Recent research suggests fascinating connections between the effects of the psychedelic drug psilocybin and personality traits related to inner experience. Personality appears to influence response to psilocybin and psilocybin can promote changes in personality, suggesting a reciprocal relationship. Further research in this area could lead to new insights into the basis of human personality and creativity.
A review of studies on factors affecting response to psilocybin found that after dosage, the strongest predictor of alterations in consciousness was the personality trait of absorption (Studerus, Gamma, Kometer, & Vollenweider, 2012). Absorption is defined as a person’s tendency to have episodes of “total” attention where a person’s awareness is fully engaged in whatever has their interest. The degree to which people had “mystical” type experiences while on psilocybin was related to their individual proneness to absorption. Absorption is associated with the broader personality trait openness to experience, which relates to a person’s receptiveness to new ideas and experiences.
What I found particularly interesting was that another study on psilocybin found that people who had never before taken the drug experienced an enduring increase in their level of openness to experience that was evident more than a year later (MacLean, Johnson, & Griffiths, 2011). In this study, people who experienced what the researchers described as a “complete mystical experience” developed increased openness to experience whereas those who did not have such an experience had no increase in openness. Because absorption is closely related to openness to experience, this suggests that there may be a two-way relationship between openness and mystical experiences associated with psilocybin. That is, people who are more open to their inner experience seem more likely to have a mystical experience and those who have a mystical experience tend to become more open as a result.
There is evidence that individual differences in absorption are associated with particular neurotransmitter receptors that are acted upon by psychedelic such as psilocybin (Ott, Reuter, Hennig, & Vaitl, 2005), which might explain why absorption-prone people are more responsive to the drug’s effects. Since psilocybin can apparently cause increases in openness to experience in some people, it seems possible that the drug might permanently increase the sensitivity of these neuroreceptors resulting in associated . This would need to be confirmed by research.
Another intriguing research question concerns what effects increased openness to experience might have. Openness to experience is associated with creativity among other things, so it would be interesting to scientifically examine whether psilocybin use leads to long-term improvements in creativity or other aspects of behaviour associated with openness to experience. In the 1960s many popular musicians experimented with psychedelic drugs such as LSD and this apparently influenced their music. Unfortunately, research into these drugs was effectively banned around this time and only recently has there been a revival of scientific activity in this area. Such research could lead to some intriguing findings about the relationship between the, personality, and consciousness.
(via Psychology Today)
Human emotions are highly contagious. Seeing others’ emotional expressions such as smiles triggers often the corresponding emotional response in the observer. Such synchronisation of emotional states across individuals may support social interaction: When all group members share a common emotional state, their brains and bodies process the environment in a similar fashion.
Researchers at Aalto University and Turku PET Centre have now found that feeling strong emotions makes different individuals’ brain activity literally synchronous.
The results revealed that especially feeling strong unpleasant emotions synchronised brain’s emotion processing networks in the frontal and midline regions. On the contrary, experiencing highly arousing events synchronised activity in the networks supporting vision, attention and sense of touch.
Sharing others’ emotional states provides the observers a somatosensory and neural framework that facilitates understanding others’ intentions and actions and allows to ‘tune in’ or ‘sync’ with them. Such automatic tuning facilitates social interaction and group processes, says Adjunct Professor Lauri Nummenmaa from the Aalto University.
The results have major implications for current neural models of human emotions and group behaviour. It also deepens our understanding of mental disorders involving abnormal socioemotional processing, Nummenmaa says.
Participants’ brain activity was measured with functional magnetic resonance imaging while they were viewing short pleasant, neutral and unpleasant movies.
(via Medical Xpress)
There are lots of metaphors floating around in creativity. We talk about ‘thinking outside the box’, ‘putting two and two together’ and ‘seeing both sides of the problem’.
But are these only metaphors or can we boost our creativity by taking them literally? We know our minds interact in all sorts of interesting ways with our bodies, so what if we enacted these metaphors physically?
