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DNA Dynamism

Just in at PhysOrg.com. Non-dividing brain cells quickly undergo epigenetic changes.

“It was mind-boggling to see that so many methylation sites — thousands of sites — had changed in status as a result of brain activity,” Song says. “We used to think that the brain’s epigenetic DNA methylation landscape was as stable as mountains and more recently realized that maybe it was a bit more subject to change, perhaps like trees occasionally bent in a storm. But now we show it is most of all like a river that reacts to storms of activity by moving and changing fast.”

So much for the view that the genome is rather static, and that the major dynamical changes to it involve random mutations. Instead, we have a view of a dynamical DNA that is entirely capable of change via interactions with its environment. Only integrated systems can function dynamically like this. And Darwinism trying to explain the rise of this level of dynamism is like trying to put a square peg into a round hole.

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12 Responses to DNA Dynamism

  1. DNA methylation represses gene expression. Off switch. Transcription is regulated, and very responsive to the environment (google transcription factors).

    So it isn’t really a “dynamical” change to the genome, just the regulation of gene expression. Another of many mechanisms of dynamic gene regulation.

    The surprise here is that DNA methylation is sometimes thought to be a stable mark (as was histone methylation, until demethylases were discovered).

  2. DrREC:

    There are two important points to be considered:

    a) For transcription to be not only regulated (which is obvious), but also “very responsive to the environment”, there must be a very complex system of coded procedures for that, and we have no idea of where they are, how they are coded, and least of all how they originated (well, on that last point we in ID have some ideas). Please note that here we are not talking of simple feedback regulations from environment (a la lac operon), buth rather of transcription adaptation in the CNS, physical adaptations of neural cells at the genome level that very likely have a meaning connected to brain function. That is something.

    b) DNA methilation is an epigenetic regulation. That means that it can be tranferred when it happens in gametes. Well, neural cells are not gametes, but we are just discovering a new scenario here, and in the general trend towards neo Lamarkism, who know what we are going to find?

  3. PaV:

    Thank for the very interesting post.

    DNA is certainly much more dynamic that we think. And let’s remember that we still miss practicall all the important procedures that make life possible bot in a single cell and in a multicellular being. I have pointed out many times that how the same DNA generates millions (or probably more) of different, specific, functionally determined transcriptomes in single cells of a multicellular organism is still a complete, and fascinating, mystery.

    We are debating darwinists mainly on protein genes information for the moment, because at least we know where and how it is coded, and it is easier to discuss. But when we discover where the procedures are, and how they are coded, and how complex they are… Well, I am happy I am not in the shoes of our interlocutors :)

  4. Yes. THis is exactly correct. I read of a study one done on the brains of Monks from different regions around the world, who prayed all day and indeed their brains showed unusual patterns of activity even at rest. What we think about and do with our minds effects it physically. once again this shows that there are physical consequences for our spiritual decisions and actions. This can cut both ways as well of course. That is, if our minds are concerned with the wrong things it may do damage, but if our minds are focused on good things, or challanging things that build us up, over time that could pay off. Once again this gets into the REAL power of consciousness, and the power of prayer. Mind over matter.

  5. Frost:

    Once again this gets into the REAL power of consciousness, and the power of prayer. Mind over matter.

    Absolutely! :)

  6. of few notes:

    The following video clearly shows just how extremely ‘plastic’ the brain can be to accommodate the ‘stable’ soul/mind of a person:

    Miracle Of Mind-Brain Recovery Following Hemispherectomies – Dr. Ben Carson – video
    http://www.metacafe.com/watch/3994585/

    Removing Half of Brain Improves Young Epileptics’ Lives:
    Excerpt: “We are awed by the apparent retention of memory and by the retention of the child’s personality and sense of humor,” Dr. Eileen P. G. Vining; In further comment from the neuro-surgeons in the John Hopkins study: “Despite removal of one hemisphere, the intellect of all but one of the children seems either unchanged or improved. Intellect was only affected in the one child who had remained in a coma, vigil-like state, attributable to peri-operative complications.”
    http://www.nytimes.com/1997/08.....lives.html

