Biochemical Implications of
Molecular Coupled Oscillators
Secure radio? stereochem forces? a nervous system for Paramecium?
William Beaty 2001

billb wrote:
 > If photons didn't exist, and if molecules are quantized resonant
 > circuits, then a light-emitting molecule emits a single frequency
 > of EM waves, and molecules in your retina will interact resonantly
 > to strongly absorb that frequency.

On Thu, 4 Jan 2001, Dustin Soodak wrote:
 > But this would imply that if you took a light-bulb and gave it a modest
 > velocity away from you(faster than the speeds of any of the individual
 > molecules in the light bulb), you would no longer see it! 

I see that I have to expand my thinking. Perfect oscillators with zero linewidth certainly would become invisible to perfect resonant absorbers if there was any doppler shift going on. What about hot filaments? Well, since "photonless" physics is just classical physics, the explanation for the above must already be in the textbooks.

Because a light bulb is not like a neon sign, the tungsten atoms in the light bulb filament don't emit the tungsten line spectrum. Instead, they couple together and form complicated 3D "collective oscillators" where the frequency depends on the coupling between atoms (like the QM-textbook example of a shoebox filled with bells, as opposed to individual bells hanging in space and ringing.) All the crazy, time-varying coupling inside the light bulb filament makes its oscillators transmit "white light". A distant single atom with zero linewidth would still "see" this light every time the frequency swept across the atom's absorption freq. A distant collection of molecules (such as a hunk of tungsten) would also "see" this light (and become heated) when one of the collective multi-line-frequency patterns of the light bulb happened to hit one of the the collective multi-line absorption patterns of the distant cold tungsten metal.

In conventional terms, the light bulb would become invisible only if it was moving at a relativistic velocity, so that its thermal spectrum moved down into radio waves, or up into x-rays, so that distant solid materials no longer interacted.

But now we're talking about something very cool: collective frequency patterns of groups of coupled oscillators. This is hidden within QM physics, inside the wave-functions in Solid State statistical concepts (Fermi surface and similar stuff.) But if we ignore the textbooks and instead look at atoms as being individual "superregen radios", something extremely interesting is revealed. It's something that's not in any physics textbook, as far as I know. It has direct engineering applications. Check it out:

Single atoms are obviously analogous to conventional radio transmitters and receivers: if their tuning doesn't match, then the "receiver" cannot hear the "transmitter".

Ah, but groups of coupled atoms are a little bit like spread spectrum radio transmitters: they give out multispectral "white light". On the other hand, they are not like spread-spectrum radio at all, because a fixed group of atoms puts out a weird multi-peak signal, and a distant but identical group of atoms... will be resonant, and will receive that strange multi-peak signal by the "energy sucking" resonance effect discussed elesewhere.

Here's the simplified version. Suppose that rather than having two separate tuned circuits which act as transmitter and receiver, instead we have resonator pairs. Suppose the "transmitter" is two coupled oscillators, and puts out a "line splitting" double-peaked spectrum. The transmitter would have two knobs: a tuning knob to set the center frequency, and a "coupling" knob which sets the distance between the two spectral peaks. If the "receiver" was identical, then the receiver could only pick up the transmitter's signal whenever the receiver's tuning knob AND the coupling knob was set the same as the transmitter's knobs. It's a radio with two tuning knobs rather than one. A 2D planar display rather than a frequency display resembling a wooden ruler.

I suspect that this is what N. Tesla was talking about when he claimed to have an "unbreakable" radio cryptography system back at the turn of the century. It's a molecular-analogy radio system. The five tuning knobs mentioned above correspond to the atoms in a five-atom molecule.

