[Taxacom] Molecular dates are NOT necessarily minimums

Sun Oct 20 21:19:48 CDT 2019

Stephen - there is more to life (and evolutionary biology) than just naming
species. For those for whom naming species is the primary concern I would
not gainsay, anymore than those for whom there are other interests or
primary concerns. Questions concerning the validity of biogeographic
methods may well be bizarre and pointless to the priorities of many just as
much as some taxonomic or nomenclatural questions. All depends on what you
like for breakfast.

John Grehan

John Grehan

On Sun, Oct 20, 2019 at 9:50 PM Stephen Thorpe via Taxacom <
taxacom at mailman.nhm.ku.edu> wrote:

>  Well, the whole debate seems bizarre and pointless. Rob steams in saying
> that the dates aren't wrong because they are minimums, they can be wrong
> for other reasons too! I'm not sure that Michael need disagree with that!
> It just goes to reinforce what a monumental waste of time and effort
> biogeography and indeed also phylogeny is. The data is too unreliable and
> the assumptions too big to be confident of any theory being anywhere close
> to "the truth". Meanwhile, perhaps most species on Earth haven't even been
> given a name yet, and lack even a basic modern taxonomic description! In my
> opinion, people need to stop all this "academic chest beating" and get back
> to the basics of increasing knowledge of the inventory of life.
> Stephen
>     On Monday, 21 October 2019, 01:19:39 am UTC, JF Mate via Taxacom <
> taxacom at mailman.nhm.ku.edu> wrote:
>
>  "Seems to me that Rob's argument is essentially that the dates aren't
> EVEN minimums, but may also be overestimates due to various kinds of
> error. If so, then what use are they at all?"  They provide a probable
> temporal window for events based on a few assumptions, (some better
> supported than others) and the available data at hand. They are still
> useful if nothing else if as a way to anchor the discussion along a
> more limited range of dates.
>
> "However, if Rob were inclined to use the Principle of Charity more in
> debates he might attribute to Michael the more sensible view that the
> dates CAN only be minimums, EVEN WHEN free of the kinds of error which
> in practice may result in overestimates."
>
> I am not sure what you mean by this Stephen. The resident
> panbiogeographer´s position, made time and time again can be (overly)
> simplified as follows: molecular rates are flexible; models based on
> these rates are fallible; fossils can only be used to estimate a
> minimum. Ergo, any distribution can be explained solely by vicariance
> (by the judicious stretching and compressing of molecular rates to
> suit this view). And since the molecular based rates are flexible (and
> did I mention fallible) they can´t falsify my hypothesis. In fact,
> neither can fossils because lack of fossils (even in very well
> researched localities) can be explained away by the difficulty of
> fossilization, etc. All perfectly "logical" but a clear rejection of
> the abductive process on which science is also (mostly?) based. This
> perspective would be fine if it weren´t accompanied by the constant
> trickle of little jabs to get some sort of discussion going.
>
> The accusation of sophistry is not wide off the mark either when you
> consider other prior arguments (i.e. "dispersal"). If you can´t recall
> previous exchanges on Taxacom let´s just say that the tag applies as
> well.
>
> My take on Rob´s post is that constant baiting is irritating and that
> some circumspection on their part is advisable. If they have fresh
> epistemological ideas that are clearly fleshed out then great, it is
> always good to spar as better understanding ensues. But if the whole
> exercise becomes yet another tit-for-tat mud slinging exercise based
> on the same sacred texts, then it is pointless and default reaction is
> to shrug shoulders and move on (although sometimes you make the
> mistake of taiking the bait and you throw a salvo their way to detox).
>
> Jason
>
> On Mon, 21 Oct 2019 at 10:32, Stephen Thorpe via Taxacom
> <taxacom at mailman.nhm.ku.edu> wrote:
> >
> >  Seems to me that Rob's argument is essentially that the dates aren't
> EVEN minimums, but may also be overestimates due to various kinds of error.
> If so, then what use are they at all? However, if Rob were inclined to use
> the Principle of Charity more in debates, he might attribute to Michael the
> more sensible view that the dates CAN only be minimums, EVEN WHEN free of
> the kinds of error which in practice may result in overestimates.
> > Stephen
> >    On Monday, 21 October 2019, 12:15:03 am UTC, 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.
> >
> >
> >
> >
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