NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.

Madame Curie Bioscience Database [Internet]. Austin (TX): Landes Bioscience; 2000-2013.

Cover of Madame Curie Bioscience Database

Madame Curie Bioscience Database [Internet].

Show details

The Origin of Complexity

.

Clearly, molecular complexity was a precondition for biogenesis. Contiguous molecular structures are monkey bars for electrons that provide the stream of energy required to extend that complexity to a level not observed in the abiotic world and to constantly renew the framework of life. Electrons built these structures via overlapping orbitals but for that to happen one needs solvated molecules dancing about each other to the tune of thermal motion until they stick together as their tiny magnets click. Long structures, branches, triangles, pentagons fused to hexagons; quite a panorama. One would observe, if possible, that molecules sort themselves by structural fit, leaving out the bulk of molecules which, in turn, may associate in different affinity groups. Nucleotides were favored structures which were produced in large amounts because the monomers were removed from the equilibrium by polymerization to form long chain nucleic acids, and that constantly shifted the equilibrium to produce more monomers and so on, leapfrogging to the first plateau in biogenesis, the potential genomic material. So, it was not a desert and it was not an ocean of infinite dilution, it was a field of perfect opportunity with moisture and temperature cycles that supported primordial chemistry under the unique condition that an earthlike planet produces only once in its history.

After decades of dramatic advances in science could enough have remained unknown for so long as to give substance to a new global paradigm of evolution based upon a different view of what chemistry can cause and how? The point is that every thing needed for the new model is known, it was all there, but nobody examined it from a different perspective and put it together accordingly. Just looking at something from a different angle can indeed give rise to a totally different model, every hypothesis in science has been conceived that way. Relativity is merely a different perspective of the universe that was Newtonian until 1915. The Genomic Potential Hypothesis is the result of viewing a Darwinian world from a chemist’s perspective and the two models are at least as different as the old and new astronomy.

So, let us ask once more what caused organic material to assemble itself into those delicate structures within structures in multi-dimensional symmetry that form the skeleton of life? What pushed immortal equilibrium chemistry onto the precarious perch that non-equilibrium chemistry occupies? The answers must lie in the realm of chemistry for the simple reason that, when life assembled itself, there was nothing else. The organizing principle is chance in the old model while the new model points to atomic orbital steering effects; the difference lies in the predictions that arise from each model as exemplified by the single origin versus the multiple origins paradigm of life. Let me elaborate upon these rather basic observations.

If such an eternal phenomenon is indeed responsible for biota then one might suspect that earth and life could have come about at the same time. Well, it almost did! About 4.5 billion years ago the earth did provide the harsh milieu for uncatalyzed chemical reactions, which include temperature gradients, reduction potential, and the necessary elements. The escape of gas from the earth's interior and the reduction of carbon compounds to hydrocarbons were early events. More carbon was brought in by carbonaceous chondrites (carbon-containing meteorites) and water was probably added to the earth's surface in small increments by comets which are lumps of water ice (as opposed to ammonia- or CO2-ice). The earth's atmosphere consisted of heavy gases such as carbon monoxide (CO), nitrogen (N2), hydrogen cyanide (HCN), and methane (CH4), that could not escape from the gravitational field. Free oxygen, however, was absent or minimal.1–3 The stage was set for an interesting play, the actors were simple organic gases, and the hot rocks of the earth's surface were interactive props. Volcanoes added sulfur and the traces of water wherein organic compounds stewed for about three-to-four hundred million years, or so goes the story that is quite familiar to the reader.

Still, all of this is chaos, a hodge-podge of molecules zooming about each other seemingly unmanageable, and that certainly invites the thoughts of an all-pervading organizing principle to which everybody agrees, albeit under different names. The evolution of this concept goes from the gods of religions to the chance of Darwinism to the atomic structure of genomism. Where then do the new Genomic Potential Hypothesis concepts enter the old picture? It happens at this very point that a genomist notes that the order is inherent and appears from within very subtly to give viscosity to the mixture. Carbon is the thixotropic agent, the atom that organizes the world around itself in five dimensions, one for each corner of the 4 sp3 orbitals and time as the fifth.

