Taxacom: Censorship by a New Zealand museum

Wed Aug 10 06:28:29 CDT 2022

 Hi Robert,
You say "(1) the calibration only indicates the most recent possible time but it could have happened earlier"
My point is that it could also have happened later!
If A and B are 5% genetically distant, you need to calibrate to find out how long it took to get that 5% divergence, right?Two options:(1) if you know how long it took to get n% divergence for a pair of near relative taxa, then assume the same rate for A and B divergence. The problem with this is that it assumes that divergence rates are approximately constant within closely related lineages, when in fact they might not be, for various reasons, one being that divergence rates might be more a result of environmental factors like temperature. It also poses a problem of where do you start? You need the answer for one case to answer the question for another case.(2) if you know the date when a relevant vicariance event took place, then assume that is t=0 for the divergence of (allopatric) A and B. The problem here is that divergence could begin at any time after the vicariance event, possibly having to wait until climatic temperature increases or something. Also, each sister species might drift into different climate zones, so they could mutate at very different rates.
Am I missing something here?
Cheers, Stephen
    On Wednesday, 10 August 2022 at 10:50:37 pm NZST, Lücking, Robert <r.luecking at bo.berlin> wrote:  

 <!--#yiv4782602108 _filtered {} _filtered {} _filtered {}#yiv4782602108 #yiv4782602108 p.yiv4782602108MsoNormal, #yiv4782602108 li.yiv4782602108MsoNormal, #yiv4782602108 div.yiv4782602108MsoNormal {margin:0cm;margin-bottom:.0001pt;font-size:11.0pt;font-family:"Calibri", sans-serif;}#yiv4782602108 a:link, #yiv4782602108 span.yiv4782602108MsoHyperlink {color:blue;text-decoration:underline;}#yiv4782602108 a:visited, #yiv4782602108 span.yiv4782602108MsoHyperlinkFollowed {color:purple;text-decoration:underline;}#yiv4782602108 p.yiv4782602108msonormal0, #yiv4782602108 li.yiv4782602108msonormal0, #yiv4782602108 div.yiv4782602108msonormal0 {margin-right:0cm;margin-left:0cm;font-size:11.0pt;font-family:"Calibri", sans-serif;}#yiv4782602108 span.yiv4782602108E-MailFormatvorlage18 {font-family:"Calibri", sans-serif;color:windowtext;}#yiv4782602108 .yiv4782602108MsoChpDefault {font-size:10.0pt;} _filtered {}#yiv4782602108 div.yiv4782602108WordSection1 {}-->
Dear Stephen,

yes, of course you have at least two levels of uncertainty: (1) the calibration only indicates the most recent possible time but it could have happened earlier. (2) there is a large variation in the node age estimates that actually take these issues into account. In a molecular clock, you do not get a simple number but you get a range and the range depends on a number of factors. But numbers such as (40-)30(-20) Mya for a node is a typical result. As a consequence, one should not use these numbers as precise measures but rather as "ballpark" figures.

Your example of comparing two sister lineages (A, B) is a good example of the underlying issues. When you calculate the genetic distance, you assume it is symmetrical, i.e. both branches have exactly the same length. However, this is rarely the case. Once you add the next outgroup lineage, you often get asymmetric branch lengths, i.e. A has a different number of changes relative to the outgroup than B. This then automatically means that A evolved either faster or slower than B. In a molecular clock, the two branch lengths will be adjusted to exactly the same, as both have a single origin and are extant. As a result, the substitution rate for A and B will be different, reflecting exactly this phenomenon. When you only compare A and B pairwise, you do not see this. So a clock does work, and it does reflect these evolutionary dynamics, only that one has to be very careful to take the exact numbers for granted.

Robert

Von: Stephen Thorpe <stephen_thorpe at yahoo.co.nz> 
Gesendet: Mittwoch, 10. August 2022 08:34
An: Andy Mabbett <andy at pigsonthewing.org.uk>; John Grehan <calabar.john at gmail.com>; Lücking, Robert <R.Luecking at bo.berlin>
Cc: taxacom <taxacom at mailman.nhm.ku.edu>
Betreff: Re: AW: Taxacom: Censorship by a New Zealand museum

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.

