[Annelida] Traditional taxonomy discussion

[J. Kirk Fitzhugh]

I'll try to place into some context the question I asked yesterday, "How 
is 'traditional descriptive taxonomy' any less scientific than 'only 
molecular taxonomists' [sic!]?" and my statement "None of us should 
condone a world of 'only molecular taxonomists". Last week I had 
extensive discussions about the Boreo paper with Sergio Salazar-Valejo. 
Below is what I sent to Sergio, as this might make my concerns a bit 
more clear. I've also added in some references where I have analyzed 
these issues extensively:

    Sergio,
    Thank you for forwarding the article. I'll offer my own opinions on
    the state of 'biodiversity' studies. I suggest that the problems
    outlined by Boreo are not the real causes. The greater problems
    include (1) the lack of emphasis on the scientific nature of
    biological systematics (_not_ taxonomy), and (2) the inability of
    the biological community to develop a rational consensus for what we
    mean by terms like 'species' and 'taxon.' I suggest that it is
    because systematists have failed to fully address these issues that
    it is primarily the systematics community that must be blamed for
    the current mess we find ourselves in with regard to 'biodiversity'
    policies and practices.

    Problem (1) is a great example of using words without any real focus
    on what the words really mean. I'm a systematist, not a taxonomist
    (Fitzhugh 2006a, 2008b). The difference is critically important.
    Systematics is a field that is consistent with the broader goal of
    doing science: to causally understand the objects and phenomena
    around us (Fitzhugh 2005a, b, 2006a, b, 2008a, b, c, 2009a, in
    review). Taxonomy deals with classification. Classification does not
    necessarily entail causal ordering, and as such, none of us should
    claim to be doing taxonomy if we are also claiming that what we do
    is part of the more general endeavor of doing science.

    Without solving problem (2), the term 'biodiversity' remains an
    empty term. I wholly deny the characterization of species as things
    in time and space, and I have published enough to justify my
    position (Fitzhugh 2005b, 2009a). I don't study species. In fact, in
    my entire career I've never seen a species, much less any other
    taxon. The reason is simple: species, or taxa for that matter, are
    not things that exist around us. Yet, we (including Boreo) speak as
    if species are all around us and actually exist. We talk in terms of
    'species diversity,' 'describing species,' or 'barcoding species.'
    But if, as I have claimed, species and all taxa are nothing more
    than our explanatory hypotheses we apply to the organisms we
    observe, then we find that the entire industry of 'biodiversity'
    rests on a myth.

    But, doing science is a social affair. We want the acceptance of our
    work by our peers. We need that acceptance to get funding and to
    keep our jobs. The consequence is that our education system teaches
    that to be a good scientist means to do things just like everyone
    else does it. Copy what the 'good scientists' are doing because they
    are the ones getting the money to do 'good' science. Don't question
    why or how we should blindly follow the use of terms like
    'biodiversity' or 'species' or 'barcoding' (Fitzhugh 2006d) It's
    more important to get as many papers published as possible, because
    everyone thinks that's what makes a scientist a 'good' scientist.

    The consequence is that we use words and 'do' science without
    critically thinking about why we are using those words or doing
    activities in a particular way. Policies are only as good as the
    foundations upon which they are built. My opinion is that the
    foundations upon which 'biodiversity' and biological systematics are
    built are so poorly formulated that it's time we realize that we
    face a critical, long-term problem that will only become worse. I
    claim that the solution is a fundamental reorganization of our
    education system when it comes to actually teaching the nature of
    science. A solution I strongly doubt will ever happen. The social
    character of science won't allow it.

This then brings us back to the question I posed yesterday on Annelida, 
"How is 'traditional descriptive taxonomy' any less scientific than 
'only molecular taxonomists' [sic!]?" and my statement "None of us 
should condone a world of 'only molecular taxonomists."

Systematics has as its goal the act of placing our observations of 
objects and events into a causal framework, such that we increase our 
opportunities to acquire understanding. This is the very reason we place 
so much importance on the theories in evolutionary biology - those 
theories are the conceptual bases for developing the explanatory 
hypotheses we call cladograms and taxa (including species; Fitzhugh 
2008b, 2009a). What we do is not classification. We are systematists, 
not classificationists. Systematics falls squarely in line with what all 
fields of science attempt to attain.

But, if it is our goal to explain the properties of the objects, i.e. 
organisms, that we study, then we have to fully accept the implications. 
And the biggest implication is that there is no rational procedure in 
reasoning to actively disregard some relevant observations over other 
relevant observations. I've raised this issue numerous times here on 
Annelida and in my research (Fitzhugh 2006a, b, 2006d, 2008c, 2009b) 
under the traditional phrase, 'requirement of total evidence.' For 
instance, the goal of producing a cladogram via a computer program is 
not just to get a 'tree' or 'phylogeny.' The intent is far, far more 
encompassing. The very reason we make observations of the characters of 
organisms is because we strive to provide explanations for those 
observations. By the very nature of that action, the requirement of 
total evidence precludes knowingly excluding some set of observations, 
then producing a cladogram and recursively referring back to the 
excluded characters. Yet, we see this done all the time, where one has a 
set of DNA sequences and do not give consideration to all other 
available characters. The consequence, as I've pointed out very often, 
is that any sequence-based cladogram can say nothing about all of the 
characters that were excluded from the analysis. Indeed, the veracity of 
the hypothesis is compromised for the fact that all relevant evidence 
has not been considered. This is the very reason why none of us should 
ever accept as 'normal systematics' the process of violating the 
requirement of total evidence. There simply are no principles of 
reasoning that would support such a view, and the view is less than 
minimally rational.

