måndag 20 februari 2012

The mystery of Life solved?

Biochemist, PhD Erik Andrulis, expert on RNA metabolism and life, has published a paper "Theory of the Origin, Evolution, and Nature of Life," and you can download the whole thing for free from the peer-reviewed journal Life, in the Special Issue "Origin of Life - Feature Papers" (with 6 papers, of which S. Kauffman also contributed). The paper created a violent rejection of 'mainstream' scientists, so they call in a journalist Jesse Emspak for their defense. The whole thing reminds much of the way Benveniste, 'the heretic' was treated, when the magicer Randi was called in to disclaim his work. Why is such things happening? This man Andrulis belongs to mainstream himself, but his insights took a giant jump, and so he is rejected, because the ordinary scientists are too ignorant. They cannot even discuss it? This is a shame for the scientific world. He thinks of the Holy Grail of Life, the billion research industry of today, and is rejected without discussion, just misunderstandings and misquotes? What a pity! So, lets take a look.

Earth as a lifelike self-organized state, the Gaia theory.
So, what did he say that was so dangerous? Earth is living! The Gaia hypothesis by James Lovelock (and Lynn Margulis). (The theory homeside here.) But there are actually hints for it being true. Even Lubos discusses this (negatively still). It says that all organisms and their inorganic surroundings on Earth are closely integrated to form a single and self-regulating complex system, maintaining the conditions for life on the planet. The self-organizing system and Gaia theory is also here with plants as a part of the biota Earth. Phil Gibbs: At 86 Lovelock is no longer considered a crank. He is appreciated as the founder of a new area of science investigating the relationship between biological systems and the atmosphere. Without his insight we would have been much slower to understand the negative effects we have been having on our climate through pollution.
A book
by Eileen Crist and H. Bruce Rinker from 2009 Gaia in Turmoil, Climate Change, Biodepletion, and Earth Ethics in an Age of Crisis.

Gaian theory, which holds that Earth's physical and biological processes are inextricably bound to form a self-regulating system, is more relevant than ever in light of increasing concerns about global climate change. The Gaian paradigm of Earth as a living system, first articulated by James Lovelock and Lynn Margulis in the 1970s, has inspired a burgeoning body of researchers working across disciplines that range from physics and biology to philosophy and politics. Gaia in Turmoil reflects this disciplinary richness and intellectual diversity, with contributions (including essays by both Lovelock and Margulis) that approach the topic from a wide variety of perspectives, discussing not only Gaian science but also global environmental problems and Gaian ethics and education.
...focus first on the science of Gaia, considering such topics as the workings of the biosphere, the planet's water supply, and evolution; then discuss Gaian perspectives on global environmental change, including biodiversity destruction and global warming; and finally explore the influence of Gaia on environmental policy, ethics, politics, technology, economics, and education.
... breaks new ground by focusing on global ecological problems from the perspectives of Gaian science and knowledge, focusing especially on the challenges of climate change and biodiversity destruction.
David Abram, Donald Aitken, Connie Barlow, J. Baird Callicott, Bruce Clarke, Eileen Crist, Tim Foresman, Stephan Harding, Barbara Harwood, Tim Lenton, Eugene Linden, Karen Litfin, James Lovelock, Lynn Margulis, Bill McKibben, Martin Ogle, H. Bruce Rinker, Mitchell Thomashow, Tyler Volk, Hywel Williams.
Al Gore wrote a book entitled Earth in the Balance, where he wrote sympathetically about the Gaia hypothesis of an earth spirit. Dr. Stephen H. Schneider (with many books, latest from 2009, Climate Change Science and Policy one of the most comprehensive and current reference resource on climate change available) a climatologist and Penelope Boston, complex systems bioloy, cited the Gaia theory in his book, Scientists on Gaia, on global warming. “...is there a Goddess of the Earth?” and "The Gaia hypothesis suggests that life is an active participant in shaping the physical and chemical environment on which it depends." This is a common way to charachterize Life in biology. He is one of several scientists who contributed to the 2004 book, Scientists Debate Gaia. A description of the book declares, “Despite initial dismissal of the Gaian approach as New Age philosophy, it has today been incorporated into mainstream interdisciplinary scientific theory, as seen in its strong influence on the field of Earth System Science.” Schneider won the 2007 Nobel Peace Prize together with Al Gore. He has been threated many hundred times also death-threats, but he died of heart-attack at 65. Sad with such stress. Has it made his death? He has written another book Science as a Contact Sport: Inside the Battle to Save the Earth's Climate about science as a network of 'best brothers' scientists.

So Andrulis is in good company.

The critizing article:

The trans-disciplinary theory demonstrates that purportedly inanimate, non-living objects—for example, planets, water, proteins, and DNA—are animate, that is, alive . . .
He didn't say so. A misquote. He [Andrulis] doesn't say that everything is alive, exactly, though he says gyres have "lifelike characteristics." So Andrulis doesn't say what Emspak just told us he does say? Maybe the space spinors should be extended? Today we have spacelike, timelike and lightlike spinors, maybe there should be lifelike too? Or can the lifelike charachteristics have something with the lightlike Universe to do? In this case it is clearly not life, but maybe its precusors? TGD actually talk of these same things. Essential for life is a consciousness, coherence and synchrony.

