Molecular Creation by J.C. Collins PhD_Rev8-2011

8/6/2019 Molecular Creation by J.C. Collins PhD_Rev8-2011

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MOLECULAR PRESENTATIONS

178 West Shore Drive, Valatie, NY 12184

[email protected]

A STORY OF MOLECULAR EVOLUTION

Dedicated to the late Dr. Stanley J. MooreVisit www.linearwater.com for background and references.

FROM ATOMS TO THE LIVING CELL

J. C. Collins, PhD


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Dr. Collins received his degrees in Chemistry from Wayne University

The Author:

in Michigan and the University of Wisconsin. After employmentat General Motors Research, E. I. Dupont and Sterling Drug, heaccepted a position at I lli nois Wesley an Univ ersi ty as Chairmanof the Chemistry Department and Associat e Profes sor. I n 1967,he returned to Sterling Drug to direct drug research at SterlingWinthrop Research Institute until l987 when he retired to devotefull time to his driving interest in the role of water in the livingcell. He has a number of publications and patents to his creditand has had a synthetic organic reagent The Collins Rea gentnamed after him. However, natural molecular shape and cellularhydration have been his primary interests for many years. In thisshort treatise, he provides a pictorial view ofhow the dynamicl inearizing properties of water molecules might well havedirected the formation of natural moleculesto those which could function harmoniously

and spontaneously together to produce

living cells.

Strange as it may seem, this work has beenplaced on the Internet for your enjoyment.Download it if you like and share it with whom-ever you like. My only desire, is that you enjoy it.

Questions and comments can be addressed to the

W e b S i t e s :

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I l l u s t r a t i o n s w e r e d e v e l o p e d o nA p p l e M a c i n t o s h a n d D e l l c o m -p u t e r s u s i n g A d o b e I l l u s t r a t o r .D a t a f o r s t r u c u r a l a n a l y s e s a n dt h e p r e p a r a t i o n o f d r a w i n g s w e r eo b t a i n e d f r o m t h e p u b l i s h e d l i t e r -a t u r e . C u s t o m p h y s i c a l mode l -b u i l d i n g w a s p e r f o r m e d p r i m a r i l yw i t h F r a m e w o r k m o l e c u l a r m o d e lp a r t s ( P r e n t i c e H a l l , E n g l e w o o dC l i s , N J 0 7 6 3 2 ) .

Q u a n t i z e d S p a t i a l C o n t r o l W i t h i n L i v i n g C e l l s

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H y d r a t i o n Q u a n t i z a t i o n o f R e c e p t o r B i n d i n g S i t e s

w w w . m o l e c u l a r c r e a t i o n . c o m

A C r e a t i o n S t o r y f r o m A t o m s t o t h e L i v i n g C e l l

A C r e a t i o n S t o r y f r o m A t o m s t o t h e L i v i n g C e l l

author at molepres2000@aol .com

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Sixth years ago, a little book appeared which helped to ch ange the course of biochemic

with James Watson in constructing the model for DNA in 1953, credits the book with givin

him the idea that DNA might be the molecule. But, within that book, Dr. Schrodinger als

pointed out that liquid water, as the environment in which the development of vital molecul

ook place, reversed the laws of physics. Based on the second law of thermodynamics, molecul

ystems should move spontaneously from order to disorder but natural molecular developmen

history and, with a recent discovery, may help to change it once again. In 1944, Erwi

Schrodinger, one of the fathers of quantum mechanics, wrote in What is Life? that the genet

nformation for reproduction is within a molecule in living cells. Francis Crick, who collaborat

has moved from extremely simple forms, like formadehyde and methane, to proteins and biomembran

The purpose of the story which follows is to provide the reader, whether experienced in th

ield of chemistry or not, with a pictorial view of how this incredible phenomenon w

call life could have been produced spontaneously from the simple molecules whicarrived on the early earth. Of course, the probability that these natural molecules could hav

formed spontaneously in the air around us is zero. However, it most likely occurred in liqu

water in which linear segments of water molecules continually form adjacent to surface

As you read what follows, you will be amazed how the bondin g properties of wate

molecules and each type of atom set in motion the spontaneous formation of the molecula

omponents of life. In other words, the omega was defined by the alpha: if life should ceas

oday and the conditions which brought it forth are here tomorrow, it will begin again.

which are so complex and function with such incredible efficency that they may never be fully understoo

PrefaceFrom Atoms to the Living CellMolecular Evolution


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Forty years ago, in an ex tensive molecular model-building program, the dimensions of

aqueous environment in which they had evolved.

Since water molecules were known to form linear, hydrogen-bonded elements adjacent

o surfaces, a proposal was presented at the American Chemical Society Meeting in Toronto Canada

n 1993 that spatial order within living cells and spaces within receptor sites might be defined

by transient linear elements of water molecules. However, little or no evidence was available for

regulator molecules, like hormones and neurotransmitters, were found to mimic linear

hydrogen-bonded segments of water molecules. At first, it seemed that the correlations

were simply a coincidence, but, as even more correlations were noted, including lipids and proteins,

t appeared that natural molecules might simply be spatial a nalogs of ordered units of the

he existance of linear elements in liquid water and limited information was available on the structures

of binding sites, so the proposals were rejected as pure speculation.

books and three web sites were presented to promote the concept of Transient Linear Hydration.Based on recently-published evidence that the molecules of liquid water do, in fact

exhibit quantum mechanical properties and that dynamic linear elements continually form

adjacent to surfaces thousands of times more rapidly than the movement of the molecules, the

hree web sites have been modified to incorporate this corroborating evidence for the Hypothesis

Hopefullythis articl e will permit you to see how water, in providing order around natural molecules as

hey evolved, produced sets of molecules which could perform harmoniously in that order. Actually, it

In spite of that rejection and the rejection of multiple submissions to scientific journals, two

Introductionfrom Atoms to the Living CellA Story of Molecular Evolution

was Erwin Schrodinger who proposed that water provides spatial order in living cells back in 1944.


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Atoms, Molecules and Water

Based on astronomical studies, it is believed that space within the emerging universe

contained hydrogen nuclei (protons) with a mass of 1 and a charge of +1 and electrons

with little or no mass and a charge of -1. As oppositely-charged entities, they combined

to form hydrogen atoms with the negative electron circling the proton. But the electronnot only circles the proton, it spins around its own axis and, in spinning, generates a

magnetic field. To neutralize that field, electrons form pairs and bond two hydrogenatoms together to form the hydrogen molecule, H2.

Atoms of the other elements appear to have been formed by the fusion of hydrogen nucleiin the stars. In these nuclear fusions, a small portion of the mass of the proton was

converted into energy to fuel the stellar furnace. However, as the store of hydrogen in thestars declined, they began to decrease in size. Remaining hydrogen, helium and othernuclei became compressed with such incredible forces that massive, nuclear fusion events

occurred. Small nuclei were compressed together in an instant to form heavier nuclei, like

oxygen, nitrogen and iron, which were discharged into space to combine with electrons to

yield new atoms and then new molecules, like oxygen, O2, nitrogen, N2 and water, H2O.


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Of all the molecules produced in these celestial explosions, those of water possessed the

unique structural feature of bonding two positively-charged hydrogen atoms at two

corners while leaving two negatively-charged electron pairs at the other two corners.

To neutralize surface charges, these small polarized units behaved like spinning magnets

which spontaneously aligned together and then hydrogen-bonded together to form shortlinear segments.


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As these short segments soared through space, additional water molecules hydrogen-

bonded to the ends to extend the chains, then bonded to the sides to form two-

dimensional, hexagonal forms and then to the other side to produce three-dimensionallattices of solid ice - all composed of linearly, hydrogen-bonded water molecules. But

the ice lattices which formed in space were not the same as those which form on earth.

As snowflakes form in the upper atmosphere at temperatures of 60 degrees below zero,water molecules assemble as linear elements - the same as they did in outer space.

However, as the snowflakes fall to earth, the water molecules gain sufficient energy to

rearrange and produce the spatial form of ice with which we are more familiar hexagonal. In this form, molecules in the horizontal planes are still in linear elements,

but they have rearranged diagonally to position the hexagonal units above each other. The

rearrangement increases the overall thermodynamic stability of the water moleculesrelative to each other but, at the same time, disrupts linearity in the vertical planes.


