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

John Grehan calabar.john at gmail.com
Mon Dec 28 15:57:26 CST 2020


One interesting thing about De Baets et al is that one of the
authors, Philip Donoghue, is a molecular biologist who has published on
molecular systematics. Makes one wonder (or it should) that a molecular
systematists resorts to referring to molecular divergence practice as a
'dark art'. If a molecular systematists can't make scientific sense of it,
who can? I am assuming that Donoghue isn't stupid.

On Mon, Dec 28, 2020 at 1:07 PM Michael Heads via Taxacom <
taxacom at mailman.nhm.ku.edu> wrote:

> 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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> >
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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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> Nurturing nuance while assaulting ambiguity for about 33 years, 1987-2020.
>


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