Taxacom: Philosophy of Systematics course

Wed Mar 30 22:14:05 CDT 2022

Colleagues,

My Philosophy of Biological Systematics course will be offered 16 May ? 29
June 2022 via Zoom. The course is free, limited to a maximum of 100
participants, and open to anyone involved in systematics research or with
an interest in systematics. You are encouraged to only consider the course
if you can commit to attending all lectures since each lecture provides a
foundation for subsequent lectures.

Contact me at kfitzhugh at nhm.org regarding registration. Please share this
announcement with anyone you think might be interested.

The schedule of lectures is shown below.

Thanks,
Kirk

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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 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 readily judge such phylogenetics-related concepts
as ?parsimony,? ?likelihood,? ?Bayesianism,? and their relations to
systematics; we can evaluate what is required to test phylogenetic
hypotheses; how to properly judge empirical support for hypotheses; and why
popular approaches such as separate phylogenetic analyses of partitioned
data, cladogram comparisons, and character mapping are scientifically
unacceptable.

*Schedule of lectures:*
? Each lecture will be via Zoom
Mondays, Wednesdays, Fridays
10 am ? 1:15 pm Pacific daylight savings time (-7 UTC), with a 15-minute
break

? Twenty lectures, during seven weeks:
Week 1 - May 16, 18, 20
Week 2 - May 23, 25, 27
Week 3 - May 30, June 1, 3
Week 4 - June 6, 8, 10
Week 5 - June 13, 15, 17
Week 6 - June 20, 22, 24
Week 7 - June 27, 29

? Topics to be covered:
1. Introduction ? 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, hypothesis, and theory
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. the ?species problem? and its solution
b. specific and phylogenetic hypotheses/taxa

9. Some implications for ?phylogenetic? methods
a. the limits of phylogenetic hypotheses
b. relations between types of evidence in systematics
c. abductive reasoning versus ?parsimony?
d. abductive reasoning versus ?likelihood?
e. abductive reasoning versus ?Bayesianism?

10. Dating cladograms: a brief critique
a. what do dates refer to on cladograms?
b. are all relevant causal events even considered when adding
dates?

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 errors of cladogram comparisons and character mapping

12. Homology & homogeny & homoplasy
a. Richard Owen?s use of homologue and homology
b. confusing homology with homologue
c. E.R. Lankester?s (1870) replacement terms, homogen,
homogeny, and homoplasy
d. implications of abductive reasoning for the utility of these
concepts
e. can pluralism work for homology definitions?
f. do we really need the concept of homology in biology?

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
d. can we consider behavior as characters?

14. Sequence data and phylogenetic inference: implications of top-
down causation on the inclusion of sequence data
a. why-questions and sequence data
b. explanatory hypotheses and sequence data ? drift versus
natural selection
c. the concept of downward causation in relation to natural
selection
d. inherent limitations on explaining sequence data ? drift versus
selection via downward causation

15. DNA barcoding: Caveat emptor
a. barcoding as ?systematics? inquiry
b. barcoding as ?applied science?

16. 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.

17. Implications for nomenclature
a. the goal of scientific inquiry versus the goal of a nomenclatural
system
b. the necessity of considering abductive reasoning in a
nomenclatural system
c. uninomial species names are ideally preferred
d. the myth of monotypic supraspecific names
e. the myth of nomenclatural stability
f. formal definitions of systematics names = accurately
representing explanatory hypotheses
g. confusing description and diagnosis

18. Defining biodiversity and conservation
a. biodiversity must be defined in the context of taxa-as-
explanatory hypotheses
b. biodiversity determines the limits on conservation
c. taxa determine the realization of conservation
d. implications of considering individuals/semaphoronts
-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.org
https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.nhm.org%2Fsite%2Fresearch-collections%2Fpolychaetous-annelids&amp;data%7C01%7Ctaxacom%40lists.ku.edu%7C4082b9bde9a14ee8d4df08da12c48a31%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637842932711066283%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=S5n3XEfPNUuxtrTMYr7s6u7UQ1q23yi0I3l2HHnJKUw%3D&amp;reserved=0
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