[Taxacom] Taxacom Digest, Vol 185, Issue 14

[John Grehan]

Hi Brendon,

Great to have your comment and viewpoint. Taken in a non-combative spirit
as always. When you say you disagree, I presume you are disagreeing with my
assertion that priors are just guesses. At this point your description does
not help me see anything to the contrary. You say that you "set my fossil
priors as the evidence-based stratigraphic range for the given deposit or
formation." So what does that really mean?

I actually have no problem with anyone assigning priors on how much older
than the oldest fossil they think a taxon might be, or even making up
probabilities for that. The problem arises when these are transformed into
empirical limits that are supposed to falsify earlier origins predicted
from tectonic correlation (for example). Also, the means of the priors are
very often presented as actual ages so that taxa are said to have
originated at (or about) such and such a date (and precluding earlier
tectonically mediated origins).

I had one colleague note to me that one of the probability models (might be
long normal, not sure) did not set an upper limit on the possibilities, yet
in practice that is what most authors do when they say they refute earlier
origins predicted by tectonic correlation. I might have less of an issue if
priors were presented in the form of a probability that the oldest age, or
even the mean age, was AT LEAST such and such age. One might take the view
that prioris make Mesozoic origins for extant taxa, even species or genera,
very 'improbable', but that is not the same as impossible, and heck, there
are an awful lot of Mesozoic (not to mention Cenozoic) tectonic
correlations. To attribute that all to 'chance' coincidence (which would
seem to be the only explanation) is hardly productive. It's kind of like
saying that God only made all the evidence of Creation only look like
evolution occured.

Cheers, John



On Sun, Sep 19, 2021 at 11:51 AM Brendon E. Boudinot via Taxacom <
taxacom at mailman.nhm.ku.edu> wrote:

> 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
> > >
> >
> >
> > ------------------------------
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> > ------------------------------
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> > End of Taxacom Digest, Vol 185, Issue 14
> > ****************************************
> >
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