    The ‘major dynamical changes’ in the brain pointed out in the OP, and as is obvious in preceding hemispherectomy study, as the result of ‘activity in the brain’, simply makes no sense from the atheistic/materialistic point of view, as if consciousness were merely ‘emergent’ from the brain, but these studies make complete sense from the Theistic point of view of the mind having a primacy of existence over the brain. Moreover reality itself points to this primacy of mind over matter:

    Quantum mind–body problem
    Parallels between quantum mechanics and mind/body dualism were first drawn by the founders of quantum mechanics including Erwin Schrödinger, Werner Heisenberg, Wolfgang Pauli, Niels Bohr, and Eugene Wigner
    http://en.wikipedia.org/wiki/Q.....dy_problem

    “It was not possible to formulate the laws (of quantum theory) in a fully consistent way without reference to consciousness.” Eugene Wigner (1902 -1995) from his collection of essays “Symmetries and Reflections – Scientific Essays”; Eugene Wigner laid the foundation for the theory of symmetries in quantum mechanics, for which he received the Nobel Prize in Physics in 1963.
    http://eugene-wigner.co.tv/

    Here is the key experiment that led Wigner to his Nobel Prize winning work on quantum symmetries:

    Eugene Wigner
    Excerpt: To express this basic experience in a more direct way: the world does not have a privileged center, there is no absolute rest, preferred direction, unique origin of calendar time, even left and right seem to be rather symmetric. The interference of electrons, photons, neutrons has indicated that the state of a particle can be described by a vector possessing a certain number of components. As the observer is replaced by another observer (working elsewhere, looking at a different direction, using another clock, perhaps being left-handed), the state of the very same particle is described by another vector, obtained from the previous vector by multiplying it with a matrix. This matrix transfers from one observer to another.
    http://www.reak.bme.hu/Wigner_.....io/wb1.htm

    i.e. In the experiment the ‘world’ (i.e. the universe) does not have a ‘privileged center’. Yet strangely, the conscious observer does exhibit a ‘privileged center’. This is since the ‘matrix’, which determines which vector will be used to describe the particle in the experiment, is ‘observer-centric’ in its origination! Thus explaining Wigner’s dramatic statement, “It was not possible to formulate the laws (of quantum theory) in a fully consistent way without reference to consciousness.”

    further note, Jeffery Schwartz, from his observation of the brain’s ‘plasticity’, in response to treatment for obsessive compulsive disorder, has also come to the conclusion that ‘mind’ has primacy over the brain:

    Dr. Jeffrey Schwartz – “You Are Not Your Brain”
    http://www.youtube.com/watch?v=u0lPuN03b40

    further notes on the ‘non-local’ quantum mind:

    Quantum Coherence and Consciousness – Scientific Proof of ‘Mind’ – video
    http://www.metacafe.com/watch/6266865/

    Particular quote of interest from preceding video;

    “Wolf Singer Director of the Max Planck Institute for Brain Research (Frankfurt) has found evidence of simultaneous oscillations in separate areas of the cortex, accurately synchronized in phase as well as frequency. He suggests that the oscillations are synchronized from some common source, but the actual source has never been located.”
    James J. Hurtak, Ph.D.

    corroborating evidence;

    Brain ‘entanglement’ could explain memories – January 2010
    Excerpt: In both cases, the researchers noticed that the voltage of the electrical signal in groups of neurons separated by up to 10 millimetres sometimes rose and fell with exactly the same rhythm. These patterns of activity, dubbed “coherence potentials”, often started in one set of neurons, only to be mimicked or “cloned” by others milliseconds later. They were also much more complicated than the simple phase-locked oscillations and always matched each other in amplitude as well as in frequency. (Perfect clones) “The precision with which these new sites pick up on the activity of the initiating group is quite astounding – they are perfect clones,” says Plen
    http://www.uncommondescent.com.....ent-399098

