Posts Tagged ‘DNA’

Neuroplasticity and Neurogenesis

June 8, 2016

Chapters 2 and 3 of Sharon Begley’s “Train Your MInd, Change Your Brain” cover neuroplasticity and neurogenesis.  Prior to discussing neuroplasticity, how learning takes place needs to be discussed.  To explain how learning takes place psychologist Donald Hebb conceived of cell assemblies.  He proposed that learning and memory were based on the strengthening of synapses.
Somehow either the neuron that fires first in the chain (the presynaptic neuron) or the neuron that fires next (the postsynaptic neuron), or both, change in such a way that the firing of the first is more likely to cause the firing of the second.  Learning and memory involve the firing of large assemblies of these cells.  Hence Hebb’s theory is called cell assembly theory.  Hebb’s maxim is that cells that fire together wire together.

Virtually all the research on neuroplasticity involved animals.  This is because surgery was almost always required. Sensory  or motor connections might be severed, and then observations would be made regarding the effects of these operations.  Sometimes connections were rewired so that animals would see sound or hear light. The late nineteenth psychologist William James had wondered , were scientists were able to alter neuron’s paths so that exciting the ear activates the visual cortex and exciting the eye the auditory cortex, we would be able to  “hear the lightning and see the thunder.”  So James was correct.  And all this research invalidated the longstanding dogma that the nervous system could not be rewired or rewire itself underscoring the reality that the nervous system can and does rewire itself.

The longstanding dogma that new neurons  could not be created, neurogenesis, was more difficult to disprove.   Before cells divide, they make a copy of their DNA.  As cells can’t conjure the double helix out of thin air, biochemicals snag the requisite ingredients from within the cell and assemble them.  One element of DNA, thymidine, lets a radioactive  molecules glom on to it.  When the thymidine becomes incorporated into the brand-new DNA, the DNA has a spot of radioactivity, which can be detected experimentally.  Old DNA does not have this glow.

Joseph Altman, a new neuroscientist at MIT, decided to try the new trick on brains.  By scanning neurons for tell tale glows he figured he would be able to detect newborn DNA, and newborn cells.  He found neurons of adult rats, cats,  and guinea pigs with thymidine—indicating that they had been born after Altman had injected them with the tracer.  He published these finding in three prestigious scientific journals in 1965, 1967, and 1970, yet his claims were ignored,   Altman was denied tenure at MIT and joined the faculty of Purdue University.

Research was done using nonhuman  animals with rich environments.  That is animals who lived in enriched environments with exercise wheels and novel features were compared to animals living in impoverished environments.  The formation and survival  of new neurons increased 15% in a part of the hippocampus called the dentate gyros, which is involved in learning and memory.

To this point humans had not been involved in the research, the reason being that noninvasive brain imaging could not address this issue.  Brains needed to be taken from   dead research participants.  Oncologists injected BrdU into cancer patients because is marks every newborn cell.  This allowed them to assess how many new cancer cells were developing.  The researchers were able to enlist the cooperation of oncologists and their patients.  After these patients succumbed to cancer, their brains could be examined to see if any new  noncancerous cells had been generated.  Thanks to these patients and their oncologists, new neurons, indicating neurogenesis, were found in the hippocampus.

An interesting find was that forced exercise does not promote neurogenesis.  The neuroscientist Gage explained to the Dalai Lama, “Running voluntarily increases neurogenesis and increases learning even in very, very old animals.  It seems like the effects of running on neurogenesis and on learning are dependent on volition.  It has to be a voluntary act.  It is not just the physical activity.

When the neuroscientist Fred Gage sat down with the Dalai Lama it was clear that new neurons arise from neural stem cells in the adult human brain, which persist and support ongoing neurogenesis.  This discovery expanded the possibilities for neuroplasticity.  The neural electrician is not restricted to working with existing wiring, he can run whole new cables through the brain.

In humans new neurons might do more than help with learning.  The hippocampus plays an important role in depression.  In many people suffering from depression, the dentate gyrus oaf the hippocampus  has drastically shrunk.  There is a question of cause and effect, whether another factor caused the hippocampus to shrink leading to depression, or whether depression caused the shrinkage.

New research suggests that people who are suffering from depression are unable to recognize novelty.  Gage said this to the Dalai Lama, “You hear this a lot with depressed people.  Things just look the same.  There is nothing exciting in life.”  “There is also evidence,” Gage said, “that if you can get someone with depression to exercise, his depression lifts.”  So neurogenesis might be the ultimate anti-depressant.  When it is impaired for any reason, the joy of seeing life with new eyes and finding surprises and novelty in the world vanishes.  But when it is restored the world is seen anew.

