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4- http://mbscientific.org/wiki/The_Proto-Biotic_Cascade

ch4- Creation of Protobiota

1- Creation of intermediate organic material from base material
2- Creation of biotic material from intermediate organic compounds
3- What is life anyway?

So far we have traced the morphological flow of energy throughout the particle, atomic and molecular realms. A class of carbon based molecules, called organic molecules continue the cascades of creation, forming the protobiotic material. These materials form the foundations from which protocells evolve. Although organic material has been detected in space as well as in meteorites that have fallen to earth, the creation cascades suggest that there must be direct pathways that describe the creation of biotic matter from the base material present on earth. The starting point of the flow would be base material that was abundant in the primordial earth some 4 billion years ago: volcanic base organic gasses (CO,CO2, N2, SO2, H2S, HCl, B2O3, and smaller quantities of H2, CH4, SO3, NH3, HF), solid material such as compounds of Si, Fe, Mg, K, Na, P, Ca among others, oh and water. The biotic matter would be nucleotides, amino-acids, lipids, sugars, etc. Here I'm going to lay out a morphological flow, represented by chemical reactions, that will take the base materials through to organic materials, to biotic materials that form the basis of cellular functions. That part is pretty straightforward. Then we'll speculate as to how proto-cells can be constituted from the biotic matter. 
Some of the reactions you see will occur naturally. Others need a large amount of energy. Many experiments have shown that base organic material will cook into intermediate and proto-biotic compounds. These include Miller type experiments which introduce electrical arcs into base organic material mixes (simulating lightning in the primitive earth atmosphere),  Fischer-Tropsch reactions that expose base organics to high temperature/pressures with the presence of catalysts (simulating volcano aquifer regions), as well as experiments such as impacting canisters full of base organics with high impact projectiles (simulating flash temperature-pressure of volcanic eruptions in volcano-aquifer regions). All of these experiments consistently produce intermediate and biotic compounds from base organics.
It must be noted that complex organic material has been detected in space as well found in asteroids. So these coalescence process which give rise to successively more complex organic material is not unique to earth, there may have even been notable contribution of organic material from cosmic objects to earth. But for our current purposes we will cover morphological flow processes that can be verified as occuring here on earth, thereby establishing direct pathways for evolution of proto-biotic material from base organic on earth.

The early atmosphere would have naturally produced some organic material, e.g. as in the following reactions:

2CH4 + N2 ==> 2HCN +3H2

CO + NH3 ==> HCN +H2O

HCHO + NH3 ==> H2N-CH2OH ===> HN=CH2 + H2O

HN=CH2 + HCN ==> H2NCH2CN

H2NCH2-CN + 2H2O ==> H2NCH2COOH + NH3

Further, as highlighted by the Miller experiments in the 1950's, volcanic gas mixtures, forming the early earth atmosphere, when subjected to lightning and in proximity of water (transport) do produce a wealth of organic matter, including:

H-COOH formic acid

H2N-CH2-COOH glycine

HO-CH2-COOH glycolic acid

H2N-CH(CH3)-COOH alanine

HO-CH(CH3)-COOH lactic acid

H2N-CH2CH2-COOH beta-alanine

CH3-COOH acetic acid

CH3-CH2-COOH propionic acid

CH3-NH-CH2-COOH sarcosine

HOOC-CH2CH2-COOH succinic acid

H2N-CO-NH2 urea

HOOC-CH2CH2CH(NH2)-COOH glutamic acid

HOOC-CH2CH(NH2)-COOH aspartic acid

Biotic material consist of sugars, amino-acids, lipids and purines and piramidines (base material for nucleotides, DNA/RNA). Sample reactions depicted below demonstrate pathways that create biotic material from intermediary organic material. Such reactions can be shown to occur naturally in Miller, Fischer-Tropsch, and high impact experiments.

