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

[John Grehan]

Hi Ken,

Understand that you feel that way since it seems that you and Jason are
frustrated when your claims or interpretations are contested. But
regardless, the bottom line remains the same:

1) fossil calibrated molecular divergence estimates are minimums only
(claims for anything else is indeed transmogrification)
2) Priors are just guesses
3) molecular clocks are not set in stone as the only arbiter of
phylogenetic age
4) Older tectonic ages are not falsified by fossil calibrated ages (since
the latter are just minimums)
5) tectonic correlations are empirically observable
6) No one (to my knowledge) has provided an empirically grounded
falsification of any proposed tectonic correlation (i.e. demonstrated that
taxa are younger than the correlated tectonics)
7) Panbiogeographic studies have generated novel geological predictions
that have subsequently been corroborated by geologists - its one case where
evolutionary theory is not simply a matter of belief, but an actual means
of predicting new knowledge that was later found to be true (I notice those
who dismiss panb biogeography step around this one :)

Cheers, John Grehan

On Sat, Jan 2, 2021 at 4:52 PM Kenneth Kinman via Taxacom <
taxacom at mailman.nhm.ku.edu> wrote:

> Thank you Jason,
>         You present an excellent critique of "CP" panbiogeographers
> arguments.   Almost always the same old rigmarole of cherry-picking,
> quoting out of context, sophistry, circular argumentation, and other
> methods of muddying the waters.  And it is often cloaked within a barrage
> of other verbiage, so I agree that it is important to warn newcomers.
>
> ________________________________
> From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> on behalf of JF Mate
> via Taxacom <taxacom at mailman.nhm.ku.edu>
> Sent: Saturday, January 2, 2021 12:35 AM
> To: Taxacom <taxacom at mailman.nhm.ku.edu>
> Subject: Re: [Taxacom] Molecular evidence (in 2017) supports my 2014
> theory about rafting killifish
>
> I think that Rob was on the right track but not precise enough. It is not
> that panbiogeography is akin to creationism, it is that the defence John
> and Michael are mounting is reminiscent of creationists. I may be wrong in
> your intention but the arguments I hear are cherry-picking, sophistry,
> circular argumentation and in general muddying the waters so as to create a
> gap for a "Panbiogeography of the gaps". This, however, is a mistake and
> has left you holding an untenable arcane view of biogeography whilst
> ignoring the last 60 years of advances in phylogenetics. The debate
> strategy seems to me to be a kafkaesque attempt to neutralize any
> possibility of criticizing Croizat or panbiogeography by labelling as
> suspect all other contenders, molecular phylogenetics (you call it
> phenetics), fossil calibration (using minimum age as a the fine edge of the
> wedge to push arguments such as confusing point calibration with log
> distributions), molecular clocks (your definition is "strict clock" from
> the 1960´s but you don´t care), and generally weaponizing the widely
> acknowledged limitations of all of these and more fields.
>
> John, you asked me to argue why I said that your position on Croizatian
> Panbiogeography (CP) was untenable. Succinctly, because of two main
> reasons. Firstly because Croizat quite simply rejected cladistics, and if
> you accept cladistics you are a vicariance cladist by definition and
> arguing otherwise is rejecting reality Secondly, because CP rejects
> dispersal (“Interestingly it is dispersalism that invokes miracles and
> mysteries.”) in spite of evidence that demonstrates that, however
> infrequently, it happens. Trying to relabel cases of dispersal as "range
> expansion" is sophistry aimed at making panbiogeography unfalsifiable.
>
> This pattern of muddying the waters is particularly noticeable when you
> selectively quote, for example with Donoghue and De Baets. From the same
> 2016 publication: "Biogeographic and fossil calibrations are complementary,
> not competing, approaches to constraining molecular clock analyses,
> providing alternative constraints on the age of clades that are vital to
> avoiding circularity in investigating the role of biogeographic mechanisms
> in shaping modern biodiversity." (2016). I don´t think any biogeographer
> would disagree with this statement, but it is anathema with CP because, as
> John has said: “If molecular clock models incorporating a tectonic
> correlation result in unacceptable results, that does not invalidate the
> tectonic correlation. But it does raise questions about the molecular
> model. Nothing ridiculous about it at all.”  The unfalsifiability of CP in
> all its glory. If something disagrees with CP, CP is not at fault because
