The Proto-Biotic Cascade
From Mbscientific_wiki
[edit] Creation of Proto-Biota
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. Here we are going to trace the cascades of chemical reactions that produce complex biotic compounds from simple organic and inorganic compounds.
The starting point of the flow would be base material that was abundant in the primordial earth some 4 billion years ago: volcanic gases (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. We will build a series of naturally occurring chemical reactions that build up the complexity of organic compounds, eventually producing biotic matter: nucleotides, amino-acids, lipids, sugars, etc. Then we'll speculate as to how proto-cells can be constituted from the biotic matter.
Some of the reactions you see will occur under normal, low energy conditions. Others need a large amount of energy. Many experiments have shown that base material will cook into intermediate and proto-biotic compounds. These include Miller type experiments which introduce electrical arcs into base material mixes (simulating lightning in the primitive earth atmosphere). Fischer-Tropsch reactions expose base material to high temperature/pressures with the presence of catalysts (simulating flash conditions in volcano-aquifer regions). High impact collision experiments smash canisters full of base material with high impact projectiles (simulating high impact collisions in space as well as on earth). All of these experiments consistently produce intermediate and biotic compounds from base matter.
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. And that should come as no surprise. After all the distinction of earth versus space is an artificial one. Earth, after all, is part of space. But for our current purposes we will cover morphological flow processes that can be verified as occurring here on earth, thereby establishing direct pathways for evolution of proto-biotic material from base material on earth.
[edit] Creation of intermediate organic material from base material
The early atmosphere would have naturally produced some organic material, e.g. as in the following reactions:
2CH4 + N2 ==> 2HCN +3H2
CO + NH3 ==> HCN (hydrogen cyanide) + H2O (water)
HCHO + NH3 ==> H2N-CH2OH (hydroxylamine) ===> HN=CH2 (Methanimine) + H2O (water)
HN=CH2 + HCN ==> H2NCH2CN (aminoacetonitrile)
H2NCH2-CN + 2H2O ==> H2NCH2COOH (aminoethanoic acid, or glycine)+ NH3 (amonia)
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
[edit] Creation of biotic material from intermediate organic compounds
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: 6(CH2O) ===> C6H12O6 (glucose)
B) Amino-acids, e.g. Serine from formaldehyde through the following reactions; first set of reactions can occur in the atmosphere:
HCHO + HCHO ===> HOCH2CHO (glycolaldehyde)
HOCH2CHO + NH3 ===> HOCH2CH(OH)NH2 (ammonium acetate)
HOCH2CH(OH)NH2 ===> HOCH2CH=NH (acetamide) + H2O
HOCH2CH=NH + HCN ===> HOCH2CH(NH2)-CN (imidazolidinone)
And finally, hydrolysis of imidazolidinone occurs in the primeval ocean, producing Serine:
HOCH2CH(NH2)-CN + 2H2O ===> HOCH2CH(NH2)-COOH (Serine) + 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
Note: Fischer-Tropsch reactions can also yield guanine, along with adenine, uracil, and thymine; e.g.
5CO + H + 5NH3 ==> C5H8N5O (guanine) + 4H2O
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.
[edit] Proto-cell Bakery: Volcano-Aquifer Environment
The next step requires the creation of protocells. Proto-cells 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 (ala Fischer-Tropsch type reactions). 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 pyrimidines, 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 (among others):
1) metabolic functions- breaking down material to gain useful energy
2) structural functions- building and maintaining the membranes, cytoskeletons, 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
6) Defense and Immunity - Inward and outward mechanisms for self-preservation
Please note that there are other functions not enumerated above. But to make the next point, these will suffice. So, we have the after picture, i.e. cells with the above 6 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 6 functions (metabolic, structural, replicative, motor/sensory, signaling, defense) 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.
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 6 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 6 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 6 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.
[edit] Chapter Key
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
biotic organics == constructor? ==> biotic aggregates manifesting defense/immunity functions
Biotic Organics exhibiting cellular functionalities == accretion constructor? ==> proto-biota (??)
[edit] Courses
From MIT OpenCourseWare:
http://ocw.mit.edu/OcwWeb/Earth--Atmospheric--and-Planetary-Sciences/12-007Spring2003/CourseHome/index.htm - MIT - 12.007 Geobiology
http://ocw.mit.edu/OcwWeb/Earth--Atmospheric--and-Planetary-Sciences/12-301Fall-2006/CourseHome/index.htm -MIT - 12.301 / 12.842 Climate Physics and Chemistry
[edit] links
Origin of life:
http://www.science.siu.edu/microbiology/micr425/425Notes/14-OriginLife.html - Where I got a lot of the chemical reactions
http://www.syslab.ceu.hu/corliss/Nature.html - Article: The Emergence of Living Systems in Archaean Submarine Hot Springs
http://www.ucmp.berkeley.edu/education/events/deamer1.html - Another article on origin of life
http://www.geocities.com/ResearchTriangle/Node/5345/ - Details on thermosynthesis and origin of life
http://mccoy.lib.siu.edu/projects/bio315/index.htm - History of evolutionary molecular biology
http://www.lawrenceroberge.com/RNAWORLD.htm - RNA World- some say its RNA's fault, it started it all
http://ool.weizmann.ac.il/Segre_Lipid_World.pdf - Lipid World- some say it was the lipids fault.. those damned lipids
http://www.dhushara.com/book/bchtm/biocos3.htm - Article on bio-Cosmology
http://www.panspermia.com/ - Panspermia - space aliens, oh noooo
All about the cell:
http://www.accessexcellence.org/AB/GG/ - From atoms to molecules and cells to tissues - DNA, RNA, proteins, sugars, etc. a great site
http://www.bact.wisc.edu/MicrotextBook/BacterialStructure/Introduction.html - Introduction to bacteria
http://www.cat.cc.md.us/courses/bio141/lecguide/unit1/index.html - More on bacterial microbiology
http://cwx.prenhall.com/bookbind/pubbooks/brock/ - Yet more on bacterial microbiology
http://www.nature.com/celldivision/milestones/index.html - Milestones in cell division
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/CellCycle.html - Cell cycle: details of cell division
http://www.bact.wisc.edu/bact303/b1 - Life at high temperatures
http://www.sbuniv.edu/%7Eggray.wh.bol/CHE4104/cp15answers.htm - Some details on cell motility
http://www.msstate.edu/dept/geosciences/4site/nannobacteria.htm - Nanobacteria- what the hell is that?!
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