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LIQUID WATER

Classically, the term Hydrogen Bond, has been used to explain why water has suchhigh melting and boiling points relative to other substances. For example, each water

molecule in liquid water often is viewed as being hydrogen-bonded to three or four other

water molecules and compared with methane molecules, CH4, which have about the samesize and mass (or weight) but essentially no surface charge.

The difference in attraction between molecules in water and those in methane, as

displayed by the boiling points above, is spectacular: 470 degrees F (243 degrees C).

Usually, this is attributed to the hydrogen-bonding of three or four water moleculesaround a central water molecule, as shown above. However, recent studies at the

Stanford Linear Accelerator Center provide evidence that, at any instant, each watermolecule in liquid water is hydrogen-bonded to a maximum of two water molecules toform a short linear triplet. High-speed infrared spectroscopy supports the view that a

maximum of three water molecules are hydrogen-bond together at any instant in liquid

water.

It is important to realize that, even though these high-speed techniques illustrate that thistype of linear triplet forms in liquid water, it lasts for less than a billionth of a second,

about 10-12

seconds; then the molecules return to separate, random, spinning forms which

are held together by their polarity - by the opposite charges on their surfaces - not by

specific hydrogen bonds.


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However, our concept of the structural and structuring nature of liquid water has changed

dramatically over the past few years. In 2003, Professor Chatzidimitriou-Driesmann and

his group in Germany reported that only 1.5 protons were scattered per water moleculerather 2 when pure liquid water was irradiated with ultra high speed neutrons at 10

-18

seconds. The result indicated, not only that the spins on the two protons on water

molecules couple but spins on neighboring water molecules couple to produce quantizedentanglement waves. Since these waves form at speeds of about 10-15

seconds,

thousands of times more rapidly than the movement of molecules dissolved in water,

linear ordering is continually being expressed on their surfaces. Thus, it appears that

three types of structuring exist in liquid water: 1) water molecules are continually drawninto lines by polarity, 2) they form short hydrogen-bonded units which last about 10

-12

seconds and 3) they form proton-coupled linear waves which last about 10-15

seconds.

INTERFACIAL WATER

Of course, at the interface with air, water molecules are stopped by impact - energy of

motion and rotation is momentarily lost and they are held side by side long enough to be

drawn together and aligned to form even more triplets and slightly longer linear elements,like they do in the upper atmosphere.

In 1972, Drs. Narten and Levy deflected X-rays off the surface of pure water and used thediffraction pattern produced to determine the structural character of water molecules at

the air/water interface. As illustrated above, most of the water molecules on the surface

are about 2.9 angstroms apart but short hydrogen-bonded units involving three and fourmolecules also are present. Since a much smaller number of these ordered units exist at

any instant and the distances between molecules on the ends vary as much as 0.4

angstroms, the peaks are much smaller and wider. Thus, even though water molecules atthe air/water interface form a multitude of short, transient, one-dimensional segments of

hydrogen-bonded molecules, there is little evidence that two-dimensional, hexagonalforms, like those present in ice, are formed. For example, pure liquid water in cleancontainer can be supercooled well below the freezing point of 0

oC (32

oF) without

crystallizing to form ice. However, if iodine crystals, with iodine molecules on their

surfaces in the same positions as water molecules in ice, are placed in contact with

supercooled water, ice forms immediately. If iodine crystals are in contact with water,supercooling is impossible. Substances with surface atoms in the same hexagonal

positions as water molecules in the surface of ice serve as seeds for ice formation.


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The same type of two-dimensional seeding occurs if gasoline or oil is placed on the

surface of water. Supercooling is impossible because liquid hydrocarbon molecules incontact with water molecules assemble in the same hexagonal arrangement as the iodine

molecules in solid iodine. As shown below, hydrocarbon molecules in contact with water

assemble side-by-side and spin around their axes - they can exchange positions but arerestricted from rotating end-over-end. At the same time, water molecules are restricted in

their motion by continually being drawn into linear and hexagonal bonding relationships.

The surface of water is smoothed and calmed by this increase in strength of hydrogen-

bonding and by the formation of transient elements oflinear and hexagonal order.However, the molecules have too much energy to be held in these ordered forms for verylong they want to be free. Thus, ordered arrangements last for only about 10

-9

seconds and then the molecules return to their rotating, spinning forms and others take

their place as transiently-ordered units. In fact, hydrocarbon and water moleculesspontaneously move away from each other to minimize contact and increase their

freedom of motion; to increase Entropy, so they can move and spin more freely. Two

simple little experiments demonstrate this Second Law of Thermodynamics. If oil andwater are mixed rapidly, small droplets form. However, if the mixture is permitted to

stand, the droplets coalesce into a single layer the liquids move spontaneously to

minimize the contact intersurface between oil and water molecules.

If water is placed on an oil or wax surface, it forms balls, once again, to minimize two-

dimensional order between water and hydrocarbon in favor of contact with air.


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Paradoxically, it was this spontaneous movement of water and hydrocarbon molecules

away from each other to reduce two-dimensional order and increase freedom that drovethe development of natural molecules to ever-increasing levels of higher order. As you

will see when we view the spatial structures of natural molecules, it is the distribution and

nature of atoms on each surface which defines the degree and orientation of linear orderin water on those surfaces. Just as the hydrocarbon molecules in oil spontaneously move

away from contact with ordering water in favor of associations with their own kind,

water-ordering (hydrophobic) surfaces on molecules, such as polypeptides, spontaneously

assemble side-by-side to permit water to leave. As water-ordering regions assemble to produce the internal regions of natural molecules, water-ordering regions on external

surfaces continue to influence the orientation of surface water to integrate motions and

interactions with other molecules.

For example, the insulin molecule shown below is produced from a single linear strand of

polypeptide which spontaneously wraps into linear coiled segments with water-ordering

and disordering regions on their surfaces. By spontaneously fitting the ordering regionsof the coils together to release water, a finished molecule is produced with an external

geometry which continues to permit transient linear elements of water to form on its

surfaces. It is these transient linear surface elements which regulate its interactions withregions of water-ordering on molecules and membranes around it.

Although external surfaces of finished insulin molecules have enough water-disorderinggroups to provide for water solubility, they still have enough ordering regions to permitsurface water to form structure-stabilizing linear elements and guide it into

complimentary-ordered regions in membranal proteins to regulate glucose uptake. Thus,

as molecules were produced at random during the early phases of molecule formation,spontaneous assembly produced sets of molecules with unique functions. A molecular

world was produced in which surface water provided for spatial control and in which

movement in one molecule was instantly communicated to others by protonentanglement. It was a world in which the rules of spontaneity were reversed: random

small molecules assembled, utilizing energy from the sun, to produce more complex

molecular systems. Molecular surfaces and adjacent linearizing water operatedsymbiotically to produce the phenomenon we call life.


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IONS AND PROTONIC CHARGE

However, there was another property of atoms which played a critical role in theassembly of molecules and the development of living cells. When sodium atoms come in

contact with chlorine atoms, the lone electron on sodium moves into the open orbital of

chlorine to form a pair the sodium atom becomes a positively chargedsodium ion

; thechlorine becomes a negatively charged chlorine ion.

In the solid crystalline form of salt, sodium and chloride ions are in a ridged lattice but, asthey dissolve in water, both ions become surrounded by water molecules to delocalize

their charge.

In this way, surrounding water molecules accept part of the positive charge of the sodiumion and those around the chloride ion, part of its negative charge. In fact, small ions like

sodium tightly bind four or six water molecules around them and have several additionallayers of water molecules more loosely bond in a spherical form. However, even though

these hydrating water molecules accept a portion of the charge on the ions, their positive

and negative charges are so strong that they continually draw a finite number of spinning,polarized water molecules between them.

If the ions are far apart, water molecules between them simply orient their spins to help

neutralize the charge. However, the strong opposite charges on the ions continually draw

water molecules within hydrogen-bonding distances from each other.


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When this happens, a unique type ofcharge-transfer reaction occurs in the triplets.