That’s the question Leung et al. (2012) examine in a new study published in the journal Psychological Science. This brings together two of my favourite topics here on PsyBlog: creativity and embodied cognition. Across five studies they tested ways of making people more creative by simply changing postures.
Creative ideas are often arrived at by bringing together two apparently unrelated thoughts. When we can think about a problem in terms of two different sides, we are more likely to find a way to integrate them. This is encapsulated by the phrase “On the one hand…on the other hand…”
So, what if while trying to solve a problem you physically hold up one hand followed by the other? Might this send a signal to the unconscious to encourage it to consider the problem from more than one angle?
Leung et al. had participants doing this and found that those who gestured with both hands came up with more novel ideas than those who gestured with just one hand.
'Thinking outside the box' is an awfully overused cliché. Nevertheless it does capture the idea that in creativity you have to try and explore new areas.
In their research Leung et al. had participants literally either sitting in boxes or sitting next to boxes while doing creativity tests. Magically just this simple manipulation worked. People quite literally sitting outside the box came up with more ideas than those sitting in the box.
If you don’t have a box handy, you might like to try just wandering around randomly, but whatever happens don’t walk in a square.
Leung et al. found that people came up with more ideas when they wandered around randomly than when they walked in a square or than when they didn’t walk at all.
Not all creative thinking is about plucking amazing ideas out of the ether.
Sometimes we need to do the grunt work of logically fitting together ideas or objects we’ve already got in front of us. We’ve got to put two and two together and make sure the answer isn’t 17, metaphorically speaking.
This is what psychologists call ‘convergent thinking’ and it’s where we bring our logic, knowledge and skills to bear on a problem.
A fourth study tested the idea that sorting piles of cards from two stacks into one would encourage convergent thinking.
It did. Participants who sorted the cards from two piles into one did better on a test of convergent thinking than those who just fiddled around with the cards in one pile.
Too lazy to get a box or wander around randomly? Then this last study is for you. Here participants either watched a Second Life avatar wandering freely or walking in a square.
According to the results this also worked as those watching the freely wandering avatar came up with more unconventional ideas for gifts than those watching the square-walking avatar.
This one is cool because it shows that the postures aren’t as important as the state of mind that they encourage. The mere suggestion that someone might adopt these postures was enough to cue a more creative state of mind.
This new research joins previous studies which have suggested that simple postures can affect creativity.
In one study people lying down were better at solving anagrams (Lipnicki & Byrne, 2005); in another their concentration was boosted by wearing a white coat. And another used mind-body dissonance—e.g. thinking an unhappy thought while smiling—to boost creativity (How To Promote Visionary Thinking).
All of these studies show how the position of our bodies feeds back into the state of our minds. And it also shows how deeply metaphors are planted in our consciousness.
Related Reading: 10 Simple Postures That Boost Performance
Stress management techniques can have a host of health benefits such as better mood and lower blood pressure, but relaxation response techniques may also alter the body at a deep, fundamental level — by influencing the expression of certain genes. Harvard Medical School’s recently updated Special Health Report Stress Management: Approaches for Preventing and Reducing Stress explains how this is possible and also how a person can learn to identify stress warning signs and develop new tools to better manage stressful situations.
The genetic changes associated with the relaxation response were identified several years ago. A study examined the effects of the relaxation response on certain sets of genes and found that the relaxation response can turn certain genes on and off. The genes were involved with controlling how the body handles free radicals, inflammation processes, and cell death. While further research is needed to confirm these findings, the study has enhanced the credibility of the connection between mind and body, and could have important implications for how diseases are treated.
The study compared the activity of genes — whether the genes were being activated or suppressed—in 19 healthy adults who were long-term users of relaxation techniques and in 19 healthy adults who hadn’t used relaxation techniques. Those who used relaxation techniques used a variety of methods—such as meditation, yoga, breath focus, or repetitive prayer. The researchers found that the activity of certain genes differed between these two groups. In order for the genetic changes to persist, relaxation response techniques have to be done regularly.