It is clear that chronic stress impairs neurogenesis, at least in mice.  Gage’s colleague, Peter Ericsson suspects that holds lessons for humans also.  “In lab animals, chronic stress dramatically decreases neurogenesis as well as spatial memory..  When people under stress experience severe memory problems—forgetting their way to work, going into the kitchen and then no remembering why they went in—it is likely that what they’re experiencing is the very negative of stress on the function of the hippocampus due to decreased neurogenesis.”


Why False Confessions Trump Evidence

June 30, 2015

Perhaps the most blatant example of the title  is the case of the Central Park Five.  This case attracted enormous attention as it supposedly characterized “wildings”  that were taking place.  Here five black men were convicted of raping and brutalizing a young woman.  There is a video piece on this that I encourage you to watch should you get the opportunity. You will see how the police interrogated these suspects, not with the hope of getting at the truth, but rather at getting them to confess, which they did.  However, it was quite clear from the physical evidence that the police were intent on getting confessions rather than seeking the truth.  The physical evidence at the scene indicated that this was not a gang rape.  And the DNA evidence, which is regarded as close to a gold standard as one can find for legal proceedings, completely exonerated these five men.

One of the reasons that confessions are regarded so highly is that juries ask themselves “Why would individuals incriminate themselves?  Don’t they know about their Fifth Amendment rights?
If you have viewed or get the opportunity to view the interrogations of the Central Park Five  you will see the extreme pressure these individuals are placed under in uncomfortable conditions for prolonged periods of time.  Moreover, there is psychological research showing that people can be falsely convinced that they did actually commit the crime (see the healthy memory blog post “False Memories Leading to Confessions” ).  And they are told that the investigation will continue, so being desperate or wrongly convinced, they reason that eventually truth will out and that they will be exonerated.

Research has indicated why these false confessions are so powerfully persuasive.  Common sense informs people that people will not incriminate themselves, these confession contain credible narratives (which often are created during the interrogation process), these narratives corrupt other evidence and undermine the truth-seeking process.

So what can be done about this?  First of all,  people, police, prosecutors, judges, juries, and appeals courts should be made aware of this research and question the reliability of these confessions.  Interrogations should be videotaped and reviewed.  There are recommended procedures for these interrogations and these procedures need to be followed.

You Are Not Prisoner of Your DNA

November 8, 2014

Unfortunately, the belief that we are prisoners to our own DNA is used as a cop out from personal responsibility. It is also the first key thing that Dr. Dharma Sing Khaisa, who is the Founding President and Medical Director of the Alzheimer’s Research and Prevention Foundation, would like every person to understand about his/her own brain, thinks that is commonly misunderstood. The second key thing is, “You can improve your brain function, regardless of your age and stage in life. He is an MD who has been working in this area for more than 20 years, and he says that he is more excited than ever about the possibilities for enhanced mental performance and brain longevity for everyone.

When he started his research he discovered that chronic stress , via release from the adrenal glands, kills brain cells by the thousands in the hippocampus, which is critical to memory performance. He realized that this could lead to Alzheimer’s Disease and other problems. He also knew from his own research and personal experience that lifestyle modifications, especially including yoga and meditation could remedy that. He is continuing his research looking into the integrative approach to the preventon of Alzheimer’s. He is especially interested in continuing to explore the multiple positive benefits of a simple brain-enhancing yoga meditation exercise called Kirtan Kriya, or KK.

He believes that it is important to champion the belief that lifestyle can influence brain fitness and to encourage people to make their brain health their top priority. Personally, he remembers to put his brain health first. He practices yoga and meditation every day, has a serious work out regimen five times a week, and watches his diet. As for mental exercise, he writes songs and plays music, which is also great fun.

This post reiterates the goals of the healthymemory blog, which is important to do periodically.

The following URL is the reference for this blog post.

A Key Component Generating Conscious Experience?

October 29, 2014

The November/December 2014 issue of Scientific American Mind included an article by Christof Koch, who is a former collaborator with Francis Crick, who with James Watson won the Nobel Prize for discovering the structure and the function of DNA. The title of the article is “A Brain Structure Looking for a Function.” The brain structure in question is the claustrum. The claustrum is a thin, irregular sheet of cells, tucked below the neocortex, which is the gray matter that allows us to see, hear, reason, think, and remember. It is surrounded on all sides by white matter, the tracts, or wire bundles, that interconnect cortical regions with one another and with other brain regions. There are two claustra one for each side of the brain. They lie below the general region of the insular cortex, underneath the temples, just above the ears. They have a long, thin wisp of a shape that can be easily overlooked when inspecting the topography of the brain region.