In liquid water, the small, positively-charged, proton nucleus of a hydrogen atom on one

water molecule moves into the electron pair lobe of the adjacent molecule. This convertsthe acceptor molecule into a positively-charged hydronium ion and leaves the donor as a

negatively-charged hydroxide ion. In pure water, only about one in a million molecules

undergoes this spontaneous ionization reaction at any instant, but in water containingions like sodium and chloride, it is another mechanism by which the charge potentials on

ions and molecules are minimized and neutralized.

By transferring protons from one hydrogen-bonded water molecule to the next, incascade fashion, water molecules bound to each ion can assume an opposite charge and

provide even broader, spatial distribution and neutralization of the charge. Although the

process appears complex, proton pulses continually resonant as quantized waves backand forth between the ions. By the above mechanisms, about 90% of the charge on ions

is transferred to water.

Since ionization in pure water is extremely low, it is an insulator, but sea water, like

water within cells, is a good conductor because it contains about 3% sodium chloride. At

low external voltages, current is carried through salt water primarily by the ions but, if

the voltage is high enough, water molecules align between the ions and pulses aretransferred like lightening bolts by protons cascading through polarized linear segments

of water molecules from one ionic center to the next. In the axons of nerve fibers, thislinear transfer of protonic charge along the inner surfaces of the membranes permitsextremely rapid, almost superconductive transfer of positive pulse.


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Just as the assembly of polypeptides, based on the association of water ordering surfaces,

played a critical role in the production of early proteins, the linear conduction of charge

between ions and charges on surfaces played a vital role in the early development offunctional nucleic acids as well. Although the small RNA molecule pictured above has no

lipid-ordering surfaces like those in the insulin molecule, strong internal hydrogen-bonds

hold the molecule in a geometric form that, once again, permits dynamic linearization of

water on its surfaces. In this case, transient linear elements serve the vital role oftransmitting the high negative charge on its surfaces to positive ions, like sodium and

calcium, around it. Once again, the internal coiled segments, as they packed together tooptimize hydrogen-bonding, produced a molecule with external geometry which

permitted transient linear elements of water molecules to stabilize the structure and

provide for spontaneous assembly and function on the water-ordering surfaces of huge

ribosomal molecules which produce genetically-coded polypeptides.

Thus, in the early formation of natural molecules, it was energy from the sun which tied

small molecules together to produce large complexes but it was the transient linearizationof water adjacent surfaces and between oppositely-charged ions that dramatically-limited

the options of molecular forms which could form and function spontaneously together.As you will see, molecules which satisfied the spatial requirements of surfacelinearization were stabilized and survived - those that did not were unstable and

hydrolyzed back to the molecules from which they came.

Now we will look at the spatial features of a molecule which reflects the hexagonalgeometry of water, which provided the spatial template for all future molecules and

which became the most abundant molecule on earth.


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1

SUGARS AND POLYSACCHARIDES

Although we have been speaking about pure water and pure saline water, primordial seas

were far from pure. If you can imagine turning all the plants and animals on earth into

the small molecules from which they came and dissolving them in the sea, it would have

been a soup of toxic chemicals interacting with each other in billions of different ways.Many of the chemicals that arrived from space were relatively stable in water, but some

were not. Formaldehyde, for example, once dissolved in water, becomes highly reactive.

In the presence of cyanide ion, formaldehyde molecules (CH2O) couple together

spontaneously to form a vast variety of sugars with the formula (CH2O)x.

Glucose and Arabinose are only two of the many sugar molecules that are produced

when formaldehyde molecules couple together - all of them in equilibrium - all

converting back and forth between each other. However, as illustrated above, when the

chains reach five to six units in length, they circle around and form a ring. Sugars in this

cyclic form are more stable and no longer react with formaldehyde to form longer chains.

In fact, beta-D-glucose, because of its spatial structure, is one of the most stable of all thesugars in aqueous medium. Thus, glucose, which is the most abundant molecular form

on earth today and the primary source of carbon and energy within living cells, might

well have become the most abundant molecule in the early seas. It would have formed

spontaneously in alkaline tidal pools containing formaldehyde and cyanide ion and might

well have accumulated rapidly. In fact, beta-D-glucose, C6H1206, is the carbon and

spatial analog of hexagonal water, H12O6, the same hexagonal unit that forms

spontaneously on water-ordering hydrocarbon surfaces.


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2

However, formaldehyde is an extremely reactive chemical and, in the presence of

ammonia and other molecules from space, would have produced an incredible variety of

molecular forms. But glucose would have been produced so readily, with only cyanide

ion as catalyst, that it merits special attention. In order to do that, the molecule must be

viewed as spatial ball and stick models which reduce the size of the atoms and do not

show the hydrogens.

In its solid crystalline form, glucose exists as the alpha-D form with the oxygen on

carbon 1 perpendicular to the ring but, when dissolved in water, the oxygen on carbon 1can flip to the beta position in the plane of the ring. As will be seen shortly, the alpha

form might have played an important role in the further development of natural

molecules.

But there is another form of glucose that would have been produced by cyanide catalysis

in equal amounts to beta-D-glucose; it is beta-L-glucose. A first glance, this beta-L form

looks like alpha-D but then it is realized that, in fact, it is the mirror image of beta-D, like

your right and left hand. For some unknown reason, nature produces only the D, right-

hand form of glucose and only one form of most other natural molecules. All sorts of

explanations have been advanced to explain how this could have happened but none are

really satisfactory. Of course, for creationists, only one form of glucose would have beenproduced but, for the evolutionist, it is a dilemma. One possibility, that appears not to

have been advanced before, is that a polymer of D-glucose may have been involved in

this next step of spontaneous production of natural molecules.


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3

If an aqueous solution containing glucose is evaporated to dryness and heated, the

molecules chemically bond together by alpha-type linkages to produce a variety of

polysaccharide polymers. If redissolved in water, heated, dried and heated multiple times,

polymers with uniform, internally hydrogen-bonded structures would have accumulated

at the expense of all others. Those that did not form stable structures in hot water would

have broken down and hydrolyzed back to glucose. It turns out that one of the moststable polysaccharide polymers is the one shown above - today it is produced

enzymatically in abundance in plants and animals - it is starch.

If, by chance, eight D-glucose molecules bonded together with alpha linkages before L

molecules, they would have coiled around and formed an internally hydrogen-bonded D

helical unit. On repeated drying, heating, redissolving and heating, this first short D

helical segment would have selectively bound more D-glucose molecules to form an

extended D coil. If then the coil broke into shorter units, each one would have grown to

produce more D-starch molecules. Although it may have taken many years for the first

D-coil to form, once it formed, the process might well have proceeded rapidly to yield

huge gelatinous masses of straight and branched D-starch molecules, as well as a numberof other D-polysaccharides that were stable to hydrolysis. Today, D-starch is produced

by enzymes and is the most abundant polysaccharide on earth - as might be suspected,

both plants and animals use it to store glucose.

D-cellulose, which is produced from D-glucose with a beta rather than alpha linkage,

most likely was not present in the early world because enzymes are required for its

synthesis.


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4

Now, if we look at the issue of order/disorder of water on the surfaces of the molecular

forms shown above, we can see that the beta-D-glucose molecule is flat with four of its

six oxygen atoms in perfect positions to hydrogen-bond with short, linear elements of

water molecules above and below the plane of the ring. This would induce transient

linearization of water molecules in the free, unbound water regions on both its upper

and lower surfaces.

On the other hand, water molecules in the plane of the glucose molecule are held in

positions by hydrogen-bonding that do not support linear order, they disorder water and

provide for freedom of the molecule to move rapidly in that plane in search of other

water-ordering surfaces, like that shown schematically above, where it can free water

molecules above and/or below. Thus, glucose molecules have surfactant properties, they

spontaneously move to water-ordering regions on the outer membranes of cells where

they can displace triplets of water molecules in membranal proteins and be transported

into cells.

It is the unique structure of the glucose molecule and the way its alcoholic groups direct

the order of water around it that guides it to transport and functional sites on and within

living cells. If, now, we look at linear starch molecules, either in their tubular or filament

forms, we find that the central cores of the tubules are relatively hydrophobic; water

molecules do not tend to bind within. On the other hand, the alcoholic oxygen groups on

the outer surfaces of the coils disorder water permitting the tubules and filaments to be

extremely flexible and highly hydrated with water molecules in dynamic, random motion

around them. In contrast, cellulose blades and sheets are flat with high water ordering on

both sides. They tend to lie side by side to form flat structural units with the order and

strength required to produce the structural elements of plants.