So, between what we know of the goal of biological systematics as a 
field in science, and the rules for rational reasoning that transcend 
all the sciences, it is obvious that no particular, exclusive set of 
characters can be used to make systematics a better science. DNA won't 
save us, just as any other classes of characters won't. We need to move 
away from the view that we need a 'tree of life." The goal of 
systematics is to explain within the evolutionary context of organisms. 
That goal cannot be attained by filtering out only the desired 
characters to the exclusion of all others that are also relevant to 
explanation.

What is often referred to as descriptive taxonomy really isn't that at 
all. It is, instead, a part of systematics, and as such has just as much 
scientific merit as other endeavors to present explanatory hypotheses. 
This becomes especially clear when we recognize that species are one 
class of hypotheses that we develop in reaction to our observing 
organisms, just as are all taxa a variety of such classes of hypotheses 
(Fitzhugh 2008b, 2009a). As a consequence, I agree with Geoff that we do 
need to worry about the ICZN, which for the most part is at odds with 
our scientific endeavors (Fitzhugh 2008b, 2009a; Nogueira et al. in 
review). But, in order to sort out ICZN problems, just as to sort out 
the problems identified by Boreo, we need to address the more 
foundational problems in systematics and the way our education system 
teaches the nature of science.

Kirk

References:

Fitzhugh, K. 2005a. Les Bases Philosophiques de L'inférence 
Phylogénétique: Une vue d'ensemble. Biosystema  24: 83-105.
Fitzhugh, K. 2005b. The inferential basis of species hypotheses: the 
solution to defining the term 'species'. Marine Ecology 26: 155-165.
Fitzhugh, K. 2006a. The abduction of phylogenetic hypotheses. Zootaxa 
1145: 1-110.
Fitzhugh, K. 2006b. The 'requirement of total evidence' and its role in 
phylogenetic systematics'. Biology & Philosophy 21: 309-351.
Fitzhugh, K. 2006c. The philosophical basis of character coding for the 
inference of phylogenetic hypotheses. Zoologica Scripta 35: 261-286.
Fitzhugh, K. 2006d. DNA barcoding: an instance of technology-driven 
science?  BioScience 56: 462-463.
Fitzhugh, K. 2008a. Fact, theory, test and evolution. Zoologica Scripta 
37: 109-113.
Fitzhugh, K. 2008b. Abductive inference: implications for 'Linnean' and 
'phylogenetic' approaches for representing biological systematization. 
Evolutionary Biology 35: 52-82.
Fitzhugh, K. 2008c. Clarifying the role of character loss in 
phylogenetic inference. Zoologica Scripta 37: 561-569.
Fitzhugh, K. 2009a. Species as explanatory hypotheses: refinements and 
implications. Acta Biotheoretica 57: 201-248.
Fitzhugh, K. 2009b. Between macro and molecular. BioScience 59:85-86.
Fitzhugh, K. in review. 'Evidence' for evolution versus 'evidence' for 
intelligent design: parallel confusions. Acta Biotheoretica
Nogueira, J.M.M, K. Fitzhugh and M.C.S. Rossi. in review. A new genus of 
Sabellinae (Polychaeta: Sabellidae) from Atlantic and Pacific Oceans. 
Zootaxa.

Kirk Fitzhugh wrote:
>
> "Personally I tend to agree with the outsiders that traditional 
> descriptive taxonomy has a weak claim to be real science. Soon only 
> molecular taxonomists will exist. This is not a bad thing as long as 
> they can also handle and include organism phenotype descriptions."
>
> How is 'traditional descriptive taxonomy' any less scientific than 
> 'only molecular taxonomists' [sic!]? I'd be fascinated to know of the 
> definitive text book on doing science that substantiates your claim 
> that presenting hypotheses isn't a fundamental part of doing science. 
> None of us should condone a world of 'only molecular taxonomists.' To 
> do so would be a bastardization of the very principles of science.
>
> Kirk
>
>
>
> -----Original Message-----
> From: annelida-bounces from oat.bio.indiana.edu on behalf of Geoff Read
> Sent: Sun 2/7/2010 12:49 PM
> To: Annelida from magpie.bio.indiana.edu
> Subject: [Annelida] Traditional taxonomy discussion
>
> Hello,
>
> This commentary is being discussed. Personally I tend to agree with 
> the outsiders that traditional descriptive taxonomy has a weak claim 
> to be real science. Soon only molecular taxonomists will exist. This 
> is not a bad thing as long as they can also handle and include 
> organism phenotype descriptions. Many can't at the moment. I worry 
> more about the problems with the Zoological Code, and lack of 
> consensus on the way forward, and the energy wasted on futility of  
> archaisms such as gender agreement, minutiae of revisionism in 
> publication dates, obscure priorities, and especially keeping to 
> print-only validity of names, and not registering all new names, than 
> the issues raised here. Politics is everywhere.
>
> Boero F 2010. The Study of Species in the Era of Biodiversity: A Tale 
> of Stupidity. Diversity 2: 115-126.
>
> [Open access]
> http://dx.doi.org/10.3390/d2010115
> http://www.mdpi.com/1424-2818/2/1/115
>
> Geoff
>

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