[Taxacom] [iczn-list] GENERAL CALL TO BATTLE

Mon Feb 15 17:12:32 CST 2021

Thanks, Stephen.  But you didn’t answer my questions.  I’ll repeat them here:

Do you object to taxa based only on DNA characters because the idea is fundamentally flawed (i.e., it will never be justifiable)?  Or, like me, do you object to it simply because we do not *yet* understand DNA characters well enough to use them to infer/define taxa in a way that is consistent with how taxa have been defined for the past couple of centuries?  If the former, then can you give me examples of morphological characters useful to inferring/defining taxa that are not controlled by information stored in the DNA?

Or better yet, maybe you could indicate which of the following 5 perspectives most represents your own:

1.	DNA characters are fundamentally flawed. DNA evidence is not (and never will be) legitimate as the only basis for inferring/defining taxa because it doesn’t contain the same information that morphology does and/or fails to accurately reflect what the essence of “taxa” should be.

2.	DNA characters are limited because they are hard to access. DNA evidence may be useful as the only basis for inferring/defining taxa, but it’s only useful to people who have access to sequencing technology, and therefore should be avoided as the only type of character to base taxa on.

3.	DNA characters are limited because we don’t yet know how to interpret them. DNA evidence may be useful as the only basis for inferring/defining taxa, but even with access to sequencing technology we don’t really understand it well enough (yet) to infer/define taxa in ways that are consistent with the long history of morphologically-based taxa, and we shouldn’t rely on it entirely until we can ensure continuity of general taxonomic practice.

4.	We should prepare for a new way of defining/inferring taxa. Because DNA evidence has the potential to be extremely useful as the only basis for inferring/defining taxa once we understand it a bit better, we should start transitioning to a new way of inferring/defining taxa now and facilitate this transition to happen gracefully.

5.	We should embrace a new way of defining/inferring taxa *now*. We already understand DNA evidence well enough, and we should embrace a new way of inferring/defining taxa now, even if it is disharmonious with the “old ways” of inferring/defining taxa based on morphological characters.

Or feel free to define a new one that represents your perspective.  I invite John (and anyone else) to do the same.

Aloha,
Rich

Richard L. Pyle, PhD
Senior Curator of Ichthyology | Director of XCoRE

Bernice Pauahi Bishop Museum

1525 Bernice Street, Honolulu, HI 96817-2704

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From: Stephen Thorpe <stephen_thorpe at yahoo.co.nz> 
Sent: Monday, February 15, 2021 9:54 AM
To: Richard Pyle <deepreef at bishopmuseum.org>; John Grehan <calabar.john at gmail.com>
Cc: iczn-list at afriherp.org; Taxacom <taxacom at mailman.nhm.ku.edu>
Subject: Re: [Taxacom] [iczn-list] GENERAL CALL TO BATTLE

Rich,

James may have proposed a putative answer to my comment, but that doesn't mean my view was an "error", not yet anyway. I still maintain (to answer your question) that DNA sequencing isn't taxonomy, but may however have a secondary support role for taxonomy. Taxonomy is not simply about attaching names to species via type specimens. That is nomenclature. Taxonomy is about circumscribing species. There is an obvious (imperfect, but nevertheless obvious) correlation between morphology and species (=more or less: groups of individuals who freely interbreed and have the same basic interactions with other species and the abiotic environment). If all individuals of all species looked the same, then taxonomy would be pointless. The whole point of taxonomy is to be able to infer interactions from morphology. Sometimes there are problem cases that may benefit from DNA sequencing in a supporting role. However, if you define species by DNA sequence, you provide no link between morphology and interactions. You simply leave the hard work for someone else down the track to try to find that link, putting many potential hurdles in their way, such as the difficulty in obtaining usable DNA for many rare or inaccessible species.

I am not convinced that simply claiming that this or that base in a sequence can vary within the same species ("consensus sequences"), based on a limited sample, amounts to a meaningful circumscription of the species. How do they (a hypothetical "they") know the different sequences are the same species?? Because they are judging by morphology! They are just not sharing with the reader the details of this all important morphology! They are withholding these details because they cannot be bothered taking the time to present them! Instead they just churn out the sequences ... thanks, but no thanks!

Cheers, Stephen

On Tuesday, 16 February 2021, 08:25:20 am NZDT, John Grehan via Taxacom <taxacom at mailman.nhm.ku.edu <mailto:taxacom at mailman.nhm.ku.edu> > wrote: 

Some misplaced 'humor' - Is it a cat or a dog I have as a pet? Looks like a
cat, but I can't trust that. It could be a cryptic elephant. Wait.... I'll
just get my DNA tricorder and we will know for sure (and which pet food to
buy).

cheers, John Grehan

>
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