Thomas Cavalier-Smith

Thomas (Tom) Cavalier-Smith, FRS, FRSC, NERC Professorial Fellow (21 October 1942 – 19 March 2021[1]), was a professor of evolutionary biology in the Department of Zoology, at the University of Oxford.[2]

Thomas Cavalier-Smith
Thomas Cavalier-Smith drawing.png
Born(1942-10-21)21 October 1942
London, United Kingdom
Died19 March 2021(2021-03-19) (aged 78)
NationalityBritish
Alma materGonville and Caius College, Cambridge King's College London
Known forCavalier-Smith's system of classification of all organisms
AwardsFellow of the Royal Society (1998)
International Prize for Biology (2004)
The Linnean Medal (2007)
Frink Medal (2007)
Scientific career
FieldsZoology
InstitutionsKing's College London, University of British Columbia, University of Oxford
ThesisOrganelle Development in Chlamydomonas reinhardii' (1967)
Websitewww.zoo.ox.ac.uk/people/view/cavaliersmith_t.htm

His research has led to discovery of a number of unicellular organisms (protists) and advocated for a variety of major taxonomic groups, such as the Chromista, Chromalveolata, Opisthokonta, Rhizaria, and Excavata. He was known for his systems of classification of all organisms.

Life and careerEdit

Cavalier-Smith was born on 21 October 1942 in London. His parents were Mary Maude (née Bratt) and Alan Hailes Spencer Cavalier Smith.[3]

He was educated at Norwich School, Gonville and Caius College, Cambridge (MA) and King's College London (PhD). He was under the supervision of Sir John Randall for his PhD thesis between 1964 and 1967; his thesis was entitled "Organelle Development in Chlamydomonas reinhardii".[4]

From 1967 to 1969, Cavalier-Smith was a guest investigator at Rockefeller University. He became Lecturer of biophysics at King's College London in 1969. He was promoted to Reader in 1982. From the early 1980s, Smith promoted views about the taxonomic relationships among living organisms. He was prolific, drawing on a near-unparalleled wealth of information to suggest novel relationships. In 1989 he was appointed Professor of Botany at the University of British Columbia. In 1999, he joined the University of Oxford, becoming Professor of evolutionary biology in 2000.[5]

Thomas Cavalier-Smith died in March 2021 following the development of cancer.

TaxonomyEdit

Cavalier-Smith was a prolific taxonomist, drawing on a near-unparalleled wealth of information to suggest novel relationships. His suggestions were translated into taxonomic concepts and classifications with which he associated new names, or in some cases, reused old names. Cavalier-Smith did not follow or espouse an explicit taxonomic philosophy but his approach was closest to evolutionary taxonomy. He and several other colleagues were opposed to cladistic approaches to taxonomy arguing that the goals of cladification and classification were different;[6] his approach was similar to that of many others' broad-based treatments of protists.[7][8]

The scope of Cavalier-Smith's taxonomic propositions was grand, but the numbers and composition of the components (taxa), and, often, their relations were not stable. Propositions were often ambiguous and short-lived; he frequently amended taxa without any change in the name. His approach was not universally accepted: Others attempted to underpin taxonomy of protists with a nested series of atomised, falsifiable propositions, following the philosophy of transformed cladistics.[9] However, this approach is no longer considered defensible.[10]

Cavalier-Smith's ideas that led to the taxonomic structures were usually first presented in the form of tables and complex, annotated diagrams. When presented at scientific meetings, they were sometimes too rich, and often written too small, for the ideas to be easily grasped. Some such diagrams made their way into publications, where careful scrutiny was possible, and where the conjectural nature of some assertions was evident. The richness of his ideas, their continuing evolution, and the transition into taxonomies that gave Cavalier-Smith's investigations into evolutionary paths (phylogeny) and the resulting classifications, its distinctive character.

Four major influencesEdit

Thomas Cavalier-Smith worked at a time when there was a pervasive presumption that classification should reflect evolutionary pathways. How this should be done had four major influences, as described in the following subsections.

