Taxacom: Taxacom Digest, Vol 214, Issue 7

Thu Feb 15 13:37:51 CST 2024

Thanks, Brendon. As I indicated in my previous email, I provide a pdf of
all material in the course. I agree the time commitment is substantial, but
this is no ordinary systematics course.

Kirk

On Thu, Feb 15, 2024, 10:40 AM Brendon E. Boudinot via Taxacom <
taxacom at lists.ku.edu> wrote:

> 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.
> 
>
> 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:
>
> > Daily News from the Taxacom Mailing List
> >
> > When responding to a message, please do not copy the entire digest into
> > your reply.
> > ____________________________________
> >
> >
> > 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%7C3e9729e69102493a681e08dc2e5da118%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638436226887372293%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=sGzPSFpsInsBg9bLelPKbF19s3SF8hpB9UleB%2Ff8NVg%3D&reserved=0
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >
> >
> > ------------------------------
> >
> > Subject: Digest Footer
> >
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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
> > ***************************************
> >
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> You can reach the person managing the list at: taxacom-owner at lists.ku.edu
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>
> Nurturing nuance while assailing ambiguity for about 37 years, 1987-2024.
>
> Made weak by time and fate, but strong in will, To strive, to seek, to find, and not to yield. Tennyson, Ulysses.
>
>