(via Harvard Medical)
For thousands of years, human beings have looked down on their emotions. We’ve seen them as primitive passions, the unfortunate legacy of our animal past. When we do stupid things – say, eating too much cake, or sleeping with the wrong person, or taking out a subprime mortgage – we usually blame our short-sighted feelings. People commit crimes of passion. There are no crimes of rationality.
This bias against feeling has led people to assume that reason is always best. When faced with a difficult dilemma, most of us believe that it’s best to carefully assess our options and spend a few moments consciously deliberating the information. Then, we should choose the alternative that best fits our preferences. This is how we maximize utility; rationality is our Promethean gift.
But what if this is all backwards? What if our emotions know more than we know? What if our feelings are smarter than us?
While there is an extensive literature on the potential wisdom of human emotion – David Hume was a prescient guy – it’s only in the last few years that researchers have demonstrated that the emotional system (aka Type 1 thinking) might excel at complex decisions, or those involving lots of variables. If true, this would suggest that the unconscious is better suited for difficult cognitive tasks than the conscious brain, that the very thought process we’ve long disregarded as irrational and impulsive might actually be more intelligent, at least in some conditions.
The latest demonstration of this effect comes from the lab of Michael Pham at Columbia Business School. The study involved asking undergraduates to make predictions about eight different outcomes, from the Democratic presidential primary of 2008 to the finalists of American Idol. They forecast the Dow Jones and picked the winner of the BCS championship game. They even made predictions about the weather.
Here’s the strange part: although these predictions concerned a vast range of events, the results were consistent across every trial: people who were more likely to trust their feelings were also more likely to accurately predict the outcome. Pham’s catchy name for this phenomenon is the emotional oracle effect.
Consider the results from the American Idol quiz: while high-trust-in-feelings subjects correctly predicted the winner 41 percent of the time, those who distrusted their emotions were only right 24 percent of the time. The same lesson applied to the stock market, that classic example of a random walk: those emotional souls made predictions that were 25 percent more accurate than those who aspired to Spock-like cognition.
What explains these paradoxical results? The answer involves processing power. In recent years, it’s become clear that the unconscious brain is able to process vast amounts of information in parallel, thus allowing it to analyze large data sets without getting overwhelmed. (Human reason, in contrast, has a very strict bottleneck and can only process about four bits of data at any given moment.) But this raises the obvious question: how do we gain access to all this analysis, which by definition is taking place outside of conscious awareness?
Here’s where emotions come in handy. Every feeling is like a summary of data, a quick encapsulation of all the information processing that we don’t have access to. (As Pham puts it, emotions are like a “privileged window” into the subterranean mind.) When it comes to making predictions about complex events, this extra information is often essential. It represents the difference between an informed guess and random chance.
How might this work in everyday life? Let’s say, for example, that you’re given lots of information about how twenty different stocks have performed over a period of time. (The various share prices are displayed on a ticker tape at the bottom of a television screen, just as they appear on CNBC.) You’ll soon discover that you have difficulty remembering all the financial data. If somebody asks you which stocks performed the best, you’ll probably be unable to give a good answer. You can’t process all the information. However, if you’re asked which stocks trigger the best feelings – your emotions are now being quizzed – you will suddenly be able to identify the best stocks. According to Tilmann Betsch, the psychologist who performed this clever little experiment, your feelings will “reveal a remarkable degree of sensitivity” to the actual performance of all of the different securities. The investments that rose in value will be associated with the most positive emotions, while the shares that went down in value will trigger a vague sense of unease.
But this doesn’t meant we can simply rely on every fleeting whim. The subjects had to absorb all that ticker-tape data, just as Pham’s volunteers seemed to only benefit from the emotional oracle effect when they had some knowledge of the subject. If they weren’t following college football, then their feelings weren’t helpful predictors of the BCS championship game.
