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The Twisted Tree of Life (tTOL) Awards

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Talk for the DOE JGI #NELLI19 Meeting on - The Twisted Tree of Life (tTOL) Awards

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The Twisted Tree of Life (tTOL) Awards

  1. 1. The Twisted Tree of Life (tTOL) Awards April 2, 2019 Jonathan A. Eisen @phylogenomics University of California, Davis
  2. 2. Trees of Life
  3. 3. New Information Reaching Many People
  4. 4. Also Some Misrepresentation
  5. 5. Extreme Misrepresentations of Evolution Common
  6. 6. Some Are Silly
  7. 7. Some Are (Kind of) Funny
  8. 8. Some Are Perplexing
  9. 9. Some Are Dangerous
  10. 10. Some Are Dangerous But Embraced
  11. 11. Misrepresentations Matter https://theconversation.com/the-five-most-common- misunderstandings-about-evolution-54845 https://evolution.berkeley.edu/evolibrary/misconceptions_faq.php
  12. 12. Trees of Life
  13. 13. Twisted Trees of Life
  14. 14. Twisted Tree of Life Awards
  15. 15. Twisted Tree of Life Awards
  16. 16. The Twisted Tree of Life tTOL Awards Category 1: Inaccurate Tree Representations
  17. 17. tTOL Innacuracies: Stuck on the Five Kingdoms
  18. 18. However, all living organisms may be placed into one of five kingdoms, e.g., see Margulis and Schwartz tTOL Innacuracies: Stuck on the Five Kingdoms
  19. 19. Fungi are one of the five kingdoms of life (six, if you’re American), the other four being plants, animals, monera (unicellular organisms that don’t have a nucleus, like bacteria), and protists (an assortment of creatures that are eukaryotic, ie, having nucleus in their cells). tTOL Innacuracies: Stuck on the Five Kingdoms
  20. 20. tTOL Innacuracies: Stuck on the Five Kingdoms
  21. 21. tTOL Innacuracies: Stuck on the Five Kingdoms
  22. 22. tTOL Inaccuracies: Prokaryotes vs. Eukaryotes
  23. 23. tTOL Inaccuracies: Prokaryotes vs. Eukaryotes
  24. 24. tTOL Inaccuracies: Prokaryotes vs. Eukaryotes
  25. 25. tTOL Inaccuracies: Prokaryotes vs. Eukaryotes
  26. 26. Same Issues w/ New Models
  27. 27. Pervasive Issue: Birds Are Dinosaurs
  28. 28. Figure 27.1 The Evolution of Plants (Part 2)
  29. 29. Figure 30.1 A Phylogenetic Tree of the Animals
  30. 30. “Prokaryotes” in Pubmed Titles 0 250 500 750 1000 1952 1958 1964 1967 1969 1971 1973 1975 1977 1979 1981 1983 1985 1987 1989 1991 1993 1995 1997 1999 2001 2003 2005 2007 2009 2011 2013 2015 2017
  31. 31. International Committee on Systematics of Prokaryotes
 