Thus, D-glucose, by mimicking the spatial properties of hexagonal water, directs its own

motion through water and produces two polymers with unique water-bonding and

structural properties. As we shall see, all natural molecules within living cells perform

their vital functions by regulating the orientation and order/disorder of hydrating water on

their surfaces.


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1

NUCLEOSIDES AND NUCLEIC ACIDS

But starch has another property that might have been involved in the production of the D-

forms of other natural molecules. The D-form of starch, which is shown below, exists as

helical filaments that coil clockwise from back to front. The unnatural, L-form, coils in

the mirror-image, counter-clockwise direction. As mentioned above, the outer surfacesof D coils are highly hydrated but the cores are hollow with oxygen atoms strategically

positioned on the inner walls like those in the reaction sites of enzymes.

Iodine molecules spontaneously move into the cores to form a blue complex but larger

molecules, like one shown above, bind to the ends, increase the diameter and move intothe expanded cores in a spontaneous manner as well. Since the cores are anhydrous and

similar to the reaction sites in enzymes, they might well have served a similar function as

they opened to admit reacting molecules and then closed. On heating, molecules mightwell have been bonded together. In fact, asymmetric positioning of the oxygens in theinner cores of D starch might well have bonded asymmetric molecules together.

Although the idea has not been tested experimentally, it is distinctly possible that small

molecules like adenosine and D-ribose, as shown above, might have been held in the

proper positions to bond together to produce adenosine. Ribose is one of the sugars thatwould have been produced spontaneously from formaldehyde in the same reaction as D-

glucose and adenine is one of many flat, aromatic molecules that are produced when

aqueous mixtures of formaldehyde and ammonia are dried and heated.


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2

However, the molecular mixtures produced by this type of dehydration mechanism would

have been so complex that it seems almost impossible for enough adenosine to have beenformed to continue biomolecular development without the aid of some sort of more

efficient enzymatic process. To complicate matters, three other nucleosides, uridine,

guanosine and cytidine, had to be produced by the same type of non-enzymatic process in

order to continue the development of molecules essential to the living cell.

Since each of these four molecules (A, U, G and C) can exist in a mirror-image form, the

environment where they were first produced also must have been asymmetric, like right-handed core of D-starch. The fact that they form strong, selective hydrogen-bonded pairs

with each other of the type shown above (A with U and G with C) might well have aidedin their formation but the synthesis of these complex molecules in sufficient quantities to

produce subsequent molecules was essential to continue the process of producing a living

cell. Obviously, experiments should be performed before any of the above hypothesescan be accepted as valid but there is little doubt that polysaccharides might have been

involved because they and related sugars were most likely the most abundant molecular

forms on the early earth. But the next stage in biomolecular development was equally

complex.

As illustrated above, this stage required the attachment of three anionic phosphates, in

sequence, to the alcoholic group on the end of the adenosine molecule. In contrast tomost of the reactions mentioned above, the attachment of an ion, like phosphate, to the

terminal alcoholic group requires substantial energy. In living cells, the energy for thisphosphate bond formation is provided by the sun or the combustion of molecules like

glucose in complex enzyme systems. However, once again, if aqueous solutions

containing phosphate ions are evaporated to dryness and heated, the phosphates attach to

each other to form long chains of phosphate units like the triphosphate on the end ofATP. Surprisingly, these polyphosphates, even though they store tremendous amounts


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3

of energy in their POP bonds, are relatively stable in water. If dissolved in water with a

mixture of molecules like adenosine and glucose, evaporated to dryness and heated, onewould expect a complex mixture of phosphorylated molecules to be produced.

On dissolving the heated mixture in water and heating again, most of the molecules

produced by this solar-heated process would have been returned by hydrolysis back to theoriginal forms. However, the ATP molecule, by wrapping around itself as the sodium

and calcium complex, is surprisingly stable in saline water.

Not only does the triphosphate chain wrap over the ribose ring to form a hydrophobic

core with all of the polar oxygen and nitrogen atoms directed outward to hydrogen-bond

with water molecules, it has hexagonal symmetry to conform to linear hydration around

it. Thus, like the stable forms before it, ATP and the other nucleoside triphosphatesmight well have accumulated at the expense of less stable forms on repeated heating and

cooling.

No studies appear to have been performed to determine what types of molecules would

be produced by this type of sequential heating and cooling but, with the analytical tools

available today, one might be able to perform such experiments. However, it is virtually

impossible to imagine the combinations of chemicals and salts which might have beeninvolved in catalyzing these processes over the millions of years which were required in

this early phase of biomolecular development. But, of course, even if the studies were

successful, it would not prove that early formation occurred as described above.

However, there is little doubt that an entire world of complex polysaccharides would

have been produced in the cyanide-catalyzed phase of molecule formation and that thosemolecules most likely were involved in the production of the nucleosides, their

triphosphate esters and the nucleic acids which were to follow. Today, polysaccharides

of many types are attached to the outer surfaces of cells and serve as external, antigenic

fingerprints. However, very few studies have been done to determine if they perform anyenzymatic functions. Once again, it is difficult to perform experimental studies on water-

soluble polysaccharides: they are difficult to purify and isolate, they do not crystallize

well and, if dehydrated, change their molecular form. Obviously, at this point in the story,

creationists have an advantage - they can simply say: All natural molecules andmechanisms were produced at time X without worrying about how they might have been

formed originally.


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4

For them, the entire life-system was produced at a single moment in time the chicken

and the egg were produced together. But, for the evolutionist, the study of how naturalmolecules originally formed, how they function today and how changes occur in living

systems are extremely important to understand in order to know how they can be altered

to address problems of health that either are inherited or imposed. For example, in living

cells today, it is important to know that adenosine triphosphate, ATP, is a pivotalmolecule. By transferring energy-rich phosphate and diphosphate groups to oxygen and

nitrogen atoms on other molecules, it activates them and gives them a negative charge.

All mechanical motion and all chemical syntheses, in both the plant and animal worlds,

depend on ATP for energy. Detailed analyses to determine where inadequate energy isgetting into particular organs to produce proper levels of ATP and proper function are

essential to define proper therapies.

Once again, before proteins were available to catalyze the synthesis of ATP, UTP, GTP

and CTP, their syntheses had to be catalyzed by some other molecules, perhaps

polysaccharides. But, no matter what synthetic systems were involved, the interfacial

and patterning properties of linear water were involved, defining the spatial properties for

stability and functionality and dramatically limiting the options of molecular forms.However, once mechanisms were available to produce the above nucleoside

triphosphates in volume, progress toward more catalytic, spontaneously-functioning,reproductive systems most likely proceeded at a much more rapid rate. By rapid, we

do not mean hoursit means thousands or millions of years.


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5

Based on available evidence, the next stage in cellular development was the coupling of

nucleoside phosphates together to form nucleic acids. Today this coupling is carried outby enzymes that align the nucleoside triphosphates next to strands of DNA so that

specific sequences of A, U, G and C are produced in the RNA strands. But the original

strands most likely were produced simply by heating the triphosphates on some ordering

mineral or polysaccharide surface. Preliminary experiments suggest that this is areasonable possibility.

As strands of nucleic acids formed with random sequences of nucleosides, theyimmediately would have begun searching in the aqueous environment for complimentary

sequences with which they could couple to form specific A/U and G/C attachments - like

a zipper with a programmed sequence of attaching units.

As shown, the strongest attachments are achieved when the strands are oriented in

opposite directions. If nucleotides in the sequence do not form a paired linkage, like theU/U pair at the top, a water molecule between the units destabilizes and breaks the

coupling.

But coupled strands are not straight; bonding within the chains causes them to coil around

each other to form a helix. If a sequence of uncoupled nucleosides is present in a strand,

they bend back on themselves in search of complementary sequences. If a sequence isfound that can form A/U and G/C couplings, it forms a helical loop as illustrated.


