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The quantum foundations of life.

The great debates that swirl around the nature of life and its evolution are couched in the basic concepts of classical physics such as solid matter and spatial separation.

The quantum revolution in the basic sciences, however, has firmly established that such classical concepts are wrong, they are at best useful approximations to how the real world functions beneath appearances.

Material objects are made of atoms. In the classical approximation, atoms are treated as tiny solid objects that stick together in chemical combinations. Such molecules are themselves are treated as extended solids which, like a lock and key, can fit together surface to surface.

At the foundations of life are macromolecules, such as protein, that involve thousands of atoms in long linear chains. In the classical view, such a macromolecule is a tiny solid rather like a lumpy rope.

This classical view of an extended amino acid chain suggests that for the amino acids A and Z to get together, they are going to have to bodily move through space--dragging the chain to which they are attached behind them--in order to meet up and lock-and-key together.

All of the proteins of life are generated in such an extended state as they reel off their natal ribosome. The next step is for this rope to fold up in the active form and arrange the layer of water molecules surrounding it into an ice-like capsule that almost completely surrounds the protein. The little patch that remains ice-free after folding is called the active site, and it is this patch that determines what role the mature folded protein plays in the cell.

As with egg white protein, high temperature can blast apart a properly folded protein back into the extended state; it is denatured. Unlike egg white, however, many protein enzymes are reversibly denatured; when cooled the enzyme active reappears as the chain refolds and assembles its water coat about it in the precise and correct form.

The folded shape and the resultant active site are very precise. It is exactly the same for each type of protein. In our example, A has to end up next to Z for the chain to end up as the active enzyme. In the classical view of the amino acid chain as a solid rope, it naturally takes time for amino acid A to move around and find its proper position at amino acid Z.

Classical concepts of solids, spatial separations and thermal movement suggest that it should take a billion years or so for a single chain to find the correct configuration as the solution cools. (The mathematical treatment of this appears under the rather cute name of the "traveling salesman" problem.) This is a situation where the incorrect, if occasionally useful, concepts of classical physics lead us totally astray: the folding occurs on a timescale of fractions of a second as trillions of enzyme molecules correctly refold into the active enzyme as the solution cools.

Such an off-the-mark classical prediction is similar to the classical expectation that the electron in a hydrogen atom should fall onto to the proton; that atoms should be 1/100,000,000,000,000 the size they are actually observed to be.

Quantum atom

In order to solve this disparity between prediction and reality we have to understand what atoms actually are. As we shall see, in the quantum description of reality, atoms are nothing like little sticky solid balls and amino acid chains are nothing like little solid ropes.

There are two types of fundamental particles involved, the fermions and the bosons (see my earlier article on quantum probability: "Inside the Quantum Atom Revolution," May 2006, Article #25025). Fermions are (relatively) permanent, and they interact with each other by exchanging ephemeral bosons. They do this in a complex quantum probability form that inhabits an abstract, mathematical space with an extension in the external world as a real probability.

A proton, for instance, involves three fermion-quarks embedded in a whole mess of exchanged boson-gluons taking up the external (real number) probability form of the internal (complex number) quantum probability form. This color interaction, as it is called, is very intense. It is actually the energy in this drop of gluon fluid that gives a proton--and hence the atom--almost all its heft and mass. The "naked" quarks like the electrons, having a mass just 1/2000 that of the proton's.

In a cold, ground state hydrogen atom, the three quarks embedded in this tiny drop of QPF-shaped gluon fluid (with an astonishing energy density of about 100,000,000 tons per cubic inch) also exchange bosons with the atomic electron, the virtual photons of light underlying the electromagnetic interaction. The quarks, gluons, electron and photons take up the external probability form of the internal QPF called the 1s orbital. The energy in this photon field is minuscule compared to that of the color field in the range 1/100,000 the mass of an electron. This is the realm of energy involved in chemical change (think dynamite) as compared to the energy involved in nuclear change (think hydrogen bomb).

Note that this diagram is decidedly not to scale. Magnify the spatial extension of the electron and bare quark to the size of a dust mote. The gluons have a much larger wavelength and, on this scale, the external extension of the proton QPF-shaped quarks-in-gluon-drop would be Yankee Stadium-sized. The QPF-shaped electron-in-photon drop is now the size of the entire earth. (This is why the diagram cannot be to scale.)

So, this is the new picture of the atom. The electron quantum jumps to a new probable position, stays a few quantum ticks and couples a few photons with the far distant quarks, quantum jumps to a new probable position, couples, jumps, etc. It does this incessantly, zillions of times a second. From our slow-time perspective, the electron seems smeared out to fill in the (real) probability form of the (complex) QPF 1s orbital.

It is this smearing out, on our time scale, that makes the atom behave on occasions like a little solid ball; but it is not. A familiar example of this is the air we breathe. It seems like a smooth gas to our senses, but the reality is quite different (even in the classical view). The molecules of air are so far apart that they rarely collide; they move so fast that they bounce back and forth between the walls of a room one hundred times a second. Trillions of these little projectiles bombard us each moment, but our senses smear them all out and we perceive a gas with a gentle pressure that flows smoothly in and out of our lungs.

