by Greg Mayer
Our second installment of Teaching Evolution is a paper by A.W.F. Edwards on the history and logical justification of methods of phylogenetic inference. In teaching evolution, the idea of the history of life is very important. Most students intuitively see the closer genealogical relationship between, say, a man and an ape than a dog, or among any of those as compared to a salmon. But the precise logic of doing so, especially when the degree of genealogical propinquity is less evident, is not easy to convey. I now teach this subject using a likelihood-based logic of justification, and Edwards was a pioneer in this area. Although we are accustomed now to think and speak of the phylogenetic tree as a “tree of life”, Darwin at first referred to it in his notebook as “the coral of life”, which is a more apt analogy, in that only the tips are alive, while the bases of the branches are dead.
For the first installment of what Jerry has called our “mini-MOOC” on evolution– an extract from the Origin by Darwin– I left out the title I gave to that week’s topic in my course: “Unity of type and adaptation”. I’ve now revised the title of that installment to include this in its title. Unity of type and adaptation were the two great classes of organic phenomena that Darwin sought to explain with his theory of descent with modification; with the chief means of modification– natural selection— accounting for the fit of organic beings to their conditions of existence, i.e. their adaptations. Thus Darwin proposed to solve these two great unsolved problems of biology in the first half of the 19th century with a single, unified explanatory theory.
Anthony William Fairbank Edwards (b. 1935) is a British statistician, geneticist, and evolutionary biologist. He is a Life Fellow of Gonville and Caius College and Emeritus Professor of Biometry at the University of Cambridge. An undergraduate student of R. A. Fisher, he has written several books and numerous scientific papers. He is best known for his pioneering work, with L. L. Cavalli-Sforza, on quantitative methods of phylogenetic analysis, and for strongly advocating Fisher’s concept of likelihood as the proper basis for statistical and scientific inference. He has also written extensively on the history of genetics and statistics, including an analysis of whether Mendel’s results were “too good” (they were). His most influential book is Likelihood (expanded edition, 1992), in which he argues for the centrality and sufficiency of likelihood as an inferential principle, often using genetic examples to illustrate his argument.
Study Questions:
1. What was Edwards’ purpose in writing this paper?
2. What is Ockham’s razor? What is the “Darwin principle”? What is the relationship between them?
3. What are some of the various ways in which a method of minimum evolution may be used to estimate phylogeny? What, according to Edwards, is the justification for any of these methods?
[For further discussion of the history of phylogenetic methods, see chapter 10, “A digression on history and philosophy”, in Joe Felsenstein‘s Inferring Phylogenies (Sinauer, 2004).]
Thanks, Greg. Could I ask that these entries be tagged MOOC, or something else specific to them? Science education, and teaching evolution will bring in a lot of other things, if we want to get to these quickly. Cheers.
I’ve added MOOC as both a category and a tag; this should make keeping track of the installments easier. Thanks for the good suggestion!
GCM
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I have read several articles expressing doubt that a “tree of life” can be drawn for prokaryotes, because the multiple horizontal gene transfers make it web-like. But I think we shouldn’t give up hope so easily.
I would be interested in hearing from the evolution experts on this.
Of the many genes that have been sequenced, a smallish minority (last I heard, about 15%) show genealogies that seem consistent with the tree of cells. The rate of horizontal gene transfer is low — the average replication of a bacterial cell does not involve any HGT. But as the depth of the tree of cells is great, even a small rate of HGT leads many genes to show discrepancies between their genealogies and the tree of cells.
So yes, there is a tree, but most genes have genealogies that don’t follow it.
Eukaryotes are another matter, with much less HGT.
Interesting, since the spread of antibiotic resistance is thought to be mediated largely by HGT in some species. Maybe a byproduct of the “unnatural” nosocomial environment? I’d be curious to hear thoughts on this.
“Unnatural” nosocomial environment or natural human gut environment containing hundreds of different bacterial species or strains?
