Physics of Biology

1409 Submissions

[6] viXra:1409.0193 [pdf] submitted on 2014-09-26 06:45:13

Morphogenesis, Morphostasis, and Learning in TGD Framework

Authors: Matti Pitkänen
Comments: 10 Pages.

According to Michael Levin, concerning morphogenesis and morphostasis the basic challenge is to understand how the shape of the organism is generated and how it is preserved. The standard local approach based on belief on genetic determinism does not allow one to answer these questions satisfactorily.

The first approach to this problem relies on a self-organization paradigm in which the local dynamics of cells leads to large scale structures as self-organization patterns. In TGD framework 3-D self-organization is replaced with 4-D self-organization (the failure of strict determinism of the classical dynamics is essential motivating zero energy ontology (ZEO)). One can speak about 4-D healing: expressing it in somewhat sloppy manner, the space-time surface serving as a classical correlate for the patient is as a whole replaced with the healed one: after the 4-D healing process the organism was never ill in geometrical sense! Note that in quantal formulation one must speak of quantum superposition of space-time surfaces.

Second approach could be seen as computational. The basic idea is that the process is guided by a template of the target state and morphogenesis and healing are computational processes. What Levin calls morphogenetic fields would define this template. It is known that organisms display a kind of coordinate grid providing positional information that allows cells to "decide" about the profile of genetic expression. In TGD framework magnetic body forming coordinate grid formed from flux tubes is a natural candidate for this structure. They would also realize topological quantum computation (TQC) with basic computational operations realized at the nodes of flux tubes to which it is natural to associate some biological sub-structures.

The assumption about final goal defining a template can be argued to be too strong: much weaker principle defining a local direction of dynamics and leading automatically to the final state as something analogous to free energy minimum in thermodynamics might be enough. Unfortunately, second law is the only principle that standard physics can offer. Negentropy Maximization Principle (NMP) provides the desired principle in TGD framework. Also the approach of WCW spinor field to the maximum of vacuum functional (or equivalently that of Kähler function) gives a goal for the dynamics after the perturbation of the organism causing "trauma". If Kähler function is classical space-time correlate for entanglement negentropy, these two views are equivalent.

TGD thus suggests an approach, which could be seen as a hybrid of approaches based on self-organization and computationalism. The magnetic body becomes the key notion and codes also for learned behaviors as TQC programs coded by the braiding of flux tubes. The replication of the magnetic body means also the replication of the programs behind behavioral patterns (often somewhat misleadingly regarded as synonymous with long term memories): both structure and function are replicated. This hypothesis survives the killer tests provided by the strange findings about planaria cut into two and developing new head or tail while retaining its learned behaviors: the findings indicate that behavioral programs are preserved although planaria develops a new brain.
Category: Physics of Biology

[5] viXra:1409.0191 [pdf] submitted on 2014-09-26 06:52:00

Pollack's Findings About Fourth Phase of Water: TGD View

Authors: Matti Pitkänen
Comments: 8 Pages.

The discovery of negatively charged exclusion zone formed in water bounded by gel phase has led Pollack to propose the notion of gel like fourth phase of water. In this article this notion is discussed in TGD framework. The proposal is that the fourth phase corresponds to negatively charged regions - exclusion zones - with size up to 100-200 microns generated when energy is fed into the water - say as radiation, in particular solar radiation. The stoichiometry of the exclusion zone is H1.5O and can be understood if every fourth proton is dark proton residing at the flux tubes of the magnetic body assignable to the exclusion zone and outside it. This leads to a model for prebiotic cell as exclusion zone. Dark protons are proposed to fork dark nuclei whose states can be grouped to groups corresponding to DNA, RNA, amino-acids, and tRNA and for which vertebrate genetic code is realized in a natural manner. The voltage associated with the system defines the analog of membrane potential, and serves as a source of metabolic energy as in the case of ordinary metabolism. The energy is liberated in a reverse phase transition in which dark protons transform to ordinary ones. Dark proton strings serve as analogs of basic biopolymers and one can imagine analog of bio-catalysis with enzymes replaced with their dark analogs. The recent discovery that metabolic cycles emerge spontaneously in absence of cell support this view.
Category: Physics of Biology

[4] viXra:1409.0185 [pdf] submitted on 2014-09-26 07:03:56

TGD View About Homeopathy, Water Memory, and Evolution of Immune System

Authors: Matti Pitkänen
Comments: 6 Pages.

This article represents a brief sketch of TGD based model of water memory and homeopathy as it is after two steps of progress. First one was due to Pollack's findings about exclusion zones of water explained in terms of fourth phase of water. Second step or progress was inspired by an anomaly claimed by Tajmar et al and known as strong gravimagnetism. The attempt to understand the claim led to heff = hgr=hem hypothesis unifying two TGD views about the notion of hierarchy of Planck constants proposed to characterize the phases of dark matter.

In this framework the attempt to understand homeopathy leads to additional insights about about water as living system and about prebiotic life as being based on the dark realization of genetic code realized in terms of dark proton strings which are nothing than dark variants of nuclei. Formation of exclusion zones would be formation of primitive lifeforms and primitive form of metabolism. Homeopathy could be seen as a manifestation of a fundamental form of immune system based on the recognition of invader molecules using reconnection mechanism for magnetic flux tubes and on mimicking the braiding of the magnetic bodies of invader molecules using dark variants of proteins (later proteins) and and eventually representing them symbolically in terms of dark DNA (later ordinary DNA) coding for the dark proteins. Genetic code might have geometric interpretation as coding for the 2-braiding of 3-D coordinate grids represented by magnetic flux tubes serving as the 4-D template coding not only for the structure of the organism but also its functions as spatio-temporal patterns. Protein folding would represent a behavior of protein and DNA would code also for it.
Category: Physics of Biology

[3] viXra:1409.0183 [pdf] submitted on 2014-09-26 07:07:47

New Results About Microtubules as Quantum Systems

Authors: Matti Pitkänen
Comments: 18 Pages.