The 1s orbital is just shape that the internal QPF has, it also has a variety of excited states where the shapes can look like inflated petals or doughnuts. The electron in such a state, however, will quickly spit out a real photon of light and quantum jump back to the ground state. The energy of such photons make up the absorption/emission lines in the characteristic spectrum of an atom.

For an atom like hydrogen, such a quantum spectrum is to be found in the visible and ultra-violet range.

Quantum molecules

When atoms covalently link up to form molecules, the internal molecular orbital QPF is now reflected in the external form of the molecule. Just as in the atom, this quantum probability form is expressed in the history of the electrons (now in pairs), the photons and the quarks confined in their gluon drops. We are still talking dust motes flitting about an earth-sized molecule getting smeared out over time and appearing as solid molecules on familiar time scales. But a molecule is no more solid, really, than an atom.

It should be quite apparent, at this point, that the lock-and-key classical concept of molecules fitting their surfaces together is just an occasionally useful approximation.

Just as the case with atomic orbitals, the shape of a ground state molecular orbital is highly specific in shape and size. The two atoms of hydrogen make an exact angle, an open triangle with the electron-hugging oxygen atom in the center.

The molecular QPF also has more complex and higher-energy states. For most molecules at room temperature, the changes involve the quark-gluon droplet atomic nuclei as they oscillate and vibrate in relationship to each other. The nuclei jump from such excited states to the lowest energy state available (in quantum terms, the state of least action and highest probability), in this case emitting and absorbing photons in the microwave region.

The photosynthesis that powers all plant and animal life is stripped of all detail, a clever way of capturing the energy of a pair of electrons kicked into an excited QPF at the far end of a chlorophyll molecule by a red photon of light. Before the electron pair can jump back by emitting a red photon, they are redirected into QPF chute that captures the energy jump as a high-energy ATP bond instead. A very useful quantum phenomenon.

Water and other "polar" molecules also connect up with each other using the hydrogen bond where the internal QPF spans both molecules with a proton in the center that belongs to both molecules at the same time.

Quantum macromolecules

We are now in a position to state just what quantum science has to say about something as large as a protein. No new principles are involved, just the number of participants. An extended amino acid chain and the water molecules H-bonded to it are just as above, a QPF being filled in by quarks, gluons, electrons and photons.

Now you might think the electrons and quarks in amino acid A at one end of the extended chain would inhabit a different QPF to the ones at the other. Nevertheless, you would be wrong. For one of the most basic aspects of internal quantum probability is that it is not limited by time and space considerations.

The experimentally verified phenomenon of entanglement illustrates such distain by quantum probability for spatial separation:
   This bizarre quantum connection isn't mediated by fields of force
   such as gravity or electromagnetism. It doesn't weaken as the
   particles move apart because it actually doesn't stretch across
   space. As far as entanglement is concerned, it is as if the
   particles were just right next to each other; the effect is as
   potent at a million light years as it is at millimeters. And because
   the [quantum probability] link operates outside of space, it also
   operates outside time. What happens at A is immediately known at B.
   No wonder Einstein used words such as "spooky" and "telepathic" to
   describe--and deride--it. ("Teleportation," p. 93.)


If a QPF has no problem spanning ten million light years it clearly will not be a problem for it to span the millimicrometers from one end of an extended amino acid chain to the other.

The multitude of electrons and quarks in the extended amino acid chain and associated water inhabit the same QPF; they are quite capable of jumping the considerable distances from one end of the chain to the other, if it's a quantum probable thing to do.

The extended chain is in a high-energy state (mainly by its disruption of the water structure around it.) The electrons and quarks jump from this high-energy state to the ground state. There is no movement of matter involved, no chains to drag around, no solid water molecules to shove aside; the quarks and electrons just jump from one configuration to the ground state; the correctly-folded mature protein with its partial ice capsule. Note that it is impossible to state that an electron that was in amino acid A in the extended state ends up in A in the folded state. They all just jump from an improbable state to most probable state; very little actual movement is involved.

The excited state has a very short lifetime and so that extended chain jumps to the active form very rapidly. While the classical prediction involves billions of years, the quantum perspective predicts rapid folding which accords with observations.

The energy differences are in the microwave region. So, we can predict that a folding chain should emit microwaves of a specific wavelength, a line spectrum, when folding, and be excited to a denatured state when the appropriate photon appears on the scene. This will have to remain in the realm of prediction, as I cannot find any reference to the blackbody radiation spectrum of folding simple proteins as the temperature falls below the renaturation temperature.

A similar argument holds for catalytic activity and the base-pair alignment so crucial to the functioning of RNA and DNA; all key molecules at the very foundations of life and its evolution. I shall explore this next level of quantum science in an essay on quantum bacteria.

Learn more about quantum physics by visiting The World & I Online archives:

--"Inside the Quantum Atom Revolution," by Richard Llewellyn Lewis, May 2006 (Article # 25025).

--"Can an Electron be in Two Places at the Same Time?" by the Max Planck Society, January 2006 (Article #24806).

--"Coherence in an Incoherent World," book review by Richard Lewis, August 2001 (Article #21168).

Richard LLewellyn Lewis, PhD

Richard LLewellyn Lewis, who holds a doctorate in biochemistry, is a freelance author based in New York City.
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Title Annotation:proteins
Author:Lewis, Richard LLewellyn
Publication:World and I
Geographic Code:1USA
Date:Jun 1, 2006
Words:2226
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