Go over cladistics slides here

Comments on a "natural taxonomy".
Shared derived vs shared primitive characters, groups from homoplasies (see cladistics -- Ashlock (Ernst Mayr, Lynn Margulis, and others) versusHennig (Woese, Pace, and others --- for discussion see here, here and here; Jan Sapp's review of the history is here) 

Here is example providing an impression on the heatedness of the ongoing debate: "Oddly, the school of ‘phylogenetic systematics’ founded by Hennig (1966) grossly downplayed the phylogenetic importance of progressive change compared with splitting, seen by them as so all-important that many Hennigian devotees dogmatically insist that ancestral groups like Bacteria, Protozoa and Reptilia be banned. Hennig called such basal groups with a monophyletic origin ‘paraphyletic’ and redefined monophyly to exclude them and embrace only clades, likewise redefined as including all descendants of their last common ancestor. This redefinition of ‘clade’ is universally accepted, but Hennig's extremely confusing and unwise redefinition of monophyly is not. Though accepted by many, sadly probably the majority (especially the most vociferous and over self-confident, and those fearful of bullying anonymous referees, of whom I have encountered dozens mistakenly insisting without reasoned arguments that paraphyletic taxa are never permissible), it is rightly firmly rejected by evolutionary systematists who consider the classical distinction between polyphyly and paraphyly much more important than distinguishing two forms of monophyly (paraphyly and holophyly, using the precise terminology of Ashlock (1971), where holophyletic equals monophyletic sensu Hennig)."
- from Tom Cavalier Smith http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842702/

Questions on commandline blast

Why is %identity not a good measure for the significance of blast hits? See blast output and histograms in demo file

• late heavy bombardment and an aside on human origins (compare also Olga's timeline of the Universe)
  
  
  

  How old is life on Earth? The Earth is about 4.6 Ga old, but no crustal rocks has survived from that time. The oldest rocks are no older than 4.0 Ga. But zircon crystals dated to 4.4 billion years BP are found in rocks, are considered evidence for Earth's crust having had formed and being in contact with water already 4.4 billion years BP (here and here) Morphological Fossil Evidence: For about a decade the oldest microfossils were considered to be about 3.5 Ga old (see here). The fossils (as interpreted by Bill Schopf) look like "modern" Cyanobacteria. Compare the time to to molecular trees of life: Is this a problem? However, the evidence for these fossils was questioned. 3.2Ga old filamentous fossils, probably of thermophilic chemotrophic prokaryotes (Rasmussen, 2000) 1.8Ga old fossils from Gunflint formation: iron-loving bacteria and cyanobacteria Biological Signature Evidence (examples): Oldest geological evidence for life - 3.8 Ga ago - is based on 13C discrimination (carbon derived from living systems often have lower delta 13C values than inorganic carbonates) [here]. The rocks are from Akilia island off the coast of Greenland, and severely altered by metamorphism. However, recently the evidence for that was reassessed. 3.7 billion year of rocks from the Isua formation in Greenland contain structures described as stromatholites. here in NYT, report in Nature The amount of carbon in the Issua formation (and its discrimination against agains 13C) is interpreted by Minik Rosing to indicate a highly productive biosphere. (See Minik's presentation at the 2011 ISSOL meeting. Especially slides 6 ff are interesting - the handwritten slides were written with the sedimentary rocks - containing lots of graphite.) 2.7Ga old: probable biomarkers of cyanobacteria and of eukaryotes (Roger Summons, Roger Buick and Jochen Brocks) See Olga's Timeline of the Universe here