Physics of Biology

What I Was Doing When I Was Einstein's Age of Discovery

Authors: David Martin Degner
Comments: 37 pages

AWhen I was in my twenties I worked on the problem: What is Life? In 1980/81 I was a research associate in molecular genetics at the University of California at Berkeley working for a professor in bacteriology. I wrote for the professor a 57 legal sized page, hand written and unedited essay in the form of a sequence of 72 questions and answers that focused on Gram (+) prokaryotic cells, the hydrogen of biology. The professor failed to comment or ask a single question. Back then I was into equilibrium and non-equilibrium thermodynamics, reversible and irreversible processes, chemical interactions and kinetics, static and dynamic phase organization, mass/energy and information flow, information definition and information processing, and modeling biological cells as chemical computers, i.e. Turing machines. I've faithfully transcribed that unedited sequence of questions and answers here. It's at times quite tedious and there were some major errors but there also is some really good science. There is always chaos embedded in new work. This is a qualitative, phenomenological model of the central processing unit of the prokaryotic cell that is the first step in obtaining a fully quantitative model for biology.

What is Life?

Authors: David Martin Degner
Comments: 12 pages

A static and dynamic physical model is presented for the Gram (+) prokaryotic cell, the hydrogen of biology. It is discovered that cells are chemical computers and the fundamental Turing machine architecture of biology is laid out.

Teilhard de Chardin Prophet of the Information Age

Authors: John A. Gowan
Comments: 9 pages. This paper has also been published as a Google "Knol".

Teilhard de Chardin's notions of the "Noosphere" and the "Omega Point" are explored in the context of current knowledge and theory, especially J.E. Lovelock's conception of "Gaia" - planet Earth as a superorganism. Space-faring humans are seen as the "seeds" or dispersal agents of Gaia's reproductive phase, carrying Earth-life into the Galaxy. "Noah's Ark" is a vision of the future, not the past.

The Fractal Organization of Nature

Authors: John A. Gowan
Comments: 13 pages. This paper has also been published as a Google "Knol".

A General Systems model of the Universe is presented, based on a fractal paradigm. A 4x3 "metric" or fractal algorithm is proposed as the organizing principle of the Microphysical, Biophysical, Astrophysical, and Metaphysical realms. The algorithm is expressed through the conservation laws and forces of physics, the families of elementary particles, the dimensions of spacetime, the quantum rules of atomic order, the structure of baryons, alpha particles, carbon atoms, carbon's molecular and crystal bonds, DNA, the genetic code, gravitation, and the nucleosynthetic pathway of stars. The human mind has discovered this order both intuitively and rationally, where it finds expression in the 4x3 (and 4x4) patterns of mythological, occult, religious, philosophical, and scientific "world systems" and cosmologies. A general model of the human "metaphysical realm", and a model of the unified field theory are presented as examples of how the fractal algorithm may be used in system modeling. In its most general form, the 4-part algorithm consists of an input of energy, followed by two complementary conservation modes, concluding with a restorative force which either returns the system to its original state, or elevates it to a "harmonic complexion" or resonant analog of the original state (the various levels of the model

Section 12: Man's Role in Nature

Authors: John A. Gowan
Comments: 4 pages, This paper has also been published as a Google "Knol".

Man's role in nature seems to divide naturally in two parts: 1) the dispersal of Earth-Life into the galaxy; 2) the enhancement and development of the self-awareness and creativity of the Cosmos. Humanity is, in the first instance, the practical, scientific tool of Gaia, or Mother Earth, evolved as her reproductive agent; and in the second instance, humanity is the perceptual or intelectual tool of the Cosmos, evolved to carry the intelligence and self-awareness of the Cosmos, the agent by which the Cosmos explores, understands, and appreciates itself, including exploring new modes of creativity. Our native spiritual awareness appears to be our intuitive recognition of this cosmic connection. The first role is Earth-oriented, manifesting socially as Science; the second role is Universe-oriented, manifesting socially as Art and Religion, in all their forms. It should be obvious that the first role is in no way intrinsically at odds with the second.

Section 8: General Systems, Complex Systems

Authors: John A. Gowan
Comments: 9 pages, This paper has also been published as a Google "Knol".