Advanced brain-imaging techniques have revealed white matter fibers coursing to and from the two claustra that it is a neural Grand Central Station. Almost every region of the cortex sends fibers to the claustra. These connections are reciprocated by other fibers that extend back from the claustra to the originating cortical regions. Although each claustrum receives inputs from both cortical hemispheres, but only project back to the overlying cortex on the same side.

Crick looked at these facts and believed that a reliable guide to understanding function, is to study structure. And he, working with Koch formulated the idea that the claustra are a key component of the networks generating conscious experience. This work turned out to be Crick’s Swan Song to science as he was suffering from end-stage colon cancer. He finished his paper with Koch before passing away,

“What is the Function of the Claustrum?, Philosophical Transactions of the Royal Society B, Vol. 360, No.1458, pages 1271-1279.

Additional research supporting this contention of Crick and Koch is cited in the Koch piece in Scientific American Mind. Nevertheless it is always fascinating to speculate about conscious. It is the only product of the brain with which we have direct experience. Yet the brain is raging with activity 24 hours a day. There are many reasons to believe that we can use our conscious experience to improve our focus and ability to attend. We can also use it to control our emotions and it lets us take a third person look at our own interactions with other. Fundamentally, meditation and mindfulness is a matter of learning to control our conscious experience to advantage.

© Douglas Griffith and, 2014. Unauthorized use and/or duplication of this material without express and written permission from this blog’s author and/or owner is strictly prohibited. Excerpts and links may be used, provided that full and clear credit is given to Douglas Griffith and with appropriate and specific direction to the original content.

How Physical Exercise Contributes to a Healthy Memory

January 9, 2013

Enter “exercise” into the search block on the healthymemory blog and you will find a listing of many articles. Although the majority of them are discussing the benefits of cognitive exercise, you can still find many on the benefits of physical exercise. So a reasonable question is how can physical exercise benefit memory? Research indicating how this might happened in an article1 in Scientific American Mind,which, in turn, was reporting the results from a study in the Journal of Applied Physiology. This study, conducted by J. Mark Davis and his colleagues at the University of South Carolina, used mice. They found that quantities of a signaling molecule, which they called a “master regulator” of mitochondria production increased in the brain after a half hour a day of running on a treadmill. These brain cells of the mice also had more mitochondrial DNA as distinguished from the regular cellular DNA found in the nucleus. The researchers said that this provided “gold standard” evidence of more mitochondria. Mitochondria generate energy, and these increased mitochondria provide additional energy that allow the brain to work faster and more efficiently.

As we age, neurons naturally lose mitochondria. This loss of mitochondria can contribute to losses in brain and cognitive function resulting in dementia and other age-related declines in brain function. By increasing the energy supply new mitochondria can be produced offsetting this mitochondria loss.

Although we’ve known for a long time that physical exercise is good for both physical and cognitive health, we are beginning to gain insights as to why this is the case.

1Sutherland, S. (2012). How Exercise Jogs the Brain: Physical activity boosts cognition by improving neurons’ power supply. Scientific American Mind, March/April, 12.

The Law and Psychological Science

January 6, 2013

Should I ever be charged with a crime, I shall not be one of those people who say that they will be proven innocence because they have faith in the legal system. Rather I’ll be saying that although I am innocent, I have no faith that I shall be exonerated. In my view there is little in common between the concept of justice and the legal system. At least in the United States, each individual gets the amount of justice that individual can afford. Say I am charged with a crime, and I am innocent. Going with a public defender would most likely increase the probability of either a conviction or some plea bargain to a lesser sentence. If I want to reduce my chances of being wrongfully convicted, I will pay for the best judicial defense I can afford. If I am exonerated, there is a good chance that I have gone into bankruptcy. So, even in that case, can we say that justice has prevailed?

I am annoyed by the instructions the judge provides to the jurors in criminal cases. In a criminal case it is usually to be convinced beyond a reasonable doubt, or some variant thereof. Now what does that mean? There needs to be some trade-off here. How many innocent people would we be willing to convict to prevent a guilty person from going free? Is it one in one hundred? One in twenty? One in ten? One in five? The instructions need to be more specific.

Here are some statistics from an article in Scientific American Mind.1 412 is the number of people exonerated in the U.S. After being implicated by mistaken witness testimony as of September 2012. 137 is the number of people exonerated in the U.S. after being implicated by false confessions as of September 2012. All too frequently we read about prisoners being released from prison on the basis of DNA evidence. Often this occurs after they have spent many years in prison.

