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New Brain, New Day, New You

New cells are born every day in the brain's hippocampus. This is the long term memory area, the hard drive for those of us who think better with metaphors. Neuroscientists at the Johns Hopkins University School of Medicine have discovered that the birth of new cells, which depends on brain activity, also depends on a protein that is involved in changing epigenetic marks in the cell's genetic material.

Epigenetic changes are fairly cool to think about as a Fiction writer, for example;

Epigenetic changes have also been observed to occur in response to environmental exposure—for example, mice given some dietary supplements have epigenetic changes affecting expression of the agouti gene, which affects their fur color, weight, and propensity to develop cancer
The idea of changes in fur color and weight (physical manifestations) because of a epigenetic change, which has been induced by the researcher, and the change being predictable has long reaching possibilities, and certainly helps with the story of Winter's Harvest.

It also appears (without being scientific, but as a fiction writer), these changes in the hippocampus's affect on these epigenetic changes, can be induced by the neuropeptides.

Neuropeptides are small protein-like molecules used by neurons to communicate with each other. They are neuronal signaling molecules, influence the activity of the brain in specific ways and are thus involved in particular brain functions, like analgesia, reward, food intake, learning and memory.

Neuropeptides are expressed and released by neurons, and mediate or modulate neuronal communication by acting on cell surface receptors. The human genome contains about 90 genes that encode precursors of neuropeptides. At present about 100 different peptides are known to be released by different populations of neurons in the mammalian brain. Neurons use many different chemical signals to communicate information, including neurotransmitters, peptides, cannabinoids, and even some gases, like nitric oxide.

Of course, altering the physical description of the human body, for even short amounts of time (or perhaps, especially for short amounts of time), would be in the purely fictional areas of reality.


Rita Rebollo, Beatrice Horard, Benjamin Hubert, Cristina Vieira, Jumping genes and epigenetics: Towards new species, Gene, In Press, Corrected Proof, Available online 25 January 2010, ISSN 0378-1119, DOI: 10.1016/j.gene.2010.01.003.
(http://www.sciencedirect.com/science/article/B6T39-4Y7MM1X-1/2/cd3af5316c22e7ec728046a95e5a6ecf)
Abstract:
Transposable elements (TEs) are responsible for rapid genome remodelling by the creation of new regulatory gene networks and chromosome restructuring. TEs are often regulated by the host through epigenetic systems, but environmental changes can lead to physiological and, therefore, epigenetic stress, which disrupt the tight control of TEs. The resulting TE mobilization drives genome restructuring that may sometimes provide the host with an innovative genetic escape route. We suggest that macroevolution and speciation might therefore originate when the host relaxes its epigenetic control of TEs. To understand the impact of TEs and their importance in host genome evolution, it is essential to study TE epigenetic variation in natural populations. We propose to focus on recent data that demonstrate the correlation between changes in the epigenetic control of TEs in species/populations and genome evolution.
Keywords: Transposable elements; Evolution; Rapid speciation; Natural populations; Epigenetic control

Covington III, Herbert E., Vincent Vialou, and Eric J. Nestler. “From synapse to nucleus: Novel targets for treating depression.” Neuropharmacology 58, no. 4-5 (3, 2010): 683-693.


Crews, D. “Epigenetics and its implications for behavioral neuroendocrinology.” Frontiers in Neuroendocrinology 29, no. 3 (6, 2008): 344-357.


Feder, Adriana, Eric J. Nestler, and Dennis S. Charney. “Psychobiology and molecular genetics of resilience.” Nature Reviews Neuroscience 10, no. 6 (6, 2009): 446-457.


McCarthy, M. M., A. P. Auger, T. L. Bale, G. J. De Vries, G. A. Dunn, N. G. Forger, E. K. Murray, B. M. Nugent, J. M. Schwarz, and M. E. Wilson. “The Epigenetics of Sex Differences in the Brain.” Journal of Neuroscience 29, no. 41 (10, 2009): 12815-12823.


Rebollo, Rita, Beatrice Horard, Benjamin Hubert, and Cristiana Vieira. “Jumping genes and epigenetics: Towards new species.” http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T39-4Y7MM1X-1&_user=10&_coverDate=01%2F25%2F2010&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1218544581&_rerunOrigin=scholar.google&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=1b16997d95d731440cf0c3c168003112.


Shepard, Kathryn N., Vasiliki Michopoulos, Donna J. Toufexis, and Mark E. Wilson. “Genetic, epigenetic and environmental impact on sex differences in social behavior.” Physiology & Behavior 97, no. 2 (5, 2009): 157-170.