This reading differs a little from the dimensions of physics but viewed from the nucleus of a carbon atom it seems natural (Fig. 1). Hydrogen, nitrogen and oxygen have not been mentioned but if we admit them, 98% of the constituents of living systems are accounted for, it merely remains to activate them. The directionality and number of the orbitals is unique for each element and all substituents not only take their position in space4 but also dictate to a point what atoms may react at the remaining sites. Liberal as these limits are they select against millions of other interactions, with further selectivity introduced as the molecules get larger and by specific conditions of pressure, temperature, pH and oxido/reduction status. In fact, the chemistry of the origins of life was most likely dependent upon a gradient of conditions (c) dc, as a function of time (t) dt, beginning with hot organic syntheses of components and continuing with less energetic chemistry of polymerization; and lastly, the low temperature era of structure-mediated catalysis which ended with the appearance of cells. This scene actually matches what earth science tells us about the conditions on the post-accretion earth.

Figure 1. The four lobes of the carbon atom evolving from the nucleus are probability distribution ranges of the bonding electrons.

Figure 1

The four lobes of the carbon atom evolving from the nucleus are probability distribution ranges of the bonding electrons. Lobes 1 and 3 project above the plane of the page and lobes 2 and 4 below. Thus carbon organizes the world around it in four directions (more...)

Bonding orbital disposition and reaction conditions are all that is required, but what to do with that information? Can we take these conditions and properties to reconstruct in detail the biogenic path? No, and that does not mean that the concept is incorrect but rather that it is not knowable down to sufficient detail by human brainpower. It is not the complexity of data but rather the number of constants and the miniscule difference between them that prevents us from developing life from first principle. Even if we were able to solve the Schrödinger equation it would not get us very far into biogenesis;5 physics is to simple to explain life beyond its atomic basis! Mono-and bimolecular reactions are fairly predictable, but to see where, in very complex reaction mixtures, the various atoms end up one must surrender to empiricism. A number of years ago an intriguing experiment was performed by Stanley Miller.6 (Fig. 2) Regular laboratory glassware was used to assemble a closed system fitted with in- and outlets, an electric spark gap, a bottle full of water and a heat source. Oxygen was removed from this system and the same “primordial” gases were entered that exist in the interstellar space.

Figure 2. The “Miller-Urey” apparatus for abiotic synthesis of biochemicals from primordial gases is shown.

Figure 2

The “Miller-Urey” apparatus for abiotic synthesis of biochemicals from primordial gases is shown. Before each experiment the system was thoroughly evacuated, flushed with interstellar-type gases, and sealed. Water is brought to a boil (more...)

The water in the closed system was brought to a boil and the vapors, rising through a discharge chamber, were condensed and led back into the reservoir. After a few days of recycling, the apparatus was opened and the contents analyzed. The result was so amazing that more and more proof was demanded by the editors, but when the amino acid glycine was crystallized from the mixture there was no escape, Dr. Miller had produced amino acids and the bases of nucleic acids from primordial gases by a random process! At least that is the prevalent interpretation today.

