Jeff’s Notebook
Reading List
Next papers to read
Papers from early 2021
- Take notes on 2016 Doolittle Brunet What is the Tree of Life? Short PLOS Genetics article on Darwin’s Tree of Life (TOL); modern attempts re: Forest of Life (FOL), Nearly Universal Trees (NUTs) etc.
- Take notes on 2012 Pace, Sapp, Goldenfeld Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life. See notes here.
- look up references 71, 72, 73, 74, 75 in the first paragraph of “is there really a tree of life?”
- also norman pace 1997 ref 24 re: how we agreed to 97% SSU rRNA sequence similarity as threshold for classiying bacteria as unique species…
- Annotate and review Rose and Oakley 2012
- 2010 Norman Pace Mapping the Tree of Life: Progress and Prospects
- Homologous genes are the superset. (p. 566) These are divided into: (a) orthologs which have a common function among different organisms post-speciation; (b) paralogs often have different functions but are the result of duplication and subsequent evolution and generally within same species; and (c) xenologs which are the result of LGT and so have evolved independently of the usual cellular line of descent.
- List of rRNA sequence databases p. 566
- Reread 2016 Booth, Mariscal, and Doolittle, The Modern Synthesis in Light of Microbial Genomics and JH notes here
- 2009 W. Ford Doolittle, The practice of classification and the theory of evolution, and what the demise of Charles Darwin’s tree of life hypothesis means for both of them
- 2007 de Queiroz, Species Concepts and Species Delimitation
- 2017 Doolittle and Brunet, On causal roles and selected effects: our genome is mostly junk
- 2020 Kapli, Yang, and Telford Phylogenetic tree building in the genomic age. Paper behind Nature Reviews Genetics paywall, despite Nature subscription.
Other papers and books to read
- Robert L. Carroll Patterns and Processes of Vertebrate Evolution (1997)
- James W. Valentine On the Origin of Phyla (2004)
- L.G. Wade Organic Chemistry, 7th Edition
- Snyder et al Molecular Genetics of Bacteria, 4th Edition
- MBOC sections on DNA Replication/Repair, Transcription, Translation
- 2010 Theobald, A formal test of the theory of universal common ancestry. See full list of PDF articles at Douglas Theobald’s lab website.
- 2015 Bacteria Culturomics by Lagier, Hugon, et al., The Rebirth of Culture in Microbiology through the Example of Culturomics to Study Huma Gut Microbiota
- 2020 Xuhua Xia, A Mathematical Primer of Molecular Phylogenetics
- 2007 Shotgun sequencing of ocean prokaryotic by Shibu Yooseph, Steven E. Brenner, J. Craig Venter et al. The Sorcerer II Global Ocean Sampling
Expedition: Expanding the Universe
of Protein Families
Progress
September, 2020
October, 2020
November, 2020
December, 2020
- Started rereading Valentine On the Origin of Phyla (2004)
- 12/06/2020:
First read through 2016 Booth, Mariscal, and Doolittle, The Modern Synthesis in Light of Microbial Genomics
- 12/06/2020:
1988 de Queiroz, Systematics and the Darwinian Revolution – good diagrams illustrating monophyletic vs. paraphyletic vs. polyphyletic, and strict speciation ancestry vs. interbreeding ancestry (Fig. 4)
- 12/07/2020:
1988 de Queiroz and Donoghue, Phylogenetic Systematics and The Species Problem - interbreeding populations vs. monophyletic definitions
- 12/09/2020:
2016 Etienne G.J. Danchin, Lateral gene transfer in eukaryotes: tip of the iceberg or of the ice cube? suggests that minimal LGT has happened recently in Eukaryota. However, common not just within Archaea and Bacteria but between those two domains as well even in relatively recent times
- 12/12/2020:
completed Sapp The New Foundations of Evolution: On the Tree of Life (2009)
- 12/12/2020:
History and Graph Theory (hierarchies, trees, networks, etc.)
- 12/13/2020:
2007 Rose and Oakley, The New Biology: Beyond The Modern Synthesis.
- JH notes here
- Excellent review of how 21st century biology is a reintegration on the order synthetic revolutions of Darwin (1859), Modern Synthesis (1930s-1940s).
- 12/21/2020:
Researched phylogenetics journals and conferences.
- 12/30/2020:
Restarted annual subscription to Nature.
January, 2021
1/08/2021: continued reading 2012 Pace, Sapp, Goldenfeld1/11/2021: continued reading Quammen The Tangled Tree1/12/2021: Reviewed some chapters of 2nd edition of Dawkins and Wong The Ancestor’s Tale (2016), esp. chapters on bdelloid rotifers, “light harvesters” (cauliflower, redwood tree, humped bladderwort and C-value, Mixotrich protist within Australian termite and four levels of symbiosis including multiple endosymbionts), Archea, and Bacteria.1/13 - 1/14: More reading on Quammen, including main reference to inosculation. Need to start a new page for all Tangled Tree notes.1/14: Finished Doolittle’s 2000 Scientific American article Uprooting the Tree of Life1/15: Completed Quammen’s The Tangled Tree. began sketching phylogeny of jawless, bony, ray-finned, and lobe-finned fish.1/16: First issue of Nature with history of humerus1/17: Sketched our Ring of Life, Historical Cone of Life1/24: started annotating 2016 Doolitle and Brunet1/27: Received Xu’s Comparative Genomics1/28: Received by Molecular Evolution: A Phylogenetic Approach by Rod Page and Edward Holmes (1998)
February 2021
- 2/02/2021: Listened to a16z Bio Eats World interview with Rick Young from MIT about how only 2% of the human genome codes for protein, but a significant fraction does code for RNA or plays other regulatory functions.
- 2/06: Joseph’s Felsenstein’s 2004 textbook Inferring Phylogenies arrived.
- 2/09: Built new page for MIT 7.QBWX course; started Matlab tutorial.
- 2/11: Browsed February 4, 2021 issue of Nature (Vol. 590, Issue 7844).
- Review Function and regulation of the divisome for mitochondrial fission
- p. 171 - Mental health crisis among US grad students
- p. 173 - Reasons to love the command line
- p. 40, 89 - Bayesian optimization machine learning to optimize synthetic chemistry reactions
- p. 41, 151 - Mouse gut immune response to bacterial infection leads to post-infection abdominal pain when eating antigen-carrying food
- p. 67 - Math research: builidng a systematic way of generating polymonial continued fractions (PCFs) and more generally mathematical relations of fundamental constants