Jesse Emspak (not scientist) just published an article at Space.com titled “Crackpot Theory of Everything Reveals Dark Side of Peer Review.” talking about the peer review process, and the dark side of modern science propaganda.

Erik Andrulis of Case Western suggest everything around us oscillates between excited and ground states as objects pivot around the center of these lifelike gyres, or spinning spirals. CREDIT: R.T. Wohlstadter | Shutterstock

On the University page Andrulis writes:
My group has been asking two broad questions: How does the spatiotemporal control of RNase interactions and post-translational modifications relate to RNase recognition and metabolism of specific classes of RNAs in living cells? How does RNase activity relate to cell structure and function? To answer these questions, we are studying Dis3, Rrp6, and the ribonucleometabolic exosome. Dis3 is a processive, sequence-nonspecific 3' to 5' RNase that is homologous to eubacterial RNase R/II. Rrp6 is a distributive, sequence-nonspecific 3' to 5' RNase similar to eubacterial RNase D. The exosome is a multi-subunit complex or set of complexes that contain(s) putative RNases (Rrp41, Rrp42, Rrp43, Rrp45, Rrp46, Mtr3 are eukaryotic homologs of the eubacterial RNase PH) and the S1 RNA-binding domain proteins Rrp4, Rrp40, and Csl4. We have proposed and are testing the hypothesis that these subunits assemble into multiple independent, functionally interrelated complexes called exozymes.

Extending upon this RNA research, I recently compiled an incommensurable, trans-disciplinary, neologistical, axiomatic theory of life from quantum gravity to the living cell.
The article says:
To test his paradigm, Dr. Andrulis designed bidirectional flow diagrams that both depict and predict the dynamics of energy and matter. While such diagrams may be foreign to some scientists, they are standard reaction notation to chemists, biochemists, and biologists. Dr. Andrulis has used his theory to successfully predict and identify a hidden signature of RNA biogenesis...the exozyme model.
So he has some kind of proofs? The abstract: Full text here.
Exosome complexes are composed of 10 to 11 subunits and are involved in multiple facets of 3' → 5' RNA processing and turnover. The current paradigm stipulates that a uniform, stoichiometric core exosome, composed of single copies of each subunit, carries out all RNA metabolic functions in vivo. While core composition is well established in vitro, available genetic, cell biological, proteomic, and transcriptomic data raise questions about whether individual subunits contribute to RNA metabolic functions exclusively within the complex. Here, we recount the current understanding of the core exosome model and show predictions of the core model that are not satisfied by the available evidence. To resolve this discrepancy, we propose the exozyme hypothesis, a novel model stipulating that while exosome subunits can and do carry out certain functions within the core, subsets of exosome subunits and cofactors also assemble into a continuum of compositionally distinct complexes-exozymes-with different RNA specificities. The exozyme model is consistent with all published data and provides a new framework for understanding the general mechanisms and regulation of RNA processing and turnover.

In TGD Matti talks of 'Gaias womb' in evolution. Earth is a coherent field body that acts as controlling agent. Also with consciousness and lifelike properties. Did Life evolve in the womb of Gaia? Matti also talks of DNA and life, water, plasmoids, lightnings etc. as lifelike. We have looked at the exosome and its 1:10-fold fractality as in electron:proton.

The gyre model?
In a wry article about Andrulis' work, Ars Technica's John Timmer summed the paper up:
The basic idea is that everything, from subatomic particles to living systems, is based on helical systems the author calls "gyres," which transform matter, energy, and information. These transformations then determine the properties of various natural systems, living and otherwise. What are these gyres? It's really hard to say; even Andrulis admits that they're just "a straightforward and non-mathematical core model" (although he seems to think that's a good thing). Just about everything can be derived from this core model; the author cites "major phenomena including, but not limited to, quantum gravity, phase transitions of water, why living systems are predominantly CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur), homochirality of sugars and amino acids, homeoviscous adaptation, triplet code, and DNA mutations."
First the 'gyres'. What are they? Andrulis:
One reason for their theoretical appeal is that gyres are detectable throughout the cosmic and tellurian realms.
Astronomically, galaxies, solar systems, comets, and lunar bodies gyrate.