What is infuriating is that even when there is compelling evidence, such as DNA evidence, that someone has been wrongfully imprisoned, the so-called justice system is reluctant to release the individual. This supports the idea that lawyers, both defenders and prosecutors, are not interested in justice; they are interested winning.

So what does psychological science have to offer the legal system if it does want to pursue justice? Psychological science studies how we perceive, think, solve problems, make decisions, how we process information and how our memories work. I think the relevance should be obvious here. We know that we have two systems for processing information: System One which is fast and does the initial processing of information. System Two is slow and deliberative, and has the responsibility for checking the accuracy of System One output. Our default when we encounter new information, absent cues to the contrary is to believe it. If it is wrong, the hope is that it will eventually be corrected by System Two. So when judges inform jurors that they are to disregard something said or introduced in court, research has shown that it is unlikely to be disregarded just because the judge said so. Research has indicated that a short and to the point explanation as to why the information should be ignored is effective (See the healthymemory blog post, “Solutions and Good Practices for Misinformation”).

Extensive research has been done showing that eyewitness testimony is highly unreliable, yet courts and jurors have historically weighted it highly. Although it is true that recognition is worse for people of differing ethnic or racial groups, it remains unreliable even within the same group. The Innocence Project, a national organization focused on correcting wrongful convictions through DNA testing and judicial reform, has freed 301 individuals on the basis of DNA testing. In about 75% of these cases, a principal cause of the erroneous guilty verdict was faulty eyewitness testimony. In about 35% of these cases the testimony stemmed from two or more incorrect observers. This demonstrates that consistency should not be confused with correctness. That is, reliability is not necessarily validity. The method for doing facial recognition is extremely important. Rather than present pictures together in groups, they should be presented individually. Moreover, there should be no guarantee or suggestion that the guilty party is one of the photographs shown. And the officers, themselves, should be blind regarding the identity of the suspect. The same procedure applies to line-ups, that they should be done individually with no guarantee or suggestion that the suspect is there.

One study indicated that 63 percent of the respondents believe that “memory works like a video camera.” Research has shown that nothing could be further from the truth. Memory is fallible and is easily influenced by suggestions and contexts. Moreover, each time we recall information, there are changes. Questioning by investigators, even if not intended, can lead to faulty recall and erroneous convictions. The cognitive interview is a procedure that has been developed by psychologists that might lead to more accurate eyewitness testimony. It relies on techniques derived from scientifically supported principles of memory. It asks open-ended rather than suggestive question. It reminds witnesses of the context of the crime and offers them reminders of the crime, and discourages them from guessing.

Confessions should not be regarded as conclusive. There were 200 people who confessed to the kidnapping of Charles Lindbergh‘s baby. The Innocence Project found that up to 27% of individuals initially found guilty but later cleared by DNA evidence had confessed in spite of their clean hands.

This indicates that the videotaping of interrogations is essential. It is also important to videotape the interrogators as well as the suspect.

Psychologists are also skilled in designing experiments and research projects to minimize bias. Correct sampling procedures are essential. This is true for juries. It is not surprising that mixed -race juries are fairer to black defendants. It also appears that diversity improves the accuracy and critical thinking of jurors. Perhaps you do not need training in psychology to know realize this. It would appear to be a matter of common sense. The legal system has been slow to realize this.

In the United States, the Supreme Court sits atop the legal system. There are different approaches to interpreting the Constitution of the United States. There is a progressive view that the Constitution is to be viewed as a living document, and is to be interpreted in the view of new knowledge. The competing view is the Strict Constructionist view. According to this view the Constitution is to be viewed as the original writers intended. Remember that at the time the Constitution was written, slavery was legal and thrived in the southern states. Black people were regarded as being three-fifths of a human being. Women could not vote. At that time Benjamin Franklin was one of the most knowledgeable scientists in the world. Today a high school science student knows much more science than Benjamin Franklin ever did. Currently five of the nine justices on the Supreme Court are regarded as strict constructionists. This might account for some of their decisions and for some of the difficulties the United States currently finds itself.

1Lilienfeld, S.O., & Byron, R. (2013). Your Brain on Trial, Scientific American Mind, January/February, p.7 & pp.44-53.

© Douglas Griffith and, 2012. Unauthorized use and/or duplication of this material without express and written permission from this blog’s author and/or owner is strictly prohibited. Excerpts and links may be used, provided that full and clear credit is given to Douglas Griffith and with appropriate and specific direction to the original content.

Electrical Activity, Chemical Activity, Connectivity, and Epigenetic Activity

October 24, 2012

All of these are involved in making our memories. Our short term or working memories are held in fleeting changes in the brain‘s electrical and chemical activity. They quickly fade as our attention wanders, but they provide the basis of our conscious awareness.

