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'''Philosophy on Rails: An Introduction to Ontology''' Special Topic PHI 579 

Fall Semester 2020, Monday 1-3:40pm

'''Venue:''' Online

'''Registration''': Class#: [http://www.buffalo.edu/class-schedule?switch=showclass&semester=fall&division=GRAD&dept=PHI&regnum=24202 24202]

'''Instructor''': [http://ontology.buffalo.edu/smith/shortcv.htm Barry Smith]

'''Prerequisites''': Open to all persons with an undergraduate degree and some knowledge of philosophy.

'''Office hours''': By appointment via email at [mailto:phismith@buffalo.edu phismith@buffalo.edu] 

== '''The Course''' ==
''Course Description'': Progress in philosophy has been hampered by the fact that philosophers have no shared, controlled vocabulary which they can use as a common starting point when defining their terms. Even mundane terms like ‘world’, ‘fact’, and ‘harm’ have such a variety of meanings that when competing theories use such terms their defenders can often be accused of talking past one another and of engaging in merely verbal disputes. This is in contrast to what is the case in the natural sciences, where consistent terminology – as codified for example in the Periodic Table and the International Standard System of Units – is recognized as indispensable. To put it bluntly, because of the use of standards, the natural sciences are collectively more successful than philosophers at resolving divergent points-of-view in their respective fields. Of course, the idea of developing a shared system of philosophical terms and definitions has been advanced in different forms already, for example by Aristotle in the ''Categories'', by Leibniz in ''De Arte Combinatoria'', by the early Wittgenstein, and by Carnap in his ''Logical Structure of the World''. Similar methods are nowadays being successfully applied, but this is occurring primarily outside philosophy, in areas such as biomedical informatics and industrial engineering. 

This course will address four goals: 

:'''First''', it will explore how to create and use a standard philosophical vocabulary. This will include exploiting modern developments in computational ontology, including the world’s first [https://www.iso.org/standard/74572.html international standard ontology]. 
:'''Second''', it will explore the ways in which building a restricted philosophical vocabulary can help to arbitrate philosophical disputes in areas such as time, mental content, modality, and obligation. 
:'''Third''', it will provide an introduction to the methods of contemporary applied ontological that are being used both inside and outside philosophy. 
:'''Fourth''', it will take students through all the steps involved in writing a paper and submitting it for publication and/or for presentation at a conference. Some of these papers will be authored by teams of up to 3 people (students can write alone, or belong to up to two teams).

''Course Structure'': This is a three credit hour graduate seminar, with a practical exercise forming part of each class.  Students will be trained in the basic tools and methods of ontology, and of how ontology can be used to help consistent formalization of philosophical and other theories.
In the initial weeks the practical exercise will take the form of one-to-one interactions with Dr Smith determining the topics and strategy for paper writing. In the middle weeks it will take the form of presentation of critiques of submitted drafts. In the final sessions it will be structured around preparation of powerpoint slides to support class presentations by students of their written work, presentations which will be recorded. .

''Target Audience'': The course is open to all interested students with an undergraduate degree and some knowledge of philosophy.

----

== Preamble ==

Background Reading: [https://buffalo.box.com/v/Whats-wrong-with-AP What's wrong with analytic philosophy?]

The philosophical methodology that underlies this course produced Basic Formal Ontology (BFO), which was approved by the International Standards Organization in 2019 as standard ISO/IED 21838-2. A textual version of BFO is available [https://buffalo.app.box.com/v/BFO-2020-Supplementary-Files/file/647823963055 here]. A BFO textbook is available ;https://mitpress.mit.edu/books/building-ontologies-basic-formal-ontology here]. 

Students are invited to explore possible ways of doing philosophy constrained by BFO or by similar top-level ontologies.  

They are invited to identify ways in which using BFO and ontologies conformant to BFO might be of benefit to philosophers, for example in tagging philosophical literature to make it more easily discoverable. How would one build out an ontology, whose terms could be used to tag philosophical literature? How does the categorization strategy used by PhilPapers measure up to the standards of what would be needed by an ontology-grounded tagging system?

A collection of uses of BFO can be found [http://basic-formal-ontology.org/users.html here].