    The preceding ‘quantum evidence’ provides a foundation for a plausible ‘transcendent mechanism’ for the following study:

    Study suggests precognition may be possible – November 2010
    Excerpt: A Cornell University scientist has demonstrated that psi anomalies, more commonly known as precognition, premonitions or extra-sensory perception (ESP), really do exist at a statistically significant level.
    http://www.physorg.com/news/20.....ition.html

    As well, Stuart Hammeroff has done some interesting work, spanning 35 years, establishing the ‘non-local quantum connection’ for the mind to the brain:

    TEDx Brussels 2010 – Stuart Hameroff – Do we have a quantum Soul? – video
    http://www.youtube.com/watch?v=iIyEjh6ef_8

    etc.. etc.. etc..

  7. of few notes:

    The following video clearly shows just how extremely ‘plastic’ the brain can be to accommodate the ‘stable’ soul/mind of a person:

    Miracle Of Mind-Brain Recovery Following Hemispherectomies – Dr. Ben Carson – video
    http://www.metacafe.com/watch/3994585/

    Removing Half of Brain Improves Young Epileptics’ Lives:
    Excerpt: “We are awed by the apparent retention of memory and by the retention of the child’s personality and sense of humor,” Dr. Eileen P. G. Vining; In further comment from the neuro-surgeons in the John Hopkins study: “Despite removal of one hemisphere, the intellect of all but one of the children seems either unchanged or improved. Intellect was only affected in the one child who had remained in a coma, vigil-like state, attributable to peri-operative complications.”
    http://www.nytimes.com/1997/08.....lives.html

    The ‘major dynamical changes’ in the brain pointed out in the OP, and as is obvious in preceding hemispherectomy study, as the result of ‘activity in the brain’, simply makes no sense from the atheistic/materialistic point of view, as if consciousness were merely ‘emergent’ from the brain, but these studies make complete sense from the Theistic point of view of the mind having a primacy of existence over the brain. Moreover reality itself points to this primacy of mind over matter:

    Quantum mind–body problem
    Parallels between quantum mechanics and mind/body dualism were first drawn by the founders of quantum mechanics including Erwin Schrödinger, Werner Heisenberg, Wolfgang Pauli, Niels Bohr, and Eugene Wigner
    http://en.wikipedia.org/wiki/Q.....dy_problem

    “It was not possible to formulate the laws (of quantum theory) in a fully consistent way without reference to consciousness.” Eugene Wigner (1902 -1995) from his collection of essays “Symmetries and Reflections – Scientific Essays”; Eugene Wigner laid the foundation for the theory of symmetries in quantum mechanics, for which he received the Nobel Prize in Physics in 1963.

    Here is the key experiment that led Wigner to his Nobel Prize winning work on quantum symmetries:

    Eugene Wigner
    Excerpt: To express this basic experience in a more direct way: the world does not have a privileged center, there is no absolute rest, preferred direction, unique origin of calendar time, even left and right seem to be rather symmetric. The interference of electrons, photons, neutrons has indicated that the state of a particle can be described by a vector possessing a certain number of components. As the observer is replaced by another observer (working elsewhere, looking at a different direction, using another clock, perhaps being left-handed), the state of the very same particle is described by another vector, obtained from the previous vector by multiplying it with a matrix. This matrix transfers from one observer to another.
    http://www.reak.bme.hu/Wigner_.....io/wb1.htm

    i.e. In the experiment the ‘world’ (i.e. the universe) does not have a ‘privileged center’. Yet strangely, the conscious observer does exhibit a ‘privileged center’. This is since the ‘matrix’, which determines which vector will be used to describe the particle in the experiment, is ‘observer-centric’ in its origination! Thus explaining Wigner’s dramatic statement, “It was not possible to formulate the laws (of quantum theory) in a fully consistent way without reference to consciousness.”

    further note, Jeffery Schwartz, from his observation of the brain’s ‘plasticity’, in response to treatment for obsessive compulsive disorder, has also come to the conclusion that ‘mind’ has primacy over the brain:

