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Applying quantum thinking to biology

New Scientist

From Michael Brooks at New Scientist (03 October, 2011), we learn about “Quantum life: The weirdness inside us”:

We all run on adenosine triphosphate, or ATP, a chemical made in cells’ mitochondria by moving electrons through a chain of intermediate molecules. When we attempt to calculate how speedily this happens, we hit a problem. “In nature the process is much faster than it should be,” says Vlatko Vedral, a quantum physicist at the University of Oxford.

Vedral thinks this is because it depends on the quality of “superposition” which allows the sort of quantum-mechanical wave that describes electrons to be in two places at once. He reckons quantum omnipresence might speed the electrons’ passage through the reaction chain. “If you could show superposition is there and it’s somehow also important for the electron flow, that would be very interesting,” he says.

Vedral’s first calculations support the idea, but he says it is too early to make any claims.

Still, he’s asking some good questions.

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2 Responses to Applying quantum thinking to biology

  1. Thanks, Cool reference: I found this one on the flagellum:

    INFORMATION AND ENERGETICS OF QUANTUM FLAGELLA MOTOR
    Hiroyuki Matsuura, Nobuo Noda, Kazuharu Koide Tetsuya Nemoto and Yasumi Ito
    Excerpt from bottom page 7: Note that the physical principle of flagella motor does not belong to classical mechanics, but to quantum mechanics. When we can consider applying quantum physics to flagella motor, we can find out the shift of energetic state and coherent state.
    http://www2.ktokai-u.ac.jp/~shi/el08-046.pdf

    Further notes that may be of interest:

    Quantum entanglement holds together life’s blueprint – 2010
    Excerpt: When the researchers analysed the DNA without its helical structure, they found that the electron clouds were not entangled. But when they incorporated DNA’s helical structure into the model, they saw that the electron clouds of each base pair became entangled with those of its neighbours. “If you didn’t have entanglement, then DNA would have a simple flat structure, and you would never get the twist that seems to be important to the functioning of DNA,” says team member Vlatko Vedral of the University of Oxford.
    http://neshealthblog.wordpress.....blueprint/

    The relevance of continuous variable entanglement in DNA – July 2010
    Excerpt: We consider a chain of harmonic oscillators with dipole-dipole interaction between nearest neighbours resulting in a van der Waals type bonding. The binding energies between entangled and classically correlated states are compared. We apply our model to DNA. By comparing our model with numerical simulations we conclude that entanglement may play a crucial role in explaining the stability of the DNA double helix.
    http://arxiv.org/abs/1006.4053v1

    Quantum Information/Entanglement In DNA & Protein Folding – short video
    http://www.metacafe.com/watch/5936605/

    Quantum Computing in DNA – Stuart Hameroff
    Excerpt: Hypothesis: DNA utilizes quantum information and quantum computation for various functions. Superpositions of dipole states of base pairs consisting of purine (A,G) and pyrimidine (C,T) ring structures play the role of qubits, and quantum communication (coherence, entanglement, non-locality) occur in the “pi stack” region of the DNA molecule.,,, We can then consider DNA as a chain of qubits (with helical twist).
    Output of quantum computation would be manifest as the net electron interference pattern in the quantum state of the pi stack, regulating gene expression and other functions locally and nonlocally by radiation or entanglement.
    http://www.quantumconsciousnes.....InDNA.html

    Quantum Action confirmed in DNA by direct empirical observation;

    DNA Can Discern Between Two Quantum States, Research Shows – June 2011
    Excerpt: — DNA — can discern between quantum states known as spin. – The researchers fabricated self-assembling, single layers of DNA attached to a gold substrate. They then exposed the DNA to mixed groups of electrons with both directions of spin. Indeed, the team’s results surpassed expectations: The biological molecules reacted strongly with the electrons carrying one of those spins, and hardly at all with the others. The longer the molecule, the more efficient it was at choosing electrons with the desired spin, while single strands and damaged bits of DNA did not exhibit this property.
    http://www.sciencedaily.com/re.....104014.htm

    Can Quantum Mechanics Play a Role in DNA Damage Detection? (Short answer; YES!) – video – as well at about 27 Minute mark in the video – Fröhlich Condensation and Quantum Consciousness
    http://www.scivee.tv/node/25476

    In the preceding Quantum DNA video, ‘Gretchen’ had asked if quantum information could also somehow be measured in protein structures, besides just DNA, and it turns out that quantum information has already been confirmed to be in protein structures;

    Coherent Intrachain energy migration at room temperature – Elisabetta Collini & Gregory Scholes – University of Toronto – Science, 323, (2009), pp. 369-73
    Excerpt: The authors conducted an experiment to observe quantum coherence dynamics in relation to energy transfer. The experiment, conducted at room temperature, examined chain conformations, such as those found in the proteins of living cells. Neighbouring molecules along the backbone of a protein chain were seen to have coherent energy transfer. Where this happens quantum decoherence (the underlying tendency to loss of coherence due to interaction with the environment) is able to be resisted, and the evolution of the system remains entangled as a single quantum state.
    http://www.scimednet.org/quant.....d-protein/

    Quantum states in proteins and protein assemblies:
    The essence of life? – STUART HAMEROFF, JACK TUSZYNSKI
    Excerpt: It is, in fact, the hydrophobic effect and attractions among non-polar hydrophobic groups by van der Waals forces which drive protein folding. Although the confluence of hydrophobic side groups are small, roughly 1/30 to 1/250 of protein volumes, they exert enormous influence in the regulation of protein dynamics and function. Several hydrophobic pockets may work cooperatively in a single protein (Figure 2, Left). Hydrophobic pockets may be considered the “brain” or nervous system of each protein.,,, Proteins, lipids and nucleic acids are composed of constituent molecules which have both non-polar and polar regions on opposite ends. In an aqueous medium the non-polar regions of any of these components will join together to form hydrophobic regions where quantum forces reign.
    http://www.tony5m17h.net/SHJTQprotein.pdf