Atmospherically, tornadoes, hurricanes, eddies, and vortex streets are all gyres. Oceanographically, there are seven major gyres.
Molecularly, numerous nucleic acid and protein structures—DNA double helix, RNA hairpins, pseudoknots, α-helices, coiled coils, and β-propellers—all gyrate. Cellularly and organismally, shells, horns, antennae, flagellae, and the cochlea all carry a spiral imprint.
Given its theoretical pedigree, empirical ubiquity, and dynamic character, the gyre appears, a posteriori, to be a prime candidate for a core model of natural systems.
Gyre - a round shape formed by a series of concentric circles (as formed by leaves or flower petals) The Free Dictionary.
curl, curlicue, ringlet, scroll, whorl, coil, roll A spiral oceanic surface current
corolla - (botany) the whorl of petals of a flower that collectively form an inner floral envelope or layer of the perianth; "we cultivate the flower for its corolla"
calyx - (botany) the whorl of sepals of a flower collectively forming the outer floral envelope or layer of the perianth enclosing and supporting the developing bud; usually green
round shape - a shape that is curved and without sharp angles
verticil - a whorl of leaves growing around a stem

Wikipedia says: A gyre is any manner of swirling vortex, particularly a natural phenomenon. It can refer to
Yeah, is this a physical description? Why on Earth go to this? Why use 'a black box' for the physical description, and say he has gone to quantum mechanics level, when physicists are trying to explain things with first principles and basic natural laws. To only use simplicity and Occams razor isn't enough? Eintein said: "Simple, but not simpler than it is". He didn't explain his motives for doing like this in the text. A 'core model'? Yeah, but the core is ad hoc used to tie togeteher microcosmos and macrocosmos. The idea is good, though, but it must be deduced from physical principles. Wikipedia:
A vortex is a spinning, often turbulent, flow of fluid. Any spiral motion with closed streamlines is vortex flow. The motion of the fluid swirling rapidly around a center is called a vortex. The speed and rate of rotation of the fluid in a free (irrotational) vortex are greatest at the center, and decrease progressively with distance from the center, whereas the speed of a forced (rotational) vortex is zero at the center and increases proportional to the distance from the center. Both types of vortices exhibit a pressure minimum at the center, though the pressure minimum in a free vortex is much lower.
The outcome of his fundamental gyre functions is 13 additional gyreprinciples or axioms. A gyre glossary is added to the article. Andrulis tries to introduce a novel idea.

Life is complex and perplexing. It should come as no surprise that modeling life is a complicated procedure. Likewise, explaining a theory of life is an arduous task. Thus, prior to proceeding, I issue several warnings regarding the model and theory. The gyromodel is incommensurable with prior and existing theories. Thus, the reader must judge this theory by two criteria: the principle of parsimony, or Ockham’s Razor—the scientific principle dictating that things behave or are connected in the simplest and most economical fashion—and the ability to explain the available scientific data. Another challenge is discovered in the lexicon, where I have redefined established terms and created and applied ~100 new words to identify, explain, and interconnect distinct aspects of the theory. Creating a new vocabulary yields, on the one hand, a single, tight system to unify multiple disparate scientific languages. On the other hand, simultaneously supplanting the vernaculars of physics, chemistry, and biology may cause a high degree of frustration. Together, the foreign symbolism, semantics, and lexicon make comprehending the gyromodel difficult. As more is different, one must think differently to interpret more. Finally, this theory challenges long-held assumptions, guiding philosophies, ad hoc models, cherished paradigms, ossified boundaries, and, quite regrettably, patience.
These warnings represent a full and sincere disclosure of the difficulties in effectively presenting my model and theory and of convincing the reader of its scientific merit.
Ye??? And restricted references, but still p66-105. He use only one or two references to defend a position or to guide the reader.

A schematic picture of a gyre from Andrulis article. It starts from the lepton in ordinary matter, and is both expanding and compressing etc. at the same time depending on energy movement (thermodynamics). It also makes up for the relations between elements as oxygen (O), carbon (C), phosphor (P) , amins (A) etc. up to cell. In this model microcosmos cannot be divided from macrocosmos.

Here, for brevity, I highlight only one theoretical solution for each gyrosystem. The electrogyre explains quantum gravity, unifying quantum mechanics and general relativity in a frame beyond the standard model [753]; the oxygyre explains the mysterious properties of water [133]; the carbogyre explains the emergence of hydrocarbons in the Earth’s mantle and crust, resolving the biotic/abiotic petroleum debate [754]; the phosphogyre explains why phosphorus is “life’s bottleneck [755]” and the dominant roles of phosphate in biology [756]; the ribogyre solves the problem of novel genetic information [757-759]; the aminogyre explains the origin and nature of the translation apparatus, one of theoretical biology’s grand unsolved problems [488,760]; the genogyre clarifies the correct relationship of DNA, protein, and RNA, quelling anonymous protestations against the central dogma [761,762]; and the cellulogyre reveals that life originates in any biosphere wherever the thermodynamics of information, energy, and matter are accommodating, consistent with ideas regarding hierarchical complexification of and in the universe [763]. Together, the theoretical framework confirms what many modern theoretical physicists have proposed: that the classical world is “quantum all the way [764].” p 62.

Some forms of gyres: (a) Electrogyre, (b) Oxygyre, (c) Carbogyre, (d) Phosphogyre, (e) Ribogyre, (f) Aminogyre, (g) Genogyre, (h) Cellulogyre, photograph of Cirripathes spiralis, a coral species, p 29.

