased expression of pro-inflammatory genes (RIPK2 and COX2) in meditators compared with controls. We found that the expression of RIPK2 and HDAC2 genes was associated with a faster cortisol recovery to the TSST in both groups.

Conclusions: The regulation of HDACs and inflammatory pathways may represent some of the mechanisms underlying the therapeutic potential of mindfulness-based interventions. Our findings set the foundation for future studies to further assess meditation strategies for the treatment of chronic inflammatory conditions.

Monday, December 09, 2013

An Online Debate Erupts Around David Dobbs' Aeon Article Dismissing the Selfish Gene


A few days ago, I posted David Dobbs' excellent article (Die, selfish gene, die) on the need for Richard Dawkins' selfish gene theory to go the way of the dinosaurs. As noted by Ed Yong in his weekly science link-fest, I've Got Your Missing Links Right Here, the perspective Dobbs offered has been, uh, a wee bit controversial.

David Dobbs’ beautifully written but controversial take on the selfish gene metaphor. Reactions have been fierce. PZ Myers liked it and expanded on some of the ideas, Jerry Coyne loathed it and deconstructed it in two postsLarry Moran agreed with Coyne’s criticism but has his own gripes with the metaphor, Dawkins defends himself, and Dobbs defends himself (twice). All of this, I think, is enlightening and well worth reading.
These responses are certainly worth a little time to read . . . this may be a pivotal moment in evolutionary biology.

Sunday, September 08, 2013

David Dobbs - The Social Life of Genes (on Epigenetics)


This is an exceptionally well-written science article on the field of epigenetics, the ways in which experience, feelings, thoughts, people, and our environment can flip on/off switches in our genes (gene expression).
When it comes down to it, really, genes don’t make you who you are. Gene expression does. And gene expression varies depending on the life you live.

Every biologist accepts this. That was the safe, reasonable part of [Gene] Robinson’s notion. 
But this limited perspective did not account for genetic changes he was seeing in the bees he was studying. He believed there was more going on - that social environment could alter large portions of the genome, not just specific genes.
Robinson, however, suspected that environment could spin the dials on “big sectors of genes, right across the genome”—and that an individual’s social environment might exert a particularly powerful effect. Who you hung out with and how they behaved, in short, could dramatically affect which of your genes spoke up and which stayed quiet—and thus change who you were.
This was provocative - and similar ideas espoused by E.O. Wilson had made him the target of criticism by materialist scientists since the publication of Sociobiology: The New Synthesis in 1975. The criticism became ridicule and personal attacks earlier this year when Wilson released The Social Conquest of Earth.


Wilson argued that our innate, biological need for group membership - not just family, but clan - can be both a blessing and a curse.

Another researcher, Steven Cole, whose background was in psychology (UC Santa Barbara), and then in social psychology, epidemiology, virology, cancer, and genetics at UCLA, speculated that the gene’s ongoing, real-time response to incoming environmental information
is where life works many of its changes on us. The idea is both reductive and expansive. We are but cells. At each cell’s center, a tight tangle of DNA writes and hands out the cell’s marching orders. Between that center and the world stand only a series of membranes.
Here is more:
“We think of our bodies as stable biological structures that live in the world but are fundamentally separate from it. That we are unitary organisms in the world but passing through it. But what we’re learning from the molecular processes that actually keep our bodies running is that we’re far more fluid than we realize, and the world passes through us.”
One of his important findings:
“We typically think of stress as being a risk factor for disease,” said Cole. “And it is, somewhat. But if you actually measure stress, using our best available instruments, it can’t hold a candle to social isolation. Social isolation is the best-established, most robust social or psychological risk factor for disease out there. Nothing can compete.
This is an excellently written, well-researched article - and this is the future of medicine. It's well worth your time to read - via Pacific Standard Magazine.

The Social Life of Genes 

Your DNA is not a blueprint. Day by day, week by week, your genes are in a conversation with your surroundings. Your neighbors, your family, your feelings of loneliness: They don’t just get under your skin, they get into the control rooms of your cells. Inside the new social science of genetics.