General Systems, as I use the term, denotes a repeating pattern of natural organization - a fractal algorithm or ordering principle in the Cosmos. While not enforced with the same stringency as a natural law (such as energy conservation), the pattern-forming impulse is nevertheless all-pervasive in nature and seems to proceed from such fundamental principles as resonance and the pathway of least energy or least resistance. It is just simpler, more efficient, and takes less energy to create a universe using self-similar repeating patterns than following any other plan. The "Tetrahedron Model" of cosmic order presents a General System based on a 4x3 universal fractal algorithm.

The Human Connection

Authors: John A. Gowan
Comments: 12 pages, This paper has also been published as a Google "Knol".

I discuss some specifically human (meta-physical) connections with the Cosmos. Life is the information pathway by which the universe awakens to and explores itself; humans are (locally) the most advanced expression of this evolving cosmic self-awareness and consciousness. Human life is significant to the extent it enriches the self-awareness, knowledge, creativity, general and personalized experience of the Cosmos.

The Information Pathway

Authors: John A. Gowan
Comments: 18 pages, This paper has also been published as a Google "Knol".

The Fractal Organization of Nature is seen as an information pathway whereby the Universe becomes selfaware through the spiritual awakening of humanity. The natural hierarchy is modeled as a sort of "Jacob's ladder" whereby Homo sapiens ascends to the astrophysical realm, realizing our destiny as galactic citizens, and dispersing Earth-life into the Cosmos.

Electro Mechanical Contributions to Low Frequency Dielectric Responses of Biological Cells in Colloidal Suspension

Authors: Andrew Beckwith
Comments: 18 pages. Part of a different analogy to bio phyics dielectric constants explored by the author with Dr. Patrick Xie and Dr. James Claycomb at the Texas center for super conductivity, Houston, Texas, in early 2002.

We investigate electro-mechanical contributions to the low frequency dielectric response of biological cells in colloidal suspension. Prior simulations of biological cells in colloidal suspension yield maximum dielectric constant values about 10³ in magnitude as the frequency of applied electric fields drops below the kHz range. Experimentally measured relative dielectric values in yeast cells , on the other hand, have maximal values up to 10⁷ - 10⁸ . We consider both electrical and mechanical energy stored in cellular suspension and show that low frequency mechanical contributions can give rise to dielectric constant values of this magnitude.

Photorefractive Protein Bacteriorhodopsin, BR , as a Material for Holographic Data-Recording

Authors: Rafael-Andrés Alemañ-Berenguer, María Gomariz
Comments: 7 pages

The search of materials of biological origin with specific estates of potential technologic applications whose structure and functions come out from a process of adaptive evolution experienced by the organisms in extreme environments, is one of the most active fields in the modern biophysics. In short, the protein bacteriorhodopsin, acts like a protonic bomb whose photocycle has demonstrated interesting implications in the technologies of optic storage of information by means of holographic methods. In the present work some results of the investigation undertaken by our group are exposed, consistent mainly in the study of the influence that working conditions (pH, state of aggregation of the environment, intensity and time of illumination, etc.) have over photophysical and photochemical states of bacteriorhodopsin as well as in the tracking of the possible presence of bacteriorhodopsin proteins and xantorhodopsin, in the salines of Santa Pola (Alicante, Spain).

Genes and Memes

Authors: Matti Pitkänen
Comments: 554 pages

The first part of book discusses the new physics relevant to biology and the vision about Universe as topological quantum computer (tqc). Second part describes concrete physical models.

1. The notion of many-sheeted DNA and a model of genetic code inspired by the notion of Combinatorial Hierarchy predicting what I call memetic code are introduced. The almost exact symmetries of the code table with respect to the third letter inspire the proposal that genetic code could have evolved as fusion of two-letter code and single-letter code.
2. A model for how genome and cell membrane could act as tqc is developed. Magnetic flux tubes containing dark matter characterized by large value of Planck constant would make living matter a macroscopic quantum system. DNA nucleotides and lipids of the cell membrane would be connected by magnetic flux tubes and the flow of the 2-D liquid formed by lipids would induce dynamical braiding defining the computation.
3. The net of magnetic flux tubes could explain the properties of gel phase. Phase transitions reducing Planck constant would induce a contraction of the flux tubes explaining why biomolecules manage to find each other in a dense soup of bio-molecules. The topology of the net would be dynamical and ADP ↔ ATP transformation could affect it. The anomalies related to ionic currents, nerve pulse activity, and interaction of ELF radiation with vertebrate brain find an explanation in this framework.
4. The discoveries of Peter Gariaev about interaction of ordinary and laser light with genome combined with ideas about dark matter and water memory lead to a model for the interaction of photons with DNA. Dark ↔ ordinary transformation for photons could allow to "see" dark matter by allowing ordinary light to interact with DNA.
5. A physical model for genetic code emerged from an attempt to understand the mechanism behind water memory. Dark nuclei which sizes zoomed up to atomic size scale could represent genes. The model for dark nucleon consisting of three quarks predicts counterparts of 64 DNAs, 64 RNAs, and 20 aminoacids and allows to identify genetic code as a natural mapping of DNA type states to amino-acid type states and consistent with vertebrate genetic code.

