Abiogenesis & Evolution

Sections
. In the Beginning . Illogical Deceit theory . RNA . DNA . Basic Physical Chemistry . Basic Biochemistry . Biochemical Energetics . Informational Macromolecules . Lipids & Membranes
. Darwin . Diversity . Selection . Logic & Science . Neo-Darwinism . Computer Modeling . Tree of Life . Protists . Fossils . Paleogeology & Paleoclimate . Proterozoic & Archaean . Cambrian Explosion . Extinction Events . Hominids . Hominid Migrations . Fallacies of Logic . Godspell Follies

Click on the title of any item to return to the original site – or explore other sites: Abiogenesis & Evolution : Algorithms of Evolution : Cell Biology : Chemistry of Life : Cyanobacteria : Endosymbiosis : Eubacteria & Archaea : Evo Devo : Godspell Follies : Mechanisms of Evolution : Molecular Biology : Molecules : Organics : Origin of Life : Paleogeology : Pathways : Photosynthesis : Serial Endosymbiosis : Stromatolites : Taxonomy Phylogeny

Algorithms of Evolution

* directional epistasis * epistasis * horizontal gene transfer * lateral gene transfer * multilinear epistatic model

Click on the title of any item to return to the original site – or explore other sites: Abiogenesis & Evolution : Algorithms of Evolution : Cell Biology : Chemistry of Life : Cyanobacteria : Endosymbiosis : Eubacteria & Archaea : Evo Devo : Godspell Follies : Mechanisms of Evolution : Molecular Biology : Molecules : Organics : Origin of Life : Paleogeology : Pathways : Photosynthesis : Serial Endosymbiosis : Stromatolites : Taxonomy Phylogeny

Cancer

∞ Cancer

Cell Biology

Items• CELL BIOLOGY • active transport • apoptosis • cell membranes • centrioles • cilia• communication • concentration gradients • cytoplasm • cytoskeleton • death of cells• energy transducers • endoplasmic reticulum • endosomes • eukaryotic • exosome• Golgi apparatus • ion channels • lysosome • meiosis • microtubules • mitosis• mitochondrion • nuclear membrane • nuclear pore • nucleolus • nucleus • peroxisome• phagocytosis • photosynthesis • physiological function • pinocytosis • plant cell• prokaryotic • protein degradation • pumps • receptor proteins• receptor-mediated endocytosis • reproduction • ribosomes • spindle • structure• transport • vacuole • vesicle • CELL SIGNALING • GPCRs • GPCR families • hormones • Nitric Oxide• neurotransmission • neuronal interconnections • phosphotransfer-mediated signaling pathways • Protein Kinase Signaling Networks • signaling gradients• MOLECULAR BIOLOGY • amino acids • caspases • proteins

Click on the title of any item to return to the original site – or explore other sites: Abiogenesis & Evolution : Algorithms of Evolution : Cell Biology : Chemistry of Life : Cyanobacteria : Endosymbiosis : Eubacteria & Archaea : Evo Devo : Godspell Follies : Mechanisms of Evolution : Molecular Biology : Molecules : Organics : Origin of Life : Paleogeology : Pathways : Photosynthesis : Serial Endosymbiosis : Stromatolites : Taxonomy Phylogeny