Prior representationEdit

First, was a residue of the 'traditional' approach that admitted speculation and which lacked any explicit rigor as to how a particular evolutionary insight should be translated into the arrangement and ranks of taxa. Inherent to this approach were narratives about character evolution and classifications that included paraphyletic taxa, and in which degree of difference would influence the rank assigned to taxa.

Popperian philosophy of scienceEdit

The second influence was the philosophy as to how scientific progress was made. It had been articulated by K. Popper[11][12] and had shifted the emphasis from verification of ideas to the falsification of hypotheses.

Popper saw that science progressed by a process that eliminated unsound hypotheses, so whittling down of the array of possible explanations leading towards the explanations which were more likely correct. To fit into this process, hypotheses needed to be falsifiable.

CladisticsEdit

The third influence was 'cladistics' – an explicit way of presenting (and then 'falsifying', although see[10]) evolutionary hypotheses. This was initially articulated by Willi Hennig,[13] and was increasingly (but not universally[6]) accepted by many as how taxonomy should be done.[14][15] The justification of the cladistic approach in terms of Popperian hypothetico-deductivism was popular in the 1970-80s but is no longer considered defensible (see Sober[16] and reviewed in Rieppel[10] ).

Genetic sequencingEdit

Fourthly, technical advances in sequencing technology led to a massive growth of hypotheses about evolutionary relationships based on the similarities among sequences of compared organisms. Algorithms were used to analyse sequence data, with the results being usually presented in the form of dendrograms.

Cavalier-Smith's narrative styleEdit

Cavalier-Smith was courageous in his adherence to the earlier traditionalist style characterized by Charles Darwin, that of relying on narratives. One example was his advocacy for the Chromista that united lineages that had plastids with chlorophylls a and c (primarily chrysophytes and other stramenopiles, cryptophytes, and haptophytes) despite clear evidence that the group corresponded to a clade.

It was Cavalier-Smith's claim hat there was a single endosymbiotic event by which chlorophyll a c containing plastids were acquired by a common ancestor of all three groups, and that the differences (such as cytological components and their arrangements) among the groups were the result of subsequent evolutionary changes. This interpretation that chromists were monophyletic also required that the heterotrophic (protozoan) members of all three groups had arisen from ancestors with plastids.

The alternative hypothesis was that the three chromphytic lineages were not closely related (to the exclusion of other lineages) (i.e. were polyphyletic), likely that all were ancestrally without plastids, and that separate symbiotic events established the chlorophyll a/c plastids stramenopiles, cryptomonads and haptophytes. The polyphyly of the chromists has been re-asserted in subsequent studies.[17]

Cavalier-Smith's lack of an objective and reproducible methodology that would translate evolutionary insights into taxa and hierarchical schemes, were often confusing to those who did not follow his publications closely. Many of his taxa requiring his frequent adjustment, as illustrated below. In turn this led to confusion as to the scope of taxa a taxonomic name was applied to.

Cavalier-Smith also reused familiar names (such as Protozoa) for innovative taxonomic concepts. This created confusion because Protozoa was and still is used in its old sense,[18] alongside its use in the newer senses. Because of Cavalier-Smith's tendency to publish rapidly and to change his narratives and taxonomic summaries frequently, his approach and claims were frequently debated.

Cavalier-Smith's contributionsEdit

 
Tree of life and major steps in cell evolution after Cavalier-Smith, c. 2010, before his 2015 revision.

Cavalier-Smith wrote extensively on the taxonomy and classification of all life forms, but especially protists. One of his major contributions to biology was his proposal of a new kingdom of life: the Chromista, even though it is not widely accepted to be monophyletic (see above).

He also introduced new taxonomic groupings group for eukaryotes such as the Chromalveolata (1981), Opisthokonta (1987), Rhizaria (2002), and Excavata (2002). Though well known, many of his claims have been controversial and have not gained widespread acceptance in the scientific community. His taxonomic revisions often influenced the overall classification of all life forms.

