[Taxacom] Mayr vs. Woese debate over Metabacteria/Archaebacteria (as a third Empire/Domain?)

Wed Dec 20 13:04:54 CST 2017

Dear all,

       In their 1977 paper, Woese and Fox actually say that "Table 1 shows the three urkingdoms to be equidistant from one another."  It was Hori, Itoh and Isawa who showed a few years later that the Three Urkingdom concept was wrong, and they said Metabacteria was a more appropriate name for Archaebacteria. Now that is what I would call a great contribution. Others (such Lake, and also Gogarten) also showed that Archaebacteria and Eukaryota were more closely related to one another.

       It wasn't until 1990 that Woese finally conceded his three Urkingdoms were not equidistant, and he simply morphed them into Three Domains (Bacteria, Archaea, and Eukarya).  So let's give those other workers their due credit for their great contributions showing Woese's Three Urkingdom concept was erroneous and that Archaebacteria (a.k.a. Metabacteria) and Eukaryota are closely related.

                  --------------Ken Kinman

P.S.  Monera or Prokaryota do form a natural group.  It's only called unnatural by those who claim that paraphyletic taxa are unnatural.

________________________________
From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> on behalf of Dilrukshan Wijesinghe <dpwijesinghe at yahoo.com>
Sent: Wednesday, December 20, 2017 5:41 AM
To: taxacom
Subject: Re: [Taxacom] Mayr vs. Woese debate over Metabacteria/Archaebacteria (as a third Empire/Domain?)

As anyone who has taken (or taught!) general biology within the last 2-3 decades knows Carl Woese's great contribution was the discovery that prokaryotes ("Bacteria" as then conceived, or "Monera") do not form a natural group and that the Archaea and Eukarya form sister lineages more closely related to each other than either is to true Bacteria. A substantial body of works exists that corroborates the hypothesis regarding the close relationship between the Archaea and Eukarya. Recent work has revealed the diversity within the "Archaea" itself and has led to the idea that a group "Archaea" distinct from Eukarya may not be monophyletic, since some archaean lineages (e.g. Lokiarchaeota) may share a more recent ancestry with Eukarya. See for example the following:
Spang, A., Saw, J.H., Jørgensen, S.L., Zaremba-Niedzwiedzka, K., Martijn, J., Lind, A.E., van Eijk, R., Schleper, C., Guy, L. & Ettema, T.J.G. 2015. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521(7551; 14 May 2015): 173–179. doi:10.1038/nature14447.

Priyantha
D. P. Wijesinghe
dpwijesinghe at yahoo.com

    On Tuesday, December 19, 2017, 9:15:31 PM EST, Kenneth Kinman <kinman at hotmail.com> wrote:

 Dear All,

      I was just reading a 2009 paper by Cavalier-Smith (Deep Phylogeny, ancestral groups and the four ages of life).  In the abstract he says"
The tree of life is a useful metaphor for organismal genealogical history provided we recognize that branches sometimes fuse. Hennigian cladistics emphasizes only lineage splitting, ignoring most other major phylogenetic processes. Though methodologically useful it has been conceptually confusing and harmed taxonomy, especially in mistakenly opposing ancestral (paraphyletic) taxa."

      Later in the paper, he criticizes the Three Domain classification in particular, saying: "As I have shown (Cavalier-Smith 2002a<http://rstb.royalsocietypublishing.org/content/365/1537/111#ref-20>, 2006a<http://rstb.royalsocietypublishing.org/content/365/1537/111#ref-24>,c<http://rstb.royalsocietypublishing.org/content/365/1537/111#ref-26>), ignoring organismal structure, cell biology and palaeontology led to a now widespread fundamental misinterpretation of the history of life, the three-domain system, in which it is incorrectly assumed that eubacteria are holophyletic and not substantially older than archaebacteria and eukaryotes and that the tree is rooted between neomura and eubacteria (Woese et al. 1990<http://rstb.royalsocietypublishing.org/content/365/1537/111#ref-119>). These serious errors stemmed not only from failing to integrate sequence evidence with other data, but also from unawareness of the often extremely non-clock-like nature of sequence evolution and of grossly misleading systematic errors in sequence trees for molecules that do not evolve according to naive statistical preconceptions (see Cavalier-Smith 2002a<http://rstb.royalsocietypublishing.org/content/365/1537/111#ref-20>, 2006a<http://rstb.royalsocietypublishing.org/content/365/1537/111#ref-24>,c<http://rstb.royalsocietypublishing.org/content/365/1537/111#ref-26>). "
[http://rstb.royalsocietypublishing.org/sites/default/files/highwire/royptb/365/1537.cover.gif]<http://rstb.royalsocietypublishing.org/content/365/1537/111#ref-119>

Deep phylogeny, ancestral groups and the four ages of life ...<http://rstb.royalsocietypublishing.org/content/365/1537/111#ref-119>
rstb.royalsocietypublishing.org
Organismal phylogeny depends on cell division, stasis, mutational divergence, cell mergers (by sex or symbiogenesis), lateral gene transfer and death. The tree of ...