September 3, 2013 • By David Dobbs

(ILLUSTRATION: JEREMY DIMMOCK) 

A few years ago, Gene Robinson, of Urbana, Illinois, asked some associates in southern Mexico to help him kidnap some 1,000 newborns. For their victims they chose bees. Half were European honeybees, Apis mellifera ligustica, the sweet-tempered kind most beekeepers raise. The other half were ligustica’s genetically close cousins, Apis mellifera scutellata, the African strain better known as killer bees. Though the two subspecies are nearly indistinguishable, the latter defend territory far more aggressively. Kick a European honeybee hive and perhaps a hundred bees will attack you. Kick a killer bee hive and you may suffer a thousand stings or more. Two thousand will kill you.

Working carefully, Robinson’s conspirators—researchers at Mexico’s National Center for Research in Animal Physiology, in the high resort town of Ixtapan de la Sal—jiggled loose the lids from two African hives and two European hives, pulled free a few honeycomb racks, plucked off about 250 of the youngest bees from each hive, and painted marks on the bees’ tiny backs. Then they switched each set of newborns into the hive of the other subspecies.

Robinson, back in his office at the University of Illinois at Urbana-Champaign’s Department of Entomology, did not fret about the bees’ safety. He knew that if you move bees to a new colony in their first day, the colony accepts them as its own. Nevertheless, Robinson did expect the bees would be changed by their adoptive homes: He expected the killer bees to take on the European bees’ moderate ways and the European bees to assume the killer bees’ more violent temperament. Robinson had discovered this in prior experiments. But he hadn’t yet figured out how it happened.

He suspected the answer lay in the bees’ genes. He didn’t expect the bees’ actual DNA to change: Random mutations aside, genes generally don’t change during an organism’s lifetime. Rather, he suspected the bees’ genes would behave differently in their new homes—wildly differently.

This notion was both reasonable and radical. Scientists have known for decades that genes can vary their level of activity, as if controlled by dimmer switches. Most cells in your body contain every one of your 22,000 or so genes. But in any given cell at any given time, only a tiny percentage of those genes is active, sending out chemical messages that affect the activity of the cell. This variable gene activity, called gene expression, is how your body does most of its work. 

Sometimes these turns of the dimmer switch correspond to basic biological events, as when you develop tissues in the womb, enter puberty, or stop growing. At other times gene activity cranks up or spins down in response to changes in your environment. Thus certain genes switch on to fight infection or heal your wounds—or, running amok, give you cancer or burn your brain with fever. Changes in gene expression can make you thin, fat, or strikingly different from your supposedly identical twin. When it comes down to it, really, genes don’t make you who you are. Gene expression does. And gene expression varies depending on the life you live.

Every biologist accepts this. That was the safe, reasonable part of Robinson’s notion. Where he went out on a limb was in questioning the conventional wisdom that environment usually causes fairly limited changes in gene expression. It might sharply alter the activity of some genes, as happens in cancer or digestion. But in all but a few special cases, the thinking went, environment generally brightens or dims the activity of only a few genes at a time.

Robinson, however, suspected that environment could spin the dials on “big sectors of genes, right across the genome”—and that an individual’s social environment might exert a particularly powerful effect. Who you hung out with and how they behaved, in short, could dramatically affect which of your genes spoke up and which stayed quiet—and thus change who you were.

Robinson was already seeing this in his bees. The winter before, he had asked a new post-doc, Cédric Alaux, to look at the gene-expression patterns of honeybees that had been repeatedly exposed to a pheromone that signals alarm. (Any honeybee that detects a threat emits this pheromone. It happens to smell like bananas. Thus “it’s not a good idea,” says Alaux, “to eat a banana next to a bee hive.”)

To a bee, the pheromone makes a social statement: Friends, you are in danger. Robinson had long known that bees react to this cry by undergoing behavioral and neural changes: Their brains fire up and they literally fly into action. He also knew that repeated alarms make African bees more and more hostile. When Alaux looked at the gene-expression profiles of the bees exposed again and again to alarm pheromone, he and Robinson saw why: With repeated alarms, hundreds of genes—genes that previous studies had associated with aggression—grew progressively busier. The rise in gene expression neatly matched the rise in the aggressiveness of the bees’ response to threats.

