Monthly Archives: February 2017

Pre-Biotic Evolution: II. Pre-Biotic Chemical Oscillations and Linked Reaction Sequences

Joseph H. Guth*

Published by the

Society for the Advancement of Metadarwinism, Volume 2 

2015

One Scientist’s Overview and Perspectives

Introduction

The complexity of modern living cells and organisms has always been one of the most baffling features when trying to understand how life could have begun spontaneously. This second installment focuses on finding a plausible mechanism that explains how the different highly complex biochemical pathways that are integrated into the overall metabolic pathway design could have individually evolved, self-assembled and formed spontaneously.  We then find an even more surprising mechanism for how they could have become incorporated into the earliest membrane-sequestered, chemically-active units that were self-selected for having some kind of long-term stability.  That long-term stability included many of the characteristics we attribute and define modern living cells with.  The timeline continues from the first installment1 and describes the next steps of a reasonably logical progression of chemical and physical developments and changes in the chaotic march from a pre-biotic earth to the formation of the first biologically-recognizable life forms.

The initial steps were described in the first part of this series of articles.1  Previously we saw how the ordinary astrophysical processes in the universe led to a broad range of different types of atomic building blocks.  Under early earth geochemical conditions, those building blocks possessed the necessary properties to allow the combinatorial creation of millions of different bonded atomic combinations or configurations we call molecules.  And this molecular pantheon at the beginning formed a massive number of different kinds and sizes of molecules at and below the surface of earth.

Figure 1.  A modern day leftover microenvironment or niche in which keragen-rich carbon-based molecular diversity and complexity could continue to form.  Gas bubbles reaching the surface in the La Brea Tar Pits.

As a testimonial to its longevity and continuity going back to early life forms, a recent study by David E. Crowley and Jong-Shik Kim revealed that hundreds of species of bacteria and Archaea also continue to thrive in the La Brea asphalt seeps.24 One key part of the microorganisms’ adaptation to, if not original genesis from within such a niche that straddles the pre-biotic to early life transition is that they are obviously adapted or evolved to thrive within the asphaltic carbon sources present.  They metabolize petroleum, growing by breaking down and rebuilding the petroleum hydrocarbons into biomolecules, which are incorporated into their cells.  And in such an environment, dating the “age” of the Archaea lines would be a significant challenge.

Such chemical complexity on pre-life earth was a necessary starting step in the longer maze that had to be navigated in moving towards the first permanently self-sustaining, free living systems.

With such a wide ranging tool box, it was not difficult to extrapolate and accept that a broad set of molecular properties and new possible molecular interactions and reactions would then come into existence.  Many studies have demonstrated this diversity of pre-biotic chemical potential.  Extreme molecular complexity of these pre-biotic molecular libraries leads to all manner of possible combinations of pairwise and multi-component interactions and linking of sequential chemical reactions.  When occurring in differing unique environmental niches they would result in molecular collections with variously skewed reactivity and composition profiles.  I proffer that this massive range of initially low numerical probability molecular encounters, interactions and events would be the main driving and selective forces that led to the specific self-organization and complexity of the first free-living terrestrial protocells.

During this early stage of pre-biotic chemical evolution, the atoms within and between simple low-molecular weight species were rearranged, leading to a huge increase in overall chemical complexity of the structures present.  Once these melting pots of chemistry reached sufficiently complex conditions, it should be a given that self-propagating subsets of linkable chemical reactions and their associated assemblies of catalytically-active molecules and macromolecules would have inevitably arisen and become more efficient through mutually-evolving aggregates.  Such highly-selective super-molecular associations are regularly observed to form in various kinds of affinity-based biochemical purification and analytical procedures.  They are also found throughout present day metabolic pathway enzyme complexes.  These macromolecular aggregates could have started to generate the potential for other different chemical and physical properties or for development of higher order chemical-based behaviors that we now attribute to living systems.

At that step of maximum complexity generating the starter set of biomolecules required to complete metabolic pathway activities, the overall complexity of the molecular library on earth could then have begun to shrink, likely now providing much of the fuel-rich substrates (needed for energy maintenance) as well as basic building blocks for those first “living” systems to feed upon and increase their mass and ability to persist indefinitely.  At this stage we should picture an ever-increasing mass of proteinaceous gel-sol like liquid pools without any membrane-based boundaries.  After those centers of living chemical processing became established, other naturally-occurring phenomena and molecular species also co-present in their immediate environment (initially perhaps a multi-layer surface sheen of lipid-like precursors) would have, with aerosol generation, been capable of capturing and sequestering them within thin, semi-permeable vesicles.  Such repackaging would have reduced the rate of water evaporation and helped those first molecular metabolic systems to endure even longer and thence begin to evolve even more rapidly.  Smaller volumes to maintain higher concentrations, higher surface area-to-volume ratios and a partial self-sealing membrane-like barrier to act like an ultrafilter and keep the diffusion forces from continually dispersing such colloidal macromolecular system components then made it more probable that even greater persistence and self-propagating potential would likely emerge from them in future versions.

Thus were born some of the basic subsequent structural patterns of biologically important molecules, coordinated molecular processing (i. e., individual metabolic pathways),  gross membrane-based cellular design and interlinking separate chemical reaction sequences (i. e., linking of different individual metabolic pathways housed in different subcellular compartments) common to all terrestrial life.

We may anticipate these as the preliminary selection events leading to the minimum initial “starter set” of necessary molecules needed to construct the first autonomous, persistent, self-sustaining protocells.   Such protocells would have spontaneously formed in countless numbers when the chemical composition and physical conditions allowed.  Temperature, pH, ionic content, membrane composition and phase transition temperature and osmotic pressure would be major determinants for defining the average size of the self-assembling protocells.  Such units being formed for the first time would have to have most of the properties that have been described as being needed for the first autopoietic unit capable of long-term persistence and of surviving and reproducing in the early earth’s chemical and physical conditions existing at that time.2  Following that initial self-assembly of such first-life units, they would have had to have been transferred by some physical process (e. g., through aerosol generation, and as a drifting airborne mist or dripping liquid-to-liquid transfer) from their formative microenvironments into their next stage, nutritionally-supportive environments.  In the latter, they could build their mass and/or numbers.  A different set of evolutionarily important selection events would then have begun to select for even greater speed, efficiencies and competitiveness in a higher level of evolutionary upgrading.  This also could be viewed as a Darwinian type of survival of the fittest contest amongst various versions of protocells, with the winning combinations of internal chemistry and its packaging attaining an even more self-sustainable and aggressive set of capabilities.  The less prolific in such a proto-cellular jungle would likely have been overwhelmed or lost completely.  More rapidly-proliferating forms out-competed them for limited resources and/or they became prey to the more aggressive (or optimized!) proto-cellular varieties.  But to better understand it, let us continue examining in more detail the final pre-life stages before this milestone was passed and thence first lit the fuse of life.

A living cell is a highly organized, interlinked, homeostatically rebalancing, and internally multiply-controlled system.  These properties, in and of themselves, still would not produce a living cell under near steady-state oscillatory conditions.  But homeostatic behavior, combined with a steady-state metabolic pattern does confer unpredictably higher potential for indefinite maintenance, unlimited propagation, and long term stability.   What is meant by that?

A particular combination of starting molecules would have to be captured and packaged in the right kind of container along with a simultaneous initial “charge” of electrochemical or electromotive potential energy.  These would be needed to initiate a unidirectional membrane-based flow of the intermediary metabolic reactants and products.  Such a simultaneous capture provides the initial impetus and directionality for the subsequent flow of the activities of the coupled metabolic pathways.  This set of requirements would be equivalent to the charged battery being used to start an automobile’s internal combustion engine.  Such a needed constraint would have had to be present at the beginning to give the first protocells a source of continuing chemical momentum and access to other useful energy forms.  This chemical momentum can be equated to and has often been referred to as the “life force” or the spark of life.  It is one of the main focal points of the biophysics subspecialty known as bioenergetics.  What follows in parallel with all of these pre-biotic developments is a version of Darwinian selection at the molecular and super-molecular levels.  But even as the first protocells come into existence, they must quickly become linked to a continuing source of energy and nutrients compatible with their internal processing schemes.  It will take further molecular and “proto-biological” developments to confer some of the additional properties we now commonly attribute only to natural terrestrial life forms.  Those will be examined in future installments.

 

The Importance of Chemical Complexity and Complex Chemistries

The earliest atmospheres were likely to have been composed, to varying extents, of a few simple low molecular weight gaseous molecules such as hydrogen, methane, ammonia, water vapor, hydrogen cyanide, hydrogen isocyanide, carbon monoxide, formaldehyde, formamide3, nitrogen, hydrogen chloride and hydrogen sulfide.  Smaller amounts of other gases, vapors, aerosols, smokes, dusts and fumes probably also existed along with solid ices and/or liquid deposits of the same molecular species.  They could have changed physical states as the earth’s temperatures gradually dropped to lower ranges.  Many important reaction chemistry energy sources, catalytically-active surfaces, and reactive compounds were likely to have been present.  Various levels of acidity or alkalinity would have been prevalent throughout the ponds, lakes, streams and oceans of water to support all kinds of oxidation-reduction reaction chemistry.  All of those microenvironments would have been necessary to drive or catalyze the intensely complex molecular chemistry that followed this initial period of low molecular weight chemical accumulation.  Then a period of concentration and consolidation of starter molecules needed to feed into the pre-biotic, life-building processes would likely have followed.  Examples of such energy sources could include heat (solar flare plasmas, extra-solar high energy particle showers from nearby periodic stellar binaries, polar region auroras, aerosol-induced lightning-related electrical arcing, volcanic/submarine vent radiant heat, geothermal geysers, fumaroles, superheated steam, geothermal pyrolysis, heat from natural radioactive decay, high temperature lava reaction chemistry and thermal degradation). It could also include ultraviolet and visible light-catalyzed photochemistry, ionizing radiation-induced nuclear chemical reactions (radioisotope particle emission/x-ray emission decay with attendant changes in atomic number/mass or subatomic particle-induced ionization of existing chemical bonds.  High altitude atmospheric reaction chemistry including that occurring within the aurorae at either polar region is also a strong contender.  Cosmic ray bombardment certainly has such capabilities to incite chemical bond scissions and reformations.  Highly exothermic inorganic combustion/oxidation processes, as well as high impact pressure/shock/sound wave-driven chemical reactions could likely have contributed sufficient chemical energy for molecular reactions and atomic rearrangements.  All of such energy sources probably operated at one time or another and in one location or another over the pre-biotic period in earth’s history.  And all would have contributed their particular range of chemical transformations leading to even more overall complexity to early earth’s pre-biotic chemical “biome”.

 

Catalysts: The More the Merrier

As mentioned before, other naturally-occurring materials were readily available to catalyze the differing types of chemistry.   Such co-present, catalytically-active materials would assist the formation of a broad range of reaction products that would have ensued.  Such reactions could have been based upon the known and yet-to-be discovered catalytic activity of various minerals, metals, salts, clays and soils.  Catalysts don’t usually provide additional energy to assist a thermodynamically favored process.  Instead they lower the activation energy barrier between the reactants and the reaction products.  Once lowered, the reaction can proceed to its equilibrium point or continue unimpeded as part of a non-equilibrating steady-state reaction sequence.  Thus all possibly-present solid surfaces must bear a thorough study for catalytic capabilities when experimentally exploring the combinatorial reaction conditions of early earth’s pre-biotic period.  In such studies, it will be most helpful to include the broadest array of such materials rather than restrict it to only a very few.

Various kinds of dissolved, colloidal gel-state, crystalline surfaces, and non-crystalline solid phase molecules, macromolecules and ions can act as catalysts for different types of chemical and electrochemical reactions.  Catalysts not only reduce the energy barrier for reactants to more rapidly proceed to products, they can provide a preferred path or selective filter for which specific products will be favored in a given reaction.  For stereoisomeric compounds, this could introduce a simplifying stage, which could have sped evolution by eliminating half of all duplicated reactions involving such isomerics.  Without such preferred stereoisomeric selection or catalytic bias involving the formation and transformations needed, stereoisomeric compounds of any single type (e. g., L- versus D-forms of amino acids or monosaccharides), this could lead to a completely parallel development of two totally opposite sets of biochemistries and life, each being based on opposing chiralities.

Within a given kind of macromolecular class, such as proteins, there should be a strong selective pressure to favor the co-assembly of like-handed monomers.  Thus if one were to be able to find proteinoids in pre-life earth niches, their likelihood to be all D- or all L- amino acid polymers would be dramatically more favored because a protein chain made up of a random mixture of D-amino acid residues and L-amino acid residues would likely  be unable to form any real tertiary structure such as long α helix sequences.  The range-limited flexibility conferred to a protein’s active site, whether an enzyme or a different functional protein, retains its evolutionary need and stability for α-helicity formation.  Such tertiary protein structure and its variable movement allows for much of the specific molecular dynamics that catalytically-active proteins, microtubule-microfilament proteins, and trans-membrane transport proteins undergo when performing their catalytic or other functional changes.  As a consequence, racemic mixtures would not have been expected to be long-lasting during early chemical and pre-membrane evolution.  As one type of stereoisomer began to predominate in a niche, simple pH-assisted slow racemization could form the short-cut needed to allow a rapid reverse conversion of the lesser form back into the more functional form.  This would speed up the process of selection of one form over the other.

In fact, if two chirally-opposite stereoisomer-based proto-cellular systems were to have equally co-evolved together, it might actually have interfered with or reduced the rate of subsequent evolution of either single chirality-based, stereoisomerically-mirrored pre-biochemistry as it moved towards formation of the first life forms.  They would have reduced the rates of appearance of new reaction sequences that began with initial reactants that were needed by both.  Initial reactants, such as methane, would not have had developed any preferentially conserved asymmetric carbon atoms or other stereoisomerism-generating features.  But some subsequent reactions occurring during each version of those opposite chiral reaction sequences would have generated such stereoisomers.  Thus they could have interfered with each others’ ability to take in the starting reactants by reducing the available reactant pool through a mutually competitive-but-inhibitory mechanism.

One of the classical hallmarks of a truly chaotic system is the well-known phenomenon popularly known as the “Butterfly Effect”.  Water flowing very slowly through a tube can flow in a highly organized laminar flow pattern.  The molecules at the inner wall flowing the slowest, with each more interior ring of liquid moving somewhat faster.  At the innermost column of liquid, the fastest moving molecules each progress as cars in a railroad train, with none advancing any faster than would be allowed.  If this overall average velocity of flow were gradually increased, at some repeatable value the laminar flow pattern becomes disrupted and turbulence patterns now form.  Simple linear flow can no longer exist above that critical value of flow.  This is the point where the system now begins to exhibit its first forms of chaotic motions.  Such transformation of linear to non-linear motions relies on subtle irregularities that may occur and become amplified at the transition point.  This point demonstrates a system going from a regular, well-behaved, predictable dynamic pattern to one that is irregular, non-predictable and chaotic.  The Butterfly Effect only occurs in systems that are deterministic but operating above such critical points and within their chaotic dynamic ranges.  The underlying principle is that chaotic systems are all extremely sensitive to the starting conditions.  Even the tiniest variation in a single parameter at the beginning can and will lead to much greater and less predictable outcomes later on.  It will subsequently also lead to non-linear dynamic properties or non-predictable system activity while maintaining a basic pattern throughout all of its ranges of varying chaotic behaviors.  Accordingly, even a slight preponderance of even a single isomer’s configuration can create an ever-increasing amplification of its growing concentrations and numbers over countless reaction cycles that follow. That would be a strongly probable outcome since the overall operation of such reaction sequences includes the generation of even more of the same exact copies of that reaction sequence.  At the molecular level, this would be the analogue of the property of reproducibility in living cells.  And any reaction sequence that finds itself initially in a more hospitable niche could have everything it needed to become the eventual “winner-take-all” in the stereoisomeric molecular evolution towards the first living cellular type systems.

For reaction sequence portions of biochemically important pathways involving both stereoisomeric and non-stereoisomeric compounds and reactions, the increased numbers of resultant intermediate compounds (derived from the combinatorial chemical environment) would have provided the fastest solution to the search for new, interactive middle- and end-of-pathway chemical product combinations.  Thus the more complexity that the mixture spun off in the beginning, the more likely some of those could act to catalyze later-developing molecular reactions.  And as longer reaction sequences evolved, more chemically useful end-products would have become available.  Ultimately, the most useful ones would have been the beginning monomers that would be needed to recreate more of the same macromolecular and super-molecular structures ultimately required for increased amounts of protocell building blocks.  In this context, super-molecular structure could be any much larger structure composed of much smaller, independent molecules.  Examples might be a lipid membrane, multi-subunit protein complexes or dynamic filamentous structures.

Though not absolutely necessary, it is my expectation that each of the final assembled metabolic pathways that developed, did so in a stepwise, sequential fashion from their beginning input points to their final reaction steps.  This does not mean that more than one version of such a pathway could not have existed at any time.  It is more likely that many versions co-existed simultaneously and competed with one another for pre-eminence.  But in considering the evolution of a longer, more complex sequence of function and structure, thermodynamics as well as increased opportunities for functional cooperativity would favor such a progression of growing complexity.  In an evolving metabolic pathway, each individual catalyst in such a reaction sequence underwent its own molecular evolution to perfect its structure in ways that increased the catalytic rate of that reaction step.  During such optimization, it would have provided some organizational improvements, allowing it to become a more coordinated part of an even larger group.  Such perfecting of structure and function through repeated testing and self-selection should have eventually made the overall reaction sequence it was a part of more controllable with respect to all of the other chemical reactions it would eventually become linked to or integrated with.  Thus the multi-enzyme complex containing multiple related catalysts was born, and this design obviously thrived thereafter.

