Molecular Creation (logo) A Story of Natural Molecular Evolution from Atoms and Water to the living Cell



Until recently, the paradox between Biochemical Evolution and the Second Law of Thermodynamics has had no viable explanation. However, recent studies have completely changed our concepts of the structural and structuring properties of water and the way in which it most likely drove and directed the evolution of natural molecules.

Based on current concepts, each water molecule in the liquid state is hydrogen-bonded to three or four other molecules by dynamic point-charge attachments to form coordinated clusters.5 Bonding is weak (1.3 to 2.8 kcal./mole relative to the gaseous state) and involves rapid exchanges between the molecules.5 However, recent neutron irradiation studies indicate that, at any instant, linear trimers form spontaneously with two water molecules more-firmly hydrogen-bonded to a central molecule.12 The trimer is unstable, lasts only about 10-12 seconds (a million millionth of a second)13 and, in contrast to most molecules in liquid water, is tied together by “covalent” hydrogen bonds with electron clouds enveloping a central proton - the same as in ice.6 Since the energy of the covalent bond is 4 to 5 kcal./mole lower than the point-charge bond,6 trimers lose 8 to 10 kcal./mole of energy as they form and absorb similar units of quantized energy as each spins and moves back into point-charge bonding.9,10 This energy exchange is important because it corresponds to that of the terminal phosphate bond of the adenosine triphosphate molecule which provides the energy for most processes in the living cells.

The same trimer and a linear tetramer form on the surface of water at 25oC with terminal oxygen atoms of the trimer 4.5 Angstroms apart (6.8A for the tetramer) - 2.76A between adjacent oxygen atoms.14 Most of the molecules are 2.9A apart, far enough to permit rotation but close enough to form point-charge bonding. Although the high surface tension of water may be due primarily to integrated point-charge hydrogen bonding, repetitive trimer and tetramer formation may contribute as well.

On hydrophobic non-hydrogen-bonding surfaces of polypeptides and proteins15 as well as on hydrocarbon molecules like those in gasoline and oil,16 molecular orbital calculations and NMR analyses indicate that five or six molecules of water kinetically bond together to form short linear elements of hydration.7 Although they do not last long enough to establish thermodynamic equilibria (10-12  to 10-10 seconds),13 they form so repetitively in in the same orientations on surfaces9 that, when integrated over-time, it is as if the surfaces are coated by layers of hexagonally-bonded water molecules – like those in ice.8

In fact, as each covalent bond forms between water molecules on a hydrocarbon surface, it loses 4 to 5 kcal/mole of energy to adjacent water molecules, the same as in trimers.6 However, as these covalent bonds break and water molecules rotate and move back into point-charge-bonding,9 similar units of quantized energy are absorbed from the hydrocarbon molecules17 and they are moved from randomness toward order. Thus, as small water molecules oscillate rapidly back and forth between two types of hydrogen-bonding on hydration-ordering surfaces, energy moves unidirectionally from more massive, slower-moving hydrocarbon molecules to transform them from multiple options of motion toward coordinated order.17,18 By conforming to the Second Law of Thermodynamics and moving spontaneously from order toward disorder, surface water absorbs energy from hydration-ordering surfaces and moves molecules within those surfaces from high-energy and high entropy to lower-energy and higher order, just as Schrodinger proposed.1

The same reversal in thermodynamics drives the spontaneous assembly of proteins in living cells.8 As polypeptides are released from ribosomes, transient covalent linear elements of hydration, which form adjacent to series of peptides with hydrocarbon side-chains, remove energy from those peptides and transform them into coils and sheets. As surface water moves from its unstable covalent state to its more dynamic higher-energy point-charge state, free-energy is removed from polypeptides and they move toward order. By forming and degrading rapidly in particular orientations on polypeptide surfaces, covalent linear elements of hydration not only drive polypeptide folding and assembly but, most likely, assist in directing assembly as well.7,8

Thus, as proteins form, most peptides with hydrocarbon side chains are left inside forming an anhydrous core while most small water-binding peptides, like glycine and serine, are left on the outside increasing stability and solubility. However, some hydration-ordering regions remain on surfaces of proteins to permit associations with other proteins, to complex with substrates for reactions and with regulator molecules to activate functions. Since water in covalent states must bind within those ordering regions in their unstable open states, it should come as no surprise that the dimensions of neurotransmitter and hormone molecules correspond to mean dimensions of linear elements of hydration.11 Thus, as primordial polypeptides began to form, covalent linear elements of hydration which formed in surface water and confined spaces might well have played a critical role, not only in forming stable functional proteins, but in the selection of the small natural molecules as neurotransmitters, hormones and vitamines.11