[http://rstb.royalsocietypublishing.org/sites/default/files/highwire/royptb/365/1537.cover.gif]<http://rstb.royalsocietypublishing.org/content/365/1537/111#ref-20>

Deep phylogeny, ancestral groups and the four ages of life ...<http://rstb.royalsocietypublishing.org/content/365/1537/111#ref-20>
rstb.royalsocietypublishing.org
Organismal phylogeny depends on cell division, stasis, mutational divergence, cell mergers (by sex or symbiogenesis), lateral gene transfer and death. The tree of ...

[http://rstb.royalsocietypublishing.org/sites/default/files/highwire/royptb/365/1537.cover.gif]<http://rstb.royalsocietypublishing.org/content/365/1537/111#ref-20>

Deep phylogeny, ancestral groups and the four ages of life ...<http://rstb.royalsocietypublishing.org/content/365/1537/111#ref-20>
rstb.royalsocietypublishing.org
Organismal phylogeny depends on cell division, stasis, mutational divergence, cell mergers (by sex or symbiogenesis), lateral gene transfer and death. The tree of ...

http://rstb.royalsocietypublishing.org/content/365/1537/111#sec-8 )
[http://rstb.royalsocietypublishing.org/sites/default/files/highwire/royptb/365/1537.cover.gif]<http://rstb.royalsocietypublishing.org/content/365/1537/111#sec-8>

Deep phylogeny, ancestral groups and the four ages of life ...<http://rstb.royalsocietypublishing.org/content/365/1537/111#sec-8>
rstb.royalsocietypublishing.org
Organismal phylogeny depends on cell division, stasis, mutational divergence, cell mergers (by sex or symbiogenesis), lateral gene transfer and death. The tree of ...

________________________________
From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> on behalf of Kenneth Kinman <kinman at hotmail.com>
Sent: Friday, December 15, 2017 9:32 PM
To: taxacom
Subject: [Taxacom] Mayr vs. Woese debate over Metabacteria/Archaebacteria (as a third Empire/Domain?)

Dear All,

      (1)  In his paper entitled "Two empires or three?", Ernst Mayr seems to have correctly assessed the inadvisability of a Three Domain/Empire classification, probably best summarized by this paragraph:

      "Woese baptized the newly discovered organisms archaebacteria, thinking they would have been the first organisms on the newly habitable earth because of their ability to live in an anoxic atmosphere and in hot springs, sulfur springs (thermo-acidophiles), brines (halophiles), and other unusual habitats, presumably common on the new earth. However, when it later appeared probable that they were not the most ancient bacteria and might have a common stem with the eubacteria, Osawa and Hori (7<http://www.pnas.org/content/95/17/9720.full?ijkey63a0329305db671f86ee684020b2ee3d6a883f&keytype2=tf_ipsecsha#ref-7>) suggested replacing the misleading name archaebacteria by metabacteria. Neither Woese (8<http://www.pnas.org/content/95/17/9720.full?ijkey63a0329305db671f86ee684020b2ee3d6a883f&keytype2=tf_ipsecsha#ref-8>) nor other microbiologists accepted this change of name. Instead Woese renamed them Archaea, retaining the inappropriate component—archae—and discarding the informative component—bacteria, which revealed their prokaryote nature."

      (2) In his response to this, Woese concluded: "The prokaryote–eukaryote dichotomy. This dichotomy, which Dr. Mayr proposes to reinstitute, is a failed taxonomic theory that was never recognized as theory, and so tested in a timely fashion, with the consequence that it has adversely affected the development of biology, especially microbiology, in the latter half of this century."

      (3) It seems to me (and others) that it was actually the Three Domains (an unfortunate, warmed over version of Woese's discredited Three Urkingdoms which he proposed 13 years earlier), both of which turned out to be simplistic and being what actually "adversely affected the development" of microbiology in the latter half of the 20th Century.  Cavalier-Smith on the other hand admits his occasional mistakes, incorporates new information, and moves on. The importance of Archaebacteria (a.k.a. Metabacteria) is actually their close relationship to Eukaryota, and is far too young to have anything to do with the origins of life.  The still unanswered question is whether Archaebacteria (a.k.a. Metabacteria) is the sister group of Empire Eukaryota (as Cavalier-Smith believes), or if the sister group of Eukaryota is actually a particular subgroup within Archaebacteria (different subgroups being suggested by different researchers as the sister group).

<http://www.pnas.org/content/95/17/9720.full?ijkey63a0329305db671f86ee684020b2ee3d6a883f&keytype2=tf_ipsecsha>http://www.pnas.org/content/95/17/9720.full

http://www.pnas.org/content/95/19/11043.full
Default taxonomy: Ernst Mayr’s view of the microbial world<http://www.pnas.org/content/95/19/11043.full>
www.pnas.org
National Academy of Sciences

Default taxonomy: Ernst Mayr’s view of the microbial world<http://www.pnas.org/content/95/19/11043.full>
www.pnas.org<http://www.pnas.org>
Proceedings of the National Academy of Sciences<http://www.pnas.org/>
www.pnas.org
Multidisciplinary journal covering the biological, physical, and social sciences. Published biweekly. Archives go back to January 1996. Subscription required for full ...

National Academy of Sciences

                ----------------Ken Kinman

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