[Taxacom] Molecular evidence (in 2017) supports my 2014 theory about rafting killifish

Michael Heads m.j.heads at gmail.com
Mon Dec 28 12:07:06 CST 2020


Ken, you write:  'It is interesting that Heads quotes De Baets *et al*.,
2016 as saying ‘could be considered a dark art’, but their source for that
"dark art" comment was Heads himself (Heads, 2012; "Bayesian
transmogrifcation..."'). That's not correct.

De Baets et al wrote: '...molecular clocks must be calibrated
by estimates of divergence timing and so it has become necessary [if you're
relying on fossils] to
provide a probabilistic judgement of the degree to which fossil minima
approximate
divergence timing. The established means of achieving this could be
considered a dark art (Heads, 2012)'. But I did not use the phrase 'dark
art' in my own paper or anywhere else.

On Mon, Dec 28, 2020 at 9:57 AM Kenneth Kinman via Taxacom <
taxacom at mailman.nhm.ku.edu> wrote:

> Thanks Jason,
>         Your post was very good.  It was then followed by Heads who (like
> Grehan) just repeats the same old arguments.  It is interesting that Heads
> quotes De Baets *et al*., 2016 as saying ‘could be considered a dark art’,
> but their source for that "dark art" comment was Heads himself (Heads,
> 2012; "Bayesian transmogrifcation...").
>         I don't understand why Heads and Grehan have to bash those who
> disagree with them, using phrases like "dark art", twaddle,
> transmogrification, "geological data manipulation", "magical black box",
> and on and on.  Especially when it appears in scientific papers.
>        By the way, I was reading a published reply to Heads, 2011 (in
> which he repeatedly accused his opponents of transmogrification).  In that
> reply, they say: "We demonstrate here that calibration using tectonic
> events, as suggested by Heads (2011), generates an unrealistic hypothesis
> where the evolution of Asteraceae must have taken place contemporary with
> or earlier than the Cambrian explosion. This would be hundreds of million
> years earlier than the origin of the asterids."
>       This reply to Heads can be read here:
> https://academic.oup.com/sysbio/article/61/3/522/1670654
>
> ________________________________
> From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> on behalf of Michael
> Heads via Taxacom <taxacom at mailman.nhm.ku.edu>
> Sent: Sunday, December 27, 2020 1:26 PM
> To: JF Mate <aphodiinaemate at gmail.com>
> Cc: Taxacom <taxacom at mailman.nhm.ku.edu>
> Subject: Re: [Taxacom] Molecular evidence (in 2017) supports my 2014
> theory about rafting killifish
>
> '...not a magical black box'.
>
> No, it's definitely a magical black box. You can get any date you want.
> Here's a section from a recent manuscript:
>
> *The problem of the priors*
>
> In the Modern Synthesis approach, ‘Fossils record the origins and
> disappearance of organisms’ (Herrera, 2017). However, a clade’s actual age
> is older than its oldest fossil’s age by an unknown amount of time. In most
> studies, clade ages are calculated from fossil-calibrated molecular-clock
> analyses. However, fossil calibrated studies on their own can provide only
> minimum ages. In Bayesian analyses, these *fossil* ages are converted into
> estimates of absolute (not minimum) *clade* ages by imposing priors that
> stipulate how much older than its oldest fossil a clade is. Naturally, the
> estimates of clade age are extremely sensitive to the time priors (Warnock
> *et
> al*., 2015).
>
> The problem is that the choice of the priors is left up to the author, and
> the priors that are chosen are invariably very narrow; in other words, a
> clade used for calibration is assumed to be not much older (often <10 Myr)
> than
> its oldest fossil. This use of very narrow priors represents the formal
> imposition of an old belief – that fossil age more or less equals clade
> age.
>
> Choosing priors is ‘highly arbitrary’ (Pirie and Doyle, 2012), ‘...often
> subjective…’ (Ho & Duchêne, 2014), ‘invariably established without
> justification’ (Warnock *et al*., 2015) and, in sum, ‘could be considered a
> dark art’ (De Baets *et al*., 2016). Thus, while the clade ages generated
> in Bayesian studies are extremely precise and have excellent statistical
> support, becaue of the problem of the priors they can be ‘grossly
> inaccurate’ (dos Reis *et al*., 2016) and could be tens or even hundreds of
> millions of years too young. As Hauenschild *et al.* (2018) observed, clade
> ages that are too young may be calculated ‘based on too narrowly set
> priors, and vicariance thereby may be erroneously ruled out’.
>
> On Mon, Dec 28, 2020 at 2:59 AM JF Mate via Taxacom <
> taxacom at mailman.nhm.ku.edu> wrote:
>
> > John, you are not discussing the points nor answering the questions but
> > simply repeating "twaddle" in an attempt to rescue a point of view
> > (Croizatian Panbiogeography) which is simply untenable nowadays. All
> > biogeographers consider vicariance and dispersal, and their definition of
> > dispersal does not depend on accepting Panbiogeography.
> >
> > As for node calibration, exponential and lognormal bounds are not maximum
> > ages but probability curves which extend the "minimum" node age into the
> > past as a first step. The model then works the best fit based on the data
> > at hand and gives you estimated ages with ranges. That is a transparent
> > model, not a magical black box as you are claiming.
> >
> > It is fair to argue if the model parameters are adequate, if the fossils
> > used are properly interpreted, or to reanalyze the data. These are all