The larger lesson, then, is that our emotions are neither stupid nor omniscient. They are imperfect oracles. Nevertheless, a strong emotion is a reminder that, even when we think we know nothing, our brain knows something. That’s what the feeling is trying to tell us.
Underground neuropharmacologist discusses his phantom limb inspired work with dissociative designer drugs.
There are medicinal chemists who work on an unseen side of the pharmaceutical industry. Like their legally sanctioned counterparts, they work to synthesize drugs they hope will produce therapeutic effects in their users. But they do not work with billion-dollar budgets or advertising agencies; doctors are not bribed to distribute their products with ergonomic pens or fine terrycloth beach towels. Their advertising comes solely from word of mouth and semicautionary articles like the one you are about to read.
The creation of these chemicals is an extraordinary feat of interdisciplinarity; often the pharmacologist, the chemist, the posologist, the toxicologist, and the experimental animal are all the same human being. This is the way drugs have been developed since the beginning of medical history—it is only in recent years that the practice of self-experimentation has become stigmatized, and accordingly these experimenters, like M., must remain shrouded in mystery.
M. is one of the most respected chemists in his underground field. Singlehandedly, he has popularized and discovered numerous novel drugs for gray-market distribution. His most recent investigation of ketamine and its chemical variations produced a new dissociative anesthetic named methoxetamine, which has recently made its way into the nostrils and anuses of lay experimenters worldwide. Methoxetamine is an exemplary product of rational drug discovery; each of its atoms is the result of arduous study and consideration, all created independently on a minuscule budget. But the success of drugs like methoxetamine does not entail great profits for their inventors. Indeed, it is they who wring their hands most over the unknown fate of the chemicals they conceive. Herein we shall explore the great bioethical quandary faced by the underground medicinal chemist.
How did your interest in the chemistry of dissociatives begin?
Well, when I was a young boy, only 13, I was badly hurt in an IRA bombing in London. My left hand had to be amputated after the explosion, and I knew I’d lived through a psychological stress that most people cannot even conceive. I would definitely say this triggered my interest in altered states. When you lose a limb, especially when the limb is exposed to serious trauma before the loss, there is a significant chance you’ll be left with an agonizing phantom limb.
Right, treatment for phantom limb has been one of the great riddles of neuroscience. Have you tried Ramachandran’s mirror-box therapy?
Oh yes, I’ve read Phantoms in the Brain and tried an awful lot of things. It’s a complete bastard to treat. God knows how many drugs I’ve been prescribed. Antidepressants, anti-epileptics, muscle relaxants—none of them really worked. For the worst excesses of phantom-limb pain, traditional painkillers like opiates don’t even touch it. You might as well not even bother with them. I was prescribed high doses of pethidine [also known as Demerol] but returned the bottle to my doctor because it wasn’t doing me any good whatsoever. When I came back, my doctor was agog. He said, “Nobody returns pethidine!” The pain involved can be so bad as to effectively detach your mind from consensus reality. Without suitable analgesia I end up looking like a psychiatric inmate, just rocking backward and forward, unable to do anything, sometimes for more than a day. All that considered, anything that does work is an absolute godsend.
And what works?
I discovered a long time ago that ketamine and cannabinoids helped my phantom hand. I’m quite convinced these classes work by distorting body image so severely that you phase out triggers for the pain. I have experienced profound proprioceptive distortions after intramuscular PCP injection, as if my whole body were a proportional model of the sensory homunculus. But in a sense, what I feel is not hallucination or a distortion, I actually find dissociatives corrective, that is, they make the phantom disappear. This is not just an idiosyncratic response on my part; there are at least three articles published on the effectiveness of ketamine in treating phantom-limb pain…
Shown here are the effects of psilocybin that the researchers observed. Regions labeled in blue indicate a decrease in brain activity. Many people have either had or heard of mind-bending experiences attributable to psilocybin — so if you or someone you know has experimented with mushrooms, the fact that the researchers’ observations reflected a decrease in brain activity during a trip will probably strike you as odd. What’s going on here, man?
