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The Evolutionary Origins of the Metabolism and Biosphere

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Introduction: The Metabolic & Cellular Transformations Of Geosphere Into Biosphere

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The Krebs Cycle, also known as the Citric Acid Cycle (CAC) or Oxidative Citric Acid Cycle (OCC), is generally encountered running in the oxidative direction and dismantles acetate into carbon dioxide while using the energy derived to reduce coenzymes and ultimately produce ATP. It has a counterpart, the Reductive Citric Acid Cycle (RCC) that runs in the reverse direction, assembling carbon dioxide and water into larger complex molecules with carbon backbones.
 
 

It appears on the basis of available facts that the circumstances surrounding the origin of life on Earth are inextricable from the origin of the solar system and Earth itself - the biosphere rising off the geosphere is the one continuous biochemical reaction that has persisted from the beginning of life on earth to the present.

The emergence of a metabolic network capable of autocatalytically building and decomposing the monomeric components required for macromolecular polymerizaion, and cellular encapsulation, marks the crossing point from the inanimate to the animate. The emergence of cellular encapsulation would facilitate the global spread of that metabolic network - thereby, effecting a transformation of the geosphere into bioshpere as the chemistry of the planet changed in response to the input and output of materials derived from the geological substrate (as well as the hydrological and atmospheric environ) through the metabolic networks of the globally distributed cellular populations.

The primary setting for the origin point is postulated to be hydrothermal vent systems forming just after the last major extraterrestrial impactor to boil off the Earths oceans had struck, ~3.9 bya at the end of the Great Bombardment period. As the water vapor condensed and rained down, the first stable terrestrial oceans emerged. Although subsequent impactors would strike that were capable of boiling the oceans, by 3.9 bya the enduring body of water we know as the ocean had been established and would persist long after the last of these impactors struck, up until this day. The planetary dynamics sought equilibrium in the aftermath of planetary accretion and extraterrestrial bombardment. Through the fissures and hydrothermal vents that formed on the surface of the early Earth flowed an up-welling of organic material moving across the mineral surfaces of the vent systems giving rise to a complex environmental chemistry.

Following the work of Graham Cairns-Smith and Günter Wächtershäuser, I will depart from the primordial soup theories of Alexander Oparin, Stanely Miller, Leslie Orgel and others -and, take the position that the metabolism was ignited in the form of a surface-catalyzed reaction system that evolved into a dissipative structure synergistically organized as an autocatalytic Surface Metabolist on the sides of the hydrothermal vent systems of the newly formed Earth. Although it appears that Wächtershäuser (and others) appropriately focused on the reductive citric acid cycle (RCC) as the starting point for the auto catalytic core of the metabolism, I will deviate from Wächtershäuser in that I feel Thomas Cavalier-Smith has appropriately identified Archea and Eukaryotes as sister domains and of relatively recent origin (950 mya), not ancient and primordial (3.5 bya) as had been originally proposed by Carl Woese - an idea that gained widespread acceptance but appears to be a flawed interpretation of the molecular and fossil data.

The goal, ala Elie Metchnikoff, is to elucidate a series of mechanistically continuous and physiologically viable transitions between each stage in the evolution and diversification of life.

Jtwsaddress42 (discuss • contribs) 19:49, 20 November 2022 (UTC)

Stage I - Surface-Catalyzed Ignition of the Metabolism and Biosphere (4.6-3.85 bya)

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Stage I - Surface-Catalyzed Ignition of the Metabolism and Biosphere (4.6-3.85 bya)

Phase I - Gaia-Genesis (4.6-4.5 bya)

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 Earth/Moon 
 

 Moon 

 
 
 Stationary 
 
 

 Core 

 Metallic 
 

 Mesosphere 

 
 

