Quantum criticality in biologic protein systems (Introduction)
by David Turell 
, Wednesday, August 15, 2018, 21:17 (2290 days ago)
The movement of electrons is poorly understood in the biochemistry of life:
https://phys.org/news/2015-04-quantum-criticality-life-proteins.html
"Stuart Kauffman, from the University of Calgary, and several of his colleagues have recently published a paper on the Arxiv server titled 'Quantum Criticality at the Origins of Life'. The idea of a quantum criticality, and more generally quantum critical states, comes perhaps not surprisingly, from solid state physics. It describes unusual electronic states that are are balanced somewhere between conduction and insulation. More specifically, under certain conditions, current flow at the critical point becomes unpredictable. When it does flow, it tends to do so in avalanches that vary by several orders of magnitude in size.
***
"The potential existence of quantum critical points in proteins is a new idea that will need some experimental evidence to back it up. Kauffman and his group eloquently describe the major differences between current flow in proteins as compared to metallic conductors.
"By contrast, this kind of a mechanism would appear to be uncommon in biological systems. The authors note that charges entering a critically conducting biomolecule will be under the joint influence of the quantum Hamiltonian and the excessive decoherence caused by the environment. Currently a huge focus in Quantum biology, this kind of conductance has been seen for example, for excitons in the light-harvesting systems. As might already be apparent here, the logical flow of the paper, at least to nonspecialists, quickly devolves into the more esoteric world of quantum Hamiltonians and niche concepts like 'Anderson localization.'
***
" Turin.. notes that the question of how electrons get across proteins is one of the great unsolved problems in biophysics, and that the Kauffman paper points in a novel direction to possibly explain conduction. Quantum tunnelling (which is an essential process, for example, in the joint special ops of proteins of the respiratory chain) works fine over small distances. However, rates fall precipitously with distance. Traditional hole and electron transport mechanisms butt against the high bandgap and absence of obvious acceptor impurities. Yet at rest our body's fuel cell generates 100 amps of electron current.
***
"In suggesting that biomolecules, or at least most of them, are quantum critical conductors, Kauffman and his group are claiming that their electronic properties are precisely tuned to the transition point between a metal and an insulator. An even stronger reading of this would have that there is a universal mechanism of charge transport in living matter which can exist only in highly evolved systems. To back all this up the group took a closer look at the electronic structure of a few of our standard issue proteins like myoglobin, profilin, and apolipoprotein E.
***
"However, in asking why life just uses the molecules that does, the authors don't explicitly address the question of just how many potential small biomolecules and or proteins would be expected to quantum critical in the first place. They do note that some biomolecules are actually fairly good conductors.
"We might call to mind at this point that others have looked for similar kinds of extreme behaviours in other examples of life's proteins. Stuart Hameroff has been a long time champion of networks of polymerized tubulins in the conduction of information in the cells through as yet fully defined mechanisms. In particular, we should mention recent work on driving the rapidly polymerization of microtubules through external electromagnetic fields raises the question of what new kinds of physics may be at play here. I discussed some of this in more detail elsewhere the other day, together with some of the researchers here for anyone interested to read a little more."
Comment: I am convinced that quantum mechanics underlies whatever is present in our universe and is actively present in the biochemistry of life. Foe example, in the past I have presented articles on photosynthesis, where quantum activity has been identified, as emphasized by my bold above. This is such a highly technical and theoretical field it is difficult to fully understand it, but then quantum theory is still at the outer edges of what it all means. Note this abstract:
http://iopscience.iop.org/article/10.1088/1742-6596/626/1/012023/pdf
"Abstract. Why life persists at the edge of chaos is a question at the very heart of evolution. Here we show that molecules taking part in biochemical processes from small molecules to proteins are critical quantum mechanically. Electronic Hamiltonians of biomolecules are tuned exactly to the critical point of the metal-insulator transition separating the Anderson localized insulator phase from the conducting disordered metal phase. Using tools from Random Matrix Theory we confirm that the energy level statistics of these biomolecules show the universal transitional distribution of the metal-insulator critical point and the wave functions are multifractals in accordance with the theory of Anderson transitions. The findings point to the existence of a universal mechanism of charge transport in living matter. The revealed bio-conductor material is neither a metal nor an insulator but a new quantum critical material which can exist only in highly evolved systems and has unique material properties."
Quantum criticality in biologic protein systems
by David Turell , Saturday, January 12, 2019, 01:06 (2141 days ago) @ David Turell
An article on the new interest in quantum mechanics in biologic systems. I've mentioned that photosynthesis shows quantum activity:
https://cosmosmagazine.com/biology/indeterminate-nature-the-resurgence-of-quantum-biology
"An old and quirky collaboration between seemingly incompatible scientific fields is producing fascinating new insights into the nature of the living world.
