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The New Foundations of Evolution: On the Tree of Life

Chapter 1: Animal, Vegetable, or Mineral? p. 3-16

  • Robert Hooke (1635–1703) updated the compound microscope by adding a third lens and drew beautiful illustrations in Micrographia (1665). p. 4
  • Antony van Leeuwenhoek (1632–1723) made simpler and better microscopes than Hooke’s models.
    • In the mid-1670s, Leeuwenhoek was able to magnify by 270x and drew pictures of animalcules, later identified as yeast, protists, bacteria, hydra, and rotifers. p. 4
    • Leeuwenhoek first discovered bacteria in 1676. p. 4
  • Carl Linnaeus (1707–1778) p. 6-8
  • Georges-Louis Leclerc Buffon (1707–1788) p. 8-9
  • Jean Baptiste Lamarck (1744–1829) p. 9-14
  • Georges Cuvier (1769–1832) p. 14
  • Étienne Geoffroy Saint-Hilaire (1772–1844) p. 14
  • Jean Baptiste Bory de Saint Vincent (1780-1846) “proposed the kingdom Psychodaire (being with two souls) for those that are ‘at the same time Animals, Plants, or Minerals, and which can not therefore be put exclusively in one or the other three kingdoms’…Bory de Saint Vincent further explained that ‘those beings that Linnaeus had called zoophytes had only thrown confusion on the two empires and tortured the minds of naturalists who attached too much importance on distinguishing plants from animals’…Indeed, that is precisely how Buffon had interpreted them: they were gradations in a continuum.” p. 15-16

Chapter 2: Microbes First p. 17-27

Chapter 3: The Germ of Phylogeny p. 28-44

Chapters 1 - 3

Chapter 4: Creatures Void of Form

  • p. 45-46, Louis Pasteur, Robert Koch, and Joseph Lister
  • p. 46: fission fungi aka Schizomycetes coined by Carl von Nägeli in 1857 as a class in Kingdom Plantae.
  • Ferdinand Cohn (1828–1898) seems to have first used the term “bacteria” in the modern sense in his 1872 paper Research on the Bacteria. p. 47
    • Other contributions. Helped Robert Koch with anthrax bacillus life cycle, isolation of dormant spores, etc.
    • p. 48: Cohn’s studies of heat resistance of spores might have contributed to the end of abiogenesis (doctrine of spontaneous generation) even more than Pasteur’s work
    • Cohn pushed for people to see bacterias not just agents of disease but the foundation of all life on earth
    • Cohn disagreed with Haeckel (who thought that bacteria and blue-green algae formed by spontaneous generation). Cohn agreed with Charles Wyville Thomson’s speculations on panspermia p. 49

[…continue with notes from p. 50-56]

Chapter 5: About Chaos p. 57-70

[…take notes on this period from p. 57-67]

Bergey’s Manual p. 67

  • In 1920, the Committee on Characterization and Classification of Bacterial Types published a final report about the family Nitrobacteriaceae, stating that this scheme was “the most reasonable outline for true biological relations among the bacteria which can be drawn up in the state of present knowledge”.
  • That outline and its methods formed the foundation for the first edition of Bergey’s Manual of Determinative Bacteriology, published in 1923
    • see also discussion of realists vs. idealists in Chapter 7, p. 86-87

