January – April 2023

The Tangled Tree: A Radical New History of Life, David Quammen, 2018. These are my chapter by chapter notes. Besides having very good reviews and being by a well-regarded author, this book got a (rare) very high rating from Reid Priedhorsky…

Read this with CS.

Contents

Timeline

Key
Items from Part II [A Separate Form of Life] in black;
from Part III [Mergers and Acquisitions] in purple;
from Part IV [The Big Tree] in light blue
from part V [Infective Heredity] in red
from part VI [Topiary] in bold-grey-with-blue-highlighting

————

1832: Charles Darwin embarks on the Beagle for his famous five year voyage.
`1838: Charles Darwin read’s Thomas Malthus‘ 1798 publication: An Essay on the Principle of Population for amusement, and has epiphany.
1838: Charles Darwin figures out the three key principles of his theory and records them in Notebook B:
(1) hereditary continuity,
(2) with variation among offspring
(3) in the context of population growth always outrunning the means of sustenance
1858: Alfred Wallace Russell develops idea of natural selection during a bout of fever: writes it up and sends it in a letter to C. Darwin. Darwin, afraid of being scooped but feeling honor-bound to acknowledge Russel, following advice of Charles Lyell, arranges joint paper presentation (in abstentia) at symposium, but ideas receive little attention.
1859: Charles Darwin publishes On the Origin of Species, which garners attention and discussion; one paragraph is devoted to ‘the tree of life.’
1864: Ernest Haeckle publishes book on Radiolarien; sends a copy to Charles Darwin.
1865: Ernest Haeckle publishes book on General Morphology.
1867: Ernest Haeckle publishes “Natural History of Creation,” a popular book on evolution and morphology that was widely read and translated
1874: Ernest Haeckle publishes “The Developmental History” of Man.
1900’s – 1920’s: Constantin Merezhkowsky and Ivan Wallin advance early ideas about endosymbiosis about chloroplasts and mitochondria, respectively.
1909: The term gene is coined, although no one knows what it is or even when molecules it consists of.
1910: Constantine Merezkhowski sketches a tree of life showing horizontal gene transfer.
1920’s: Ivan E. Wallin develops ideas about endosymbiosis (sybmionticism)
1928. Fred Griffith publishes “On the Significance of Pneumococcal Types,” in which he describes transformation, and its hypothesized mechanism, pabulum.
1942. Oswald Avery, Colin Macleod, and Maclyn McCarty publishe “Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumoccal Types,” in which they make the case that DNA is the chemical basis of the gene.
1946. Joshua Lederberg and E. L. Tatum describe genetic exchange and recombination among ecoli.
1948. Joshua Lederberg and Norton Zinder describe
1952. Joshua Lederberg, Luigi L. Cavalli, and Esther Lederberg describe the F-Factor in bacteria.