"Psychedelics are thought of as ‘mind-expanding’ drugs, so it has commonly been assumed that they work by increasing brain activity. Surprisingly, we found that psilocybin actually caused activity to decrease in areas that have the densest connections with other areas.”
Did you catch that? The most important thing to take away from this study isn’t the fact that brain activity decreased, it’s where the activity decreased. The greatest dips in activity were observed in regions of the brain known as the medial prefrontal cortex (mPFC) and the anterior and posterior cingulate cortices (ACC and PCC, respectively). And as if that wasn’t enough, the researchers’ findings also suggest that psilocybin takes its disabling effects one step further by disrupting connections between the mPFC and PCC.
You can think of your mPFC, PCC, and a third region of your brain called the thalamus, as transportation hubs that coordinate the flow of information throughout your brain. Decreased activity within and between the brain’s hubs allows for "an unconstrained style of cognition."
What the hell does that mean? Mo Costandi fleshes things out for us, with a little help from Aldous Huxley:
In his 1954 book The Doors of Perception, novelist Aldous Huxley, who famously experimented with psychedelics, suggested that the drugs produce a sensory deluge by opening a “reducing valve” in the brain that normally acts to limit our perceptions.
The new findings are consistent with this idea, and with the free-energy principle of brain function developed by Karl Friston of University College London that states that the brain works by constraining our perceptual experiences so that its predictions of the world are as accurate as possible.
Why We Need To Start Taking Magic Mushrooms Seriously
Psilocybin. It’s the psychoactive substance in those "sacred mushrooms" that causes hallucinations and other novel mental experiences. The effects of those mushrooms have been explored and appreciated by members of the ancient Capsian culture in North Africa, Aztec shamans, and modern college students. But they’re now the subject of serious study by scientists.
A team from the Johns Hopkins University School of Medicine recently published results from a roughly year-long experiment. The researchers worked with 18 volunteers who were given pure psilocybin to measure how it affected people and how different dosages changed the experience. The subjects were screened for psychological health and given the drug in a pleasant environment, after preparatory guidance. They even had a soundtrack consisting of “classical and world music chosen to complement the arc of the psilocybin action, from onset, through the peak of the effects, and subsiding back to baseline.”
The results? At high dosages people occasionally experienced fear, anxiety, or delusions. But the negative effects of those “bad trips” were easily mitigated by the reassuring researchers and didn’t outlast the session. At more moderate doses, the results were almost unambiguously positive. Moreover, people didn’t just appreciate the experience as fun; they found it spiritually meaningful, with lasting benefits.
As a piece on Newswise explains:
Looking back over a year later, most of the experiment’s 18 volunteers (94 percent) rated a psilocybin session as among the top five most or as the topmost spiritually significant experience of his or her life. […] Most volunteers (89 percent) also reported positive changes in their behaviors, and those reports were corroborated by family members or others, the researchers say. The behavior changes most frequently cited were improved relationships with family and others, increased physical and psychological self-care, and increased devotion to spiritual practice.
Reading the volunteers’ first-hand reports of how the experiences affected them is a testament to their value. “More and more, sensuality and compassion and gratitude continue to unfold around me.” “I try to judge less and forgive more.” “I feel that I relate better in my marriage. There is more empathy.” “I need less food to make me full. My alcohol use has diminished dramatically.”
I’m not saying we should all start doing mushrooms. These were carefully measured doses, taken in a setting designed to be comfortable and supportive. There are certainly situations in which it would be dangerous or irresponsible to take psilocybin.