The third part of the book discusses number theoretical models of the genetic code based on p-adic thermodynamics and maximization of entropy or negentropy. These models reproduce the genetic code but fail to make killer predictions.

Quantum Hardware of Living Matter

Authors: Matti Pitkänen
Comments: 552 pages

This book represents a view about quantum hardware of living systems in TGD framework. Since the vision is bound to look highly speculative, it is good to emphasize that the most important predictions follow almost without any reference to the classical field equations using only quantum classical correspondence. The new conceptual elements are the notion of many-sheeted space-time having fractal hierarchical structure, 4-D spin glass degeneracy of the preferred extremals of Kähler action providing huge information storage capacity, topological field quantization, the notion of magnetic/field body serving as intentional agent using biological body as sensory receptor and motor instrument, zero energy ontology leading to a new view about energy and about the relationship between experienced and geometric time, dark matter hierarchy realized in terms of book like structure of 8-D imbedding space with pages labeled by values of Planck constant, the assumption that the phase transitions changing the value of Planck constant provide a key control tool in living matter, and p-adic length scale hypothesis allowing quantitative grasp to the situation.

1. Three chapters of this book are devoted to the model of high T_c super-conductivity relying strongly on the notions of quantum criticality and dark matter.
2. Two chapters discuss quantum antenna hypothesis inspired by topological light rays (M(assless) E(xtremals)) and the notion of wormhole magnetic fields. Notice that the notion of wormhole magnetic field was introduced much before the hypothesis that bosons have a natural identification as wormhole contacts emerged.
3. Two chapters are devoted to the possible biological implications of the hypothesis that dark matter corresponds to macroscopic quantum phases characterized by a large value of Planck constant and is the key actor in living matter.
4. A possible identification of quantum correlates of sensory qualia is discussed assuming that qualia are in one-one correspondence with the increments of quantum numbers in quantum jump. Also a simple model for sensory receptor is introduced.

I must apologize the fact that the introduction is somewhat ahead of the chapters of the book which have developed slowly during the last decade. In particular, the implications of the dark matter revolution which has occurred during last year and still continues, have not been thoroughly considered. Same applies to the implications of zero energy ontology.

Bio-Systems as Self-Organizing Quantum Systems

Authors: Matti Pitkänen
Comments: 288 pages

The quantum theory of self organization represents a rather old layer of TGD inspired theory of consciousness.

1. Self organization is a non-deterministic process and corresponds to the evolution of conscious entities - selves - to asymptotic self-organization patters via quantum jumps. This requires macroscopic quantum coherence.
2. Space-time surfaces are analogous to Bohr orbits and the failure of the classical non-determinism in the conventional sense of the word makes it possible to interpret space-time surfaces as representations of both quantum states and sequences of quantum states assignable to the sequences of quantum jumps. The huge vacuum degeneracy of Kähler action implies spin glass degeneracy in 4-dimensional sense providing maximal resources to represent information about external world by mapping its states to its own internal states. Space-time sheets would be four-dimensional statues gradually carved by a sequence of quantum jump to a shape representing asymptotic self-organization pattern.
3. Magnetic body is the intentional agent controlling the biological body. The fractal hierarchy of copies of standard model physics involving in particular a hierarchy of electro-weak bosons and gluons with increasingly longer weak/confinement length scale is an essential piece of the story. The concrete quantum model for how intentions are transformed to actions provides additional insights to quantum self-organization.
4. The new view about time and energy justifying time mirror mechanism involving sending of negative energy phase conjugate photons to geometric past is crucial for the models of long term memory, intentional action, and remote metabolism.
5. The model of self organization involves cyclotron radiation from the cyclotron transitions assignable with the Bose-Einstein condensates of charged bosons at the magnetic bodies and Josephson radiation from Josephson junctions assignable to the cell membrane and also other layer like structures (electrets).