1958: Francis Crick publishes “On Protein Synthesis,” in which, in a side comment, he proposes protein taxonomy (now called molecular phylogenetic) as a way of deducing evolutionary relatedness.
1958. Fred Sanger wins his first Nobel prize for figuring out techniques for sequencing Bovine insulin, which go on to enable general DNA sequencing.
1961, Tsutomu Wantanabe and Toshio Fukasawa describe transfer of antibiotic resistance both within and between bacterial species; the coin the term “episome“for the unit of transfer.
1962: Hans Ris and Walter Plaut publish paper arguing for endosymbiosis based on their electron microscopic studies of chloroplasts
1962: Roger Stanier and C. B. Van Niel argue that life consists of two groups: prokaryotes and eukaryotes.
1964: Emil Zuckerkandl and Linus Pauling, conclude a series of papers on “chemical paleogenetics,” with Molecules as Documents of Evolutionary Historythey argue that by looking a the degree of differences among organisms one can tell:
(1) how much time has passed,
2) what the ancestral molecules must have looked like, and
(3) how much time has passed since the lineages split.
1964: Sol Spigelman recruits Carl Woese, then 36 years old, to the University of Illinois, Champaigne-Urbana. Woese viewed the nature of the DNA code as inseparable from the nature and origin of the decoding mechanism, and felt that the origin of DNA and its decoding mechanism was the central question of biology.
1967. Lynn Margulis publishes paper: On the Origin of Mitosing Cells.
1968: Sol Spiegelman leaves UI,C-U and gives his equipment to Woese; Woese tasks his new graduate post-doc, Mitch Slogin, to learn all he can about sequencing from Michael Bishop, Spiegleman’s post-doc, who had come to Spielgelman from Fred Sanger’s lab.
1968. Fred Doolittle does postdoctoral work in Sol Spiegelman‘s lab at UI-CU on RNA maturation, and develops biochemical techniques for studying cleaving of RNA. Doolittle becomes friends with Woese.
1969: Woese writes a letter to Francis Crick, asking for advice and support, regarding his intention to unravel the course of events leading to the origins of prokaryotes. Woese decides to focus on structural RNA in ribosomes as the molecule to follow: specifically 16S rRNA.
1969 Robert Whittaker publishes a paper arguing for five kingdoms, adding Fungi as the new kingdom.
1970. Lynn Margulis publishes book: Origin of Eukaryotic Cells, elaborating endosymbiotic hypothesis, claiming that chloroplasts, mitochondria and (incorrectly) undulipodia (flagella, cilia) were all the descendants of captured bacteria.
1970. Lynn Margulis publishes book: Origin of Eukaryotic Cells, elaborating endosymbiotic hypothesis, claiming that chloroplasts, mitochondria and (incorrectly) undulipodia (flagella, cilia) were all the descendants of captured bacteria.
1970. Fred Doolittle arrives at Dalhousie; gets interested in applying his rRNA maturation techniques to blue-green algae because he likes the color.
1973: Wosese’s lab has become the foremost user of Sanger-type RNA sequencing technology in the world. This work proceeded from 1968-1977.
1974. Linda Bonen (from Worse’s lab) arrives at Dalhousie and begins working with Doolittle.
1975: Woese shifts direction a little to look at methanogen bacteria in collaboration with Ralph Wolfe. First methanogen sequenced appears to be anomalous: 16S-rRNA unlike prokayotic RNA.
1975. Paper on Sequence Studies on 16S rRNA from a Blue-Green Alga by Doolittle, Ford, Woeses, Sogin, Bonen, and Stahl.
1976. Fred Doolittle, aided by Linda Bonen who came from Woese’s lab, demonstrate that the RNA in the chloroplasts of red algae is radically different from that of the RNA in its cytoplasm, another bit of support for endosymbiosis.
1976: Woese’s lab sequences five more methanogen’s, with similar anomalous results.
1976. Doolittle and Bonen publish a paper offering evidence for two claims: blue-green algae are not algae but cyanobacteria, and that chloroplast’s in some complex organisms had originated as cyanobacteria.
1977: Woese’s lab produced three papers culminating in a major paper coauthored with George Fox, making the claim that methanogen’s are a new form of life that differ from plants, animals and bacteria. Press release debacle tarnishes Carl Woese’s reputation.
1978: French lab publishes complete sequence of 16S rRNA.
1978: Robert Whittaker and Lynn Margulis publish a paper noting that classification is a human pedagogical convenience and arguing that classification s of life, so far as possible, should reflect phylogenetic relationships.
1977-80: Woese makes contact with Germans (Kandler, Zillig, Stetter), and they individually and collectively establish that methanogens, halophiles, thermophiles and acidophiles are all anomalous with respect to prokaryotes both in their RNA and in their cell walls and lipids.
1980: Fox and Woese (and many others) coauthor “On the Phylogeny of Prokaryotes.”
1981: First international workshop on Archaea.
1984: James Lake et al publish an analysis of ribosome shapes, and suggest that there are four kingdoms of life, with sulphur-loving organisms being their own kingdom.
1987: Woese publishes a single-authored review paper on bacterial evolution, which, of ccourse, argues for his view that there are three kingdoms and puts forward the concept of a prognote (developed in 1977: an organisms capable of self-replication but with a genome probably consisting of RNA rather than DNA, and an imprecise mechanism for generating proteins that kept it small and inefficient..
1990: Worse, Kandler, and Wheels publish “Towards a Natural System of Organisms,” arguing that (1) classification should be phylogenetic; (2) and that there should be three domains of life than trascend kingdoms.
1995: Craig Venter et al publish first full genetic sequence of a Bacterium.
1996: “Another team” publishes first full genetic sequence of a Eukaryote: Brewers Yeast, a fungus.
[1996: Craig Venter et al publish first full genetic sequence of an Archaeon. Of 1736 genes, over half are entirely new to science, bolstering claim for Archaea as its own kingdom..
1997: Jim Brown and Fred Dolittle publish trees for 67 organisms; the trees do not match.
1999: Fred Dolittle publishes a review article in Science – “Phylogenetic Classification and the Universal Tree” – that calls the current consensus of a universal tree into question, and contains his drawing of a reticulated tree.
2002: Peter Gogarten, Jeffrey Lawrence and Fred Dolittle write a paper making the case for the advantages of HGT – basically HGT provides a vast repertoire of instant adaptations which can be rapidly shared and subjected to natural selection.
2009: New Scientist publishes an issue titled “Darwin was Wrong: Cutting Down the Tree of Life.”
19xx