A) Sugars, e.g. Glucose from 6 Formaldehyde molecules: C6H12O6 = (CH2O)6

B) Amino-acids, e.g. Serine
Glycolaldehyde from formaldehyde in the atmosphere:

HCHO + HCHO ===> HOCH2CHO (glycolaldehyde)

HOCH2CHO + NH3 ===> HOCH2CH(OH)NH2

HOCH2CH(OH)NH2 ===> HOCH2CH=NH + H2O

HOCH2CH=NH + HCN ===> HOCH2CH(NH2)-CN

Hydrolysis of the cyanide group occurs in the primeval ocean:

HOCH2CH(NH2)-CN + 2H2O ===> HOCH2CH(NH2)-COOH + NH3

C) nucleotide bases e.g. Purine Adenine

 
D) Lipids

Fischer-Tropsch type reactions can produce a variety of hydrocarbons, including fatty acids from CO and H2, passed over catalysts such as nickel, iron, etc.:

e.g. Palmitic Acid: 16CO + 30H2 ===> CH3-14CH2-COOH + 14H2O

So, we have shown pathways for creation of biotic material from base organic material. We also know that primitive cells (extremophile archaea) abound. The morphological flow model suggests that pathways must exist that connect the two.

The next step requires the creation of protocells. Protocells would be the aggregation of various permutations of sugars, proteins, lipids and nucleic acids (RNA,DNA). This step is the Holy Grail of origin of life theories. For this we need an environment where biotic material can mix and pick up other necessary components such as potassium, sodium, calcium and phosphorous. This environment should be subject to high-energy thermal flashes as well as possess catalytic properties in order to carry on the construction/destruction cascades repeatedly, thus creating various permutations of biotic matter. Secondly this environment must provide water transport to accumulate the produced protobiota in sheltered areas. Such an environment, seemingly, is the interface zone between volcanoes and aquifers. Such zones would be the convergent environments where biotic material created from atmospheric electrical flashes mix with the biotic material produced within the region itself. Recent discovery of primitive extremophile archaea in such zones lends credence to this idea. Furthermore, it has been shown that these extremophile archaea metabolize inorganic material. So not only such zones possess the environment that produces biotic compounds, they also contain the food sources for the emergent proto-cells once they have formed.

The ongoing work here, for the research community in general, is to establish a pathway for evolution of proto-cells in the volcano-aquifer environment. The work looks to establish evolutionary pathways for creation of nucleic acid chains (DNA/RNA) from the base ingredients of purines and piramidines, sugars (ribose specifically) and phosphates. At the same time, it looks to show how a wide variation of protein and lipid structures would arise in combination with nucleotide chains and sugars. So one could write a simple cascade metaphor:

Lipid vesicles + catalytic proteins + nucleotide chains +sugars ==> more Lipid vesicles + catalytic proteins + nucleotide chains + sugars ==> more Lipid vesicles + catalytic proteins + nucleotide chains + sugars ==> and so forth

Now, if we look at a cell as a series of related control functions, we find these major functions:

1) metabolic functions- breaking down material to gain useful energy

2) structural functions- protein manufacturing, building and maintaining the membrane, cytoskeleton, etc.

3) replication functions- building copies of nucleic acid strands from templates and producing offspring.

4) Sensor - Motor functions - building sensory organelles, motor organelles and establishing stimulus/response pathways

5) Signaling functions- building pathways for inter-cellular an intra-cell signaling

Please note that there are other functions not enumerated above, including defense and immunity functions. But to make the next point, these will suffice.  So, we have the after picture, i.e. cells with the above 5 functions. We have the before picture, that is the biotic material that can aggregate to perform those functions. We also know a probable environment for incubating proto-cells, i.e. the volcanic-aquifer zones. The holy grail of evolution of life theory is to come up with the pathways that could get us from there to here.

Judging from what we have learned from morphological flows, it is quite likely that the proto-biotic aggregates that manifest the 5 functions (metabolic, structural, replicative, motor/sensory, signaling) might well have their separate evolutionary construction pathways. Then somewhere along the line accretion pathways kick in, thereby coalescing these separate aggregates within the body of proto-cells. And evidence shows, as in the case of viruses, that structural and replicative aggregates might have coalesced to create an alpha type proto-cell. Then as metabolic, motor/sensory and signaling aggregates are further coalesced, you'd get all of the 5 functions within the body of a say beta proto-cell.