Eight kingdoms modelEdit

Cavalier-Smith's first major classification system was the division of all organisms into eight kingdoms. In 1981, he proposed that by completely revising Robert Whittaker's Five Kingdom system, there could be eight kingdoms: Bacteria, Eufungi, Ciliofungi, Animalia, Biliphyta, Viridiplantae, Cryptophyta, and Euglenozoa.[19]

In 1983, he revised his system particularly in the light of growing evidence that Archaebacteria were a separate group from Bacteria,[20] to include an array of lineages that had been excluded from his 1981 treatment, to deal with issues of polyphyly, and to promote new ideas of relationships. In addition, some protists lacking mitochondria were discovered.[21] As mitochondria were known to be the result of the endosymbiosis of a proteobacterium, it was thought that these amitochondriate eukaryotes were primitively so, marking an important step in eukaryogenesis. As a result, these amitochondriate protists were given special status as a protozan subkingdom Archezoa, that he later elevated to kingdom status.[21] This was later referred to as the Archezoa hypothesis.[22] In, 1993, the eight kingdoms became: Eubacteria, Archaebacteria, Archezoa, Protozoa, Chromista, Plantae, Fungi, and Animalia.[23]

The kingdom Archezoa went through many compositional changes due to evidence of polyphyly and paraphyly before being abandoned.[24][25] He assigned some former members of the kingdom Archezoa to the phylum Amoebozoa.[26]

Six kingdoms modelsEdit

By 1998, Cavalier-Smith had reduced the total number of kingdoms from eight to six: Animalia, Protozoa, Fungi, Plantae (including Glaucophyte, red and green algae), Chromista, and Bacteria.[27] Nevertheless, he had already presented this simplified scheme for the first time on his 1981 paper[19] and endorsed it in 1983.[28]

 
Table 11 From Eukaryote kingdoms: seven or nine?

Five of Cavalier-Smith's kingdoms are classified as eukaryotes as shown in the following scheme:

The kingdom Animalia was divided into four subkingdoms: Radiata (phyla Porifera, Cnidaria, Placozoa, and Ctenophora), Myxozoa, Mesozoa, and Bilateria (all other animal phyla).

He created three new animal phyla: Acanthognatha (rotifers, acanthocephalans, gastrotrichs, and gnathostomulids), Brachiozoa (brachiopods and phoronids), and Lobopoda (onychophorans and tardigrades) and recognised a total of 23 animal phyla.[27]

Cavalier-Smith's 2003 classification scheme:[29]

Seven kingdoms modelEdit

Cavalier-Smith and his collaborators revised the classification in 2015, and published it in PLOS ONE. In this scheme they reintroduced the division of prokaryotes into two kingdoms, Bacteria (previously 'Eubacteria') and Archaea (previously 'Archebacteria'). This is based on the consensus in the Taxonomic Outline of Bacteria and Archaea (TOBA) and the Catalogue of Life.[30]

Proposed root of the tree of lifeEdit

In 2006, Cavalier-Smith proposed that the last universal common ancestor to all life was a non-flagellate Gram-negative bacterium ("negibacterium") with two membranes (also known as diderm bacterium).[31]

Awards and honoursEdit

Cavalier-Smith was elected Fellow of the Linnean Society of London (FLS) in 1980, the Institute of Biology (FIBiol) in 1983, the Royal Society of Arts (FRSA) in 1987, the Canadian Institute for Advanced Research (CIFAR) in 1988, the Royal Society of Canada (FRSC) in 1997, and the Royal Society of London in 1998.[32]

He received the International Prize for Biology from the Emperor of Japan in 2004, and the Linnean Medal for Zoology in 2007. He was appointed Fellow of the Canadian Institute for Advanced Research (CIFAR) between 1998 and 2007, and Advisor of the Integrated Microbial Biodiversity of CIFAR.[33] He won the 2007 Frink Medal of the Zoological Society of London.[5]