And what about the question of the evolution of multi-pathway linkages?  As more types of pathway-like, reaction sequence-catalyzing, multi-component complexes came into physical existence, new combinations of these would undoubtedly find greater chemically-meaningful survival benefits.  That would be favored if their final products could also become the initial reactants for different and separately evolved metabolic pathway-like complexes that happened to drift by.

Another increase in the stabilization of such multi-complex assemblies would have occurred when some molecular variants generated combinatorially had external molecular properties offering non-covalent, mutually-compatible binding sites with which to temporarily connect them together in a chemically meaningful fashion.  In other words, the complexity of the system invariably could tend to increase and that in turn could lead to even more possible interactive chemical species.  This spontaneous, entropically-assisted tendency applied to developing chaotic systems for greater complexity in composition and inter-actability could be argued to be the first driving force for molecular evolution in pre-biotic systems.  It is actually the opposite of the underlying assumptions derived from the Miller-Urey and similar experimental interpretations held by many today.  Where they assumed that only a smaller set of biologically relevant molecules would have been necessary to be generated through non-living processes, their experimental designs terminated the experiments much too quickly to observe the predictably longer, slower process of increasingly-growing molecular complexity and its possible universe of outcomes.  Had those experiments patiently continued to operate for months or years, and with varying energy sources, chemical and physical conditions, catalytic alternatives, and hydration conditions, much different outcomes might have been found.  This could be performed by repeated monitoring of the different chemical species formed under one set of conditions. When the composition changes slow down or stop, a new set of reaction conditions would be introduced with continued monitoring.  Such an experimental protocol could go on for a great deal of time to maximize all possible compounds formable under such combinatorial reaction conditions.  It is my suggestion that the first proto-biotic systems approaching the definition of living systems as potentially formed under early earth conditions must be experimentally sought with extended trials that produce the greatest diversity and number of combinatorially-generated compounds.

New pathway end-products meant new future biochemical and ultimate biological potentials would become possible.  For instance, nucleic acid base-synthesizing pathways and associated pentose and nucleotide generating pathways offered a more stable future form of molecular information storage, replication and translation into other useful structures and functions.  Pentose sugar pathway genesis provided the main building block for the backbones of such information-storing macromolecules.  Only after such end products were formed could nucleic acid polymerases involving such building blocks become more chemically relevant to the pool of evolving proto-biochemical pathways.  Thus once integrated to the preceding connected pathways, each added pathway’s multi-enzyme complex, through trial and error evolutionary steps, enhances the likelihood for the final appearance of what is present-day terrestrially-based biochemistry, cell biology and molecular genetics.

 

Homeostasis, Oscillatory Dynamism and Chaos

Our considerations up to now have yet to focus on the dynamic properties and self-regulation of such newly developing chemical systems.  Also of relevance during selection between different versions of some developing molecular system are those that could behave with homeostatic recovery from various kinds of perturbations or influences.  Homeostasis allows persistence of the status quo, whatever that state actually is.  It represents an active corrective mechanism for retention or conservation of the molecular assemblage it imbues.  Even more significantly, it can influence its immediate environment as well as the chemical species that tend to be of most utility for it.  Thus the mechanism of homeostasis brings not only a uniqueness into the self-selection process for the kinds of assemblages that have the greatest stability, but it further allows those self-modulating assemblages to tailor their chemical environments to favor their persistence and thus longevity.

Capabilities for homeostatic behavior are also based on and provide a control mechanism for operation of oscillatory chemical reactions.  Oscillatory systems such as the Belousov-Zhabotinsky and  Briggs–Rauscher reactions are based on the earlier work of Bray.4  These time-dependent, non-linear, multi-step, complex oscillatory chemical changes are exemplified in some synchronized systems of linked chemical reactions which are capable of becoming chaotic under various conditions.5,6,7,8,9  These well-defined reactions can display both well-behaved and fractal behavior in some states of organization.

Figure 1A.   Regular oscillating electrochemical potential in a set of coupled time-dependent chemical reactions.  EMF (vertical axis) versus Time (horizontal axis).  Taken from Dupuis and Berland.10

Figure 1B.  A modified Belousov-Zhabotinsky reaction displaying areas of well-regulated and chaotically-escaping (bottom right area) spatial oscillations when operating in a shallow layer of diffusion-limiting agar gel over a period of time.  Taken from Dupuis and Berland.10

Such coordinated and internally-interlinked chemistry is postulated here to be one of the earliest appearances of higher chemical processing complexity.  Such complexity is both an unrecognized feature for the definition of terrestrial life, as well as a necessary one for defining the living process in a more general chemical-based context.  This aspect has become more formalized in the specialized field of chemical reaction network theory.

Looking past the inanimate-to-animate boundary in pre-biotic times, we can understand how these aspects ultimately became our present day reality.  Modern day, fluid-filled, membrane-bounded, subcellular organelles such as mitochondria, contain different networked chains of sequentially-coupled reaction catalysts, energy carriers, and reaction intermediates.  They can easily be induced to perform synchronized, repetitive oscillations.11  Such internal oscillations can and do occur within eukaryotic cells as well.12

Figure 2.   Mitochondrial-Based, Intracellular Calcium Oscillatory Behavior in Neurons.  Taken from Jackson and Thayer.12

During the oscillations, the internal biochemical, trans-membrane transported substances and bioenergetics-related reactants and products flow forward and then in reverse through their respective macromolecular catalysts or through semi-permeable membrane transporters during each cyclic oscillation. Subcellular compartment pH and osmotic changes and membrane electrical charges and potentials vary at the same time in a closely-choreographed coordination and synchronicity with each oscillatory cycle.  Such flows of chemical changes are accompanied by measurable membrane and matrix compositional changes.  Molecular synchronization in such kinetic design represents a dynamic organization of different but interdependent biochemical, electrochemical and biophysical reactions.  They all can operate in conjunction with selective trans-membrane transport and electrically-charged ion separation processes.  Synchronization implies cooperativity, specificity and coordination between the underlying components with some kind of rapid feedback and self-regulatory control to provide a varying rate of change at critical control points.

In multicellular organisms, these oscillatory, homeostatically-operating reaction sequences can also form the ultimate basis for a time-measuring, physiological mechanism of variation.  Time-dependent chemical and transport phenomena form the basis for the various biological clocks as defined by chronobiology (e. g., circadian and circannual) found in most living terrestrial organisms today.13,14    Any theory of pre-biotic evolutionary development needs to also explain how this important characteristic of most living systems was realized during the origination of the living process.  With circadian-type rhythms being found throughout the plant and animal kingdoms from the most primitive to advanced forms, it is quite probable that this represents an important feature, if not mandatory requirement for organic life to be capable of forming and surviving to evolve on a planetary surface.  For these reasons it is suggested that in the search for extraterrestrial life, exoplanets with the rotational periods and seasonal variations similar to earth may present the most likely sites to find more highly developed life forms.

 

Chaos in Pre-Biotic Evolution

Chaos in dynamically-developing systems can lead to even greater levels of chaos.  An aerodynamically well-designed airplane cuts smoothly through the air at normal speeds while under control, its motion predictable and well-behaved and continuously being readjusted to the small scale irregularities of its immediate atmospheric environment.  Slow it down to its stall speed and it begins to drop out of the sky with different aerodynamics modifying is actual path through the atmosphere.  It can then display low amplitude chaotic mechanics.  Perhaps it flutters back and forth like a dropping an autumn leaf from a tree.  If a bit of cross-wind catches it at the wrong angle of attack, it might begin to wildly oscillate or spin completely out of control.  This even more chaotic motion becomes less predictable and of greater impact on its ultimate path of movement.  It reduces the ability to recover from such a condition.  A catastrophic destructive event can then eliminate it from the landscape.   Similar things happen in all kinds of chaotic phenomena.

Chaotically patterned, complex, interdependent, coupled behavior through various action-reaction linkages are also well-known to exist down to the cellular and subcellular levels.  It is a repeating chaos-based design pattern found first in the pre-biotic chemical cauldron of early earth.  Which came first?  It is most likely that the molecular evolutionary pattern formed first purely as a result of the inherent properties of the different elements and the laws of chemistry.  It was then perpetuated and conserved at all scales thereafter during the formation of the major underlying biochemical pathways, their development of homeostatic control capabilities, and then subsequent development of membrane-based phenomenology and circadian rhythms observed in most living systems.  Thus we may allude to their pervasive and expanding presence and term this development as the first appearance of the “pulsatile nature of life”.  It could also be argued that life was a process occurring even before it became housed within a complex molecular framework we now call the “cell”.  But once the multi-compartmented cell evolved and formed spontaneously, that allowed it to move all of its now-internalized chemical activities anywhere across the landscape.  In its new packaging, it incorporated new design features.  It began to evolve new potent structure that produced new capabilities.  It was no longer simply a physical housing of the fluxes and simultaneous conversions of various molecular structures passing through the chemical reaction pathways.  It could now develop new potentials such as the long-term storage of molecular design information.   It could now develop a means of abruptly acquiring new energy-collecting capacity, such as photosynthesis.  At this stage, it was accomplished by symbiotically internalizing other developing prokaryotic protocells, such as proto-blue-green algae.  These large structural changes occurred and continued from that point on.  Continued evolution of metabolic and control pathways remained as an on-going feature.  The continued perfecting of these protocells’ catalytic landscapes for the molecules and reactions within them remain to this day.  Cellular metabolism continues to evolve, become more complexly integrated and more toti-potential. 

In multicellular organisms, the overall metabolic needs could be met through a similar integration of more specialized cell types that evolved to work in a cooperative and integrated fashion with each other.  In the big chaotically-based picture, this evolutionary synergy existed at the individual metabolic pathway level, the subcellular organelle level, the multi-cellular colony-forming level, the integrated specialized tissues and organ system level in differentiated multicellular organisms, and in the overall development and evolution of multi-species food chains.  Chaos is not randomness.  Chaos is not complete disorganization.  Chaos maintains underlying patterned behavior.  It is deterministic but simply behaves in an unpredictable manner.  However chaotic behavior can be analyzed probabilistically.  Any chaos-based dynamic phenomenon, whether chemical or membrane-based, is typically continuous, predictable and well-behaved up to certain limiting values.  Above those limits it remains deterministic but becomes chaotic and unpredictable in its moment to moment behavior.  In the chaotic ranges, abrupt and discontinuous behavior is the norm.  Rather than gradual, smoothly continuous analog operation with attendant, well-behaved transmembrane transport occurring across the overall surface of a membrane-enclosed cell, small abrupt triggered fluxes of different chemical species and a moving wave of semi-permeability is usually found.  This action potential impulse pattern for all metabolic and transmembrane flows allows the internalized biochemical systems to operate dynamically but in a triggered pulsatile-like fashion.  Triggered phenomena are designs that must incorporate chaotically-based systems.  The nerve impulse, the membrane action potential in contracting muscle cells, the motilility mechanism controlling ciliary beats in Paramecia, and the eukaryotic cell division cycle are all modern day representatives of this connection.

Chaotic design and its attendant behavior of pre-biotically formed, complex chemical mixtures could be proffered as the main underlying organizational principle for the original genesis of individual free-living systems in general.  It also explains the integrated molecular dynamics operating within each membrane-bounded compartment within a single living eukaryotic-type cell.  It ultimately translates and evolves into the chaotic design and behavior of more complex multicellular systems (e. g., simple multicellular colonial organisms and aggregated cells that make up tissues).  It seems to extend to multicellular organs, entire multicellular organisms, and even more loosely-associated societies of separate multicellular organisms.

What would have been necessary to finalize the overall organized integration of multiple pathways needed in the living process of the first generation proto-cells is  when they just began to form liposomal membranes, they would have also required the nearly simultaneous capture of some of their other interacting sequential pathways.  Thus all main integrated pathways normally found in the modern cell’s cytosol would have been sequestered or packaged during a single event.  This capture point would have had the greatest likelihood of maintaining itself if occurring during an active phase of the oscillatory reaction cycles already operating in the pre-existing unbounded primordial soup.  Other organelle-specific metabolic pathways would have become sequestered at an earlier or later stage of proto-cell evolution.  That subject will be reserved for a future installment.

An already-oscillating multiply-linked chemical system involves a reversible exchange of chemical species transformations with a complementary variation of their chemical energy content.  That added energy content would have then kept echoing its oscillatory chemical changes from that point forward through to the cells present today.  But this would not be a perfect, perpetual, undamped oscillator.  Instead it would be like a slightly damped oscillator that required a continuing but periodic input of new energy to keep it ticking away.  Like a stick repeatedly hitting a bicycle wheel rolling down a country path, a child pumping their legs in a swing, or perhaps a reciprocating and periodically-renewed swinging of the balls of a Newton’s Cradle, continuing input from energy-producing or energy-capturing pathways would have indefinitely kept such oscillations from dying out.  The periodic energy input ultimately developed into the regular intake of food to keep a cell or organism alive.  It was needed to counter losing the proto-cell’s complex integration and integrity.  The continued increase in protocellular mass, that is the continued conversion of inanimate to animate matter, became the original defining behavior of these first “life-like” systems.  If the various pathway molecules were not in an already-oscillating condition when initially captured, simple steady-state flow of reactants to ultimate products would have been the kinetic pattern that resulted.  That steady kinetic picture would not have introduced the strong need for homeostatic control to be selected for in evolutionary terms.  And without homeostatic control of its integrated architecture, the uncontrolled proto-cell would not have immediately possessed the ability to sense and react to its external environment as well as its moment-to-moment internal needs.  It never would have developed any source-seeking trophic capabilities such as chemotropism, thermotropism, phototropism or gravitropism.  Without that, finding additional fuel and nutritional sources in its environment or escaping unfavorable changes in conditions would have doomed it to an early extinction.  And without that, cell-to-cell and intra-organismal communication through various chemical substances (e. g., hormones) would ultimately not have developed.

During the earliest portion of the pre-biotic period, a set of changes in the composition, complexity, connectivity and range of possible interactions would have had to take place.  Ultimately this would have been followed by a sorting out of more successful from less successful molecular ensembles.  This sorting of the more successful from the less successful chemical reaction sequences could also be considered an analogue to Darwin’s selection of the fittest species but restaged within a pre-biotic chemical evolutionary process.  With some coupled reaction sequences, enhanced overall net throughput rates would have been one of the critical factors for their longevity and conservation.  For other more beneficial molecular combinations, new property appearance could lead to linking to a new energy source or to a lasting new functional development in future chemical compositions.  An example of a new property might be the development of the feedback control loop with all of its dynamic ramifications.  It is at this moment in our timeline that we may start the formal pre-biotic to proto-biotic evolutionary stopwatch.  At this point we now would see an evolution of the molecular precursors to the eventual biochemical systems that will ultimately find their way into the first independently self-repairing, growing, self-surviving, homeostatically-rebalancing, and ultimately self-propagating proto-cells.  The evolutionary paths that were followed during this pre-biotic time and during the time to follow, however, might generally be unrecognizable when viewed through the standard Darwinian models.

 

Combinatorial Molecular Evolution: from Molecules to Macromolecules to Linked Chemical Reactions

Let us look at this timeline from the broadest unifying viewpoint.  During the earliest stage of pre-biotic chemical development, it is commonly assumed that a relatively small number of ultimately successful pre-biotic starter molecules evolved in a rather straight-forward and somewhat simplistic manner from even simpler compounds present under reducing conditions on early earth.  But this is not necessarily the direction or path that was originally followed in evolving into modern, post-life times.   As described earlier, it probably originated from a surprisingly more complex background.

Moving to the next higher level of organization, let us not assume that the ultimate complexity in modern day biochemistry first had to originate and then build up in a straight-line manner from a simpler, limited mixture of smaller-sized molecules.  Additionally we may assume that over time new and more complex reaction pathways developed until the mixture of different partially-formed pathways became complex enough to provide for all of the subsequent overall chemistry needed to self-regenerate and self-propagate.  As noted, we begin with a highly complex and multitudinous mixture derived through a combinatorial genesis process.  We know that such keragen-like complex mixtures are actually found extraterrestrially in carbonaceous meteorites.  They were probably first generated when a star nucleosynthesized the carbon atoms through a triple alpha helium fusion process and then eventually blew apart in old age.  They may have even earlier been part of a former, fully-developed planet that ultimately was destroyed in some kind of cataclysm.  The first self-sustained chemical systems behaving as early versions of living processes actually would have originated through sorting out from a higher level of complexity rather than from gradually growing out of a lower level of complexity.