But any EM receiver would "hear" the signal at least partially, so how can it allow secure transmissions? Ah, but normal receivers aren't "resonant" in this odd way. Normal receivers might sense the existence of the signal, yet be unable to decode it. Suppose a knob on the multi-peak transmitter is changed back and forth. Then the multi-peak receiver's resonance with the transmitted signal will be spoiled periodically, yet 3rd-party listeners won't detect any obvious change because the transmited signal still resembles pink noise. We can send a sort of "FM" frequency modulation to which the multi-peak receiver responds strongly, while a normal single-resonator receiver won't even notice the modulation. For a secure transmitter, use fifty coupled oscillators and hundreds of coupling adjustments, then tune an identical receiver to the same pattern (so the receiver is in "bizarro-resonance" with the transmitter.) Now transmit a continuous signal. I believe such a receiver will respond very strongly, just like the "energy sucking" mode of a crystal radio's resonator. Now modulate the transmitter by varying one or more of the transmitter adjustments slightly, and the overall amplitude of the signal received by the receiver will vary enormously. You can communicate via a sort of "FM radio" effect. But anyone who tries to listen in will hear nothing but constant unmodulated "thermal noise spectrum."

This is "geometrical" tuning, where the "virtual shape" of the receiver must match the "virtual shape" of the transmitter, and where similar "shapes" can communicate by a nasty-complicated signal which looks like plain old thermal noise. Sounds more like Sympathetic Magic than physics, eh?

Here's an added thought (Dec 2005.) Throw a small bit of nonlinearity into both transmitter and receiver, and then the multi-peak transmitted spectrum will fill with Fractals (the waveform will become Deterministic Chaos rather than just narrowband noise.) And the transmitter and receiver will still lock together as the transmitted Chaos signal causes the receiver's own Chaos to become synched coherently. The transmitter and receiver would have to have the same nonlinear elements in the same spot in their circuits. Communication by synchronized chaos, eh?

If you think THAT's cool, then how about this: molecules which can sense each other at a distance. A programmable Van der Waals force.

Go back to the crystal radios: hang two identical crystal radios on the ends of long threads, then "illuminate" them with a transmitter. They will resonate and therefore oscillate strongly. But the AC magnetic field surrounding one crystal radio's inductor touches the other radio's inductor. When the two resonators are weakly coupled, their fields are identical in phase, so this will cause "DC" physical forces to arise between the floating radios. Do they attract each other? Repel? Repel first, then rotate until they start attracting? I'll have to try it and see. If they attract, then boy do I ever have something cool on my hands.

If the two crystal radios are pulled together, yet when they are detuned, the attraction force turns from DC to AC (and weakens or vanishes...) then we have an analogy for atomic bonding. Atomic bonding without covalent electron sharing?!!! We also have an electromagnetic analogy for stereochemical key/lock bonding in biological molecules, where the "key" is electromagnetically attracted by the "lock" from quite a distance away (from at least a quarter wavelength distance at the frequencies used,) but only if the tuned resonance is there. (Just how ARE those ribosomes able to pull in the T-RNA units to assemble proteins at a rate of hundreds of Hz? How do the ribosomes find the nuclear membrane pores? If the ribosome can electromagnetically yank in the next required amino acid, or navigate itself to a membrane pore a hundred nanometers away then it doesn't have to wait for diffusion to try all possible combinations of nearby "keys" in the waiting "lock."

In the above, by "resonance", I don't mean spectrum lines, I mean complicated spectrum bands, bands with identical hidden dynamical substructures; I mean the weird sort of resonance that occurs between two clusters of coupled oscillators which have identical patterns of internal resonance frequencies and coupling. It's an electromagnetic version of atomic bonding force, but where one molecule can yank in a desired distant molecule which has the matching spectrum-peak code. A radio transmitter which physically attracts distant radios, dragging them in, but only if they're tuned to receive the transmissions.

I just about soiled myself when this idea appeared in my head a few months back. :) But it was too big for my brain, so I forgot all about it until now. It's like trying to recall a dream upon waking.