"Meet the discipline known as “quantum biology”: the idea that the oddities of quantum mechanics such as entanglement, quantum tunnelling, superposition of wave states, the uncertainty principle and quantum coherence play vital roles in the biology of living things.
***
"Quantum biology is one such meeting point. And while it is producing remarkable and novel findings about olfaction, photosynthesis and the action of enzymes, the interdiscipline is as old as the quantum revolution itself.
***
"As early as 1929, Niels Bohr was making vague allusions to the role of quantum thinking in biology, and although such a vision was not yet fleshed out by Bohr himself....
***
"Bohr returned to the topic, too, this time arguing that complimentarity, or wave-particle duality (the idea that quantum objects act as both particles and waves, but never both at the same time) was the organicist “new law” that would uncover the mysteries of the living world. Together with Werner Heisenberg, Bohr wondered if such quantum phenomena played an undiscovered role in the mutation and selection of Darwinian evolution.
"In the 1940s Erwin Schrödinger argued that genes and the laws of heredity were sensitive to quantum mechanical dynamics and that the mutations necessary for natural selection arose through quantum tunnelling (the phenomena whereby subatomic particles can reach lower energy states by bypassing, or tunnelling through, intervening higher energy states).
***
" Several scientists kept thinking about the connection between quantum mechanics and life, however, with some, such as British mathematical physicist Roger Penrose, even drawing connections between the quantum world and consciousness. But for the most part, many of the early claims of quantum biology were discredited and the classical sciences remained dominant in biology.
"However, in the past few decades quantum biology has experiencing something of a revival. There is now, the authors state, “sound experimental evidence for quantum coherence in photosynthesis and quantum tunnelling in enzyme action; together with strong theoretical arguments and some experimental evidence supporting the role of quantum entanglement in avian navigation and quantum tunnelling in olfaction".
"There are also some tantalising findings to suggest that the “hot, wet and complex” biological systems, non-equilibrium systems fundamentally connected to their environment, might actually promote interesting quantum dynamics, rather than rule them out has had been thought in the sixties.
"The question has now become how quantum phenomena affect biology, rather than if they do. And given that evolution has had three and half billion years to devise ways to harness the oddities of quantum mechanics, there seems much for quantum biology to explore."
Comment: It will be fascinating. If teh vasis of reality is quantum mechanics, it has to have a basis in biology.
Quantum mechanics rule life
by David Turell , Thursday, May 30, 2019, 05:42 (2003 days ago) @ David Turell
The important Pauli exclusion principle:
https://www.forbes.com/sites/startswithabang/2019/05/28/this-little-known-quantum-rule-...
"It might make you wonder how this occurs. How do atoms, made of atomic nuclei and electrons, which come in less than 100 varieties, give rise to the enormous diversity of molecules, objects, creatures and everything else we find? We owe the answer to one underappreciated quantum rule: the Pauli Exclusion Principle.
***
"Most of us barely give a second thought to the Pauli Exclusion Principle, which simply states that no two identical fermions can occupy the same exact quantum state in the same system.
"Big deal, right?
"Actually, it's not only a big deal; it's the biggest deal of all. When Niels Bohr first put out his model of the atom, it was simple but extremely effective. By viewing the electrons as planet-like entities that orbited the nucleus, but only at explicit energy levels that were governed by straightforward mathematical rules, his model reproduced the coarse structure of matter. As electrons transitioned between the energy levels, they emitted or absorbed photons, which in turn described the spectrum of each individual element.
***
"The Pauli Exclusion Principle — and the fact that we have the quantum numbers that we do in the Universe — is what gives each individual atom their own unique structure. As we add greater numbers of electrons to our atoms, we have to go to higher energy levels, greater angular momenta, and increasingly more complex orbitals to find homes for all of them. The energy levels work as follows:
***
"Each individual atom on the periodic table, under this vital quantum rule, will have a different electron configuration than every other element. Because it's the properties of the electrons in the outermost shells that determine the physical and chemical properties of the element it's a part of, each individual atom has its own unique sets of atomic, ionic, and molecular bonds that it's capable of forming.
"No two elements, no matter how similar, will be the same in terms of the structures they form. This is the root of why we have so many possibilities for how many different types of molecules and complex structures that we can form with just a few simple raw ingredients. Each new electron that we add has to have different quantum numbers than all the electrons before it, which alters how that atom will interact with everything else.
