Brain cells have different lineages?

_{Denyse O'Leary

October 1, 2015

Genetics, News}

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Our brain cells have different genomes from one another. The study shows for the first time that mutations in somatic cells — that is, any cell in the body except sperm and eggs — are present in significant numbers in the brains of healthy people. These mutations appear to occur more often in the genes a neuron uses most. Patterns of mutation allow researchers to trace brain cell lineages.

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The study, published Oct. 2 in Science, shows for the first time that mutations in somatic cells–that is, any cell in the body except sperm and eggs–are present in significant numbers in the brains of healthy people. This finding lays the foundation for exploring the role of these post-conception mutations in human development and disease.

“A lot of people have been asking lately whether somatic mutations contribute to a range of neurodevelopmental and neurodegenerative diseases, but they couldn’t answer the question because of the limitations of technology,” said the study’s co-senior author, Peter Park, associate professor of biomedical informatics at HMS.

Whatever happened to one gene, one protein? And all the other simplicities?

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A natural history of neurons - Diverse mutations reveal lineage of brain cells - October 1, 2015 Excerpt: The researchers found that each neuron contained about 1,500 single nucleotide variants.... Many phenomena can create somatic mutations. Ultraviolet light causes them in skin cells. Errors in DNA replication cause them in rapidly dividing cancer cells. "What we found in the brain was neither of those things," said Walsh. "We thought the dominant source of mutation would be faulty DNA replication and were surprised to find that instead, it's faulty DNA expression."... "I'm full of mutations but I'm walking around, pretty healthy," said Park. "It just goes to show that there are a lot of things we don't understand." http://www.sciencedaily.com/releases/2015/10/151001153926.htm
Actually, contrary to what the researchers believe from the central dogma of the modern synthesis, (that they were, apparently, erroneously taught in school via neo-Darwinism), it has been known for a while now that mutations to DNA caused by ultraviolet light and errors in DNA replication are not the only source of variations to DNA. In fact, replication errors and ultraviolet damage are now known to not even be the main source of variations to DNA as was, and apparently still is, presupposed in neo-Darwinian thought.
How life changes itself: the Read-Write (RW) genome. - 2013 Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences. http://www.ncbi.nlm.nih.gov/pubmed/23876611 Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009 Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf
Also of interest from the preceding paper, on page 22, is a simplified list of the ‘epigenetic’ information flow in the cell that directly contradicts what was expected from the central dogma (Genetic Reductionism/modern synthesis model) of neo-Darwinism. In fact mutations, instead of occurring randomly as is presupposed in neo-Darwinian thought, are now best thought of as being 'directed':
"mutations don’t occur randomly in the genome, but rather in the genes where they can help to address the challenge. But there is more. The gene’s single stranded DNA has certain coils and loops which expose only some of the gene’s nucleotides to mutation. So not only are certain genes targeted for mutation, but certain nucleotides within those genes are targeted in what is referred to as directed mutations.,,, These findings contradict evolution’s prediction that mutations are random with respect to need and sometimes just happen to occur in the right place at the right time.,,," Cornelius Hunter - New Research Elucidates Directed Mutation Mechanisms - January 7, 2013 Failed Darwinian Prediction – Mutations are not adaptive – Cornelius Hunter – 2015 Excerpt: In the twentieth century, the theory of evolution predicted that mutations are not adaptive or directed. In other words, mutations were believed to be random with respect to the needs of the individual.,,, But that assumption is now known to be false.,,, (References on site) https://sites.google.com/site/darwinspredictions/mutations-are-not-adaptive "It is difficult (if not impossible) to find a genome change operator that is truly random in its action within the DNA of the cell where it works' James Shapiro - Evolution: A View From The 21st Century - (Page 82)
Besides the neurons of the brain, the tissues and cells of the body, as they differentiate, are also found to modify their DNA to suit their needs. As Dr. Jonathan Wells states in the following article, "It's the organism controlling the DNA, not the DNA controlling the organism."
Ask an Embryologist: Genomic Mosaicism - Jonathan Wells - February 23, 2015 Excerpt: humans have a "few thousand" different cell types. Here is my simple question: Does the DNA sequence in one cell type differ from the sequence in another cell type in the same person?,,, The simple answer is: We now know that there is considerable variation in DNA sequences among tissues, and even among cells in the same tissue. It's called genomic mosaicism. In the early days of developmental genetics, some people thought that parts of the embryo became different from each other because they acquired different pieces of the DNA from the fertilized egg. That theory was abandoned,,, ,,,(then) "genomic equivalence" -- the idea that all the cells of an organism (with a few exceptions, such as cells of the immune system) contain the same DNA -- became the accepted view. I taught genomic equivalence for many years. A few years ago, however, everything changed. With the development of more sophisticated techniques and the sampling of more tissues and cells, it became clear that genetic mosaicism is common. I now know as an embryologist,,,Tissues and cells, as they differentiate, modify their DNA to suit their needs. It's the organism controlling the DNA, not the DNA controlling the organism. http://www.evolutionnews.org/2015/02/ask_an_embryolo093851.html