 https://www.the-icsp.org tTOL Inaccuracies: Prokaryotes vs. Eukaryotes
  32. 32. Autocorrect “Prokaryotes” to “Bacteria & Archaea”
  33. 33. Autocorrect “Prokaryotes” to “Bacteria & Archaea” https://phylogenomics.blogspot.com/2013/01/just-say-no-to-prokaryotes-lesson-in.html
  34. 34. tTOL Inaccuracies: Prokaryotes vs. Eukaryotes
  35. 35. The Twisted Tree of Life (tTOL) Awards Category 2: Bad Use of Terminology
  36. 36. tTOL Terminology: Primitive Primitive: Relating to, denoting, or preserving the character of an early stage in the evolutionary or historical development of something
  37. 37. tTOL Terminology: Higher vs. Lower Higher Organism: More evolved organism? Lower Organism: Less evolved organism?
  38. 38. tTOL Terminology: Higher vs. Lower
  39. 39. tTOL Terminology: Higher vs. Lower
  40. 40. tTOL Terminology: Higher vs. Lower
  41. 41. tTOL Terminology: Higher vs. Lower after all, this is the predominant form of signaling in higher organisms The roots of most higher plant species form arbuscular mycorrhiza
  42. 42. The DOXP pathway functions in some bacteria, algae and higher plants
  43. 43. CO2 assimilation in higher plants, algae, and most characterized autotrophic prokaryotes relies on the ribulose-1,5-bis- phosphate carboxylase (RubisCO)
  44. 44. tTOL Terminology: Ancient Ancient: belonging to the very distant past and no longer in existence
  45. 45. tTOL Terminology: Basal Terms like 'basal', 'early-diverging', and 'first-branching' reflect persistent misconceptions about evolution and phylogenies Of course, the tree has a base, and there is a most basal branching and a next most basal branching, but there is no such thing as the most basal clade. Because branchings are rotatable, there are always two most basal clades http://for-the-love-of-trees.blogspot.com/2016/09/the-ancestors-are-not-among-us.html Basal: nodes near the root of a rooted phylogenetic tree
  46. 46. tTOL Terminology: Other Terms • Deeply branching, early diverging • Simple vs complex • Missing Link • Similarity vs. Homology
  47. 47. The Twisted Tree of Life (tTOL) Awards Category 3: Misrepresentation of Process
  48. 48. tTOL Proccess Twists: Adaptationism Adaptationism: “the belief or assumption, now generally held, that each feature of an organism is the result of evolutionary adaptation for a particular function.”
  49. 49. tTOL Proccess Twists: Adaptationomics Adaptationomics: “the belief or assumption, now generally held, that each genomic feature of an organism is the result of evolutionary adaptation for a particular function.” Adaptationomics Award Well, I have decided to start a new award. For years I have been fighting against the tide on the tendency for people doing genomics work to resort to silly adaptationist arguments for observations. The argument goes something like this. We sequenced a genome (or did some type of genomics). We made an observation of something weird being present (take your pick - it could be a gene order or a gene expression pattern or whatever). We conclude that this observation MUST have an adaptive explanation. We have come up one such adaptive explanation. Therefore this explanation must be correct.
  50. 50. You're talking about a significant portion of its DNA that is now from Wolbachia," says Julie Dunning Hotopp, a geneticist at the J. Craig Venter Institute in Rockville, Maryland, who led the study. "There has to be some sort of selection to carry around that much extra DNA." Just the right amount of wrong instructions and wasteful habits — that’s what evolution has built into all of us. tTOL Proccess Twists: Adaptationomics
  51. 51. YAGS - Yet Another Genome Sequence “Scientists have sequenced the genome of species X. Their research, published today in the Journal of Terribly Important Studies, will lead to new insights about this important species. Maybe it will even cure cancer or eliminate world hunger!”
  52. 52. tTOL Proccess Twists: Anthropomorphizing https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2948194 Anthropomorphizing: attributing human characteristics or behavior to (a god, animal, or object).
  53. 53. tTOL Proccess Twists: Anthropomorphizing https://www.youtube.com/watch?v=URFundw8bfc Talk by Dr. Heidi Elmendorf
  54. 54. tTOL Proccess Twists: Anthropomorphizing
  55. 55. tTOL Process Twists: More • Evolution is not “trying” to do anything • There are no “bad” or “good” microbes • Existence of LGT means there is no tree or phylogeny • Differences between organisms are called mutations • Organisms at the end of long branches in phylogenetic trees are “primitive” • Anything anomalous is due to lateral gene transfer
  56. 56. The Twisted Tree of Life (tTOL) Awards Category 4: Darwin = Evolution
  57. 57. tTOL Darwin Twists
  58. 58. tTOL Darwin Twists
  59. 59. Conclusions
  60. 60. Twisted Trees of Life
  61. 61. Don’t Get Your Tree in a Twist
  62. 62. Further Reading • https://theconversation.com/the-five-most- common-misunderstandings-about- evolution-54845 • https://evolution.berkeley.edu/evolibrary/ misconceptions_faq.php • Correcting some common misrepresentations of evolution in textbooks and the media .. https://evolution-outreach.biomedcentral.com/ articles/10.1186/1936-6434-6-11

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