Chapter 6: Kingdoms at Biology’s Borders p. 71-84

  • Edwin and Herbert Copeland were a father-son pair of biologists
  • Edwin Copeland (1873–1964) p. 72 taught at University of the Phillipines and originally began a classication system that placed bacteria in an independent kingdom as early as 1914.
    • However, Edwin did not publish this until a small note in a 1927 issue of Scienceand it did not gain notice until his son Herbert published another monograph in 1938 with a complete taxonomy in Quarterly Review of Biology.
    • Interestingly, it was considered obvious that bacteria and blue-green algae (aka Phylum Schizophyta) still belonged to Kingdom Plantae in the 1920s-30s.
    • “‘a plant kingdom comprised of all the organisms listed in the texts of botanical taxonomy is no more ‘natural’ than a kingdom of the stones.’” p. 72
    • “[Edwin Copeland] suggested there might be other kingdoms [beyond bacteria]. He reassured botanists that to grant bacteria a kingdom of their own would not reduce botany’s holdings. ‘These various creatures do not disappear from the course in botany just because they are not plants.’ Botany was ‘still the most convenient place to study them’.” p. 72
    • “Convenience aside, Copeland asserted, ‘there is no other one thing so important in systematic biology as the fact that the grouping of organisms reflects and expresses their true relationships. It is inconsistent and unreasonable to begin the course in botany by doing violence to this basic principle.’” p. 72
  • Herbert Copeland (1902–1968) p. 72
    • “‘When it became my turn to [teach elementary biology as my father had once taught me and many other introductory students], my efforts to recognize a series of natural kingdoms led me to distinguis four of them, called Monera, Protista, Plantae, and Animalia.’” p. 73

The Map is Not the Territory

  • Anastomosis - when edges in a network start from a small set of nodes, branch out into many nodes, and then converge back again into a small set of destination nodes. Somewhat like arteries and veins in the human body. p. 76
  • Edwin Copeland believed that phylogenetic evolutionary trees did *not * exhibit anastomosis; “natural systems consist of lines which divide, diverge, and redivide, and are incapable of anastomosis.” p. 76
  • Edwin Copeland’s three conventions of constructing taxonomic systems:
    1. “Natural groups” are formed by common descent and a prepondarance of common characters indicating that descent. p. 77
      • For example, “because the plant and animal kingdoms posessed such characters they were undoubtedly natural groups.”
      • “The Protista was a natural group; its members include the original form of nucleated life and all of its descendants except those two specialized secondary developments, the familiar kingdoms of plants and animals.” In modern parlance, we would call Protista a monophyletic taxon.
    2. Paraphyletic groups were not allowed.
      • First the delimitation of any particular group assigned a taxonomic category was “always artificial, arbitrary, and decided by convenience.” But, one could not cross phylogenetically divergent lines.
      • Edwin did not believe any of the seven common ranks (kingdom, phylum, class, order, family, genus, species) were objective categories determined by nature.
      • In contrast, Alexander Agassiz perceived the seven ranks (kingdoms…species) to be “realities, facts of nature; they were natural kinds to be discovered, not invented categories” probably because of his belief in divine categories as opposed to Darwinian gradualism
      • Copeland wrote of Agassiz “We know that he was mistaken. All taxonomic groups are parts of a branching system considered separately for purposes of human thought.” p. 77
    3. The type method
      • A group is named with a specific “paragon” example representing the group. “The type meant the exemplar of the group whose members possess many but not all group characteristics. As Copeland put it, ‘it was a standard and allowed for diversity within the polythetic group.”
      • Another rule related to the type method was the importance of priority, i.e., recognizing the oldest valid name and only that name. On this basis, Edwin Copeland in 1947 abandonded the terms protista and monera because he had come to learn of Richard Owens’ and John Hogg’s earlier proposals as well as Haeckel’s exemplar of Protoamoeba turned out to simply be a broken-off fragment of a whole amoeba. p. 77

The New Systematics

  • In 1940, Julian Huxley published The New Systematics which had contributions from 22 biologists across many fields but did not include microbiologists. p. 80
  • The Modern Synthesis also did not incorporate microbiology or embryology/development (p. 78 and see Chapter 6, footnote 40 - p. 336 and Sapp 1987).
  • The New Systematics (1940) and Ernst Mayr’s Systematics and the Origin of Species (1942) both included “discussions of the philosophical and methodological principles of taxonomy. What is meant by ‘natural classification’? Are such taxonomic categories as species, genus, and family artificial creations of the systematist, merely matters of convenience, or are they real natural groups with an objective reality? Could and should taxonomy be based on phylogeny? Can the course of evolution be visualized as a tree? To what extend is the course of evolution reticulated?

Are Species Real?

