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

John Grehan calabar.john at gmail.com
Thu Dec 31 14:13:40 CST 2020


Smissen, Chambers and Garnock-Jones 2005 stated

"We agree with Head’s general points that dating nodes in molecular
phylogenies is a difficult process of approximation with most data, and
that the inadequacy of the fossil record, and the apparent variation in
rates of substitution, both among lineages and over time,present major
impediments to accurate dating"

Problem here is that it was not over impediments to accurate dating, but
the misrepresentation of  fossil calibrated minimum dates as anything else
but minimum.

"our conclusion that Scleranthus is capable of long-distance dispersal is
based on the observation that conspecific samples from Australia and New
Zealand differ by as little as one substituted site in ITS sequences"

This is a classic argument that if disjunct populations have not diverged
much then the disjunction must be recent. It has no empirical basis that I
know of.

"If this was then extrapolated to the tribal-level divergences (around 0.4
substitutions per site) within the Caryophyllaceae that we used as
a calibration for our dating, then the Caryophyllaceae are projected to be
in excess of 10 billion years old."

Only if the 'clock' was constant throughout. Maybe it's not.

John Grehan

On Thu, Dec 31, 2020 at 3:59 AM Rob Smissen <SmissenR at landcareresearch.co.nz>
wrote:

> I think this sort of argument is why people consider panbiogeography to be
> analogous with creationism. Personally, I don’t think it’s a fair analogy.
> Creationism is significantly less credible than panbiogeography, but that
> is not saying much. It is not enough to say that clades might be older than
> guestimated from the fossil record, or that molecular clocks are very bad
> clocks. I would like to see the panbiogeographers accounts of how among
> lineage rate variation and older ages of fossils combine to explain
> patterns in DNA sequence data. It’s a black art, put in whatever priors you
> want, give us some actual results.
>
> -----Original Message-----
> From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> On Behalf Of John
> Grehan via Taxacom
> Sent: Tuesday, 29 December 2020 10:57 AM
> To: Michael Heads <m.j.heads 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
>
> 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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> > >
> > > 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/He
> > ads/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&sou
> > rce=gbs_navlinks_s
> > >
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> > The Taxacom email archive back to 1992 can be searched at:
> > http://taxacom.markmail.org
> >
> > Nurturing nuance while assaulting ambiguity for about 33 years,
> 1987-2020.
> >
> _______________________________________________
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>
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