Robinson had not expected that. “The pheromone just lit up the gene expression, and it kept leaving it higher.” The reason soon became apparent: Some of the genes affected were transcription factors—genes that regulate other genes. This created a cascading gene-expression response, with scores of genes responding.

This finding inspired Robinson’s kidnapping-and-cross-fostering study. Would moving baby bees to wildly different social environments reshape the curves of their gene-expression responses? Down in Ixtapan, Robinson’s collaborators suited up every five to 10 days, opened the hives, found about a dozen foster bees in each one, and sucked them up with a special vacuum. The vacuum shot them into a chamber chilled with liquid nitrogen. The intense cold instantly froze the bees’ every cell, preserving the state of their gene activity at that moment. At the end of six weeks, when the researchers had collected about 250 bees representing every stage of bee life, the team packed up the frozen bees and shipped them to Illinois.

There, Robinson’s staff removed the bees’ sesame-seed-size brains, ground them up, and ran them through a DNA microarray machine. This identified which genes were busy in a bee’s brain at the moment it met the bee-vac. When Robinson sorted his data by group—European bees raised in African hives, for instance, or African bees raised normally among their African kin—he could see how each group’s genes reacted to their lives.

Robinson organized the data for each group onto a grid of red and green color-coded squares: Each square represented a different gene, and its color represented the group’s average rate of gene expression. Red squares represented genes that were especially active in most of the bees in that group; the brighter the red, the more bees in which that gene had been busy. Green squares represented genes that were silent or underactive in most of the group. The printout of each group’s results looked like a sort of cubist Christmas card.

When he got the cards, says Robinson, “the results were stunning.” For the bees that had been kidnapped, life in a new home had indeed altered the activity of “whole sectors” of genes. When their gene expression data was viewed on the cards alongside the data for groups of bees raised among their own kin, a mere glance showed the dramatic change. Hundreds of genes had flipped colors. The move between hives didn’t just make the bees act differently. It made their genes work differently, and on a broad scale.

What’s more, the cards for the adopted bees of both species came to ever more resemble, as they moved through life, the cards of the bees they moved in with. With every passing day their genes acted more like those of their new hive mates (and less like those of their genetic siblings back home). Many of the genes that switched on or off are known to affect behavior; several are associated with aggression. The bees also acted differently. Their dispositions changed to match that of their hive mates. It seemed the genome, without changing its code, could transform an animal into something very like a different subspecies.

These bees didn’t just act like different bees. They’d pretty much become different bees. To Robinson, this spoke of a genome far more fluid—far more socially fluid—than previously conceived. 

Gene Robinson, an entomologist at the University of Illinois, found that when European honeybees are raised among more aggressive African killer bees, they not only start to become as belligerent as their new hive mates—they come to genetically resemble them. (PHOTO: COURTESY OF GENE ROBINSON)

ROBINSON SOON REALIZED HE was not alone in seeing this. At conferences and in the literature, he kept bumping into other researchers who saw gene networks responding fast and wide to social life. David Clayton, a neurobiologist also on the University of Illinois campus, found that if a male zebra finch heard another male zebra finch singing nearby, a particular gene in the bird’s forebrain would “re up—and it would do so differently depending on whether the other finch was strange and threatening, or familiar and safe.

Others found this same gene, dubbed ZENK ramping up in other species. In each case, the change in ZENK’s activity corresponded to some change in behavior: a bird might relax in response to a song, or become vigilant and tense. Duke researchers, for instance, found that when female zebra finches listened to male zebra finches’ songs, the females’ ZENK gene triggered massive gene-expression changes in their forebrains—a socially sensitive brain area in birds as well as humans. The changes differed depending on whether the song was a mating call or a territorial claim. And perhaps most remarkably, all
of these changes happened incredibly fast—within a half hour, sometimes within just five minutes.

ZENK, it appeared, was a so-called “immediate early gene,” a type of regulatory gene that can cause whole networks of other genes to change activity. These sorts of regulatory gene-expression response had already been identified in physiological systems such as digestion and immunity. Now they also seemed to drive quick responses to social conditions.

