Tuesday, May 29, 2012

Study of photosynthesis reveals new physics

The experimental study of photosynthesis is beginning to reveal new physics. Already now it has become clear that quantum effects in much longer scales as believed in orthodoxy are involved. The latest revelation is decribed in a Science News article. The title is Unusual Quantum Effect Discovered in Earliest Stages of Photosynthesis. When photon excites the cell, it excites one electron inside chromophore. The surprising finding was that single photon actually excites several chromophores simultaneously!

What does this statement mean? One could think photon as a finite sized object (in TGD Universe space-time sheet that I have used to call "massless extremal") with size scale of wavelength which for visible photons is of order cell size. The photon would excite a superposition of states in which one of the chromophores is excited. The system formed by chromophores behaves as quantum coherent system. If quantum coherence is not present, one can say that photon excites just single chromophore at time.

Quantum coherence makes possible amplification for the rate of process. In incoherent situation the rate would be proportional to the number N of chromophores. In coherent situation it would in the optimal case be proportional to N2 (constructive interference). Note that one could imagine also second option in which photon literally excites several electrons belonging to different chromophores separately but this does not make sense to me.

This kind of simultaneous excitation would make sense in TGD framework if photo space-time sheet has size of order wave length, which is indeed of the order of cell size. If photon is dark then its size is scaled by the ratio hbar/hbar0 so that even chromophores in several cells could be excited simultaneously!

For TGD based model of photosynthesis see the chapter Macroscopic quantum coherences and quantum metabolism as different sides of the same coin: part I of "TGD Universe as a Conscious Hologram".


Ulla said...

Look at this: http://www.eskesthai.com/2012/05/embodied-cognition-and-icub.html

Ulla said...

"In coherent situation it would in the optimal case be proportional to N2 (constructive interference). Note that one could imagine also second option in which photon literally excites several electrons"

For cAMP the amplification is 1000-fold. The same molecule is used many times, like a ferry (wave?). The bridge is open as long as the coherence is there?

N^2 is the quantization making virtual particles visible/measurable?

See also the Pauling link given by O'Dowd
about resonance created by energetic differencies from excitations compared to basic energetic level, usually required for the quantum charachters to be visible.

also http://www.nature.com/news/2008/080123/full/451385a.html

When the amoeba Physarum polycephalum is subjected to a series of shocks at regular intervals, it learns the pattern and changes its behaviour [for hours]
Stochastic resonance?

http://www.nature.com/nature/journal/v474/n7350/full/nature10120.html Direct measurement of the wavefunction.

Ulla said...

Russian scientific research directly or indirectly explains phenomena such as clairvoyance, intuition, spontaneous and remote acts of healing, self healing, affirmation techniques, unusual light/auras around people (namely spiritual masters), mind’s influence on weather patterns and much more. In addition, there is evidence for a whole new type of medicine in which DNA can be influenced and reprogrammed by words and frequencies WITHOUT cutting out and replacing single genes.
The Russian biophysicist and molecular biologist Pjotr Garjajev and his colleagues also explored the vibrational behavior of the DNA...

matpitka@luukku.com said...

To Ulla:

The Nature article tells about memory at cellular level. Neuroscientists assign memory the synaptic strengtths of synapses connecting neurons. This paradigm does not explain memories at cellular level. Basic associative learning is in question however.

I would start to model from basic principles and see stochastic resonance as a tool of amplifying weak signal.

The memory representation for shocks would be in terms of braidings between various biomolecules. The shocks induce liquid flows at the liquid crystals formed lipids at cell and nuclear membranes and these in turn change the braiding of flux tubes connecting lipids to DNA nucleotides. Shocks affect of course also any other braidings possibly present.

Change of braiding changes the topological quantum computer programs involved and cell's behavior changes. This is of course very abstract: one should develop this to a concrete model for the change of behavior.

