About protons and atoms.

The highest resolution image of a single atom ever taken.

Ben Norton and supervisor David Kielpinski, of Griffith University's Centre for Quantum Dynamics in Australia, developed new techniques to capture an atom, which is about 400th billionths of a meter across. The research areas of the Centre include attosecond science, atomic and molecular dynamics in ultrafast fields, atom optics, quantum optics, quantum information and computation, and fundamental quantum mechanics. The team also took the first-ever image of the shadow of a single atom, at their smallest, are only one tenth of a millionth of a millimetre across.

Norton has captured the highest resolution images ever of a single atom with the help of a special lens. The atoms were imaged in an ion trap that was built from the ground up. By cooling the atoms down to absolute zero (-273.25 degrees Celsisus), he is able to reduce any movement. Norton then traps the atoms in an ultra-high vacuum that contains less air than outer space and holds them in place for a 'photo opp' using electric fields. These lenses can be made so small and light that they can be put inside the vacuum chamber with the atoms, allowing to collect as much light as possible.


Ben Norton's remarkable image of an atom was runner up in the CiSRA Extreme Imaging Competition. Credit: Griffith University. From Phys.org.
The smallest trapped ion spot size that they captured high resolution images of was 370nm. Here is the link to the paper by Ben Norton et al, Millikelvin spatial thermometry of trapped ions. New Journal of Physics 13 (2011) 113022.

The strong Coulomb coupling makes laser-cooled trapped ions attractive for sympathetic cooling at millikelvin temperatures in investigations of fundamental physics [7], dynamics of complex molecular [8, 9] and biomolecular [10] ions, nano-mechanical oscillators [11, 12], resonant electric circuits [13] and Bose–Einstein condensates [14].

Look, what pictures! They cannot be bringed here!
Images of a trapped ion for three different external heating rates.
Errors were dominated by systematic uncertainty. All images were taken with the laser detuned 15MHz from resonance. The ion signal was integrated for 2 s in all three images.

Norton's basic research is in atomic physics, using lasers to interact with atoms. The team is now hoping to use the high resolution images of single atoms to understand how atoms behave.
Precise imaging of atoms can help scientists understand physics as a whole, the new field of quantum computing, and possibly even ultra-high resolution imaging of cells in the body.
The dynamics of quantum systems are systems composed of microscopic particles such as photons, electrons, and atoms, the behaviour of which is governed by quantum mechanics, and is very different from the familiar behaviour of macroscopic systems.

A crystal of 8 ions trapped by electric fields, from the Centre for Quantum Dynamics.
Another one! The February 21, 2012 press release from the Centre for Quantum Dynamics is entitled “Single atoms talk to electric circuits at Griffith."

Scientists at Griffith University’s Centre for Quantum Dynamics have advanced quantum computing in a big way with their ability to manipulate one atom within an electrical circuit, what is called atom-based quantum communications. They have been able to use a single atom to transfer information within an electrical circuit.
The scientists involved with this research compare their ability to manipulate a single atom to communicate within an electrical circuit with the much older process of getting “voices … transmitted over radio.”
By this Australian-American team “… could have far-reaching implications for the future of secure communications and code breaking.”
Dr. Dave Kielpinski, the chief investigator on this project and a professor at Griffith University, from the press release: "Atom-based quantum communication is guaranteed to be secure by the laws of physics, so the atom-circuit interface can extend this security to electronic devices. They are also excellent sensors for acceleration, gravity, and electrical fields. But working with them requires exotic laser and vacuum technologies. The atom-circuit interface will let us plug atom-based devices into more widespread electronic technology such as computers. This is the first time that the quantum theory of a single atom has been combined with a quantum electrical model. Quantum mechanics normally manifests itself on a microscopic scale. While well isolated single atoms can readily be controlled on the quantum level, large objects such as computers normally behave classically.”
The paper highlighting this work will be published in the journal Physical Review Letters -- within the February 24, 2012 issue.
"Proton Smaller Than Thought—May Rewrite Laws of Physics." from 2010. The hydrogen atom is also seen as the “Rosetta Stone” of quantum physics.