Book Notes

Introduction, notes, and index

The book is about molecular phylogenetics, and how this method has reconfigured our understanding of how life has evolved from its primitive origins to “the florescence of diversity and complexity we see now.” The method has produced three critical insights

First, that there exists a separate kingdom of life, called Archaea, that was unknown until circa 1980
Second, that horizontal gene transfer is a major mechanism in the evolution of life, occurring not just between related species but across wider gaps, even across kingdoms
Third, that all plants, animals, fungi, and organisms that contain DNA within a cell nucleus evolved from Archaea.

The book will also trace the history of the development of this method, and of the accompanying perspective on evolutionary biology. It will animate a cast of characters, including Carl Woese (everything having to do with horizontal gene transfer), Fred Griffith (antibiotic resistance), Barbara McClintock (corn genetics), Lynn Margulis (endosymbiosis), and Ford Dolittle (“Uprooting the Tree of Life”).

Other materials: About 400 notes, mostly to scientific articles, especially review articles. Thirty-seven page bibliography, from which we can see a focus on: Doolittle, Gogartin, Kooning, Lederberg, Margulis, Martin, Pace, Wallin and especially Woese.

Part I: Darwin’s Little Sketch

[1] Charles Darwin came from a well-to-do family with a significant intellectual pedigree, including his grandfather, Erasmus Darwin. In 1832 at the age of 22 he took his only long voyage, a 5 year trip to South America (and also Australia), where he amassed evidence that he drew on throughout his life.
[1] Darwin kept two notebooks labeled “A” and “B.” A contained notes on geology. B started in 1837, nine months after he returned from his 5 year voyage on the Beagle; notebook B was secret, and contained his notes on ideas that eventually led to his theory of evolution.
[2] At the time scientific dogma included the notion of “the stability of species,” that is that species were immutable and never changed, though more radical thinkers would admit that they might go extinct. “The tree of life should perhaps be called the coral of life, base of branches dead.
[3] A discussion of some of the predecessors to the idea of a tree of life, including Aristotles ‘Scale of Nature,’ and Charles Bonnet’s ladder-like” “Scale of Life.’ By the late 18th Century natural scientists were gravitating to tree-like forms to capture the progression and interrelatedness of organisms. However, this use of a tree-like form did not represent any thinking about evolution…
[4] Lamark and the inheritance of acquired traits; early on this mechanism was preferred by many to natural selection as an evolutionary mechanism. Note that Darwin also included interitance of acquired traits as a minor part of his threory.
[5] Edward Hitchcock’s religiously-conformant ‘trees’ of organisms, versus Charles Lyell‘s Principles of Geology which challenges the scriptural model of natural history and geology. Darwin read Lyell’s work during his voyage on the Beagle.
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- [6] Although Darwin figured out the key ideas of his theory in 1838, he did not publish On the Origin of Species until 1859, and he only went public then because Alfred Russell Wallace had submitted a paper along the same lines.
- [6] The key ideas were (1) hereditary continuity, (2) with variation among offspring (3) in the context of population growth always outrunning the available means of sustenance. The last idea was due to Thomas Malthus’ An Essay on the Principle of Population, published in 1798 which Darwin read in early 1838 “for amusement.”
- [7] In 1858 Wallace had hit upon the idea during a bout of fevers during during a collecting trip in Malay. However, Wallace was a poor man with only a few publications to his name — he worked as paid natural history collector — and so he sought an ally to help him get the paper published: Charles Darwin, whom he knew only as an eminent naturalist, as Darwin had kept his evolutionary theorizing secret. Darwin assisted in getting Russell’s paper publicly presented (with help and advice of Charles Lyell), but at the advice of colleagues he also had a paper of his own on the topic presented at the same time. Seventeen moths later Darwin published On the Origin of Species, which is what got public attention.
- [8] Darwin explored the tree metaphor in one extended paragraph in his book.

