Any comments?

Arlin Stoltzfus arlin at ac.dal.ca
Tue Oct 24 21:58:40 EST 1995

Agneta.Guillemot at historia.umu.se (Ludvig Mortberg) wrote:

[quotations from abstracts of two studies that disagree]
>Who do you belive, and why? More studies? But how many?

The existance of conflicting abstracts is not evidence of anything.  
This is how creationists try to discredit science, and its quite silly.  
I'm sure we could find lots of conflicting abstracts in other areas as 
well.  Ludwig, do you mean to tell us that all classically-based 
phylogenies agree on the bird-mammal-reptile problem, or the 
artiodactyl-perissodactyl-cetacean problem?  NO!  Does this mean that 
the methods of systematics (molecular or otherwise) are useless?  NO!  
The solution is for scientists to stop exaggerating about the strength 
of their conclusions (we, including myself, do this too often), and for 
critics to be less superficial.  

Being critical, and reading further than the abstracts, one finds that 
Saccone, et al. have made a number of exaggerations or errors in 
judgment that reveal cracks in the confident abstract that they wrote:

1. they used a subset of available glutamine synthetase genes;
2. they "rooted" their rRNA tree based on a so-called molecular clock 
that is known not to exist, dismissing the contradictions with the 
fossil record that this "clock" implies; 
3. they presented bootstrap values without emphasizing that these values 
are inflated (relative to standard bootstraps) by their procedure of 
treating a string of related sequences as a 'supersequence' (sometimes 
even repeating the same sequence to make a supersequence);
4. in drawing conclusions about the relationships of organisms (as 
opposed to genes) they did not take seriously enough the possible 
confounding effects of gene duplication and lateral transfer.  Some of 
these effects had been suggested previously be other groups.

Although the abstract seemed to state very clearly that a group 
"archaebacteria" was a sister to "eubacteria", there were not coherent 
groups of either in the glutamine synthetase tree, and in the rRNA tree, 
the statement is unreliable because it is based on the clock-rooted 

>The idea that there is something inherrently wrong with the
>method has to be considered!
And it is being considered constantly by the molecular systematists you 
are so quick to disparage.  Are bootstraps accurate?  Can different base 
compositions be taken into account?  What about different rates of 
change in different lineages?  Different rates at different sites?  Each 
of these questions corresponds to an active area of methods development 
& testing in molecular phylogeny.  

>(1) A "close distance" between proteins or DNA sequences does not
>always reflect close relationship (within an organim and between
>organims). That is because mutations accumulate at different speeds at

bla, bla, bla.  The same thing could be said about any other type of 
comparative data.  

>(2) When a cladistic approach is used, "shared derived
>sequences/mutations" have been found that apparently could be used in
>a cladogram. The problem is that of information content. A cladogram
>with morphologic characters should not be put aside for one where the
>characters are a few nucleotide substitutions.

"A few" meaning several thousand?  Stop exaggerating and post some real 
numbers if you want to make the comparison.  There are plenty of studies 
in Systematic Biology and other places comparing molecular and 
morphological data.   Why don't you count the number of characters and 
the inferred numbers of changes per character?  Want to make any bets 
about where is the weight of information content?


Arlin Stoltzfus (arlin at ac.dal.ca)
Department of Biochemistry
Dalhousie University
Halifax, NS  B3H 4H7 CANADA
ph. 902-494-3569; fax 902-494-3569

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