  • “The problem of conceptuatlizing species was characterized by the dispute between Darwin and Agassiz, a lifelong opponent of the theory of evolution. For Agassiz, species were real, natural types around which individual variations occurred; they were the ‘thought of God’.”
  • “For Darwin, like Lamarck before him, species were not real–if real meant eternal or immutable, or if the boundaries between them had to be sharp.” p. 80
  • J.S. Mill’s theory of natural kinds p.81
  • More interesting quotes from p. 80 - 84

Chapter 7: The Prokaryote and the Eukaryote p. 85-99

Chapter 8: On The Unity of Life p. 100-114

Chapter 9: Symbiotic Complexity p. 115-126

Chapter 10: The Morning of Molecular Phylogenetics p. 127-144

Chapter 11: Roots in the Genetic Code p. 145-161

  • A new approach to microbial classification, “far removed from the many-characters methods of numerical taxonomy (aka phenetics see p. 133) and from the molecular methods of the 1960s based on amino aid sequence, GC values, and nucleic acid hybridization.” p. 145
  • Carl Woese (1928–2012) finished his doctoral research in biophysics in 1953 at Yale, outside of the mainstream of microbiology.
    • He attended medical school for “two years and two days” at University of Rochester from 1953 to 1955 but quit after just a few days in the pediatrics ward during 3rd year rotations. p. 146
    • Woese subsequently returned as a postdoc to the lab of his PhD advisor Ernest Pollard at Yale. Pollard was the founder of the biophysics group at Yale and created the Department of Biophysics at Penn State.
  • Cosmologist George Gamow (1904–1968) proposed that the genetic code consisted of triplet codons that fit into the diamond-sshpaed cavities of dsDNA. He also believed that the code was overlapping. e.g, the codon ACG could only be followed by CGA, CGT, CGC, or CGG. “However, as the peptide sequence data accumulated, it became increasingly clear that no such ‘neighbor restrictions’ existed.” p. 147
  • Woese kept working on the DNA-amino acid coding problem, testing the hypothesis of Martynas Yčas that “in viruses, one nucleotide rather than a triplet codon encoded one amino acid.” p. 148
  • In 1961, Marshall Nirenberg and Heinrich Matthaei at the NIH in Bethesda, MD showed that a triple-uracil codon (UUU) coded for phenylalaninine. And a poly-U RNA of many uracils leads to a long polypeptide of polyphenylalaninine. The called it the U-3 incident after the U-2 spy plane incident of 1960.
  • By 1965, the entire table of RNA–>amino acid was filled out. p. 149

On the Origin of Translation p. 149-150

  • In 1962, Woese was a visiting researcher at the Pasteur Institute in Paris.
  • That same year, Sol Spiegelman from the University of Illinois visited Paris looking for new faculty to add to the campus at Urbana-Champaign.
  • Spiegelman and Benjamin Hall had “developed a DNA-RNA hybridization technique using E. coli and bacteriophage T2 that…acted much like [the messenger RNA system] conceived by Jacques Monod, François Jacob, and Matt Meselson.”
  • Spiegelman offered Woese a tenured position at UIUC starting in 1964 which allowed him to explore “high-risk problems far off the main paths of biology”.
    • Why did UUU or UUC encode phenylalanine, and CCC proline? In 1965, Woese wrote ‘While it is important to know what the genetic code codon assignments are, it is more important to know why they are, i.e., to know the mechanisms giving rise to the particular assignments observerd. Only when the latter question is answered can we truly claim to begin to understand the genetic code.

Frozen Accident Theory p. 151-153

  • Crick was an advocated of the essential accidental nature of the mapping between RNA and amino acid. At some point early in the history of life, these assignments were randomly made and because the translation machinery is so fundamental, this accident was forever “frozen” for all descendants from one of the early common ancestors of all life on earth.
  • Review of Crick’s adaptor hypothesis for tRNA at the ribosome from 1955 onwards p. 151
  • Since the discovery of tRNA (formerly called “soluble RNA”), all intro bio courses and textbooks have claimed that tRNA is the empirical validation of Crick’s adaptor hypothesis.
  • But this is not true. In fact, the “size and molecular complexity of tRNA are nothing like what Crick had proposed or required.” p. 152
    • Whereas Crick had pictured triplet codons 3 nucleotides in length, real tRNA molecules contained between 25 to 200 nucleotides.
    • In fact, Crick was initially skeptical that tRNA could be the adaptors he had hypothesized. In 1958, he said that tRNA “was too short ot code for a complete polypeptide chain, and yet too long to join onto template RNA by base pairing.” p. 152
  • In contrast, Woese believed that: (a) the adaptor model was a little too neat; (b) it was based on the “erroneous assumption about how codon mappings originated in the form of a frozen accident”; and (c) that one needed to have a better accounting for the anomalous size and complexity of tRNAs.
    • “Woese doubted that tRNA functioned passively merely as a static adaptor. He developed an alternative view based on the idea that tRNA was active and had different functional states like protein enzymes.”