One of the most startling early demonstrations of such a response occurred in 2005 in the lab of Stanford biologist Russell Fernald. For years, Fernald had studied the African cichlid Astatotilapia burtoni, a freshwater fish about two inches long and dull pewter in color. By 2005 he had shown that among burtoni, the top male in any small population lives like some fishy pharaoh, getting far more food, territory, and sex than even the No. 2 male. This No. 1 male cichlid also sports a bigger and brighter body. And there is always only one No. 1.

I wonder, Fernald thought, what would happen if we just removed him?

So one day Fernald turned out the lights over one of his cichlid tanks, scooped out big flashy No. 1, and then, 12 hours later, flipped the lights back on. When the No. 2 cichlid saw that he was now No. 1, he responded quickly. He underwent massive surges in gene expression that immediately blinged up his pewter coloring with lurid red and blue streaks and, in a matter of hours, caused him to grow some 20 percent. It was as if Jason Schwartzman, coming to work one day to learn the big office stud had quit, morphed into Arnold Schwarzenegger by close of business.

These studies, says Greg Wray, an evolutionary biologist at Duke who has focused on gene expression for over a decade, caused quite a stir. “You suddenly realize birds are hearing a song and having massive, widespread changes in gene expression in just 15 minutes? Something big is going on.”

This big something, this startlingly quick gene-expression response to the social world, is a phenomenon we are just beginning to understand. The recent explosion of interest in “epigenetics”—a term literally meaning “around the gene,” and referring to anything that changes a gene’s effect without changing the actual DNA sequence—has tended to focus on the long game of gene-environment interactions: how famine among expectant mothers in the Netherlands during World War II, for instance, affected gene expression and behavior in their children; or how mother rats, by licking and grooming their pups more or less assiduously, can alter the wrappings around their offspring’s DNA in ways that influence how anxious the pups will be for the rest of their lives. The idea that experience can echo in our genes across generations is certainly a powerful one. But to focus only on these narrow, long-reaching effects is to miss much of the action where epigenetic influence and gene activity is concerned. This fresh work by Robinson, Fernald, Clayton, and others—encompassing studies of multiple organisms, from bees and birds to monkeys and humans—suggests something more exciting: that our social lives can change our gene expression with a rapidity, breadth, and depth previously overlooked.

Why would we have evolved this way? The most probable answer is that an organism that responds quickly to fast-changing social environments will more likely survive them. That organism won’t have to wait around, as it were, for better genes to evolve on the species level. Immunologists discovered something similar 25 years ago: Adapting to new pathogens the old-fashioned way—waiting for natural selection to favor genes that create resistance to specific pathogens—would happen too slowly to counter the rapidly changing pathogen environment. Instead, the immune system uses networks of genes that can respond quickly and flexibly to new threats.

We appear to respond in the same way to our social environment. Faced with an unpredictable, complex, ever-changing population to whom we must respond successfully, our genes behave accordingly—as if a fast, fluid response is a matter of life or death.

ABOUT THE TIME ROBINSON was seeing fast gene expression changes in bees, in the early 2000s, he and many of his colleagues were taking notice of an up-and-coming UCLA researcher named Steve Cole.

Cole, a Californian then in his early 40s, had trained in psychology at the University of California-Santa Barbara and Stanford; then in social psychology, epidemiology, virology, cancer, and genetics at UCLA. Even as an undergrad, Cole had “this astute, fine-grained approach,” says Susan Andersen, a professor of psychology now at NYU who was one of his teachers at UC Santa Barbara in the late 1980s. “He thinks about things in very precise detail.”

In his post-doctoral work at UCLA, Cole focused on the genetics of immunology and cancer because those fields had pioneered hard-nosed gene-expression research. After that, he became one of the earliest researchers to bring the study of whole-genome gene-expression to social psychology. The gene’s ongoing, real-time response to incoming information, he realized, is where life works many of its changes on us. The idea is both reductive and expansive. We are but cells. At each cell’s center, a tight tangle of DNA writes and hands out the cell’s marching orders. Between that center and the world stand only a series of membranes.

