[Taxacom] Molecular dates are NOT necessarily minimums

Sun Oct 20 21:30:00 CDT 2019

 That's not quite a fair assessment of the situation John. The point is that there is no point doing biogeography, or indeed very much at all, on entities that are undescribed (not just because they lack a name, but because it means that the basic taxonomy, as opposed to just nomenclature, hasn't been done, so we don't really have much idea what we are dealing with). The taxonomy (not necessarily the nomenclature) is the basis upon which all else depends. Additionally, it has the advantage of being a bit more concrete to describe actual biodiversity, as opposed to making endless inconclusive hypotheses about a small random subset of described biodiversity. So, it is not just a matter of taste, but about which is more fundamental to science and pragmatically useful.
Stephen
    On Monday, 21 October 2019, 02:20:26 am UTC, John Grehan <calabar.john at gmail.com> wrote:  

 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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