"The net result is that each individual atom offers a myriad of possibilities when combining with any other atom to form a chemical or biological compound. There is no limit to the possible combinations that atoms can come together in; while certain configurations are certainly more energetically favorable than others, a variety of energy conditions exist in nature, paving the way to form compounds that even the cleverest of humans would have difficulty imagining.
"But the only reason that atoms behave this way, and that there are so many wondrous compounds that we can form by combining them, is that we cannot put an arbitrary number of electrons into the same quantum state. Electrons are fermions, and Pauli's underappreciated quantum rule prevents any two identical fermions from having the same exact quantum numbers.
"If we didn't have the Pauli Exclusion Principle to prevent multiple fermions from having the same quantum state, our Universe would be extremely different. Every atom would have almost identical properties to hydrogen, making the possible structures we could form extremely simplistic. White dwarf stars and neutron stars, held up in our Universe by the degeneracy pressure provided by the Pauli Exclusion Principle, would collapse into black holes. And, most horrifically, carbon-based organic compounds — the building blocks of all life as we know it — would be an impossibility for us.
"The Pauli Exclusion Principle isn't the first thing we think of when we think of the quantum rules that govern reality, but it should be. Without quantum uncertainty or wave-particle duality, our Universe would be different, but life could still exist. Without Pauli's vital rule, however, hydrogen-like bonds would be as complex as it could get."
Comment: As usual quantum mechanics is at the base of our reality.
Quantum mechanics rule life; double slit confusion
by David Turell , Saturday, December 14, 2019, 19:49 (1804 days ago) @ David Turell
The double slit experiment is still not explained satisfactorily:
https://aeon.co/essays/the-elegant-physics-experiment-to-decode-the-nature-of-reality?u...
Note the title of this long essay:
"How a sunbeam split in two became physics’ most elegant experiment, shedding light on the underlying nature of reality."
***
"In its simplest form, the experiment involves sending individual particles such as photons or electrons, one at a time, through two openings or slits cut into an otherwise opaque barrier. The particle lands on an observation screen on the other side of the barrier. If you look to see which slit the particle goes through (our intuition, honed by living in the world we do, says it must go through one or the other), the particle behaves like, well, a particle, and takes one of the two possible paths. But if one merely monitors the particle landing on the screen after its journey through the slits, the photon or electron seems to behave like a wave, ostensibly going through both slits at once.
***
"In the mid-1920s, a few fabulously talented physicists, among them Heisenberg, Pascual Jordan, Max Born and Paul Dirac in one group, and Erwin Schrödinger on his own, developed two ways of mathematically depicting the behaviour of the quantum underworld. These two ways turned out to be equivalent. It boils down to this: the state of any quantum system is represented by a mathematical abstraction called a wavefunction. There is a single equation – called the Schrödinger equation – which tells us how this wavefunction, and hence the state of the quantum system, changes with time. This is what allows physicists to predict the probabilities of experiment outcomes.
***
"Did the photon go through both slits at once? Does the photon have a trajectory, as it leaves the source and is eventually detected at the photographic plate? And given that the mathematics says that there are many regions where the photon can be found with a non-zero probability, why does it end up in one of those regions and not others? Finally, if the photon didn’t go through both slits, but rather the wavefunction did, is the wavefunction real?
***
"For any given photon, you can never predict with certainty where it will be found: all you can say is that it will be found in region A with probability X, or in region B with probability Y, and so on. These probabilities are born out when you do the experiment numerous times with identical photons, but the precise destiny of an individual photon is not for us to know. Nature at its most fundamental seems indeterminate, random.
***
"The opposite of locality – nonlocality – gets highlighted by something as simple as the double-slit experiment. When the photon’s wavefunction nears the photographic plate, the photon is in a quantum superposition of being in many places at once (this is not to say that the photon actually is in these places simultaneously, it’s just a way of talking about the mathematics; the photon itself is not yet ascribed reality in the standard way of thinking about it). Upon observation, the wavefunction is said to collapse, in that its value peaks at one location and goes to near-zero elsewhere. The photon is localised – and thus found to be at one of its many possible locations.
***
"But our classical minds rebel. We cannot disregard the conviction that the photon has to go through one slit or the other. So we put detectors next to the slits (let’s assume that our detectors work without destroying the photons). Something weird happens. The photons will now go through one or the other slit. Curiously, this time they will not form an interference pattern. They act like particles and they will go to those regions on the photographic plate that they shunned when acting like a wave.
