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Taxacom: Censorship by a New Zealand museum

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Wed Aug 10 01:33:46 CDT 2022 

 Thanks Robert, but I still don't understand the crucial bit."Regarding your example " If A and B are 5% divergent, you don't know if it was 1 year of 5% divergence, or 5 years of 1% divergence", you precisely have that problem in a pairwise comparison but it will be resolved in a well-done molecular clock using an independent calibration."That is just the question! If mutation rates depend more on environmental conditions (e.g. temperature, background radiation levels) then calibrating with related taxa isn't going to work. If you calibrate with a geological event of known date, which opens up the possibility for divergence, then that still assumes that divergence happens soon after it could start, but maybe things remian the same for a while until environmental conditions change to facilitate greater mutation rates. There just seems to be too many unknowns in the equation. The main point is that any conclusions are based on assumptions. All science is based on assumptions (except perhaps, strictly technological science which either works or it doesn't). It seems to me that underlying assumptions are often downplayed. You can't demonstrate when two taxa diverged. You can only demonstrate when they diverged given certain assumptions which may or may not be correct. There is a big difference here!Cheers, Stephen
    On Wednesday, 10 August 2022 at 05:21:39 pm NZST, Lücking, Robert <r.luecking at bo.berlin> wrote:  
 
 Dear Stephen,

the molecular clock does work, but obviously it has to be relaxed, because otherwise in a phylogram all terminals would end along the same vertical line, which is never the case. The "relaxation" is the tricky part, because it variously adjusts the branch lengths in a phylogram to obtain an ultrametric tree, trying to achieve the best balance given the data and the chosen model. Therefore, there is variation in the outcome which can be reduced by certain settings, although that does not mean it is more precise. Such a clock tree can be run without any calibration, e.g. setting the root to 1. The calibration of a particular node is then done to add a real time scale, i.e. it interpolates the inferred age for all other nodes. Calibrations should be done closer to the root and not to the tips, as especially towards the tips there might be a the problem of lack of resolution if the chosen markers have ambiguously aligned regions that need to be removed (happens easily in broader taxon sets), and calibrations close to the tip may give highly unreliable age estimates towards the root (a problem often seen in early clock studies).

The estimation of a divergence time based on genetic difference between two lineages is in my view tricky and less accurate and reliable than a molecular clock, because one simplifies the issue. For instance, between two sequences, differences are assumed to represent direct substitutions and identities as conserved, but in a tree context, it may turn out that a simple difference is a more complex one (e.g. two substitutions in a row) and identities may sometimes be homoplasies, which then puts the divergence time further into the past. Regarding your example " If A and B are 5% divergent, you don't know if it was 1 year of 5% divergence, or 5 years of 1% divergence", you precisely have that problem in a pairwise comparison but it will be resolved in a well-done molecular clock using an independent calibration.

Robert


-----Ursprüngliche Nachricht-----
Von: Taxacom <taxacom-bounces at lists.ku.edu> Im Auftrag von Stephen Thorpe via Taxacom
Gesendet: Mittwoch, 10. August 2022 00:54
An: Andy Mabbett <andy at pigsonthewing.org.uk>; John Grehan <calabar.john at gmail.com>
Cc: taxacom <taxacom at mailman.nhm.ku.edu>
Betreff: Re: Taxacom: Censorship by a New Zealand museum

 PS: I don't know much about molecular divergence estimation, but I found an interesting summary here: 

The Molecular Clock and Estimating Species Divergence
By: Simon Ho, Ph.D. (Australia National University) © 2008 Nature Education Citation: Ho, S. (2008) The molecular clock and estimating species divergence. Nature Education 1(1):168



I had to laugh a little at "Subsequent research has shown that Kimura's assumption of a strict molecular clock is too simplistic, because rates of molecular evolution can vary significantly among organisms. However, there has been a general reluctance to abandon the molecular clock entirely, because it represents such a valuable tool in evolutionary studies. Instead, researchers have undertaken efforts to retain some aspects of the original clock hypothesis while "relaxing" the assumption of a strictly constant rate."
This sounds to me a bit like scientists saying "well we know it doesn't work, but it is so convenient and useful that we will use it anyway!"
Anyway, what I don't understand is "Thus, to calibrate the molecular clock, one must know the absolute age of some evolutionary divergence event, such as the split between mammals and birds. An estimate of the timing of this event can be gained by examining the fossil record, or by ..."
This seems odd. Does the divergence event used for calibration purposes have to be relevant to the particular case, or can it be the same one across the board? Either way, I don't understand how it helps. If A and B are 5% divergent, you don't know if it was 1 year of 5% divergence, or 5 years of 1% divergence, etc., etc. You could find that out if you knew the divergence date, of course, but that is exactly what you are trying to find out from the degree of divergence, so it seems circular! So, I suppose if you knew the divergence date of a pair of closely related species, then you could work out their divergence rate from their level of divergence, and assume the same rate for A and B. The problem, of course, it that this makes all sorts of assumptions, such as that divergence rates are lineage dependent more than environmentally dependent (local differences in background radiation levels, temperature, etc.) Can anyone explain how it is supposed to work, in simple terms, so that even I can understand?
Stephen    On Wednesday, 10 August 2022 at 10:02:12 am NZST, Stephen Thorpe via Taxacom <taxacom at lists.ku.edu> wrote:  
 
  John, This is just the way that the online world works. People or institutions put things up on the internet, with an open commenting facility, but they own and control the webpage, so they commonly "moderate" comments by allowing comments that they agree with and blocking comments that they disagree with. It is a universal strategy. At they end of the day, nobody really cares what Te Papa puts on its website. It can be a load of old rubbish. It might be frustrating to you if you think you know better, but you don't have to correct them on their own forum. You can either (1) just sit back and let them be wrong; or (2) find another forum on which to disagree with them. The problem with (2) is that another forum is unlikely to reach the same audience as the original forum. Hence, I suggest that we just have to learn to live in a world where all sorts of people and institutions are claiming all sorts of garbage in a variety of forums. Not much you can do about it, I'm afraid!Cheers, Stephen
    On Wednesday, 10 August 2022 at 05:24:34 am NZST, John Grehan via Taxacom <taxacom at lists.ku.edu> wrote:  
 
 And don't forget, this comes on the heels of the Royal Society of New Zealand endorsing suppression and censorship of panbiogeography. New Zealand is a small and relatively homogenous society where there is a strong pressure for conformity to the prevailing milieu - which shows up in its science.

On Tue, Aug 9, 2022 at 1:16 PM John Grehan <calabar.john at gmail.com> wrote:

> Sorry Andy, but you are not correct. It is censorship by Te Papa. Of 
> course Taxacom does not engage in censorship of scientific arguments. 
> But Te Papa evidently does. Cheers, John
>
> On Tue, Aug 9, 2022 at 12:53 PM Andy Mabbett via Taxacom < 
> taxacom at lists.ku.edu> wrote:
>
>> On Tue, 9 Aug 2022 at 17:33, John Grehan via Taxacom 
>> <taxacom at lists.ku.edu> wrote:
>>
>> > Te Papa has refused to post this comment.
>>
>> This is not censorship. You are able to post your views here - at 
>> length - as you have demonstrated, and presumably there is nothing 
>> and no one preventing you from publishing them on your own blog or 
>> website.
>>
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