Zero energy ontology and hierarchy of Planck constants complete this vision. Zero energy ontology justifies time mirror mechanism and explains how arrow of subjective time emerges. Dark matter hierarchy implies macroscopic quantum coherence, inspires vision about bio-catalysis and quantum computation in living matter, explains evolutionary leaps, and suggests generalization of the notion of genome and new realizations of genetic code. The topics of the book are following. The first chapters explain the vision about biological self organization in TGD framework. The last chapters of the book discuss quantum control and coordination in living matter according to TGD.

Wheeler-Feynman Generalized Bohm Quantum Potential for Open Far-from-Equilibrium Biological Dissipative Structures with Non-Unitary Post-Quantum Retro-Causal Signal Nonlocality

Authors: Jack Sarfatti
Comments: 6 pages

Bohm's micro-quantum ontological interpretation for closed systems in sub-quantal thermal equilibrium is generalized to open macro-quantum coherent systems using the Wheeler-Feynman-Cramer Ansatz. A connection to the Freeman-Vitiello model of the brain is suggested.

The Information Pathway

Authors: John A. Gowan
Comments: 19 pages, This paper has also been published as a Google "Knol".

The Fractal Organization of Nature is seen as an information pathway whereby the Universe becomes selfaware through the spiritual awakening of humanity. The natural hierarchy is modeled as a sort of "Jacob's ladder" whereby Homo sapiens ascends to the astrophysical realm, realizing our destiny as galactic citizens, and dispersing Earth-life into the Cosmos.

The Information Pathway

Authors: John A. Gowan
Comments: 19 pages, This paper has also been published as a Google "Knol".

The Fractal Organization of Nature is seen as an information pathway whereby the Universe becomes selfaware through the spiritual awakening of humanity. The natural hierarchy is modeled as a sort of "Jacob's ladder" whereby Homo sapiens ascends to the astrophysical realm, realizing our destiny as galactic citizens, and dispersing Earth-life into the Cosmos.

Genes and Memes

Authors: Matti Pitkänen
Comments: 602 pages

The first part of book discusses the new physics relevant to biology and the vision about Universe as topological quantum computer (tqc). Second part describes concrete physical models.

1. The notion of many-sheeted DNA and a model of genetic code inspired by the notion of Combinatorial Hierarchy predicting what I call memetic code are introduced. The almost exact symmetries of the code table with respect to the third letter inspire the proposal that genetic code could have evolved as fusion of two-letter code and single-letter code.
2. A model for how genome and cell membrane could act as tqc is developed. Magnetic flux tubes containing dark matter characterized by large value of Planck constant would make living matter a macroscopic quantum system. DNA nucleotides and lipids of the cell membrane would be connected by magnetic flux tubes and the flow of the 2-D liquid formed by lipids would induce dynamical braiding defining the computation.
3. The net of magnetic flux tubes could explain the properties of gel phase. Phase transitions reducing Planck constant would induce a contraction of the flux tubes explaining why biomolecules manage to find each other in a dense soup of bio-molecules. The topology of the net would be dynamical and ADP ↔ ATP transformation could affect it. The anomalies related to ionic currents, nerve pulse activity, and interaction of ELF radiation with vertebrate brain find an explanation in this framework.
4. The discoveries of Peter Gariaev about interaction of ordinary and laser light with genome combined with ideas about dark matter and water memory lead to a model for the interaction of photons with DNA. Dark ↔ ordinary transformation for photons could allow to "see" dark matter by allowing ordinary light to interact with DNA.
5. A physical model for genetic code emerged from an attempt to understand the mechanism behind water memory. Dark nuclei which sizes zoomed up to atomic size scale could represent genes. The model for dark nucleon consisting of three quarks predicts counterparts of 64 DNAs, 64 RNAs, and 20 aminoacids and allows to identify genetic code as a natural mapping of DNA type states to amino-acid type states and consistent with vertebrate genetic code.