But did chemical complexity completely originate on the earth alone?  Under highly reactive chemical conditions that can exist in shockwave-rich, interstellar plasma and dust clouds and similar localized environments, various kinds of complex chemistry must also occur.  This would be most favorable in the cooler regions of such high energy processes.  It could lead to a multitude of chemical species by having both the density of matter and the reaction conditions conducive to dissociation and re-formation of many kinds of inter-atomic chemical bonds.  Pure carbon is relatively abundant in interstellar and peristellar space.  Carbonaceous meteorites are a common class of space rocks containing all kinds of interesting carbon compounds.  They have been found to contain elemental carbon, hydrocarbons, larger organic molecules, amines and amino acids, carboxylic acids, water, alcohols, sulfides, reactive intermediates and similar primordial starter compounds.  Graphite, graphene, fullerenes, nanocarbon structures, and soot provide a virtual infinitude of molecular skeletons composed of pure carbon atoms that could also be found in these extraterrestrial locations.  Free protons and electrons, as well as mono-atomic, reactive hydrogen atoms are abundant in stellar vicinities.  Whenever they encounter or collide with carbon atoms and carbonaceous molecules at temperatures cooler than plasmas, they can begin reacting with such carbon-rich structures to form the broad range of hydrocarbon-based categories and chemical species also found on earth and in its geological strata.   Atoms of other elements are also present to react as chance permits.  They could also react and form many kinds of hetero-atomic hydrocarbon molecules.   Under such conditions, a huge library of differing molecular structures and sizes could more rapidly form in deep space and be found in massive amounts anywhere in the universe.  It might be like a reaction vessel in an organic chemistry laboratory that simultaneously contained all of the reactants, catalysts and intermediates that could ever be mixed together and allowed to synthesize a huge combinatorial library of compounds.  All of them could thus be generated extra-terrestrially15.  So we can anticipate that such “organic” molecules not only occur in quantity on planetary surfaces but may be widely pervasive throughout interstellar space.  This expectation alone provides a high expectation that living, carbon-based systems may be common throughout the cosmos.

These early-stage libraries of chemical compounds, whose developing molecular compositions would in part be dictated by the availability and concentrations of differing species, could have had to emerge from a process in which many combinations and permutations of primary molecular structure might begin to form more energetically-stable compounds.  Smaller atomic fragments and neutral molecules could tend to grow into larger molecular sizes, functional group content and complexity.  Delocalized electron bonding, as abundantly found in the ubiquitous graphene molecules in interstellar space as well as within the stacked base-pair core of the DNA double helix, would enhance the probabilities for the long term complex molecular stability.  In the more stable DNA, the additional stabilization energy occurs through pi-pi molecular orbital overlaps and sharing of pi electrons (i. e., delocalization) between successive pairs of stacked aromatic base pairs.  This makes their interior base components less prone to dissociation at normal temperatures compared with non-resonance stabilized monomer units in other types of macromolecular polymers.  Such an exceptionally stable molecule as DNA lends itself to multiple evolution-enhancing functions.  When considered along side the lower molecular stabilities and higher chemical reactivities of polysaccharides, RNA or most readily-denaturable proteins, DNA’s 3-dimensional sterically-hindered and electronically delocalized structure demonstrates the value of maintaining long-term genetic information in a higher fidelity, more durable molecular repository.  It makes sense that the most stable macromolecules would become the best Darwinian-selected candidates for long term maintenance of system design instructions.  It makes even more sense that such higher stability would provide a more difficult-to-corrupt molecular format that then led to a very long period of conservation between error-generating molecular events.

So earlier periods of pre-biotic combinatorial chemistry would have been richer in simpler and smaller polyatomic molecules.  Only later, as the molecular size and structure of smaller types of monomeric molecules built up and became more complex, could they have created even more stable types of macromolecules with more elaborate life-related functions.  In evolving macromolecular terms, this implies that DNA and its double helical structure did not develop as early as polysaccharides, proteins or RNA.  The assembly of molecules within those classes involved the repetitive addition of similar smaller units generating larger overall molecular structures.  This polymer growth tended to reduce the total number of chemically-reactive groups within the combinatorial mixtures that involved differing types of chemical bond formation.  Thus pre-biotically-formed polymers may very well have originally formed not only as homopolymers, created from identical chemical monomers, but would have also included all manner of heteropolymers as well (e. g., covalently-bonded glycopeptides and glycopolypeptides, glycolipids, and precursor t-RNA amino acid-RNA hybrids).  Through this combinatorially-driven complex chemical evolution, some developed greater stability relative to the environmental conditions while others developed only moderate stability and remained relatively labile under the same conditions.  In certain cellular processes, ease of molecular modification could provide an evolutionary advantage, so we have examples of both stability-seeking and modifiable-seeking evolutionary end-products within the same developing life paradigm.

Long-term information storage could likely take advantage of the more persistent nature of the longer-lasting varieties.  The ultimate and eventual development of RNA and DNA as the genetic information repositories rather than other more complicated heteropolymer combinations may have more to do with the limited number of potential monomer combinations that the resulting genetic code would need to conduct trans-generation information storage and transfer.  That would work against the continued ever-increasing expansion of molecular complexity once the earliest versions of a living process developed.  Continued generation of an unlimited pool of combinatorial possibilities after the first self-sustaining and self-selecting living systems began operating would have been both counter-productive and less likely.  Those first living systems already had strong survival potentials built into their operating chemistry.  The latter situation creates a reverse pressure on the open-ended evolutionary possibilities generated from a combinatorially source of starter compounds.  So the final set of successfully performing co-operating molecular species that were to eventually become the basis of all terrestrial metabolic pathways would now become structurally and reactively optimized somewhere between an overly-simple and overly-complex mixture.  This represented the next stage of growing complexity of the pre-biotic chemical world.  The evolutionary development of the genetic information system within the previously developing protocellular chemical framework will be discussed more at length in a future installment of this series.

 

The Advent of Specificity

We can’t describe parallel events in detail when written communications are of a singular, simple linear and sequential nature.  The development of intermolecular specificity of each component’s interactions with the substrates, intermediates and other components with which it must form complexes provides the ultimate basis for true growth, repair and reproduction of life processes.  Stereoisomeric specificity would also now be capable of developing within the evolutionary context.  To examine this new property we need to return to the earlier portion of the combinatorial period.  With the advent of an era of all manner of polymer formation, new combinatorial libraries would more rapidly spring into existence across the landscape.  Large molecules capable of developing secondary structure and finally tertiary superstructure would have appeared and then be found interacting in many ways with each other.  At this stage of molecular evolution, high reactant and product specificity would now become possible for the first time during the overall operation of chemical catalysis on early prebiotic earth.  And for the first time, optimized, sequential, multi-step catalysis could become a practical possibility.  Two or more chemical reactions could now become linked together such that the reaction products of the first would become the reactants of the second.  And when the specific catalysts formed super-molecular complexes or assemblages, the close juxtapositioning of the two reaction sites and presentation geometry of intermediate metabolites produced a tremendous enhancement in the overall maximum kinetic throughput of that multi-step pathway.  With the invention of molecular selection and reactant/end-product specificity in catalysts, the more highly selective nature of catalytically-based compositional changes dramatically improved and accelerated all subsequent chemical evolution.

Extrapolating that specificity-based enhancement factor to a longer sequence of chemically linkable reactions, the ability for each step’s catalyst to become a member of a functionally-optimized complex of macromolecules for the combined range of catalysts provides a further Darwinian quantum jump in the kinetic throughput of that pathway, and coincidentally, the Darwinian superiority for its conservation.   During this period, the proto-metabolic pathway potential was born.

 

Did All Life Spring From a Single-Type Protocell?

Biology has as one of its core assumptions that the “tree of life” sprang from a single taproot.  All of these described chemical progressions, digressions and changes were inevitable because of the inherent chemical, physical and functional properties of each resultant compound present.  Within the same range of temperature and other environmental conditions, these molecular processes could occur anywhere in the universe.  But Chaos Theory allows us to imagine that subtle differences in the contents and conditions of one pool or niche versus others would lead to major differences if allowed to proceed indefinitely.  So let us re-examine one of our earlier assumptions within this new context.

To summarize and further elaborate, after the formation of many kinds of smaller molecules through non-living processes, the more reactive (less stable) ones would have preferentially tended to combine or exchange atoms with others they encountered.  They could also break down to smaller-sized molecules that possessed altered and unique structural features.  But some of the reactions would have led to increased molecular sizes, and over sufficient time, ultimately to molecules we now term macromolecules.  Differences in native stability of each kind of reactive species, and the physical and chemical conditions existing in that unique niche could, according to Chaos Theory’s Butterfly Effect, have biased the structure and composition of the future chemical products that would subsequently form.  Such composition bias would have expanded the combinatorial repertoire of possible chemical species formed during this earlier period of pre-biotic earth.  In this primordial soup, we find pre-biotic evolution self-sorting itself out into successful combinations, while destroying or degrading and recycling less successful ones.  In such a molecular free-for-all we have the very first instance of the dynamic combinatorial chemical experiment, with life as the final, distant, self-propagating, negatively-entropic reward.  If one wished to make an analogy with later biological evolution, this “jungle” of pre-biotic chemistry resulted in the survival of the fittest or most chemically functional.  It occurred through spontaneous self-selection and without involving any genetically-directed form of mutation-based mechanism of evolution.  But the later composition of such evolving mixtures certainly were dependent upon the “blending” of preceding chemical reactions and molecular properties.  It might be characterized as both Darwinian (i. e., selection) and Lamarckian (i. e., non-genetically produced) in those respects.

If we could have visited pre-biotic earth at this time, what would we have found?  These smaller, simpler molecules, such as amino acids, monosaccharides, polyols, aldehydes, organic acids, amines, and nucleic acid bases accumulated, concentrated and further dehydrated on all kinds of heated dry surfaces in various protected niches.  Some then  dissolved into more water-rich environments like rain puddles, dew droplets, wet mud, thermal hot springs, submarine hydrothermal vents, air-water interfaces and rock crevices.28  Under such sequential or cyclic reaction conditions, larger molecules such as dipeptides, oligopeptides and polypeptides would have been more likely to have formed during the higher temperatures through simple dehydration reactions in the presence of such simple and relatively unspecific catalysts.25, 26  Simple catalysts could certainly include various minerals, zeolites, clathrates, organo-metallics (e. g., metal-porphyrin and metallic ion-captured fullerene hybrids), graphite, free radicals, photochemically-activated compounds, and acidic, alkaline and metal ion-rich waters.27  And at the point where oligo- and poly- peptides of a minimum length and complexity formed abiotically, new catalytic possibilities and starting materials for more complex chemistry to follow would have rather quickly become available to the pre-biotic chemical world.

Besides simple dehydration chemistry, more complex chemical reactions and molecular structure rearrangements would undoubtedly have also been occurring.  Simple random ring-opening polymerization of N-carboxyanhydrides of a mixture of amino acids will lead to an even broader library of polypeptides with mixed amino acid sequences and chain lengths.16, 17   Some of these early oligo- and poly- peptides could have contained the same or similar amino acid sequences as found in modern day active sites and binding sites of biochemically important enzymes.  Unusual amino acids were also produced and incorporated into macromolecules as have sometimes been found in primitive microbes and meteorites.  Important functional molecular sites are also found within the structure of motility-associated, cytoskeletal and other non-enzymatic proteins.  For enzymatic forerunners, these primitive “naked active site sequences” would likely have possessed rudimentary, low-specificity catalytic activity.  As an outcome of their very simple and unselective nature (due to lack of the additional assistive tertiary structure and geometries) they could have generated many more kinds of possible chemical products for the types of reactions they catalyzed during that earlier period.  Consequentially another door opened into creating even more complexity of composition of the starter sets of chemical species present in the earliest versions of pre-biotic chemistry of the primordial soup.  At that earlier time, that would have provided an evolutionary advantage for the development of more potential products and molecular speciation through now-favored, pre-biotic, linked reactions.  Such increased diversity of chemical species present could have thus promoted the development of more complex, inter-connected chemical reaction systems they could participate in.  This was not a linear or simple branched-tree development.  It would have followed many branched and closed looped flows of chemical structure modification, with any given chemical reactant potentially being available for two or more competing reaction sequences to follow.  The overall library of compounds finally formed within one location could, with further changing conditions, have become skewed in its composition many different times in this early formative and evolutionarily molecular selective phase.  Even in this finer detail involving chemical reactions, we see a familiar kind of molecular analogy to classical Darwinian evolution.  That is suggested to have occurred in this pre-biotic battle ground of molecular evolution.

Such molecular diversification might easily be anticipated given that so many compounds would have contained a variety of chemical bonds of varying strengths and reactivities.  Continual cleavage and rearranging of atoms and small atomic groupings within and between somewhat larger molecules would have led to all manner of permutations and combinations of molecular structures.  At this stage the primordial soup of pre-life would have been indistinguishable from a modern day, well-stocked chemistry lab in which all the chemicals have been stirred and reacted together; that is, a version of a massive combinatorial chemistry experimental library of chemical compounds.  Extremely complex inter- and intra-molecular reaction chemistry would have been continuously taking place within it.  It would have reached complexities of millions of different chemical compounds and chemical reactions being co-present and operating.   Then, as posited earlier, a wide variety of niches subjected to a variety of different reaction conditions over a very long period of time led to many differing versions of early life processes and designs.  In such a model, we have not just a single original protocell becoming the first generation of all subsequent life.  We have numerous variations on a theme popping into existence and becoming self-propagating at somewhat different times and locations.  Each then would lead to a similar, but independent line of descendants.  This model seems more consistent with our currently emerging understanding of early cellular evolution of structure.

 

A Well-Stirred Soup is Not Always Needed Before Serving

Novel compounds would, more likely than not, have been formed and modified or consumed in a long-term set of reactions leading up to the first successful “living” forms.  This period could easily have lasted many millions of years, beginning just after the Hadean period.  It is likely to have continued into and beyond the end of the Massive Heavy Bombardment in earth’s geological history.  It is suspected by many that during this latter phase of earth’s geological history, most of its water arrived principally in the form of cometary impactors.  And the atmosphere was much less dense then.

During this early part of the transition from non-life to life, we see multiple routes in the progressions involving the evolution of available molecular compounds.  It pre-biotically began as an unorganized, uncoordinated, and somewhat chaotically-generated collection of molecules and individual macromolecules that had localized spurts of rapid increase in complexity interspersed in larger areas of more slowly progressing chemical changes.  Different locales provided different chemical and physical conditions and catalytic actions.

In our model of pre-biotic evolution, the amino acid sequences and chain lengths were somewhat randomly formed in the beginning.  Of those that possessed some kind of catalytic activity for assisting other molecular reactions to occur, those niche-like micro-environments and their chemical contents would have tended to evolve more rapidly than micro-environments with only non-catalytic amino acid sequences.  In this manner, as amino acids condensed into short peptides, oligo-peptides and polypeptides, the evolution of final enzyme structure would have begun with the active site sequences, and then the non-active site sequences would have been added on at later times.  And in enzymes that possess more than one segment of their primary sequence composing an active site, these “accessory” sequences confer added specificity to the catalyzed reaction.  With specificity enhanced, the enzyme and the resulting chemistry it supported would have simply evolved more rapidly.

And what about the origins of similar, but non-identical enzyme molecular structure in analogous enzymes as found in prokaryotes and eukaryotes?  In a world that would have had various niches of differing molecular compositions we might even expect to see a chemical version of inter-niche competition for chemically-based dominance.  Perhaps this is how the most prevalent biochemical pathways found in both prokaryotes and eukaryotes, such as the glycolytic pathway, or the parallels between the structure of prokaryotic and eukaryotic ribosomes, first began.  Many other similar comparisons beg for a rational explanation and plausible mechanism within a pre-biotic and evolutionary model that deal with the earliest origins of life on earth.   The model presented here, mostly derived from the work of many others, offers some insights towards those ends and reflects a Darwinian and meta-Darwinian type of style of progression even in the chemistry operating prior to the first protocell development.

This progression was anything but a simple linear set of steps as many have assumed.  Complexity and non-random behavior were abundant.  Repeating patterns of interactive behavior at different scales of size continued to persist.  They progressed and morphed from molecular to cellular to multicellular to organismal scales with all operating through competition, selection of the most efficient, adaptable and dominating over lesser forms and the end result was an indefinitely persistent collection of self-replicating units.  One localized niche of more rapid chemical evolution might lead to a particular catalytically-active protein with a specific amino acid sequence in its active site, while in a different niche, a similar but non-identical sequence could have developed that concurrently provided an analogous, but subtly different starting point for the continued evolutionary development of the modern versions of that same specific enzyme-like polypeptide.  As in the Butterfly Effect, Chaos Theory predicts that if one begins with subtle differences, the subsequent steps of evolution or progression can lead to quite different outcomes over time.  Thus we can envision the somewhat parallel evolution and development of at least two separate-but-similar basic pre-biotic chemical design patterns that would eventually become incorporated into or captured by the ever-present, membrane-forming packaging chemistry and lead to independently formed but separate categories of living cells.   This parallel chemical evolution conserved certain minimally-necessary chemical pathways while allowing other unique pathways to develop and become integrated with those “core” pathways.  Such roughly parallel evolutionary development would have been most easily seen to have occurred during an early period of coordinated organization of sets of different molecular catalysts.  It would not have been as facile if developing after the membrane capturing stages for packaging such complex integrated pathways of catalysts.

 

Other Enhancement Factors Come to the Party

Abiogenically produced, catalytically-active, amino acid-based molecules, with and without more reactive atomic adducts like Fe(II), Zn(II), porphyrins (and related heterocyclic cofactors) and S are postulated to have possessed and conferred some longer term survival advantages to the local primordial soup they were a part of.18,19,20  Capable of capturing and temporarily photochemically storing electromagnetic energy of visible wavelength photons, porphyrins and other light-capturing pigments in particular became an open doorway for direct solar energy injection into the formation of higher energy content chemical compounds (photosynthesis).  The advent of photochemically-excited molecules and their ability to link to the energy needs of the growing chains of linked chemical reactions developing proved indispensable to providing a long-term solution for life’s ultimate staying power.  It provided the ultimate delivery of chemical and electrochemical energy that fed into subsequent biochemical operations (e. g., electron transport chain).  Thus an inexhaustible supply of energy was finally married to the earlier, finite-sized chemical energetics scheme (i. e., chemosynthesis) originally developed during evolution of pre-biotic molecular structural changes and the attendant synthetic reactions.