Chemistry of Life

~ Molecular Genetics Overview ~ allele ~ alternative splicing ~ base ~ base excision repair ~ capping ~ chromosome ~ cis versus trans-acting factors ~ codon ~ DNA ~ DNA damage by ROS
~ DNA repair ~ DNA polymerases ~ DNA mutation and alkylation ~ double strand breaks ~ enhancer ~ epigenetics ~ exon ~ genes ~ gene regulation ~ genome ~ targetted genetic repair
~ helicases ~ heterochromatin ~ insulator ~ intron ~ mRNA ~ miRNAs ~ mismatch repair ~ nonsense-mediated decay ~ nonstop decay ~ nuclear speckles ~ nucleic acids ~ nucleosome ~ nucleotide ~ nucleotide excision repair ~ open reading frame ~ oxidative stress and DNA damage ~ oxoG repair ~ polyadenylation ~ pre-mRNA ~ pre-mRNA splicing ~ promoters ~ proteome ~ regulatory proteins ~ replication ~ repressor ~ response elements ~ restriction enzymes ~ reverse transcriptase ~ ribosomes ~ ribosomal structure ~ ribozymes ~ ribozymes in repair of RNA and DNA ~ RNA ~ RNA polymerase ~ RNA processing ~ rRNAs ~ self-splicing
~ silencers ~ snoRNAs ~ splice-site ~ spliceosome ~ SSOs ~ transcription ~ transcription factors ~ transcription initiation ~ termination of transcription ~ translation ~ trans-splicing ribozymes and therapeutics ~ tRNA ~ Research techniques ~ BIOCHEMISTRY ~ Biochemistry overview ~ amines ~ amino acids ~ amphipathic ~ chemical gradients ~ cofactor ~ enzyme
~ heterocyclic ~ hydrogen bond ~ hydrophilic ~ hydrophobic ~ peptide ~ phospolipid ~ proteins
~ thermochemistry

Click on the title of any item to return to the original site – or explore other sites: Abiogenesis & Evolution : Algorithms of Evolution : Cell Biology : Chemistry of Life : Cyanobacteria : Endosymbiosis : Eubacteria & Archaea : Evo Devo : Godspell Follies : Mechanisms of Evolution : Molecular Biology : Molecules : Organics : Origin of Life : Paleogeology : Pathways : Photosynthesis : Serial Endosymbiosis : Stromatolites : Taxonomy Phylogeny

Cyanobacteria

~ The Cyanobacteria ~ Photochemistry ~ Phylogenetic relationships ~ Fossilized cyanobacteria

Click on the title of any item to return to the original site – or explore other sites: Abiogenesis & Evolution : Algorithms of Evolution : Cell Biology : Chemistry of Life : Cyanobacteria : Endosymbiosis : Eubacteria & Archaea : Evo Devo : Godspell Follies : Mechanisms of Evolution : Molecular Biology : Molecules : Organics : Origin of Life : Paleogeology : Pathways : Photosynthesis : Serial Endosymbiosis : Stromatolites : Taxonomy Phylogeny

Comments on nonexistence . . .

A-Deistic
Adeistic
Black Out
cosmic
Eine Kleine Nattermusing
eMusings
eVolition
Galaria
Godborygmi
Godspell Follies
Gray Matters
MetaThoughts
Mimble Wimble
Naturalism
BLogodaedaly
palimpsest
Salient
Science of Evolution
Sechuam
Sintheist
Tabula Flexuosa
The Scarlet A
Weltschauung

Endosymbiosis

• Serial Endosymbiosis Theory (SET) • Diagrams of endosymbiotic cells • Secondary endosymbiosis • Endosymbiotic transfers • Endosymbiotic Gene Transfer • Evidence for Endosymbiosis • Mitochondrial origins • History of ideas concerning endosymbiosis

Click on the title of any item to return to the original site – or explore other sites: Abiogenesis & Evolution : Algorithms of Evolution : Cell Biology : Chemistry of Life : Cyanobacteria : Endosymbiosis : Eubacteria & Archaea : Evo Devo : Godspell Follies : Mechanisms of Evolution : Molecular Biology : Molecules : Organics : Origin of Life : Paleogeology : Pathways : Photosynthesis : Serial Endosymbiosis : Stromatolites : Taxonomy Phylogeny

