[Taxacom] New paper: Ruggiero et al. "A Higher Level Classification of All Living Organisms"

Fri Jul 10 19:52:03 CDT 2015

Hi John,

I think you would need to read the full paper (not just the two lines of text I quoted from the abstract) before you could make an assessment as to whether or not their work fits within your own personal definition of “science”.  Considerably more investigation would be required before you could confidently infer whether or not the work falls within the authors’ own personal definitions of “science”.

Aloha,

Rich

From: John Grehan [mailto:calabar.john at gmail.com] 
Sent: Friday, July 10, 2015 1:00 PM
To: Richard Pyle; taxacom
Subject: Re: [Taxacom] New paper: Ruggiero et al. "A Higher Level Classification of All Living Organisms"

Yes I was implying (explicitly) that the authors of the paper appear to have a definition of science (assuming that the classification was being represented as science) where science is a 'consensus' of opinion compromising conflicting information. When one comes up with a compromise of the sort it does not appear to be a process that is attempting to reflect reality (whatever that might be), but just a compromise between different opinions. A good example of this is how so-called ecological areas were defined in New Zealand (Under the Protected Natural Areas program, and with lots of money to boot) according to compromises over different opinions about where the boundaries between the areas were to be drawn (said boundaries having no reality anyway, hence the ability to 'compromise').

Perhaps I am being awfully presumptuous, but if it is presumptuous to regard consensus opinions as outside science then so be it.

John Grehan

On Fri, Jul 10, 2015 at 4:06 PM, Richard Pyle <deepreef at bishopmuseum.org> wrote:

The “nature of reality” is sufficiently vague that it could be interpreted just as broadly as “science” can be.

My only point is that the outer boundaries of “science” are not well defined.  Controlled experimentation following the scientific method is squarely within the realm of science, and most would argue that things like Astrology are pretty clearly at the very outskirts.  In between those is a very broad range of activities, such as phylogenetics, taxonomy, nomenclature, informatics, and a whole host of other things that may or may not conform to some particular person’s definition of “science”.

Your comment, to which I was responding, seemed to imply that we all (including the authors of the paper) share a definition of science that would unambiguously exclude their paper from “science” (i.e., the notion that the authors self-evidently “admit” that their work is not science).  That seemed awfully presumptuous of you.

Aloha,

Rich

From: John Grehan [mailto:calabar.john at gmail.com] 
Sent: Friday, July 10, 2015 9:52 AM
To: Richard Pyle

Subject: Re: [Taxacom] New paper: Ruggiero et al. "A Higher Level Classification of All Living Organisms"

Perhaps, but what do you think is incorrect about the one I gave? Are you saying consensus opinion is science?

John Grehan

On Fri, Jul 10, 2015 at 3:30 PM, Richard Pyle <deepreef at bishopmuseum.org> wrote:

We all like to believe our own definition of “science” is the correct one.

Sigh….

Rich

From: John Grehan [mailto:calabar.john at gmail.com] 
Sent: Friday, July 10, 2015 9:23 AM
To: Richard Pyle
Cc: TAXACOM

Subject: Re: [Taxacom] New paper: Ruggiero et al. "A Higher Level Classification of All Living Organisms"

At least the quotes show that the authors admit their work not be science (if science is understood to be about the nature of reality beyond 'consensus' opinion).

John Grehan

On Fri, Jul 10, 2015 at 3:07 PM, Richard Pyle <deepreef at bishopmuseum.org> wrote:

Hmmm....  I've been deliberately quiet on this thread as well.  I appreciate the viewpoints of Ken and others in terms of holophyly, the value of acknowledging paraphyletic taxa through Linnean nomenclature, etc.  This is all good philosophical grit, and I enjoy the intellectual stimulation as much as anyone.

However, this thread began (and remains?) relevant to the PLoS ONE publication of Ruggiero et al., which provides a generalized **CONSENSUS CLASSIFICATION**.  Perhaps there is some misunderstanding on what is meant by this term (and the associated classification)?  Anyone who read as far as the abstract of this paper should at least know that:

"This classification is neither phylogenetic nor evolutionary but instead represents a consensus view that accommodates taxonomic choices and practical compromises among diverse expert opinions, public usages, and conflicting evidence about the boundaries between taxa and the ranks of major taxa, including kingdoms."

And:

"Beyond its immediate use as a management tool for the CoL and ITIS (Integrated Taxonomic Information System), it is immediately valuable as a reference for taxonomic and biodiversity research, as a tool for societal communication, and as a classificatory “backbone” for biodiversity databases, museum collections, libraries, and textbooks."

In this context, it is ABSOLUTELY CORRECT that the subtaxa within a taxon are alphabetically arranged!  It is absolutely NOT intended to reflect any sort of "naturalness" in patterns of evolution.  Yes, it probably does kinda- sorta- happen to reflect modern views of evolutionary relationships (otherwise there wouldn't be much consensus behind it).  But its function is to serve as a tool for informatics and generalized (i.e., highly simplified) organizational representation of life on Earth.  As such, it is overwhelmingly valuable to the people for whom it was intended (see second quote above).

Aloha,
Rich

> -----Original Message-----
> From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf
> Of Richard Zander
> Sent: Friday, July 10, 2015 7:51 AM
> To: TAXACOM
> Subject: Re: [Taxacom] New paper: Ruggiero et al. "A Higher Level
> Classification of All Living Organisms"
>
> Maybe now is the time to add my perspective, backing up that of Ken.
>
> Phylogenetic classification is artificial. Artificial classifications use one set of
> traits to group taxa, e.g., molecular races, shared traits (only). Artificial
> classifications are repeatable, yet repeatability is not the only requirement of
> science. Alphabetization is repeatable.
>
> Principles of phylogenetic classification are artificial. Some principles include
> strict monophyly (so long Aves), putting known taxa at the top of a tree of
> relationships ("tree-thinking") rather than in the tree when known (stem-
> thinking), ignoring the probability of extinct paraphyly that casts doubt on
> molecular trees, ignoring the evolutionary importance of autapomorphies,
> asserting that only zero length branches imply a surviving ancestral taxon,
> pretending that a cladogram is "the evidence" (when it is only some
> evidence) and evolutionary theory is mere narrative . . . you can probably
> think of more phylogenetic principles of classification that do violence to
> evolutionary theory developed only after long struggle with artificial
> classifiers of the past.
>
> Classification by phylogenetic principles is actually quite unprincipled, and
> serves only to preserve a modification of older methods of numerical
> taxonomy.
>
> Richard
>
>
> -------
> Richard H. Zander
> Missouri Botanical Garden – 4344 Shaw Blvd. – St. Louis – Missouri – 63110 –
> USA richard.zander at mobot.org Web sites:
> http://www.mobot.org/plantscience/bfna/bfnamenu.htm and
> http://www.mobot.org/plantscience/resbot/
>
>
> -----Original Message-----
> From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf
> Of Nico Franz
> Sent: Friday, July 10, 2015 12:16 PM
> To: TAXACOM
> Subject: Re: [Taxacom] New paper: Ruggiero et al. "A Higher Level
> Classification of All Living Organisms"
>
> Computational logic? Nico
>
> Reasoning over taxonomic change:
> http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118247
> Taxonomy - for computers:
> http://biorxiv.org/content/early/2015/07/09/022145
>
> -----
> Date: Thu, 9 Jul 2015
> From: Kenneth Kinman
>
> Hi Stephen,
>        Logically, we must remember that [...]
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Celebrating 28 years of Taxacom in 2015.