    Myosin Coherence
    Excerpt: Quantum physics and molecular biology are two disciplines that have evolved relatively independently. However, recently a wealth of evidence has demonstrated the importance of quantum mechanics for biological systems and thus a new field of quantum biology is emerging. Living systems have mastered the making and breaking of chemical bonds, which are quantum mechanical phenomena. Absorbance of frequency specific radiation (e.g. photosynthesis and vision), conversion of chemical energy into mechanical motion (e.g. ATP cleavage) and single electron transfers through biological polymers (e.g. DNA or proteins) are all quantum mechanical effects.

    etc.. etc..

  2. I liked this comment from the article:

    Quantum life: The weirdness inside us – 03 October 2011 by Michael Brooks
    Excerpt: “It sounds harsh but we haven’t learned a thing apart from the obvious.” A better understanding of what is going on might also help us on the way to building a quantum computer that exploits coherent states to do myriad calculations at once. Efforts to do so have so far been stymied by our inability to maintain the required coherence for long – even at temperatures close to absolute zero and in isolated experimental set-ups where disturbances from the outside world are minimised.
    http://www.newscientist.com/ar.....?full=true

    And indeed the quantum computation in life, that is the little we have managed to barely catch a glimpse of yet, completely dwarfs anything man has yet achieved in his attempts at quantum computation:

    Notes:

    Quantum Information/Entanglement In DNA & Protein Folding – short video
    http://www.metacafe.com/watch/5936605/

    Quantum Dots Spotlight DNA-Repair Proteins in Motion – March 2010
    Excerpt: “How this system works is an important unanswered question in this field,” he said. “It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It’s akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour.” Dr. Bennett Van Houten – of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot.
    http://www.sciencedaily.com/re.....123522.htm

    Whereas in man’s best concerted efforts thus far:

    14 quantum bits: Physicists go beyond the limits of what is currently possible in quantum computation – April 2011
    Excerpt: They confined 14 calcium atoms in an ion trap, which, similar to a quantum computer, they then manipulated with laser light. The internal states of each atom formed single qubits and a quantum register of 14 qubits was produced. This register represents the core of a future quantum computer.
    http://www.physorg.com/news/20.....imits.html

    Two atoms entangled using microwaves for the first time – August 2011
    Excerpt: Physicists at the National Institute of Standards and Technology have for the first time linked the quantum properties of two separated ions (electrically charged atoms) by manipulating them with microwaves instead of the usual laser beams, suggesting it may be possible to replace an exotic room-sized quantum computing “laser park” with miniaturized, commercial microwave technology similar to that used in smart phones.
    http://www.physorg.com/news/20.....waves.html

    Large scale qubit generation for quantum computing
    Excerpt: “Many people are trying to build a quantum computer,” Olivier Pfister tells PhysOrg.com. “One to the problems, though, is that you need hundreds of thousands of qubits. So far, scalability has been something of a problem, since generating that many qubits is difficult.”,,,Pfister points out that quantum computers of this sort cannot actually replace classical computers. However, quantum computers can be used for processing some types of information faster. “This is an attractive model for experiments that need cluster states. The big deal is that we got all these little quantum registers, and the entanglement is remarkably consistent.”,,, The next step, Pfister says, is to entangle the already-entangled qubits into a bigger register. “It requires additional complexity to entangle them all together, and we’re on our way to this.,,, We have shown that our control of entanglement is pretty good, but we need even better control to make entangled sets bigger than four.”,,,
    http://www.physorg.com/news/20.....antum.html

    ,,,LOL, engineers can just stare at the quantum computation/information processing in cells, and even though they can examine it all day long, they still haven’t come anywhere near matching it. too funny!, And even though this should drastically humble any sane man, neo-Darwinists will come along and deny (read Lie!) that any of this points to intelligent design;

    further note:

    Three subsets of sequence complexity and their relevance to biopolymeric information – Abel, Trevors
    Excerpt: Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC (Functional Sequence Complexity). FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,,

    Testable hypotheses about FSC

    What testable empirical hypotheses can we make about FSC that might allow us to identify when FSC exists? In any of the following null hypotheses [137], demonstrating a single exception would allow falsification. We invite assistance in the falsification of any of the following null hypotheses:

    Null hypothesis #1
    Stochastic ensembles of physical units cannot program algorithmic/cybernetic function.

    Null hypothesis #2
    Dynamically-ordered sequences of individual physical units (physicality patterned by natural law causation) cannot program algorithmic/cybernetic function.

    Null hypothesis #3
    Statistically weighted means (e.g., increased availability of certain units in the polymerization environment) giving rise to patterned (compressible) sequences of units cannot program algorithmic/cybernetic function.

    Null hypothesis #4
    Computationally successful configurable switches cannot be set by chance, necessity, or any combination of the two, even over large periods of time.

    We repeat that a single incident of nontrivial algorithmic programming success achieved without selection for fitness at the decision-node programming level would falsify any of these null hypotheses. This renders each of these hypotheses scientifically testable. We offer the prediction that none of these four hypotheses will be falsified.
    http://www.tbiomed.com/content/2/1/29

    verse and music:

    John 1:1-3
    In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made.

    The Word – Sara Groves – music video
    http://www.youtube.com/watch?v=0ofE-GZ8zTU

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