 Lithosphere 

 Ionic 
 Geosphere 
 

 Cryosphere 

 Ice 
 Phase 
 Mobile 
 

 Liposphere 

 Nonpolar 
 

 Hydrosphere 

 Polar 
 

 Atmosphere 

 Gases 
 Phase 
 Earth 
Biosphere
 System 

Planetary Accretion, Bombardment, and Equilibration

  • Formation of the Heliosphere and planetary solar system (4.6-4.5 bya)
  • Accretion of Earths Primordial Geosphere and Atmosphere
  • Initial atmosphere of H2, He, CH4, N2, NH3, H2O, Metallic Vapors, Noble Gases. Rapid loss of lighter non-polar gases. Gradual accumulation of volcanic outgassing - CO, CO2, H2O, H2S
  • Low abiotic concentrations of molecular oxygen scavenge electrons from other elements resulting in the formation of oxides and an anaerobic environment.
    • H2O, CO, CO2, P2O5
    • Na2O, K2O
    • MgO, CaO, Al2O3, SiO2, TiO2
    • FeO, Fe2O3, Fe3O4
  • Collisional Lunar Event and extraterrestrial bombardment (4.5-3.9 bya)
  • Last impactor large enough to completely boil off Earths oceans. and the first "prebiotic broths", strikes. Large impactors are still capable of boiling the Earths Oceans periodically, but the Great Bombardment is waning and the primary solvent base of the ocean is established permanently.
  • The Ten Million Year Rain - The Condensation of Atmospheric Water Vapors and establishment of the hydrosphere.
  • The final "Prebiotic Soup" of organic and inorganic constituents in a mineral-rich aqueous broth cooked by geological and atomospheric processes surge through the fissures of the Earths crust and mantle and then work their way back to the surface. This solution becomes increasingly dilute as water continues to condense out of the atmosphere and enters the hydrosphere. Non-polar substances partition from aqueous phase and give rise to prebiotic liposphere.
  • Establishment of permanent oceans/beginning of dynamic equilibration of the Geosphere/Hydrosphere (3.9 bya) - [Mantle-Crustal-Atmospheric Redox Couple, Na+,K+,Cl- osmolality]
  • Fe2+ and H2S abundant in seawater precipitates Iron Sulfide.
  • Primordial upwelling of inorganic and abiotic thiorganic molecules from hydrothermal and volcanic sources flow over precipitated Iron Sulfide chimney/vent systems in a continuous flux.
  • Substantial seawater concentrations of Ca2+,Mg2+ limits free/soluble phosphate. Phosphate is sequestered as precipitates of Mg, Ca, Fe, and other metals.

Phase II - Iron-Sulfur World & The Chemoautotrophic Ignition (3.9 bya)

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 CS2,COS,CO2 
 FeS/H2S ⇒ FeS2 + 2 H+ + 2 e‑ 
 FeS/H2S ⇒ FeS2 + H2O 

 Fe-S Clusters 

 Exergonic 
 R‑COSH + CO2 ⇒ R‑CO‑COSH 
 Thiols,Thials,Thiones 

 Thioacetal 
 Chemistry 

 Carbonyl [H] Rxns 
 α‑Ketoacids 
 

 Chemoautotrophic 
 RCC Core 

 
 

 Iron-Sulfur World 

 
 Autocatalytic Cycle 
 Thiocarboxylates 
 & Carbon Fixation 
 Chemoautotrophic 
 Ignition 

4.56 - 3.9 GYA 

Pyrite-Pyrrhotite
 
Hydrothermal "Black Smoker" vent

Hyperbarometric Hyperthermophily/Thermophily, Transition Metals, Organosulfur, and Carboxylate Surface-bonders

  • Iron-Sulfur World - Thio-organic Chemistry occurring on the Iron Sulfide/Pyrite surface of a Hydrothermal Vent System generating sulfur-analogs of the primary metabolites from inorganic monomers CS, CO, CS2, COS, CO2, H2S, H2O, HCN
  • Iron Sulfide conversion to Pyrite serves as a kinetically inhibited source of energetic electrons for the reduction of inorganic carbon to organic carbon (Geoenergetic)
    • H2S/(Fe,Ni,Co) Sulphides ⇒ Iron-Sulfur Clusters  
    • H-R-COS- + CO2 + FeS + 2 H2S ⇒ R=CSH-COS- + FeS2 + 2 H2O
  • Anionic Surface-anchored Thiocarboxylates anchored on a positively charged iron sulfide/pyrite surface - (Carboxypeds)
    • Polycarboxylic Acids possess enhanced surface-bonding and retention by the iron sulfide/pyrite surface
  • Pyrite-pulled Autocatalytic Proto-Reductive Citric Acid Cycle (RCC) ⇒ Chemoautotrophic Surface Metabolist (RCC Metabolic Core)
    • Thiols /(Thio)Aldehydes /(Thio)Ketones ↔ Thioenols /(Thio)Carboxylates / Alpha-Keto-Acids ↔ Alpha-Thioenol-Acids
    • Fatty Acids  
  • Surface-anchored Thio-analogs of Proto-coenzyme moieties
    • 2-mercaptoethanesulfonate ⇒ Coenzyme M  
    • ? ⇒ Lipoic Acid  
    • ? ⇒ Coenzyme Q  

