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

Wed Dec 20 13:43:46 CST 2017

If Monera/Prokaryota is paraphyletic then it means that some members of the
group are more closely related to another group than to each other. In
which case Monera/Prokaryota is not a natural group phylogenetically. It
could be said to be a 'natural' grouping of primitive characters I suppose
(this is just my observation in general, not a judgement about the actual
validity of this taxon for which I not read the systematic literature).

John Grehan

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On Wed, Dec 20, 2017 at 2:04 PM, Kenneth Kinman <kinman at hotmail.com> wrote:

> 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?ijkey=
> 0063a0329305db671f86ee684020b2ee3d6a883f&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?ijkey=
> 0063a0329305db671f86ee684020b2ee3d6a883f&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?ijkey=
> 0063a0329305db671f86ee684020b2ee3d6a883f&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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