Smaller Proton Size Revealed by Lasers.
In a ten-year experiment, a team led by Randolf Pohl of the Max-Planck Institute of Quantum Optics in Garching, Germany, used a specialized particle accelerator to alter hydrogen atoms into 'muonic hydrogen'. The team replaced the atom's electron with a particle called a muon, which is 200 times more massive than an electron.
"Because the muon is so much heavier, it orbits very close to the proton, so it is sensitive to the proton's size," said team member Aldo Antognini, of the Paul-Scherrer Institute in Switzerland.
Muons are unstable, and they decay into other particles in just 2.2 microseconds. The team knew that firing a laser at the atom before the muon decays should excite the muon, causing it to move to a higher energy level—a higher orbit around the proton. The muon should then release the extra energy as x-rays and move to a lower energy level. The distance between these energy levels is determined by the size of the proton, which in turn dictates the frequency of the emitted x-rays.
Errors possible:
- the Rydberg constant hasn't been correctly measured. This value describes the way light gets emitted from various elements—a key component of spectroscopy.
- the smaller size of a proton could mean the equations in QED theory will fail
The spectroscopic determination of the Lamb shift of the energy levels in muonic hydrogen in 2010 yielded a value for the proton radius which was significantly smaller than deduced from previous measurements – a fact that still puzzles the scientific community. Present knowledge of the (root-mean-square) proton charge radius which does not depend on hydrogen spectroscopy comes from electron scattering experiments. A recent reanalysis of all electron-proton scattering data [1], accounting for Coulomb distortion and using a parametrization that makes it possible to include data at higher q², finds a radius of 0.895(18) fm, i.e. the uncertainty is as large as 2%. A measurement of the muonic Lamb shift with 30 ppm precision will determine the proton radius with 0.1% precision.
For years the accepted value for the radius of a proton has been 0.8768 femtometers, where a femtometer equals one quadrillionth of a meter. Now the scientists detected x-rays at an assumed proton radius of 0.8418 femtometers—4 percent smaller than expected. If it proves correct, it means something fundamental is wrong in particle physics.
The size of a proton is an essential value in equations that make up the 60-year-old theory of quantum electrodynamics, a cornerstone of the Standard Model of particle physics. The Standard Model describes how all forces, except gravity, affect subatomic particles. But the proton's current value is accurate only by plus or minus one percent—which isn't accurate enough for quantum electrodynamics, QED, to work perfectly.

See:

• Animation of the experiment
• Movie about experimental setup
• Press release
• Homepage
  
  • Introduction
  • Motivation
  • Experiment
  • People
  • Publications
  • Links

Awards: “European Research Council Starting Grant” in August 2011.
Spectroscopy of muonic hydrogen in 2010 yielded a tenfold precision in the measurement of the protonic radius. However, the result showed a large discrepancy with previous measurements. The new project “Charge Radius Experiment with Muonic Atoms” is meant to solve this puzzle. By extending the spectroscopy of muonic hydrogen to muonic helium it will be possible to measure the size of its nucleus with tenfold precision. This will also shed some light on the proton size puzzle. “I have spent twelve years on measuring the charge radius of the proton”, Randolf Pohl says. “It may again take a long time to find the resonance of muonic helium. On the other hand, when we are successful, the gain will be huge, as progress in fundamental physical constants is notoriously slow.”

Professor Stefan Kuhr: “Single-atom-resolved detection and manipulation of strongly correlated fermions in an optical lattice” was the other reciever.
Because the interaction of fermions with each other is quite different from the interaction of bosons, the new project requires a completely new experimental setup. Among others, this work will lead to a deeper understanding of the mechanisms that give rise to macroscopic properties of matter such as magnetism or superconductivity.

...and Gustav Hertz Award of the German Physical Society, DPG, in nov 2011. with Antognini, will be given Stuttgart in March 2012.

From the homepage: in order to improve the determination of

• the proton charge radius by a factor of 20 (to 1x10^-3 relative accuracy)
• the deuteron charge radius by a factor of 20 (to 1x10^-3 relative accuracy)
• the Rydberg constant by a factor of 6 (to 1x10^-12 relative accuracy)
• the proton magnetic radius (Zemach radius) to 1x10^-2 relative accuracy
• the deuteron polarizability

and extend the test of bound-state quantum electrodynamics (QED) theories in hydrogen and deuterium to a level of 3x10^-7.

Latest publications:
Randolf Pohl, Aldo Antognini, et.al. The size of the proton, Nature, vol. 466, issue 7303, pp. 213-216 (2010).
Randolf Pohl, Aldo Antognini, et al. The Lamb shift in muonic hydrogen, Can. J. Phys. vol. 89, pp. 37–45 (2011).
Aldo Antognini, et al. Illuminating the proton radius conundrum: the muonic helium Lamb shift, Can. J. Phys. vol. 89, pp. 47–57 (2011).