 

Complex Complexations

Besides new energy-source development, other molecularly-based properties would also have offered evolutionary advantages that might have conveyed a longer-lasting character to their particular version or niche of the primordial soup.  Thus overall chemical species that developed in one particular niche might have followed a more divergent course than those that occurred in other niches.  We would expect that many niches might have ultimately failed to finally produce the first definable self-replicating living systems with only a much smaller number finally attaining such successful compositions.  Those successful compositions would not likely have resulted in identical chemical potpourri at such an end point.

With increasing molecular structure, these evolving polypeptide-like, catalytically-potent sequences of amino acids with built-in specificities acquire new complex-forming capabilities.  Each new configuration generates new chemical reaction potentials.   Macromolecular complexes of multiple polypeptides would also have been forming at this stage.  Other growing macromolecules, such as ribonucleic acids, could additionally become complexed with such polypeptides complexes, such as occurs in ribosomes and RNA polymerase/depolymerase.  The added non-active site structure could allow integration of protein-based catalytic processing with nucleic acid-based information control in a small number of molecular locations.  With this event an important new capability offered new and important evolutionary possibilities for the first time.  High fidelity, long-term, indefinite replication through directed synthesis of polymeric and monomeric molecules could now become a reality in the evolutionary mixing pots around primeval earth.

The earliest self-organized, chemically integrated, self-modulating assemblages of all kinds of macromolecules could then have formed at this time.  These would take the form of multi-macromolecular complexes.  With their advent, some would become self-sustaining.  Up until then, their “pre-life” structure would have only formed  combinatorially.  And such a process was very slow due to the low probabilities of each species being generated in that fashion within complex mixtures containing many interfering or inhibitory substances.  Ultimate integration of the functions of two related catalysts would have sped up its selective evolutionary advantages.  Finding a third combinatorial component would have again been a long shot, but once present, major compositional changes would become exponentially more rapid and available.  These multi-enzyme type complexes would have become the brightest stars and most conserved forms of carbon-based catalysts in the pre-biotic chemical world.  Their evolutionary advantages were revolutionary as well.

In any watery environments where they thrived, their appearance would have been deceiving.  Viewing such pond scum and bubbling tar pit fumaroles, important but invisible changes were incubating.  For convenience, we might refer to such unbounded, open chemical systems lacking an enclosing membrane as a form of “proto-cytosol”.  With liquid water present, it could have had a colloidal or semi-fluid gel-sol consistency.  If kept in a relatively viscous liquid condition or trapped on a mineral surface, such functionally-related, macromolecular assemblages would have added longevity.  That longevity due to surface adsorptions could have been extended almost indefinitely while other processes and changes continued to evolve and be tested for complementarity with it.  This kind of unbounded assemblage only needed to eventually define and permanently unify itself through enclosure and capture by a proteolipid or liposomal structure.

 

Gift Wrapping

Liposomes are well known to be capable of spontaneous self-association from abiotically or pre-biotically synthesized lipid molecules.  When that occurs, they can then form the platform for a more complex boundary membrane.  Essentially this already-described proto-cytosol is envisioned as quite similar to present day eukaryotic cellular cytoplasm without the other normally existing cellular and subcellular structures (mitochondria, endoplasmic reticulum, Golgi apparatus, lysosomes, peroxisomes, cytoskeleton, cilia, centrosomes, etc.).  It would have also lacked the control information repository (the nucleus) to indefinitely support it’s operational and replicational designs or require things from.  The proto-cellular liposome-style membrane was functionally very primitive and lacking in the many modern cell components, functions and capabilities.  Initially the proto-cytosol might not have had any structural or dynamic components, such as microtubules and microfilaments to enhance internal transport, mixing and bulk liquid flows.  But once such subcellular dynamic molecular structures were present through their appearance from combinatorial generation, they could have provided a large kinetic advantage to the macromolecular milieu in which they resided.  At that point it would be likely to encounter various versions which ultimately would increase its rate of further evolutionary changes.  At such a point in evolution, the proto-cytosol might not have to remain reaction rate-limited by simple laws of diffusion.  It could now carry starting nutrients and final reaction end products to and from sites of reactions within it more quickly.  It could now bring various macromolecules into proximity with one another to explore new potential interactions and novel chains of sequential catalysis or other higher functional relationships.  The beginnings of the self-assembly of complexes and super-complexes of protein-based catalysis and full metabolic pathway development could now proceed even more quickly from this point on.  A Darwinian form of Survival of the Fittest would accurately describe how such successful versions of multi-enzyme complexes became the most dominant types in such highly complex and dynamically mixed combinatorial soups.

At this stage let us now imagine further details of the developing proto-cytosol prior to the period of membrane capture.  Through combinatorial protein formation, rudimentary polypeptides possessing the molecular functions of tubulin plus actin- and myosin-like molecules are present.  Perhaps naturally-occurring inorganic pyrophosphates, formed in hot pockets of waterless rocks, were then dissolved into the mixture.  Inorganic pyrophosphate contains high energy bonds capable of phosphorylating other molecules much as ATP provides in modern biochemical terms.  That would have provided the necessary chemical energy to allow the phosphate-based biochemical functions underlying more dynamic activities, such as activation/deactivation control, to evolve.  The microniches where this molecular-based dynamic mixing and transport occurred would have greater chemical reaction rates.  Such accelerated behavior allows those motile microniches to dominate the scene.  They would be able to out-compete the relatively quiescent, non-motile locales adjacent to them.   In our protocell-free world, we could still have proto-cytosol flow that would mix and transport the millions of different kinds of molecules throughout the reactive protoplasm-like masses.  Perhaps inorganic pyrophosphates or organo-polyphosphates provided the chemical energy for this molecular dynamism.  This active flow might appear similar to the microscopic phenomenon seen within a leaf cell of the Elodea plant, or the cytoplasmic flow of a slime mold, or a neuron’s axonal flow, or inside the extending pseudopod of an amoeboid cell.  Very small scale concentration gradients of calcium ions could have induced and sustained such streaming behavior.  This type of fundamental protoplasmic motility occurs in a very broad range of present day cell types.  The main difference from them might be that in the developing, complex, pre-life soups on pre-biotic earth this unbounded, free-flowing, hyaline-like, light brownish- or amber-colored proto-cytosol would have been filled with polypeptide macromolecular supercomplexes.  It also contained the smaller reactive molecular building blocks that were being processed to build the larger molecular structures present.  Some of the smaller-sized chemical species could then become involved in various kinds of chemical reactions and conversions catalyzed by the super-complexes.  Internal mixing would not only speed up the overall reaction rates, it would enhance the rates for self-selection of more integrated and efficient dynamic changes.  There would have been an evolution of the streaming phenomenon culminating in the most effective combination of participating molecules, as seen in the broad range of modern cell types.  As most chemists learn, rapid and adequate mixing is almost always beneficial to synthetic and other multi-molecular chemical reactions.  It should only be avoided when uncontrollable reaction rates are possible, as in the formulation of nitroglycerin and other explosives.

Proto-cytosol at this stage could exist and remain sustained without any nuclear structures or functional equivalents.  No subcellular membrane-bounded organelles or outer boundary membranes would yet exist. This means that no semi-permeable membranes would be found separating or compartmenting this unbounded cytoplasm into differing regions of pH or other chemically important modifications.  No outer plasma membranes would be found separating this cytoplasm from a more chemically deficient, chemically hostile or toxic external watery environment.  The physical boundaries for the pools of the pre-biotic, water-based reactive mixtures would have been the gross physical mineral surfaces and finely-packed mineral particulates that formed those ponds, pools and puddles.  These were the initial de facto vessels housing the proto-life chemical processes.  Those would also have presented catalytically-active surface sites to their contained mixtures.

A major advantage would have finally been conferred on such complex chemistry through any means of sequestering and consolidating its component mixtures.  Semi-permeable membranes would have served this role once they could spontaneously form and capture these complex dynamic aqueous mixtures.  And without systems of membranes, active transport or other kinds of subcellular compartmentation-based control could not exist to help maintain marginally-stable macromolecular complexes and optimum conditions for their activity.  Many, if not most, of such unsequestered complexes might ultimately have failed to thrive.

But there is more to this stage of pre-biotic chemical evolution.  As stated, there could be irregularly-shaped masses of gelled regions made primarily of large macromolecular and super-macromolecular complexes.  Some would have collections of sequences of catalytically-active polypeptide/protein-like macromolecules.  And perhaps a few of these could form more molecularly coordinated units capable of assisting other chemical conversions.  Such integration and complexity could speed up the process of creating even more kinds of molecular species within the combinatorial libraries of compounds forming spontaneously all over the planet.  Such sequential macromolecular complexes could take a small molecule in and process it rapidly through a series or chain of stepwise chemical transformations.  The result would yield whatever inherently useful products that could produce more of the same components involved in this rudimentary form of metabolism.  Such complexes of functionally-related macromolecules could constitute the first primitive physical states of what might later be termed a metabolic pathway in more modern day life forms.  In one sense it was the very first example of the assembly line.  The actin-based movements within this semi-liquid milieu might likely present the classical appearance of a reversibly-changing sol-gel much like that of the modern eukaryotic cell cytoplasm.  But once lipids appeared, membrane-bounded vesicles would have also co-existed.  As has been seen in experimental, geological and meteorite samples, fatty acids, glycerol and other simple lipid compounds can be produced abiotically.21

We view this transition through a systems biology lens rather than the classical reductionistic one.  Thus the reversibly-associated assemblages of metabolically-related groups of enzymes self-aggregate through formation of weak chemical bonds into super-macromolecular complexes.22  Many enzymes possess a multiple subunit kind of structural design for optimal operation and regulation.  As such all subunits are usually needed to be present for maximal reaction rates or at least maximum controllability.  Often some subunits function as control switches that are linked with other parts of the metabolic and life processes within the cell.  With many such multi-component complexes, the main catalytic site resides in either one of the components or in a commonly shared site involving identical or complementary subunits.  So even without the control components, such catalytic compounds could have first appeared and operated as catalysts for long periods prior to a final control structure being overlaid on such complexes.  And once a complete active catalytic site for a single enzyme had finally evolved, such enzymes would themselves become physically associated with other enzymes.  Multi-enzyme super-complexes now would appear as the dominant design feature.  When such enzymatically active entities find themselves closely associated with others that also catalyze related reactions, super-molecular complexes capable of performing longer chains of rapid reaction sequences would likely arise.  If complexed with other enzymes not well-coordinated with them, such mis-matched complexes would not operate to produce an abundance of end product that was beneficial to its long-term conservation.  We see various versions of each subunit and sequential enzyme interacting on an evolutionary time scale until the optimum geometric juxtapositioning of the linked active sites was found through trial and error combinations.  At that point the fully evolved advantages for that optimized operating arrangement becomes self-determined and self-selected.

As this strategy is repeated with other multi-protein complexes, the rate of new and more complex super-macromolecular arrangements can be expected to increase dramatically.  It is even possible to expect that more than one version of these macromolecular complexes could operate well enough to have good survival potential.  In such cases, that would give rise to slightly different-but-persistent self-propagating molecular forms.  This could be the origin of differing groups of subsequently evolving organisms.

These kinds of quantum leaps in super-molecular complexity of the early pre-biotic soups around the world are quite different and unique compared with the smaller step changes characteristic of more Darwinian evolutionary theory. In living cells of today, these super-macromolecular complexes could be found making up the “gel” rather than the “sol” portion of the extra-organelle (as well as intra-organelle) cytosol.  Gel-sol transitioning in modern cells’ cytoplasms is typically associated with various activities, such as internal regions of motility and formation and breakdown of structural proteins making up the cell’s cytoskeleton.  This segregation of gelled macromolecular supercomplexes are considered to be the initial integrative step towards the consolidation of the first highly complex and organized structural and functional framework we ultimately will call “the living cell”.  Sol-gel transitioning of the proto-cytosol has been a classic description of the behavior of cytoplasm forming the basis of amoeboid movement of some types of cells.  This macromolecular complex self-assembly, disassembly and self-selection might also be argued to be the earliest preliminary stage of the combined non-Darwinian and Darwinian evolution of life on earth (or anywhere else in the universe that conditions would allow).

The ultimate driving force for this stage of pre-biotic evolution is seen as physicochemical and thermodynamic in nature.  Its combinatorial beginnings and initially unbounded operation would have allowed for the eventual  formation of a panoply of macromolecular super-complexes.  Once all possible versions of super-macromolecular complexes were generated, the Darwinian self-selection through a competitive, survival-of-the-fittest type of model provide the next mechanism along the path to the development of independent, free-living systems.  Greater complexity could inevitably lead to greater capabilities for such macromolecular complexes.  Through increasing complexity, such proto-cytosols would develop new ways to survive and ultimately to propagate with higher fidelity.  More successful combinations of enzymatically-active reaction sequences could simply outperform their slower combinatorial kin.  The most successful could minimize the transfer distances and transfer times that metabolites took to move from one reaction site on one catalyst to the next during a sequential set of reactions.  That might occur whenever a specific set of enzymatic macromolecules would combinatorially develop appropriate non-active site structure to allow multiple enzyme complexing to occur.  And such complexes would initially be found in many different geometric juxtapositions with respect to each other.  The more optimized complex structure versions would be more likely to have the fastest overall throughput from initial reactants to final products.  This could initially bias the overall molecular composition in favor of the most rapid overall metabolic effectiveness.  Once such complexes attained their optima in overall throughput rates, the next evolutionary challenge of control and modulation of that throughput could begin to exert additional self-selectivity on the longevity of those macromolecular complex structures.  The ultimate end-point in this molecular evolution would likely be of a complex, metabolically-integrated design of various self-regulating pathways.  Those pathways could then be coupled together in terms of their raw starting materials and their final synthetic end products.  And when the collection of end products from each type of integrated pathway happened to be the generation of all of the necessary building blocks for formation of new proto-cellular structure, we might just have arrived at the first definable, self-perpetuating system we could argue was now imbued with the living process.  With the advent of metabolic control points and feedback inhibition of metabolic throughput, multiple independent proto-cells would be more able to feed and reproduce in a coordinated manner, allowing colonial and multicellular association to evolve.  Without an internal down-regulation built into each proto-cell, raw starting materials (i. e., foodstuffs) would be quickly depleted and the entire population might then die out.  This molecular jungle just described is part and parcel of earth’s early pre-biotic molecular evolution.

 

A Definition of Terrestrial Living Systems

Perhaps it would be reasonable at this point to lay the ground work for describing first life by offering a more rational and detailed description of what is meant by life.   “Life” has been defined, supplemented, redefined and extrapolated to many systems over the centuries.  Our earliest definitions had very little to do with basic biology.  Ancient humans and even lower animals have an intrinsic understanding and recognition of a previously animated and alive organism from its non-animated, decomposing form after some mortal injury, illness or natural death occurs.  That is insufficiently detailed for this subject to be framed within.

Computer scientists have for decades worked at identifying various properties of living systems and attempting to emulate them through a combination of hardware, firmware and software with varying degrees of success.  It is likely at some future point, the improvements of artificial intelligence, fuzzy logic and neural networks that can learn and reason and synthesize new information in more human or animal psychological ways will be combined with a vast database of human-acquired knowledge.  At that time they will become psychologically and sociologically indistinguishable from a living human being.  Such a system, interfaced with robots, could extract all of the raw resources needed to make such machines and to utilize automated equipment to process those resources into finished components.  Those could then be assembled into duplicates of all of the components of such systems.  Thus such computer-controlled robots making complete copies of themselves from scratch, transmitting their operational programming, and being able to sense and respond to their environments would become an even more complicating reality in the continuing definition of life.  But are we putting those characteristics ahead of the chemical-based ones that terrestrial life began with?  I leave that argument to others while returning to the chemical-based life forms and their origins.  It is this question that must be understood.  Panspermia, or the seeding of life on earth from other extraterrestrial sources, simply kicks the can down the road.  It still does not explain how our carbon-based life sprang from inanimate matter.  Whether on primeval earth or from elsewhere, this story must be told.  It must be experimentally verifiable if we are to see our origins clearly.