The cell should learn to behave so that shocks do not destroy its negentropic resources (its health!). This relates directly to ATP: compensation of lost negentropy requires metabolic energy and ATP: the new behavior should minimize metabolic costs due to the shocks. Cell should learn to flight since fight does not work in laboratory;-).

Ulla said...

The ATP has been thought to be too little for all cascades and receptors. Only brain would need so very much. One step amplify 100-fold and there are many steps, so there can be a six number amount ATP. This all happen within short time, almost immidiately.

No wonder sprinters are so adrenalin-filled and nervous (sympaticus active) Ca is needed for the muscles.

Adenylate cyclases are coincidence detectors, meaning that they are activated only by several different signals occurring together. Linked to Ca-signaling, and resonance.

In cancers this cAMP/kinases is also important. http://www.nature.com/onc/journal/vaop/ncurrent/full/onc201250a.html
Cancers are said to be very greedy, but the amplifying is also halted. Think at the effect in a nerve where there are so many mitochondrions.

Could the quantum coherence above be seen as a Schrödinger cat? Superposition of one induce it in all chromatophores, note their form. Like a song.

matpitka@luukku.com said...

To Ulla:

Quantum coherence can amplify. If you have N particles in coherence then emission by them can be N^2 times that for single particle: this requires that all emission amplitudes are in same phase. Without coherences there is N-fold emission as compared to single particle case.

Cancer cells behave much like cells after only few steps of differentiation: Becker's DC currents manage to take them to the primordial omnipotent state after which normal genetic machinery allows to build from the healthy specialized cells.

Maybe the problem with cancer cells is that they do not obey genetic machinery requiring further differentiation and have become ultrahedonistic money-making individuals of postmodern market economy;-). Coherence is certainly lost.

The entire cell and thus chromatophores behaves as single unit when responding to visible photon whose wavelength is of order cell size.

Hamed said...

Dear Matti,
In these days, I have some free times to learn TGD :). I come back to my process on testi.pdf, On gauss-bonnet theorem.
I write what I understand:
in according to Stokes theorem in language of differential forms, one can write integral of dA on M is equal to integral of A on boundary of M (A is gauge potential and dA is gauge field).
You wrote: “integral of 2-form Riemann curvature tensor defining the analog of gauge field reducing to a 1-D integral of a gauge potential by Stokes theorem supports strongly this”
Therefore I think one can equal dA with 2-form Riemann curvature tensor. then to obtain A from 2-form Riemann curvature tensor, second cartan equation is needed?
Also you wrote it is equivalent to “The reduction of the integral of curvature scalar to total divergence reducing by Gauss law to a 1-D integral”. Then how I can use from stokes theorem to proof this? In really in this case oppose to above case, I can’t equal dA with curvature scalar.
I am reading a chapter of a book about gauge potential to understand more about what you say ;).

matpitka@luukku.com said...

Dear Hamed,

fine that you contact. Take contact whenever you feel so. I have been very busy for various reasons and have not contacted.

I must look about what you could learn. One could think of learning about the geometric variatonal principles and variational principles in general. We could continue the discussion privately about these points.

R= domega+omega wedge omega would be the definition of curvature tensor as a complete analog of gauge field strength in non-abelian field theory. Omega is vielbein connection analogous to gauge potential in gauge group SO(n) for n-D Riemann manifold.

In 2-D case one has SO(2) gauge group so that the situation is abelian, and essentially Maxwell theory is obtained. Therefore R= domega holds true now and the flux of R over 2-D region is integral of omega along its boundary.

Zephir said...

The pigment array in thylakoid lamellas, i.e. quantasomes appear pretty similar to quantum dots arrays. Each quantasome contains about 230 to 300 chlorophyll molecules. They're regularly spaced in 150 x 180 A lattice, like quantum vortices in superconductors. All the molecules in each of these photo-synthetic units are spaced and oriented in such a way, captured photons are transferred from molecule to molecule by inductive resonance and the energy absorbed is transferred to as exciton.

