1) Frozen-accident – once the complete code was formed this defined the universal

1. Possible explanations for the unity of the genetic code entertained by Crick 1) Frozen-accident – once the complete code was formed this defined the universal common ancestor from which all life evolved. 2) Steric constraint - The current code is functionally constrained because because of a chemical fit between codon and amino acid.

2. Possible explanations for the unity of the genetic code entertained by Crick 1) Frozen-accident – once the complete code evolved this defined the universal common ancestor from which to all life evolved. 2) Steric constraint - The current code is functionally constrained because because of a chemical fit between codon and amino acid. But there was a third possible explanation Genetic code is unified because of natural selection for unity per se – i.e. horizontal gene transfer is essential to evolution itself.

3. Ribosomal protein tree Yeast Sulfolobus Plasmodium Aeropyrum Neurospora Pyrobacae C.elegans Human Pyroco-ab Catfish Rice Mettheth Metpyrka Archaefu Aquifex Metcocja Thermo ac Thermot ma Metsar ma Haloba ma CAUCR Strep coe Ecoli B.subtilus Synecococ 0.1 Chlamy tr Chlorote

4. Quartet partitions gram (+) archaea Tree 1 gram (-) eukaryote eukaryote archaea Tree 2 gram (+) gram (-) gram (+) archaea Tree 3 gram (-) eukaryote

5. What was found was support for NONE of the three trees, instead: archaea gram (+) eukaryote gram (-) Star phylogeny

6. 18 of the 26 homologue submitted to the quartet analysis displayed the star phylogeny. They include: argD ornithine carbamoyl transferase argT arginine tRNA synthetase argH arginine biosynthesis trpA tryptophan synthetase α trpB tryptophan synthetase β mutS,H mismatched DNA repair purA purine biosynthesis purB “ pur5 “ pur6 “

7. Ribosomal protein tree Yeast Sulfolobus Plasmodium Aeropyrum Neurospora Pyrobacae C.elegans Human Pyroco-ab Catfish Rice Mettheth Metpyrka Archaefu Aquifex Metcocja Thermo ac Thermot ma Metsar ma Haloba ma CAUCR Strep coe Ecoli B.subtilus Synecococ 0.1 Chlamy tr Chlorote

8. Ornithine carbamoyl transferase Bifurcated tree aquifex Streptomyc pyrobac B.subtilis aeropyrum E.coli mettheth metpyrka halobacter thermo ma chlorobium rice pyrococab CAUCR Arabidopsi metsar ma Neurospora themoc ac synecoc metcocja C.elegans Zebrafish Human 0.1 Drosophila sch pombe Yeast

9. Ornithine carbamoyl transferase Colapse unsupported bifurcations aquifex pyrobac Streptomyc B.subtilis aeropyrum mettheth metpyrka E.coli halobacter thermo ma chlorobium rice pyrococab CAUCR Arabidopsi metsar ma Neurospora themoc ac synecoc metcocja C.elegans Zebrafish Human 0.1 Drosophila sch pombe Yeast

10. Trptophan synthase (α and β) Bifurcated tree candida nodulisp spathosp neucra Halobacte coprinus Clostrid trametes arabidopsi Guillard oryza Nostoc Acantham haloferax buchnera Methanolob E.coli bacillis thet Methanosar Archaeog legionel Pseudomo 0.1 Rhodomic Caucre thermus zymonas

11. Trptophansynthase (α and β) Collapse bifurcations candida nodulisp spathosp neucra Halobacte coprinus Clostrid trametes arabidopsi Guillard oryza Nostoc Acantham haloferax buchnera Methanolob thet E.coli Archaeog Methanosar bacillis legionel Pseudomo Rhodomic 0.1 Caucre thermus zymonas

12. Arginine-tRNA ligase Chlorobium Thermot ma Thermo ac B.subtilis Aguifex sulfolobus Archaefu Aeropyrum Haloba ma Metpyr ka Pyrobacae Metcoc ja Mettheth Pyroco-ab Metsar ma Zebra fish Human HumanMt C.elegans D.melanoga Neurospora Plasmodium Chlamytr Yeast Orzya Sch.pombe Synecococ E.coli Strep coe 0.1 CAUCR

13. Tryptophan-tRNA Ligase haloba su1 Plasmodium Neurospora sulfolobus schizop pyrocoab Rice pyrobacae Human metsar ma haloba su2 archaefu Aeropyrum Yeast methe th metcoc ja strmy co metpyrka E.col thermo ac B.subtilis C.elegans synecoc thermot ma CAUCR Aquifex 0.1 chlamy tr Chlorobium

14. MutS protein family arabidopsi schpom neucra seaurchin zfish gallus ciona mouse human drosophila oryza saccer ecoli metbar thermmar celegans dictyoste plafal halmar clotet caucre natrpha bacanth strpne 0.1

15. Whole matrix rate test comparing Ornithine carbamoyl and Aspartate carbamoyl Transferases Distance OCTase Distance ACTase 1 E.coli/Salmonella; Pea/arabidopsis 2 E.coli/Haemophilis; Yeast/neurospora 3 Plants/metazoa; plants/ fungi

16. Whole matrix rate test comparing Tryptophan synthetase and Aspartate carbamoylTransferases Distance trpA Distance ACTase

17. I have shown that the evolution for multiple genes in the tryptophan and arginine biosynthetic pathways, as well as their tRNA ligases show unusual phylogenies. If we discard functional constraint arguments (i.e. that some kind of peculiar protein chemistry is driving their evolution) then we can offer the following interpretation: These genes “found in the three kingdoms that are not just unusually highly conserved but whose topologies, when deduced from their sequences, strongly suggest that they evolved after Archaea, Bacteria and Eukaryotes had already diversified. In other words, these universal genes appear to be younger than the taxonomic groups in which they are found today “ That is to say, there was a time when Archaea, Bacteria and Eukaryotes existed but that they lacked the amino acids arginine and tryptophan. If so, then LUCA, if it ever existed, could not have had those two amino acids. Thus the current universal distribution of arginine and tryptophan is not explained by LUCA. Once we start down this road of reasoning there is no reason why we cannot imagine the the entire genetic code evolved within multiple demes that are linked together by Horizontal gene transfer.

18. Possible outline for the emergence of tryptophan (W) tRNA ligase by duplication and horizontal spread of tyrosine (Y) tRNA ligase Archaea Ytl Eukarya Ytl Bacteria Ytl Ytl + Wtl Ytl Ytl Ytl + Wtl Ytl + Wtl Ytl+ Wtl ?? ?? ??

19. XianchiDong,MinyunZhou, Chen Zhong1, BeiYang,NingShen and JianpingDing (2010) “Crystal structure of Pyrococcushorikoshiitryptophanyl-tRNA synthetase and structure-based phylogenetic analysis suggest an archaeal origin of tryptophanyl-tRNA synthetase” Nucleic Acids Research Volume 38, . 1401-1412 “Our results raise the possibility that  present day tyrosyl- and tryptophanyl-tRNA synthetasesappeared after the separation of  nucleated cells from eubacteria.”

20. Darwin’s notion of the Tree of Life

21. “There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.” ― Charles Darwin, The Origin of Species