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6

However, if a complementary sequence is not found, it will search in other strands to find

a match. The spatial structure of the transfer RNA molecule which is shown below willgive you an idea of the unique way the chains bend back on themselves to form new

couplings to produce a finished form. Once again, the finished molecule has a geometry

that uniquely fits into the linearization of surface water.

If transfer RNA molecules of this type are heated in saline water, they unwrap to form a

single strand which waves around in the heat-disordered medium. However, on cooling,the strand spontaneously wraps to form the same original structure. This means that, if

the sequence of nucleotides that forms these RNA molecules were produced at random,

they also would have wrapped to form these tight hydration-stabilized structures.

Sequences of nucleic acid that could wrap to form stable spatial forms would haveaccumulated, while those that could not wrap would have been hydrolyzed by water back

to the nucleosides from which they came. Like polysaccharides before them, over

millions of years of synthetic cycling, spatial forms that were stable in the linearizingenvironment of surface water would have accumulated at the expense of all others.

Fifty years ago, only proteins were considered to have unique catalytic properties; today,

even relatively short segments of nucleic acids have been shown to be able to hold othernucleic acid strands together, attach new strands to the ends, remove sections and

perform almost all of the functions that, at one time, only proteins were considered to be

capable of performing. Thus, it is likely that the Age of Polysaccharides, was followed

by an Age of Nucleic Acids, all driven by energy of the sun and directed by the

linearizing property of environmental water to yield the most stable, functional forms.

Strong evidence for the proposed sequence in biomolecular production is provided by the

fact that the catalytic regions of the huge ribosomal complexes that exist today are not

protein, they are primarily nucleic acid. Thus, as we shall see in the next section,catalysis of polypeptide and protein formation is performed by nucleic acids, not theother way around.


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1

AMINO ACIDS, POLYPEPTIDES AND PROTEINS

As mentioned above, some of the simplest and most stable forms of nucleic acid to be

produced were the transfer RNA molecules - probably at random at first but later by

specific catalytic mechanisms.

Every single cell in our bodies and in every other living organism contains about 20 of

these structures, one for each natural aminoacid of the type shown below. These transferRNA molecules bind a specific amino acid to the terminal adenosine (A) end and have a

specific sequence of three nucleosides (the triplet code) on the loop at the other end. Inother words, they attach a specific three-letter code to each amino acid.

The transfer RNA triplet code for phenylalanine is AAA, for serine, AGA, for leucine,GAG. As you can see in the chart above, each amino acid has a unique structure but they

all contain the same CO2 (acid) and N (amine) so they can be attached together, as shown

below, to form long polypeptide chains, sometimes composed of thousands of peptide

units, all arranged in specific sequences.


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2

Each peptide in a chain serves a unique role relative to water adjacent to it. Those with

positively and negatively-charged side-chains attract each other and transfer chargeslinearly through adjacent water. Lipophilic, hydrocarbon groups order water adjacent to

them; they repel water away from them and associate as closely as possible with other

hydrocarbon, lipid regions. Sections containing small aminoacids like glycine, serine and

proline, bind water molecules on all sides, disrupt linear hydration order and are

extremely mobile.

Polypeptide segments with charged or hydrocarbon side chains often produce straight

beta-sheet or helical coil regions but sequences of two or more small peptides usually

cause chains to change direction in beta turns while segments with a number of the smallpeptides have the freedom to coil in space and permit beta-sheet and coiled regions to

find close packing arrangements to bring opposite charges together and permit lipid,

water-ordering regions to fit tightly together.

Although many of the amino acids involved in current polypeptide syntheses can be

produced by subjecting ammonia and the gaseous components in the atmosphere to

electrical discharges, we really do not know how they were formed originally possiblyon crude nucleic acid enzymes. What we do know is that polypeptides of the type

shown above were not formed simply by heating the amino acids. Heating amino acids

does not produce polypeptides, it simply converts them into cyclic molecules, most of

which are not found in nature.

Thus, it is likely that the formation of biochemicals on earth passed through four stages:

sugars and polysaccharides, nucleosides and nucleic acids, polypeptides and proteins and,as we will see later, fatty acids and membranes. However, the synthesis of functional

polypeptides was much more complex than that of the polymers before them.


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3

Random synthesis of polypeptides may have occurred periodically prior to thedevelopment of functional nucleic acids but it was not until structurally-stable nucleic

acids were available which could catalyze the attachment of specific amino acids to the

ends of transfer RNA molecules could specific sequences of amino acids in polypeptides

be produced.

One of the unique features of the transfer RNA molecule is that the loop with the triplet-

coded is flat, it permits two molecules to lay side-by-side with their triplet codes bound to

adjacent complimentary codes on a single linear strand of (messenger) RNA as shownbelow.

If, now, the amino acids attached to the other end were brought close together by lying on

another RNA surface, the amino acid on the second molecule could bond with that of thefirst and a dipeptide could be formed. Coupling one aminoacyled t-RNA after another to

their complimentary codes on m-RNAs would have yielded coded polypeptides. Once

nucleic acid surfaces were available which could produce a variety of aminoacyled t-RNA molecules and hold them together on segments of messenger RNA, the synthesis ofspecific sequences of polypeptides must have proceeded at a relatively rapid rate.

Obviously, we do not know what the nucleic acids looked like that performed these firstcatalytic functions but we do know that nucleic acid segments which hold them together

today might well have been very similar to, if not identical, to those in early forms.


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4

At first, there was probably little selectivity for amino acids and dry heating might have

provided energy for the attachment of the amino acids to the transfer RNAs. However,once aminoacylated transfer RNAs began to form, their relatively flat structures must

have permitted them to produce a tremendous variety of polypeptides. Once again, those

that could wrap to form stable functional units survived, those that could not were

hydrolyzed back to aminoacids. Since the reactions were not catalyzed well, they mostlikely were extremely slow and with a tremendous variety of sequences produced for

millions of years.

However, it is likely that some of the first polypeptides to be produced bound to the RNA

molecules which had produced them. Some of them blocked further synthesis; others

provided improved stability and functionality. As the size and stability increased, somenucleic acid complexes became more efficient - those are the ones that have survived and

become the critical functional parts of the huge ribosomal particles that exist today.

Although ribosomal particles in living cells today are large enough to be seen with amicroscope, nucleotide sequences that bind messenger RNAs (mRNAs) and aminoacyltransfer RNAs (Aa-tRNAs) today might very well be the same as those that produced the

first polypeptides. Today, ribosomes are composed of 3 long nucleic acids and 55

proteins. The proteins are primarily on the outer surfaces - they control the beginningand end of syntheses, provide ATP power to draw m-RNAs through the complex and fill

voids in surfaces to remove water, increase structural stability and improve control in

coding and production of correct sequences of polypeptides.

In ribosomes today, a single strand of m-RNA is drawn by ATP power across a nucleic

acid platform in Particle A which holds two adjacent Aa-tRNAs so that their triplet codes

perfectly match complimentary codes on the mRNA strand. Once the amino acids areattached together in particle B, the resulting polypeptide chain passes down a channel inB. As polypeptides emerge into the aqueous environment they immediately begin

wrapping to produce functional proteins. Sometimes, chaperone proteins bind to

newly-formed polypeptides as they exit particle B and help them wrap into their lowestenergy forms but it is the sequence of peptides in the chain, their interaction with each

other and with linearizing surface water that determines the final protein structure.


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5

In spite of the structural complexity of these huge ribosomes, if heated in an aqueous

ionic medium similar to that in the cell, they separate into the 3 nucleic acids and the 55polypeptide parts. On cooling, they spontaneously assemble, once again, to form the

original, functional particles. It is absolutely amazing that all nucleic acids and all

polypeptides in living cells have the capacity to spontaneously assemble into their

functional forms. However, if the medium is denatured, by leaving out critical salts or byadding additional salts or liquids like alcohol, the linearizing property of water is

disrupted, spontaneous wrapping does not occur and molecular messes are produced.

Thus, the saline medium, with its dynamic linearizing and ordering properties,systematically directs surface charges into close association and hydrophobic,

hydrocarbon regions into close proximity to produce unique, geometric functional forms.