Silicon is similar to carbon in that it can form tetrahedral and pi bonds with hydrogen, carbon and other more electronegative elements.  In the tetrahedral valence, stereoisomers can form and form analogous chirality in the compounds they are part of.  Other silicon-plus-chlorine-based “life” forms have been previously postulated by some as being potentially capable of most or all of the molecular complexity and reactivity that terrestrial carbon-oxygen life chemistry is found in.  It could have evolved in a parallel extraterrestrial environment with significantly different chemical and physical conditions.  Is life an inevitable process that simply depends upon the environmental conditions and absolute amounts of specific elements available?  Is non-carbon life possible and a fluke of the location in the universe where average temperatures are higher and various elements may richly or sparsely occur?  Stars in different stages of nucleosynthesis that have undergone collisions, disruptions or stellar-sized explosions can eject different collections of elements into their neighboring regions as plasmas, gases and dust which would reflect the composition of those stars just prior to their mass ejections.  Some of these more unusual chemically-based life forms could develop and evolve in environments quite different from those on earth.  Any environmental variables, such as temperature, pressure, presence of ionized elements or molecules, the presence of radioactively decaying isotopes or intense levels of gamma/x-ray/ultraviolet/visible wavelengths of light could skew much of the “bioenergetics” and molecular “biochemistry” that results.  Even whether the biochemistry takes place in a fluid or gaseous milieu could provide new molecular bases for “life” forms.  All of these variations on a theme are of interest and will be the subject of future articles and discussions.  The current series of articles is focused on early terrestrial chemistry and the virtually universal carbon-based chemistry of life that ultimately developed from that shopping list of materials and conditions believed to have been present on early earth.23

In any attempt to understand the origin of life, a clear description of what constitutes a collection of “living” molecules from “non-living” ones must be addressed.  This is not a trivial issue.  A water molecule outside of a living cell is considered “non-life”.  But should that same water molecule transport into a living cell, we immediately consider it a vital part of that living cell.  If that water molecule reacts and combines with another molecule synthesized within the cell, its atoms become even more an active part of what we identify as a living cell.  Water molecules are, in fact, the major molecular species found in most terrestrial living cells.  We cannot imagine animated biological life of any kind without the presence and active participation of water molecules.  A similar change of identity and definition accompanies any other atomic or molecular species moving into or out of a living cell as well.

When an amoeba slowly locomotes along a surface, encounters a smaller bit of detritus or a clump of bacterial cells and then engulfs and digests it, it is said to be alive.  When that same amoeba eventually consumes sufficient organic matter to stop its search of food and enters a cycle of cell duplication through mitosis, it adds to our understanding of what the living process is capable of.

What is at first clear in this example is that an intact, functioning plasma membrane literally defines the boundary between the “living” molecules inside from the “non-living” ones outside.  Larger physical objects, such as a knife blade, and particles, such as asbestos fibers,  can cut, stretch, tear or puncture the plasma membrane of the amoeba.  And that fragile membrane continually creates, regenerates and maintains the amoeba’s living state.  It has apparently done so in a continuous fashion for billions of years since the first living proto-cells formed.  And should that two-molecule thick membrane of any cell be physically breached and lose its integrity, it loses its integrity and semi-permeable functions.   Any kind of stressor capable of causing membrane-level injuries allows an uncontrolled leakage of extracellular fluids into the cell and an equally devastating and uncontrolled leakage of intracellular fluids and/or organelles out of it.   That cell becomes irreversibly changed and damaged.  It loses all of its earlier patterns of behavior, its organization and structure, and ability to resist the never-ending call for its dissipative destruction through the Second Law of Thermodynamics.  In other words, it dies.  Its life processes, even with its DNA still intact initially, are no longer under any kind of organized control, management or energy linkage.  Any concentration or electrochemical gradients that initially existed across the membrane are discharged and lost with the resulting equilibration of those gradients.  It ceases all previous functions and slowly falls apart.  Membrane integrity and semi-permeability are absolutely mandatory for living systems to continue their existence.

As a general rule of physical chemistry, any difference in a single substance’s concentration between two different points in space within a bounded volume involves a spontaneous tendency to equalize those concentrations if allowed to.  This involves the thermodynamic difference in energy content between the initial state and the final equilibrium state.  It also involves the system’s spontaneous change and resulting positive entropy as derived from those two differing states.  That spontaneous tendency to move towards an equilibrium concentration is what can be coupled with to drive other net energy-requiring processes if properly linked to them.  That latter connection involves extracting useful work out of the concentration gradient as it relaxes.  In living systems, that gradient is continually regenerated with isolation of incompatible chemistries through membrane sub-compartmentation of the cell.  Various active trans-membrane transport phenomena are coupled and maintained within different membrane types defining the subcompartments of the modern living eukaryotic cell.  This is not unlike the continued generation of electricity (useful work) by hydroelectric dams using continuing water flow regenerated through the atmospheric water cycles.  If the two points are totally separated and isolated by a completely enclosing semi-permeable membrane, this provides all the necessary elements for creating an energized electrochemical or concentration gradient battery.

This continuing, permanent existence and duplication of asymmetric chemical gradients can be thought of as an equivalent, chemical-based analogy or redefinition for the “life force”, “living energy field”, or “energy of life” that is colloquially assumed by most Vitalists to imbue “inanimate” matter with life force but here we can define it in physicochemical terms.

Therefore it should be a prerequisite that the formation and continued survival of the first living protocells include a means of capturing and then regenerating various chemical gradients across the newly-forming membrane boundary-enclosures.  Such an energy-charged condition must have occurred during the initial envelopment process.  With that starting charge, the protocell would be capable of then becoming internally linked with the specific endergonic reactions that led to regenerating those charged conditions.  With a self-regenerating chemical energy source linkable to other reaction pathways, this allowed a continued supplying of the various materials needed by the different parts of the molecular self-renewal processes.  The sum total at this stage of living process genesis was a single, membrane-bounded entity that continuously grow new proto-cell mass.  But since this must have occurred at many locations over long periods, these living and growing masses would have been found wherever the resources and conditions allowed.  Slightly different compositions amongst them would have provided ultimately different “bloodlines” in future evolutionary developments.  In our next installment, the large growing masses begin to seed the earth with the advent of a rudimentary division process, development of simple mechanisms of mobility, and chemotactic behavior.

With so many such aspects simultaneously needed to renew different molecular components of the living protocell, many co-mingled chemical gradients must have been initially captured, regenerated and then maintained during the original packaging events.   Once that was accomplished it assured that those proto-cells’ persistence, with proper nutritional and environmental needs supported, could have extended from that time on up to the present.

A note on transmembrane gradients:  This minimal collection of chemical gradients must have been simultaneously captured at the same moment and within the same membrane housing to give birth to that first self-persistent living protocell.  It is clear that the internal cytosol of that first protocell must have had a different chemical composition both qualitatively and quantitatively in comparison to the extracellular fluid it was transferred to or deposited in.  That sudden shift in the extracellular medium’s composition was needed to generate the initial gradients that would become the driving force for continued chemical and electrochemical activity. What has and is being proposed is that the multiplicity of precursory chemical species and their gradients were generated through natural combinatorial synthetic processes. During this initial primitive membrane capture, there would have had to follow an immediate transfer to a different extracellular milieu.  Only at this moment would the establishment of the first energy-charged, living protocells have occurred.

But terrestrial life possesses many other defining characteristics.  General biological texts use 7 characteristics to define living matter and distinguish it from inanimate matter.  These life characteristics would occur in most cells meeting the definition of having a biological living state.  Some of these activities or properties could be postponed, as occurring in such entities as spores or dormant seeds, hibernation or other temporary conditions of suspended animation, but must eventually return to an active living state to continue the indefinite existence of that species.  These characteristics of life can be listed as follows:

  • Homeostasis: The operation of control mechanisms that continuously operate to maintain a balanced condition of the internal environment of a living cell or multicellular organism.
  • Organization: Non-random, optimized structure that provides the continuing framework that a cell or organism operates within.
  • Metabolism: The chemical processing that goes on in cells and organisms which derives useful energy, consumes nutrients, and produces and assembles the various building blocks for all other life processes.
  • Growth: The net increase of living cellular components.  Self repair and replacement of lost components are also included in this feature of living systems.
  • Adaptation: To change over time in response to environmental stresses or new opportunities. This extinction-fighting ability is at the basis of evolution and operates through heredity, diet, and external selective factors.  It is not always accomplished through a Darwinian selection
  • Irritability or Responsiveness: A dynamic response by a cell or multicellular organism as a direct consequence to a specific external stimulus, stressor, or change of any kind.
  • Reproduction: Proliferation or replication of new cells or organisms through either a form of asexual or sexual genetic duplication.  In our narrative, we may have to broaden our definition and accept non-genetic replication to allow for the early development of genetically-based reproductive processes.

Once proto-cells attained this minimal number of characteristics, little would be left to argue as to their being “alive”.  But even if they acquired only some of these characteristics, the question of life might still be viewed in the affirmative.  There is nothing in this list that is unique to carbon-based terrestrial life in these features.  These can all be simulated in simpler systems biological, robotic, physical or chemical-based systems.  But the totality of self-propagation and self-repair of present day living cells is more apparent in those cells than in such manmade simulacra.  Our challenge is to recreate a present day life form from initial inanimate components without resorting to previously living or life-generated materials.

 

Next:  Pre-Biotic Evolution.  Part III.  Transitioning to Animacy

* Scientific and Forensic Services, Inc., Delray Beach, FL. and Norfolk, VA  scientificandforensicservices@gmail.com

References

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  15. Greenberg, J. M., N. Zhao, and J. Hage. (1989)  “Chemical Evolution of Interstellar Dust, Comets and the Origin of Life”.  Phys. (Paris)  14: 103-31
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© Copyrighted by Joseph H. Guth, 2015.  All rights reserved.

Pre-Biotic Evolution: I. From Stellar to Molecular Evolution

By Joseph H. Guth*

One Scientist’s Overview and Perspectives

Introduction

The principle intent of this collection of essays is to conceptualize and provide a stepwise, detailed and plausible path for the formative and evolutionary processes before and up through when “life”, per se, began on earth.  It explores and synthesizes some of the most relevant recent experimental, technological and theoretical developments.  This series of essays will attempt to provide a road map for the experimental probing of the specific events and mechanisms which produced the very first origins of living systems.  An understanding of what the minimum requirements are for a collection of abiotically created molecules being able to become organized into a “living” protocell may now be at hand for scientific exploration, experimentation and verification.  Should science one day finally produce a pre-biotic-to-biotic laboratory model system to simulate the origin of life forms on earth, it could offer real guidance to our efforts to understand our actual chemical and physical origins.  More importantly, it could allow us to develop new and more plausible approaches in exploring the universe at large for extraterrestrial life and all of its possible definitions and variations.  Its ultimate impact will be immeasurable on human history.

Outline of this essay series

The overall phenomenon known as life begins with and is inextricably connected to the nucleosynthesis of the major elements of the Periodic Table.  The production of those elements occurred in various stellar and astrophysical processes.  Past supernovae provide just one of many sources of our elemental atomic building blocks.  As Cosmos astronomer Carl Sagan observed, “We are made of star stuff”.  Without the availability of so many resultant and differing types of atoms with their various symmetries and geometries, bonding potentials, and electronic energy states, life as we know it could not even have begun.  By extension, the subsequent molecules that inextricably formed and evolved from them, constituting the matter making up living systems on earth today, also could not exist.

The lens through which the earliest stages of the origin of life may be illuminated begins with the basic tenets of physical chemistry, combinatorial reaction chemistry, biochemistry, bioenergetics, membrane biophysics, chaos theory, complexity theory and evolutionary theory.  The challenges that are ultimately addressed are as follows:

  • How could a complex, dynamically balanced and interactive system made up of so many parts ever have come into existence?
  • How could this extraordinarily unlikely “whole” originate from the piecemeal addition of each of its “parts”?
  • How could the inherently low probabilities for each of these presumed pre-biotic steps actually have led to an inexorably predictable outcome for the genesis of life?
  • Life is a dynamic and complex process. What are the exact events that caused forms of molecular evolution to change into forms of process evolution?
  • What is the physical nature of life’s “energy” and how was it generated in the first living cell?
  • With a multitude of different “molecules of life” finally generated, how could such a collection in a state of relative thermodynamic equilibrium ever become assembled into a dynamic, exergonic, energy-containing assembly that continued to take in various forms of energy and matter and build new biomass?

It is usually the complexities and unknown or uncertain workings of living systems that baffles the scientific reductionist trying to probe or analyze the beginnings of life.  But that classical scientific mindset is exactly what needs to be overcome in order to embrace a process that had innumerable components, steps, stages, variations and possible outcomes.  It is the complexity and non-linearity of the living process that imbues “life” to inanimate matter.  Life does not greatly depend upon random, stochastic processes.  In fact, it is commonly described in opposite terms as being thermodynamically of a negative entropic nature.  Though molecular biology is useful in observing and describing the structure of the living cell, it is a misnomer in that it does not actually address the complex “living” state.  It only looks at snippets of the bigger, overall picture and that is where we must be able to have a clear view and understanding.  When looking for the origin of life, a firm definition and operational design of life is quite indispensable.  But in this series of essays, the underlying, non-stochastic patterns of molecular behavior and dynamic linkages create the necessary chaotic complexity that is required to more accurately describe the living state.  The complexity of the living cellular system must not be dissected back into its parts to understand it.  It is the way those parts interact and work together that provides the whole being greater than the sum of its parts.  Can one understand how the space shuttle could fly and carry out its missions from just its parts list?

Our scientifically-based genesis story begins with inanimate atoms and logically carries through to the biophysical formation of the first proto-cells.  In this series of essays, we find some new and interesting pieces of the puzzle fit together naturally.   These stages of molecular and early cellular evolution might rationally end at a waymark in this narrative after prokaryotic and the earliest eukaryotic cells made their appearances for the first time.   The level of presentation is less rigorous and specific in order to facilitate understanding by a wider, enlightened scientific audience.  As such, brief introductory comments about specialized theories will hopefully benefit the majority of readers while not trying the patience of those more specialized in this subject.

After bringing the universal collection of various kinds of atoms into existence, we also must find common ground to agree on certain basic assumptions.  Such assumptions as all atoms of a given element, no matter where they occur in the universe, are indistinguishable in their makeup, chemical and physical behavior and characteristics.  Another assumption is a corollary to that which implies that all atomic reactions between atoms of identical or differing elements behave the same anywhere in the universe when under the same environmental conditions.  That leads to the next corollary that all specific molecules formed from such reactions will have the same identical properties no matter where they occur if under the same environmental conditions.  And the last corollary is that all molecules with the same structure will behave indistinguishably from one another if under the same conditions anywhere in the universe.  These fundamental assumptions allow us to accept spectroscopically-derived astronomical data and interpreting it as being mechanistically identical with comparable laboratory or locally-generated data.  Such assumptions are commonly accepted in astrophysics, astrochemistry and astrobiology.

We follow a similar trail to that which others described in which the pattern for protein-based metabolism could have preceded the appearance and functioning of a nucleic acid-connected, information-containing, accurately-transmitted, highly specific (genetic) molecular replication scheme.1  We begin with describing a picture of nonmembrane-bounded molecular evolution preceding that first membrane-packaged “cell” formation (i.e., the proto-cell).

There will be a very prominent role for the development of permanently oscillating, self-propagating, oxidation-reduction chemistry that provides the first form of life energy storage and conversion that future living systems will be built upon.  Such systems can involve purely inorganic reactions assisted by catalytic species or can be found in organic chemically-based systems which can range from relatively simple to highly complex.  In modern biochemistry, such oscillatory behavior is found in both cell-free and intact subcellular biochemical pathway dynamics.  It is also reflected by oscillatory behavior in various transmembrane fluxes of different biochemicals and bioenergetically-important compounds and membrane-based ion transport mechanisms as well.  Such oxidation-reduction coupled oscillations will ultimately become packaged as one of many forms of protocells which then survive as dynamic, chemically-reactive entities.  Those protocells then would have been able to merge with other different, chemically-dynamic, oscillating protocells containing differing supermolecular complexes that were carrying out different sets of chemical reaction sequences.  This aspect will be focused on in more detail in the coming installments.

Think of this as a time when there were different subpopulations of protocells, each of which contained all of the main enzymatic protein complexes for different future metabolic pathways such as glycolysis, electron transport, tricarboxylic acid cycle, pentose shunt, etc.  Each subpopulation may have arisen in a single body of water with a combinatorial collection of all kinds of supermolecular complexes incompletely mixed together or in different adjacent or nearby bodies of water.  Each pond or lake contained a variety of molecular mixtures and with hot rocky surfaces nearby.  In this chemically-evolving, catalytically active world, complexity drives this natural tendency for molecular structure and reactivity to always spontaneously increase.  As the different mixtures’ complexities grow, even low probability outcomes become more likely.  Such is the power of combinatorial chemical catalysis.  As newer molecules form, some of them will possess other catalytic capabilities that lead to even more subpopulations of molecular species.  That increasing complexity provides the driving force for the development of highly complex, integrated systems.  That ever-increasing complexity can increase the likelihood of protocells and living systems eventually appearing.  Once such more complex assemblages of molecules and structure appear, if the selection conditions are present, those more complex units become the dominant subpopulation if they have developed any survival or propagational benefit from their environment at that time.

Protocell fusions occurred countless times between differing types to eventually result in complex, highly-structured protocells with multiply-integrated, dynamically-oscillating pathway activities.  It is reasonable to expect that only pathways that could be in resonance with one another in terms of their input reactants and output products would be capable of long term stability and homeostatic behavior.

It will be noted that the self-sustaining collection or set of chemically-reacting molecules (both substrates and catalysts) that possessed many of the later characteristics of biochemistry and biological life were likely to have been already generated abiotically and assembled well before the membrane packaging of those molecular reactions and their enzyme-like assemblies.  Those chemical reactions began with simple available starting materials self-sorted out of a complex, abiotic mixture generated combinatorially.  The chemical reaction sequences within those mixtures that also became self-amplifying by generating more of the same catalytic capabilities in the end products they formed would have become more abundant.  Those would have become established sooner than those that could not.

