Taxacom: Philosophy of Biological Systematics Course

[Kirk Fitzhugh]

Colleagues,

I am again offering my international Philosophy of Biological Systematics
course via Zoom, from 15 May to 30 June 2023. The course is open to anyone
involved in systematics research or with an interest in systematics.

Contact me at kfitzhugh at nhm.org to register or if you have any questions.

Please share this announcement with anyone you think might be interested.

Thanks,
Kirk
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*PHILOSOPHY OF BIOLOGICAL SYSTEMATICS: a short course*
Kirk Fitzhugh, Natural History Museum of Los Angeles County

Systematics has become a field of research with many different and often
conflicting perspectives and methods. How does one decide among these
options? Is there a basis for critically evaluating how systematics should
function as a science? Approaching the subject from the perspective of the
philosophical foundations of science, Philosophy of Biological Systematics
is a unique course offering critical examinations of the principles
required to judge the scientific merits of systematics. During this 21-day
course, we will examine the nature of scientific inquiry and what is
required for systematics to operate within established principles of
rational reasoning. From those basics we can more readily (a) judge such
concepts as “parsimony,” “likelihood,” “Bayesianism,” and their relations
to systematics; (b) evaluate what is required to test phylogenetic
hypotheses; (c) determine how to judge the empirical support for
hypotheses; and (d) understand why popular approaches such as separate
phylogenetic analyses of partitioned data, cladogram comparisons, and
character mapping are scientifically unacceptable.

*Course logistics:*
• Contact Kirk Fitzhugh, kfitzhugh at nhm.org, to register or if you have any
questions

• Registration is free

• Registered participants should plan to attend all lectures since each
lecture provides a cumulative foundation for subsequent lectures

• Registered participants will receive a 1,400+ page pdf containing all
course slides and notes

• A course certificate will be provided upon request after course completion

• Lectures will be via Zoom; Mondays, Wednesdays, Fridays
10 am ‒ 1:45 pm Pacific daylight savings time (-7 UTC), with a 15-minute
break, and 30-minute question/comment period at the end of each day’s
lecture period

• Twenty-one lectures, during seven weeks:
Week 1 - May 15, 17, 19
Week 2 - May 22, 24, 26
Week 3 - May 29, 31, June 2
Week 4 - June 5, 7, 9
Week 5 - June 12, 14, 16
Week 6 - June 19, 21, 23
Week 7 - June 26, 28, 30

*The following topics will be addressed:*
1. Introduction ꟷ what this course offers

2. The goal of science; the goal of biological systematics
a. the nature of understanding
b. basic foundations of scientific inquiry
c. systematics versus taxonomy

3.  Causal relationships in systematics
a. taxa and causal understanding

4.  The nature of why-questions

5.  The three forms of reasoning: deduction, induction, abduction

6.  The uses of deduction, induction, and abduction in science
a. defining fact, theory, and hypothesis
b. background knowledge
c. mechanics of theory and hypothesis testing
d. the meanings of evidence and support

7.  Systematics involves abductive reasoning

8.  Inferences of systematics hypotheses, i.e., taxa
a. taxa are explanatory hypotheses, per the goal of scientific inquiry
b. the “species problem” and its solution
c. abductive inferences of specific and phylogenetic hypotheses/taxa

9.  Some implications for “phylogenetic” methods
a. the limits of phylogenetic hypotheses
b. beware of “tree thinking”
c. relations between types of evidence in systematics
d. abductive reasoning versus “parsimony methods”
e. abductive reasoning versus “likelihood methods”
f. abductive reasoning versus “Bayesian methods”

10.  Dating cladograms: a (very) brief critique
a. to what explanatory hypotheses implied by cladograms are dates applied?

11. The requirement of total evidence (RTE)
a. relation of RTE to inference
b. relation of RTE to systematics
c. implications for systematics
d. the significant errors of cladogram comparisons and character mapping

12.  Homology & homogeny & homoplasy: are these terms needed?
a. Richard Owen’s use of homologue and homology
b. E.R. Lankester’s replacement terms, homogen, homogeny, and homoplasy
c. implications of abductive reasoning and the RTE for the utility of these
concepts

13.  Character coding
a. why character coding is necessary for systematics
b. accurately representing observation statements
c. character coding, why-questions, and the data matrix

14.  Sequence data and phylogenetic inference: implications of top-down
causation on considering sequence data
a. sequence data, genetic drift, natural selection
b. sequence data, why-questions, and the data matrix
c. top-down causation
d. can we really explain shared nucleotides?

15.  The “species delimitation” myth
a. once again, species are explanatory hypotheses, not entities, things,
individuals, etc.
b. “species delimitation” methods
c. the misconceptions of “gene trees” versus “species trees”
d. implications of the RTE for “delimitation” methods
e. examples of the failure of “delimitation” methods
f. take-home message: inferences of specific hypotheses cannot be
accomplished via phylogenetic inferences

16.  DNA barcoding: caveat emptor
a. barcoding as pure research versus barcoding as applied research
b. barcoding cannot be justified as part of pure systematics research,
i.e., inferring specific or phylogenetic hypotheses
c. barcoding is justified as applied research under very limited conditions

17.  The mechanics of hypothesis testing in biological systematics
a. traditional misconceptions about testing phylogenetic hypotheses
b. mechanics of testing explanatory hypotheses, revisited
c. the uses of evidence, revisited
d. what is actually required to test phylogenetic hypotheses
e. the limits on acquiring causal understanding via phylogenetic hypotheses
f. the myths of support measures: bootstrap, jack-knife, Bremer, etc.

18.  Implications for nomenclatural systems

19.  Defining biodiversity and conservation; do we need the term
“biodiversity?”

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-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
J. Kirk Fitzhugh, Ph.D.
Curator of Polychaetes
Invertebrate Zoology Section
Research & Collections Branch
Natural History Museum of Los Angeles County
900 Exposition Blvd
Los Angeles CA 90007
Phone: 213-763-3233
FAX: 213-746-2999
e-mail: kfitzhug at nhm.orghttps://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.nhm.org%2Fsite%2Fresearch-collections%2Fpolychaetous-annelids&data=05%7C01%7Ctaxacom%40lists.ku.edu%7C110cb169a771458a800508db1a95ea6b%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638133003410966169%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=aWhcBWbsuojLKqyN2%2FzqAwbz8FjAbO1YpblvKkJ6Afo%3D&reserved=0
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