Thakker-Varia, S., J. J. Krol, J. Nettleton, P. M. Bilimoria, D. A. Bangasser, T. J. Shors, I. B. Black, and J. Alder. “The Neuropeptide VGF Produces Antidepressant-Like Behavioral Effects and Enhances Proliferation in the Hippocampus.” Journal of Neuroscience 27, no. 45 (11, 2007): 12156-12167.



Cloning and the copying of beings..

In most fiction (since that is where human clones exist at present), there is always the assumption that a clone is an exact copy. In fact the angst of the young Picard in the movie Nemisis, is that he is a clone a copy of Captian Picard, and therefore not his own person.

Going through some of the research on DNA, cells, nueropeptides and epigenetics, I have come across several papers in the search listings which suggest quite positivly that there is no such thing as an exact copy of a clone. That in fact, each clone would be a separate person, and that even the DNA markers used for Criminal Fingerprinting would be different enough to tell which clone murdered the original evil genius responsible for their creation.

For me this changes some of the underlying assumptions of what clones would be if they were created, and who they would be as well. Even minor changes to the structure of the brain would alter the chemistry and personality of the brain as a whole, so that the perception of events would be interpreted differently. With these changes in perception, would come changes in personality, and experience, even knowledge.

In a very short time, the physical resemblance of the clones would be enough that they would be only as close as twins, and very possibly not even this close by the time ten to fifteen years had passed.

Critical Mass in San Diego

Regarding the post I made last night about the bicyclist in Downtown, the group is called Critical Mass, which I'm sure I knew, but flaked out on. When I was in San Fransisco I saw them hit the downtown area with a much larger group. It was, brilliant, to put it mildly.

Critical Mass is all over the world now. Of course, not everyone thinks they are as cool as I do.

Critical Mass is an idea that started in San Francisco in 1992 and was originally called Commut Clot. The idea was to show that they are no longer going to take the effects that automobile transportation has on the environment and the world. In order to emphasize this point the riders would take to the streets clogging up lanes, making commuters frustrated and protesting live on the streets in a disorganized but brilliant fashion.

Soon after its conception in the U.S., Critical Mass begun to catch like wild fire and eventually spread to over 325 cities world wide. Even Budapest has Critical Mass twice a year where they have reached numbers of 80,000 participants. Wherever and whenever it started, Critical Mass is definitely catching on in a growing environmentally conscious culture.

Even with all of the angst, and some very good points coming in from the other side, I still believe it is better to be alive, than a fungus.


The things that change our DNA

The possible factors that can change the human DNA are being discovered all the time. These changes mostly affect the Germline DNA.

Germline cells are immortal, in the sense that they can reproduce indefinitely. This is largely due to the activity of the enzyme known as telomerase. This enzyme extends the telomeres of the chromosome, preventing chromosome fusions and other negative effects of shortened telomeres. Somatic cells, by comparison, can only divide around 30-50 times due to the Hayflick limit.
That little tid-bit I found rather interesting for several other reasons...

Changes in the DNA due to Diabetes


That article is an example of a change occuring through 'natural causes', however, by using retro-viral vectors that infect a wide range of cells in a wide range of tissue types, changes are theoretically possible as well. Problem is, most such vectors target fairly specific cell types.

Retrovirus vectors are the agent most commonly used to insert, or change, genes in multi-cellular organisms. They are the agent used for the retroviral based flu vaccine. Also, there have been some other gene therapies developed on retroviral vectors. The problem with them, as disease treatment agents, is that they are finite; that is, the immune system eventually clears them, and any cells with altered DNA are eventually lost due to normal tissue turn over. So, the "cure" is not permanent.

And, of course, mutagens can impact and alter DNA on a cell by cell basis. And, several environmental toxicants are now known to exert an "epigenetic" effect on DNA. Exposure to these after birth leads, especially during early development, to a change in DNA structure in many or all cells. The change is not a mutation. Rather, it is a change in DNA methylation or histone phosphorylation, that alters gene expression. This epigenetic mechanism is now recognized as one of the primary ways that environmental substances may cause disease later in life.

The field of molecular biology and genetic engineering began in the 1970's with the discovery of restriction enzymes. The structure of DNA was understood. From the 1970's, our ability to manipulate DNA has exploded as we have developed an ever increasing repertoire of tools with which to manipulate DNA, and as we have elucidated the sequence of the human genome.

Seldom a week goes by without the discovery of a gene for yet another disease. Genetic explanations are touted for everything from cancer and heart disease to more diffuse conditions like alcoholism, homosexuality, and crime. It's been suggested that there may even be a gene for shyness! Biologists believe that new gene technology will revolutionize our understanding of disease and will have a greater impact on us than nuclear power or the computer.

What will make an even greater impact, however is the discovery of being able to alter these markers and genes which create traits such as shyness. What will we be when we can alter our base personality? What happens when the effect wears off?