Based on the hypothesis that dielectric transient linear elements of hydration form between ions and molecules,7 it is those linear elements which provide for quantized integrated of motion between the tremendous variety of molecules within living cells. In fact, it was recently reported that the spin of protons in water molecules, at significant distances apart, couple them together in a Quantum Mechanical process called “entanglement”.19 Entanglement coupling is so rapid (10-15 seconds) that it is independent of time and space. (Einstein called the state “spooky.”) In fact, it may be that entanglement between remotely-ordered water molecules may tie our bodies together as one gigantic molecule. Hydrating elements of mean lengths may provide for local energy exchange while entanglement may provide for quantized long-range communication.8,11,19 In fact, it may be that it is the integration of entanglement waves within our brains which provide for consciousness, thought and extra-sensory perception.

If Dr. Schrodinger had been informed of these properties of water, he would have said they should have been expected – protons in water are like electrons in metal – they are sub-atomic entities which should exhibit both wave and particle properties.20 Protons in water provide the same property of energy exchange as electrons in a wire, except that water molecules in the liquid state have more freedom to align between charge centers than orbital electrons in solid-state systems.11 Although conduction of charge by protons through water requires transient linearization, anionic phosphates on the heads of phospholipid molecules which form the inner walls of myelinated nerve fibers are the same distances apart as trimers.11,12 As high charge potentials develop between nerve endings and nodes during depolarizations, water most likely aligns along the inner walls to permit proton pulses to pass through at almost super-conductive speeds with very little resistance.21 If our nerves were filled with metal rather than water, we would be combusted by the resistance. Nanotechnology today is searching for superconductivity in electrons - nature may have already found it in protons.

The question is: “When is the scientific field going to acknowledge that biological systems, based on protons and ions in water, assemble spontaneously and function far more efficiently than electrons in solid-state systems?” “When are they going to realize that it was water, as quantized transient linear elements of hydration on surfaces and between charge centers, which drove and directed the formation and selection of diverse sets of molecules which could function in such an integrated and harmonious fashion that they could spontaneously assemble and produce the living cell?”29

Sunlight provided the energy to tie atoms together as biomolecular evolution began, but it was the kinetic, thermodynamic and hydrolytic properties of surface water, along with internal bonding energy between atoms, that defined which ones would be stable, which ones would spontaneously form functional complexes and which ones would be torn apart hydrolytically by surface water.18 If we look closely at the surfaces of molecules which compose living cells, we find that each one has a unique spatial distribution of ionic, polar and non-polar groups to regulate the orientation and degree of order in surface hydration.11,29 Spectroscopic, NMR and crystallographic studies of fully-hydrated polysaccharides, nucleic acids, collagen and muscle, as far back as the 1970’s, supported the view that water adopts preferred orientations and distances on surfaces7,15 and, as pointed out above, studies now support the view that it may be the protons in water molecules within living cells which may tie all parts together in almost instant communication.

However, the first vital molecules to be produced on earth most likely were not amino acids or fatty acids but formaldehyde (CH2O). For, if formaldehyde is dissolved in water containing calcium hydroxide and cyanide ions, its molecules spontaneously couple together to form a complex mixture of sugars with the formula (CH2O)X22 with glucose, (CH2O)6, as one of the most stable molecules.23 In fact, the same reaction is utilized catalytically in plants today to convert carbon dioxide into formaldehyde and then into glucose.24 Thus, glucose, as the carbon and spatial analog of the hexagonal form of water, (H20)6, is one of the most abundant molecules on the earth and may have been one of the most abundant when molecular evolution began.18,29

As you read what follows, you will be amazed, not only by correlations in spatial properties between natural molecules and transiently-ordered elements of surface water, but that even the most complex molecular systems, like ribosomes, which contain huge nucleic acids and numerous proteins, assemble spontaneously and perform their functions with extreme precision as long as they are in unadulterated ionic water. In fact, the same property of covalent linearization in surface water which assisted in bringing forth those molecules in the beginning, continues to provide for the incredible phenomenon we know as life. As you continue reading, you will realize that water is, indeed, “The Matrix and Mother of Life”25 and each living cell “A Miraculous Molecular Creation.”29

If you would like more information with regard to the possible role of water in the formation of proteins, the binding of regulator molecules in receptor sites or the stabilization of double Helix DNA, check out or

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