“Porous membranes,” notes Cole.

“We think of our bodies as stable biological structures that live in the world but are fundamentally separate from it. That we are unitary organisms in the world but passing through it. But what we’re learning from the molecular processes that actually keep our bodies running is that we’re far more fluid than we realize, and the world passes through us.”

Cole told me this over dinner. We had met on the UCLA campus and walked south a few blocks, through bright April sun, to an almost empty sushi restaurant. Now, waving his chopsticks over a platter of urchin, squid, and amberjack, he said, “Every day, as our cells die off, we have to replace one to two percent of our molecular being. We’re constantly building and re-engineering new cells. And that regeneration is driven by the contingent nature of gene expression.

“This is what a cell is about. A cell,” he said, clasping some amberjack, “is a machine for turning experience into biology.”

When Cole started his social psychology research in the early 1990s, the microarray technology that spots changes in gene expression was still in its expensive infancy, and saw use primarily in immunology and cancer. So he began by using the tools of epidemiology—essentially the study of how people live their lives. Some of his early papers looked at how social experience affected men with HIV. In a 1996 study of 80 gay men, all of whom had been HIV-positive but healthy nine years earlier, Cole and his colleagues found that closeted men succumbed to the virus much more readily.

He then found that HIV-positive men who were lonely also got sicker sooner, regardless of whether they were closeted. Then he showed that closeted men without HIV got cancer and various infectious diseases at higher rates than openly gay men did. At about the same time, psychologists at Carnegie Mellon finished a well-controlled study showing that people with richer social ties got fewer common colds.

Something about feeling stressed or alone was gumming up the immune system—sometimes fatally.

“You’re besieged by a virus that’s going to kill you,” says Cole, “but the fact that you’re socially stressed and isolated seems to shut down your viral defenses. What’s going on there?”

He was determined to find out. But the research methods on hand at the time could take him only so far: “Epidemiology won’t exactly lie to you. But it’s hard to get it to tell you the whole story.” For a while he tried to figure things out at the bench, with pipettes and slides and assays. “I’d take norepinephrine [a key stress hormone] and squirt it on some infected T-cells and watch the virus grow faster. The norepinephrine was knocking down the antiviral response. That’s great. Virologists love that. But it’s not satisfying as a complete answer, because it doesn’t fully explain what’s happening in the real world.

“You can make almost anything happen in a test tube. I needed something else. I had set up all this theory. I needed a place to test it.”

His next step was to turn to rhesus monkeys, a lab species that allows controlled study. In 2007, he joined John Capitanio, a primatologist at the University of California-Davis, in looking at how social stress affected rhesus monkeys with SIV, or simian immunodeficiency virus, the monkey version of HIV. Capitanio had found that monkeys with SIV fell ill and died faster if they were stressed out by constantly being moved into new groups among strangers—a simian parallel to Cole’s 1996 study on lonely gay men.

Capitanio had run a rough immune analysis that showed the stressed monkeys mounted weak antiviral responses. Cole offered to look deeper. First he tore apart the lymph nodes—“ground central for infection”—and found that in the socially stressed monkeys, the virus bloomed around the sympathetic nerve trunks, which carry stress signals into the lymph node.

“This was a hint,” says Cole: The virus was running amok precisely where the immune response should have been strongest. The stress signals in the nerve trunks, it seemed, were getting either muted en route or ignored on arrival. As Cole looked closer, he found it was the latter: The monkeys’ bodies were generating the appropriate stress signals, but the immune system didn’t seem to be responding to them properly. Why not? He couldn’t find out with the tools he had. He was still looking at cells. He needed to look inside them.

Finally Cole got his chance. At UCLA, where he had been made a professor in 2001, he had been working hard to master gene-expression analysis across an entire genome. Microarray machines—the kind Gene Robinson was using on his bees—were getting cheaper. Cole got access to one and put it to work.

Thus commenced what we might call the lonely people studies.