''Proposed Topics for Papers''

The topics listed under successive dates, below, are intended at this stage only to provide an initial set of ideas for possible papers. We will decide as the semester proceeds on what the focus should be for each week. Here are some further ideas for possible papers:

:[https://ndpr.nd.edu/news/when-words-are-called-for-a-defense-of-ordinary-language-philosophy/ How did Austin's military experience in WWII influence his mode of doing philosophy] (Or: Can philosophy be performed through teamwork?)
:How can the [https://philpapers.org/categories.pl Philpapers category system] be improved? 
:How can the [https://philpapers.org/help/categorization.html rules for categorizing papers in Philpapers] be improved?
:Formalizing the [https://plato.stanford.edu/entries/capability-approach/ Amartya Sen/Martha Nussbaum ontology of capabilities]
:In many cases papers would consist in presentations of ontologies or classifications or sets of formal or semi-formal definitions of philosophical relevant terms. Examples of the such classifications might be: 
::1. A classification of responses to the Gettier argument
::2. A classification of (a) definitions of disease coupled with (b) proposed counterexamples for each disease-type. 
::3. A comprehensive catalogue of definitions of 'harm'
::4. A comprehensive catalogue of definitions of causality
:Formalization of the content of any philosophical work, as for example in [https://www.jstor.org/stable/20115250?seq=1#metadata_info_tab_contents Charles Jarrett, "The Logical Structure of Spinoza's ''Ethics'', Part I", ''Synthese'', 37 (1), 1978]

==August 31: Introduction: Philosophy on Rails==

Philosophy on Rails
:[https://buffalo.box.com/v/Philosophy-on-Rails Slides]
:[https://www.youtube.com/watch?v=w5I8kxqDSeo Video] (28 minutes)

Driverless Philosophy 
:[https://buffalo.box.com/v/Driverless-Philosophy Slides]
:[https://www.youtube.com/watch?v=29GE_p5GEtY Video] (73 minutes)

Example: The Emotion Ontology
:[https://buffalo.box.com/s/jli8soa96pwixvs4e4r2yyq6qumt8tar Slides]
:[https://www.youtube.com/watch?v=BYAT8vHZ8ik Video] (38 minutes)

Readings 
:Amanda Bryant, "[https://philpapers.org/rec/BRYKTC Keep the chickens cooped: the epistemic inadequacy of free range metaphysics]", ''Synthese'' 197 (5): 1867-1887. 2020.

Precursors

:[https://books.google.com/books?id=858AHFXOt5EC&printsec=frontcover&source=gbs_ge_summary_r&cad=0#v=snippet&q=smith&f=false Chisholm]
:[https://philpapers.org/archive/MILICA-6.pdf Ingarden]
:Armstrong, D. M. ''[https://www.oxfordscholarship.com/view/10.1093/acprof:oso/9780199590612.001.0001/acprof-9780199590612 Sketch for a Systematic Metaphysics]'', Oxford University Press, 2010.
:[https://github.com/BFO-ontology/BFO/raw/master/docs/bfo2-reference/BFO2-Reference.pdf BFO 2.0]

==September 7: The Ontology of Philosophy ==

Making the Content of Philosophy Accessible Systematically 

Pierre Grenon and Barry Smith, “[http://ontology.buffalo.edu/smith/articles/Ontology_of_Philosophy.pdf Foundations of an Ontology of Philosophy]”, Synthese, 2011, 182 (2), 185-204.

Describes an ontology of philosophy that is designed to help navigation through philosophical literature, including literature in the form of encyclopedia articles and textbooks and in both printed and digital forms. The ontology is designed also to serve integration and structuring of data pertaining to the philosophical literature, and in the long term also to support reasoning about the provenance and contents of such literature, by providing a representation of the philosophical domain that is orientated around what philosophical literature is about. 
:[http://ontology.buffalo.edu/philosophome/pdcphilontology-v1.owl OWL]
:[http://ontology.buffalo.edu/philosophome/philonto/philontologyX013.gif gif]
:[https://www.youtube.com/watch?v=5HV3M0NvyPM Video] 40 minutes
 

Overview
:[http://philosophome.org/ The Philosophome]


