This document outlines categories for the "Twisted Tree of Life Awards", which recognizes common misrepresentations and inaccuracies in depictions of evolutionary trees and processes. Category 1 focuses on inaccurate tree representations, such as outdated models of the kingdoms of life that ignore modern evidence. Category 2 examines problematic terminology like "primitive" and "higher/lower". Category 3 critiques misrepresentations of evolutionary processes, including excessive adaptationism. Category 4 notes the common conflation of Darwin and evolution. The document provides examples for each category and concludes that correcting misunderstandings is important.

1. The Twisted Tree of Life (tTOL) Awards
April 2, 2019
Jonathan A. Eisen
@phylogenomics
University of California, Davis

2. Trees of Life

3. New Information Reaching Many People

4. Also Some Misrepresentation

5. Extreme Misrepresentations of Evolution Common

6. Some Are Silly

7. Some Are (Kind of) Funny

8. Some Are Perplexing

9. Some Are Dangerous

10. Some Are Dangerous But Embraced

11. Misrepresentations Matter
https://theconversation.com/the-five-most-common-
misunderstandings-about-evolution-54845 https://evolution.berkeley.edu/evolibrary/misconceptions_faq.php

12. Trees of Life

13. Twisted Trees of Life

14. Twisted Tree of Life Awards

15. Twisted Tree of Life Awards

16. The Twisted Tree of Life tTOL Awards
Category 1:
Inaccurate Tree Representations

17. tTOL Innacuracies: Stuck on the Five Kingdoms

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. 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. tTOL Innacuracies: Stuck on the Five Kingdoms

21. tTOL Innacuracies: Stuck on the Five Kingdoms

22. tTOL Inaccuracies: Prokaryotes vs. Eukaryotes

23. tTOL Inaccuracies: Prokaryotes vs. Eukaryotes

24. tTOL Inaccuracies: Prokaryotes vs. Eukaryotes

25. tTOL Inaccuracies: Prokaryotes vs. Eukaryotes

26. Same Issues w/ New Models

27. Pervasive Issue: Birds Are Dinosaurs

28. Figure 27.1 The Evolution of Plants (Part 2)

29. Figure 30.1 A Phylogenetic Tree of the Animals

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. International Committee
on Systematics of
Prokaryotes
https://www.the-icsp.org
tTOL Inaccuracies: Prokaryotes vs. Eukaryotes

32. Autocorrect “Prokaryotes” to “Bacteria & Archaea”

33. Autocorrect “Prokaryotes” to “Bacteria & Archaea”
https://phylogenomics.blogspot.com/2013/01/just-say-no-to-prokaryotes-lesson-in.html

34. tTOL Inaccuracies: Prokaryotes vs. Eukaryotes

35. The Twisted Tree of Life (tTOL) Awards
Category 2:
Bad Use of Terminology

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. tTOL Terminology: Higher vs. Lower
Higher Organism: More evolved organism?
Lower Organism: Less evolved organism?

38. tTOL Terminology: Higher vs. Lower

39. tTOL Terminology: Higher vs. Lower

40. tTOL Terminology: Higher vs. Lower

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. The DOXP pathway functions in some bacteria, algae and higher
plants

43. CO2 assimilation in higher plants, algae, and most characterized
autotrophic prokaryotes relies on the ribulose-1,5-bis- phosphate
carboxylase (RubisCO)

44. tTOL Terminology: Ancient
Ancient: belonging to the very distant past and no longer in existence

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. tTOL Terminology: Other Terms
• Deeply branching, early diverging
• Simple vs complex
• Missing Link
• Similarity vs. Homology

47. The Twisted Tree of Life (tTOL) Awards
Category 3:
Misrepresentation of Process

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. 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. 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. 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. 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. tTOL Proccess Twists: Anthropomorphizing
https://www.youtube.com/watch?v=URFundw8bfc
Talk by Dr. Heidi Elmendorf

54. tTOL Proccess Twists: Anthropomorphizing

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. The Twisted Tree of Life (tTOL) Awards
Category 4:
Darwin = Evolution

57. tTOL Darwin Twists

58. tTOL Darwin Twists

59. Conclusions

60. Twisted Trees of Life

61. Don’t Get Your Tree in a Twist

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