One example of that self-amplification is the modern day Polymerase Chain Reaction (PCR) used to replicate small amounts of DNA in vitro for analysis.  Another is the replication mode of PrPSC prion proteins which is thought to be devoid of any DNA-directed involvement.  It is even possible to place the first virus-like precursors within such a milieu if enough of their needed molecular replication machinery and molecular building blocks were co-constituents within our pre-biotic combinatorial ponds.  Those “proto-viruses” would become the first self-replication genes and genomes existing before the first complete genomes, chromosomes or independent living cells were formed.   But in our early earth case, those products were initially amino acid-based polymers possessing the same types of catalytic activity that initially produced them.  And what allowed this to happen with a high probability?  It was that they were most likely organized as multiple step, integrated reaction sequences that operated in a controlled feedback loop-like fashion.2, 3, 4, 5

Molecular Simplicity to Complexity

A Stellar Beginning

Let us start at the beginning.  Our story of the origins of life began with simple chemistry and its universal occurrences.  Hydrogen, carbon, nitrogen, oxygen, sulfur, sodium, potassium, calcium, magnesium and phosphorus are found throughout the universe.  Astronomically large clouds of these elements are found throughout the galaxy having been transmuted through a sequential nucleosynthetic process occurring from the life and death of stars and other high temperature, high energy sources.  Depending on the temperatures present, differing nuclear reactions and states of matter can exist within them.  At higher temperatures, those elements are found primarily as atomically individual, electrically ionized plasmas with unassociated, free-moving electrons.  At lower temperatures the oppositely-charged particles can remain associated with one another, and form ionized as well as neutrally-charged atoms and molecules.  During this cooling down, mixtures of plasmas containing nuclei of different elements will form heteroatomic chemical bonds.  Simple gaseous molecules like hydrogen (H2), oxygen (O2), water, all carbon-based fullerenes and graphite, methane (CH4), ammonia (NH3), nitrogen (N2), carbon monoxide (CO), formaldehyde (CH2O) and similar compounds will have readily formed.  Many of these have been identified in spectra of stars, nebulae and molecular clouds.  Formation of larger molecules might not be favored in space-based clouds however.  Larger molecules would likely have to await the less severe ionizing conditions of planetary surfaces.

Once these smaller molecules collect and concentrate on cooler planetary and sub-planetary bodies, various chemical reactions and physical processes can continue to lead to larger molecular structures under more molecularly stable conditions.  The production of life’s complex mixture of starting chemical compounds could have formed in large quantities on post-Hadean period earth as well as many other places in the universe.  Such is the inevitable driving tendency of synthetic dynamic combinatorial chemistry.  When there are a few different kinds of atomic building blocks and sufficient energy available to break chemical bonds along with conditions that allow new bond reformations, small simple molecules becoming increasingly larger and more complex in structure.  And as new kinds of chemical structures come into existence in our mixtures, new catalytic potential is introduced with them.  New catalytic potential spurs even faster development of ever-expanding libraries (i. e., collections) of newer compounds which hadn’t previously existed.  Complexity in our early chemical incubators will ultimately lead to collections of linked chemical catalysis.  Linked reactions form the basic pattern and framework for modern cell-based metabolism.  And in our case it comes together on a cooling earth a little less than 4.5 billion years ago.   The physical incubator for abiogenesis became available on the still hot, asteroid-bombarded surface of earth.

The chemical compounds which collected there initially must have originated from a combination of meteorite/asteroid plus cometary deposition and higher-temperature chemical reactions.  These latter are known to occur between very simple molecules composing the early earth surface deposits and atmosphere.  Similar high energy-associated chemistry could have already been occurring extra-terrestrially within the Oort cloud surrounding the infant solar system.  The solar wind and the ionizing electromagnetic radiation it emitted bathed such frozen water- and methane-rich icy bodies with high energy particles and chemical bond-ionizing photons.  Low- to extremely high-energy protons, electrons, neutrons, and other elementary particles (which are commonly known as cosmic rays) catalyzed new element nucleosynthesis and chemical bond formations after they traveled in on the solar wind, as well as from deeper interstellar and intergalactic sources.  Physical shock waves due to impacts and sound vibrations and deep earth zones under very high compressive forces and temperatures can induce unusual chemical reactions to occur (such as crystallization of elemental carbon to diamond).  In addition to the previously-generated elements, new elements formed from these cosmic ray transmutations and subsequent radioactive decay.  These collected within the populations of chemical compounds on each of the various proto-planetary bodies orbiting the young sun.

This early earth setting frames the period and some of the necessary steps, stages and events leading up to and into the formation of the first cells on pre-biotic earth.  It must be a brief overview since there are publication limitations in time, space and reader attention span.  Such limitations were not present during the original story.  That original reality had the advantage of having all the time in the world to play out.  It evolved over the time span from approximately 4.2 to 3.6 billion years ago.  This pre-life reaction chemistry began almost immediately after the earth cooled sufficiently and limited amounts of liquid water became available.

Molecular Evolution Leading to Pre-Life Chemistry

During the pre-biotic period, simple molecules were produced through a variety of chemical and physical processes.  Some were generated on early earth in manners already described.6, 7, 8, 9, 10, 11, 12   Hydrogen, the most abundant (reducing) element in the cosmos, will usually be part of the early gases that collected as atmospheres on cooling planetary bodies.  The hydrogen-rich reducing atmosphere, composed of gases found throughout space as nebulae and molecular clouds in the galaxy, were generated from within supernovae. And as modern exo-planetary research has repeatedly shown, they could have been expected to be abundant around our youthful Sun.13, 14, 15  The simple atoms and molecules of the periodic table found throughout the cosmos could have not only been plentiful, they could have been gravitationally attracted to any sizable body in an infant solar system.  They collected on our newborn planet as it slowly swept through them.

This reducing atmosphere was originally low in molecular oxygen content and oxidizing potential.  That was first postulated by Oparin and Haldane in the 1920s.  It could have coalesced and formed over the solid surface of primitive earth soon after it finished cooling and solidifying out of a previous supernova cloud full of lighter and heavier elements.  Through high temperature processes such as volcanism, geothermal steam, simple pyrolysis, high energy impacts, electrical arc heating (lightning) and ionizing radiation, it is likely that brownish-black, tarry, keragen-rich ooze would have developed and continuously accumulated over large land-based areas.  Such organic molecule building generally is not found in oxidizing conditions.1  Growing molecular sizes for the organic compounds being generated abiotically would have built up over a great amount of time on or within various heated rock, sand and clay surfaces scattered around the globe.  This was an early period of not just fairly arid conditions, it could have also been predominantly water-poor, dehydrating conditions for early reactive carbon chemistry to become relatively facile.

Differences in the area-specific mineral and gaseous contents, volcanism, temperature, pH, sun light intensity and spectrum, and other chemically important conditions at these different locations imparted complex but important nuances by way of the Butterfly Effect to the variety of chemical reactions taking place from one oasis of pre-biotic chemical genesis to another.  But liquid water would likely have been sparse at this earliest part of the Hadean Eon.  Volcanically-heated steam could likely have been found in a widely distributed niches amidst the water-poor areas.  The conclusions of Lazcano and Bada regarding Miller’s experiment only portrayed a watery womb for the development of surprisingly high concentrations of a few more simple structured, biochemically-important, starting compounds in that primitive soup.16  The genesis of even more molecular complexity would likely have been seeded in a water-poor, higher temperature environment that favored condensation polymer formation.17, 18, 19  Thus the original drier and higher temperature range starting molecular recipe created one large population of larger molecular weight polymers.  Once lower temperatures became the norm, and after more water became available, the conditions changed sufficiently so that a much more diverse and now biochemically-meaningful population of chemical compounds was available.  That population worked better in aqueous environments and began to produce the next generation of products ultimately needed for the life process to finally organize and become self-propagating.  During that phase, only integrated and highly effective molecular subpopulations that could resist or overcome the slow rate of hydrolysis would win a place in this post-combinatorial chemical water-world.

As an example, the transition from the arid to aqueous world during earth’s early history would have involved water-requiring chemical reactions.  Water would be both a supporting solvent and a reactant.  Variations in the yields of various products might have depended upon the availability of super-heated steam above certain reaction temperatures.  When such water-based chemistry occurs along side anhydrous heated surfaces, many interesting compounds could result.20  Such closely juxtaposed reaction sites, as are found in present day geothermal environments like Yellowstone National Park in the United States, could have also more quickly modified the plethora of molecular species that could combinatorially form.  Reaction products from dehydration-driven conditions would easily transport into more aqueous conditions where water-requiring oxidation-reduction electrochemical reactions would have been incubating.  And as changes in the latter pools led to newer compounds, those could have been recycled back to the hotter dehydration conditions building up larger molecular species that were more resistant to hydrolysis and yet possessing of newer and unique molecular reactivities and properties.  The complexity of the resultant molecular mixtures becomes the most important determinant as to whether the right combination of molecular species form abiotically.  Without a minimum number of necessary interactive molecules being present, a living process would not be possible.  Which is what we view as the origin of life’s greatest challenge.  It defines the highly improbable nature of the generation of living cells from non-living matter that make them up.  But if that minimum threshold number of compounds does come into existence in our mixtures, then what are the chances for life to spontaneously follow?

Complexity at the Beginning

Dynamic combinatorial chemistry is a specialized synthetic technique that is now a sub-discipline of the chemical sciences and was first developed by Merrifield in the 1960s21 and later by others.22, 23, 24  It has since become highly popular and a powerful technique for finding specific “needle-in-the-haystack” molecular interactions and associations from highly complex and undefined mixtures.  It is commonly found in synthetic chemistry and analytical chemistry applications.  In most applications, combinatorial chemistry is based upon the principle that if one allows all manner of possible chemical reactions to proceed unhindered, unselected, and without limitations, a broad range of possible reactions will occur and reaction products will form.  Within that complex mixture of perhaps millions of different, uncharacterized compounds there could, through random chance, be some very small numbers of specific interactions of important biochemical or pharmaceutical consequence.  Once the library of all those resultant compounds becomes available, then very specific conditions, probes or selectors can be introduced to dissect out just a few compounds from the astronomically large number of possibilities.  If successful combinations occur, those have the necessary molecular structure, affinities, and reactivity needed for the end purpose.  In chemical laboratory applications, those rare compounds can be quickly identified, filtered and isolated using appropriate affinity-based selection techniques.  But under primeval earth conditions, the selection for those rare combinations would be made through a process of self-selection.  In our origin-of-life experiment under combinatorial conditions, only those molecules that can react in just the ways that current metabolic pathways operate would have been spontaneously self-selected for.  It could include any ultimate subset of catalytically-active, catalytically-controllable, self-amplifying, and self-perpetuating collections of molecules that might become the most prevalent and thus most likely to ultimately become packaged into proto-cells that form later.  That packaging process will be detailed in subsequent parts of this essay.

Comets carrying large amounts of water, rock, frozen gases, and dust also started becoming more plentiful during this early period in earth’s history.  They subsequently added sufficient free liquid water as the earth further cooled to begin forming pools, ponds, lakes, seas and eventually-frozen polar caps.  After that hydration phase passed some critical threshold, membrane-bound life forms would have had an environment they could call home.

The originally dehydration-based pre-biotic chemistry now began to dissolve and suspend a growing variety of small, medium and larger molecular weight precursory pre-biotic molecules. It is this limited collection of compounds we shall refer to as the “starter set”.  Niches and pockets of dehydration-based chemistry continued to generate the earlier reaction products while the water-based chemistry began to form a newer collection of pre-cursor, pre-biotic molecules.  This latter group in part contained water-derived oxygen atoms within their structure.  That increased their inherent polarities, water solubilities and reaction chemistry potentialities.  Such wide climatic fluctuations simply emulate what we can still find anywhere on earth.  Even arid deserts can experience infrequent flooding rainfall and rain forests can die off from drought-provoking climate changes.   Chemical complexity now becomes the new paradigm.  Virtually every chemical reaction pathway found in current synthetic organic chemistry could be co-existing at some location under these early earth conditions.

Pockets of minerals containing more reactive elements and atomic species (such as inorganic carbon, iron, manganese, cobalt, phosphorus, silicon, selenium, arsenic, iodine, sulfur, or copper) would provide even greater richness of molecular diversity in their own niche-like locations.  A long-standing question has been “Why are so many inorganic elements found in key metabolic sites within living cells?  How did they evolve to be there?”

Such an early history of exotic chemical reactions might have led to conservation and parallel evolutionary paths for various metallo-organics (such as metallo-porphyrins), metallo-enzymes, thiol/disulfide-containing proteins and unusual biochemical pathways.  Examples of the latter group are the selenium-based superoxide dismutase enzymes, the iron-sulfur containing P450-FeS and cytochrome complexes in mitochondria and inner cytoplasmic membrane systems, the hydrogen peroxide-hydroquinone defense mechanism of the bombardier beetle, and the hydrogen, methanogenic and carbon/nitrogen/sulfur-fixing pathways of the Archaea.  The high G-C DNA base composition and thermal stability of proteins in thermophiles in this latter group of ancient microorganisms also provide present day examples of such likely long-term conserved lineages.

After dry-cooking for millions of years, new classes of carbon-based chemistry began becoming common in water-rich pockets.  It is the aqueous environments that are typically referred to as the “primordial or primeval soup” by many authors.  Most theories involving the origin of life speculate that first “life” began in such a liquid environment.  But without the earlier abiotic conditions and chemistry previously occurring in the dehydration zones, the genesis of a complex mixture of higher molecular weight polymers might have been much slower and present a statistically less-likely outcome.  In proteins, nucleic acids, and polysaccharides, the bonds forming the primary monomer linkages are virtually all formed through the net removal of a water molecule and subsequently are usually easily hydrolyzed through simple addition reaction with a water molecule.  Phospholipids are similarly formable through condensation under dehydration conditions.

The higher temperature conditions the molecules are subjected to typically favor the forward reaction for the reversible hydration-dehydration type reaction.  The larger molecular skeleton aids in favoring the formation of somewhat more stable bonds.  Loss of water is a common biochemical reaction found in biochemically important molecules.  And the formation of those is favored and preferentially induced under higher temperature-driven, anhydrous reaction conditions.  Increased temperatures will increase the stretching and vibration modes in covalent bonds.  As the mean bond lengths increase even slightly, the bond dissociation energy is reduced and the bonds can more easily come apart.  When two heated molecules contain a more labile H atom and OH group and are close together, they can thus form even stronger inter-molecular covalent bonds while expelling a water molecule.  And at elevated temperatures, the volatile H2O molecule is quickly driven off, leaving a less volatile larger or polymeric molecule as the remaining reaction product.  Besides condensation polymer formation, cyclic anhydrides of varying compositions could also be a common class of reaction products occurring from dehydrating conditions.

Thus our increasingly complex pool of abiotically generated molecules all began from some very common, simple, low molecular weight and universally available starter molecules.  All types of natural energy sources supplied the necessary energy to break simpler compounds into reactive fragments and allow those fragments to rearrange and reform into more complex and larger molecules.  The process occurred over and over.  Different elements became caught up in various locations within these molecular card shuffles.  Hetero-atomic molecules brought a greater diversity of characteristics and capabilities to the growing morass.  With the increasing complexities of the resultant mixtures, low probability events became more likely to occur.  Certain combinations of molecules found themselves more closely associated with one another than the vast majority of the mixture components.  Some of those closer associations had catalytic capabilities that when the associated chemical reactions occurred, the products of those coordinated reaction sequences generated more molecules of the same types.  When those complexes continued to generate more of their own types, a Darwinian-like molecular competition occurred in which one very well-established survival pattern was born.  Those complexes continued evolving at the expense of the less capable molecular species surrounding them.  Non-self propagating molecular species began to break down in thermal and non-thermal bond dissociation events leading to their atoms becoming recycled into the growing populations of self-propagators.  It was the molecular analog of a predator-prey pattern, and helped to clear the early environment of non-useful molecular species that did not provide any useful paths to a greater level of overall collaborative organization.  What is meant by that is that in ecological terms, we have food chains that have been established over time through evolutionary refinements.  The biosphere is considered a complete, self-sustaining system.  Such was not the case at the molecular level just after the appearance of self-propagating molecular complexes and their associated chemistries.  The less useful molecular species were cleared out while the survivors perfected their higher level coordination of structure.

Next:  Pre-Biotic Evolution.  Part II.  Pre-Biotic Chemical Oscillations and Linked Reaction Sequences

* Scientific and Forensic Services, Inc., Delray Beach, FL. and Norfolk, VA  scientificandforensicservices@gmail.com

References

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Sex, Psyche and Evolution

By   Tam Hunt, J.D.

Most people now realize that sexual attraction is in the mind, even though we often forget this insight in practice. The growth of phone sex and online sex is testament to the ability of imagination to titillate as much or more than actual human contact. And the presence of pornography in all cultures throughout history is an ongoing reminder that people can be turned on by the strangest things and certainly don’t need a live human being for this purpose.

Why is sex so central to our lives? The facile answer is that it’s because we need sex to reproduce. But this is only partly true. Many species reproduce without sex, including some complex vertebrates like lizards and fish. So why do we have sex? No one really knows the answer to this question, but there are many theories. I won’t delve much into why our species reproduces sexually; rather, I’m going to delve into what sex is, as a general principle, and the role of sex in evolution. I’ll also suggest that thinking deeply about sex leads to perhaps a more general theory of evolution than natural selection.

Natural selection is the key agent in Darwinian evolution. Natural selection is the label we give to the idea that traits that confer some reproductive advantage will, by definition, spread. But Darwin didn’t stop there. His second book focused almost entirely on sexual selection, another agent of evolution. “Sexual selection” is the bridge between Darwin and Lamarck and sexual selection is Lamarckian through and through. This is not generally acknowledged by today’s biologists and it may in fact be a novel interpretation. (Darwin was a Lamarckian in many ways, but this is not commonly known).