    Dr. Jeffrey Schwartz – “You Are Not Your Brain”
    http://www.youtube.com/watch?v=u0lPuN03b40

    further notes on the ‘non-local’ quantum mind:

    Quantum Coherence and Consciousness – Scientific Proof of ‘Mind’ – video
    http://www.metacafe.com/watch/6266865/

    Particular quote of interest from preceding video;

    “Wolf Singer Director of the Max Planck Institute for Brain Research (Frankfurt) has found evidence of simultaneous oscillations in separate areas of the cortex, accurately synchronized in phase as well as frequency. He suggests that the oscillations are synchronized from some common source, but the actual source has never been located.”
    James J. Hurtak, Ph.D.

    corroborating evidence;

    Brain ‘entanglement’ could explain memories – January 2010
    Excerpt: In both cases, the researchers noticed that the voltage of the electrical signal in groups of neurons separated by up to 10 millimetres sometimes rose and fell with exactly the same rhythm. These patterns of activity, dubbed “coherence potentials”, often started in one set of neurons, only to be mimicked or “cloned” by others milliseconds later. They were also much more complicated than the simple phase-locked oscillations and always matched each other in amplitude as well as in frequency. (Perfect clones) “The precision with which these new sites pick up on the activity of the initiating group is quite astounding – they are perfect clones,” says Plen
    http://www.uncommondescent.com.....ent-399098

    The preceding ‘quantum evidence’ provides a foundation for a plausible ‘transcendent mechanism’ for the following study:

    Study suggests precognition may be possible – November 2010
    Excerpt: A Cornell University scientist has demonstrated that psi anomalies, more commonly known as precognition, premonitions or extra-sensory perception (ESP), really do exist at a statistically significant level.
    http://www.physorg.com/news/20.....ition.html

    As well, Stuart Hammeroff has done some interesting work, spanning 35 years, establishing the ‘non-local quantum connection’ for the mind to the brain:

    TEDx Brussels 2010 – Stuart Hameroff – Do we have a quantum Soul? – video
    http://www.youtube.com/watch?v=iIyEjh6ef_8

    etc.. etc.. etc..

  8. “well, on that last point we in ID have some ideas”

    Do share.

  9. Dr Rec, pardon the instrusion, I answered your questions from a day or two ago here:

    http://www.uncommondescent.com.....ent-401213

    I was wondering if your care to respond.

  10. DrREC:

    Regulation networks and adaptive procedures are very complex. In software, they represent a big part of the whole. Indeed, software is mainly about regulation and response to inputs.

    The protein genes, in human genome, are only the final effectors of the complex mechanism of life. And yet, they ar by far funcionally complex enough that we can infer design for them.

    But the regulation networks, especially the transcription regulation networks, which may include the methylation mechanism, are certainly much more complex.

    Just think of how finely tuned the transcriptome regulation must be:

    1)It must choose, among the about 20000 protein coding genes, those that must be transcribed in that specific cell

    2)It must control how much each gene is transcribed

    3) It must control when (in a temporal seqeunce) each gene is transcribed

    4) It muist choose and control how each gene is transcribed, according to the current one gene – many proteins model

    5) It must control all post transcriptional events

    6) And finally, translation and post translational modifications must ne under strict check, too.

    Moreover, the transcriptome, beyond being specific for the cell type, is dynamic, and constantly changing according to stimuli from within and without the cell (or even the body), including the state of cell division, checkpoints of DNA integrity, cytokines, hormones, neural control, and so on.

    The procedures that efficiently manage the genome to comply with all that, although still not understood both in their nature and their implementation, must necessarily be so complex that design can be easily hypothesized for their origin, even more than for the origin of protein information.

  11. 11

    cha-ching

  12. OT: Body Code is a selection of biomedical animations that explore the human body at the microscopic and molecular scale. Body Code was designed for museum and art gallery exhibition, with the goal of reaching public audiences who do not usually seek out or are exposed to the details of scientific knowledge.

    Body Code – video
    http://www.youtube.com/watch?v=mDZLiZB0iPY

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