[Taxacom] Molecular dates are NOT necessarily minimums

[John Grehan]

Rob, I don't understand how the statement  "As discussed,
fossil-calibrated, molecular clock dates for clades can only ever be
minimums." is 'self serving, and even if it were, it is still a valid
statement.

When you note that “Current Bayesian molecular dating software gives a
probability distribution of dates. How can a distribution of dates (a
range) be a minimum?” one migh tjust as well ask how can one empirically
generate a range (which implies a maximum as well as a minimum)? It seems
that such ranges are just arbitrary guesses (I have yet to see anything to
support the contrary).

Rob – interesting comments, but my understanding is that Heads does not
take the oldest date from a published range and transmogrifies that into
minimum. He only points out that the 'oldest' date cannot be generated from
fossil-calibrated estimates that are only minimums. So the 'only ever
minimum' is not an argument – it is about as basic a truth that one can get
to in this life. It also does not ignore other sources of error in
molecular calculations at all.

Regarding other sources of error – none of these contradict the fact that
fossil-calibrated estimates are minimums. The incorrect attribution of
fossils to exant lineages and the problem of correct dating has been
discussed by Heads. It is a real problem when clades are defined purely on
molecular grounds, and especially where fossil morphology may contradict
molecular clades (as with fossil hominids).

Need to explain how “Heads transmogrifies an age of millions of years into
a so called minimum'” Not obvious to me what you are syaing.

“ I do mind the slogan that they are necessarily minimum. That is
sophistry.” Need to explain how. Actually it is only fossil-calibrated
esimtes that are minimums. Efforts by some molecular researchers calibrate
by tectonic features which generates an estimate of an actual date.

“Using the current generation of software, it is possible to explore the
effect of using different priors.” Problem here is that the priors are all
arbitrary.

“Heads...could make the calibrations as old as he likes.” Actually he does
not do that, but offers tectonic calibrations as estimates.

“Heads seems remarkably slow to provide analyses of how much older than
their oldest fossils clades needs to be to fit his paradigm.” Not sure how
to understand that. All Heads does is offer tectonic calibrations as
divergence estimates. How much older than the oldest fossil depends on the
group concerned.

John Grehan

On Sun, Oct 20, 2019 at 8:14 PM Rob Smissen via Taxacom <
taxacom at mailman.nhm.ku.edu> wrote:

> Once again Michael Heads promotes his self-serving slogan, claiming "As
> discussed, fossil-calibrated, molecular clock dates for clades can only
> ever be minimums."
> Current Bayesian molecular dating software gives a probability
> distribution of dates. How can a distribution of dates (a range) be a
> minimum? Well, Heads takes the oldest date from a published range and
> transmogrifies that into minimum.
>
> But that is only the beginning. The "only ever minimum" argument ignores
> the fact that other sources of error can contribute to misleadingly old
> date estimates. These include
>
>   1.  Ancestral polymorphism (splits in gene lineages are older than
> splits among populations). This has the opposite effect to the missing
> fossil problem. Gene lineage divergences necessarily predate population
> divergences, and therefore one might (wrongly) infer using Heads' logic
> that molecular date estimate are necessarily maximum.
>   2.  Rate variation among lineages.
>   3.  Miss-specified models.
>   4.  Incorrect attribution of fossils to extant lineage.
>   5.  Imprecise ages of fossils (often themselves given as ranges).
>   6.  Stochastic effects when sequences are short.
>
> Sometimes the data underpinning molecular dating papers is consistent with
> a 0 age (by which I mean that the samples could as well have been taken
> from a single panmictic population), yet Heads transmogrifies an age of
> millions of years into a so called minimum. I don't believe intelligent
> people would support that, at least not if they were honest.
>
> We should all take molecular clock dates with a big grain of salt, but
> slogans don't make for good science. I don't mind an argument that
> molecular date estimates may be underestimates, but I do mind the slogan
> that they are necessarily minimum. That is sophistry.
>
> Using the current generation of software, it is possible to explore the
> effect of using different priors. In fact it is quite easy. In particular,
> it is easy to explore the effect of increasing a calibration age to make
> dates older. It is also easy to constrain or relax the allowed rate
> variation among lineages.  If Heads was serious he could undertake these
> analyses. He could make the calibrations as old as he likes. Or stipulate
> that conspecific allopatric populations diverged in the Mesozoic as he oft
> claims. Then he could quantify how much rate variation, and how old the
> earth has to be, to accommodate his "biogeographic" assumptions. Despite
> claiming an understanding of molecular data and the workings of Bayesian
> analyses, and the fact that the software is free, Heads seems remarkably
> slow to provide analyses of how much older than their oldest fossils clades
> needs to be to fit his paradigm.
>
>
>
>
> ________________________________
>
> Please consider the environment before printing this email
> Warning: This electronic message together with any attachments is
> confidential. If you receive it in error: (i) you must not read, use,
> disclose, copy or retain it; (ii) please contact the sender immediately by
> reply email and then delete the emails.
> The views expressed in this email may not be those of Landcare Research
> New Zealand Limited. http://www.landcareresearch.co.nz
> _______________________________________________
> 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 assaulting ambiguity for 32 some years, 1987-2019.
>