Alterations in the ID of a DNA Fingerprint

Of course the panacea of DNA Fingerprinting for criminals, is to be able to alter the existing DNA finger print, either for the duration of the crime, or for the investigation afterward.

Just the idea of mucking about with your core DNA areas, sounds like an invitation for primate mutation (and an ape appetite for vegetation), the thought of actually doing it is, well ... fairly creepy. But then, some criminals are fairly creepy...

A study titled: Changes in DNA induced by toxic agents
(Forensic Sci Int. 1996 Apr 23;78(3):169-78, Sawaguchi T, Wang X, Sawaguchi A. Department of Legal Medicine, Tokyo Women's Medical College, Japan.)

Seems to suggest that it is possible, although from this publication, most of the methods would be fatal.

This is a preliminary report on significant alterations in the DNA profile caused by toxic substances which potentially has profound implications for the use of DNA techniques in identification. Acute DNA changes in the globus pallidus of the brain in man caused by carbon monoxide poisoning were detected by DNA profiling with probe 33.15. Chronic DNA changes in rabbits caused by methamphetamine were detected by DNA profiling with probe 33.15, AmpFLP on D1S80, TH01, CSF1PO and TPOX loci. Pre-intoxication bands appeared, disappeared or were discoloured after intoxication. With PCR-dot blot hybridization testing for HLADQ alpha, pre-intoxication positive spots became negative after intoxication and pre-intoxication negative spots became positive after intoxication. Intravenous injection of 10 mg/kg of methamphetamine every 2 days for 2 weeks was a large enough dose for inducement of genetic changes. In this investigation, clear changes in DNA due to intoxication were confirmed.

The results of the study, do suggest the possibility of a market for criminal re-sequencing for the purpose of acquittal. The repercussions of such an action, I can't imagine, are going to be better than going to prison, since all we are able to confirm through this study is that the DNA changes. There is no mention of a Predictable change... just A Change... so place your bets... monkey time!

Bicycle Protesters hit San Diego




















Just after 8:00pm a group of bicycle protesters emerged downtown, numbering well over 500. I wasn't able to count them as they went by, but considering my first estimate was 1000(based on the amount of times the traffic lights cycled as they road through the intersection of 4th and Broadway), I'm betting "over 500" is at the very least, accurate.

Three groups of bicycle cops were in the garden area of Horton Plaza (is the front of Horton Plaza an eye-sore these days or what?) when the protesters emerged. The bike-cops where ineffectual, as were the squad cars which were attempting to stem the tide as the cycles poured on through.

After the first group, a second group emerged which continued on down 4th street, turning left on Fst and into the Gas-lamp main area, disrupting traffic, to the cheers of hundreds as they passed by.

Most of the drivers who were paused in their travel to find parking and start their Friday night revelry cheered the bicyclists on, I noticed a few drivers who boiled into a state of road rage, but not many.

Most of the cyclists were in the college student age bracket, but there were more than a few 30 and 40-somethings out there in that pack, shouting "Go, go go!" when the police hit the sirens, attempting to disperse the pack -- It is good to have silver-backs around at times like those, to keep the youngsters from panicking themselves into a ticket.

In a city where the greater portion of people bitch and do nothing, it was great to see that many people out doing "something" because they felt change was required.

And for you City Council Members, recall that these were all voters, the riders and those cheering them on.


A Introduction look at DNA Finger Printing

I've posted a few "overview" looks at DNA Finger Printing so far on this blog, this time the link is to an article on JSTOR, An Introduction to DNA Finger Printing

Personally, getting the same information from different authors helps my writing on the subject. While the information is basically the same, the choice of words, vocabulary and the focus of importance is often different between two different authors, which not only provides me with a larger vocabulary, but often a new set of search criteria for further information.

This is one of the methods I developed working as a Google Researcher, to speed up the absorption of a new topic, and develop answers, and a technique that is invaluable as a freelance writer.

Passing the Buck - Homeless in San Diego

The Museum of San Diego History, for its NOW! program starting Feb 25th is showing the Passing the Buck: Homeless in San Diego exhibit.

"Although there is great concern for assisting the homeless, where to house them in San Diego is a political hot button."

Time for the show is 6:00pm - 7:30pm Admission is Free, and promises to be an informative look at what is really being done for the homeless in San Diego.

The Chimera

In Greek mythology, "chimera," derived from the Greek word for "billy goat," referred to a fire-breathing she-demon that was part lion, part goat, and part dragon or snake. Getting rid of this killer was quite an achievement, and Bellerophon was heaped with praise and riches for his courageous and clever dispatch of the beast. The term "chimera" has come down to us through the ages with 3 definitions: the original monster, an impossible and fanciful creation of the imagination (eg, Woody Allen's malefactor with the body of a crab and the head of social worker), and an organism containing tissues from at least 2 genetically distinct parents. It is this last definition that is of compelling medical interest, based largely on the work of Ray Owen.