But these results illustrate the artificial dichotomy between medicine and recreational drugs in America. Stateside, Prozac is regarded as medicine, but psilocybin is a schedule 1 controlled substance like heroin. Americans assume that if some substance is made by nature instead of Eli Lilly, it can’t be medicine. But if psilocybin has true psychiatric and emotional benefits, what’s the difference? Sure, you can have a bad experience with psilocibin, but antidepressents like Prozac have been linked to suicidal thoughts, and it’s hard to imagine a worse side effect than that. We also think that if a drug is used for fun, there must be something bad about it. But Vicodin and OxyContin are all still on the market. There are plenty of FDA-approved drugs that get used (and abused) recreationally.
We should aim to evaluate any drug objectively, whether it’s made by an enormous pharmaceutical company or grows in the forest. If an engineered antidepressant generated reports like those from the volunteers in this study, it would be regarded as a breakthrough in psychiatric medicine.
The scientists found that the slow waves that characterize sleep didn’t occur throughout the brain. In fact, they found that only local clusters of neurons switched voltage in a slow pattern. From time to time, the clusters would crackle and shift to a faster frequency—in effect, waking up. When EEGs pick up slow sleep waves, Tononi and his colleagues found, only a third of the brain was actually participating in the event. Tononi has thus found a shocking symmetry: parts of our brain sleep when we’re awake, and parts of our brain are awake while we sleep.
A new study finds that young children are less likely to help a person after seeing that person harm or intend to harm someone else. The study placed nearly 100 German 3-year-olds in scenarios where they observed an adult help, harm, intend to harm, or accidentally harm another. The children were less likely to subsequently help that adult in a game if the adult had harmed or intended to harm another person in the initial scenario.
Young children’s helpfulness is tempered when they see that the person they intend to help has harmed another person. But it also diminishes when they see that the object of their attention meant to harm another, even if no harm was done. That’s the conclusion of two new studies of 3-year-olds conducted by researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. The research appears in the November/December 2010 issue of the journal Child Development. "In finding that children are quite sophisticated and discriminating helpers, our studies show that youngsters are sensitive not only to others’ moral behaviors, but also to the intentions behind those behaviors," according to Amrisha Vaish, postdoctoral researcher at Germany’s Max Planck Institute for Evolutionary Anthropology and the studies’ lead author. Researchers carried out two studies with almost 100 middle-class German 3-year-olds. The children participated in several scenarios in which adult actors carried out various actions involving helpfulness (taping together a drawing that someone else tore), harmfulness (tearing another person’s drawing), intentions to harm (wanting to but not being able to tear another person’s drawing), and accidental harmfulness (accidentally tearing another’s drawing). The adults then began playing a game; children’s helpfulness was gauged by whether or not they gave the adults a game piece they were missing. The studies found that the children helped an adult less not only when they saw that the person harmed another person, but also when they saw that the person intended to harm another person without causing actual harm. When the adult was helpful and when he or she accidentally caused harm, the children were helpful, too. This suggests that children are sensitive not only to others’ moral behaviors, but also to the intentions behind them. The research sheds light on our understanding of children’s moral development. And it raises questions about our assumptions that young children are not discriminating helpers, but help everyone in the same way. (via ScienceDaily)
Young children’s helpfulness is tempered when they see that the person they intend to help has harmed another person. But it also diminishes when they see that the object of their attention meant to harm another, even if no harm was done.
That’s the conclusion of two new studies of 3-year-olds conducted by researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.
The research appears in the November/December 2010 issue of the journal Child Development.
"In finding that children are quite sophisticated and discriminating helpers, our studies show that youngsters are sensitive not only to others’ moral behaviors, but also to the intentions behind those behaviors," according to Amrisha Vaish, postdoctoral researcher at Germany’s Max Planck Institute for Evolutionary Anthropology and the studies’ lead author.
Researchers carried out two studies with almost 100 middle-class German 3-year-olds. The children participated in several scenarios in which adult actors carried out various actions involving helpfulness (taping together a drawing that someone else tore), harmfulness (tearing another person’s drawing), intentions to harm (wanting to but not being able to tear another person’s drawing), and accidental harmfulness (accidentally tearing another’s drawing). The adults then began playing a game; children’s helpfulness was gauged by whether or not they gave the adults a game piece they were missing.