Natural selection is supposed to be a general theory of evolution. To be a general theory of evolution, however, it seems that a theory must possess at least the following features: 1) applicable in all times and places (at least until we are forced to conclude otherwise); 2) testable; 3) falsifiable.

Sexual selection, however, is arguably a more general theory than natural selection. Historically, these two selective forces have been presented as parallel forces, but with natural selection as by far the more important force. In recent years, sexual selection has been re-framed as a subset of natural selection. In reality, of course, there is no “force” behind natural selection. It’s just physics and chemistry in action, as the sum total of environmental forces on each organism and population, so when we talk about natural selection as a force or an agent, it’s reification of a sort at work. Rather than being an actual force, natural selection is just a label we use for the collective phenomena of differential reproduction given different traits in different environments.

Sexual selection is different, however, because there really is supposed to be a selective agent at work, which may not be explained wholly through the currently conceived physical and chemical forces because the conventional view of these forces ignores, for the most part, the role of mind in nature. Contemplating evolution requires that we consider whether mind (and thus choices made by minds) can in fact be explained through current physical and chemical theories, and the degree to which mind plays a role in evolution.

Current physical theories cannot plausibly explain mind because the constituents of matter are defined by modern physics as wholly mindless. (See Thomas Nagel’s 2012 book, Mind and Cosmos, or Christof Koch’s 2012 book, Consciousness: Confessions of a Romantic Reductionist, for extended arguments on these issues). We are thus left with a system of modern physics that seems to exclude that which is most real to each of us: ourselves, our own minds. Even though some interpretations of quantum theory appeal to the role of an “observer” in collapsing the wave function, the observer doesn’t actually have to be a conscious observer. Moreover, there is no explanation of how mind emerges or otherwise is derived from matter in quantum theory or any other branch of today’s physics.

Our own subjective awareness, our minds, surely should be included in an adequate theory of physics and the role of mind in the universe. I have, over the course of two decades in thinking about these issues, come to the view that this impasse requires the inclusion of mind, in a highly rudimentary form, in all forms of matter. This view is known generally as panpsychism.

Under this view, as matter complexifies, the tiny bit of mind in each little piece of matter complexifies and eventually reaches our highly complex type of mind due to the highly complex matter that comprises our brains and bodies. There is nothing necessarily mystical about panpsychism. Rather than positing the emergence of mind at some seemingly arbitrary level of complexity, as the conventional view suggests (whether that level of complexity at which mind emerges is cats, bats, rats, bacteria or what have you), panpsychism suggests instead that there are at least some rudimentary mind qualities present in even the simplest forms of matter. As matter complexifies, so mind complexifies. Rather than posit an arbitrary moment of emergence, ontogenetically and phylogenetically, as is the case in the conventional notion of mind in relation to matter, panpsychism simply re-defines matter to include some rudimentary subjectivity, all the way down.

This raises the question: how did we, and life forms like us, reach such a high level of complexity? How did we evolve? This is where evolutionary biology and the philosophy of mind intersect.

If we acknowledge that all matter has some degree of mind, no matter how small, we realize that choice must be inherent in all matter. This is the case because mind without some kind of choice seems to be contradictory: the essence of mind is the selection (choice) between alternative courses of action made available through perception of the universe around us. Mind without choice would be simply a passive observer and have no causal role. If we accept that mind has a causal role, as it certainly seems to based on the abundant evidence from our own lives, we can reasonably infer that some rudimentary choice-making ability plus some rudimentary perceptive ability are key features of even rudimentary consciousness.

One of today’s preeminent physicists, Freeman Dyson (Professor Emeritus at Princeton’s Institute for Advanced Study, the same institution where Einstein resided for a number of years before his death in 1955) makes this point explicit: “[T]he processes of human consciousness differ only in degree but not in kind from the processes of choice between quantum states which we call ‘chance’ when made by electrons.”[i]

What Dyson is saying is that what physicists normally interpret in electron behavior, an extremely rudimentary type of matter, as pure chance is better interpreted as choice. Choice, not chance. Choices can be fickle, so what seems to be random is in fact a result of unpredictable choices by these tiny entities. Thus, even electrons make choices, but these are very simple choices compared to the infinity of choices possible to our advanced human consciousness. Choice at the level of the electron is apparently limited to how the electron will manifest and move in the next moment. Particles such as electrons are not static, timeless entities. Thinking of the fundamental constituents of reality as unchanging particles is the fallacy of substantialism that the panpsychist approach attempts to correct.

If choice is inherent at the level of electrons, a universal principle of evolution is made apparent. I call this universal principle “generalized agentic selection,” or “generalized sexual selection.” The essence of sexual selection is choice–female choice (generally, but not always), to be more specific, as Darwin described in The Descent of Man. Darwin recognized that many traits, such as the peacock’s tail, could not be explained strictly through natural selection. Rather, female choice led to pronounced features in males who competed for females’ attention, so Darwin argued.

To be entirely clear, the peacock’s tail is not considered adaptive because its weight and size make it harder for male peacocks to escape predators and to forage for food. But if the tail’s disadvantages are outweighed by increased mating opportunities for the male who carries the showy burden, it will continue as a trait in male peacocks.

Darwin’s division of natural selection and sexual selection into two distinct agents of evolution, which continues to this day, is not, however, warranted when we think through what’s really going on. There are some major problems with natural selection as a theory of evolution. Generalized agentic selection (GAS) may solve these problems in an elegant way. Here’s why.

The simple structure of natural selection theory has just two parts: 1) random variation of traits (based on random mutation of genes); 2) “selection” of those traits through increased offspring of the parents bearing traits that confer a survival or reproductive advantage. (Again, there is not really any “selection” going on, but the end result is “as if” there was some selection process).

The problems with this two-part structure can be summarized quickly: 1) truly random variation is highly unlikely to lead to the adaptive traits we see in nature, even over the course of billions of years because beneficial mutations are so rare; 2) “natural selection” as a theory is unhelpful because it is either tautological or it is highly provisional in nature and needs way more data to support it before it can be considered a general theory of evolution.

GAS can help this situation, in the following re-framing: 1) variation in traits comes about through male competition for mating opportunities and striving of males, more generally, to improve themselves, which can sometimes be incorporated into the germ line of the male[ii]; 2) female choice is the selective agent that leads to greater reproduction of those males with the most desirable traits to the females who choose them, incorporating their germ line into their own. In other words, variation is not random, it is directed, with increasing mating opportunities as a significant motivation, and an innate desire for survival and other desires surely at work also in this complex process. Perhaps more importantly, selection is not blind, it is conscious at every level of nature through the conscious choices made generally by females in terms of mate selection.

I call this generalized agentic selection because it applies to situations that don’t involve sex in the traditional sense. Most species on our planet don’t reproduce sexually. Bacteria, for example, often reproduce asexually, as do protists. And even many vertebrates reproduce asexually, such as certain species of lizards and fish. However, bacteria are constantly exchanging genetic information, which is a rudimentary kind of sex, which I define at this level as the mixing of genetic information from at least two entities. This type of sex is known as “horizontal gene transfer” because it occurs without simultaneous reproduction.

Bacteria seem to transfer genes spontaneously, giving rise to many problems in defining species of bacteria. If individuals and populations are constantly exchanging genes directly, how can we define each species as a semi-stable collection of genotypes and consequent phenotypes (the most sensible definition of “species”)? The answer to this question is beyond the scope of this essay, but it presents an interesting current question in biology.

But here’s why GAS applies beyond traditional sexual reproduction. The terms “male” and “female” are not as clearcut as we generally assume. And in GAS, “male” refers to any genetic donor and “female” to any genetic recipient, as Lynn Margulis and Dorion Sagan describe in their 1986 book, The Origins of Sex. Thus, a bacterium that gives some genetic material to another is a male and the recipient is a female. These roles can and do change on a regular basis, thus the “gender” of each bacterium changes regularly. What is important, then, is not gender, per se, but actions.

The principle extends even deeper, however, when we consider further the panpsychist notion of matter. If all matter has some degree of mind or subjectivity, as it must if we are to avoid the “and a miracle occurs” crude materialist explanation of consciousness that is currently popular, then GAS applies to literally all matter, not just biological life forms. This is the case because the most sophisticated panpsychist thinking, that of Alfred North Whitehead (Science and the Modern World, Process and Reality, Adventures of Ideas) and his intellectual descendants, recognizes each of the ultimate constituents of matter–what Whitehead calls “actual entities”–as oscillating between a subjective aspect and an objective aspect in each moment. Thus, physical and mental aspects of each unit of reality oscillate with each step forward in time. This oscillation is extremely rapid.

This moment-to-moment-to-moment process of perpetual creation is Whitehead’s “creative advance.” The mental aspect of each actual entity is informed by the immediately prior physical aspects of all other actual entities available to it. Each actual entity, in its mental aspect, chooses what information to accept and rejects everything else. Thus, the mental aspect of each actual entity can be considered to be “female” insofar as it chooses what information from the universe around it to include in its objective manifestation–like the female bower bird accepting the attention of a hard-working showy male. By “objective,” I mean the entity is now available as a datum for other actual entities in their mental, subjective, aspects. When the actual entity becomes objective, it becomes “male” insofar as its manifestation now constitutes information for the next round of actual entities to consider in their mental/female aspect.

Wipe your brow as I wrap up this essay. GAS is a potentially powerful re-framing of evolution in a way that recognizes the unbroken continuum of the complexity of matter, which is inherently experiential/subjective all the way up and down. I won’t delve into further details about the testability and falsifiability of GAS here, but it is my view that GAS presents a more adequate theory of evolution than the prevailing adaptationist view of natural selection–which generally denies the role of mind and choice in evolution beyond a supplementary role in shaping certain sexual traits a la traditional sexual selection theory.

Sexual selection theory was for the first hundred years after Darwin first proposed his theory in 1872 largely ignored. In the last 20 or so years, however, it has experienced a resurgence of interest and scholarship. Helena Cronin’s The Ant and the Peacock and Geoffrey Miller’s The Mating Mind are excellent reviews of current thinking in this area. So sexual selection theory is making something of a comeback. However, because it is generally grouped as a type of natural selection, most biologists have not considered the implications of sexual selection and the role of mind in nature to the degree that is warranted.

Mind/choice/subjectivity is the missing ingredient in the secret sauce of evolutionary theory. GAS is an attempt to provide that missing ingredient.

See my 2012 paper, “The Middle Way of Evolution” for some more detail on GAS and my 2014 paper, “Reconsidering the Logical Structure of the Theory of Natural Selection” for more on the problems with natural selection theory. Last, see my 2014 collection of essays, Eco, Ego, Eros: Essays in Philosophy, Spirituality and Science for more on panpsychism and its implications for philosophy, biology and physics.

Tam Hunt is a philosopher, lawyer and biologist. He lives in Santa Barbara and is a

[i]
[i]   Dyson, 1979, Disturbing the Universe. A similar point is made by Bohm and Hiley (1993, pp. 384-387).

[ii]
[ii] There is, contrary to the popular view, abundant evidence that somatic changes acquired during an organism’s lifetime can sometimes be incorporated into the germ cells. See Lamarck’s Signature, by Robert Steele, et al., for a good introduction, as well as Jablonka and Lamb’s Evolution in Four Dimensions. The most recent work in this area seems to be from Laura Landweber’s lab at Princeton University: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18046331.

Bio-Logic

Bio-Logic

 Like Prometheus discovering fire, Archimedes in the bathtub, Copernicus declaring that the sun is the center of the solar system, or Einstein’s Relativity Theory, we need an ‘aha!’ moment for biology. This essay describes just that.

The ‘Problem’

When we think of evolution in terms of contemporary biologic phenotypes, we make the systematic error of reasoning backwards from the present to the past. Yet reasoning after the fact, by definition, is illogical. All of biology is formed from and by cells, which emerged from the primordium 3-4 billion years ago, likely as primitive micelles formed from lipids. Such structures are semi-permeable, generating intracellular chemical gradients, a process referred to as chemiosmosis, ultimately allowing for the reduction of entropy within the cell, transiently circumventing the second Law of Thermodynamics. It was under these conditions that life began on Earth, initiated and perpetuated by the perennial competition between prokaryotes and eukaryotes, a battle which rages on to this day.

The Solution to the Problem

We have identified a mechanism that integrates development and physiologic homeostasis- cell-cell interactions. Why not apply that mechanism to Evolutionary Biology as the long-term basis for phylogenetic change? Using that approach at the cell-molecular level offers the opportunity to determine how cellular composition has accommodated adaptation. In a recently-published book, entitled Evolutionary Biology, Cell-Cell Communication and Complex Disease, we exploited this approach to understand how the lung evolved to accommodate metabolic drive, based on the role of surfactant in facilitating both the developmental and phylogenetic increases in lung alveolar surface-area for gas exchange. By reducing this process to ligand-receptor interactions and their intermediate down-stream signaling partners, we are able, for example, to envision the functional homologies between such seemingly disparate structures and functions as the lung alveolus and kidney glomerulus, the skin and brain, and the skin and lung.

Using such a reductionist approach to functional genomics has led to a mechanistic understanding for how internal selection pressure, brought on by physiologic stress within Claude Bernard’s milieu interieur, may have given rise to such disparate diseases as Goodpasture Syndrome and asthma. By linking together the cell-molecular pathways for basic physiologic mechanisms, independently of their overt structural and functional appearances, particularly as they relate to extrinsic ecologic selection pressures, one can discern the ‘how and why’ of evolution. By literally starting from the ‘middle’ of the mechanism, tracing the signaling pathways linking genes to phenotypes, one can see how such pathways evolved across the space and time of biology as ontogeny and phylogeny.

One fundamental insight from such molecular analyses is that the time and space dimensions for evolutionary processes are artifacts of descriptive biology; once the underlying mechanisms are identified, the dimension of time falls out of the analysis, other than as the sequence of events. Once achieved, vertical integration literally and figuratively eliminates time and space. This point of view opens up to a very different perspective on life actually being simple, rather than complex. Moreover, it begs the question whether metazoans are merely a further extrapolation of such prokaryotic, pseudo-metazoan traits as lateral inheritance, biofilm and quorum sensing. Perhaps protozoans evolved their metazoan phenotype as a way of monitoring the environment iteratively. After all, H.G. Wells wanted to teach us such humility by having bacteria save mankind in The War of the Worlds.

Putting Humpty Dumpty back together again based on epigenetic principles

A systematic error in the reductionist approach to Evolutionary Biology is our failure to recognize that it is a mechanism, not a ‘thing’, namely DNA. In order to understand how and why evolution functions, one must first reduce it to its smallest functional unit of activity- the cell. In contrast, evolutionists describe the process dichotomously as mutation and selection, overarching the cell. That is why Cell Biology is not part of the conventional analysis- it is not considered to be necessary, yet it is the fundamental mechanism of ontogeny- it is only in the recent past that we have been able to determine the mechanisms underlying morphogenesis based on cell-specific production of soluble growth factors and their cognate receptor signaling partners on the surfaces of neighboring cell-types. These developmental mechanisms culminate in homeostatic control, providing a unified functional basis for physiology, repair and regeneration. And since such processes are amenable to modification under selection pressure, they are also the mechanisms for phylogeny. Such cellular signaling mechanisms common to both ontogeny and phylogeny provide insights to the mechanisms of evolution, complying with the ‘emergent and contingent’ nature of the evolutionary process.

We humans have succeeded as a species because of our highly-evolved central nervous system. We have an obligation to both our ancestors and offspring to use our minds effectively so that we don’t destroy ourselves and the environment in the process. If we understood where we evolved from perhaps we would act in more socially responsible and humane ways. The key is to deconvolute Evolutionary Biology, which has become so complicated as to be useless in utilizing the Human Genome for the prediction and prevention of disease. The solution to the puzzle of evolution is right under our noses, but instead we generate more and more neologisms and metaphors that allow us to circumlocute and evade the solution.

Paracrine Growth Factors- from morphogenesis to homeostasis

Contemporary molecular embryology is based on growth factors signaling via their cognate receptors, depending upon spatio-temporal relationships that determine morphogenetic patterns. As such, these mechanisms provide a predictive magnitude and direction for the formation of structure and function. In this sense, it is no different from what we expect of a mechanistic basis for Evolutionary Biology, which is also trying to comprehend the magnitude and direction of biologic change, though the time scales are (seemingly) very different. But perhaps that’s just an artifact of the descriptive modality. Once we transition to a mechanistic approach, such time and space considerations are independent of the mechanisms of interest, other than providing the nominal sequence of events.

So what is the value added in using a cellular-molecular mechanistic approach? We have been able to envision this continuum, and how it has fostered the evolution of the lung, for example. Based on our working knowledge of how paracrine growth factor-receptor interactions have mediated the development of the mammalian lung, we considered the overall ontogeny and phylogeny of the lung phenotype, i.e. its evolution, as an overall selection pressure for increased surface area, from fish to man in service to the metabolic drive underpinning the water-to-land transition. This has been realized by a progressive decrease in the size of the alveoli, increasing the gas-exchange surface area-to-blood volume ratio over phylogeny and ontogeny (see Schematic, Fig. 2).