> it is perfect. Other examples of cherry-picking involve the numerous out of
> context quotes of researchers acknowledging the caveats of phylogenetics
> and calibration as evidence of the inferiority and mendaciousness of non CP
> researchers (“magic”, “dark art”, “lies”, etc).
>
> This pattern is so extensive it is tiring pointing out the examples:
>
> “...keep in mind that some molecular systematists are recognizing that
> fossil calibration only provides minimum ages and are looking to tectonic
> correlates instead - which is another way of saying that they have adopted
> this panbiogeographic method.” ML or Bayesian models do not assume point
> dates but a probability distribution into the past. Please stop confusing
> the terms.
>
>
> “The idea that there has to be a constant molecular clock throughout the
> phylogenetic history of a group is not an empirical finding. It is a model
> of evolution that may not be true. … Like priors, molecular clocks are also
> theoretical models (and there are different models) and open to question or
> refutation. I would like to see you, Ken, show how a constant molecular
> clock” A molecular clock model does not assume monotonic (constant) rates
> within genes or within lineages nor are clocks assumed a priori.  This is a
> straw man argument. Nobody assumes the strict clock a priori except in very
> specific cases like viruses and even then after testing. I can´t believe
> that this is a mistake when you guys selectively quote dos Reis et al 2016:
> “Thus, while the clade ages generated in Bayesian studies are extremely
> precise and have excellent statistical support, because 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.” Cherry
> picked quote: “Errors in the time prior and in the rate prior can lead to
> very precise but grossly inaccurate time estimates. Great care must always
> be taken in the construction of fossil calibrations and in the
> specification of priors on times and on rates in a dating analysis.” Not
> quite the same meaning, in particular with the added sentence ending “tens
> or hundreds of millions of years…”. That is a misquote if I ever saw one.
>
> “We see this in the morphological aspect of molecular genetics where
> different groups separated or dislocated by a tectonic feature show
> different levels of morphological divergence (for example with the NZ
> Alpine fault dislocation where correlated distributions may be conspecific
> or species level differences even after more than 20 million years. So the
> panbiogeographic implication of tectonic correlation is that this provides
> an approximation of age for the correlated groups.”
> You are assuming as axiomatic that the taxa on either side of the fault
> have been unable to cross since the tectonic event.
>
> “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’.”
>
> Again, cherry-picked, out of context quote. It is followed by: “If the
> importance of vicariance in the course of the Gondwanan breakup is to be
> evaluated via the pragmatic criterion of mismatch between age estimates and
> geological history, the priors defining the molecular dating analyses have
> to be solid. As those are predominantly influenced by fossil attribution
> (Magallón, 2014; Pirie, Litsios, Bellstedt, Salamin, & Kissling, 2015; Shen
> et al., 2016), taxonomy and phylogeny of the study group are of crucial
> importance. Consequently, taxonomically resolved groups with a rich fossil
> record should constitute ideal model groups, because they are more likely
> to uncover accurate age estimates (e.g., Favre et al., 2016; Muellner‐Riehl
> et al., 2016).”
> And what did the authors find?
> “Results: Our biogeographic analyses illustrate that the ziziphoid lineage
> was influenced by both long‐distance dispersal and Gondwanan breakup
> vicariance events. Yet, these vicariance events cannot explain all
> divergence events at the backbone of this lineage.” Shocker, they find both
> mechanisms at play. I can´t wait to see how you ignore this part of the
> paper whilst using the bits that you agree with (usually the necessary
> acknowledgement of study limitations).
>
> This is a pattern. I have kept correspondence for the last 10 years on
> these exchanges and it is always the same rigmarole. But I still bite
> because it is important to warn newcomers.
>
> Happy New Year everyone.
>
> Jason
>
> On Sat, 2 Jan 2021 at 09:03, John Grehan via Taxacom <
> taxacom at mailman.nhm.ku.edu> wrote:
>
> > p.s. keep in mind that some molecular systematists are recognizing that
> > fossil calibration only provides minimum ages and are looking to tectonic
> > correlates instead - which is another way of saying that they have
> adopted
> > this panbiogeographic method.
> >
> > John Grehan
> >
> > >
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> Nurturing nuance while assaulting ambiguity for about 33 years, 1987-2020.
>