Gyre thermodynamics and forms:
Gyres are open thermodynamic entities that require energy and matter mobilization to establish and maintain themselves. Being open systems, gyres import energy and matter from their surroundings into themselves, ebb and flow energy and matter within themselves, and dissipate energy and matter from themselves into their surroundings. Reducing or increasing amounts of energy and matter elicits gyre contraction or expansion, respectively. When efflux or influx is acute, extreme, or unsustainable, a gyre collapses. A gyre staves off collapse through autoregulation: a gyre feeds into itself, regulating its own rotational rate, size, composition, motion, and trajectory. Gyre autoregulation is spatiotemporally internal and/or external, proximal and/or distal, negative and/or positive. Consistent with its autoregulatory bent, a gyre maintains homeostasis—internal responsiveness and balance—by oscillating material around its singularity, a consequence of alternating between extreme countervailing forces within itself. Previewing the application of the gyromodel to life, the cell is an open thermodynamic entity that has numerous, discrete layers of autoregulation

The geometric form created is called a hypersphere; this shape is compatible with ideas regarding the thermodynamic expansion of the universe [42,43]. Still, in nature, there is manifest directionality, such as that observed in the N- to C-terminal orientation of the protein chain or 5’ to 3’ orientation of nucleotide polymers. Though gyromodels are depicted as having a left-to-right vectorization, this is simply a two-dimensional restriction of the artistic approach. From this two-dimensional perspective, one revolution of a gyre is seen as a circle or oval. A circle, when viewed in three dimensions, is a cycle. Closing this circle of thought: a cycle viewed in the context of time, or four dimensions, looks like a rotating spiral, helix, or gyre. Foreshadowing, any cycle that exists in nature—in physical, chemical, or biological systems—may be viewed as a gyre.

Fourth Law of Thermodynamics. The theoretical framework sheds light on how life maintains order and complexifies in spite of entropy: the repulsive force of the gyradaptive singularity elevates a particle to its excited state, offsetting the effects of it cycling to the ground state. The gyromodel thus confirms the existence of the fourth law of thermodynamics [770], the ordering law of the universe. p 63.
Given the law of relativity, IEM order and disorder are demonstrated to be relative to the singularity. Further, given the law of complementarity, universal order and disorder paradoxically co-exist. In proving this contradictory fact, my theory does not “collapse in deepest humiliation [781],” but rather reflects and honors the true nature of the physical world. p 64.

All natural gyres harbor two countervailing forces: attraction and repulsion. Paradoxically, the gyre singularity both attracts and repels energy and matter and thus is “attractorepulsive.” These unified yet contradictorily dual (diune) forces exert paradoxical effects. Gyre forces occur both within an individual gyre and also between and among gyres. For example, two transverse gyres exhibit constructive interference when synchiral (same chirality) and destructive interference when antichiral (opposing chirality). Alternatively, the fine-tuning and balancing of two contradictory forces results in neutrality, immutability, and immobility—identifiable characteristics of physical systems.
Gravity and antigravity? Or positive and negative energy? Like a Zero Energy Ontology and Kähler action behind massivation inTGD?
The identification of the spectrum of light particles reduces to two tasks: the construction of massless states and the identification of the states which remain light in p-adic thermodynamics. The latter task is relatively straightforward. The thorough understanding of the massless spectrum requires however a real understanding of quantum TGD. It would be also highly desirable to understand why p-adic thermodynamics combined with p-adic length scale hypothesis works. A lot of progress has taken place in these respects during last years.
Zero energy ontology providing a detailed geometric view about bosons and fermions, the generalization of S-matrix to what I call M-matrix, the notion of finite measurement resolution characterized in terms of inclusions of von Neumann algebras, the derivation of p-adic coupling constant evolution and p-adic length scale hypothesis from the first principles, the realization that the counterpart of Higgs mechanism involves generalized eigenvalues of the modified Dirac operator...

About formative forces in TGD:

The string world sheets in Euclidian regions would de ne the analogs of the minimal surfaces in Euclidian AdS5 and the string world sheets in Minkowskian regions the analogs of Minkowskian AdS5. The magnitudes of the areas would be identical so that they might be seen as analytical continuations of each other in some sense. Note that partonic 2-surfaces would belong to the intersection of Euclidian and Minkowskian space-time regions. This argument tells nothing about possible momentum space analog of M4 x CP2.
The strong form of General Coordinate Invariance implies e ffective 2-dimensionality (holding true in finite measurement resolution) so that also a strong form of holography emerges. The expectation is that Chern-Simons terms in turn reduces to 2-dimensional surface terms. The only physically interesting possibility is that these 2-D surface terms correspond to areas for minimal surfaces de fined by string world sheets and partonic 2-surfaces appearing in the solution ansatz for the preferred extremals. String world sheets would give to Kähler action an imaginary contribution having interpretation as Morse function. This contribution would be proportional to their total area and assignable with the Minkowskian regions of the space-time surface. Similar but real string world sheet contribution de fining Kähler function comes from the Euclidian space-time regions and should be equal to the contribution of the partonic 2-surfaces. A natural conjecture is that the absolute values of all three areas are identical: this would realize duality between string world sheets and partonic 2-surfaces and duality between Euclidian and Minkowskian space-time regions.
Zero energy ontology combined with the TGD analog of large Nc expansion inspires an educated guess about the coeffcient of the minimal surface terms and a beautiful connection with p-adic physics and with the notion of nite measurement resolution emerges. The t'Hooft coupling should be proportional to p-adic prime p characterizing particle. This means extremely fast convergence of the counterpart of large Nc expansion in TGD since it becomes completely analogous to the pinary expansion of the partition function in p-adic thermodynamics. Also the twistor description and its dual have a nice interpretation in terms of zero energy ontology. This duality permutes massive wormhole contacts which can have off mass shell with wormhole throats which are always massive (also for the internal lines of the generalized Feynman graphs).
Actually Andrulis comes out with the same figures as in TGD, with Matrioshka dolls, hierarchy (sub/supragyres resp CD-diamonds) and infinite fractality, nesting/wormholes etc.
Stuart Kauffman talks about work cycles as thermodynamic entities too. About the history of the independent invention in 1971 by T. Ganti, M. Eigen and Kauffman of three alternative theories of the origin of molecular replication: the Chemotron, the Hypercycle, and Collectively Autocatalytic Sets, CAS, respectively.