> > limitations, but simply using them to disregard studies out of hand
> because
> > they don't support your point of view is not helpful.
> >
> > Best
> >
> > Jason
> >
> >
> >
> > On Sat, 26 Dec 2020, 01:57 John Grehan, <calabar.john at gmail.com> wrote:
> >
> > >
> > > Jason – thank you for elaborating on the defense of minimums
> > > misrepresented as maximums. Comment below:
> > >
> > > “0.5 SD on the fossil's age seems a reasonable and conservative range”
> > >
> > > 'reasonable or not' it's still just made up out of thin air. It is
> magic.
> > >
> > > “Are you arguing for a minimum hardbound and if so what is your
> > > justification? “
> > >
> > > Yes, although not sure what you mean by 'hardbound'.  A minimum is a
> > > minimum so it is hardbound in that respect. Justification is simple,
> > > fossils provide minimum ages and no data on potential older ages of
> > origin
> > > for the taxon in question.
> > >
> > > “why not use lognormal or exponential for both points and maybe some
> > > sensitivity analysis in regards to this but other than that I wouldn't
> > call
> > > it twaddle”
> > >
> > > You are welcome to use anything you like, but it's still magic and the
> > > result is twaddle. A minimum cannot be turned into a maximum. That is
> the
> > > reality. The rest is an invention of the imagination.
> > >
> > > “This argument is at best specious. Molecular calibrations have been
> > using
> > > soft calibrations for well over a decade now to account for the
> > > uncertainties that you mention “
> > >
> > > Wrong, the molecular calibrations misrepresent minimum ages as maximum.
> > >
> > > “ majority use either lognormal or exponential bounds “
> > >
> > > So what? They are both inventions of the mind – magical transformation
> of
> > > minimum into maximum.
> > >
> > > “In other words, there is already the acknowledgement that known
> fossils
> > > may not be the oldest exemplars of a taxon, but you have to work with
> > what
> > > you have
> > >
> > > of course. But if fossils may not be the oldest exemplars then the
> > > molecular extrapolations may not be either. To say otherwise is to
> > invoke a
> > > magical transformation - not science as I understand it.
> > >
> > > “ and, when new fossil evidence is discovered, corrections will be
> made.”
> > >
> > > Corrections to what? Corrections to a maximum that never was in the
> first
> > > place?
> > >
> > > “What you are asking for is the legal equivalent of proving someone's
> > > innocence.”
> > >
> > > Rubbish. I am asking that the empirical reality be recognized – that
> > > fossil calibrated molecular divergence dates be recognized as minions
> > that
> > > cannot falsify earlier origins or biogeographic correlations that may
> > > suggest earlier origins.
> > >
> > > Molecular transformations of minimums into maximums is perhaps the only
> > > modern case of magic being used in science that I am aware of (other
> than
> > > perhaps some political inventions with COVID). Just to be sure that
> there
> > > is no misunderstanding (as has happened in the literature),
> > > panbiogeographic approaches do not ignore or disregard molecular
> > divergence
> > > ages, but accept and incorporate those findings as MINIMUM ages only.
> > That
> > > is science.
> > >
> > > Cheers,
> > >
> > > John Grehan
> > >
> > >
> > > On Fri, Dec 25, 2020 at 7:01 AM JF Mate <aphodiinaemate at gmail.com>
> > wrote:
> > >
> > >> Michael, regarding the calibration method used: "It corresponds to the
> > >> origin of the crown European cyprinodontoid clade [39], which was
> > estimated
> > >> to have occurred at least 33 Ma on the basis of the oldest
> identifiable
> > >> clade member, the
> > >> fossil Prolebias stenoura Sauvage, 1874 from the Lower Stampien (Lower
> > >> Oligocene) of Puy-
> > >> de-Dome, France [40] (prior setting: lognormal distribution, mean = 33
> > >> and standard devia-
> > >> tion = 0.5). ( [40] Costa WJEM. Oligocene killifishes (Teleostei:
> > >> Cyprinodontiformes) from southern France: relationships, taxonomic
> > >> position, and evidence of internal fertilization. Vertebr Zool. 2012;
> > 62:
> > >> 371–386.)
> > >>
> > >> John:
> > >> 0.5 SD on the fossil's age seems a reasonable and conservative range,
> > >> with a lognormal distribution for the node. My only quibble is why not
> > use
> > >> lognormal or exponential for both points and maybe some sentivity
> > analysis
> > >> in regards to this but other than that I wouldn't call it twaddle. Are
> > you
> > >> arguing for a minimum hardbound and if so what is your justification?
> > >>
>
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> Nurturing nuance while assaulting ambiguity for about 33 years, 1987-2020.
>


-- 
Dunedin, New Zealand.

My books:

*Biogeography and evolution in New Zealand. *Taylor and Francis/CRC, Boca
Raton FL. 2017.
https://www.routledge.com/Biogeography-and-Evolution-in-New-Zealand/Heads/p/book/9781498751872


*Biogeography of Australasia:  A molecular analysis*. Cambridge University
Press, Cambridge. 2014. www.cambridge.org/9781107041028


*Molecular panbiogeography of the tropics. *University of California Press,
Berkeley. 2012. www.ucpress.edu/book.php?isbn=9780520271968


*Panbiogeography: Tracking the history of life*. Oxford University Press,
New York. 1999. (With R. Craw and J. Grehan).
http://books.google.co.nz/books?id=Bm0_QQ3Z6GUC
<http://books.google.co.nz/books?id=Bm0_QQ3Z6GUC&dq=panbiogeography&source=gbs_navlinks_s>


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