As mentioned before, the insulin molecule, which is produced in pancreatic cells as a

single polypeptide segment, spontaneously wraps into coiled sections that associate

together to exclude water from the central region and form stable structural units. Once

the assembly is complete, section C, which contains a number of small, hydrating glycinepeptides, is clipped off enzymatically to give the functional insulin molecule. As you

can see, the final molecule, like the transfer RNA molecule discussed above, has ageometry that fits into the linearizing environment of water around it. This provides for

improved stability and functionality as it binds to complimentary linearly-ordered sites in

cell membranes to promote the uptake of glucose into cells.


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1

ENZYMES AND DNA

Just as the earliest polypeptides which were produced, most likely bound to early

ribosomes to increase synthetic efficiency, they most likely bound to the transfer RNA

molecules as well. In fact, as can be seen below, the spatial structures of the enzymatic

proteins which formed to catalyze the attachment of amino acids to t-RNA moleculesfollowed the geometry of the t-RNAs to achieve the same high structural stability.

As you can also see, the catalytic groove in the protein where ATP and the amino acid

bind and reactions occur is surrounded by coils which pack tightly together to exclude

water and provide structural stability. Since there are 21 different amino acids, there

must be at least twenty one different enzymes, with structures similar to that shown

above, to bind a specific amino-acid at one end and a specific triplet code at the other end

of each t-RNA molecule. Obviously, peptide sequences in the binding regions at both

ends of these enzyme molecules must be different for each transfer RNA molecule butsequences in the structural region areas can be the same.

Thus, it is not surprising that polypeptide sequences in the noncatalytic, structural regions

are similar in most of these enzymes. Also note that the amino acid-attachment end of

the t-RNA molecule is bent into the catalytic site on the enzyme so it can be activated by

ATP and bind a specific amino acid.

As might be expected, the production of polypeptides and proteins initiated an entirely

new phase in spontaneous biochemical development. Nucleic acids, although capable of

many catalytic functions, were highly hydrated and required close proximity of positive

ions like sodium, calcium and magnesium to neutralize negative charges on theirsurfaces. Dynamic linearization of water between charge centers provided for spatial

coordination of motion and interactions, but the molecules possessed no extended,

hydrophobic, hydrocarbon regions to exclude water and aid in forming stable complexes.

Polypeptides, on the other hand, had ionic regions that could bind to the nucleic acids as

well as hydrocarbon regions that could aid in wrapping and provide greater hydrolytic

and structural stability.


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2

It is unfortunate that there is no record of this phase of biomolecular history - it would

have been thrilling to see. Just as the formative earth was in turmoil, biomolecular

development must have been in turmoil as well - the only constant in the process was the

ionic aqueous environment which continually provided for the direction of motion and

selection of molecules that would improved reproductive functionality.

As more and more polypeptides were formed with greater structural strength and catalytic

capability, nucleic acids began to decline in importance. Sometimes these new enzymatic

proteins broke strands of nucleic acid and polypeptides in the middle - others removed

particular peptides from the ends. Carboxypeptidase A is a digestive enzyme that

removes the aminoacid tyrosine and structurally related aromatic peptides from the

acid end of polypeptide chains.

In this enzyme, the negatively-charged end of a polypeptide chain is directed into the

positively-charged reaction site by a dynamic linear segment of transiently hydrogen-bonded water molecules. As the chain moves toward the site, water molecules leave until

the terminal peptide is hydrogen-bonded to the oxygen and nitrogen atoms in the site. If

the peptide on the end of the chain completely fills the site, as shown in the cut-away, a

water molecule held in precisely the proper position next to peptide carbon of the end

group binds to the carbon, breaks the peptide bond, releases the shortened chain and then

the frees the aminoacid. However, if the peptide on the end of the chain does not fit

tightly into the site and water is not completely excluded, the rotational energy of residual


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3

water molecules propel the chain back out of the site to wait for another with a more

appropriate terminal peptide. Another important feature of the reaction site is that it is

bordered by hydrocarbon groups that repel water and direct the chain into the positively-

charged reaction site.

It seems impossible that enzymes, with structures as complex as Carboxypeptidase A,could form by aqueous selection from random polypeptides, and yet, it is equally

incomprehensible that polypeptides composed of hundreds of aminoacids like this can

spontaneously fold in an aqueous medium similar to sea water to form a single, unique

functional protein. And yet, it happens in every instant to every polypeptide produced in

every living cell. Once again, if Carboxypeptidase A is heated in saline solution, it

unfolds to yield a single polypeptide chain. If cooled slowly, it will, like it did when it

first formed on the ribosome, spontaneously wrap into the same stable functional protein.

Of course, the process of modifying the molecules that compose living cells continues

today. Viruses continuously mutate and bacteria continually develop new molecular

systems of resistance to survive treatment with antibiotics. Whether we like it or not, thecells of our body are also changingsome return to their primordial, cancerous forms to

be independent of the cells that gave them birth. Other cells become more efficient at

providing nutrients to neighboring cells. Immunological cells recognize toxic molecules

they have never seen before, bind them, signal their destruction and signal for more of

their own kind to be made. Nerve cells continually make new connections to improve

and integrate signals. We and the living organisms around us not only are the products of

the past, we are the source of new processes and new chemicals for the future.

Although the production of enzymatic proteins which could hydrolyze linear strands of

messenger RNAs back to nucleosides threatened to destroy the entire process of

polypeptide and protein production, enzymes also were produced which could remove an

oxygen atom from the ribose ring of nucleosides to give deoxy-forms. These also could

couple together to produce coded strands - they were the deoxyribonucleic acids, the

DNAs.

Just as nucleosides form specific couplings, the deoxynucleosides did as well. However,

the deoxynucleoside that binds to adenine has one extra carbon on the ring to increase

stability - it is thymidine (T). The unique feature of the deoxynucleic acids was that they

could bind much more tightly together as complimentary strands to form double helices -

so tightly, in fact, that it took enzymatic proteins to separate them.


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4

However, the reason for their increased stability was not only tight binding and exclusion

of water between the strands, it was the extremely regular arrangement of negatively-

charged phosphate groups around them that permitted hydration bridging between the

strands and dynamic linearization of water to delocalize the high negative charge.

For example, infrared spectroscopic analysis reveals that the water around DNA

filaments is ice-like that, at any instant, the water exists as straight linear elements,

like those shown in the figure. The linear elements continually transfer negative charges

back and forth between surface phosphate groups and positively-charged ions around it.

However, the linear segments last for less than a billionth of a second so the double-helix

segments have the freedom to bend and twist and move. In fact, linearization of water

around the helices is so dominant, that sodium ions, which bind water molecules in

circular patterns around them, are excluded by multiple layers of water molecules in the

same way that hydrated sodium ions are excluded from liquid water adjacent to ice as thewater molecules linearize to form more ice.

Of course, the biochemical importance of double helix DNA was that it permitted

permanent storage of the codes required to repetitively and orderly produce RNAs,

polypeptides and proteins.

Truly, when the first DNA code was translated into a specific m-RNA and then into

a specific polypeptide, we can say that the first phase of reproductive life had begun.

However, life at that stage was not the same as it is today. There were no cells as we

know them. Most likely, there were huge gelatinous masses floating in the seas and inshoreline tidal pools with compartments of reproductive molecules. Only as protein

systems developed that could utilize sunlight energy to more efficiently electrolyze water

into hydrogen and oxygen could cellular development continue.


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PHOSPHOLIPIDS AND MEMBRANES

As illustrated below, oxygen was needed to convert glucose into acetic acid, acetic-acid

was needed, as a two-carbon unit, to produce long chains and hydrogen was needed to

remove oxygen atoms from the chains to produce a variety of fatty acids.

Some of the fatty acids, like stearic acid, were totally saturated with hydrogens on the

chains while others, like oleic acid, were unsaturated with two hydrogens missing and a

double bond in the chain. At the same time, molecules like isoprenol, with carbons on

unsaturated chains, also were made from acetic acid and converted into an array of

essential molecules, particular vitamins.