Ontology of Philosophy
:[https://www.youtube.com/watch?v=5HV3M0NvyPM  Video] 40 minutes
:[https://buffalo.box.com/v/Philosophome-2015  Slides] 


History of Philosophy 
:[https://www.youtube.com/watch?v=YkYlY2jnRxc Video] 98 minutes
:[https://buffalo.box.com/v/Future-of-History Slides]
:N. Milkov, [https://philpapers.org/rec/MILALH A Logical–Contextual History of Philosophy], ''Southwest Philosophy Review'' 27 (1):21-29 (2011)


Examples of philosophical categorizations 
:[https://philpapers.org/browse/all List of philpapers.org Categories]
:Dimitris Gakis (2016) "[https://doi.org/10.1080/05568641.2016.1188547 Philosophy as Paradigms: An Account of a Contextual Metaphilosophical Perspective]", ''Philosophical Papers'', 45:1-2, 209-239.
:[https://publiscologne.th-koeln.de/frontdoor/deliver/index/docId/1363/file/MAT_Seidlmayer.pdf Eva Seidlmayer, ''An ontology of digital objects in philosophy'']

:Advancing beyond the [https://philpapers.org/browse/all PhilPapers Table of Categories]

==September 14: An Introduction to Basic Formal Ontology==

Background: Robert Arp, Barry Smith and Andrew Spear, [https://mitpress.mit.edu/index.php?q=books/building-ontologies-basic-formal-ontology Building Ontologies with Basic Formal Ontology], Cambridge, MA: MIT Press, August 2015.

The ISO Standardization Process

ISO/IEC 21838
:[https://www.youtube.com/watch?v=_0masZPGLb0 Video] (20 minutes)
:[https://buffalo.box.com/v/Ontology-Summit-2020 Slides]

Basic Formal Ontology
:[https://www.youtube.com/watch?v=p0buEjR3t8A Video] (70 minutes)
:[https://buffalo.box.com/v/ICBO-2019-BFO-Tutorial Slides]

Basic Formal Ontology Applied to the Ontology of Language 
:[https://www.youtube.com/watch?v=Y3btP1InPZY&list=PLyngZgIl3WTjK-D7L1pdtpqzxIBhjBsb_&index=5 Video] (40 minutes)
:[https://buffalo.box.com/v/Immortality-and-Turing-Test Slides]

--
Modes of Philosophical Derailment / Why Computer Science Needs Philosophy
:"... philosophical problems arise when language goes on holiday.” Wittgenstein, ''Philosophical Investigations'', §38
:Preliminary reading: "[http://hl7-watch.blogspot.com/2008/02/weight-of-baby.html The Weight of the Baby]"
:[https://www.youtube.com/watch?v=0yfhUt1LrIo Video] (51 minutes)
:[https://buffalo.box.com/s/v04c0oaywzts54m2qqnmswigwmhjc6l6 Slides]

==September 21: Philosophy of Language ==

Truth and the Ontology of Maps
:[https://www.youtube.com/watch?v=Jqqq7eBnZvE&list=PLyngZgIl3WTjK-D7L1pdtpqzxIBhjBsb_ Video] (20 minutes)
:https://buffalo.box.com/v/Truth-and-the-Ontology-of-Maps Slides]

Ontology of Language, Ontology of Terrorism, Ontology of Obligations
:[https://www.youtube.com/watch?v=G4lg1_-XpiE&list=PLyngZgIl3WTjK-D7L1pdtpqzxIBhjBsb_&index=4 Video] (88 minutes)
:[https://buffalo.box.com/v/Ontology-of-Language Slides]

Command and Control
:[https://www.youtube.com/watch?v=U8LTHhpF4Wk Video] (60 minutes)
:[https://buffalo.box.com/v/Command-and-Control Slides]

:Karl Bühler on logical vs. material derailment (''Entgleisung''). See Mulligan [https://www.unige.ch/lettres/philo/files/6614/2644/2862/mulligan_EssenceLanguageWBBB4.pdf here].

:Nosology of Continental Philosophy. See Mulligan [https://www.unige.ch/lettres/philo/files/8614/2644/2135/mulligan_PostContinentalPhilosophy1.pdf here].

