[Taxacom] Taxacom Digest, Vol 185, Issue 14

[Brendon E. Boudinot]

Hello John!

I disagree. In tip-dating analyses, I set my fossil priors as the
evidence-based stratigraphic range for the given deposit or formation.
Using this range, we can account for patterns of variation for both
morphology and molecular data, given the estimated range of possible
relationships and clades ages. The priors have strong affect when there is
little information, such as at a root node. The main point is accounting
for uncertainty regarding the most recent or oldest possible age for a
fossil. Please explain, in this context, why that is a problem. I am here
today because of curiosity in general; likewise, I am responding now
because of specific curiosity. What alternatives should one make use of to
combine genotypic, phenotypic, and stratigraphic ranges for estimating a
possible set of relationships and ages?

Noncombatively,
Brendon

On Sat, 18 Sep 2021, 19:05 <taxacom-request at mailman.nhm.ku.edu> wrote:

> Daily News from the Taxacom Mailing List
>
> When responding to a message, please do not copy the entire digest into
> your reply.
> ____________________________________
>
>
> Today's Topics:
>
>    1. Re: Snake garbage (John Grehan)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 17 Sep 2021 16:25:36 -0400
> From: John Grehan <calabar.john at gmail.com>
> To: taxacom <taxacom at mailman.nhm.ku.edu>
> Subject: Re: [Taxacom] Snake garbage
> Message-ID:
>         <CADN0ud1-28JXFunp23V6=
> v4evN7orEypWnxjf04t+TGoES5bEQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> I wrote the original note in a bit of a hurry (should not do that) and
> quite justifiably got castigated off list for not making sense. So below a
> hopefully more coherent rant.
>
> This paper carries on the time honored scientific tradition of just
> ignoring shortcomings of a method and ploughing on as if the ground was not
> already falling away beneath. In this case the paper does this by
> representing priors as some kind of empirically real source of estimating
> fossil calibrated clade ages whereas it has been shown that fossil
> calibrated ages cannot be anything but a minimum ages. Priors are just
> personal guesses about how much older than the older fossil a taxon might
> be (dressed up in numbers to look scientific). These authors just ignore
> that. And they continue the temptation of using an automated biogeography
> program as 'evidence' despite its inherent inability to distinguish between
> vicariance and dispersal where either can generate the same biogeographic
> pattern. In other words, they use a plug and play program that can render
> artificial results and they have no way to know. But the authors carry on
> the pretense that this is not the case.
>
> Cheers, John
>
> On Fri, Sep 17, 2021 at 10:20 AM John Grehan <calabar.john at gmail.com>
> wrote:
>
> > "Evolution and dispersal of snakes across the Cretaceous-Paleogene mass
> > extinction" (https://www.nature.com/articles/s41467-021-25136-y.pdf )
> >
> > This paper carries on the time honored scientific tradition of just
> > ignoring shortcomings of a method and ploughing on as if the ground was
> not
> > already falling away beneath. In this case the representation or priors
> as
> > some kind of empirically real source of estimating fossil calibrated
> clade
> > ages as anything but a minimum ages, and the continued temptation of
> using
> > an automated biogeography program as 'evidence' despite its
> > inherent inability to distinguish between vicariance and dispersal where
> > either can generate the same biogeographic pattern. I have been attacked
> > for calling this stuff 'garbage' but I have not come up with a more
> > accurate term - yet.
> >
> > John Grehan
> >
>
>
> ------------------------------
>
> Subject: Digest Footer
>
> Taxacom Mailing List
>
> Send Taxacom mailing list submissions to taxacom at mailman.nhm.ku.edu
> For list information; to subscribe or unsubscribe, visit:
> http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> You can reach the person managing the list at:
> taxacom-owner at mailman.nhm.ku.edu
> The Taxacom email archive back to 1992 can be searched at:
> http://taxacom.markmail.org
>
> Nurturing nuance while assailing ambiguity for about 34 years, 1987-2021.
>
>
> ------------------------------
>
> End of Taxacom Digest, Vol 185, Issue 14
> ****************************************
>