Taxacom: Taxacom Digest, Vol 214, Issue 7

Thu Feb 15 12:40:18 CST 2024

If the 22 lectures are made available in a digital format it might be
possible to think through the ideas you are proposing to provide.
Otherwise, the time commitment is onerous outside of the context of
university undergraduate enrollment. Please let me know if some alternative
can be provided.

–––––––––––––––––––––––––––––––––
Dr. Brendon E. Boudinot
Hymenoptera Curator & Head of Entomology II
    * Senckenberg Institut & Naturmuseum*
Subject editor

*Historical Biology*

*Journal of Hymenoptera Research*

*Myrmecological News*
     *ZooKeys*
–––––––––––––––––––––––––––––––––

On Thu, Feb 15, 2024 at 19:00 <taxacom-request at lists.ku.edu> wrote:

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> ____________________________________
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> Today's Topics:
>
>    1. Philosophy of Biological Systematics course (Kirk Fitzhugh)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 14 Feb 2024 13:27:17 -0800
> From: Kirk Fitzhugh <kfitzhugh at nhm.org>
> To: taxacom <taxacom at mailman.nhm.ku.edu>
> Subject: Taxacom: Philosophy of Biological Systematics course
> Message-ID:
>         <CABB=imm3zeYf9DTkQn=z-dd=2TEGDX-rVJ+w2kJnodH=
> 5V_3Ag at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Colleagues,
>
> I am again offering my ?????????? ?? ??????????
> ??????????? 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??
>
> --
>
> --
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 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.orghttp://
> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.nhm.org%2Fsite%2Fresearch-collections%2Fpolychaetous-annelids&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Ccd2707bad4ce4a3df5ec08dc2e55968f%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638436192340302095%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=taHLWYYgoBgKGfze8MXx5VxzJPS3OxOXDHlM3Ybwkbs%3D&reserved=0
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
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> Nurturing nuance while assailing ambiguity and admiring alliteration for
> about 37 years, 1987-2024.
>
>
> ------------------------------
>
> End of Taxacom Digest, Vol 214, Issue 7
> ***************************************
>