The studies found that the children helped an adult less not only when they saw that the person harmed another person, but also when they saw that the person intended to harm another person without causing actual harm. When the adult was helpful and when he or she accidentally caused harm, the children were helpful, too. This suggests that children are sensitive not only to others’ moral behaviors, but also to the intentions behind them.
The research sheds light on our understanding of children’s moral development. And it raises questions about our assumptions that young children are not discriminating helpers, but help everyone in the same way.
Activation of a default mode network (DMN) including frontal and parietal midline structures varies with cognitive load, being more active during low-load tasks and less active during high-load tasks requiring executive control. Meditation practices entail various degrees of cognitive control. Thus, DMN activation patterns could give insight into the nature of meditation practices. This 10-week random assignment study compared theta2, alpha1, alpha2, beta1, beta2 and gamma EEG coherence, power, and eLORETA cortical sources during eyes-closed rest and Transcendental Meditation (TM) practice in 38 male and female college students, average age 23.7 years. Significant brainwave differences were seen between groups. Compared to eyes-closed rest, TM practice led to higher alpha1 frontal log-power, and lower beta1 and gamma frontal and parietal log-power; higher frontal and parietal alpha1 interhemispheric coherence and higher frontal and frontal-central beta2 intrahemispheric coherence. eLORETA analysis identified sources of alpha1 activity in midline cortical regions that overlapped with the DMN. Greater activation in areas that overlap the DMN during TM practice suggests that meditation practice may lead to a foundational or ‘ground’ state of cerebral functioning that may underlie eyes-closed rest and more focused cognitive processes.
How do children understand fantasy-reality distinctions? Better than we had assumed. A fascinating study.
ENCODE (Encyclopedia Of DNA Elements), a massive database cataloging the human genome’s functional elements, including genes, RNA transcripts, and other products, has been created by an international team of researchers, with principal investigators at Penn State University and HudsonAlpha Institute for Biotechnology.
ENCODE is being made available as an open resource to the scientific community, classrooms, science writers, and the public. It provides an overview of the team’s ongoing efforts to interpret the human genome sequence, as well as a user’s guide for accessign the vast amounts of data and resources produced so far by the project.
ENCODE comes on the heels of the now-complete Human Genome Project, the 13-year effort aimed at identifying all the approximately 20,000 to 25,000 genes in human DNA, which used open-source data sharing to further scientific discovery and public understanding of science.
Scientists with the ENCODE Project are applying up to 20 different tests in 108 commonly used cell lines to compile the data. The ENCODE User’s Guide also explains how to apply the data to interpret the human genome.
The ENCODE project adds data such as where RNA is produced from our DNA, where proteins bind to DNA, and where parts of our DNA are augmented by additional chemical markers. These proteins and chemical additions are keys to understanding how different cells within our bodies are interpreting the language of DNA.
The researchers say that the ENCODE data can be immediately useful in interpreting associations between disease and DNA sequences that can vary from person to person (single nucleotide polymorphisms). For example, scientists know that DNA variants located upstream of a gene called MYC are associated with multiple cancers, but until recently the mechanism behind this association was a mystery.
“Very few proteins and other DNA products differ in any fundamental way between humans and chimps,” says principal investigator Ross Hardison. “The important difference between us and our close cousins lies in gene expression — the basic level at which genes give rise to traits such as eye color, height, and susceptibility to a particular disease. ENCODE is helping to map the very proteins involved in gene regulation and gene expression. The User’s Guide not only explains how to find the data, but also explains how to apply the data to interpret the human genome.”
Ref.: Peter B. Becker, Academic Editor, A User’s Guide to the Encyclopedia of DNA Elements (ENCODE), PLoS Biology (open access), April 19, 2011
Tools to facilitate data use at: http://encodeproject.org