Locality data

J.E. Shields jshields@indy.net
Wed, 31 Oct 2012 16:50:23 PDT

I apologize if I am unclear.  From these colorful discussions of "species" 
it seems clear that there is not at present a single unambiguous working 
definition for the concept.  I infer from this that the concept we are 
trying to define may in fact not exist as a single logical entity.

At 11:19 PM 10/31/2012 +0100, Christian wrote:
>Sir, I'm sorry but I don't understand your statement, although getting a
>vague idea of the global picture ("This leads me to feel that there is
>probably no such thing as a "species" but rather many ways of viewing the
>biological world.").
>You seem to disagree with the way living forms are categorized, and maybe
>are you correct if defining the tool for this categorization is an
>impossible challenge.
>But if there is no species, there must be another concept representing
>stable (yet evolving) forms of living beings.
>What would be your suggestion? Dynamic systems? How would categories be

I am at present inclined to see the cladistic view of phylogenetics as the 
most likely to reflect an historic past that we can never actually know in 
detail.   Cladistic analyses based on molecular genetics appeal to me for 
reasons previously stated.  Cladistics could in principle extend right down 
to the individual level.  It does not address what constitutes a "species" 
any more than it addresses the vexing questions of what are genera and what 
are families.  Cladistics does not appear to me to help us sort out what a 
species is.  It is however a tool that seems most useful at the present 
time in understanding phylogenetics.


You  as a morphologist are studying the physical structure of organisms, 
and this is your tool for investigating the relationships between different 
organisms.  It will give you answers that are  determined by the 
limitations of the kinds of data you utilize.  Morphology does not actually 
address genetic relatedness, as far as I can tell, although it was the 
traditional basis for all phylogenetics and, if I'm not mistaken, the sole 
basis until DNA sequencing was invented.

It seems to me that a significant limitation to morphology as a 
phylogenetic tool is the dependence it has on the interactions between the 
organisms' DNA and the various environmental conditions to which the 
organisms were exposed during development and growth.  You are filtering 
the primary data -- the DNA sequences -- through a prism of variable 
environmental conditions, in my view.  I'd be interested in your 
elaboration on this point.

Questions of structural convergence in response of similar evolutionary 
pressures seem to me to require molecular genetic analyses for 
clarification.  I am reminded of the phenomenon of "cryptic sibling 
species" in butterflies, but those were first uncovered by detailed 
morphological studies (of the male genitalia, as I recall), prompted by 
observed behavioral differences.  They still pose an epistemological question.

In any case, I think that the most useful work in plant systematics is 
including morphology along with molecular genetics at present.  I'm just 
not sure that condition will last.

At 11:51 PM 10/31/2012 +0100, Dietrich wrote:
>Hi Jim,
>I appreciate your enthusiasm about the fascinating topic and your
>apparent longing for a clear and fair discussion:
>  From my perspective as a morphologist I fully agree with the first half
>of your sentence: "the DNA sequence of the organism IS the organism ",
>but I disagree with your conclusion in the second half of your sentence:
>"so the DNA sequence perforce defines the species."
>Only the last word "species" is wrong in my opinion. It might be
>replaced by the "individual organism".
>Proposal of a proof by falsification: Every individual human has its own
>DNA sequence, but every individual human is certainly not a species of
>its own.
>Here I took your word "DNA sequence " literally, whereas you had in mind
>something like the "essential DNA sequence " of a species. How works
>your recipe to eliminate all the individual DNA sequence differences in
>order to distil the DNA sequence of a species?
>Do you understand my and your problem.
>  From your perspective as a biochemist, "Geography and morphology are 
> just approximations of the species."
>  From my perspective as a morphologist, the DNA sequence is just one 
> morphologic character (to a certain extent the most powerful one, if well 
> handled) to find out, how to circumscribe a species.
>There are different levels of morphologic characters: In botany we start 
>with the growth form and the variations of the three basal organs, at a 
>lower level we have anatomy. These levels can be called alpha-taxonomy.
>One level further down in size cytotaxonomy was the most modern taxonomy 
>for some decades.
>Again further down in size chemotaxonomy followed.
>Since about two decades molecular taxonomy is the most modern branch of 
>taxonomy, but good morphology always remains a healthy basis.

I think that a future definition(s) of "species" will attempt to 
circumscribe the "envelope" of DNA sequences that are encompassed by a 
given species.  This answer will probably be different for different 
species.  I think it will be very different for plants than for animals; 
and microbiologists seem to have already gone off on their on very separate 
track for defining populations rather than species.  Binomial nomenclature 
seems to be giving way to serial numbers that computers can more easily 
handle.  You don't draw pictures of phylogenetic trees, you calculate new 
ones using the latest data as you need them.  Today's tree won't look like 
yesterday's unless the databases were locked down overnight.

It's a really  exciting time to be alive.  A lot of my "feelings" are 
projections and extrapolations based on 60 or so years of observation of 
biological science.  I have been living through a true scientific 
revolution -- albeit purely as a spectator -- and I would not trade this 
experience for anything.

Jim Shields

Jim Shields             USDA Zone 5
P.O. Box 92              WWW:    http://www.shieldsgardens.com/
Westfield, Indiana 46074, USA
Lat. 40° 02.8' N, Long. 086° 06.6' W

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