Our long term memories are woven into webs of connections among the brain cells. The brain alters the communication between networks of cells by the creation of new receptors at the end of a neuron, by a surge in the production of a neurotransmitter, or by the forging of new ion channels that allows a brain cell to boost the voltage of its signals. The same pattern of neurons will fire when we recall the memory bringing the thought back into our consciousness. Long term memories include our autobiographical memories, our episodic memories of specific events in our lives, our sensory memories, as well as our semantic memories that comprise our knowledge of the world. One of the most important brain regions involved in this process are the hippocampi. The are located near the base of the brain and are especially important in the consolidation of new memories. When they are surgically removed or damaged, no new memories can be stored. Thus, no new learning can take place.

The preceding has been known for some time, what is new is an understanding of the epigenetic changes that are involved in memory. These involve small alterations in the structure of a gene and determine its activity within the cell. For instance, certain genes linked to the formation of memories have been shown to have fewer methyl groups attached to their DNA after learning. This is a clear example of an epigenetic change.1 Every time we recall a memory, new proteins are made. The epigenetic markers are altered changing the memory in subtle ways. So the brain is not like a video camera. It is dynamic and changes itself.

1Young, E. (2012). The Making of a Memory, New Scientist, 6 October, p.34.

© Douglas Griffith and, 2012. Unauthorized use and/or duplication of this material without express and written permission from this blog’s author and/or owner is strictly prohibited. Excerpts and links may be used, provided that full and clear credit is given to Douglas Griffith and with appropriate and specific direction to the original content.

How Much Information Is There and What Does It Mean?

September 27, 2012

A recent article by Martin Hilbert was published in the Big Data Special Issue of the publication Significance: statistics making sense titled “How Much Information Is There in the Information Society”? Hilbert together with his collaborator Priscila Lopez tackled the task of estimating the world’s technological capacity to store, communicate, and compute information over the period from 1986 to 2007/2012. The complete collection of these studies can be accessed free of charge at

In 1949 the father of information theory, Claude E. Shannon, estimated that the largest information stockpile he could think of was the Library of Congress with about 12,500 megabytes (106). The current estimate for the amount of storage for the Library of Congress has grown to a terabyte 1012. During the two decades of their study the amount of information quadrupled from 432 exabytes (1018) to 1.9 zetabytes (1021). For our personal and business computation we are familiar with gigabytes (109). Next are terabytes (1012), then petabytes (1015), the aforementioned exabytes, and zetabytes. Yottabytes (1024) await us in the future.

Although these are measures of information in the technical sense, I prefer to think of them as data. I think of information in technical transactive memory as data. When it is perceived by a human it becomes information. When it is further processed into the human information processing system, it becomes knowledge. Suppose we all disappeared and the machines kept remembering and processing. What would that be? Perhaps sometime in the future machines will become intelligent enough to function on their own. There is a movie, Colossus: the Forbin Project in which intelligent machines take over the world because they have concluded that humans are not intelligent enough to govern. Then there is Ray Kurzwiel‘s concept of the Singularity, when humans and technology become one. However, coming back to reality, I think there would just be machines storing and processing information absent true knowledge. We need to use technology to help us cope with all these data and fortunately according to Hilbert computation is grown at a faster rate than storage.

Hilbert makes some interesting comparisons between technical processing and storage of information and biological processing and storage of information. In 2007, the DNA of the 60 trillion cells of one single human body would have stored more information than all of our technological devices together. He notes that in both cases information is highly redundant. One hundred human brains can roughly execute as many nerve pulses as our general purpose computers can execute instructions per second. Hilbert asks the question why we currently spend 3.5 trillion dollars per year on our information and communication technology but less than $50 dollars per year on the education of many children in Africa? I think what he is proposing is that we not lose sight of human potential. Although our brains and DNA have phenomenal processing and storage capacities, we only have access to a very small percentage of this information in our conscious awareness. The healthymemory blog makes a distinction among potential transactive memory, available transactive memory, and accessible transactive memory. Potential transactive memory is all the information about which Hilbert writes as well as information held by our fellow humans. Available transactive memory is that information we are able to find. And accessible transactive memory is that information we are able to access readily. The goal is that this accessible transactive memory grows into knowledge, understanding, and insight, as it is in these final stages where its true value is realized.

© Douglas Griffith and, 2012. Unauthorized use and/or duplication of this material without express and written permission from this blog’s author and/or owner is strictly prohibited. Excerpts and links may be used, provided that full and clear credit is given to Douglas Griffith and with appropriate and specific direction to the original content.