***
"It was clear that whether a photon behaves like a wave or a particle depends on the choice of the experimental setup
***
"Experimentalists have also combined delayed-choice and quantum-erasure experiments into one mind-boggling delayed-choice quantum-erasure experiment – in which you not only delay the choice of what to see (particle or wave nature), but you can also randomly erase this choice. Again, the photon or any quantum system will show you only one face or the other – and what it reveals depends on the final state of the experimental apparatus.
***
"Even more enigmatically, does collapse ultimately need observation by a conscious human being? (To be clear, almost no physicist today thinks that this is the case.)
***
"physics has yet to successfully explain the double-slit experiment. The case remains unsolved."
Comment: And this is the basis of reality! We can't seem to out-think God. Worth reading it all.
Quantum mechanics rule life; double slit confusion
QUOTE: "Even more enigmatically, does collapse ultimately need observation by a conscious human being? (To be clear, almost no physicist today thinks that this is the case.)
QUOTE: "…physics has yet to successfully explain the double-slit experiment. The case remains unsolved."
DAVID: And this is the basis of reality! We can't seem to out-think God. Worth reading it all.
Thank you for the all-important bold: this seems to put paid to the absurd notion that objective reality does not exist outside our observation of it. That does not, of course, alter the fact that our perception of reality is subjective. The double-slit experiment simply takes its place alongside the origin of life, of consciousness, of reproduction and of evolution as an “unsolved case”. Whether it really is the “basis of reality” I would hesitate to say. How can we know until the case is solved?
Quantum mechanics rule life; double slit confusion
by David Turell , Sunday, December 15, 2019, 15:43 (1803 days ago) @ dhw
QUOTE: "Even more enigmatically, does collapse ultimately need observation by a conscious human being? (To be clear, almost no physicist today thinks that this is the case.)
QUOTE: "…physics has yet to successfully explain the double-slit experiment. The case remains unsolved."
DAVID: And this is the basis of reality! We can't seem to out-think God. Worth reading it all.
dhw: Thank you for the all-important bold: this seems to put paid to the absurd notion that objective reality does not exist outside our observation of it. That does not, of course, alter the fact that our perception of reality is subjective. The double-slit experiment simply takes its place alongside the origin of life, of consciousness, of reproduction and of evolution as an “unsolved case”. Whether it really is the “basis of reality” I would hesitate to say. How can we know until the case is solved?
Solved? We may not be able to out-think God.
Quantum mechanics rule life; still confusing
by David Turell , Saturday, March 12, 2022, 16:53 (985 days ago) @ David Turell
Another review:
https://www.symmetrymagazine.org/article/how-to-break-a-theory
“'What Einstein did was expose internal paradoxes of the theory itself,” says Stephon Alexander, a physics professor at Brown University. “It’s like looking at a picture of something beautiful, but then finding a new angle and the picture isn’t as beautiful or elegant as you thought.”
"Theorists must look for every possible angle, Alexander says. “As a theorist, you have the responsibility to strive for mastery and at the same time, be willing to look at things from the outside-in.”
"Today’s thought experiments sound just as bizarre as Einstein’s from 100 years ago. The internal paradoxes they reveal are just as gnarly.
***
"Theories tell stories. What are the smallest pieces of matter? What are their characteristics? What are their relationships? What is their destiny?
"But unlike the stories of Shakespeare or Kurosawa, a physics theory is told in the language of mathematics. If the math doesn’t check out, neither does the theory.
“'A lot if it is asking, ‘Is this legal?’” Keeler says. “You might write down something that seems mathematically consistent and then run into problems later. You have to ask, could any universe be constructed with this, or would it fall apart?”
"Quantum field theory, which describes physics at subatomic scales, makes many mathematicians cringe because of its “algebraic shenanigans,” says Dorota Grabowska, a fellow in the CERN Theory Group. “If I had a conversation with a mathematician about quantum field theory, they would let out a sigh of exasperation. It’s like when your mom tells you to clean your room, so you shove everything in the closet. It looks fine, but please don't open the closet.”
"Quantum field theory is rife with something mathematicians can’t stand: unresolved infinities. In a 1977 essay, Nobel Laureate Steven Weinberg wrote that “[Quantum field theory’s] reputation among physicists suffered frequent fluctuations… at times dropping so low that quantum field theory came close to be[ing] abandoned altogether.”
"But quantum field theory survives because at the end of the day, it still makes predictions that check out with experiments, such as those at the Large Hadron Collider at CERN. (my bold)
***
"The LHC’s enormous energy allowed physicists to finally find the legendary Higgs boson, which was theorized 50 years before its discovery and helps explain the origin of mass.
"But this discovery illuminated what might be the limits of current theory in the form of the Standard Model, which physicists use to describe subatomic particles, forces and fields.