ReferencesEdit

  1. ^ Saldarriaga, Juan F. (2021). "Thomas Cavalier-Smith (October 21, 1942 – March 19, 2021)". Protist (Obituary). 172 (3): 125807. doi:10.1016/j.protis.2021.125807. S2CID 235321431.
  2. ^ "Professor Dr. Tom Cavalier-Smith, FRS, FRSC, Professor of Evolutionary Biology and NERC Professorial Fellow in the Department of Zoology, Oxford University". Cavali. Archived from the original on 4 March 2016. Retrieved 11 February 2016.
  3. ^ Marriage of Alan C. Smith and Mary Maud Bratt, 1st Qtr 1942, Wayland Reg Dist. (GRO Ref 4b/743). Birth of Thomas C Smith (mother's maiden name Bratt) last Qtr 1942, Greenwich Reg Dist. (GRO Ref 1d/650). Source www.freebmd.org.uk.
  4. ^ Cavalier-Smith, Thomas (1967). Organelle development in Chlamydomonas reinhardii (PhD thesis thesis). University of London. OCLC 731219097.
  5. ^ a b "Thomas (Tom) CAVALIER-SMITH". Debrett's. Archived from the original on 15 March 2016. Retrieved 11 February 2016.
  6. ^ a b Ruggiero, Michael A.; Gordon, Dennis P.; Orrell, Thomas M.; Bailly, Nicolas; Bourgoin, Thierry; Brusca, Richard C.; Cavalier-Smith, Thomas; Guiry, Michael D.; Kirk, Paul M. (29 April 2015). Thuesen, Erik V. (ed.). "A Higher Level Classification of All Living Organisms". PLOS One. 10 (4): e0119248. Bibcode:2015PLoSO..1019248R. doi:10.1371/journal.pone.0119248. ISSN 1932-6203. PMC 4418965. PMID 25923521.
  7. ^ Margulis, L.; McKhann, H.I.; Olendzenski, L., eds. (1993). Illustrated Glossary of Protoctista: Vocabulary of the Algae, Apicomplexa, Ciliates, Foraminifera, Microspora, Water Molds, Slime Molds, and the other Protoctists. Jones and Bartlett.
  8. ^ Margulis, Lynn; Schwartz, Karlene V., eds. (1997). Five Kingdoms: An illustrated guide to the phyla of life on Earth. W.H. Freeman & Company. ISBN 0-613-92338-3.
  9. ^ Patterson, D.J. (1985). "The fine structure of Opalina ranarum (family Opalinidae): Opalinid phylogeny and classification". Protistologica. 21: 413–428.
  10. ^ a b c Rieppel, Olivier (2008). "Hypothetico-deductivism in systematics: fact or fiction?". Papéis Avulsos de Zoologia. 48 (23): 263–273. doi:10.1590/S0031-10492008002300001. ISSN 1807-0205.
  11. ^ Popper, K. (1959) [1934]. Logik der Forschung [The Logic of Scientific Discovery] (English translation ed.). ISBN 0-415-27844-9.
  12. ^ Popper, K. (1963). Conjectures and Refutations: The growth of scientific knowledge. ISBN 0-415-04318-2.
  13. ^ Hennig, W. (1966). Phylogenetic Systematics. Urbana, IL: University of Illinois Press.
  14. ^ Wiley, E.O. (1981). Phylogenetics: The theory and practice of phylogenetic systematics. Wiley.
  15. ^ Eldredge, N.; Cracraft, J. (1981) [1980]. Phylogenetic Patterns and the Evolutionary Process. Method and Theory in Comparative Biology. New York, NY: Columbia University Press. ISBN 0-231-03802-X.
  16. ^ Sober, Elliott (1988). Reconstructing the past : parsimony, evolution, and inference. Cambridge, Mass.: MIT Press. ISBN 0-262-19273-X. OCLC 17803724.
  17. ^ Burki, F.; Roger, A.J.; Brown, M.W.; Simpson, A.G.B. (2020). "The new tree of eukaryotes". Trends in Ecology and Evolution. 35 (1): 43–55. doi:10.1016/j.tree.2019.08.008. PMID 31606140. S2CID 204545629.
