Re: Article: Is the Term 'Prokaryote' Obsolete?

On Thu, 1 Jun 2006 01:10:40 -0400 (EDT),
DK <dk@xxxxxxxxxxxxxxxxxxxxxxxxx> wrote:
In article <e5kkbl$1215$1@xxxxxxxxxxxxxxxxxxx>,
"Robert Karl Stonjek" <rstonjek@xxxxxxxxxxxxxx> wrote:
Is the Term 'Prokaryote' Obsolete?

No, it is not. There is still a useful distinction to be made between
organisms that have nucleus and those that don't.

The following points are made by Norman R. Pace (Nature 2006 441:289):

..
4) The lessons of the three-domains tree are profound. Instead of two kinds
of organism, prokaryotes and eukaryotes, there are three: bacteria, eukarya
(eukaryotes) and archaea. The root, or origin, of this universal tree,
cannot be determined from ribosomal RNA sequences, but other phylogenetic
results and biochemical correlates show that the genetic lines of eukarya
and archaea have a common ancestral branch that is independent of that
giving rise to the bacteria. That is, eukaryotes and archaea are more
closely related to one another than either is to bacteria. [1-3]

Why would anyone want to proclaim this in 2006? This was pretty obvious
and almost universally accepted ~ 20 years ago.

The reason why Norm Pace has to proclaim this in 2006 is because his ideas
are losing ground. More and more people are questioning the Three Domain
Hypothesis. Most people who study molecular evolution now recognize that
there are many flaws with RNA trees and they know that it's wrong to
place all your eggs in that basket.

In spite of what Pace says in the above paragraph, there's a huge amount of
data showing eukaryotes and "bacteria" are more closely related to each other
than either is to archaebacteria.

The controversy has even attracted the attention of philosophers ...

Lyons, S.L. (2002) Thomas Kuhn is alive and well: the evolutionary
relationships of simple life form--a paradigm under siege ?
Perspect. Biol. Med. 45(3):359-76

A Kuhnian framework is used to analyze the current controversy
over whether two or three fundamental types of life forms exist.
Until the 1980s, all life was classified into two primary forms:
eukaryotes and prokaryotes. Using molecular sequencing data, Carl
Woese suggested the archaebacteria constituted a third domain. In
the mid-1990s, Radhey S. Gupta challenged the three-domain
hypothesis. While this dispute may seem to be a purely technical
debate over the analysis of protein and nucleic acid sequence data,
the controversy encompasses broader issues such as the aims of
classification and the role of microorganisms in the biosphere. At
the heart of this dispute is what kinds of data are relevant to
constructing an overall taxonomy. The prestige of molecular biology
played a large role in why the three-domain hypothesis was accepted
so readily, but supporters of the two-domain hypothesis argue that
the fossil record, morphology, and cell physiology should all play
a role in taxonomy. This case study provides a good example of a
paradigm shift in the making, demonstrating that issues beyond the
raw data will be significant factors in deciding whether the three-
domain hypothesis will prevail or a new classificatory scheme will
emerge.

You know you're in trouble when the philosophers get involved.




Larry Moran

(Cue Wilkins lecture on the abuses of Kuhn and "paradigm.")

.

Relevant Pages

  • Re: Article: Is the Term Prokaryote Obsolete?
    ... organisms that have nucleus and those that don't. ... of organism, prokaryotes and eukaryotes, there are three: ... and archaea have a common ancestral branch that is independent of that ... giving rise to the bacteria. ...
    (sci.bio.evolution)
  • Re: Article: Is the Term Prokaryote Obsolete?
    ... organisms that have nucleus and those that don't. ... of organism, prokaryotes and eukaryotes, there are three: ... and archaea have a common ancestral branch that is independent of that ... giving rise to the bacteria. ...
    (sci.bio.evolution)
  • Re: Incredible evolution
    ... known as eukaryotes, right on up to humans, Shen notes." ... at the extant organisms that have been in competition for living space ... of DNA in multiple packets called chromosomes. ... You can look up the Histone ...
    (talk.origins)
  • Re: Incredible evolution
    ... known as eukaryotes, right on up to humans, Shen notes." ... do not even use host repair genomic repair systems, ... at the extant organisms that have been in competition for living space ... They seem to be talking about conservation among eukaryotes for ...
    (talk.origins)
  • Re: Goodness is not an euphemism
    ... >> No scientist says that humans are descended from bacteria. ... that as descent from the urkaryote, ... neomura (archaea+eukaryotes) and eukaryotes as successively ... Adl et al, The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists, J. Eukaryot. ...
    (talk.origins)
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