>>  

>> --

>> Andy Mabbett

>> @pigsonthewing

>>  

>>https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpig

>> sonthewing.org.uk%2F&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cadc5

>> 29b7bc70472e6f6708da7a5a1022%7C3c176536afe643f5b96636feabbe3c1a%7C0%7

>> C0%7C637956824501173145%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiL

>> CJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sda

>> ta=6beG8O3jRmSM9i33n6rzYH2jxb9Jx0Wc3g2mhus%2BquQ%3D&reserved=0

>> _______________________________________________

>> Taxacom Mailing List

>>  

>> Send Taxacom mailing list submissions to:taxacom at lists.ku.edu For 

>> list information; to subscribe or unsubscribe, visit:

>>https://lists.ku.edu/listinfo/taxacom

>> You can reach the person managing the list at:

>>taxacom-owner at lists.ku.edu The Taxacom email archive back to 1992 can be searched at:

>>https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftax

>> acom.markmail.org%2F&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cadc5

>> 29b7bc70472e6f6708da7a5a1022%7C3c176536afe643f5b96636feabbe3c1a%7C0%7

>> C0%7C637956824501173145%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiL

>> CJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sda

>> ta=0hNSB9aJTTk1YIzb60CL5tGVQaWTpW%2Bb3LKLsX9x8xQ%3D&reserved=0

>>  

>> Nurturing nuance while assailing ambiguity for about 35 years, 1987-2022.

>>  

>  

>  

> --

>https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhepialidsoftheworld.com.au%2F&data=05%7C01%7Ctaxacom%40lists.ku.edu%7C3b38dd9ebae9488ec8d308da7ac37662%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637957277777888229%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=LUeDd7PSuD%2Fr4dUXrwaDSc5w7GaG%2B9mqcJ%2F8Z5lt2Dg%3D&reserved=0(use the 'visit archived web site'

> link, then the 'Ghost Moth Research page' link.

>  

--

https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhepialidsoftheworld.com.au%2F&data=05%7C01%7Ctaxacom%40lists.ku.edu%7C3b38dd9ebae9488ec8d308da7ac37662%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637957277777899179%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=xkf6CGnSzzfdaizGeJllUEWcoR0iQgVZTTLtElzRwNo%3D&reserved=0(use the 'visit archived web site'

link, then the 'Ghost Moth Research page' link.

_______________________________________________

Taxacom Mailing List

Send Taxacom mailing list submissions to:taxacom at lists.ku.edu For list information; to subscribe or unsubscribe, visit:https://lists.ku.edu/listinfo/taxacom

You can reach the person managing the list at:taxacom-owner at lists.ku.edu The Taxacom email archive back to 1992 can be searched at:https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftaxacom.markmail.org%2F&data=05%7C01%7Ctaxacom%40lists.ku.edu%7C3b38dd9ebae9488ec8d308da7ac37662%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637957277777899179%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=RetFVkS%2BvJCXTtxyqf5px9zL6EyPKmwUygLDCV%2FMFVc%3D&reserved=0

Nurturing nuance while assailing ambiguity for about 35 years, 1987-2022.

_______________________________________________

Taxacom Mailing List

Send Taxacom mailing list submissions to:taxacom at lists.ku.edu For list information; to subscribe or unsubscribe, visit:https://lists.ku.edu/listinfo/taxacom

You can reach the person managing the list at:taxacom-owner at lists.ku.edu The Taxacom email archive back to 1992 can be searched at:https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftaxacom.markmail.org%2F&data=05%7C01%7Ctaxacom%40lists.ku.edu%7C3b38dd9ebae9488ec8d308da7ac37662%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637957277777899179%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=RetFVkS%2BvJCXTtxyqf5px9zL6EyPKmwUygLDCV%2FMFVc%3D&reserved=0

Nurturing nuance while assailing ambiguity for about 35 years, 1987-2022.

_______________________________________________

Taxacom Mailing List

Send Taxacom mailing list submissions to:taxacom at lists.ku.edu For list information; to subscribe or unsubscribe, visit:https://lists.ku.edu/listinfo/taxacom

You can reach the person managing the list at:taxacom-owner at lists.ku.edu The Taxacom email archive back to 1992 can be searched at:https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftaxacom.markmail.org%2F&data=05%7C01%7Ctaxacom%40lists.ku.edu%7C3b38dd9ebae9488ec8d308da7ac37662%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637957277777899179%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=RetFVkS%2BvJCXTtxyqf5px9zL6EyPKmwUygLDCV%2FMFVc%3D&reserved=0

Nurturing nuance while assailing ambiguity for about 35 years, 1987-2022.