==September 28: Philosophy of Science ==

The Replication Crisis in Pharmaceutical Science 
:[https://www.youtube.com/watch?v=3QPpUhVOiPE Video] (70 minutes) 
:[https://buffalo.box.com/s/gonk4yplf5niimpwi429ii89d4r1dzmn Slides]

Quantities as Fiat Universals
:[https://www.youtube.com/watch?v=xVVUH00cMNY&list=PLyngZgIl3WTj8kH_CMlBPVhaJT45rbPWw&index=17&t=0s Video] (78 minutes)
:[https://buffalo.box.com/v/Quantities-as-fiat-universals Slides]

Functions, Dispositions and Capabilities
:[https://www.youtube.com/watch?v=gJxfZ3cq5jE Video] (47 minutes)
:[https://buffalo.box.com/s/2zgx6emfas2t9ocik7n0c5ldkafymopc Slides]

:[https://doi.org/10.1371/journal.pone.0154556 A. Bandrowski, et al., "The Ontology for Biomedical Investigations", ''PLoS ONE'', 2016]

==October 5: Ontology of Documents ==

The Ontology of Document Acts (2005)
:[https://www.youtube.com/watch?v=TvwHy2-3Lss&feature=youtu.be&t=2143 Video] (50 minutes)
:[https://buffalo.box.com/v/Bozzi-Prize-Lecture Slides]

Documents and Massive Social Agency (2013)
:[https://www.youtube.com/watch?v=I2vvVM7ff28 Video] (21 minutes)

From Speech Acts to Document Acts (2018) 
:[https://www.youtube.com/watch?v=5chInYVVypI Video] (24 minutes)
:[https://buffalo.box.com/s/4v54yvkduv2r5qrdjo1racc355ywmj03 Slides]

Searle on the Ontology of Money
:[https://www.youtube.com/watch?v=dHo-Tn_v8xM Video] (39 minutes)
:[https://buffalo.box.com/s/ipuxsaapkdne29g2lhqsg70kahnssra1 Slides]

The Documentome
:[https://buffalo.app.box.com/s/swb8dupnopuox0o9ihl8j8gv0sxxp8ay Slides]

==October 12: Introduction to Protégé ==

Includes introduction to the ontology authoring and editing software at [https://protege.stanford.edu/]

==October 19: Metaphysics ==

:Mind, Language and Emotions: From Austrian Philosophy to Contemporary Realist Ontology
:[https://www.youtube.com/watch?v=3Vw3R5UCcDI Video] (67 minutes)
:[http://ontology.buffalo.edu/14/Rijeka/Ontology-of-Documents-May-2014-Rijeka.ppt Slides]

:What are capabilities?
:[https://buffalo.box.com/s/kvvq8qjb22rc80k8j7g4w7odi1hkhztz Slides] (60 minutes)
:[https://youtu.be/gHxDOFXu6CA Video]

:The Great Debate: John Sowa vs. Barry Smith
:[https://www.youtube.com/watch?v=TDJk9xTvdqY Video of BS contribution] (30 minutes)
:[http://bit.ly/2row7xT Slides of BS contribution]
:[http://bit.ly/2robKkp First 2 hours of whole debate]
:[http://bit.ly/2rnIdHE Final part of whole debate]

==October 26: Social Ontology, Norms and Values ==

Deontic Entities 

:Deontology Ontology: Towards an Ontology of Deontic Entities
::[http://ontology.buffalo.edu/smith/ppt/documents/Deontic-Entities-Geneva-July-2016.pdf Slides] 
::[https://www.youtube.com/watch?v=WIJJlnLLWGU Video] (36 minutes)

:Document Acts and the Ontology of Social Reality
::[http://ontology.buffalo.edu/14/Rijeka/Ontology-of-Documents-May-2014-Rijeka.ppt Slides]
::[https://www.youtube.com/watch?v=4lg4z2up6HI Video] (103 minutes)

:The Ontology of the Organigram 
::[http://ontology.buffalo.edu/16/Organigram.pdf Slides]
::[https://www.youtube.com/watch?v=bp3B2GkgaB8 Video] (58 minutes)