The genomist asserts that this experiment has shown beyond reasonable doubt that chemistry is not a random process! The reader, chemist or not, can verify the genomist’s assertion by counting the atoms in the mixture (assuming that they are spheres without features) and do a simple probability calculation. The result shows that amino acids and purines and pyrimidines should have occurred at such a low concentration that they would not be detectable with our technology. Carbon, nitrogen, oxygen and hydrogen would never have come together as they did if reactivity would depend only upon the sequence in which molecules collide with each other. Important is the sequence in which they stick to each other and how tightly! Of course, molecules have to collide before they can stick, but the number of unsuccessful collisions is very large compared to the number of successful ones because of steric steering. The significance of this experiment reaches far beyond the demonstration of abiotic amino acid and nucleotide production, it gave evidence for the self-organizing principle that lies at the root of evolution. Note how far we have strayed from the Darwinian path by just taking a fresh look at the old problem. The result of the Miller/Urey experiment has been greeted as curious or remarkable but not as what it seems (to me), i.e., the discovery of the “background radiation” of the birth of biology. So much for the difference in perspective! Although Miller's findings went far beyond Darwinism, he remained a Darwinist until today, and that is astounding testimony to the unwillingness to take ever so small a step away from the polished surface of an experiment, and to dare to be distracted by its meaning in second and third intention.

The “Miller-Urey” apparatus and the primordial puddles have a number of properties in common, namely: 1. sterility, 2. no free oxygen, 3. primordial gases, 4. small amounts of recycling water, 5. energy, and 6. a mineral surface. The common argument that the ground will be different in different regions is countered by the fact that results of similar experiments done by nature under significantly different conditions in the asteroid belt have led to nearly the same result. The carbon compounds isolated from carbonaceous chondrites (meteorites) are the ones also seen in the laboratory experiments. What an impressive demonstration of the principle that is to be highlighted in this chapter. The Miller experiment made one recognize that all that was required to produce bio-molecules of great variety was to activate confined, relatively inert gases; the structure of atoms did the rest.

The experiment makes yet another exceedingly important point, namely that, no matter where such a reaction would have been set up and how activation was affected, the result would always be the same. This conclusion is supported by the data in Table 1, which lists the results of the analysis of a natural experiment done in the asteroid belt as compared to the products of a Miller experiment. In as much as our galaxy is not notably different from others, one may expect the organizing force of chemistry to be indeed a cosmic phenomenon as is life. Continuing this train of thought, are there still difficulties in imagining that organic puddles in Texas would yield chemical products similar to those located in what is now New England?

The structure of atoms is known to us in great detail down to the fact that isotopes are not totally equal to the major form of an element. Heavier isotopes react slower in enzyme-catalyzed reactions but they form stronger bonds. No uncertainty is needed for that aspect of our world. Heisenberg's Principle does not pertain to the power fields created by the atomic nuclear structure, but rather to the position of the electrons within these power fields. For the macroscopic world and its chemical basis the position of the power fields (orbitals) is important, and these positions allow carbon, very precisely and very predictably, to give rise to four bonds (or two double bonds as in CO2 or a triple and a single bond as in cyanate) that are stable under a variety of conditions and which allow carbon to form the many and varied polymers that form the skeleton of life. Chemistry does not suffer uncertainty neuroses.

The doyens of physics, Einstein, Planck, Schrödinger, and even Heisenberg, have warned against a view of the macroscopic world based upon subatomic uncertainty. Einstein, in a dialog with Murphy, calls it “not just nonsense but objectionable nonsense”.7 To no avail, once the principle was announced indeterminism became the patron saint of human dignity, superiority and free will, and luck became a legitimate adjunct to science. Karl Popper once called Darwinism an unfalsifyable hypothesis, i.e., not a scientific hypothesis until the indeterminate wave in London swept him of his pedestal into the gully of politically correct thought; he was no Giordano Bruno.

As it is, almost 99% of the human body consists of hydrogen, carbon, nitrogen, and oxygen, which are the members of the first and second period of our table of elements. It is perhaps easy to realize that the order of elements in the table reflects the same natural law that forms the elements in the first place, and it would be logical therefore to search for compatible properties among neighboring elements. What our elements of life have in common is smallness and the ability to form stable bonds by adding either one, two, three, or four electrons to their outer valence shells. From the third period of the table of elements only phosphorus (P) and sulfur (S) are important for living systems because of their specific electronic structure. Again, it is the specific atomic configuration that allows both of them to have structural roles as well as energy-transferring roles. The backbone of the genetic material (DNA and RNA) contains phosphorus, and protein cross-links contain sulfur. In addition, phosphorus is used as “currency” in biological energy transfers. The argument has been made by Edsall.8 and later by Wald,9 but the message was lost on biologists.