Eubacteria & Archaea

Prokaryote structure • Cell wall • Taxonomy and Phylogeny • Eubacteria • The Archaea
• Interactions in Bacteria • Bacterial motility • Phosphorylation switches • Photosynthetic bacteria • Control of gene expression • Recombinant DNA Restriction Enzmes Restriction Endonucleases • Horizontal Gene Transfer • Conjugation • Transduction • Transformation • Symbiosis • Domains • Kingdoms • Phylum • Division • Aquifex • Thermotoga • Green nonsulfur • Deinococcus • Bacteroides-Flavobacteria • Planctomyces • Gram-positive • Chlamydia • Cyanobacteria • Spirochetes • Green sulfur • Proteobacteria • green filamentous • prochlorophytes • purple sulfur • purple nonsulfur

Click on the title of any item to return to the original site – or explore other sites: Abiogenesis & Evolution : Algorithms of Evolution : Cell Biology : Chemistry of Life : Cyanobacteria : Endosymbiosis : Eubacteria & Archaea : Evo Devo : Godspell Follies : Mechanisms of Evolution : Molecular Biology : Molecules : Organics : Origin of Life : Paleogeology : Pathways : Photosynthesis : Serial Endosymbiosis : Stromatolites : Taxonomy Phylogeny

Evolution in Action

Evo Devo

^ Evo Devo ^ alternative splicing ^ alternative 3' splicing ^ alternative 5' splicing^ epigenetic mechanisms ^ ESE ^ ESS ^ Evo Devo ^ exon skipping ^ intron retention ^ ISE ^ ISS

Click on the title of any item to return to the original site – or explore other sites: Abiogenesis & Evolution : Algorithms of Evolution : Cell Biology : Chemistry of Life : Cyanobacteria : Endosymbiosis : Eubacteria & Archaea : Evo Devo : Godspell Follies : Mechanisms of Evolution : Molecular Biology : Molecules : Organics : Origin of Life : Paleogeology : Pathways : Photosynthesis : Serial Endosymbiosis : Stromatolites : Taxonomy Phylogeny

Diagrams & Tables

Mechanisms of Evolution

~ Beyond Darwin and Neo-Darwinism ~ The modern synthesis ~ Punctuated equilibria ~ Basic mechanisms of evolution ~ Genetic drift ~ Gene flow ~ Mutation ~ Natural selection ~ Horizontal Gene Transfer ~ Conjugation ~ Transduction ~ Transformation ~ Molecular Genetics ~ Genome and Proteome ~ Important features of the genome and proteome ~ Conserved & Consensus ~ Insertion ~ Inversion ~ Meiosis ~ Recombination ~ Population Genetics and Formulae ~ Bottleneck ~ Founder effect ~ Persistence of functional gene duplicates ~ Phyletic gradualism

Click on the title of any item to return to the original site – or explore other sites: Abiogenesis & Evolution : Algorithms of Evolution : Cell Biology : Chemistry of Life : Cyanobacteria : Endosymbiosis : Eubacteria & Archaea : Evo Devo : Godspell Follies : Mechanisms of Evolution : Molecular Biology : Molecules : Organics : Origin of Life : Paleogeology : Pathways : Photosynthesis : Serial Endosymbiosis : Stromatolites : Taxonomy Phylogeny

Molecular Biology

alternative splicing : base excision repair : capping : cis versus trans-acting factors : codon :DNA : DNA damage by ROS : DNA polymerases : DNA repair : double strand breaks :enhancer : epigenetics : exon : genes : genome : gene regulation : helicases : heterochromatin : insulator : intron : messenger RNA mRNA : micro RNAs miRNAs : mRNA : mismatch repair : nonsense-mediated decay : nonstop decay : nuclear speckles : nucleic acids : nucleosome : nucleotide : nucleotide excision repair : open reading frame : oxidative stress and DNA damage : oxoG repair : polyadenylation : pre-mRNA : pre-mRNA splicing : proteome : replication : Research techniques : ribosomal structure : regulatory proteins : ribosomal structure : ribozymes in repair of RNA and DNA : RNA : RNA polymerase : RNA processing : targetted genetic repair : transcription : termination of transcription : transfer RNA tRNA : translation : trans-splicing ribozymes and therapeutics : silencers : snoRNAs : spliceosome : SSOs :