Phase III - Thioester World & The Nitrogen Invasion

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 Nitrogen Invasion 
 Branch Pathways 
 
 FeS/H2S ⇒ FeS2 
 

 αKG ⇒ Glu (Acidic)

 
 

 OXO ⇒ Asp (Acidic)

 
 

 PYR ⇒ Ala (Neutral Non-polar)

 
 Reductive Amination 
 FeS/H2S ⇒ FeS2 
 

 Glu + Glu ⇔ αKG + Gln (Neutral Polar)

 
 

 Glu + Asp ⇔ αKG + Asn (Neutral Polar)

 
 Synthase Rxns 
 

 α-Ketoacids ⇔ α-Amino Acids

 Transanimase Rxns 
 AA Synthesis 
 
 

 Non-coded Polypeptides 

 Condensation Rxns 
 
 

 Biotin 

 
 

 Pyridoxal 

 
 

 Pantetheine 

 
 

 Proto-Thiamine 

 
 Proto‑Coenzymes 
 

 Thioester World 

 
 
 Chemoautotrophic 
 RCC Core 
 Iron-Sulfur World 

Expanding the core - Heterochemistry and The Introduction of New Elements

  • Thioester World - Kinetically Inhibited High-energy Thioester intermediates as proto-bioenergetic transferase metabolites  
  • Nitrogen Invasion - Ammonium enters the system via Pyrite-pulled Nitrogen Fixation on Fe,V,Mo Sulphide surfaces  
  • Amino Acid Pathways  
  • GSH-GSSG Redox Buffer  
  • Surface-anchored Thio-analogs of Nitrogen containing Proto-coenzyme moieties
    • ? ⇒ Biotin  
    • ? ⇒ Coenzyme B  
    • ? ⇒ Flavin  
    • ? ⇒ Nicotinamide  
    • ? ⇒ Pantothenic Acid  
    • ? ⇒ Protoporphyrin IX  
    • ? ⇒ Pyridoxamine  ⇔ Pyridoxal  ⇔ Pyridoxine  
    • ? ⇒ Tetrahydrofolate  
    • ? ⇒ Thiamine  
  • Pyrimidines  
  • Purines  

Phase IV - Phosphoester World & The Bioenergetic Takeover (3.87 bya)

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 Phosphate Invasion 
 
 Peptides 

 Proto-Kinase Rxns 

 
 Carbohydrates 

 Proto-Neoglucogenesis 

 
 Phosphorylation 
 Rxns 
 
 
 

 Aminoglycan Pathways 

 
 

 Nucleoside Pathways 

 
 
  
 
 

 Nucleotide Coenzymes 

 
 

 Energy Carriers 

 
 
 
 

 Nucleic Acid Chemistry 

 
 

 Phosphoester World 

  
 Polymerization 
 Rxns 
 Bioenergetic 
 Transfer 
 Phosphoanhydride 
 Takeover 
 Thioester World 

Vivianite-Pyrite

Mesophily, Alkaline Earths & Phosphates

  • Phosphorus Invasion - the system encounters Ferrous Phosphate (Vivianite) and polyphosphate surfaces still under a flux of H2S and pyrite formation, enabling phosphate to enter the metabolism
    • Polyanionic surface-bonded phosphates anchor organic moieties on a positively charged pyrite surface (Phosphorypeds)
        
    • Phosphoesters provide a means to couple phosphoanhydride energy stores to their organic moieties  
    • pH Buffer System: H2PO4-/HPO42-
  • Phosphorylation Pathways
  • Aldose & Ketose Pathways
  • PNPP
  • cyclicAminoacetals/purines
  • Surface-anchored protoNucleotides (protoNMP's)]
  • Reversible energy-storage carriers/NucleotidePolyphosphates (NDP's/NTP's)
  • NucleotideCoenzymes

Phase V - Nucleic Acid World

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Psychrophily, Coenzyme Handles, Polymerization