To date, only collectively autocatalytic DNA, RNA, and peptide sets have achieved molecular reproduction of polymers. Theoretical work and experimental work on CAS both support their plausibility as models of openly evolvable protocells, if housed in dividing compartments such as dividing liposomes. My own further hypothesis beyond that of CAS in themselves, of their formation as a phase transition in complex chemical reaction systems of substrates, reactions and products, where the molecules in the system are candidates to catalyze the very same reactions, now firmly established as theorems, awaits experimental proof using combinatorial chemistry to make libraries of stochastic DNA, RNA and/or polypeptides, or other classes of molecules to test the hypothesis that molecular polymer reproduction has emerged as a true phase transition in complex chemical reaction systems.

An essential feature of the CAS above is that they can be purely exergonic. Real cells link exergonic and endergonic reactions in complex webs of reactions, and perform work cycles such as chemo-osmotic pumps.
i. Consider a hypothetical world in which only exergonic reactions can be coupled;
ii. Consider a hypothetical world in which exergonic and endergonic reactions can be coupled.
Almost a Theorem: The richness of the web of coupled reactions is far greater if exergonic and endergonic reactions can be coupled, than if only exergonic reactions can couple. In turn, the more complex the web of coupled reactions, together with the chance that molecules in the web are catalysts for the same reactions, the easier it is to form collectively autocatalytic sets. There may well be a selective advantage in the formation of CAS to link exergonic and endergonic reactions.
Thus a central point.
IF exergonic and endergonic processes are linked, there is no point in eating unless a work cycle is completed. It is useless to take in food, or a renewed energy source, (the second explosive charge placed in the base of the cannon), if a work cycle is not completed. Work cycles are necessary to the efficacy of feeding if exergonic and endergonic processes are linked.


Real cells need both energy, and to perform thermodynamic work cycles by which spontaneous (exergonic) and non-spontaneous (endergonic) processes are linked into large webs of cyclic and cross cyclic processes, which are in fact work cycles. At present we know that simple substances, such as pyrophosphate, might serve as driving energy sources; but that might still be a trivial extension from purely exergonic CAS, driven by pyrophosphate.
Real cells use proton gradients, e.g., mitochondria use ATP to drive endergonic reactions. We have little theory about the emergence of work cycles in protolife, although we know that life is a non-equilibrium process. From the above, if we link exergonic and endergonic processes, there must be completed work cycles for food to be useful. As Schrodinger said in What is Life? we eat negentropy and excrete entropy. However, Schrodinger missed the need for work cycles if exergonic and endergonic processes are linked. We have had no theory for how far-from-equilibrium cells do work cycles. Carnot showed maximum energy efficiency for work cycles if performed infinitely slowly, i.e., adiabatically. Although, if the work cycle is needed for cell or protocell reproduction, such a cell will lose the Darwinian race, implying that energy efficiency must be the wrong concept.
So, why do we eat? Ingest, take in information etc. Act as a negative entropy system? We need 'negative negative entropy' to maintain the system? The same as quantum computer scientists have realized. Wells, memory... to minimize dissipation, scattering, negative interference? Negative interference destroys coherence and collapse into decoherence.

