Taxacom: Philosophy of Systematics course

Wed Mar 30 22:37:51 CDT 2022

Kirk - interesting course scope. Wish you luck with that - lots of
potential controversy in just about every topic. One item that caught my
attention was reference to " drift versus natural selection". Are you
saying these are the only valid mechanisms to explain the evolution of
sequence differences among taxa?

Also, on defining biodiversity' - I have an opinion on that recently
published. Will send it separately (you may have it, but just in case).

Cheers,  John

On Wed, Mar 30, 2022 at 11:14 PM Kirk Fitzhugh via Taxacom <
taxacom at lists.ku.edu> wrote:

> 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
>
> ----------------------------------------------------------
> 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
>
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