It is notable that as we traverse biotic evolution in the next few chapters, all we will see are body morphologies evolving to better manifest these 5 major functions (among others) based on a simple premise of what is agreeable and disagreeable to the stability (validity) of the emergent functionalities, thereby filling stable evolutionary pathways. Much more on this to come.

 
3- Exactly what is life anyway?

Let us consider the sizes of the compounds that we've covered in the course of following the morphological flows so far. The atomic scales are in the order of Angstroms (10^-10 meters), base organic molecules are in the order of nanometers (10^-9 meters), macro-molecules like ribose are in the order of 20 or so nanometers. At these scales some macro molecules display some of the 5 functions of life. Small protein and nucleotide chains can catalytically break other molecules. Protein, lipid and nucleotide chains can add to their polymer strands, then split into smaller strands, that is a form of primitive replication. In the 20-100 nanometer range, lipids can form self-sealing cells. They can let in protein and nucleotide chains, which in turn can form primitive metabolic and replication functions. They can also combine with proteins and form primitive cell walls. At this same size range we find the first organisms with recognizable (all be it partial: alpha proto-cells) signs of life, those are nano-bacteria and viruses (primitive viruses have a single RNA strand encapsulated in a membrane). At about 500 nanometers and above we start finding extremophile archaea and prokaryotes (bacteria). In the order of micrometers (10^-6 meters) we find eukaryotes (plant and animal cells).

So we find the morphological flows radiating in all possible directions, creating a host of entities. Out of that assembly of possibilities, stable cell designs emerge that have all of the functions that we require to call something alive.

My point is that it is our definition that determines what life is. In the morphological flow process itself there is no demarcation point of where the inanimate stops and where the animate life starts. It is our philosophical stance that produces a definition for the demarcation point of life, namely cells with the 5 functions. It must be noted that (and we will cover this in much more detail later on) that this philosophical stance is not universally shared. In the pantheistic philosophy everything is alive, i.e. there is no demarcation point between the animate and the inanimate. That mode of thought is more reflective of the morphological flows.

Chapter Key: Morphological Flows, entities going through functional constructs thereby creating more complex entities with more complex functionalities:

base organic molecules  == chemical reactive constructors (Electro-Magnetism) ==> intermediate organic molecules  == chemical reactive constructors (Electro-Magnetism) ==> biotic organics

biotic organics == constructor? ==> biotic aggregates manifesting structural functions

biotic organics == constructor? ==> biotic aggregates manifesting metabolic functions

biotic organics == constructor? ==> biotic aggregates manifesting replicative functions

biotic organics == constructor? ==> biotic aggregates manifesting sensory/motor functions

biotic organics == constructor? ==> biotic aggregates manifesting signaling (communication) functions

structural aggregates + replicative aggregates == accretion constructor? ==> alpha proto-biota

alpha proto-biota+ motor/sensory aggregates +  signaling (communication) aggregates + metabolic aggregates == accretion constructor? ==> beta proto-biota

Links:

Origin of life:
Article: The Emergence of Living Systems in Archaean Submarine Hot Springs

Another article on origin of life

Details on thermosynthesis and origin of life

History of evolutionary molecular biology

RNA World- some say its RNA's fault, it started it all

Lipid World- some say it was the lipids fault.. those damned lipids

Article on Bio-Cosmology

Panspermia- space aliens, oh noooo

All about the cell:
From atoms to molecules and cells to tissues - DNA, RNA, proteins, sugars, etc. a great site

Introduction to bacteria

More on bacterial microbiology

Yet more on bacterial microbiology

Milestones in cell division

Cell cycle: details of cell division

Life at high temperatures

Some details on cell motility

++++++

Nanobacteria- what the hell is that?!