Everything seems to be logical in the context of chemistry. The important atomic characters can be displayed such as to reveal the reasons for self- association in an orderly fashion. From a purely mechanistic point of view we need something that will cause inanimate matter to stick together to produce, over and over again, similar structures and variations thereof. Figure 3 shows a bare skeleton display of molecules which are coming together at specific angles at very specific distances because of the bond angles of carbon, nitrogen, and oxygen. Molecules are a little like an erector set, standard distances marked in standard components. The structural information of atomic orbitals is propagated to the molecular level.

Figure 3. This figure illustrates the “erector set” quality of carbon chemistry.

Figure 3

This figure illustrates the “erector set” quality of carbon chemistry. Carbon-carbon bonds are of unit length and produce unit angles so that electron activation will cause repetitive, spatially defined structures that, under appropriate (more...)

The corners of these stick models are carbon and the lines leading away from the corners are bonding orbitals. Dimers, trimers, and tetramers are coming together, and when they align their ends they fit precisely because the carbon-carbon bonds single, double, or triple bonds are precisely defined to give the building blocks for molecules a natural fit. It stands to reason that monomers produced in that fashion will again have functional groups displayed such as to overlap the neighboring molecules and cause the buildup of superstructures. In Fig. 4 the same stick models are drawn with their electronic clouds to show how chemistry might look if our eyes were sensitive to x-rays.10

Figure 4. This figure may be considered a window to a “chemical aquarium.

Figure 4

This figure may be considered a window to a “chemical aquarium.” The core of each of the structures is carbon and most of the hemispherical structures attached to the core represent hydrogen atoms. When these molecules collide under appropriate (more...)

Clearly, it is a mass-action phenomenon and the only selection that can occur in such a solution is the fit of specific groups to build larger molecules. In this way the bonding orbitals, the direction and strength as well as their sensitivity to competing reactions, cause the buildup of more complex molecules if reaction conditions favor such a development. In Figure 5 the concept is illustrated by an actual example of a radiation-driven, non-biological series of reactions that ends in the formation of proto-porphyrine.

Figure 5

Figure 5

From the mixture in Figure 4 a chain of reactions has been isolated to show how the guiding force inherent in the electrical orbital orientation can lead to complex bio-molecules

These pictures11 are simplified to provide an unobstructed view of one of the most important principles of the inanimate world. The power of the Genomic Potential Hypothesis stems from the realization that there is no purpose and no goal in all of this and that syntheses came about because of the predisposition of atomic and molecular structures for such reactions under certain conditions. In contrast to the chance-oriented Darwinian paradigm, this model invites experimental exploration.

Pre-biotic self-association was inevitable as well as uniform at the most fundamental level; differences are the consequence of higher level organization, i.e., the order rather than the ingredient. Once a nucleic acid sequence had been established and became part of the memory of an organism, it was maintained by the mode of complimentary self reproduction for as long as the species lasted. Again it is the uniform distance of hydrogen bonds that line up the nucleotide bases for the accurate reproduction.

Figure 6. Here the principle of bond length and angles is shown in connection with the core molecules of all of life, the monomers of DNA.

Figure 6

Here the principle of bond length and angles is shown in connection with the core molecules of all of life, the monomers of DNA. The configuration of bonding orbitals leads to the selection of bonding partners in the DNA and this arrangement again causes (more...)

Note how many distances have to be uniform in order to properly align the hydrogen bonds that stabilize the DNA helix. Here the principle of bonding orbitals is continued to the next higher level of molecular association. The next step, the covalent linkage of the bases of nucleic acid to polynucleotides, is the moment when potential memory is produced from molecules that singularly have no meaning.