“'If the Standard Model is valid across a large range of energies, we would expect the Higgs to have a much heavier mass than it does,” Renner says. “There’s no reason why the Higgs should be at the mass that it is, unless some new theory takes over at energies just out of our reach.'”
Comment: Just a reminder the basis of our reality makes no sense
Quantum mechanics rule life: fields are needed
by David Turell , Saturday, November 26, 2022, 18:10 (726 days ago) @ David Turell
Particles have fields. There are other fields that exist. All interact:
https://bigthink.com/starts-with-a-bang/quantum-fields-quantum-particles/?utm_source=ma...
"One of the most revolutionary discoveries of the 20th century is that certain properties of the Universe are quantized and obey counterintuitive quantum rules. The fundamental constituents of matter are quantized into discrete, individual particles, which exhibit weird and "spooky" behaviors that surprise us constantly. But the Universe's quantum weirdness goes even deeper: down to the fields that permeate all of space, with or without particles. Here's why we need them, too.
***
"When you reduce what’s real to its smallest components, you find that you can divide all forms of matter and energy into indivisible parts: quanta. However, these quanta no longer behave in a deterministic fashion, but only in a probabilistic one. Even with that addition, however, another problem still remains: the effects that these quanta cause on one another. Our classical notions of fields and forces fail to capture the real effects of the quantum mechanical Universe, demonstrating the need for them to be somehow quantized, too. Quantum mechanics isn’t sufficient to explain the Universe; for that, quantum field theory is needed. This is why.
***
"The more we experimented, the more of this unusual behavior we uncovered, including:
".>.the fact that atoms could only absorb or emit light at certain frequencies, teaching us that energy levels were quantized, that a quantum fired through a double slit would exhibit wave-like, rather than particle-like, behavior, that there’s an inherent uncertainty relation between certain physical quantities, and measuring one more precisely increases the inherent uncertainty in the other, and that outcomes were not deterministically predictable, but that only probability distributions of outcomes could be predicted.
***
"But what do you do when you have a quantum that’s generating a field, and that quantum itself is behaving as a decentralized, non-localized wave? This is a very different scenario than what we’ve considered in either classical physics or in quantum physics so far. You can’t simply treat the electric field generated by this wave-like, spread-out electron as coming from a single point, and obeying the classical laws of Maxwell’s equations. If you were to put another charged particle down, such as a second electron, it would have to respond to whatever weird sort of quantum-behavior this quantum wave was causing.
***
"...the enormous advance of quantum field theory, which didn’t just promote certain physical properties to being quantum operators, but promoted the fields themselves to being quantum operators. (This is also where the idea of second quantization comes from: because not just the matter and energy are quantized, but the fields as well.) All of a sudden, treating the fields as quantum mechanical operators enabled an enormous number of phenomena that had already been observed to finally be explained, including:
"...particle-antiparticle creation and annihilation, radioactive decays, quantum tunneling resulting in the creation of electron-positron pairs, and quantum corrections to the electron’s magnetic moment.
***
"One of the key things that comes along with quantum field theory that simply wouldn’t exist in normal quantum mechanics is the potential to have field-field interactions, not just particle-particle or particle-field interactions. Most of us can accept that particles will interact with other particles, because we’re used to two things colliding with one another: a ball smashing against a wall is a particle-particle interaction. Most of us can also accept that particles and fields interact, like when you move a magnet close to a metallic object, the field attracts the metal.
***
"The Universe, at a fundamental level, isn’t just made of quantized packets of matter and energy, but the fields that permeate the Universe are inherently quantum as well. It’s why practically every physicist fully expects that, at some level, gravitation must be quantized as well. General Relativity, our current theory of gravity, functions in the same way that an old-style classical field does: it curves the backdrop of space, and then quantum interactions occur in that curved space. Without a quantized gravitational field, however, we can be certain we’re overlooking quantum gravitational effects that ought to exist, even if we aren’t certain of what all of them are.
***
"In the end, we’ve learned that quantum mechanics is fundamentally flawed on its own. That’s not because of anything weird or spooky that it brought along with it, but because it wasn’t quite weird enough to account for the physical phenomena that actually occur in reality. Particles do indeed have inherently quantum properties, but so do fields: all of them relativistically invariant. Even without a current quantum theory of gravity, it’s all but certain that every aspect of the Universe, particles and fields alike, are themselves quantum in nature. What that means for reality, exactly, is something we’re still trying to puzzle out."
Comment: this is the basis of reality. dhw will complain God should have made it simpler. But since it is like it is, it must be required as God views its need in His design.