Taxacom: Philosophy of Biological Systematics course

[Kirk Fitzhugh]

Colleagues,

I am again offering my 𝘗𝘩𝘪𝘭𝘰𝘴𝘰𝘱𝘩𝘺 𝘰𝘧 𝘉𝘪𝘰𝘭𝘰𝘨𝘪𝘤𝘢𝘭
𝘚𝘺𝘴𝘵𝘦𝘮𝘢𝘵𝘪𝘤𝘴 course via Zoom, 6 May to 26 June 2024, involving 22
lectures. Details are provided below.

I would be grateful if you would share this announcement with grad
students, post-docs, faculty members, and systematics researchers you think
might be interested. Contact me at kfitzhugh at nhm.org if you have any
questions.

Thanks,

Kirk Fitzhugh
--------------------------------

*PHILOSOPHY OF BIOLOGICAL SYSTEMATICS:*
*A Short Course Via Zoom*
*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 being offered via Zoom. The course will provide critical
examinations of the principles required to judge the scientific merits of
systematics. During this 22-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 judge such issues as (a) “parsimony,” “likelihood,” “Bayesianism,”
and if their applications to systematics inferences actually matter; (b)
whether or not phylogenetic hypotheses can be inferred to explain sequence
data; (c) evaluate what is required to test phylogenetic hypotheses; (d)
determine if methods of empirical support, e.g., the bootstrap and Bremer
Index, are legitimate; and (e) understand why popular approaches such as
phylogenetic inferences of partitioned data, cladogram comparisons and
character mapping are philosophically and scientifically unacceptable.

*Course logistics:*
• Who should apply: graduate students, postdocs, professors and researchers
with prior training in systematics principles. Previous systematics
coursework highly recommended.
• Contact Kirk Fitzhugh, kfitzhugh at nhm.org, regarding questions or to
register.
• Registration fee: $100 US.
• Registration deadline: 1 May 2024.
• Participants should commit to attend all lectures since each lecture
provides a cumulative foundation for subsequent lectures.
• Registered participants will receive a 1,500-page pdf containing all
course slides and notes.
• A course certificate will be provided upon request after course
completion.
• Zoom Lectures: Mondays, Wednesdays, Fridays: 10 am − 1:45 pm Pacific
Daylight Savings Time (-7 UTC), with a 15-minute break.

*Twenty-two lectures over eight weeks:*
• Week 1 – May 6, 8, 10
• Week 2 – May 13, 15, 17
• Week 3 – May 20, 22, 24
• Week 4 – May 29, 31
• Week 5 – June 3, 5, 7
• Week 6 – June 10, 12, 14
• Week 7 – June 17, 19, 21
• Week 8 – June 24, 26

*Topics included (not an exhaustive list):*
1. Introduction - what this course offers and why

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; species theories, not concepts
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 actually
applied?

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

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 concrete entities,
things, individuals, etc., to be delimited
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 or limited to sequence data only

16. DNA barcoding: caveat emptor
a. barcoding as pure research, e.g., systematics, versus barcoding as
applied research, e.g., ecological assessments
b. implications of species as explanatory hypotheses as opposed to
ontological individuals
c. barcoding cannot be justified as part of systematics research, i.e.,
inferring specific or phylogenetic hypotheses; “dark taxa” are
epistemically unfounded
d. barcoding is marginally justified for applied ecological research under
very limited circumstances

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 of abductive reasoning and taxa as explanatory hypotheses
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%7C02%7Ctaxacom%40lists.ku.edu%7C9eb7c727e3164d3affe908dc2da3c765%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638435428667575215%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=9TolI4OZtld7RfFtGwMZlyoftQ91yfffis3pDYZNi2k%3D&reserved=0
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