With Tommi Aho and Olli Yli-Harja at the Tampere University of Technology Finland, we [27] have taken a model of E. coli metabolism, calculated biomass production rate per unit fuel use rate, plotted on the Y axis versus fuel (glucose) use rate on the X axis. We find a unimodal distribution with a maximum at a finite rate of glucose utilization per unit time, a power efficiency maximization point, which seems interesting because it picks out a preferred displacement from chemical equilibrium, maximizing the efficiency of cell reproduction per unit fuel used. This criterion is related to K, not R selection in ecology, i.e., selection, not for a high reproduction rate, but for sustained reproduction when food resources are limited. If this is a general condition in life, for example in bacterial colonies, or ecosystems, we may have found a principle for an optimal power efficiency in the work cycles of life.
Current work shows that this theory fits the empirical data available somewhat better than the standard model of “most rapid growth.” More bacteria tune their growth rate based on their density by quorum sensing, perhaps bringing bacterial colonies to a power efficiency optimum. When power efficiency is maximized, heat production should be minimized such that, a maximum amount of the energy available to cells is going into reproduction of cells, not into waste heat. If this is correct, life does NOT maximize entropy production and flattening energy gradients, but maximizes power efficiency per unit food utilized, under K selection, at a specifiable optimal displacement from equilibrium where it may minimize entropy production compared to reproduction rate.
Andrulis about particle-wave Unity (not duality):
The gyromodel clarifies how a quantum has both wave and particle qualities: as one particle oscillates between two extreme gyrostates, its gyratory path creates an undulating pattern that is detected as a wave. When many particles oscillate around the same or different singularities, they create constructive or destructive waveforms. When the gyromodel is considered as a gyre, it manifests classical wave characteristics: wavelength, amplitude, and frequency. When considered as a quantum, it exhibits particle characteristics: translational, rotational, and vibrational movement. The gyromodel thus accounts for particle spin.
A bit summaristic. I would want some description about different kinds of spin and particles. He also talk of gyres as linking macrocosmos (GR) to microcosmos (QM) but nothing about SR as link and its spacetime model. Nothing about Zero Points as infinite points, grids or dynamos, binding together. Not much of physics at all. This is a typical biologist, thinking he doesn't need physics? This I cannot accept. About antimatter:
An outstanding question in physics is why there is so little antimatter in the physical universe [119,120]. Microcosmically, the tertiary electrogyre shows the electron cycling out the thermodynamic support of the triphoton. Given synchiral organization of the tertiary majorgyre gyrobase, the electron destabilizes and ultimately collapses due to the synchiral sub2gyre (not shown) in lieu of the antichiral subgyre, modeling the positron. The extreme creatodestructive swing of the electrogyre thus provides an explanation for the fleeting presence, or absence, of antimatter in the universe.
Really no 'explanation'. (Compare to annihilation of vortex video. Abelian Higgs Model 2+1 dimensions ~ superconducting vortices annihilating to oscillons by Joel Thorarinson). Andrulis just talks of an collapse, and not the energetic addition of forces, nor the reason why we have antimatter as counterbalancing force for gravity.
He establish strict non-cognitive meanings for learning and memory. The Machine model. "Learning is a continual, unstable, and energetically demanding affair. Gyre learning, or gyrognosis, is the process by which the gyradaptor repels the particle from the gyrobase to the gyrapex. Memory, by comparison, is a relativistically stable and energetically conserving phenomenon. The process of storing IEM (energy) in gyre memory, or gyromnemesis... gyre learning and memory are relative to the gyradaptive singularity."
A Self, but no cognition nor consciousness? No true realizing of a meaning or quale? He talks about qualias: "Information, in turn, is the distinct patterns or organizations of energy and matter, with these patterns detectable by observation and quale".

Theory in eight subsections, each detailing a discrete, empirically defined system that is amenable to theoretical modeling: visible matter, water, organic matter, phosphomembrane, RNA, protein, DNA, and cell. This theoretical framework concomitantly depicts both the microcosm— the biology, chemistry, and physics of the existing living cell—and the macrocosm—the astrophysical and biogeophysichemical (geospheric, hydrospheric, atmospheric, biospheric) process underlying the evolution of life on Earth. Hence, subdividing this framework into separate parts defined by scale, by field, by topic, or by evolutionary spacetime is not scientifically appropriate for modeling life in toto.
Meaning of Life.
Life has many definitional meanings but lacks a complete and consistent scientific explanation. In this work, I have pursued and arrived at a scientific answer to the Schrödingerian question, “What is Life? [1].” Traditionally, the living cell is commonly called “animate” and all other biospheric and cellular chemicals and molecules are called “inanimate.” However, this theory and the law of vortex motion prove that all these physical systems gyrate and are, as such, “animated.” Moreover, theory-defined laws of unity and correspondence require that life and Earth evolve as one, with thermodynamically appropriate conditions (the fitness of the biosphere [788,789]). Unexpectedly, then, this theory reveals that Earth—or, for that matter, any celestial, physical, chemical, and molecular system—is alive, that is, synonymous with life. Given this definitional and conceptual upheaval, I propose that a very open and candid discussion of the meaning of life—well beyond this text—is in order. On this topic, it may be useful to consider how scientifically redefining life elucidates non-scientific, eudaemonic meanings of “life,” “living,” or “alive,” related to ontology, consciousness, sentience, behavior, vocation, or social interactions.
The gyre models the living universe perfectly. I have been unable to find one system, particle, event, or process—at any point or stage leading up to or during the origin of life—that does not consent to modeling onto the gyre form. In other words, there is no “before” or “after” the gyre in a spacetime sense; the gyre is evolutionarily and existentially omnipresent.
As concluding remark:
In science and theory, the principle of parsimony dictates that the most straightforward, plain, and frugal model of an observation or set thereof is more favorable and likely right. As my theoretical framework coalesces a vast amount of accumulated scientific evidence into one neat, lawful, and interconnected modular structure, it abides by this principle. In conclusion, this catholic theory provides an innovative and elegant solution to the origin, evolution, and nature of life in the cosmos. I humbly offer my theory as a viable system for knowing life.
This paper must be seen as premature, with no discussion and links to other ideas. And it is very far from a theory. He makes Life reductionistic, ordinary matter, like a computer intelligence, and doesn't explain how it differ from ordinary matter. Abelian and non abelian math? He says it is non-mathematical? No funding source supported this work. no, certainly not.