First, in collaboration with University of Chicago social psychologist John Cacioppo, Cole mined a questionnaire about social connections that Cacioppo had given to 153 healthy Chicagoans in their 50s and 60s. Cacioppo and Cole identified the eight most socially secure people and the six loneliest and drew blood samples from them. (The socially insecure half-dozen were lonely indeed; they reported having felt distant from others for the previous four years.) Then Cole extracted genetic material from the blood’s leukocytes (a key immune-system player) and looked at what their DNA was up to.

He found a broad, weird, strongly patterned gene-expression response that would become mighty familiar over the next few years. Of roughly 22,000 genes in the human genome, the lonely and not-lonely groups showed sharply different gene-expression responses in 209. That meant that about one percent of the genome—a considerable portion—was responding differently depending on whether a person felt alone or connected. Printouts of the subjects’ gene-expression patterns looked much like Robinson’s red-and-green readouts of the changes in his cross-fostered bees: Whole sectors of genes looked markedly different in the lonely and the socially secure. And many of these genes played roles in inflammatory immune responses.

Now Cole was getting somewhere.

Normally, a healthy immune system works by deploying what amounts to a leashed attack dog. It detects a pathogen, then sends inflammatory and other responses to destroy the invader while also activating an anti-inflammatory response—the leash—to keep the inflammation in check. The lonely Chicagoans’ immune systems, however, suggested an attack dog off leash—even though they weren’t sick. Some 78 genes that normally work together to drive inflammation were busier than usual, as if these healthy people were fighting infection. Meanwhile, 131 genes that usually cooperate to control inflammation were underactive. The underactive genes also included key antiviral genes.

This opened a whole new avenue of insight. If social stress reliably created this gene-expression profile, it might explain a lot about why, for instance, the lonely HIV carriers in Cole’s earlier studies fell so much faster to the disease.

But this was a study of just 14 people. Cole needed more.

Over the next several years, he got them. He found similarly unbalanced gene-expression or immune-response profiles in groups including poor children, depressed people with cancer, and people caring for spouses dying of cancer. He topped his efforts off with a study in which social stress levels in young women predicted changes in their gene activity six months later. Cole and his collaborators on that study, psychologists Gregory Miller and Nicolas Rohleder of the University of British Columbia, interviewed 103 healthy Vancouver-area women aged 15 to 19 about their social lives, drew blood, and ran gene-expression profiles, and after half a year drew blood and ran profiles again. Some of the women reported at the time of the initial interview that they were having trouble with their love lives, their families, or their friends. Over the next six months, these socially troubled subjects took on the sort of imbalanced gene-expression profile Cole found in his other isolation studies: busy attack dogs and broken leashes. Except here, in a prospective study, he saw the attack dog breaking free of its restraints: Social stress changed these young women’s gene-expression patterns before his eyes. 

Gene-expression microarray printouts (this one comes from a study of autistic versus non-autistic people) depict snapshots of activity across a genome. Red squares represent genes that are more active, green squares represent genes that are less active. (PHOTO: PUBLIC DOMAIN)

IN EARLY 2009, COLE sat down to make sense of all this in a review paper that he would publish later that year in Current Directions in Psychological Science. Two years later we sat in his spare, rather small office at UCLA and discussed what he’d found. Cole, trimly built but close to six feet tall, speaks in a reedy voice that is slightly higher than his frame might lead you to expect. Sometimes, when he’s grabbing for a new thought or trying to emphasize a point, it jumps a register. He is often asked to give talks about his work, and it’s easy to see why: Relaxed but animated, he speaks in such an organized manner that you can almost see the paragraphs form in the air between you. He spends much of his time on the road. Thus the half-unpacked office, he said, gesturing around him. His lab, down the hall, “is essentially one really good lab manager”—Jesusa M. Arevalo, whom he frequently lists on his papers—“and a bunch of robots,” the machines that run the assays.

“We typically think of stress as being a risk factor for disease,” said Cole. “And it is, somewhat. But if you actually measure stress, using our best available instruments, it can’t hold a candle to social isolation. Social isolation is the best-established, most robust social or psychological risk factor for disease out there. Nothing can compete.”