Part II: A Separate Form of Life

[9] Molecular phylogenetics began with a suggestion of Francis Crick‘s. Crick was interested in understanding not just DNA, but the entire mechanism of which it was part. In 1958 he published a paper called “On Protein Synthesis.” In it he mentioned that he foresaw a field called “protein taxonomy” which would involve the comparison of amino acid sequences between organisms, and which would enable one to draw phylogenetic trees.
[10] Seven years passed, and then two scientists – Emile Zuckerkandl and Linus Pauling – began pursuing the idea from different routes. Pauling had recently won his first Nobel prize, and had become interested in genetic diseases. He recruited Zuckerkandl — who had done molecular level work on crabs and their hemoglobin analog – to his lab, and suggested that he work on hemoglobin.
[10] Over the next several years Zuckerkandl and Pauling published a series of papers — many going into Festschriften which Pauling was invited to contribute to because of his eminence, and which did not go through peer review allowing for ore speculative thinking. One of those papers, Molecules as Documents of Evolutionary History, singled out molecules which encode information (such as DNA and the proteins it encodes, and argued that by looking a the degree of differences among organisms one can tell (1) how much time has passed, (2) what the ancestral molecules must have looked like, and (3) how much time has passed since the lineages split. They termed this approach “chemical paleogenetics.“
[11] In 1964, the same year Zuckerkandl presented the paper to a symposium at Rutgers, Carl Woese, 36 years old, was hired with immediate tenure at the University of Illinois, Champaigne-Urbana. Woese viewed the nature of the DNA code as inseparable from the nature and origin of the decoding mechanism, and felt that the origin of DNA and its decoding mechanism was the central question of biology. To pursue this, he needed to develop an evolutionary tree that included microbes, the oldest organisms.
[12] In 1969 Woese wrote a letter to Crick, asking for advice and support, regarding his intention to unravel the course of events leading to the origins of prokaryotes. To develop such a tree, he needed to track changes in a molecule common to all organisms: his choice was the translation apparatus: the ribosome and messenger RNA.
[12] Ribosomes consist of two units: a small unit that ‘reads’ the messenger RNA, and a large unit the concatenates the different amino acids specified by the reading unit. A single cell can contain tens of thousands (if a prokaryote) to tens of millions (if mammalian) ribosomes, and each ribosome can produce a protein at the rate of about 200 amino acids per minute (1 every 300 milliseconds)
[12] Another of Woese’s insights was to focus on the structural RNA that, along with proteins, makes up the ribosome, because they are so old and likely to change so little over time (I don’t understand why they’d be less likely to change than the proteins).
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[13] Fred Sanger had pioneered techniques for sequencing RNA: these involved cleaving RNA with enzymes, and separating the fragments using electrophoresis. Sanger won two nobel prizes for this line of work: one in 1958 for his work in sequencing Bovine insulin, and a second (1980) for his work in sequencing DNA. One of Sanger’s students had come to Illinois to postdoc in Sol Spiegelman‘s lab, and when Speigelman left suddenly, Woese inherited his equipment and had his own new postdoc, Mitch Sogin, learn as much about Sanger’s sequencing methods from Bishop as he could, and Sogin became the equipment wrangler and experimentalist that Woese, who primarily did theory, needed. (Sogin stayed in graduate school to avoid going to Vietnam.)
[14] After a short detour, Woese decided that he would sequence 16S rRNA that is a structural component of every bacterium on earth, and that also has a close analog, 18S rRNA in the ribosomes of eukaryotes. Quammen suggests this is Woese’s single most important contribution to biology.
[14] Sequencing involved growing bacteria with a radioactive isotope of phosphorous, and then doing 2-dimensional electrophoresis to characterize the fragments; sometimes it was necessary to extract fragments from a section of the gel and do a third round. By 1973 Woseses lab had become the foremost user of Sanger-type RNA sequencing technology in the world. This work proceeded from 1968-1977 during which the Woese lab sequenced a panoply of bacteria.
[15] Luehrsen joins Woese lab, and after graduating in 1975 stays to do PhD. Woese shifts direction a little to look at methanogen bacteria, in collaboration with Ralph Wolfe.
[16] Biologists struggled, with little success, to come up with a good classification system for bacteria.
[17] More on the attempt to classify bacteria, and the paper “The Concept of a Bacterium,” as signaling the abandonment of the taxonomic attempt.
[18] 1975. The first attempt to sequence 16S rRNA from the methanogen grown in Wolfe’s lab (aka delta-h) gave anomalous results — it appeared to be neither a prokaryote or eukaryote.
[19] Original films of delta-h
[20] By the end of 1976 the lab had sequenced 5 more methanogenic microbes and found similar results.].
[21] —
[22] Wolfe’s account
[23] Three papers published, leading up to the 1977 paper, coauthored with Fox, that made a claim for a new form of life different from plants, animals and bacteria.
[24] George Fox.
[25] The disastrous press release is misinterpreted and exaggerated by the press, due perhaps to Woese lack of talent at talking to ordinary people, and the publicity damages his reputation and sets back acceptance of Archea 10-15 years
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[26] Woese connects with German scientists, one being Otto Kandler, a botanist/microbiologist who had an interest in cell walls – in particular he had discovered that the cell walls of methanogens were anomalous: they did not contain peptidoglycan. This also seemed to be the case with halophiles. This sent George Fox to the library, where he learned that halophiles (and thermophiles and acidophiles) also contain ‘weird lipids,’ just like the methanogens. At this point, Woese decide he wanted to sequence halophile RNA, but as he had lost his tech had to grow them hiimself; after a few months that verified that halophiles were also archaea.
[27]The other two Germans Woese connected with were Wolfram Zillig (who had been studying methanogens) and Karl Stetter (a former student of Kandler). After hearing of Woese’s findings on methanogens, Zillig and Stetter applied their research method — analyzing RNA polymerase, to see whether there were parallels with extremophiles that were analogous to what Woese was finding. There were.
[27] In 1981 the Germans organized the first international workshop on Archaea, and made Woese the star.