In fact, in the following paper, and in direct contradiction to neo-Darwinian thought found that, from a genetic point of view, we are 'individual in the truest sense of the word' and also found that 'we need to fundamentally rethink the view of genes that every schoolchild has learned since Gregor Mendel's time'
Duality in the human genome - November 28, 2014 Excerpt: The results show that most genes can occur in many different forms within a population: On average, about 250 different forms of each gene exist. The researchers found around four million different gene forms just in the 400 or so genomes they analysed. This figure is certain to increase as more human genomes are examined. More than 85 percent of all genes have no predominant form which occurs in more than half of all individuals. This enormous diversity means that over half of all genes in an individual, around 9,000 of 17,500, occur uniquely in that one person - and are therefore individual in the truest sense of the word. The gene, as we imagined it, exists only in exceptional cases. "We need to fundamentally rethink the view of genes that every schoolchild has learned since Gregor Mendel's time.,,, According to the researchers, mutations of genes are not randomly distributed between the parental chromosomes. They found that 60 percent of mutations affect the same chromosome set and 40 percent both sets. Scientists refer to these as cis and trans mutations, respectively. Evidently, an organism must have more cis mutations, where the second gene form remains intact. "It's amazing how precisely the 60:40 ratio is maintained. It occurs in the genome of every individual – almost like a magic formula," says Hoehe. http://medicalxpress.com/news/2014-11-duality-human-genome.html
Moreover, as if all that was not bad enough for the committed neo-Darwinist, the following study revealed, contrary to neo-Darwinian thought which holds that the genome 'is a stable structure that changes rarely and accidentally', it is now found that neurons are 'dynamic' and are 'constantly rewriting their DNA':
Neurons constantly rewrite their DNA - Apr. 27, 2015 Excerpt: They (neurons) use minor "DNA surgeries" to toggle their activity levels all day, every day.,,, "We used to think that once a cell reaches full maturation, its DNA is totally stable, including the molecular tags attached to it to control its genes and maintain the cell's identity," says Hongjun Song, Ph.D.,, "This research shows that some cells actually alter their DNA all the time, just to perform everyday functions.",,, ,,, recent studies had turned up evidence that mammals' brains exhibit highly dynamic DNA modification activity—more than in any other area of the body,,, http://medicalxpress.com/news/2015-04-neurons-constantly-rewrite-dna.html
Also of related interest, it is now found that the 'mind', which neo-Darwinists do not believe in by the way, can have pronounced effects on the function of the brain in what is termed 'brain plasticity'. Jeffrey Schwartz's work in 'brain plasticity' is gone over at the 4:03 minute mark of the following video
The Case for the Soul - InspiringPhilosophy - (4:03 minute mark, Brain Plasticity including Schwartz's work) - Oct. 2014 - video The Mind is able to modify the brain (brain plasticity). https://www.youtube.com/watch?v=oBsI_ay8K70
Moreover, besides the brain, it is also now found that 'mindfulness' can reach all the way down to the molecular level of your body and 'Can Cause Specific Molecular Changes To Your Genes':
Scientists Finally Show How Your Thoughts Can Cause Specific Molecular Changes To Your Genes, - December 10, 2013 Excerpt: “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,”,,, “Most interestingly, the changes were observed in genes that are the current targets of anti-inflammatory and analgesic drugs,”,,, 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. http://www.tunedbody.com/scientists-finally-show-thoughts-can-cause-specific-molecular-changes-genes/
To say the preceding findings contradict neo-Darwinian expectations would be an understatement. The preceding findings of 'top down' control by 'mind', for both the brain and the body, are completely inexplicable to the 'bottom up' materialistic explanations of neo-Darwinism and should, if neo-Darwinism were a proper science instead of being basically a faith based religion for atheists, count as a solid refutation of the 'bottom up' modern synthesis of neo-Darwinism.bornagain77_{October 2, 2015
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We don't have a brain. I think we just gave a giant memory machine and connected with soul and body. So these genes would only be affecting memory operations. All neuro problems are memory triggering problems I'm sure. The brain is as a concept should be dead as a dodo.Robert Byers_{October 2, 2015
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Whatever happened to one gene, one protein?
It got updated in the light of new data. What do you think this study has to with that?wd400_{October 1, 2015
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