Molecular Metaphysics p. 153-156

  • In the early 1970s, “Woese came to see molecular biology as an engineering discipline ensconced in misguided reductionism and devoid of evolutionary explanation…It tended to treat the translation apparatus as a given, a machina ex deus.” p. 153
  • In 1972, Woese wrote: “If the principles of molecular biology were correct, evolution would [simply] be a mixed bag of peculiarities, a basically unrelated collection of ‘historical accidents’, an unordered wandering through an immense evolutionary space.”
  • Woese drew inspiration from Alfred North Whitehead’s process philosophy.
    • Cartesian dualism (aka classical substance dualism) has an ontology whereby reality ultimately consists of either physical Matter or mental/immaterial Mind. Furthermore, Matter consists of very small, independent bits of material.
    • In contrast, Whitehead proposed an ontology based on interrelated processes; where events, patterns, and change are considered fundamental rather than objects and matter, or as Whitehead termed it “irreducible brute matter.” Whitehead: “All Things Flow”.
    • Whitehead’s objections to what he termed scientific materialism and “irreducible brute matter”: (1) insufficient focus on the importance of change, (2) insufficient emphasis on the importance of relations versus objects.
    • In summary, Whitehead conceived of “reality as composed of processes of dynamic ‘becoming’ rather than static ‘being’, emphasizing that all physical things change and evolve, and that changeless ‘essences’ such as matter are mere abstractions from the interrelated events that are the final real things tha make up the world.”
  • Woese was inspired by Whitehead writing in 1925: In between the duality of matter and mind, lies “the concepts of life, organism, function, instanteneous reality, interaction, order of nature, which collectively form the Achilles’ heel of the whole system.”
  • Woese,1972: “Whitehead’s philosophy of organism stressed that process is fundamental…existence and evolution begin to fuse…evolution seems to define itself as the problem of how order at one ‘level’ of the universe relates to order at the adjacent level.”

Speculations about proto-tRNA p. 154

  • “In Woese’s model, the tRNA played an active role in tape reading and ‘it could well have a say in specifying the amino acid it is to carry.’”
  • This conneted with speculation about how RNA could play an enzyme-like role, esp. early in the history of life. Woese (and Crick and Orgel) played with the idea of ribozymes before the term was coined by Kelly Kruger et al in 1982.
  • tRNA was a molecular misfit, with a complicated cloverleaf molecular geometry that “resembled a protein more than RNA”.
  • The proto-tRNA might have possessed one site for selecting amino acids and another site for holding them.
  • Further speculation: perhaps the proto-tRNA simply grabbed the same amino acid repeatedly and added to a homopeptide chain (without any reading of mRNA or equivalent).
  • In later evolution, some amino acids might be transferred from one proto-tRNA to another, resulting in heteropeptides. Again, this is not modern message-reading or translation as we know it.
  • In later developments, perhaps the ‘aboriginal RNA’ would serve as an evolutionary precursor to ribosomal RNA. In 1967, Woese speculated that proto-RNA could have been the original genome” and tRNA evolved later.

Reciprocating ratchet mechanism p. 154

  • Woese proposed in 1970 that proto-tRNA would undergo conformational changes that ‘pulled’ mRNA through the ribosome during translation.
  • Woese theorized that there was a “pre-Central Dogma world” where biopolymers such as simple polypeptides floursihed but “translationally produced proteins had yet to arise; it was an era doiminated by nucleic acids.”
  • The translation appartus would have evolved from interactions between RNA and amino acids beore the origin of ribosomes.