Background
:[https://buffalo.box.com/v/Deontic-Entities-in-BFO Slides]
:[https://search.proquest.com/openview/4ddf6056e26862d1573f674fe123b20b/1?pq-origsite=gscholar&cbl=18750&diss=y Social Ontology and Social Normativity]

==November 2: Artificial Intelligence==

:"[https://arxiv.org/pdf/1901.02918.pdf Making Artificial Intelligence Meaningful Again]", ''Synthese'', [https://link.springer.com/article/10.1007/s11229-019-02192-y online first]

:"[https://arxiv.org/pdf/1906.05833.pdf There is no General Artificial Intelligence"], https://arxiv.org/pdf/1906.05833.pdf

==November 9: Capabilities ==

:Capabilities

:[https://buffalo.box.com/v/capabilities-summary-Nov11 Slides]

:''Reading''
:[https://philarchive.org/archive/MERMC Eric Merrell, et al., "Mental Capabilities", ICBO, 2019]

==November 16: Philosophy of Information ==

:The Information Ontology

:[https://www.youtube.com/watch?v=PBKsupBquok&list=PLyngZgIl3WTi9ez4OjbXDlYtLb-vSxLHc Video]

:Werner Ceusters and Barry Smith, "[https://philpapers.org/archive/CEUATF.pdf Aboutness: Towards Foundations for the Information Artifact Ontology]", ''Proceedings of the Sixth International Conference on Biomedical Ontology'' (ICBO). CEUR vol. 1515. pp. 1-5 (2015).

==November 23: Philosophy of Action ==

==November 30: Student Projects==

==December 7: Student Projects (Remote Session) ==

1:00 

=='''Reading'''== 

----

== '''Student Learning Outcomes''' ==
          
{| class="wikitable"
|-
! Program Outcomes/Competencies  
! Instructional Method(s)
! Assessment Method(s)
|-
| The student will acquire a knowledge of the principles and procedures of ontology, and an insight into the philosophical methods and theories relevant thereto. The student will also acquire a familiarity with research in formal philosophy and analytic metaphysics. 
| Lectures and class discussions
| Review of reading matter and associated online content and participation in class discussions
|-
| The student will acquire experience in using the methods employed in applied ontology, especially as applied to philosophical theories and systems

| Participation in practical experiments
| Review of results 
|-
| The student will acquire experience in communicating the results of work using ontologies and in the potential of modern applied ontology as a tool to aid philosophical understanding
| Creation of youtube presentation and of associated documentation
| Review of results
|}

=='''How to Write an Essay'''==
[https://web.archive.org/web/20191209181112/https://jordanbpeterson.com/wp-content/uploads/2018/02/Essay_Writing_Guide.docx Jordan Peterson's Essay Writing Guide]

=='''Important Dates'''==
{|
|  Sep 1 || - about now start to discuss by email the content of your essay or essays with Dr Smith
|-
|   Sep 14 || - submit proposed title and abstract
|-
|   Sep 28 || - submit a table of contents and 300 word summary plus draft of associated ppt slides
|-
|   Oct 15 || - submit first draft of essay (~1000 words) and associated powerpoint (~10 slides)
|-
|   Nov 15 || - submit second draft of essay (~2000 words) and associated powerpoint (~10 slides)
|-
|   Dec7 || - class presentation
|-
|   Dec 11 || - submit final version of essay and powerpoint and upload final version of video to youtube
|}

=='''Grading'''==

Grading will be based on two factors: 

I: understanding and criticism of the material presented in classes 1-13

All students are required to take an active part in class (and where relevant on-line) discussions throughout the semester. 

II: preparation of an essay, and associated powerpoint slides and recorded presentation. 