  • Nucleic Acid World -
  • Montmorillonite
  • Macromolecular Polymerization
  • Nucleozymes(Ligase/Nuclease/Polymerase/Replicase/AminoAcylNAsynthase/Kinase)
  • Surface-bound Amino Acid-anchored 3' AminoAcylNucleic Acids(Sb3ANA's)

Stage II - Lipid-driven Differentiation of Biosphere into Organism and Ecology (3.85-3.5 bya)

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Stage II - Lipid-driven Differentiation of Biosphere into Organism and Ecology (3.85-3.5 bya)

Phase I - Lipid World (3.85 bya)

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From Surface Metabolist to LUCA via the Obcell

 
 

 Lipid World 

 
 
 
 

 Lipid-protected NA Epoch 

 
 
 
 

 Lipid-anchored RNA World 

 
 
  
 
 

 Lipid-anchored Lipo-Ribo-Protein Epoch 

 
 
 
 

 Lipid-anchored Proteo-Ribosomal Epoch 

 
 
 
 

 Lipid-anchored Virion Epoch 

 
 
 
 

 Lipid-anchored Enzyme Epoch 

 
 
 
 

 Water-Soluble Virionic/Enzymatic Ecology 

 
 
 
 

 Cytoplasmic Cellularity 

 
 
 

 Viral-Virovore Ecology 

 
 
 
 

 Genomic Cellularity 

 
 
 
 

 Rampant HGT Epoch 

 
 

 
 

 HGT Refractory Period 

 
 
 

 Darwinian Threshold 

 
 
 
 

 Cellular Biosphere 

 
 

 LUCA 

 
 Natural 
 Selection 
 VGT 
 Amino‑Acyl tRNA 
 Synthase 
 Selection 
 RNA/DNA 
 Polymerases 
 Ribonucleotide 
 Reductase 
 Virovory 
 Obcell 
 Fusion 
 Proteolytic 
 Enzymes 
 Enzymatic 
 Takeover 
 Capsid 
 Encoding 
 Ribosomal 
 Encoding 
 Peptidyl 
 Transferase 
 
 Obcell 
 
 Lipid 
 Bilayer 

Surface Metabolist 


Surface-anchored Lipid-Obcells, Membrane-anchored Nucleic Acids, Coded Membrane-embedded Polypeptides, protoCytosol and protoPeriplasm

  • Lipid World - [Sb3ANA-anchored Lipid Bilayers, Liposomes, Micelles - AcylEsterLipids]

Phase II - Lipid-protected Nucleic Acid World

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LpNA World

  • Lipid-protected NA World - [protoObcell - protoPeptidylTransferase Nucleozyme/3' AminoAcylNucleicAcid-Oligopeptide Membrane Anchors/surface-adhesion oligopeptides]
  • Lipid-anchored RNA World - [GC-rich Ribonucleotides - PRPP/mRNA/AAtRNAs/rRNA/Ribosome/Coded Membrane-embedded Polypeptides (CMeP's)/protoPolypeptideMembraneAnchorSequence]
  • Lipid-anchored Protein World [protoCystolic-protoPeriplasmic differentiation - protoSRPrna-protoSRP CMEP's/protoRibosomal CMeP's/protoCytoskeletal-Transmembrane CMeP's/Substrate Adhesion CMeP's/protoGTPase CMep's/Septum-forming Division Proteins, Protein Translocation Signals]
  • protoPeriplasmic Murein Matrix - [protoPetidoglycan]
  • Enzymatic Takeover - [Catalytic transfer of metabolism from mineral surface and nucleozymes to Coded Membrane-embedded Polypeptides - Cofactor-Coenzyme CMeP Scaffolds(apo-proteins)/Nucleozymal catalysis transfer to Residue-catalyzed CMeP's ]

Phase III - Surface-independent Protocells, Membrane-anchored Chromosomes, Proteins, Cytosol and Periplasm (3.8 bya)