We do not know precisely how it happened but we know it did. Would that necessarily stamp evolution per se as a soft science? Not really. Or would one move physics into that category because among other things, the origin of inertia is still not known? Every living science must have its unknowns because, once all is known (which is anyway impossible) the discipline becomes history. The foundation of the Genomic Potential Hypothesis lies in chemistry, which is governed by thermodynamics, kinetics, and the laws of mass action; nothing soft about that!

These events, observations, and thoughts have brought us to the bottom of the staircase that leads to living systems. The production of nucleic acids from nucleotide monomers is not totally understood, but we know how the single units of nucleic acids are produced and we know how nucleotides need to be connected to each other to form the basis of the bio-memory (Fig. 7). Formation of these high-molecular weight, linear molecules was the crucial event that provided a path to life. Nucleotides changed to nothing new, they just joined hands (orbitals) to form the surface from which, by a circuitous route, other complex molecules could be read. Again, we do not know the details of the abiotic polymerization process for nucleic acids, but it had to have happened by fusing bonding orbitals guided by steric restrictions. Someday our studies of the chemistry of the origin of life will present us with the mechanism of abiotic polymerization of nucleotides.12 Complexity hereafter is defined by how many times and through how many levels of structure molecules are connected. The surfaces produced led to the reactions that increased the speed of growth of these structures and provided the energy for maintenance, and when all was wrapped up in a membrane the border was crossed to that “mysterious state” of life without putting anything mysterious into the reaction. The change from inanimate to living systems is not so much a change of basic materials, i.e., carbon, hydrogen, nitrogen, oxygen, but rather the change in the way they are connected to each other.

Figure 7. This figure illustrates the chemistry of memory.

Figure 7

This figure illustrates the chemistry of memory. The process is quite well known but in the new hypothesis it is given the attention it deserves. The monomers of DNA designated as containing “no information,” of course, do have the information (more...)

The structure of energy makes the emergence of life inevitable if the proper reaction conditions prevail. This, the determinist’s clarion always sounds true because its score is chiseled into the structure of energy manifest in atoms. It also is a useful sound for it tells us that, if we should learn how to get to another earthlike planet, our test for life should be based upon the very principles that led to life on this planet.

To the genomist the origin of complexity is a matter of coincident natural conditionsand, wherever those conditions are met, life like ours will arise.

References

1.
Ferris JP. The chemistry of life's origin Chem Eng News 1984August 27. [PubMed: 11541976]
2.
Canuto VM, Levine JS, Augustsson TR. et al. The young sun and the atmosphere and photochemistry of the early earth. Nature. 1983;305:281.
3.
Rebek J. Synthetic self-replicating molecules. Scientific American. 1994:48.
4.
van't Hoff JH. Imagination in Science Springer Verlag Berlin-Heidelberg-New York 1967 1967.
5.
Schrödinger E. Naturwissenschaften. 1926. p. 664.
6.
Miller SL. The atmosphere of the primitive earth and the prebiotic synthesis of amino acids. Origins of Life. 1974;5:139. [PubMed: 4842068]
7.
Planck M. Where is Science Going? 1981. OX BOW PRESS Wooddbridge, Connecticut;
8.
Edsall JT, Wyman J. Biophysical Chemistry Academic Press, 1958vol 1 New York .
9.
Wald G. Life in the Second and Third Periods 1962. In: Pullman K, ed. Horizons in Biochemistry Academic Press Inc. New York .
10.
Pauling L. Chemistry. Scientific American. 1950;182:60.
11.
Calvin M. Photosynthesis and Quantum Conversion 1962. (Pullman K, ed. Horizons in Biochemistry Academic Press Inc. New York .
12.
Ferris PJ, Hill AR, Lui R. et al. Synthesis of long prebiotic oligomers on mineral surfaces. Nature. 1996;381:59. [PubMed: 8609988]
Copyright © 2000-2013, Landes Bioscience.
Bookshelf ID: NBK6522

Views

Related information

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...