Click on the title of any item to return to the original site – or explore other sites: Abiogenesis & Evolution : Algorithms of Evolution : Cell Biology : Chemistry of Life : Cyanobacteria : Endosymbiosis : Eubacteria & Archaea : Evo Devo : Godspell Follies : Mechanisms of Evolution : Molecular Biology : Molecules : Organics : Origin of Life : Paleogeology : Pathways : Photosynthesis : Serial Endosymbiosis : Stromatolites : Taxonomy Phylogeny

Molecules

amino acids • amino acid chart • alanine • arginine • asparagine • aspartic acid • cysteine • glutamic acid • glutamine • glycine • histidine • isoleucine • leucine • lysine • N-formylmethionine • methionine • phenylalanine • proline • serine • threonine • tryptophan • tyrosine • valine• DNA, RNA and nucleotides • adenosine • CDP • DNA RNA • GDP • GMP • GTP • UDP • UMP• Lipids fatty acids• steroids• neurotransmitters • acetylcholine • dopamine • epinephrine • GABA • glycine • norepinephrine • serotonin• hormones• sugars • ribose deoxyribose • energy • chloroplast .

Click on the title of any item to return to the original site – or explore other sites: Abiogenesis & Evolution : Algorithms of Evolution : Cell Biology : Chemistry of Life : Cyanobacteria : Endosymbiosis : Eubacteria & Archaea : Evo Devo : Godspell Follies : Mechanisms of Evolution : Molecular Biology : Molecules : Organics : Origin of Life : Paleogeology : Pathways : Photosynthesis : Serial Endosymbiosis : Stromatolites : Taxonomy Phylogeny

Molecular Paths

future construction planned

Organics

• atomic orbitals • acidic amino acids • acidic and basic amino acids • basic amino acids • polar amino acids • non-polar amino acids • glycerol • DNA • chirality • bases

Click on the title of any item to return to the original site – or explore other sites: Abiogenesis & Evolution : Algorithms of Evolution : Cell Biology : Chemistry of Life : Cyanobacteria : Endosymbiosis : Eubacteria & Archaea : Evo Devo : Godspell Follies : Mechanisms of Evolution : Molecular Biology : Molecules : Organics : Origin of Life : Paleogeology : Pathways : Photosynthesis : Serial Endosymbiosis : Stromatolites : Taxonomy Phylogeny

Origin of Life

Sections
_ Abiogenesis _ Paleogeology _ Paleo-atmosphere _ Chemistry _ Models _ RNA world _ Protein world _ Submarine Vents _ Space _ Minimal Genome _ Clay _ Basic Cell _ Evolution

Click on the title of any item to return to the original site – or explore other sites: Abiogenesis & Evolution : Algorithms of Evolution : Cell Biology : Chemistry of Life : Cyanobacteria : Endosymbiosis : Eubacteria & Archaea : Evo Devo : Godspell Follies : Mechanisms of Evolution : Molecular Biology : Molecules : Organics : Origin of Life : Paleogeology : Pathways : Photosynthesis : Serial Endosymbiosis : Stromatolites : Taxonomy Phylogeny

Paleogeology

~ Hadean ~ Paleogeology and Paleoclimate ~ Timeline Earth Life ~ "Peribiotic" conditions?~ Climate and Extinction ~ Prebiotic atmosphere ~ Hydrogen

Click on the title of any item to return to the original site – or explore other sites: Abiogenesis & Evolution : Algorithms of Evolution : Cell Biology : Chemistry of Life : Cyanobacteria : Endosymbiosis : Eubacteria & Archaea : Evo Devo : Godspell Follies : Mechanisms of Evolution : Molecular Biology : Molecules : Organics : Origin of Life : Paleogeology : Pathways : Photosynthesis : Serial Endosymbiosis : Stromatolites : Taxonomy Phylogeny