See also TGD, 2010, The incredibly shrinking proton and a more detailed article here.

Interesting things! Keep the eyes open!

Addendum:  First photo of shadow of single atom July 3, 2012



In an international scientific breakthrough, a Griffith University research team has been able to photograph the shadow of a single atom for the first time.
"We have reached the extreme limit of microscopy; you can not see anything smaller than an atom using visible light," Professor Dave Kielpinski of Griffith University's Centre for Quantum Dynamics in Brisbane, Australia.
"We wanted to investigate how few atoms are required to cast a shadow and we proved it takes just one," Professor Kielpinski said.
Published this week in Nature Communications, "Absorption imaging of a single atom "is the result of work over the last 5 years by the Kielpinski/Streed research team.
At the heart of this Griffith University achievement is a super high-resolution microscope, which makes the shadow dark enough to see.
 
Holding an atom still long enough to take its photo, while remarkable in itself, is not new technology; the atom is isolated within a chamber and held in free space by electrical forces.
Professor Kielpinski and his colleagues trapped single atomic ions of the element ytterbium and exposed them to a specific frequency of light. Under this light the atom's shadow was cast onto a detector, and a digital camera was then able to capture the image.
"By using the ultra hi-res microscope we were able to concentrate the image down to a smaller area than has been achieved before, creating a darker image which is easier to see", Professor Kielpinski said.
The precision involved in this process is almost beyond imagining.
"If we change the frequency of the light we shine on the atom by just one part in a billion, the image can no longer be seen," Professor Kielpinski said.

Journal reference: Nature Communications

Provided by Griffith University

And
Scientists make quantum breakthrough
 April 20, 2011

“We have shown that when atoms in a vacuum chamber are guided inside a laser light beam, they too can create a speckle pattern - an image of which we have captured for the first time”.
The team trapped a cloud of cold helium atoms at the focus of an intense laser beam pointed downwards at the imaging system, and then gradually turned down the laser intensity until the speckled image appeared. The work was done with PhD students Sean Hodgman and Andrew Manning.
“We then made the atoms even colder,” says team leader Dr Andrew Truscott, “until they behaved more like waves than particles, forming a single quantum wave called a Bose-Einstein condensate (BEC).  When the BEC was loaded into the guide, the speckle pattern disappeared, showing that just one mode was being transmitted – the single quantum wave.”
The physicists demonstrated that by measuring the arrival time of the atoms on the imaging system, they were able to distinguish between the multimode (speckled image) guiding, and the single-mode (smooth image) guiding.
“Measurements for the multi-mode beam showed the atoms arriving in groups as a result of their interference – so-called atom bunching,” said team member Dr Robert Dall. “However, the BEC represents just a single quantum mode with no interference, so when we guided the BEC - we saw no bunching.”
The guiding behaviour agreed with a theoretical model developed by team member Mattias Johnsson.  “We have shown that atoms can be guided in a laser beam of light, with the same properties as light guided in an optical fibre made of glass,”
More information: Observation of atomic speckle and Hanbury Brown–Twiss correlations in guided matter waves, Nature Communications 2, Article number: 291 doi:10.1038/ncomms1292
Abstract
Speckle patterns produced by multiple independent light sources are a manifestation of the coherence of the light field. Second-order correlations exhibited in phenomena such as photon bunching, termed the Hanbury Brown–Twiss effect, are a measure of quantum coherence. Here we observe for the first time atomic speckle produced by atoms transmitted through an optical waveguide, and link this to second-order correlations of the atomic arrival times. We show that multimode matter-wave guiding, which is directly analogous to multimode light guiding in optical fibres, produces a speckled transverse intensity pattern and atom bunching, whereas single-mode guiding of atoms that are output-coupled from a Bose–Einstein condensate yields a smooth intensity profile and a second-order correlation value of unity. Both first- and second-order coherence are important for applications requiring a fully coherent atomic source, such as squeezed-atom interferometry.
Provided by Australian National Universit

= Flux tubes, massless extremals with Kähler language.

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

• An ocean gyre, its most common meaning.
• A cyclone or hurricane.
• A maelstrom
• A whirlpool.
• A tornado.
• USNS Gyre (T-AGOR-21), a research ship.

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.

But...

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