Part III: Mergers and Acquisitions

[28] 1967. Lynn Margulis publishes On the Origin of Mitosing Cells, presenting the theory of endosymbiosis and arguing that mitrochondria, chloroplasts, and centrioles are all descended from bacteria, citing also citing Ris, Merezhkowski, and Wallin
[29] 1962: Hans Ris and Walter Plaut publish paper arguing for endosymbiosis based on their electron microscopic studies of chloroplasts, and also citing Merezhkowski
[29] 1970. Lynn Margulis publishes book: Origin of Eukaryotic Cells.
[30] Back story on Merezhkowsky a brief summary of his thinking (1900 on…), theoretical and delusional, and his likely abuse of children.
[31] Back story on Ivan E. Wallin and his thinking on endosymbiosis (sybmionticism )in the 1920’s.
[31] Back to Margulis: She knew that chloroplasts as captured bacteria could be traced back to Merezhkowsky and mitochondria as captured bacteria could be traced back to Wallin; her contribution was to argue that flagella, cilia and centrioles (which shared a radial arrangement of nine microtubule) were also the result of captured bacteria–but in the long run the findings of phylogenetic analysis did not support her claim.
[32] 1970: Fred Doolittle (a student of Norman Pace) at Dalhousie had worked on ribosomal RNA maturation, and the cutting of it into segments (including 16S) during assembly of the ribosome. Doolittle decided to study RNA maturation in blue-green algae because he liked their color, and could just apply his earlier methodology. He did this work, got a nice note from Stanier (a senior scientist), and then read and was inspired by Margulis’ book.
[32] 1974. Then Linda Bonen (from Woese’s lab) arrived and began working with him. They analyzed RNA from red algae, and discovere, circa 1974-5, that the RNA within its chloroplasts differed radically from RNA in its cytoplasm, another bit of evidence in support of endosymbiosis.
[33] Doolittle and Woese’s friendship, formed while Doolittle was working in Spieglman’s lab in the late 1960s.
[33] A year later (1976? 1977?) Doolittle and Bonen publish a paper offering evidence for two claims: blue-green algae are not algae but cyanobacteria, and that chloroplast’s in some complex organisms had originated as cyanobacteria.
[33] 1978: French lab publishes complete sequence of 16S rRNA.
[34] Walter Gray arrives at Dalhousie, and becomes curious about why there is transfer RNA in mitochondria, and then reads Margulis’ book. His first graduate student, Scott Cunningham talks with Linda Bonen and they hit on the idea of apply Woesean methods to Wheat RNA. They discover that the rRNA of Wheat mitochondria does not resemble other wheat RNA: it resembles bacterial RNA.
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Part IV: The Big Tree