Now visualise two clusters of identical coupled oscillators which are being illuminated by infrared thermal white noise from the environment. (At the nano-scale, this illumination might also be from quantum uncertainty, or basically the virtual particle flux which creates the Casmir force.) If the two distant groups of oscillators are in close proximity, closer than a quarter-wavelength, then the EM white noise will simultaneously "twang" both molecules in phase. As a result, their synchroniced AC fields will cause both clusters to pull upon each other (or perhaps push?) If these "oscillators" are actually the active sites of two separate biomolecules, then maybe I've just solved the great riddle of how the "keys" can find the "locks" over relatively great distances in biochemistry, find each other despite the immense jostling of thermal motion. The molecules are like crypto-coded AC electromagnet coils, where the complicated non-repeating fields vary in synch, and where the "electromagnets" attract each other only if the "codes" being broadcast by each "magnet" are identical.

Is this cool or what?!!! Hmmm, not enough exclamation points. Try !!!!!!!!!!! instead!! And not only could biology be using this for selective bonding as with ribosome operations, biology might also stumble upon it as a method for *communication* between distant molecules without needing any nerve-fiber cables. The "cables" would be invisible field couplings in the Casmir force or perhaps in the thermal infrared frequency band, like a wireless LAN network. Unbeknownst to anyone, proteins might be programmably attracting/repelling each other, or might form interacting electronic components. Perhaps globs of molecules might even function as room-temperature quantum computer arrays with an "invisible EM nervous system" connecting them. If this is true, then single cells or even biological tissues become like a "brain-stuff" made out of Cray Supercomputers, and maybe Amoebas and Paramecia and neuron-free plant life are all just as intelligent as flatworms, cockroaches and snails!!!!!!

Heh.

But maybe my dangling crystal radios always repel each other, and my analogy is all wrong. Maybe van der Waals force, though definitely long-range over 100s of nM scale, is just a boring feeble thing, and contains no hidden discoveries.

> The idea about photons not really existing except as waves is a fairly
> accurate conceptual tool though. 
> 
> I've actually seen a similar idea in solid-state physics:  The
> transmition of sound can be modelled by considering each atom to be a
> simple harmonic oscillator(like a pendulum) that is weakly connected to
> its neighbors.

Bingo! In classical physics, that's "flow of heat energy." In QM, it's "acoustic mode thermal radiation" (as opposed to IR light.) And modelling phonons as quantized acoustic frequencies is not conceptually different than ignoreing photons and instead seeing them as quantized IR light frequencies emitted by hot matter.

> If one atom has a certain amount of vibrational energy,  it will 
> transfer this energy to its neighbors in discrete units (this
> conclusion came from actual mathematical proof as opposed to idle
> speculation). For this reason, they coined the term "phonon" which is
> just the audio equivalent of a photon.  In one lecture I attended, the
> professor demonstrated this with an apparatus that consisted of a piece
> of string (streched horizontally between a couple of poles) from which
> he hung two pendulums. He pushed one to give it some energy and after a
> few seconds it (relatively)suddenly stopped as all of its energy was
> transferred to its neighbor. 

Yes! And then the energy in the neighbor goes back again. This gives a double-peaked spectrum, where the difference between the two frequency peaks is the same as the "sloshing" frequency of the energy going back and forth between the two penduluma. It's called "frequency splitting" in coupled oscillators, since pairs of widely separated (non-coupled) oscillators can share a single frequency, but closely-spaced oscillators cannot. Huh. Maybe the Pauli Exclusion principle is nothing but a renamed version of electromagnetic frequency splitting? (!!!!!!!!!!!) If two classical LCR oscillators approach each other so that their coupling increases, then two different energy levels arise like magic. If you have a group of coupled oscillators, they will form a collection of emission lines, a "frequency band" just like the electron levels and infrared spectra of solid matter. If they repel when close but attract when distant, then we even have a model for chemical bonds having a bonding distance predicted via calculation.

> I'm suprised that this example isn't given as an explanation of
> wave/particle duality in Q.M. especially since this concept is regularly
> applied in solid state physics. One professor I talked to seemed to see
> no difference between the reason for the "existence" of phonons and
> photons. I didn't quite believe it, though, until I read your article,
> since the normal way Q.M. is taught makes you think that photons are
> some sort of fundamental particle. 