  18. ^ el-Bawab, F. (2020). "Chapter 3 – Phylum Protozoa". Invertebrate Embryology and Reproduction. Academic Press. pp. 68–102. doi:10.1016/B978-0-12-814114-4.00003-5. S2CID 240900596.
  19. ^ a b Cavalier-Smith, T. (1981). "Eukaryote kingdoms: Seven or nine?". Biosystems. 14 (3–4): 461–481. doi:10.1016/0303-2647(81)90050-2. PMID 7337818.
  20. ^ Cavalier-Smith, Thomas (1983). "A 6-kingdom classification and a unified phylogeny". Endocytobiology II: 1027–1034.
  21. ^ a b Cavalier-Smith, Thomas (1987). "Eukaryotes with no mitochondria". Nature. 326 (6111): 332–333. Bibcode:1987Natur.326..332C. doi:10.1038/326332a0. PMID 3561476.
  22. ^ Roger, Andrew J. (1999). "Reconstructing Early Events in Eukaryotic Evolution". The American Naturalist. 154 (S4): S146–S163. doi:10.1086/303290. ISSN 0003-0147. PMID 10527924. S2CID 32138852.
  23. ^ Cavalier-Smith, T. (1993). "Kingdom protozoa and its 18 phyla". Microbiological Reviews. 57 (4): 953–994. doi:10.1128/mmbr.57.4.953-994.1993. PMC 372943. PMID 8302218.
  24. ^ Cavalier-Smith, T.; Chao, E.E. (1996). "Molecular phylogeny of the free-living archezoan Trepomonas agilis and the nature of the first eukaryote". Journal of Molecular Evolution. 43 (6): 551–562. Bibcode:1996JMolE..43..551C. doi:10.1007/BF02202103. PMID 8995052. S2CID 28992966.
  25. ^ Simpson, A.G.B.; Bernard, C.; Fenchel, T.; Patterson D.J. (1997). "The organisation of Mastigamoeba schizophrenia n. sp.: More evidence of ultrastructural idiosyncrasy and simplicity in pelobiont protists". European Journal of Protistology. 33: 87–98. doi:10.1016/S0932-4739(97)80024-7.
  26. ^ Cavalier-Smith, T. (2004). "Only six kingdoms of life". Proceedings of the Royal Society B: Biological Sciences. 271 (1545): 1251–62. doi:10.1098/rspb.2004.2705. PMC 1691724. PMID 15306349.
  27. ^ a b Cavalier-Smith, T. (2007). "A revised six-kingdom system of life". Biological Reviews. 73 (3): 203–266. doi:10.1111/j.1469-185X.1998.tb00030.x. PMID 9809012. S2CID 6557779.
  28. ^ Cavalier-Smith, T. (1983). "A 6-Klngdom Classification and a Unified Phylogeny". In Schenk, H.E.A.; Schwemmler, W.S. (eds.). A 6-kingdom classification and a unified phylogeny. Endocytobiology II: Intracellular Space as Oligogenetic. Berlin, DE: Walter de Gruyter & Co. pp. 1027–1034. doi:10.1515/9783110841237-104. ISBN 9783110841237.
  29. ^ Cavalier-Smith, Thomas (2003). "Protist phylogeny and the high-level classification of Protozoa". European Journal of Protistology. 39 (4): 338–348. doi:10.1078/0932-4739-00002.
  30. ^ Ruggiero, Michael A.; Gordon, Dennis P.; Orrell, Thomas M.; Bailly, Nicolas; Bourgoin, Thierry; Brusca, Richard C.; Cavalier-Smith, Thomas; Guiry, Michael D.; Kirk, Paul M.; Thuesen, Erik V. (2015). "A higher level classification of all living organisms". PLOS One. 10 (4): e0119248. Bibcode:2015PLoSO..1019248R. doi:10.1371/journal.pone.0119248. PMC 4418965. PMID 25923521.
  31. ^ Cavalier-Smith, Thomas (2006). "Rooting the tree of life by transition analyses". Biology Direct. 1: 19. doi:10.1186/1745-6150-1-19. PMC 1586193. PMID 16834776.
  32. ^ "Awards and distinctions". Cavali. Archived from the original on 23 July 2016. Retrieved 11 February 2016.
  33. ^ "Thomas Cavalier-Smith". Canadian Institute for Advanced Research. Retrieved 11 February 2016.

External linksEdit