classifying life ("primitiveness")

[B. J. Tindall]

In reply to Ken:
Lot of food for thought - but:
I would suggest that the basis for placing thermophiles early in the
development/evolution of life comes from geological inferences. However,
this has been coupled to sequence data, and it is at this point where there
seem to be potential differences in what one reads. On the one hand
thermophiles are "ancient", on the other hand some of them do not show
great divergence at the 16S rDNA sequence similarity level, so they are
slowly evolving. In other cases "deeply rooting branches" are taken to be
ancient, while highly 16S rDNA sequence divergent taxa are variously either
"ancient" or "rapidly evolving". I confess I have problems here with
determining evolutionary rate without a reliable fossil record (for
prokaryotes). Again I can pull out of the hat a number of either ancient or
rapidly evolving genera which have since been fragmented into several
genera. Kind of makes me wonder, or is this just "molecular" progress?
Do I detect a dichotomy in your thinking. Firstly you state:
>Anyway, trying to couple geological age and rank of a taxon is
>obviously futile.  I'm tempted to discussing anagensis and the vast
>differences in molecular "clocks" in different taxa and at different times,
>but that is another "can of worms".
Which I won't agrue with, but then you state:
>Suffice it to say that I personally
>believe cyanobacteria generally have the slowest molecular clocks of any
>form of life still extant.
and I wonder how you conclude that, given my comments further up. Sorry,
this is just an open question, and yes I do see the case for autotrophs in
the early history of life, but I also see the case for thermophiles in the
thermophilic environments, and having worked with alkaliphiles for years I
also appreciate the theory that early seas may have been alkaline etc.
(lots of theory in all cases, no proof??). However, I base my
acceptance/rejection on the theory of the early Earth, not on the study of
modern day organisms (someone will try to strangle me for that comment!).
Just as a side line, the presence of bacteriochorophyll seems to be more
common in the Proteobacteria than the literature would indicate - I guess
genome analysis will also pick this up.

Your comment on cell membranes is interesting. Having spent a long time
doing chemotaxonomy I certainly see certain patterns, but I also see a
fantastic diversity, which standard reference works do not convey
correctly. The diversity is such that I have not been able to find one
single lipid which is common to all "prokaryotes". Of course this is also
reflected in the genetics of the organisms, but if you take a look at total
genome sequences you won't find much data on the genes simply because they
are probably located in the section allocated to "unknown function". It is
not hard to explain why either.

Oh well enogh for today - and a Happy Easter to all of you on Taxacom, and
especially to Ken who is so tolerant of me asking yet more questions.
Brian



********************************************************************
* Dr.B.J.Tindall      E-MAIL bti at dsmz.de                           *
* DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH *
* Mascheroder Weg 1b, D-38124 Braunschweig, Germany                *
* Tel.: ++ 531 2616 0 (general)                                    *
* Tel.: ++ 531 2616 224 (direct)                                   *
* Fax:  ++ 531 2616 418                                            *
* Fax:  ++ 531 2616 491 (ISDN)                                     *
*                                                                  *
* Homepage: http://www.dsmz.de/index.html                          *
* E-MAIL: help at dsmz.de (general enquiries)                         *
*         sales at dsmz.de (sales)                                    *
********************************************************************