This helps explain, for instance, why many people who work in high-stress but rewarding jobs don’t seem to suffer ill effects, while others, particularly those isolated and in poverty, wind up accruing lists of stress-related diagnoses—obesity, Type 2 diabetes, hypertension, atherosclerosis, heart failure, stroke.

Despite these well-known effects, Cole said he was amazed when he started finding that social connectivity wrought such powerful effects on gene expression.

“Or not that we found it,” he corrected, “but that we’re seeing it with such consistency. Science is noisy. I would’ve bet my eyeteeth that we’d get a lot of noisy results that are inconsistent from one realm to another. And at the level of individual genes that’s kind of true—there is some noise there.” But the kinds of genes that get dialed up or down in response to social experience, he said, and the gene networks and gene-expression cascades that they set off, “are surprisingly consistent—from monkeys to people, from five-year-old kids to adults, from Vancouver teenagers to 60-year-olds living in Chicago.”

COLE’S WORK CARRIES ALL kinds of implications—some weighty and practical, some heady and philosophical. It may, for instance, help explain the health problems that so often haunt the poor. Poverty savages the body. Hundreds of studies over the past few decades have tied low income to higher rates of asthma, flu, heart attacks, cancer, and everything in between. Poverty itself starts to look like a disease. Yet an empty wallet can’t make you sick. And we all know people who escape poverty’s dangers. So what is it about a life of poverty that makes us ill?

Cole asked essentially this question in a 2008 study he conducted with Miller and Edith Chen, another social psychologist then at the University of British Columbia. The paper appeared in an odd forum: Thorax, a journal about medical problems in the chest. The researchers gathered and ran gene-expression profiles on 31 kids, ranging from nine to 18 years old, who had asthma; 16 were poor, 15 well-off. As Cole expected, the group of well-off kids showed a healthy immune response, with elevated activity among genes that control pulmonary inflammation. The poorer kids showed busier inflammatory genes, sluggishness in the gene networks that control inflammation, and—in their health histories—more asthma attacks and other health problems. Poverty seemed to be mucking up their immune systems.

Cole, Chen, and Miller, however, suspected something else was at work—something that often came with poverty but was not the same thing. So along with drawing the kids’ blood and gathering their socioeconomic information, they showed them films of ambiguous or awkward social situations, then asked them how threatening they found them.

The poorer kids perceived more threat; the well-off perceived less. This difference in what psychologists call “cognitive framing” surprised no one. Many prior studies had shown that poverty and poor neighborhoods, understandably, tend to make people more sensitive to threats in ambiguous social situations. Chen in particular had spent years studying this sort of effect.

But in this study, Chen, Cole, and Miller wanted to see if they could tease apart the effect of cognitive framing from the effects of income disparity. It turned out they could, because some of the kids in each income group broke type. A few of the poor kids saw very little menace in the ambiguous situations, and a few well-off kids saw a lot. When the researchers separated those perceptions from the socioeconomic scores and laid them over the gene-expression scores, they found that it was really the kids’ framing, not their income levels, that accounted for most of the difference in gene expression. To put it another way: When the researchers controlled for variations in threat perception, poverty’s influence almost vanished. The main thing driving screwy immune responses appeared to be not poverty, but whether the child saw the social world as scary.

But where did that come from? Did the kids see the world as frightening because they had been taught to, or because they felt alone in facing it? The study design couldn’t answer that. But Cole believes isolation plays a key role. This notion gets startling support from a 2004 study of 57 school-age children who were so badly abused that state social workers had removed them from their homes. The study, often just called “the Kaufman study,” after its author, Yale psychiatrist Joan Kaufman, challenges a number of assumptions about what shapes responses to trauma or stress.

The Kaufman study at first looks like a classic investigation into the so-called depression risk gene—the serotonin transporter gene, or SERT—which comes in both long and short forms. Any single gene’s impact on mood or behavior is limited, of course, and these single-gene, or “candidate gene,” studies must be viewed with that in mind. Yet many studies have found that SERT’s short form seems to render many people (and rhesus monkeys) more sensitive to environment; according to those studies, people who carry the short SERT are more likely to become depressed or anxious if faced with stress or trauma.