In alkaline medium, long-chain fatty acids form semi-soluble soaps. Just as oil molecules

align perpendicular to the surface of water to form layers, negatively-charged fatty acids

align perpendicular to the surface with their lipid tails toward the air and charged heads

toward the water. However, instead of linearly-ordering water on the surface, like

hydrocarbons, the charged acid heads disorder water molecules by hydrogen-bonding to

them in arrangements that do not conform with linear water. Thus, in alkaline media,

fatty acid molecules are surfactants, they migrate rapidly to surfaces to increase water

disorder, to increase hydration entropy and reduce surface tension. By reducing surface

tension, the interface weakens and bubbles form. Fatty acids emulsify and suspend oils

in water by surrounding the droplets with their tails toward the oil and their heads towardwater - they stabilize oil as droplets but they do not form spherical cells.

However, as shown above, if glycerine, phosphate and amino alcohols are attached to the

head groups of fatty acid molecules, phospholipid molecules, like lecithin, are

produced. These molecules not only align side by side to form layers but also maintain

the linearizing order of water adjacent to the phosphate head group.


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This allows them to form double layer membranes with their tails directed toward each

other in the center of the membrane and their polar, hydrogen-bonding heads facing

linearly-ordered water on the both sides.

The large head groups on phospholipids permit the hydrocarbon tails below them to

absorb energy and be converted from their straight, relatively ridged, beta states, to

dynamic kinked, alpha states, in which chains can bend and rotate around their axes.

Thus, alpha-state double layers are extremely dynamic, with the freedom and energy to

bend around, join ends and form spherical cells.

For the first time, cellular forms were produced which could encompass molecularmachinery and protect it from changes in the external environment. Phospholipid

Membranes that produced the first cells were unique in a number of respects:

1) at low temperatures, the hydrocarbon chains in the beta state are straight and

relatively rigid but, at normal body temperatures in the alpha state, they absorb

energythey twist and turn and spin,

2) by increasing the amount of unsaturation in the chains (the number of double bonds),

the alpha-state is stabilized - mobility in the hydrocarbon region is increased,

3) in the energetic alpha state, surface groups are far enough apart to permit small

hydrocarbon molecules and molecules with long hydrocarbon regions to move into and

pass through the membrane and

4) modifications in the head groups of the phospholipids produce an almost infinite

number of characteristics on the inside and outside surfaces of the cells.

Undoubtedly, a number of proteins began entering membranes based on these properties.

Some of the most important were those with long coiled segments, as shown below, with

hydrocarbon groups on one side directed toward the phospholipid chains and polar

hydrogen-bonding oxygen and nitrogen atoms directed toward each other in the center of


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the pores. Early pore-forming proteins were probably very simple: in the closed position,

they might have permitted potassium ions, which do not bind water molecules, to pass in

and out, while, in the open position, more highly-hydrated ions like sodium and calcium

might have passed through.

Thermal energy might have opened the pores to permit the larger hydrated ions to enter

and leave. Obviously, membranal proteins, like the ribosomes before them, increased in

complexity and function.

The photoelectric complex shown above was isolated from bacteria but similar ones are

present in most plants. As you can see, it is composed of three protein complexes - one

in the membrane and one on each side. The membranal unit holds eight green


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chlorophyll molecules which absorb sunlight in a pair of chlorophylls at the top, reverse

the spin on an electron and propel it into the cell. This draws an electron from the four

red iron atoms in the outer protein and then from water molecules on the outer surface to

produce oxygen gas and positively-charged protons. The electrons that are propelled into

the cell electrolyze water into negatively-charged hydroxide ions and hydrogen atoms

which react with carbon dioxide to produce formaldehyde and then glucose. Even thoughthe process involves a number of enzymatic steps, the polymerization of formaldehyde to

give glucose is the same reaction that most likely produced it in the beginning.

It may seem unbelievable, but the protons produced on the outer surface of the

membrane, to reach the hydroxyl ions on the inside, drive rotors in molecular generators

in the membrane to force adenosine diphosphate (ADP) molecules into phosphate (P)

ions to produce high energy adenosine triphosphate (ATP) molecules. It is a molecular

machine with rotating parts which, even though extremely complex, most likely was used

within the leaves of plants to convert sunlight energy into ATP molecules long before the

organisms we call animals even existed on earth.

Even an ardent believer in evolution, on viewing the incredible complexity of this

photoelectric/ATP-generating system, must be forced to agree with creationists that these

systems are simply too Perfect to have been produced without a Plan. And yet, even

these extremely complex molecular systems, if heated in the ionic medium of the cell,

separate into their individual molecular components and, on cooling, spontaneously

reassemble to give the same functional units. Once again, it is almost impossible to

believe that, even if their parts were produced at random, at separate times, they would

have assembled spontaneously to form the functional units that exist today. It is difficult

for us to imagine how so many different parts, composed of only a dozen different types

of atoms, can store enough information within them to program their own assembly into

life-giving forms.

But remember, assembly occurred in a medium that selected the parts and directed them

together based on specific ordering rules of dimension and geometry. As we shall see, it

appears that the dynamic linearization of water not only selected functional molecules, it

selected functional membranes as well.


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For example, if we look closely at the structure of plasma membranes that encompass

many cells, we find that the distance through the lipid zone corresponds to hydrogen-

bonded segment of 19 water molecules, 9 on each side, equal to the length of the dynamic

alpha-lipid chains, and 1 in the middle for the intersection of the chains.

This type of Fluid Mosaic Structure for membrane was proposed by Singer and

Nicolson back in 1972 and, in the same year, Kirschner and Casper published the electron

scattering (ES) and neutron scattering (NS) curves rabbit nerve cell membrane. ES peaks

occur wherever charged groups are on both sides of the membrane; NS peaks occur

wherever there is maximum water. As expected, there is little or no water or ions in the

center of the membrane and both curves peak where one would expect based on the

model of membranal phospholipids in their alpha, energetic state. The helical, coiled

protein shown was isolated from a red blood cell with the same type of phospholipid

membrane. Note that the polar, charged oxygen and nitrogen atoms on the protein are

predominantly where they would be expected and that most of the side chains in the

center of the membrane are hydrocarbon.

Since linear segments of water molecules passed through membrane pores and integrated

processes on both sides when they first formed, it should not be surprising that the

average length of the fatty-acid segment of phospholipid molecules in many types of

plasma membranes correspond to linear segments of 9 water molecules. In fact, the

molecule with four rings that is shown complexed with lecithin is cholesterol - again,

with a length corresponding to a linear segment of 9 water molecules.


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Cholesterol is a particularly important molecular component of nerve and muscle

membrane because it stabilizes phospholipid chains in their energetic, alpha state. At

the same time, it provides so much energy to the internal hydrocarbon zone of the

membrane, by spinning around on its own axis, as shown below, that ions, molecules and

charges cannot pass through. It produces membranes that are extremely good insulators -

they prevent molecules and positive proton pulses from passing through the walls ofcells.

But it also fulfills another vital function. By enzymatically removing the tail section,

glands in our bodies produce and release a large number of hormone molecules which

correspond in length to six linear water molecules. With oxygen atoms in several

different configurations on the ends, these hormone molecules bind to specific receptor

sites in other organs to control a large variety of functions.

Once again, correspondence with linear segments of water molecules undoubtedly was

extremely important in the selection of these molecules as functional regulators. Since

hormones bind to sites in proteins at precisely the proper distances to activate or

deactivate functions, it is likely that ordered units of water form in those sites as they

open in response to the thermal energy around them. However, order in water is

extremely transienthydrogen-bonded segments last for only an instant and have little or

no structural strength. Only if specific hormone molecules are present that can bind

tightly to the sites and displace the water, can the sites be held open long enough for

regulator proteins to change their shape and activate or deactivate neighboring functions.

Thus, it is likely that transient linear elements of water play a critical role in the function

of receptors. Unfortunately, it is often assumed that, if evidence cannot be generated for

the presence of solvent molecules in a process, they are not involved. However, water is

so ubiquitous and so dynamic that the selective action of a few cannot be detected. If

natural systems are dehydrated to identify the ordering role of water, the systems lose


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their function because free disordered water is as essential around functional

molecules as ordered water. Often, substances are studied in their purified molecular

state but, in their natural state, they are never pure - they are always surrounded by a

colony of molecules that interact with each other in thousands of different ways. The

only constant in the processes is saline water and its capacity to form transient linear and

two-dimensional forms of unifying order.