The Chimera and the Crime

There is a fantastic paper on the subject of the Chimera as directly related to Crime Scene investigation.

CHIMERAS: DOUBLE THE DNA-DOUBLE THE FUN FOR
CRIME SCENE INVESTIGATORS, PROSECUTORS, AND
DEFENSE ATTORNEYS?
(This Link is to a PDF File)

One thing she doesn't address, which does come up in the Winter's Harvest novel, is the idea of triplets or ... more... in the make up of the Chimera.

Despite this, Catherine Arcabascio has written one of the best papers I've read on the subject so far, and just about all of the information presented is current science.

DNA Uses in Crime Investigation

A report issued by the Justice Department in 2002 indicated that two-thirds of chief prosecutors in the United States rely on DNA testing during investigations and trials. The use of DNA evidence has exonerated at least ten individuals who were wrongly convicted of murder and faced the death penalty, while the sentences of more than 100 others convicted of lesser crimes were overturned based upon DNA evidence. The FBI maintains a database that may be used to compare DNA samples from unsolved state and federal crimes. Since its inception in 1992, the FBI's database has made more than 5,000 matches, thus allowing law enforcement officials to solve crimes that might not have been solved without the use of DNA.

The FBI crime laboratory dominated research in forensic sciences for much of the 1980s and 1990s. However, allegations surfaced in 1995 that suggested scientists at the crime lab had tainted evidence related to the 1993 bombing of the World Trade Center in New York City. A former chemist in the lab, Frederic White-hurst, testified before the House Committee on the Judiciary that the FBI had knowingly drafted misleading scientific reports and pressured FBI scientists to commit perjury by backing up the false reports. These allegations injured the FBI's reputation and led to speculation in the late 1990s that prosecutors could not rely on the FBI's analysis of DNA evidence.

Even as the FBI rebuilt its reputation, other questions surrounding the use of DNA evidence have arisen since the late 1990s. In 1999, the department of justice issued a report stating that evidence from at least 180,000 unsolved rape cases had not been submitted for testing. A 2002 report by USA Today suggested that several thousand pieces of evidence from rape and Homicide cases had not been submitted for DNA testing, so they do not appear in the FBI's database. In 2000, Congress allocated $125 million to support the national DNA database system, including $45 million designated to allow states to test evidence from unsolved crimes. However, several states claim that their law enforcement officials are so swamped with current cases that they cannot test older, unsolved cases. Moreover, a small number of states—primarily New York, Florida, Virginia, and Illinois—have aggressively developed their own DNA databases and have contributed heavily to the FBI's system. These states accounted for more than half of the FBI's DNA matches between 1992 and 2002.

Use of DNA evidence to overturn criminal convictions remains a common topic of discussion among legal and criminal justice experts, as well as the popular media. One of the most closely followed cases involved the convictions of five young men for the rape of a jogger in Central Park in New York City in 1989. The five men in the case, dubbed the "Central Park Jogger Case," served sentences ranging from seven to eleven years for the incident. However, another man, Matias Reyes, who was convicted for murder in 1989, confessed to the rape. Testing confirmed that the semen found in the victim and on the victim's sock matched Reyes's DNA.

Upon receiving the new evidence, the New York County district attorney's office asked the New York State Supreme Court to overturn the convictions of the five men. Several groups, including Women's Rights groups, cited this case as an example of why law enforcement should be more proactive in pursuing unsolved rape cases through the use of DNA testing.
Further readings

Bennett, Margann. 1995. "Admissibility Issues of Forensic DNA Evidence." University of Kansas Law Review 44 (November).

"Confronting the New Challenges of Scientific Evidence: DNA Evidence and the Criminal Defense." 1995. Harvard Law Review 108 (May).

Federal Bureau of Investigation. 1994. Handbook of Forensic Science. Washington, D.C.: U.S. Government Printing Office.

National Research Council. 1992. DNA Technology in Forensic Science. Washington, D.C.: National Academy Press.

Wright, Eric E. 1995. "DNA Evidence: Where We've Been, Where We Are, and Where We Are Going." Maine Bar Journal 10 (July).

DNA Fingerprinting - An Overview




For the novel Winter's Harvest I have had to spend quite a bit of time looking into the techniques of DNA fingerprinting. This is a basic overview of how a DNA fingerprint is extracted from evidence at a crime scene, produced by the Encyclopedia Britannica.

GTP and ME and Chess

You: Give me an annotation of the following game, noting and highlighting tactics, positioning, shifts in momentum and their causes, as we...