[37] 1864: Charles Darwin receives Haeckle’s book on Radiolarien
[38] Ernest Haeckle’s early life, education and travels – his interest in art and in morphology
[39] Ernest Haeckle publishes his first book, gives a keynote, gains an academic position, marries Anna
[40] 1864: Ernest Haeckle‘s book and death of his wife
[41] 1865: Ernest Haeckle throws himself into his work and writes a two volume work “General Morphology” on morphology and evolution. In it he coins the terms “ecology,” “phylogeny,” and “ontogeny,” the biogenic law now stated as “phylogency recapitulates ontogeny,” and proposes a third Kingdom of Life: Protista. The book contains 8 drawings of trees, which distinguish themselves from earlier trees by representing he relationships among actual organisms.
[42] 1874: Ernest Haeckle publishes “The Developmental History of Man,” with his ‘Great Oak’
[43] Trees become a popular way of showing relationships among organisms and are widely used through the middle of the 20th century. In 1969 Robert Whittaker publishes a paper arguing for five kingdoms, adding Fungi as the new kingdom.
[44] 1978: Robert Whittaker and Lynn Margulis publish a paper noting that classification is a human pedagogical convenience and arguing that classification s of life, so far as possible, should reflect phylogenetic relationships; but that isn’t always possible: sometimes one must use polyphonic taxa (e.g., marine vertebrates which include both whales and fish and salt water crocodiles).
[45 & 46] 1980: Fox and Woese (and many others) coauthor “On the Phylogeny of Prokaryotes.” They have a dispute about author order, resolved in Fox’s favor, but leading to a gradual end to their collaboration. The paper draws on the 16S rRNA sequences of more than 170 organisms and makes two points: (1) that there are really not prokaryotes, but rather bacteria, archaea and eukaryotes; (2) the Lynn Margulis was right and that eukaryotes were genetic chimera with mitochondria and choloplasts originating as bacteria.
[47] 1984: James Lake et al publish an analysis of ribosome shapes, and suggest that there are four kingdoms of life, with sulphur-loving organisms being their own kingdom. Woese strongly disagrees and his geniality towards Lake shifts to hostility.
[47] 1987: Woese publishes a single-authored review paper on bacterial evolution, which, of course, argues for his view that there are three kingdoms, and puts forward the concept of a prognote (developed in 1977) as the predecessor of the three kingdoms. A prognote is anrganisms capable of self-replication but with a genome probably consisting of RNA rather than DNA, and an imprecise mechanism for generating proteins that kept it small and inefficient.
[48] 1990: Worse, Kandler, and Wheels publish “Towards a Natural System of Organisms,” arguing that (1) classification should be phylogenetic; (2) and that there should be three domains of life than trascend kingdoms.
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Part V: Infectious Heredity