Experiments have demonstrated, that the presence of the quantasome particles in chloroplast membrane is not a necessary condition for photoreduction activity of chloroplasts [J. Mol. Biol., 27, 323 (1967)] In prokaryotes pigments are distributed uniformly on or in the thylakoid lamellae.

Ulla said...

About memory. Is it also forming a topological map?


Inductive resonance, ye, but what is induction, Zephir?

Membranes makes it more efficient?

matpitka@luukku.com said...

To Ulla:

I think that the excited electron can be assigned to one particle chlorophyll molecule in thylakoid membrane forming this lattice structure. It could play important role in quantum coherence and in the phenomenon discussed in posting. One possibility is that electrons which can belong to different chlorophyll molecules form Cooper pairs. Also more complex multi-electron entanglement making the structure single coherent unit could be in question. For instance, in quantum Hall effect this kind of state of electrons is formed.

The sequence of induced resonances follows the primary excitation: this is like falling of domino pieces. Photon energy is transferred along the sequence to what is called reaction center.

Hamed said...

Dear Matti,

At “The dimension of CP2 projection as classifier for the fundamental phases of matter.”
The dimension of CP2 projection means projection of space-time surface in M4*CP2 to CP2 subspace?
Elementary particles have DCP2=3? Another fundamental phases of matter are some kind of new matters that is predicted by TGD?

at “Elementary particles have geometric representation as so called CP2 type extremals. Instead of standard imbedding of CP2 as a surface of M4+×CP2 obtained by putting Minkowski coordinates mk constant mk=const.
one considers 'warped' imbedding
mk =fk(u) u is arbitrary function of CP2 coordinates with the property that the M4+ projection of the surface is random light like curve:
mkl dmk/du dml/du =0, mkl is flat M4 metric. (A)
The condition implies that induced metric is just CP2 metric, which is Euclidian! “
Why does it need some arbitrary function u as intermediate between M4 and CP2 coordinates? It is unnatural for me.
Why the induced metric is just CP2 metric? CP2 metric obtains from mkl dmk/dXi dml/dXibar witch Xi and Xibar are complex coordinates of CP2 isn’t it?

matpitka@luukku.com said...

Dear Hamed,

the dimension of CP_2 projection is a convenient classified for space-time sheet locally. Again the notion of scale is very important.

Minkowskian regions are by holography related to macroscopic description of particles or rather many-particle states. For instances "massless" extremals characterize states of beams of massless gauge bosons.

In Minkowskian regions D is at most 3 *IF* the proposal that all preferred extremals are effectively 3-D: this requires that j^alphaA_alpha in the expression

J^alphabetaJ_alphabeta =j^alphaA_alpha+ divergence reducing to 3-D boundary terms

vanishes. Vanishing is guaranteed is j^alpha= is proportional to instanton current: in other words, it "topologizes". TGD as almost topological QFT and reduction to Chern-Simons terms weak form of electric magnetic duality is assumed at the ends of space-time surface and at light-like wormhole throats where the signature of induced metric changes.

Small deformations of CP_2 type vacuum extremals provide short scale description of particles. These regions had Euclidian signature of induced metric. In regions of Euclidian signature- in particular generalized Feynman diagrams as deformations of CP_2 type vacuum extremals and serving as counterparts of black holes in TGD - one has D=4 but now j^alpha vanishes identically so that Kahler action reduces effectively to 3-D terms also now (holography)

D=2 characterizes cosmic strings and massless extremals: again long length scale description. For their small deformation D>2 holds true but the CP_2 projection has very small third dimension.

Concerning CP_2 type vacuum extremals: there is actually nothing un-natural involved! The presence of arbitrary function only means that CP_2 vacuum extremals are an extremely general family of solutions of field equations. Since the M^4 projection is random light-like curve it can be parametrized by single coordinate u which is some function of CP_2 coordinates which can be anything. This actually gives rise to the 1-D counterpart of conformal invariance: conformal transformations correspond to the replacement of u with any function of u.