The latest news in quantum biology is the observation by the group led by Anirban Bandyopadhyay about detection of quantum vibration in microtubule scale - their lengths vary up to 50 μm. If this observation can be replicated, one can speak about breakthrough in quantum consciousness.

The findings reported in an earlier talk of Banduopadhyay give support for the general TGD inspired view about topological quantum computation (TQC) and allow for a rather detailed model in the case of microtubules. The idea is that flux tubes form a 2-D coordinate grid consisting of parallel flux tubes in two different directions. Crossing points would be associated with tubulins and the conformational state of tubulin could define a bit coding whether the braid strands defining coordinate lines are braided or not (swap or not). In this manner any bit pattern at microtubule defines a particular TQC program. If also conformations are quantum superposed, one would have "quantum-quantum computation". It however seems that conformation change is irreversible chemical reaction so that this option is not feasible.

The TGD inspired modification of the proposal in terms of flux tube coordinate grids making possible TQC architectures with tubulin dimers defining bits defining in turn TQC program looks rather natural. Coordinate grids can be fixed on basis of the experimental findings and there are 8 of them. The interpretation is in terms of different resolutions. The grids for A and B type lattices are related by 2π twist for the second end of the basic 13-unit for microtubule. An attractive interpretation for the resonance frequencies is in terms of phase transitions between A and B type lattices. If A type lattices can be generated only in phase transitions induced by AC stimulus at resonance frequencies, one could understand their experimental absence, which is a strong objection against Penrose-Hameroff model.

TGD suggests also a generalization of the very notion of TQC to 2-braid TQC with 2-D string world sheets becoming knotted in 4-D space-time. Now qubits (or their generalizations) could correspond to states of flux tubes defining braid strands as Penrose and Hameroff seem to suggest and the emergence of MTs could be seen as an evolutionary leap due to the emergence of a new abstraction level in cognitive processing.
Category: Physics of Biology

[2] viXra:1409.0182 [pdf] submitted on 2014-09-26 07:15:53

General Model for Metabolism

Authors: Matti Pitkänen
Comments: 10 Pages.

The general strategy in attempts to understand metabolism is based on the assumption that a very large class of anomalous phenomena rely on same basic mechanism. This includes life as a phenomenon, water memory and homeopathy, free energy phenomena involving over-unity phenomena related to the dissociation of water, lightning and ball lightning, anomalous effects associated with rotating magnetic systems, phenomena related to UFOs (light balls), even remote mental interactions. One must have a unified explanation for all these phenomena based on a real theory. Plasmoids are TGD inspired proposal for prebiotic lifeforms and the input from anomalies related to electrolysis of water together with TGD based proposal that sequences of dark protons define dark nuclei realizing vertebrate genetic code leads to the vision that the biochemical metabolic machinery including photosynthesis has a simple analog realized in terms of "polymers" of water molecules with one dark proton with protons bound to sequence by color bonds.

The old view about the metabolic energy quanta as energies liberated as particle "drops" to a larger space-time sheet is modified. Metabolic energy quanta are liberated when the space-time sheet at which the particles reside expands in a phase transition increasing its p-adic prime and reducing the value of Planck constant correspondingly so that the net result is that the size of the space-time sheet remains the same. This condition implies a close relationship between p-adic and dark matter hierarchies. This process is automatically coherent since all particles suffer the change simultaneously. It applies also to a situation in which particles are in magnetic field: in this case the scale of cyclotron energies changes since the strength of the magnetic field is scaled down to guarantee the conservation of magnetic flux. This transition is not cyclotron transition but liberates essentially the same energy as coherent cyclotron transition so that magnetic fields (their "motor actions") become essential players also in metabolic activities.
Category: Physics of Biology

[1] viXra:1409.0021 [pdf] submitted on 2014-09-04 03:08:03

EINSTEIN’S Work Explains Placebo Effect

Authors: Rodney Bartlett
Comments: 3 Pages.

I’ve been doing some more thinking about the miraculous improvement in my friend Karen’s (name changed for privacy) health. This improvement – a less cautious person might even call it a cure – is a real puzzle … but a good one. The surgery she had 6 years ago, and all the chemotherapy and CT scans she’s received, have obviously been absolutely essential. I saw a TV program about Professor Ted Kaptchuk’s work with the placebo effect a few nights ago (his experiments with patients show that placebos have beneficial effects even when the placebo is known to be such) and am wondering if this twist in the placebo effect could be involved. In Karen’s case, the placebo wouldn’t be a pill or other treatment but I think it might possibly be the way she thinks. When diagnosed with a CT scan, the doctor made the seriousness of her condition very clear and said she needed emergency surgery. Karen’s mind was clear at the time and she understood everything he said. But she was really calm because she had the unmistakeable feeling that everything would be fine, even if treatment lasted years. This wasn’t just wishful thinking on Karen’s part because, in her late 40s, she had the same feeling over and over telling her that her 50s would be an extremely difficult time for her health (Karen never mentioned this to anyone before because she had enough problems without being labelled a crazy woman who believes in ESP and precognition). But I think the Theory of Everything and Einstein’s Unified Field provide a rational explanation (both of her drastic improvement and supposed precognition) if they aren’t limited to mathematics but embrace all reality, and unify everything in space and time (including Karen’s beautiful, unconventional mind) into one thing.
Category: Physics of Biology