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  • Negibacterial Envelope - [Obcell fusion to form double membrane]
  • Cystolic Protein World - [Cleavage of protoSRP domain from CMep to create soluble cystolic protein]
    • DNA Stabilization of Genome - [RibonucleotideReductase/DNA]
    • Consolidation of Intermediary Metabolism
  • Beginning Rampant HGT between cells
    • Establishment of Universal Cellular Organizing Macromolecules - [Chromatin/AminoAcyltRNASynthases/Release Factors/Rubisco(?)/Peptidoglycan/Lipopolysacharride]
    • Virovory/Viral Shunt - competitive heterotropic-scavenging/virus induced-releasing of biochemical components from/to the ecology and cellularized physiology.
  • The Darwinian Threshold - [Universal Genetic Code/Vertical Heredity/HGT intensity subsides]
  • Photophosphorylation - [ElectronTransportChain/ATPsynthase]
  • Last Universal Common Ancestor (LUCA)

Stage III - The Eubacterial Biosphere

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Stage III - The Eubacterial Biosphere

Phase I - Negibacteria and the Anaerobic Biosphere (~3.5 bya)

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  • Eobacteria
  • Glycobacteria/Cyanobacteria - [Bioenergetics - Oxygenic Photosynthesis]
  • Rusting of the Ocean (2.5-1.8 bya)

Phase II - The Oxygen Crisis and the Rise of the Aerobic Bioshphere (1.9-0.95 bya)

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  • Posibacteria - Loss of outer plasma membrane/thickening of murein cell wall
  • Rise of the Ozone Layer/Rusting of the terrestrial crust/Canfield Ocean (1.9-0.9 bya)

From LUCA to Neomura

 
 

 Chlorobacteria - (Glidobacteria - Eobacteria)

 
 OM β-barrel insertion (Omp85)[k] 
 

 Hadobacteria   - (Glidobacteria - Eobacteria) 

 
 Lipopolysaccharides[j] 
 

 Cyanobacteria   - (Glidobacteria - Glycobacteria)

 
 Flagella 
 

 Gracilicutes[b]   - (Glycobacteria)

 
 Endospores[i] 
 

 Eurybacteria   - (Glycobacteria)

 
 OM Loss[h] 
 

 Endobacteria[c]  

 
 Exospores[g] 
 

 Actinobacteria  

 
 Cell Wall Loss[f] 
 Isoprenopid Ether Lipids[d] 

 Archaebacteria 

 
 Phagocytosis[e] 

 Eukaryota 

 
 Neomura 
 0.9 GYA 
 
 ~2.0 GYA 
 
 
 2.8 GYA 
 
Negibacteria
Posibacteria
Neomura
LUCA[l]  
3.5 GYA 

The Path to Proteobacteria and Mitochondria

 
 Lipooligosaccharide[n] 

 Spirochaetae  

 
 RNA polβ BBM1 insert
 Shingolipids/Sulfonolipids 

 Sphingobacteria  

 
 Type III Secretion 
 Murein Loss/Reduction 

 Planctobacteria  

 
 
 
 

 Proteobacteria  

 
 
 Endosymbiosis[m] 

Mitochondria  

 0.9 GYA 
 
 
 
 
& alanyl‑tRNA synthase 4‑aa insert 
Endosymbiotic Eukaryotic Organelle
Gracilicutes[o] 

Stage IV - The Neomuran Biosphere - Phagocytosis, Archea & Eukaryotes

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Stage IV - The Neomuran Biosphere - Phagocytosis, Archea & Eukaryotes

Phase I - The Rise of Neomurans and the Modern Aerobic Atmosphere (950-600 mya)

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  • Neomuran Revolution (950 mya) - Loss of murein cell wall
  • Archaeabacteria (850 mya) - Methanogenesis/Extremophiles
  • Eukaryotes (850 mya) - Phagocytosis & Massive HGT, Endomembrane System, Endosymbiosis
    • Protokaryotes
    • Eokaryotes
    • Orthokaryotes
    • Neokaryotes
    • Scotokaryotes & Coricates
  • Podiata
  • Opisthokonta
  • Snow Ball Earth Episodes
  • Modern Aerobic Atomsphere (600 mya)

From Neomura to Podiata

 Loss of Cell Wall 
 Isoprenopid Ether Lipids[y] 

 Archaebacteria  

 
 Phagocytosis[z] 
 Cytopharynx & Ciliary Paraxonemal Rods 

 Euglenozoa  

 
 Ventral Feeding Groove 
 Eruptive Psuedopodia[x] 

 Percolozoa[p]  

 
 Dorsal Ciliary Vane 
 

 Eolouka[q]  

 
 Ventral Ciliary Vane[w] 
 Myosin Domain Fusions 
 
 

 Neolouka[r]  

 
 Anaerobes[t] 