Metaphysical limits of molecular biology p. 155 – 156

  • Watson’s Molecular Biology of the Gene first appeared in 1965 and MBOC first appeared in 1983. Both of these books mapped the perimeters of molecular bio and barely mentioned evolution. p. 155
    • In other words, “Evolution was not considered to be important for molecular biological understanding.”
  • François Jacob wrote in 1970 about the chicken or egg problem with DNA –> RNA –> protein: “If the genetic code is universal, it is probably because every organims that has succeeded in living till now is descended from one single ancestor. But it is impossible to measure the probability of an event that occurred only once. It is feared that the subject may become bogged down in a slough of theories that can never be verified. The origin of life might well become a new center of abstract quarrels, with schools an theories concerned, not with scientific predictions, but with metaphysics.”

Need for a Phylogenetic Framework p. 156-157

  • By the time Woese finished The Genetic Code in 1976, he concluded “that one could not study these problems of deep evolution without a phylgenetic framework.”
    • “A universal tree would therefore hold the secret to its own existence as well.” p. 156
    • He wrote a letter to Crick in 1969: If we are ever to unravel the course of events leading to the evolution of the prokaryotic (i.e. simplest) celss, I feel it will be necessary to extend our knowledge of evolution backward in time by a billion years or so–i.e. backward into the period of actual “Cellular Evolution”…Therefore, what I want to do is to determine primary structures for a number of genes in a very diverse group of organisms, on the hope that by deducing rather ancient ancestor sequences for these genes, one will eventually be in the position o being able to see features of the cell’s evolution–i.e., by knowing what features of the primary structures are “locked-in” what regularities (repeats, etc.) existed, and how one ancient primary relates to another ancient primary strucutre (which gave rise to some different cellular function).
  • Consider a introductory biology textbook and the table therein of 64 codon possibilities mapped to 20 amino acids. Because this code is virtually uniform and universal among all current organisms, the lack of variation in the coding implies that this is an uninspired avenue for research into phylogenetic relationships or history.
  • “But the black-box conception of the code is deceptive. Understood as a process, the genetic code might not be universal at all or an ‘event’ that occurred only once.”
  • “One might be able to discern differences in the mechanisms of translation among such widely divergent organisms as prokaryotes and eukaryotes. Based on such ancient differences, one could make inferences about the translation machinery of their common ancestor.”
  • “Alternately, differences in the translation apparatus might not be evidence of an ancestral state but rather evidence that prokaryotes and eukaryotes had altered their coding systems after they diverged from a common ancestor, which itself possessed a fully evolved genetic code.” This possibiity seems less likely because of how damaging mutations are to the translation machinery.
  • Woese began a “lifelong task of conceptualizing [the prokaryote/eukaryote split] in terms of fundamental differences in their translation machinery” (in contrast to historical cell histology methods that distinguished the branches by visible differences in cell structure).
  • In 1970, Woese wrote “the fundamental differences in translation apparatus between prokaryotes and eukaryotes suggest that the final stages of the evolution of the genetic code may have occurred independently in the two lines.” p. 157
    • More differences between prokaryotes and eukaryotes:
      • difference in gross composition in ribosomal RNA
      • difference in antibiotic sensitivity
      • striking difference in a particular loop in the tRNA cloverleaf molecule
    • Woese’s hypotheses: (1) the split between prokaryotes and eukaryotes was more ancient than commonly assumed; and (2) prokaryotes did not give rise to eukaryotes but instead both lineages derived from an earlier nonprokaryotic lineage.