That's it exactly. Many textbooks still teach us that photons are "real", as if photons were like tiny well-localized billiard balls. Their quantum-mechanical "unreality" is only applied in the more advanced classroom like a conceptual coat of paint. And it's not a student mistake, even the textbook authors and educators seem to mostly think in these "billiard ball" terms. But in fact, the physics is "nothing but paint" and there are no localized billiard balls underneath. Photons are not particles in the billiard-ball sense. They are quanta of Gauge fields.

> I've also seen the idea of atoms absorbing energy by emitting waves that
> partly cancelled out the incoming waves but the description in class was
> fairly confusing and not detailed enough to give an explanation for what
> caused the atoms to emmit the cancellation waves in the first place. 
>
> It was also stated that this was just the classical E.M. theory.  In
> fact, when I read you "energy suction" series I suddenly realized that I
> had never actually seen an official explanation of how atoms emit and
> absorb photons (this after being a physics major for 4 years!).  Sure
> they teach you how to calculate the absorbsion and emission
> lines(frequencies) but the actual process seemed to be taken as an
> axiom (the atom CAN emit and absorb at an energy, E (which means
> frequency E/h), therefore it DOES). One of these days I am going to
> corner a physics professor and not give up until I get a straight
> answer. 

Heh. Be careful. In rare cases that's the same as penetrating the psychological defenses of a lunatic. They'll erect their system of Denial. This might seem like paranoia, but my experience on various physics forums shows that even screaming rage should not be a suprise. All the stories about "backstabbing academic politics" are no joke. After years of hearing about such things, I got a chance to witness it first-hand. It really exists. Whenever academic reputation (and especially self-image) is concerned, the physics truth becomes very very secondary as compared to the need to silence any voice which threatens to shatter their whole carefully-cultivated conviction of self-importance. Once a person thinks that they're an expert, they have to attack any radical new ideas which call their expertise into question. The really new ideas can destroy careers, or even worse, can threaten a deeply held belief. Better find a HUMBLE physics teacher who still considers himself to be a "mere student." I've met some of the opposite type, the self-nominated experts. Steer carefully away from them. They're pure poison.

LINKS

• 50nM gold particles strongly absorb light, become hot
• Non-contact friction of STM probes enhanced by resonant atoms
• Coupled oscillators as source of gravity force
• Odd longrange forces in ultra-cold atoms
• L. Turin: A spectroscopic mechanism for primary olfactory reception (PDF) (1996)
• L. Turin: Structure-odor relations: a modern perspective
• L. Turin: A method for the calculation of odor character from molecular structure

(UPDATE 1/9/2001)
Jamie C. sends this:

BioEssays (Nov 2000) 22.11 pp1018-1023.  "Random walks and cell size",
Agutter PS and Wheatley DN
  "The belief that diffusion can explain many aspects of intracellular
   movement is no longer tenable, since classical (Fickian) diffusion
   theory cannot strictly apply to conditions withing the cell as we
   currently understand them. Yet simple diffusion is still often invoked,
   or frequently assumed, to explain intracellular transport ... The
   extensive evidence against the diffusion theory will be discussed here
   and an alternative viewpoint will be presented."

Diffusion Theory in Biology: A Relic of Mechanistic Materialism
Agutter, Malone, & Wheatley, 
Journal of the History of Biology 33: 71-111, 2000.
http://www.jodkowski.pl/prywata/Diffusion.pdf



Cytoplasmic Transport of Lipids
http://dickw.ucsf.edu/papers/CompBiochemPhysiol/Symposium.html




Cellular Microtransport Processes



The refs above are interesting because they show that for decades the 
biochem
community was wrongly assuming that biomolecules can find each other by
diffusion; just by trying all possible positions at a high rate.  This 
isn't true, and we now know that filaments in the cytoplasm act like an 
internal "railroad" for moving proteins around.  Therefore, if the 
existence of such 
a necessary "transport force" was unsuspected, then there could easily be 
many other exotic forces hiding within cells, forces which have always 
been ignored and dismissed as mere diffusion or uninteresting VanderWaals
effeccts.