Kaufman looked first to see whether the kids’ mental health tracked their SERT variants. It did: The kids with the short variant suffered twice as many mental-health problems as those with the long variant. The double whammy of abuse plus short SERT seemed to be too much.

Then Kaufman laid both the kids’ depression scores and their SERT variants across the kids’ levels of “social support.” In this case, Kaufman narrowly defined social support as contact at least monthly with a trusted adult figure outside the home. Extraordinarily, for the kids who had it, this single, modest, closely defined social connection erased about 80 percent of the combined risk of the short SERT variant and the abuse. It came close to inoculating kids against both an established genetic vulnerability and horrid abuse.

Or, to phrase it as Cole might, the lack of a reliable connection harmed the kids almost as much as abuse did. Their isolation wielded enough power to raise the question of what’s really most toxic in such situations. Most of the psychiatric literature essentially views bad experiences—extreme stress, abuse, violence—as toxins, and “risk genes” as quasi-immunological weaknesses that let the toxins poison us. And abuse is clearly toxic. Yet if social connection can almost completely protect us against the well-known effects of severe abuse, isn’t the isolation almost as toxic as the beatings and neglect?

The Kaufman study also challenges much conventional Western thinking about the state of the individual. To use the language of the study, we sometimes conceive of “social support” as a sort of add-on, something extra that might somehow fortify us. Yet this view assumes that humanity’s default state is solitude. It’s not. Our default state is connection. We are social creatures, and have been for eons. As Cole’s colleague John Cacioppo puts it in his book Loneliness, Hobbes had it wrong when he wrote that human life without civilization was “solitary, poor, nasty, brutish, and short.” It may be poor, nasty, brutish, and short. But seldom has it been solitary.
“A cell,” Steve Cole said, clasping some amberjack, “is a machine for turning experience into biology.”

TOWARD THE END OF the dinner I shared with Cole, after the waiter took away the empty platters and we sat talking over green tea, I asked him if there was anything I should have asked but had not. He’d been talking most of three hours. Some people run dry. Cole does not. He spoke about how we are permeable fluid beings instead of stable unitary isolates; about recursive reconstruction of the self; about an engagement with the world that constantly creates a new you, only you don’t know it, because you’re not the person you would have been otherwise—you’re a one-person experiment that has lost its control.

He wanted to add one more thing: He didn’t see any of this as deterministic.

We were obviously moving away from what he could prove at this point, perhaps from what is testable. We were in fact skirting the rabbit hole that is the free-will debate. Yet he wanted to make it clear he does not see us as slaves to either environment or genes.

“You can’t change your genes. But if we’re even half right about all this, you can change the way your genes behave—which is almost the same thing. By adjusting your environment you can adjust your gene activity. That’s what we’re doing as we move through life. We’re constantly trying to hunt down that sweet spot between too much challenge and too little.

“That’s a really important part of this: To an extent that immunologists and psychologists rarely appreciate, we are architects of our own experience. Your subjective experience carries more power than your objective situation. If you feel like you’re alone even when you’re in a room filled with the people closest to you, you’re going to have problems. If you feel like you’re well supported even though there’s nobody else in sight; if you carry relationships in your head; if you come at the world with a sense that people care about you, that you’re valuable, that you’re okay; then your body is going to act as if you’re okay—even if you’re wrong about all that.”

Cole was channeling John Milton: “The mind is its own place, and in itself can make a heaven of hell, a hell of heaven.”

Of course I did not realize that at the moment. My reaction was more prosaic.

“So environment and experience aren’t the same,” I offered.

“Exactly. Two people may share the same environment but not the same experience. The experience is what you make of the environment. It appears you and I are both enjoying ourselves here, for instance, and I think we are. But if one of us didn’t like being one-on-one at a table for three hours, that person could get quite stressed out. We might have much different experiences. And you can shape all this by how you frame things. You can shape both your environment and yourself by how you act. It’s really an opportunity.”

Cole often puts it differently at the end of his talks about this line of work. “Your experiences today will influence the molecular composition of your body for the next two to three months,” he tells his audience, “or, perhaps, for the rest of your life. Plan your day accordingly.”