I did not provide gyrosystems to model much of the scientific evidence related to astrophysics, particle physics, and cosmology before the electrogyre, nor did I integrate organismal, ecological, and ethological data after the cellulogyre. I predict that further gyromodel application will reveal its explanatory breadth and power. For example, given that complexity theorists find there to be a unifying organization in ecosystems, language, and economics.
But the scaling-question? The problem of thermodynamics in open systems? Does this paper really 'explain' anything? Testable? He says there are tests. To me it looks more like a scientific frame or overview, very similar to the theory TGD, but lifeless, without consciousness and cognitions. He wants to redefine Life, yes, but is this the way? Everyone can feel themselves how a stone differ from a cell or animal. No, I am not satisfied. But as idea it is interesting. Just replace the gyre with a cone. This is very far from the beautiful TGD Universe.
The aminogyre makes some very profound and testable predictions about the specificity of the genetic code and how proteins behave, lengthen and shorten, and fold and unfold in response to physical and biometabolic changes or changes in genetic information content of RNA. -well this is his speciality, so he should know.
The papers in the Life Special Issue was:
Erik D. Andrulis Article: Theory of the Origin, Evolution, and Nature of Life Life 2012, 2(1), 1-105; doi:10.3390/life2010001
Victor Norris and Yohann Grondin Article: DNA Movies and Panspermia Life 2011, 1(1), 9-18; doi:10.3390/life1010009
Richard Egel Essay: Primal Eukaryogenesis: On the Communal Nature of Precellular States, Ancestral to Modern Life Life 2012, 2(1), 170-212; doi:10.3390/life2010170
Victor Ostrovskii and Elena Kadyshevich Article: Life Origination Hydrate Hypothesis (LOH-Hypothesis) Life 2012, 2(1), 135-164; doi:10.3390/life2010135
Stuart A. Kauffman Article: Approaches to the Origin of Life on Earth Life 2011, 1(1), 34-48; doi:10.3390/life1010034
Christopher H. House, Emily J. Beal and Victoria J. Orphan Article: The Apparent Involvement of ANMEs in Mineral Dependent Methane Oxidation, as an Analog for Possible Martian Methanotrophy Life 2011, 1(1), 19-33; doi:10.3390/life1010019

8 kommentarer:

  1. http://www.livescience.com/18565-life-building-blocks-chemical-evolution.html

  2. http://www.livescience.com/18632-life-surprisingly-thrives-deepest-spot-earth.html

  3. S. Kauffman on NPR blog 5.3:
    The Evolution Of The Biosphere And Econosphere Are Self Creative

    He seems to join the Gaia hypothesis? Look!

    Evolution may be the mysterious "antientropic force" that generates complexity, at least in the living world and, just perhaps, in the universe at large. (Although, of course, evolution is not a force at all.)

    The evolving biosphere and econosphere have both exhibited astonishing increases in diversity and complexity over time. One common biological ancestor diversified, we believe, into the millions of species we see today. Except for some extinction events, the diversity of species shows a steady increase.

    Similarly, the diversity of goods and production capacities 50,000 years ago across the globe might have been a few thousand. Now this diversity numbers in the billions.

    Why does this diversity increase? One view is that this process is just a "random branching, birth and death process."

    Here is the theory: consider a token "person" on an infinite-square lattice. At each discrete moment in time he takes one step north, and at random chooses to go one step east or one step to the west. This process iterates and the "person" performs a random walk, a well-studied stochastic process. Now let the single "person," divide occasionally into two "persons" at the same spot on the lattice. Call it a "birth process." Thereafter each "person" walks fully independently of the other. From time to time there are similar "birth" processes to "persons" walking. Now add "deaths" where "persons" die and disappear from the lattice. This is a random branching, birth and death stochastic process, well studied.

    On average, if births happen more frequently than deaths, the ensemble of persons will branch out on the graph in increasing numbers.

    This model is commonly in mind when considering the increase in the diversity of species, economic goods and production capacities. I think this view is deeply inadequate, if partially true.

    Instead, I want to suggest that biological and economic evolution are self-creative, supracritical and progressive.

    The heart of what I wish to say of organisms and businesses is that they both maintain their structure, evolve and literally create empty "Adjacent Possible" biological or economic niches. These new empty spaces are places where new organisms or businesses can come into existence.