This process could not have occurred without an increase in the net production of lung surfactant, which must physic-chemically compensate for the increased surface tension resulting from the decrease in alveolar diameter (by the Law of Laplace, that the surface tension is inversely related to the diameter of a sphere). The cellular regulation of surfactant production is orchestrated by interactions between the alveolar epithelial lung cells that synthesize the surfactant, known as Alveolar Type II cells, and the adepithelial connective tissue fibroblasts that underlie them within the alveolar wall. The cell-cell interactions that regulate surfactant production have evolved from the secretion of cholesterol, the simplest form of surfactant, into the lumen of the swim bladder of fish to prevent the walls from adhering to one another, to a progressively more efficient means of synthesizing and secreting a more complex biochemical surfactant mix of lipids and proteins in order to accommodate the increase in surface area, as the lung has evolved phylogenetically. Along with the decrease in the diameter of the alveoli, the alveolar walls also became progressively thinner, further facilitating the gas exchange between the alveolar space and the lung microcirculation. The ‘invention’ of tubular myelin, an extracellular latticework of surfactant proteins and phospholipids generated from the lamellar bodies secreted by the Alveolar Type II cell, provides an extracellular homolog of the lipid barrier formed by the stratum corneum of the skin, including both the lipids and the antimicrobial peptides packaged within the lamellar bodies.

Tracing the changes in structure and function that have occurred over both the short-term history of the organism (=ontogeny), and the long-term history of the organism (=phylogeny), and how the mechanisms shared in common account for both biologic stability and novelty, will provide the key to understanding the mechanisms of evolution. Like solving a fraction problem in math, the cellular-molecular approach determines the ‘least common denominator’ for both ontogeny and phylogeny, eliminating the artifactual temporal-spatial differences between these processes.

It is important to bear in mind that there are certain gene-phenotype homologous relationships that are fairly readily apparent because of their position as ‘barriers’ at the interface between the environment and the organism, such as the lung, skin, and gut, likely having originated from the cell membrane in unicellular organisms as their ‘common denominator’. And then there are other homologies that are ‘derived’ from those more readily apparent properties that must be deciphered based on their short- and long-term histories, particularly as they derive from those primary mechanisms. Instead of taking a ‘top-down’ or ‘bottom-up’ approach to understanding physiologic evolution based on superficial appearances, we have advocated for a ‘middle-out’ approach based on the underlying cell-cell communication by which to determine the evolutionary origins of cell-molecular traits.

We have demonstrated the utility of a cell-molecular developmental physiologic approach in deconvoluting lung evolution, providing a cell-molecular mechanistic continuum from development to physiologic homeostasis and regeneration. Moreover, this tack allows for understanding the interrelationships between tissues and organs at a fundamental cell physiologic level, independent of their contemporary appearances and functions, effectively replacing the need for illogically reasoning after the fact. This approach has provided novel insights to the mechanisms of evolution for both the more directly evolved structures/functions of the lung, namely skin and bone, as well as for the deeper homologies of the kidney and brain, based on cell-cell signaling as the integrative mechanism, for the first time.

We have learned from cell culture experiments that normal metazoan cells are not structurally or functionally autonomous; over time, differentiated cell-types lose their phenotypes. They exist within microenvironments created during development by cell-cell interactions between cells of derived from different cell lines. The underlying mechanisms of development, physiologic homeostasis and regeneration are mediated by soluble growth factors and their cognate receptors, which signal through second messengers to determine the metabolic and proliferative status of their surroundings. We maintain that these mechanisms are the basis for the evolution of complex biologic traits, and that by systematically analyzing these diachronic signaling mechanisms over time within and between species, the mechanistic basis for evolution can be discerned.

The Water-Land Transition, PTHrP Amplification, and the Adaptation to Land

The evolution of PTHrP signaling known to have occurred during the water-land transition (Fig.4) would provide a mechanistic explanation for the morphing of fish into land vertebrates, like Neil Shubin’s Tiktaalik, the fossil remains of the transitional tetrapod discovered in 2004.

All of the essential water-land adaptations—lung, skin kidney, gut, and brain—would have been facilitated . At first glance, this event may seem like a Just So Story for vertebrate adaptation to land, yet we know that there were at least 5 separate attempts by vertebrates to breach land based on skeletal fossilized remains; this could not have occurred independently of the evolution of the visceral organs, particularly because many of the same genetic mechanisms are common to both bone and visceral organ development (PTHrP, Wnt/βcatenin, TGFβ, PKA, PKC, Shh), so these events should also be viewed in the context of hypothetical internal selection mechanisms for cellular adaptation.

Mechanistically, the PTHrP Receptor gene is known to have duplicated during the water-land transition, amplifying the PTHrP signaling pathways for the adaptive morphing of the lung, skin and bone- all of these organs are dependent on the PTHrP signaling pathway for their development and homeostasis. Though the literature suggests that this occurred by chance, it could well have happened as a direct consequence of the generation of excess oxygen radicals and lipid peroxides due to vascular shear stress within the microcirculations of these very same tissues. On the one hand, these tissues and organs would have constrained land adaptation, but on the other, increased PTHrP signaling would have been advantaged by such gene duplication events. This process is formally known as the Baldwin Effect.

In fact, if adaptation is thought of in the context of internal selection caused by vascular shear stress, the concept of plasticity becomes much more relevant, not to mention being experimentally testable; constitutive genes are the ones that were most vulnerable to mutation, since they were the genes being targeted by such selection mechanisms. And perhaps such unconventional internal selection was followed by classic Darwinian population selection for those members of the species that were best fit to regulate those constitutive genes to survive, rendering the newly evolved homeostatic mechanisms regulatable. Theoretically, this may have been due to the fact that regulated mechanisms would be more resilient, and therefore less likely to generate mutagens than non-regulated constitutive genes. And this may also explain why humans have fewer than the predicted number of genes based on descriptive instead of mechanistic biology.

Those members of the species best able to up-regulate their PTHrP signaling in support of any one or all of the land adaptive traits- bone, skin, lung- would have had a higher likelihood of surviving on land. In turn, other tissues and organs would also have been positively selected for their amplified PTHrP signaling capacity, making them more likely to survive. This is particularly relevant to the glomeruli of fish kidneys, which range from large (salt water), to small (fresh water) to being absent in some species, but are ubiquitous in land vertebrates. Shear stress within the renal vasculature could have given rise to PTHrP signaling for glomerular function- PTHrP-mesangium signaling for water and electrolyte flux. Similarly, PTHrP is expressed in the pituitary and adrenal cortex of land vertebrates, making for a more robust physiologic stress ‘fight or flight’ mechanism since the corticoids stimulate epinephrine secretion as they course their way from the adrenal cortex through the adrenal medulla. But this amplified epinephrine response to stress is only applicable to amphibians and beyond phylogenetically since fish have an independent adrenal cortex and medulla. Such an evolved stress mechanism would have been advantageous for various physiologic adaptations to land, not the least of which would have been the positive selection for brain evolution- epinephrine inhibits flow through the blood-brain barrier, generating more neuronal interconnections within the Central Nervous System due to increased epinephrine and norepinephrine production within the brain.

This is not merely a tautologic rationalization of the data. If you experimentally delete the PTHrP gene in the embryonic mouse, the bone, skin and lung fail to develop the self-same characteristics for land adaptation- Phylogenetically, the PTHrP signaling pathway has been amplified through gene duplication, fostering stronger skeletal support, skin barrier function and lung gas exchange.

In further support of the causal relationship between the water-land transition and the evolution of specific physiologic traits that actively accommodated the adaptation to life on land, there were two other gene duplications that occurred during the water-land transition: the βAdrenergic Receptor (βAR), and the glucocorticoid receptor. The evolution of the βARs was necessitated by the demand for independent regulation of the systemic and pulmonary blood pressures to accommodate the expanding surface area of the evolving lung. The evolution of the glucocorticoid receptor from the mineralocorticoid receptor was necessitated by the increase in blood pressure due to the increased effect of gravity on land, causing increased blood-pressure, generating further selection pressure for the βAR mechanism in alleviating the constraint on the expansion of the lung surface area; the effective stimulation of  the βARs by glucocorticoids caused further positive selection pressure  for the co-evolution of both genes. Again, as in the case of the duplication of the PTHrP Receptor, the specific effects of the physiologic stress due to land adaptation on shear stress in the lung and kidney may have specifically precipitated gene duplications in these capillary beds, functionally alleviating the physiologic constraints on these tissues and organs through internal selection, further fostering these physiologic adaptations through external selection. For example (Fig.5), the episodic bouts with hypoxia due to the unmet physiologic needs of the organism as it attempted to adapt to land would have caused physiologic stress since hypoxia is the most potent stressor known,  stimulating the Pituitary-Adrenal Axis (PAA), ACTH stimulating glucocorticoid production by the adrenal cortex, and epinephrine production by the adrenal medulla; acutely, epinephrine would have alleviated the hypoxic stress by stimulating surfactant secretion by the evolving alveoli, and the glucocorticoids would have increased βARs, acting synergistically with epinephrine. As a result, the increased distension of the alveoli would have stimulated PTHrP production by the alveolar type II cells, promoting further alveolarization (Rubin et al, 1994), alveolar capillary perfusion, and angiogenesis of both the capillaries and possibly the lymphatic vessels- taken together, the evolution of alveolar PTHrP signaling coordinates the secretion and homeostasis of surfactant with gas exchange across the microvasculature at both the macro-level, and at the micro-level,  since it co-regulates calcium in the alveolar fluid hypophase with the regulation of surfactant removal from the alveolus via lymphatic drainage.  In the aggregate, this adaptive integration of the PAA and the pulmonary system would have fostered the phylogenetic adaptation of land vertebrates. And this cascade of physiologic adaptations may explain the evolution of PTHrP signaling for pituitary ACTH and adrenocortical glucocorticoid, since it would have further facilitated the positive selection for land adaptation by PTHrP Receptor gene duplication.

Bear in mind that these events didn’t occur all at once- it took place over eons of land vertebrate evolution, both within and between species. Consistent with this scenario, elsewhere we have shown that in the course of lung evolution, there were alternating intrinsic and extrinsic selection pressures for the genes that facilitated the increased surface area of the lung. This pattern may atavistically reflect the original mechanism by which the cell membrane of unicellular organisms facilitated the adaptation of the cell to the environment.

As added evidence for the interrelationship between key genetic changes that occurred during the water-land transition and physiologic stress causing internal selection, type IV collagen also evolved novel polymorphisms in the basement membranes of the lung and kidney phylogenetically from fish to humans during this period. The NC1 domain of Type IV collagen forms a natural physicochemical barrier against fluid exudation from both the lung and kidney due to its molecular electrostatic and polar properties, preventing the loss of fluid across the alveolus and glomerulus that would otherwise have occurred due to the increased physiologic demand on these structures during the water-land transition.

Contrast Evolutionary and Developmental Biology as Descriptive vs Mechanistic

 If the ‘key’ to understanding evolution is as a mechanism for spatial-temporal relationships of genes as determinants of phenotypes, and these relationships are mediated by soluble growth factors and their cognate receptors, then by following the latter we can understand the former. After all, how can you generate an ‘arrow of time’ without a mechanism for the magnitude and direction of its trajectory? Ironically, the Evolutionary Biology literature has virtually no orientation to growth factors as the mediators of evolution, or their signaling to their cognate growth factor receptors, which are the determinants of the ‘arrow of time’ described by evolutionists. As a result, Evolutionary Biology is purely descriptive, offering no biologic mechanism to explain Natural Selection.

On the other hand, as mentioned earlier, contemporary developmental biology is predicated on the functions of growth factors and their receptors as the determinants of morphogenesis. The big breakthrough in molecular embryology occurred in the late 1970s with the discovery that soluble growth factors and their receptors underlie and mediate the patterns of development. And developmental physiology as the outcome of embryonic development acknowledged that the denouement of development is integrated homeostasis. Recognition of such developmental and homeostatic mechanisms as a continuum provides deep insight into the mechanisms of evolution. By superimposing cell-cell signaling on conventional ways of thinking about descriptive evolution, one can begin to understand such otherwise nebulous terms and concepts as Survival of the Fittest, Descent with Modification, Natural Selection, the Biogenetic Law, Spemann Organizers, Canalization, Genetic Assimilation, Exaptation, Modularity, Evolvability, Systems Biology, Developmental Systems Theory, Pleiotropy, etc, etc.

Conrad Waddington invoked Canalization, aka homeostasis, in the context of evolution. When a Cell Biologist looks at Waddington’s adaptive landscapes, which resemble tents, supporting poles and all, they want to look under the canvas and see what has caused those hills and valleys (I know I do). In so doing, they have been able to determine the cellular/molecular basis for morphogenesis, which is where evolutionists began in the 19th century, but were unable to provide the mechanistic basis for Haeckel’s Biogenetic Law or Spemann’s Organizer. So the geneticists wrested the subsequent inquiry into evolution from the embryologists, and have been reducing Evolutionary Biology to mutation and selection ever since. Cell biology has literally been eliminated from Evolution Theory for these historic reasons, yet it has revealed how single cells can create whole organisms, much the same as evolution has. And suffice it to say that evolutionists are not trained in Cell Biologic methods. Therefore, it would seem productive to let the Cell Biologists back into the tent. How would this advance our understanding of the mechanisms of evolution? Perhaps by addressing some of the major concepts in Evolution Theory in cellular terms (see above), we may see how developmental biology would facilitate our thinking in this field, which has the potential for being the basis for a unifying theory of biology in practice, as well as in principle- science is deductive, not inductive. We suffer from too many metaphors and too few experimentally refutable hypotheses.

One often reads of molecular biologists alluding to the highly conserved nature of genes of interest as validation for their relevance to some biologic process or structure, but what does that mean functionally? That it is expressed far back in the history of the organism, inferring that it has been present through much of the evolution of the species. But rarely if ever is this pursued mechanistically in order to determine how and why such a conserved gene was involved in the evolutionary mechanism. Other than the process of development, there is no system in which to test such mechanisms.

Although this is a simple concept, there was considerable difficulty in actually executing studies based on the idea. Development and evolution certainly offer a facile sort of analogy to each other: both are processes of change. Although this analogy was compelling during the nineteenth century, it was sterile until the developmentalists discovered soluble growth factors and their cognate receptors, which were able to mediate the spatiotemporal aspects of the developmental process. Development is a programmed and reproducible process. If we accept Darwinian mutation and selection, evolution can be neither. Evolution can consist of internal and external selection, with internal stability being homeostasis, which can exhibit ‘reaction norms’ that are heritable based on the Baldwin Effect. The process of evolution is described as “emergent and contingent”. Canalization can be seen in the context of homeostatic regulation, which, when it fails, can generate cryptic genes that represent the history of the organism, now reprised to provide a physiologic ‘safety net’ that allows for the healing to occur; as such, it allows for reproduction even in the face of illness. The apparent inevitability of development was daunting. To connect it effectively with evolution , two major ideas had to be accepted. The first, pointed out by Garstang, is that the larval stages also face the rigors of life (reminiscent of the Barker Hypothesis, that adult diseases originate in utero). Mendelian genetics allows new traits to appear at any developmental stage, and natural selection potentially operates upon them as it does upon traits expressed in adults. The second major point is that although ontogeny appears inevitable and inextricably orchestrated in its flow, it is not a single process. There are a large number of processes at work, some more or less coupled to others. It was Joseph Needham who, in 1933, using an engineering metaphor of shafts, gears and wheels, suggested the idea of dissociability of elements of the developmental machinery. He pointed out that it is possible to experimentally separate differentiation from growth or cell division, biochemical differentiation from morphogenesis, and some aspects of morphogenesis from one another. The implication of this idea is enormous: developmental processes could be dissociated in evolution to produce novel ontogenies out of existing processes, as long as an integrated developmental program and organismal function could be maintained.

Epistemology- Maybe We Got it Backwards?

The integrated mechanism for physiology has long been accepted to be a fait accompli, yet we know that there are processes of development, evolution and regeneration-repair that comply with some unknown, underlying bauplan. The recent experimental evidence for the complete metazoan toolkit being present in the unicellular state of sponges provides the rationale for such an integration of structure and function, by definition. Mechanistically, the insertion of cholesterol in the plasma membrane of eukaryotes facilitated endocytosis, locomotion and respiration, providing the impetus for their evolution. Moreover, it is striking that the cytoskeleton collectively mediates homoestasis, mitosis and meiosis alike, suggesting the phenotypic autonomy of these unicellular organisms. The significance of this is evinced by subjecting yeast, the simplest eukaryotes, to microgravity, causing both loss of polarity and failure to bud. Without polarity, there is no calcium flux or reason to locomote- where is up, down, sideways? and budding is the reproductive strategy of yeast- loss of these fundamental traits by ‘disorienting’ the cytoskeleton underscores the adaptation to the one element in the environment that is omnipresent, unidirectional and was there from the inception of the planet. So perhaps multicellularity was merely the eukaryotic ploy used to combat lateral inheritance, biofilm and quorum sensing in our age-old competitors, prokaryotes.

Conclusion

 The multicellular form may merely be a derivative of the unicellular state, acting as a matrix for it to monitor the on-coming environment so that the gene pool knows what epigenetic marks acquired during the multicellular phase of the life cycle to include or exclude in the next generation. For example, Dictyostelium exists in two forms, a free-swimming amoeboid form and a colonial Fruiting Body. Under conditions of abundant nutrients, the Slime Mold remains in its free-swimming amoeboid form; under low food abundance conditions, the amoeboid forms colonies. Logic would dictate that this organism evolved under high nutrient abundance conditions, and therefore its unicellular form is the primary phenotype, the colonial form being derivative.

We need to better understand evolution from its unicellular origins as the Big Bang of biology.