Pathways

beta-oxidation : Calvin cycle : choline-folate-methionine : citric acid cycle : glycolysis :HMG-CoA-reductase pathway : Krebs cycle : nitrogen assimilation :pentose-phosphate pathway : photorespiration : sulfur metabolism : TCA cycle : tricarboxylic acid cycle : urea cycle : chloroplast :

Click on the title of any item to return to the original site – or explore other sites: Abiogenesis & Evolution : Algorithms of Evolution : Cell Biology : Chemistry of Life : Cyanobacteria : Endosymbiosis : Eubacteria & Archaea : Evo Devo : Godspell Follies : Mechanisms of Evolution : Molecular Biology : Molecules : Organics : Origin of Life : Paleogeology : Pathways : Photosynthesis : Serial Endosymbiosis : Stromatolites : Taxonomy Phylogeny

Photosynthesis

• Photosynthesis • Cyanobacterial cell • Plant cell • Chloroplast • Chlorosomes• Pigments and absorption spectra • Chlorophylls and accessory pigments• Oxygenic photosynthesis • Nonoxygenic photosynthesis • Light-reactions• Antenna and Reaction Center • Bacteriochlorophylls • Carotenoids • Phycobilins

Click on the title of any item to return to the original site – or explore other sites: Abiogenesis & Evolution : Algorithms of Evolution : Cell Biology : Chemistry of Life : Cyanobacteria : Endosymbiosis : Eubacteria & Archaea : Evo Devo : Godspell Follies : Mechanisms of Evolution : Molecular Biology : Molecules : Organics : Origin of Life : Paleogeology : Pathways : Photosynthesis : Serial Endosymbiosis : Stromatolites : Taxonomy Phylogeny

Serial Endosymbiosis

• Serial Endosymbiosis Theory (SET) • Experimental evidence for Endosymbiosis • Mitochondrial origins • Secondary endosymbiosis • History of ideas concerning endosymbiosis
• Endosymbiotic transfers • Endosymbiotic Gene Transfer • Horizontal Gene Transfer
• Diagrams of proposed mechanism of SET • Photosynthesis in Eukaryotes

Click on the title of any item to return to the original site – or explore other sites: Abiogenesis & Evolution : Algorithms of Evolution : Cell Biology : Chemistry of Life : Cyanobacteria : Endosymbiosis : Eubacteria & Archaea : Evo Devo : Godspell Follies : Mechanisms of Evolution : Molecular Biology : Molecules : Organics : Origin of Life : Paleogeology : Pathways : Photosynthesis : Serial Endosymbiosis : Stromatolites : Taxonomy Phylogeny

Signaling

Stromatolites

~ Cyanobacteria and stromatolites ~ Modern stromatolites – living fossils~ Stromatolite structure ~ Ancient stromatolite reefs ~ Imaging fossil cyanobacteria~ Stromatolite fossils

Click on the title of any item to return to the original site – or explore other sites: Abiogenesis & Evolution : Algorithms of Evolution : Cell Biology : Chemistry of Life : Cyanobacteria : Endosymbiosis : Eubacteria & Archaea : Evo Devo : Godspell Follies : Mechanisms of Evolution : Molecular Biology : Molecules : Organics : Origin of Life : Paleogeology : Pathways : Photosynthesis : Serial Endosymbiosis : Stromatolites : Taxonomy Phylogeny

Taxonomy Phylogeny

^ Bacteria ^ Cambrian explosion ^ Endosymbiotic transfer events ^ History of taxonomic concepts ^ Phylogenetics ^ Taxonomy

Click on the title of any item to return to the original site – or explore other sites: Abiogenesis & Evolution : Algorithms of Evolution : Cell Biology : Chemistry of Life : Cyanobacteria : Endosymbiosis : Eubacteria & Archaea : Evo Devo : Godspell Follies : Mechanisms of Evolution : Molecular Biology : Molecules : Organics : Origin of Life : Paleogeology : Pathways : Photosynthesis : Serial Endosymbiosis : Stromatolites : Taxonomy Phylogeny