    Life confronts us with something totally novel: its evolution is self-creative. It creates new niches without selection or intent. This process can be supracritical and progressive in its diversifying complexity.

  4. It is important to understand how the physics of test particle depends on the presence of parallel space-times sheets. Simultaneous topological condensation to all the sheets is extremely probable so that at classical level forces are summed. Same happens at quantum level. The superposition of various fields assignable to parallel space-time sheets is not possible in TGD framework and is replaced with the superposition of their effects. This allows to resolve one of the strongest objections against the notion induced gauge field.

    Entanglement has no interpretation in terms of everyday experience. You cannot perceive a state which is superposition of states in which Schrodinger's cat is dead and bottle of poison is open and Schrodinger's cat is alive and bottle of poison closed. Mathematically this kind of state makes complete sense but not at the level of sensory experience.

    The basic property of sensory perception indeed is that it makes state classical by state function reduction.

    Automatic consciousness is in TGD Universe a non-sensical notion. And also in the real universe: when a performance requiring learning becomes automatic it is not anymore a conscious performance. If there is still consciousness, it is at lower levels of the hierarchy, not ours, where things need not be automatic.

    This is a good example of how prevailing theories of consciousness - in this case computationalism - neglect even the most elementary facts about consciousness. Same applies also in particle physics. Seeing that which is - about which Krishnamurti talks a lot - is is very very important for a theorist;-). Too often theorists are unable to see anything from the shadow of their own gigantic ego!



  5. Machine consciousness. Can machines be murdered? Tate, M.A. et al
    'Consciousness and the Universe' emphasises the lack of depth of thinking that can be a hall mark of the functionalist approach to consciousness.
    Assumption that (combining of) particular actions will produce consciousness; no argument is presented, conclusions are merely asserted. Computers/robots are making advances in mobility, face recognition and other functions. Do the authors think that a machine performing just one of these functions could become conscious. At any rate, their main emphasis appears to be concentrated on generating some magic out of the combination of different modalities that occurs in the brain,
    Relating consciousness:combining of modalities has a certain plausibility in neuroscience, in that consciousness is correlated with the global gamma synchrony. It is possibly awareness of this arrangement in the brain that has suggested that combining a number of functions could produce consciousness,
    A general relating problem is that the synchronisation of action spikes across billions of spatially separated neurons bears little resemblance to computing. Although functionalism is probably the dominant orthodoxy, there is now more awareness of the differences between computers and brains, The operation of the gamma synchrony could be digitally replicated, although this isn't really clear. No doubt a computer could in principle replicate such connections, but this leaves open the question as to whether the basis for consciousness relates to the connections as such, or the physical/biological structures allow them. This could be a subject of some discussion,
    The working of human-made computers is fully understood, and provides no examples of structures that do not exist elsewhere in the universe without them producing consciousness. It is noticeable that while philosophy and psychology talk in terms of certainties with relation to the mind, the neuroscientific literature is hedged by 'perhaps' and 'could be'. The gamma synchrony is only a correlate of consciousness. Is it consciousness that produces the synchrony, visa versa or some interactive process between neurons and the brain-wide synchrony?
    The core of the mind-brain identity concept is that mental states and neural states are identical. In a trivial sense this appears to be true of all theories of consciousness that are not dualistic, so that even a Penrose-Hameroff theory of consciousness could be argued to be a mind-brain identity theory. Thus Penrose argued that the mind was not identical to a computer rather than not identical to a brain.
    In modern consciousness studies mind-brain theories tend to travel with a certain hidden agenda. The mind is identical to the brain as described by neuroscience text books. So far so good, except that when we read such a text book, there is nothing in it which either requires or could generate consciousness. We are presented with a closed information system from which consciousness is entirely missing. Incidentally an end chapter, which may be found in some more recent books, giving a round up of current theories of consciousness does not constitute an explanation of why consciousness is missing from the main text. The problem we have in conventional mind-brain identity theory is that the mind is claimed to be identical to a brain that, as described, has no requirement for consciousness and had no way of generating it.

  6. Has a rather confused take on some other theories of consciousness. appear to conflate quantum consciousness with epiphenomenalism. The assumption appears to be that any quantum states must be by-products of processes based on classical physics, suggesting a rather strange take on physics, and this is odder still because epiphenomenonalists tend to indignantly reject the idea of any quantum involvement. Another curious idea is the conception of persistence through time as the factor underlying consciousness. Awareness or record of lifespan to date is usually part of the contents of human consciousness, but it is another thing to say that this produces consciousness. A non-conscious computer only needs a clock to record how long it has been in existence. In a fashion reminiscent of twentieth century thinking cognition is frequently equated to (potential for) consciousness, while emotion or evaluation of sensory input is hardly mentioned.

  7. http://youtu.be/Tfi8BLca07M
    The Secret Life of Vortices: Evolution and Destruction of Vortical Flows

  8. Andrulis work as a Theory of Life can be seen at http://www.scribd.com/doc/107521682/Presentation-at-X-International-Ontology-Congress-Physis-From-Elementary-Particles-to-Human-Nature