I think I once read something about resistance genes being spread through HGT in the soil of animal farm environments, where antibiotics are heavily used.
I recall some years ago reading and understanding (I think) a review article about horizontal gene transfer in basal prokaryotes and basal eukaryotes resulting in a “ring” topology at the base of the tree, rather than a binary branching all the way down to LUCA (Last Universal Common Ancestor).
I remember it principally because it gave me a splitting headache.
From network theory (clubbed into protesting braincells for database management in mid-80s computing, when Real Programmers wrote their own tree-traversal algorithms), a multi-way split at a tree node can be represented as multiple binary splits with one leaf null or extinct. Palæontologically or in genetic species comparison, that’s simply interpreted as missing specimens.
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Thanks to Greg for a link to my book. Sinauer Associates having become an Oxford University imprint recently, the link should be to here.
Alas, it is not cheap; I wish I were allowed to post a link to a free PDF of Chapter 10.
GCM – your series is appreciated!
Am reading the 13 page PDF now
Thanks
Charles Darwin seems to have had a thing for coral.His theory on the formation of coral atolls first explained how they form. Coral polyps can only live in a certain depth of water, and he realized that as an island slowly subsides the polyps maintain their growth by building upon the coral that has subsided, so maintaining the optimal zone for growth. He developed his theory while still on the Beagle.
https://en.wikipedia.org/wiki/The_Structure_and_Distribution_of_Coral_Reefs#Theory_of_coral_atoll_formation
I watched “Reefer Madness” recently. It wasn’t about coral, atoll.
😀
You should have inhaled. That makes it much clearer.
(Darwin considered himself as a geologist more than a biologist.)
Inhale? My presidential gravitas would go up in smoke!
Here’s one that should have been picked up in proofreading/review. “Suppose we hear
that a friend has borne male twins. Are
they identical? If so, the probability that
they are both boys is 0.5,…”.
Since we’ve already been told they are male twins the probability they are both boys is 1.
Thank you very much for the series. I’m reading the pdf now, and the section on the apparent linearity of evolution really reminds me of field theories used in physics, at least in the case where there is no potential function. Will attempt to answer the questions after reading the paper.
1. What was Edwards’ purpose in writing this paper?
The purpose was to point out parsimony does not arise from assumptions purely philosophical in nature (e.g. Occam’s razor) while constructing evolutionary histories, but rather originates from statistics and probabilistic arguments.
2. What is Ockham’s razor? What is the “Darwin principle”? What is the relationship between them?
Occam’s razor is a philosophical principle which states that there should be no unnecessary assumptions in a theory. The Darwin principle is that life has a single origin. Occam’s razor is one of the justifications for the Darwin principle, as a single origin has fewer unnecessary assumptions.
3. What are some of the various ways in which a method of minimum evolution may be used to estimate phylogeny? What, according to Edwards, is the justification for any of these methods?
Phylogeny can be estimated with minimum mutation distance, discrete probability models, or phylogenetic systematics. Probability arguments justify these methods.
Ockham’s Razor, I believe, started out as a theological affirmation to the effect that simple explanations were preferred because the deity did not tolerate inefficiency. It was much after Newton that the dictum transformed into a scientific working procedure that demanded to formulation of simple explanations that simultaneously conformed to the facts and presented as few untested assumptions — and these plausible — as possible because this led to quicker resolutions. Theology has done a complete about-face and now considers, not the Razor’s affirmation of the simplicity of nature, but rather its complexity and superfluity, as evidence for the deity.
Ockham was not claiming that nature always follows the simplest course, nor that a simple explanation trumps a better, more complex one; nor yet that simplicity should overrule the need to explain all the data. Rather, he was advocating that one should not propose any more causes than are necessary to account for any phenomenon.
He wrote (translated): “Nothing ought to be posited without a reason given, unless it is self-evident or known by experience or proved by the authority of Sacred Scripture.”