Content and structure of the essay should be discussed with Dr Smith. Where the essay takes the form of the documentation of a specific ontology developed by the student it should include:
:Statement of scope of the ontology
:Summary of existing ontologies in the relevant domain
:Explanation of how your ontology differs from (or incorporates) these ontologies
:Screenshots of parts of the ontology with some examples of important terms and definitions
:Summaries of potential applications of the ontology

'''Grading Policy:''' Grading follows standard [http://grad.buffalo.edu/Academics/Policies-Procedures/Grading-Procedures.html Graduate School policies]. Grades will be weighted according to the following breakdown:

Weighting	Assignment
:20%    - class discussions  
:15%    - youtube video presentation
:15%    - powerpoint slides 
:50%    - essay 

'''Final Grades'''

Percentages refer to sum of assignment grades as listed above

Grade	Quality Percentage
{|
|  A	|| 4.0	|| 90.0% -100.00%
|-
| A-	|| 3.67	|| 87.0% - 89.9%
|-
| B+	|| 3.33	|| 84.0% - 86.9%
|-
| B	|| 3.00	|| 80.0% - 83.9%
|-
| B-	|| 2.67	|| 77.0% - 79.9%
|-
| C+	|| 2.33	|| 74.0% - 76.9%
|-
| C	|| 2.00	|| 71.0% - 73.9%
|-
| C-	|| 1.67	|| 68.0% - 70.9%
|-
| D+	|| 1.33	|| 65.0% - 67.9%
|-
| D	|| 1.00	|| 62.0% - 64.9%
|-
| F	|| 0	|| 61.9% or below
|}

An interim grade of Incomplete (I) may be assigned if the student has not completed all requirements for the course. An interim grade of 'I' shall not be assigned to a student who did not attend the course. The default grade accompanying an interim grade of 'I' shall be 'U' and will be displayed on the UB record as 'IU.' The default Unsatisfactory (U) grade shall become the permanent course grade of record if the 'IU' is not changed through formal notice by the instructor upon the student's completion of the course.

Assignment of an interim 'IU' is at the discretion of the instructor. A grade of 'IU' can be assigned only if successful completion of unfulfilled course requirements can result in a final grade better than the default 'U' grade. The student should have a passing average in the requirements already completed. The instructor shall provide the student specification, in writing, of the requirements to be fulfilled.

The university’s Graduate Incomplete Policy can be found [http://grad.buffalo.edu/study/progress/policylibrary.a-to-z.html#iugrade here].

=='''Related Policies and Services'''==

'''Academic integrity''' is a fundamental university value. Through the honest completion of academic work, students sustain the integrity of the university while facilitating the university's imperative for the transmission of knowledge and culture based upon the generation of new and innovative ideas. See http://grad.buffalo.edu/Academics/Policies-Procedures/Academic-Integrity.html. 

'''Accessibility resources:''' If you have any disability which requires reasonable accommodations to enable you to participate in this course, please contact the Office of Accessibility Resources in 60 Capen Hall, 645-2608 and also the instructor of this course during the first week of class. The office will provide you with information and review appropriate arrangements for reasonable accommodations, which can be found on the web [http://www.buffalo.edu/studentlife/who-we-are/departments/accessibility.html here].

'''University suppert services:''' Students are often unaware of university support services. For example, the Center for Excellence in Writing provides support for written work, and several tutoring centers on campus provide academic success support and resources.

'''Available resources on sexual assault:''' UB is committed to providing an environment free of all forms of discrimination and sexual harassment, including sexual assault, domestic and dating violence and stalking. If you have experienced gender-based violence (intimate partner violence, attempted or completed sexual assault, harassment, coercion, stalking, etc.), UB has resources to help. This includes academic accommodations, health and counseling services, housing accommodations, helping with legal protective orders, and assistance with reporting the incident to police or other UB officials if you so choose. Please contact UB’s Title IX Coordinator at 716-645-2266 for more information. For confidential assistance, you may also contact a Crisis Services Campus Advocate at 716-796-4399.

'''Counseiling services:''' As a student you may experience a range of issues that can cause barriers to learning or reduce your ability to participate in daily activities. These might include strained relationships, anxiety, high levels of stress, alcohol/drug problems, feeling down, health concerns, or unwanted sexual experiences. Counseling, Health Services, and Health Promotion are here to help with these or other concerns. You learn can more about these programs and services by contacting: 
:Counseling Services: 120 Richmond Quad (North Campus), phone 716-645-2720
:Health Services: Michael Hall (South Campus), phone: 716-829-3316
:Health Promotion: 114 Student Union (North Campus), phone: 716- 645-2837