[49] 1923-28. Fred Griffith‘s discovers that different types of pneumonia can transform into one another: a dead virulent strain cultured with a non-virulent strain can make the non-virulent strain deadly. He calls the process transformation, and the physical vehicle of the process pabulum.
[50] 1942. Oswald Avery, Colin Macleod, and Maclyn McCarty publishe “Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumoccal Types,” in which they make the case that DNA is the chemical basis of the gene.
[51] From 1946 – 1952 Joshua Lederberg and colleges discover (1) conjugation — ‘sexual’ exchange among bacteria, and (2) transduction — genetic transfer of a single trait via viruses, and (3) that transduction can enable conjugation by making ‘non-fertile’ bacteria fertile.
[52] 1961-63, Tsutomu Wantanabe sounds alarm about antibiotic resistance. Tsutomu Watanabe and Toshio Fukasawa describe transfer of antibiotic resistance both within and between bacterial species; the coin the term “episome“for the unit of transfer.
[53] Stuart Levy meets Wantanabe and becomes interested in resistance. In the mid-60’s publishes a paper that shows antibiotic resistance can be transferred from bacteria in chickens to bacteria in the human gut.
[54] Antibiotic resistance existed before humans discovered antibiotics.
[55] 1968: Ephraim S. Anderson comments on Wantanabe et al, and speculates that transfer factors may be important in general bacterial evolution.
[55} 1970: Dorthy Jones and Peter Sneath publish “Genetic Transfer and Bacterial Taxonomy” in which they argue that horizontal gene transfer may be very widespread and that this “could favor extremely reticulate modes of evolution, with numerous partial fusions of phyletic lines.”
[56] 1983: Sorin Sonea and Maurice Panisset publish “A New Bacteriology,” making the case that bacteria are better viewed as a single organism with a distributed genome.
[57] In the 19890s the idea caught on, and also the concept of HGT between bacteria and eukaryotes began to be more accepted. In particular, work on rotifers showed that they incorporated many different genes from bacteria and fungi. The commonality of HGT in rotifera may be due to their ability to endure desiccation and their pathogenesis.
[58] Julie Dunning Hotopp and Michael Clark use bioinformatics to show that bacterial genes have been transferred into insects, one species of fruitfly providing a notable example having accepted nearly the entire genome of the parasitic bacterium Wolbachia.
[59] Overclaims for HGT into human genome in early Human Genome Project paper.

Part VI: Topiary

[60] Story about a guy who used grafting to grow groups of trees into chairs and other furniture. Introduces the term inosculate
[61] 1910: Constantine Merezkhowski sketches a tree of life showing horizontal gene transfer.
[61] 1995: Craig Venter et al publish first full genetic sequence of a Bacterium. In 1996 Another team” publishes first full genetic sequence of a Eukaryote: Brewers Yeast, a fungus. A few months later, Venter et al publish first full genetic sequence of an Archaeon. Of 1736 genes, over half are entirely new to science, bolstering claim for Archaea as its own kingdom.. So, overall, in 1995-1996 genetic sequences of organisms from Bacteria, Archaea and Eukaryotes are published. Mixtures of genes from bacteria and archaea are common within single genomes, and some bacteria genes even show up in Eukaryotes. Horizontal Gene Transfer (HGT) as a significant impact on microbial evolution become generally accepted. Robert Feldman questions Woese’s and other’s reliance on rRNA as a principal indicator of phylogentic relationships.
[62] Fred Dolittle, influenced by Peter Gogarten, gradually comes to the conclusion the HGT may have played such a signficant role in microbial evolution that it jepordizes the concept of cell lineages.
[62] 1997: Jim Brown and Fred Dolittle publish trees for 67 organisms; the trees do not match.
[63] 1999: Fred Dolittle publishes a review article in Science – “Phylogenetic Classification and the Universal Tree” – that calls the current consensus of a universal tree into question, and contains his drawing of a reticulated tree.
[64] 2002:Peter Gogarten, Jeffrey Lawrence and Fred Dolittle write a paper making the case for the advantages of HGT – (1) allowing an organism to colonize a new niche; (2)allow organisms to acquire a new adaptation abruptly without passing through ‘dangerous’ intermediary stages; (3) and this happens fast rather than incrementally; and (4) HGT provides a vast repertoire of adaptations which can be rapidly shared and subjected to natural selection. [[These don’t seem very different to me.]]
[65] Reprises George Martin’s work on HGT, which he call endosymbiotic gene transfer.
[66] 1996: Bill Martin publishes “Is Something wrong with the Tree of Life,” in which he talks about HGT in ecoli, which acquired about a fifth of its genome from other bacteria.
[66] 199????: Bill Martin publishes “XXX,” in which he notes that only about 1% of bacterial genes are so essential and complexly entwined with the organism that they couldn’t be swapped by HGT. Woese responds to these ideas by claiming that HGT occurred only in the deep past, in an ‘RNA world,’ and that there was a later Darwinian threshold where life became complex and shifted to vertical evolution.
[67] More and more scientists find evidence of HTZ. Martin et al, in a study of 81 organisms, concluded that more than 80% of the genes arrived by HGT.
[67] 2009: New Scientist publishes an issue titled “Darwin was Wrong: Cutting Down the Tree of Life.” The incendiary headline receives a lot of criticism for its hyperbole, and because it incited creationists, et al.
[68] Interlude on Fred Dolittle and philosophy and Darwin and the tree.
[69] Kind of a hazy end to the chapter, with a return to topiary, and three final questions: (1) Was Darwin wrong? (2) What is the origin of the Eukaryotic cell? (3) What implications do these discovery carry for human identify. [[I only find question 2 of interest; I’m really interested in how does HGT actually play out?]]

