classifying life ("primitiveness")

[Ken Kinman]

Brian,
     Not much time, so this will have to be relatively  brief (which will be
a relief to some, as I admittedly do rant on too long sometimes).
     For anyone who has not yet done so, I recommend reading the 1995 paper
by Stanley Miller and Antonio Lazcano ("The Origin of Life---Did It Occur at
High Temperatures?") in the Journal of Molecular Evolution (Vol.
41:689-692).  I don't agree with everything they say, but they certainly get
across the point about how little we really know about the conditions on
Earth when life originated.  I think it is entirely plausible that the Earth
could have been a patchwork of large cold areas broken up by hot areas, with
clines of mesophilic areas in between.  We just don't know, although
eventually we probably will find evidence that narrows the possibilities.
     As for inferring thermophilic or non-thermophilic origins from sequence
data, I suspect we are still at the "toddler" stage on that front.  I think
Woese has convinced many (including himself) that we are a lot further along
than we really are, and the extent to which circular reasoning is affecting
our theories at present will probably amaze us a decade or two down the
road.  Therefore I try not to get too attached to any particular line of
evidence or pattern of reasoning.
     But the totality of the present evidence convinces me that it took
"life" up to a billion years to evolve the ability to cope with thermophilic
environments.  And although Woese's contributions were very important back
in the 1970's, I believe his undue influence in the 80's and 90's (while
many good ideas by others have been relatively ignored) has probably done a
lot more harm than good (in a number of different ways).  But science won't
be able to evaluate that any time soon.  In the meantime, I advise a very
skeptical attitude when it comes to today's prokaryotic trees.  I predict
that correctly rooted trees of the future will not have thermophiles (like
Aquifex, Thermotoga, or the Metabacteria-"Archaebacteria") anywhere near the
base.  But only time will tell.
                  Happy Holiday weekend, Ken Kinman
*********************************************************
>From: "B. J. Tindall" <bti at DSMZ.DE>
>Reply-To: "B. J. Tindall" <bti at DSMZ.DE>
>To: TAXACOM at USOBI.ORG
>Subject: Re: classifying life ("primitiveness")
>Date: Thu, 20 Apr 2000 10:34:53 +0200
>
>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)                                    *
>*******************************************************
______________________________________________________
Get Your Private, Free Email at http://www.hotmail.com