 Metamonada[s]  

 
 
 Ciliary Gliding[u] 

Podiata 

 Podiates 
 Scotokaryotes 
 Cortical Alveoli 
 Chloroplast Endosymbiont 

 Plantae[v]  

 
 Plantae Endosymbiont 
 

 Hacrobia  

 
 

 SAR supergroup  

 
 Chromista 
 Corticates 
 Neokaryotes 
 Orthokaryotes 
 Eokaryotes 
 Protokaryotes 
Archaebacteria
Eozoa[aa]
Neozoa[ab]
Corticata
Neomura[ac] 

 0.9 GYA 

From Podiata to Opisthokonta

 Ciliary Gliding 
 

 Planomonadida[ad] 

 
 Psuedopods[ah] 
 
 

 Mantamonas 

 
 

 Diphylledia  

 
 CRuMs 
 Catenins[af] 
 Broad Psuedopods 

 Amoebozoa  

 
 Narrow Psuedopods[ae] 
 

 Breviatea  

 
 
 

 Apusomonadida  

 
 Anterior Cilium Lost 

Opisthokonta 

 
 
 Obazoa 
 Unikonts[ag] 
 
Varisulca[ai]
Amoebozoa
Obazoa

Podiata 

From Opisthokonta to Metazoa

Cavalier-Smith describes the Opisthokonts as being comprised of Choanozoa, Metazoa, and Fungi.[2] In this diagram Cavalier-Smith's Fungi equates to Holomycota and Fungi is used more restrictively. Cavalier-Smith's Choanozoa equates to all Holozoans except Animals (Metozoa). Here Choanozoa is used in a more conventional and restrictive manner.

 Loss of Anterior Cilium 
 Tapering Psuedopods[al] 
 

 Cristidiscoidea  

 
 
 
 

 Rozellidea  

 
 

 Microsporidia  

 
 
 Cell Walls & Branching Hyphae 

 Fungi  

 
 
Holomycota
 Holomycota 
 Ubiquitin S‑30 Fusion 
 Cell Walls Replace Psuedopods 

 Ichthyosporea  

 
 
 

 Pluriformea  

 
 CAMs & Filose Tentacles[ak] 
 

 Filosporidia  

 
 Collar Filter 
 

 Choanoflagellatea  

 
 Epithelia & Mesenchyme[aj] 

Animalia  

 Metazoa 
 665 MYA 
 Choanozoa 
 Filozoa 
 
Holozoa
 Holozoa 
Opisthokonta[am] 

Phase II - The Multicellular Aquatic Ecology (~600 mya)

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  • Parenchemella/Phagocytella - Multicellularity with Intracellular Digestion/Germline Sequestration/Active Host Immunity/Shift in Level of Selection
  • Gastrea - Diploblastic Extracellular Digestion
  • Bilateria (570 mya) - Blastopore becomes anterior mouth/Triploblastic/HOX-Cluster defined AP-axis/Head Senses/Cognitive Map
  • Deuterostomia - Blastopore becomes posterior anus/Inversion of the DV-axis
  • Olfactores
  • Chordata (543 mya) - Notochord/Somatic Larva/Visceral Adult
  • Craniata
  • Agnatha (530 mya) - Somato-visceral fusion/Genome Duplication/Neural Crest/Unmyelinated Parasympathetic/Antibody-based Immune System
  • Gnathostoma - Genome Duplication/Trigeminal-Sympathetic System/Jaws/Fins/Myelin

Phase III - The Multicellular Terrestrial Ecology (~400 mya)

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  • Tetrapoda - Limbs/Muscle spindles/Auditory system
  • Amniota - Adrenal Gland/Head-Neck-Sensorimotor Reintegration
  • Mammalia - Endothermy/Pulmonary Loop/Isocortex/Myelinated Parasympathetic/Postural Communication/Social Engagement System
  • Primate - Dexteral-Gesterual Intelligence
  • Homo - Gene Losses/Diminished Olfactory/Bipedal
  • Homo Erectus - Myosin gene MYH16 Frameshift mutation

Stage V - The Anthropogenic Biosphere (~2.8 mya-present)

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Stage V - The Anthropogenic Biosphere (~2.8 mya-present)

Phase I - Dexterity, Language, Tools, & Fire

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Atmosphere composition diagram-en
  • Human Sapiens - Fire & Fossil Fuels
  • The Chemoplasticene - Plastics and industrial chemicals in the ecology