Part VII: E Pluribus Human

[70] Microbiome: as many as 3x microbes in a human body as human cells; to 1 – 3% by weight. They change somewhat with location, time and circumstance.
[71] 1980’s: Norman Pace develops methodology for sampling exogenous (environmental) DNA and applies it to studying organisms that can’t be raised in the lab, such as microbes from the Octopus Hot Springs in Yellowstone.
[72] Eric J. Alm looks at genomes from 2235 microbes looking for very similar genes in very different organisms (thus likely candidates for Horizontal Gene Transfer). They found over 10,000, rather than the 5 to 10 they’d expected to turn up. Analysis showed that the strongest determinate of HGT was ecological closeness, rather than phylogenetic similarity.
[73] Carl Woese strikes up collaboration with Nigel Goldenfeld, and expert in complex systems dynamics. Woese appears to accept HGT as a common and even dominant force in microbial evolution.
[74] Carl Woese and Harris Lewin friendship.
[75] When human genome is sequenced it is found to contain a lot of ‘junk DNA’ (aka transposons) base sequences of unclear purpose that are replicated throughout the genome. A precursor to this is that Barbara McClintock‘s work on maize genetics and the discovery of transposons. Unsuspected by McClintock at the time, 85% of the maize genome is comprised of transposons.
[75] Cedric Feschotte and his student John K. Pace discover the same transposon in a primate and a bat. They look more widely and find it in other mammals, marsupials and a lizard. They term the transposon “Space Invaders.”
[75] One theory about transposons is that their repetitive replication and movement (a) enable them to survive the extinction of particular organisms, and (b) provide organisms with genes that can be repurposed. [This is very curious, and I would like to understand more about how this ‘repurposing’ can happen.]
[76] More on Woese and his increasingly bad attitude towards Darwin, and his irritation with molecular biology.
[77] ~8% of human genome consists of the remnants of retroviruses.
[78] Retroviruses invade a cell, enter the nucleus, and use RNA to create DNA that it inserts into the receiving organisms genome. If it happens to do the insertion in a germ cell, the DNA will be passed along to the organism’s descendants — it is called an Endogenous Retrovirus (ERV). If it is in a human, it is called an HERV.
[78] Thierry Heidmann discovers new family of viruses in human placental tissues. When the human genome sequence was released, they scanned the genome for a particular type of gene that produces a sticky envelope around the core of a virus. They found twenty variants of it.
[78] Generically, the type of gene is called syncytin, and in placental tissue it fuses cells together into a multi-nucleated envelop that forms a layer in the placenta. It turns out that apparently syncytin has come into mammalian and other lineages many different times, testifying to its utility.
[79] Another capacity that syncytin has is immunosuppression. This is obviously useful for a virus invading a cell, but it is also useful for a placental organism, in that it enables the placenta to protect the fetus from the mother’s immune system. This is likely what allowed the transition from egg-laying organisms to those that retain the eggs internally and give birth to live young,.
[80] CRISPR: Clustered, Regularly-Interspaced Palindromic Repeats. CRISPR sequence ‘wrap’ short sequence of base pairs in microbes (both bacteria and archaea). In 2005, Francisco Monica publishes a paper arguing that CRISPRs appear to be a ‘memories’ of previous viral infections.
[80] In 2002, a Dutch team discovers cas (CRISPR-Associated-Sequences), 4 genes that appear adjacent to CRISPR sequences, and that turn out to be able to attack invading DNA that contain the CRISPR sequences.
[81] Carl Woese’s final period.
[82] Thijiss Ettema discovers an archaea from deep sea vents that appears to be a close match for the host cell that was the origin of eukaryotes. [But how did they determine that?] If true, this suggests that archaea began acquiring complexity before they acquired mitochondria, and that eukaryotes originated from archaea rather than a common ancestor of archaea and bacteria.
[83] Carl Woese’s death.
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