Back to Evolution’s Core

  • Woese focused on ribosomal RNA b/c , per Darwin’s advice about focusing on core features rather than peripheral characters that would be more prone to adaptation, the translation machinery seemed to be well-conserved in everything from the smallest bacteria to the largest metazoans and metaphytes.
  • In 1965, “Sanger announced methods for sequencing and cataloging oligonucleotide RNA.” He and his collaborators applied this method to tRNA and rRNA and showed that some common sequences like GCUCAG were common in E. coli but not in yeast.
  • In 1968, one of Sanger’s graduate students David Bishop moved to UIUC as a postdoc to help set up Sanger’s system for sequencing viral RNA in Speigelman’s lab. Bishop and Mitch Sogin built a setup for the Spiegelman lab and Woese inherited this lab at UIUC after Spiegelman moved to NY to take a position at Columbia University in 1969. (For more details, see The Tangled Tree: A Radical New History of Life p. 57-58)
  • “The sequencing technology was slow and arduous, but Woese’s team had the field virtually to themselves for a decade. Using the Sanger technique for RNA oligo sequencing [not to be confused with Sanger chain-termination DNA sequencing which would not be published until 1977], many small pieces of RNA could be separated by electrophoresis and then catalog.”
  • “The long RNA molecule was broken into small fragments several nucleotides long by cutting at every G residue with Ribonuclease T1 a restriction endonuclease that cuts RNA at every guanine…Then, these smaller fragments would be cut by other enzymes that cut at other specific nucleotides. This method allowed them to reconstruct the nucleotide sequence of each original rRNA fragment.”
  • Sogin was critical to developing and implementing the lab equipment and setup, “increasing the capacity of the lab from two to six Sanger tanks. Thanks to Sogin’s efforts, the Woese lab was able to catalog the RNA sequence for various taxa.”
  • “During the first few years, Woese and his technician Linda Bonin worked to improve the technique. It took several years of work to get to the point where it was really useful.” p. 159
  • Ribosomes have two subunits: (a) the small subunit has a 16S rRNA; and (b) a large subunit (LSU) which has a 23S RNA component and a 5s RNA component. See this Wiki table for more details.
  • After some trial and error, the team began focusing on the 16S rRNA aka the SSU rRNA.
  • The comparative cataloging approach “provided information from only about 35% of the 16S rRNA. Sequencing the entire 16S rRNA gene was not feasible unitl the late 1970s.” For more, see this 1978 paper and then this Woese lab paper on a complete archeaon 16S rRNA in 1983. p. 160
  • Slowly but surely, microbiologists from around the world began sending samples to the Woese lab for sequencing and cataloging of the 16S rRNA. Many were reluctant to use the extremely high levels of radioactive materials needed.
  • “The collaboration between Woese and George Fox was especially vibrant for many years.”

Chapter 15: In the Capital of the New Kingdom p. 199-215

  • p. 210: “In the winter of 1977, Stetter was teaching as an assistant in Kandler’s Institute at the University of Munich. He ran a lab there as well as at the Max Planck Institute in Martinsried, traveling back and forth every day. In January, Kandler informed [Stetter] about his inspiring visit with Woese and Fox in Urbana. He suggested that Stetter and Zillig extend their analysis of transcription by examining the RNA polymerase of the proposed ‘third kingdom’.”
    • The group in Martisried held their weekly Friday seminar to discuss research and ideas. Stetter informed them about Woese’s ‘third kingdom’. Zillig had known of Woese from his work on the genetic code [but had not kept up since then]. Zillig had not heard of the archaebacteria and he certainly did not at first take the idea of a third kingdom seriously. ‘A Third Reich?’, he quipped, ‘We have had enough of the Third Reich’!

Chapter 16: Out of Eden p. 216-225

  • “There was no direct phylogenetic evidence to support the view that the arcahebacteria were actually older than the eubacteria but the conjecture that the archaea were ancient persisted as that grouping grew to include extreme halophiles and termoacidophiles.” p. 216
  • p. 216-217: Increasing and productive cross-Atlantic collaboration between Woese, Fox, Kandler, Stetter, and Zillig.
  • p. 216-220: Breakdown and competition between Woese and Japanese researchersHorishi Hori and Syozo Osawa from the Institute of Nuclear Medicine and Biology at Hiroshima University.

An Aquatic Eden p. 220-222

Chapter 17: Big Tree p. 226-242

Proving Symbiosis Theory

Can Only God Make a Tree?

Chapter 18: The Dawn Cell Controversy p. 243-256

Chapter 19: Three Domains p. 257-266

Chapter 20: Disputed Territories p. 267-281

Chapter 21: Grappling with a Worldwide Web p. 282-299

Chapter 22: Entangled Roots and Braided Lives p. 300-313

Concluding Remarks p. 314-318