Notes & Commentary

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Notes & Commentary
  1. ↑ Subject to major change, revision ,and/or retraction at any moment.
  2. ↑ 4 Protein Insertions
  3. ↑ a.k.a Firmicutes
  4. ↑ Also: Reverse DNA gyrase; 2 genes split; novel stabler flagella; copious gene losses
  5. ↑ Also: Endomembranes; Endoskeleton; Mitochondria; 26S proteasomes; tricorn & TET peptidases lost
  6. ↑ Also: Cholesterol; 20S proteasomes; new ring ATPase; murein lost; Lipoproteins & ClpP lost; N-linked glycoproteins replace lipoproteins; core hisones replace DNA gyrase
  7. ↑ also: Phosphotidylinositol
  8. ↑ Also: Sortase lipoprotein secretion
  9. ↑ Also: Hsp70 & 90 deletions; MFIcc to MFIc operon; glycerol-1-P dehydrogenase
  10. ↑ Also: Hopanoids; TolC; TonB; Group I Nif
  11. ↑ Also: Photosystem Duplication; HsIVU ring protease; Cytochrome b; Type II Secretion
  12. ↑ "The last ancestor of all life was a eubacterium with acyl-ester membrane lipids, large genome, murein peptidoglycan walls, and fully developed eubacterial molecular biology and cell division. It was a non-flagellate negibacterium with two membranes, probably a photosynthetic green non-sulphur bacterium with relatively primitive secretory machinery..."[1] - Other key features: Peptidoglycan; Gliding; Lipoprotein; CLpP; Ion Proteases; Cytochrome c; group II Nif Nitrogen Fixation;
  13. ↑ Proteobacteria phagocytosed by Protoeukaryotic Neomuran. Also: Murein/LPS/Lipoprotein Loss
  14. ↑ Also: endoflagella L-ring lost;
  15. ↑ Glycobacteria possessing flagella excluding Eurybacteria. Also: 4 Protein Insertions
  16. ↑ alternative taxonomy membership: Excavata
  17. ↑ alternative taxonomy membership: Excavata - Loukozoa
  18. ↑ alternative taxonomy membership: Excavata - Loukozoa
  19. ↑ alternative taxonomy membership: Excavata - Loukozoa
  20. ↑ Also: 4 Cilia/Centrosome, loss of Mitochondria
  21. ↑ Dorsal Pellicle
  22. ↑ a.k.a. Archaeplastida
  23. ↑ Also: Novel cytochrome c biogenesis
  24. ↑ Also: 4 cilia/centrioles
  25. ↑ Also: Reverse DNA gyrase; 2 genes split; novel stabler flagella; copious gene losses
  26. ↑ Also: Endomembranes; Endoskeleton; Mitochondria; 26S proteasomes; tricorn & TET peptidases lost
  27. ↑ Ancestral aerobic, bicilate, phagotrophic Eukaryotes
  28. ↑ a.k.a. Scotokaryotes
  29. ↑ Also: Cholesterol; 20S proteasomes; new ring ATPase; murein lost; Lipoproteins & ClpP lost; N-linked glycoproteins replace lipoproteins; core hisones replace DNA gyrase
  30. ↑ a.k.a. Ancyromonadida
  31. ↑ Also: Integrins
  32. ↑ The primordial role of the Catenins is tethering other proteins to actin I suspect.
  33. ↑ a.k.a. Sarcomastigo, Amorphea
  34. ↑ Also: Myosin II
  35. ↑ Varisulca lacks molecular phylogenetic support and appear to be strongly non-monophyletic. Planomonadida are not inferred to be the sister group to CRuMs and lacks wide acceptance as such.
  36. ↑ Also: Extracellular Matrix, Oogamy
  37. ↑ Unbranched Non-tapering. Also: Cadherins
  38. ↑ Sometimes Branched.
  39. ↑ Loss of anterior cilium

Citations

[edit | edit source]
List of Citations
  1. ↑ Cavalier-Smith 2006.
  2. ↑ Shalchian-Tabrizi et al. 2007.

Sources & References

[edit | edit source]
Blochl et al.
Borgeson et al.
Drobner et al.
Hafenbradl et al.
Huber et al.
Keller et al.
Popper et al.

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