The third part of the book discusses number theoretical models of the genetic code based on p-adic thermodynamics and maximization of entropy or negentropy. These models reproduce the genetic code but fail to make killer predictions.

Quantum Hardware of Living Matter

Authors: Matti Pitkänen
Comments: 552 pages

This book represents a view about quantum hardware of living systems in TGD framework. Since the vision is bound to look highly speculative, it is good to emphasize that the most important predictions follow almost without any reference to the classical field equations using only quantum classical correspondence. The new conceptual elements are the notion of many-sheeted space-time having fractal hierarchical structure, 4-D spin glass degeneracy of the preferred extremals of Kähler action providing huge information storage capacity, topological field quantization, the notion of magnetic/field body serving as intentional agent using biological body as sensory receptor and motor instrument, zero energy ontology leading to a new view about energy and about the relationship between experienced and geometric time, dark matter hierarchy realized in terms of book like structure of 8-D imbedding space with pages labeled by values of Planck constant, the assumption that the phase transitions changing the value of Planck constant provide a key control tool in living matter, and p-adic length scale hypothesis allowing quantitative grasp to the situation.

1. Three chapters of this book are devoted to the model of high T_c super-conductivity relying strongly on the notions of quantum criticality and dark matter.
2. Two chapters discuss quantum antenna hypothesis inspired by topological light rays (M(assless) E(xtremals)) and the notion of wormhole magnetic fields. Notice that the notion of wormhole magnetic field was introduced much before the hypothesis that bosons have a natural identification as wormhole contacts emerged.
3. Two chapters are devoted to the possible biological implications of the hypothesis that dark matter corresponds to macroscopic quantum phases characterized by a large value of Planck constant and is the key actor in living matter.
4. A possible identification of quantum correlates of sensory qualia is discussed assuming that qualia are in one-one correspondence with the increments of quantum numbers in quantum jump. Also a simple model for sensory receptor is introduced.

I must apologize the fact that the introduction is somewhat ahead of the chapters of the book which have developed slowly during the last decade. In particular, the implications of the dark matter revolution which has occurred during last year and still continues, have not been thoroughly considered. Same applies to the implications of zero energy ontology.

Bio-Systems as Self-Organizing Quantum Systems

Authors: Matti Pitkänen
Comments: 288 pages

The quantum theory of self organization represents a rather old layer of TGD inspired theory of consciousness.

1. Self organization is a non-deterministic process and corresponds to the evolution of conscious entities - selves - to asymptotic self-organization patters via quantum jumps. This requires macroscopic quantum coherence.
2. Space-time surfaces are analogous to Bohr orbits and the failure of the classical non-determinism in the conventional sense of the word makes it possible to interpret space-time surfaces as representations of both quantum states and sequences of quantum states assignable to the sequences of quantum jumps. The huge vacuum degeneracy of Kähler action implies spin glass degeneracy in 4-dimensional sense providing maximal resources to represent information about external world by mapping its states to its own internal states. Space-time sheets would be four-dimensional statues gradually carved by a sequence of quantum jump to a shape representing asymptotic self-organization pattern.
3. Magnetic body is the intentional agent controlling the biological body. The fractal hierarchy of copies of standard model physics involving in particular a hierarchy of electro-weak bosons and gluons with increasingly longer weak/confinement length scale is an essential piece of the story. The concrete quantum model for how intentions are transformed to actions provides additional insights to quantum self-organization.
4. The new view about time and energy justifying time mirror mechanism involving sending of negative energy phase conjugate photons to geometric past is crucial for the models of long term memory, intentional action, and remote metabolism.
5. The model of self organization involves cyclotron radiation from the cyclotron transitions assignable with the Bose-Einstein condensates of charged bosons at the magnetic bodies and Josephson radiation from Josephson junctions assignable to the cell membrane and also other layer like structures (electrets).

Zero energy ontology and hierarchy of Planck constants complete this vision. Zero energy ontology justifies time mirror mechanism and explains how arrow of subjective time emerges. Dark matter hierarchy implies macroscopic quantum coherence, inspires vision about bio-catalysis and quantum computation in living matter, explains evolutionary leaps, and suggests generalization of the notion of genome and new realizations of genetic code. The topics of the book are following. The first chapters explain the vision about biological self organization in TGD framework. The last chapters of the book discuss quantum control and coordination in living matter according to TGD.