I actually got the stimulus leading to t the generalization of ordinary conformal invariance for 2-D Riemann surfaces to that for 3-D light-like surfaces from this conformal invariance.

That one obtains just CP_2 metric follows just by calculating the the contribution of M^4 to the induced metric. Use CP_2 coordinates (with u one of the coordinates) in which first contribution is just CP_2 metric. The M^4 contribution is

Delta g_uu= m_kl partial_um^kpartial_jm^l

But this contribution vanishes since M^4 projection is light-like so that one has just CP_2 metric. The internal geometry is just CP_2 geometry: one can speak about warped imbedding of CP_2. From the point of view of imbedding space the situation is different since the M^4 projection is light-like random curve rather than point. The shape of CP_2 is different from canonically imbedded CP_2.

In fact, random light-likeness motivates p-adic thermodynamics as a description of particles and leads to massivation. The average velocity over time intervals is smaller than c and particle behaves as if it had mass.

◘Fractality◘ said...


CORONAL HOLE: Spewing solar wind, a yawning dark fissure in the sun's atmosphere is turning toward Earth. NASA's Solar Dynamics Observatory photographed the "coronal hole" during the early hours of June 1st:


Coronal holes are places where the sun's magnetic field opens up and allows the solar wind to escape. A stream of solar wind flowing from this coronal hole will reach Earth on June 5th - 7th, possibly stirring geomagnetic storms. High-latitude sky watchers should be alert for auroras.

In TGD framework, this could theoretically have effects on consciousness?

m said...

To my opinion this is quite possible since magnetic perturbations could affect personal magnetic bodies as well as that of magnetic Mother Gaia.

One interesting effect is the possibility of quantal direct currents without dissipation flowing along flux tubes. This means gigantic electron energies since dissipation does not slow down the motion. In the case of thunderstorm relativistic electrons have been indeed observed and they are a mystery. I read just few days ago that also anomalously energetic electrons from Sun were detected.

◘Fractality◘ said...


Can those quantal direct currents manifest as plasmoids?


matpitka@luukku.com said...

These quantal direct currents are just supra currents in presence of electric field along the current carrying flux tube. For constant electric field the behavior is like a massive particle in Earth's gravitational field quantally. One can calculate and one obtains Airy functions as solutions.

What is purely quantal is that the net current depends on the boundary conditions and can be vanishing even in presence of electric field. Too strong electric field also means that the velocity for a particle leaving second end becomes very low by the condition of current conservation so that there is some critical range of field strengths allowing considerable currents. Thermal velocity defines a natural criterion here.

This leads to the notion of criticality. Criticality of cell membrane potential for nerve pulse generation would be basic example of this.

The proposal is that plasmoids are magnetic flux tube structures carrying supra currents. Flux tubes could of course carry also electric fields and the interaction with radiation could be a general mechanism generating supra current and therefore "biological" activities. Most of life would be based on universal mechanisms.

Ulla said...

One interesting question, why is symmetry breaking and decoherence necessary for Life, which is coherent?

When we look at the abundance of different atoms we see that the atoms for Life were created as the first ones. This would implicate that Life is the primordial state of matters and Life can be very different from our point of view. We just happened to be the Manifestation of Life here on Earth?

This Manifestation has happened through a violent symmetry breaking phase, guided by methane and CN. The same elements are seen as 'shields' also today. ironically we today think that this same symmetry breaking would make Life impossible. I know of your underground hypothesis, with ground acting as a stabilizer. But still...

The big difference between a silicon life and a carbon life is water, or the symmetry breaking. Today we find 'silicon life' added as instance in diatomeers, and some plants. Very rigid. Carbon instead is the most flexible element of all. made of 3 He-nucl. (alpha particles) forming a 3-body sytem, with non-locality present?

Ulla said...

This is an interesting video, but start a bit into it. At least 15 min. It talks much about chromophores. http://worldsciencefestival.com/webcasts/quantum_biology