Once again, it should not be surprising that all of the critical regulator molecules shown

above, which bind to receptor sites at nerve endings and other important cells, mimic

ordered arrangements of water molecules. Some of them simply mimic a single linear

segment while others mimic two-dimensional forms. The flat, aromatic molecules in the

right-hand chart are not all regulators but they are all critical molecular units in living

cells and they all tend to mimic the planar, hexagonal-form of water.

Since it is extremely important for molecules which regulate multiple functions within

living cells to move rapidly in and out of binding sites, it is not surprising that cyclic

adenosine monophosphate (cyclic AMP), which regulates many processes within living

cells, also mimics the linear dimension of six water molecules with hydrogen-bonding

oxygen and nitrogen atoms in three additional positions in the hexagonal water lattice.


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Undoubtedly, it as one of the most important regulators in our bodies and is an excellent

example of a molecule whose spatial structure fits uniquely into the patterning of

linearly-ordered water. It is called a second messenger because it is released inside

cells to regulate functions when regulator molecules bind to receptor sites on the outside.

With two anionic oxygens on one end and two cationic nitrogens on the other end, the

molecule is a polarized dipole which binds to oppositely-charged groups on proteins thatare separated by six linearly hydrogen-bonded water molecules.

The above simulation illustrates how a cyclic AMP molecule, in binding to a positively-

charged arginine, A, on one protein and a negatively-charged glutamate, G, on another,

brings the two together to activate an enzyme or open a pore in a membrane. Prior to

binding, both surfaces are highly hydrated but, by binding cyclic AMP, all of the water is

displaced and a stable union of the two proteins is established. Of course, the system isdynamic, so external water continually binds to the surface groups to displace the cyclic

AMP molecule. Undoubtedly, as more detailed studies are performed on binding sites, it

will be found that many molecules, as they bind to proteins and nucleic acids, displace

transiently-ordered units of water molecules.

Now let us look at the role that ions may have played in the formation of functional,

living cells.


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IONS AND LIVING CELLS

In developing functional cellular systems, nature took advantage, not only of the spatial

properties of water, but of the hydration properties of ions as well.

Calcium ion, with its two positive charges, tightly binds six water molecules.Magnesium ion, which is smaller, can accommodate only four. Sodium ion, with its

single positive charge, binds either four or six around it, depending on the environment.

Potassium ion, which is slightly larger, has eight more electrons circling its positively-charged nucleus. Its positive nuclear charge is so shielded by electrons that it does not

bind water molecules - it only forms transient associations.

Thus, potassium ions play a critical role within the cellular world. Unlike sodium andcalcium ions, they do not induce a spherical orientation of water around themselves; they

move more rapidly through water because they do not carry water molecules with them.

Of critical importance, is that they increase the freedom of water so it can assume natural,linear configurations to penetrate and relax proteins. Sodium ions, on the other hand,

dehydrate proteins - they drawing linearizing water away from them to form their own

spheres of hydration. This fundamental difference in hydration properties between

sodium and potassium ions provided a mechanism for the development of functionalcells.


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Iflecithin is mixed with water containing sodium and potassium ions, at the same levels

as they are in living cells, small synthetic cells are produced. If the levels of ions are

measured, potassium ion is found to be slightly higher inside than outside and sodium is

higher outside than outside. Many explanations have been advanced for this difference, but most likely potassium ions, with their property of increasing the freedom of water

relative to sodium, are higher inside to increase the freedom (the entropy level) of water

within the more confined space. Since normal cellular water contains more sodium thanpotassium, the cell develops a slight positive charge outside and negative inside.

The important aspect of this slightly higher distribution of potassium inside is that, as

functional ion pores developed in cells, they took full advantage of this by using ATPenergy to pump 3 sodium ions out and 2 potassium ions in. Of course, this developed an

even higher charge potential across the membrane and turned the cells into small

batteries. One way living cells use this charge potential across the membrane is to bindsodium ions with molecules like glucose in transport pores on the outside. As positively-

charged sodium ions are drawn into the cell to neutralize the negative charge inside, they

bring glucose molecules with them. Thus, in this indirect way, ATP energy is used totransport uncharged, essential molecules into cells by tying them to positively-charged

sodium ions in pores on the outside.


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As the pumping and transport capabilities improved, an entirely new and important typeof cell developed. In nerve cells, sodium ion, once again, is pumped from the cell and

binds to pores on the outer surface. However, the pores remain closed - movement of

sodium into the cell is blocked and, as the sodium/potassium ATP pumps continued torun, an even higher potential is developed across the membrane.

In this highly-charged Resting State, potassium ions inside permit water to penetrate

and linearize surfaces - proteins hydrate and relax. The pores, which bind sodium ions onthe outside, open only when specific transmitter molecules bind to adjacent receptor sites.

Neurotransmitter molecules, like those shown above, permit nerve cells to communicate

with each other, with muscle cells and with hormone-releasing cells. Once the sodiumtransport pores are triggered by the neurotransmitters, they open - sodium ions rush in

and the internal environment changes completely. As water surrounds sodium ions,

proteins dehydrate; they change their shape and function, some enzymes are turned onand some turned off and the activated end of the nerve cell develops a high positive

charge.

In this positively-charged Excited State, the nerve ending discharges a positive protonpulse down its axon to an amplifying node. There, sodium pores open, the positive pulse

is amplified and it moves on at ultra-high speed to the nerve ending where its own stores

of neurotransmitters are released to continue the process of communication. However,only if the sodium pulse produced in the nerve ending is high enough and rapid enough

will a positive pulse pass through the axon. In other words, a positive threshold must be


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reached before discharge will occur proton conduction through the axon resembles the

instant on/off passage of electrons through a vacuum cathode ray tube.

If we look at the inner surface of the axonal membrane, we can see, once again, hownature has taken full advantage of the fact that the phosphate groups on thelecithin/cholesterol complexes along the inner membrane walls are at precisely the proper

distances to transfer negative charges to water molecules in linear lines along the surface.

If the positive potential generated at the nerve ending by sodium ions is high enough,water molecules polarize and linearize along the inner, negatively-charged wall to

propagate positive proton pulses through the axon to the amplifying node. If the potential

rise there is high enough, the pulse will be continued at the same extremely high speed to

the next node and on to the nerve ending where neurotransmitters of that cell will bedischarged to activate other cells.

This dynamic, linearizing property of water adjacent to the inner membrane wall permitsaxonal nerve cells to communicate long distances at extremely rapid rates with essentially

no movement of molecules and little or no loss of energy. Proton transmission is so

much more efficient than electron transmission that, if our nerves were composed ofmetal, we would be combusted by the resistance. It is important to realize that most

communication in our bodies is not performed by electrons but ions and protons - protons

that require water, rather than metal, as the medium of transport.

In the Age of Biotechnology that is to come, photosynthetic systems of plants will be

produced by genetic engineering and provide far more efficient conversion of sunlight

into electrical energy. Membrane systems of the electric eel will be used to store high potentials and electrolysis of water into hydrogen and oxygen will be used to store

energy. Proton-driven mechanical systems, which assemble spontaneously, will be

used to perform all kinds of nanotechnology tasks.


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If we follow the positive signal transmission by neurotransmitters to muscle cells, it is the

same type of ATP-powered sodium/potassium pumps that generate high negative

potentials and high levels of potassium within the cells in their Resting States.

In the Resting State, muscle proteins are highly hydrated and relaxed with ATP

molecules bound to critical sites ready to transfer phosphate groups and provide the

power for contraction. Calcium ions, which trigger contractions, are stored in sitesnearby. When neurotransmitters release sodium into muscle cells, the character of water

and molecules change completely. In the Excited State, calcium is displaced from its binding sites by sodium, proteins dehydrate, contraction is triggered and ATP

phosphorylates small protein feet on thin protein legs in such a manner that they rotate

back and forth and take steps down beaded actin fibers. As millions of protein legs and

feet draw millions of actin fibers into millions of the large myosin fibers, musclescontract. When neurotransmitter stimulation stops and sodium is pumped out by the ATP

pumps, muscle cells, once again, move from

Molecular Creation by J.C. Collins PhD_Rev8-2011

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Transcript of Molecular Creation by J.C. Collins PhD_Rev8-2011