[Taxacom] New systematics book

[Richard Zander]

Mike:

I detailed two fatal flaws in phylogenetics, two calamitous
clarifications of cladistics. You replied with a slogan, an assertion
that "we" know all about my arguments, and can deal operationally quite
fine with any problems. Operationally meaning, I suppose, purify the
data from anything reflecting nonpseudoextinction, run it through the
sister-group software, and change classifications based on the
sister-group result. 

Can anyone on Taxacom address my two attributions of error in
phylogenetics? Directly? Without regressing into nostalgia?

Philosopher of science Lakatos, in his Research Program, averred that
rarely must any scientist defend the fundamentals on which his or her
research project is based. That "rarely" is now.

____________________________
Richard H. Zander
Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA  
Web sites: http://www.mobot.org/plantscience/resbot/ and
http://www.mobot.org/plantscience/bfna/bfnamenu.htm
Modern Evolutionary Systematics Web site:
http://www.mobot.org/plantscience/resbot/21EvSy.htm
UPS and FedExpr -  MBG, 4344 Shaw Blvd, St. Louis 63110 USA

-----Original Message-----
From: Michael A. Ivie [mailto:mivie at montana.edu] 
Sent: Thursday, September 05, 2013 6:33 PM
To: Richard Zander
Cc: mivie at montana.edu; Ken Kinman; taxacom at mailman.nhm.ku.edu
Subject: RE: [Taxacom] New systematics book


Hmmm, these arguments seem to me to be reminiscent of the logic
(certainly not the specifics) of the Intelligent Design refutation of
Evolution, in that the problems that supposedly negate Evolution are
actually not problems to those who understand Evolution.

I am a "regular taxonomist" certainly not a Big Science theoretician,
and I don't see your issues as anything that we didn't know about all
along, and can deal with operationally quite fine without regressing
into nostalgia.

Mike
>
> Expected comment, Mike. I got a review of a paper once that said "we 
> solved all these problems back in the 1980's." Really? The 1980's were

> when regular taxonomists gave up and stuck their heads in the sand. 
> The cladists took over with their version of Big Science.
>
> It has taken this long to work out that parsimony and other optimality

> analyses only work with accuracy with pseudoextinction (dying 
> ancestor, two new species). The correct optimality for branching 
> analysis is that which makes the shortest (most likely, most credible)

> tree given identified surviving ancestors and their daughter taxa 
> based on other information. This is merely, MERELY less precise, 
> correctly less precise and therefore with more uncertainty about
evolutionary relationships.
>
> It has taken this long to work out that molecular "lineages" are 
> molecular strains, and ancestral taxa in stasis generate lots of 
> molecular strains before and after generation of one or more daughter 
> species. The DNA continues to mutate in isolation while expressed 
> traits remain in stasis for millions of years. Molecular phylogenetics

> gives precise sister group analyses of extant strains, not taxa.
Evidence?
> Molecular paraphyly. What about extinct or unsampled strains? They 
> could have diverged molecularly long before or after any extant 
> strain. Oh, oh.
>
> My stance is that the alternative to cladism must be addressed now, 
> even if you see it as 1980's stuff that you and your cladist fellows
"solved"
> way back in the day.
>
>
> ____________________________
> Richard H. Zander
> Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USA 
> Web sites: http://www.mobot.org/plantscience/resbot/ and 
> http://www.mobot.org/plantscience/bfna/bfnamenu.htm
> Modern Evolutionary Systematics Web site:
> http://www.mobot.org/plantscience/resbot/21EvSy.htm
> UPS and FedExpr -  MBG, 4344 Shaw Blvd, St. Louis 63110 USA
>
>
> -----Original Message-----
> From: Michael A. Ivie [mailto:mivie at montana.edu]
> Sent: Thursday, September 05, 2013 5:34 PM
> To: Richard Zander
> Cc: Ken Kinman; taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] New systematics book
>
>
>
> Wow, it this had not just come in on a communication system not 
> invented then, I would  think I was reading something from 1976!  Is 
> this a 1980's theme party?
>
> Mike