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'''PHI 548 (seminar, 3 credits). Registration number: [http://www.buffalo.edu/class-schedule?switch=showclass&semester=fall&division=GRAD&dept=PHI&regnum=24057 24057]'''
'''PHI 637 (seminar, 2 credits). Registration number: [http://www.buffalo.edu/class-schedule?switch=showclass&semester=fall&division=GRAD&dept=PHI&regnum=]'''


'''This course is cross-listed with BMI 508, which is offered as part of the newly accredited PhD program in UB's [http://www.smbs.buffalo.edu/biomedicalinformatics/index.php Department of Biomedical Informatics]
'''Time''': 1:00-3:50pm, selected Mondays (TBD), Fall Semester 2024


'''Time''': 4:00-6:50pm, Mondays, Fall Semester 2016
'''Room''': Park 141, UB North Campus


'''Room''': Baldy 200-G, UB North Campus
'''Instructors''': [http://ontology.buffalo.edu/smith/ Barry Smith] (Philosophy) and [https://www.philosophie.uzh.ch/en/seminar/people/research/politics_cheneval/martinelli.html Emanuele Martinelli] (Philosophy, University of Zurich)


'''Instructors''': [http://ontology.buffalo.edu/smith/ Barry Smith] (Philosophy) and [http://www.referent-tracking.com/RTU/?page=ceusters_vita Werner Ceusters] (Biomedical Informatics)
'''Office hours''': BS: by appointment via [mailto:phismith@buffalo.edu email]; EM: by appointment via [mailto:emanuele.martinelli@uzh.ch email]


'''Office hours''': BS: by appointment via [mailto:phismith@buffalo.edu email]; WC: TBA
'''Course Description'''  


'''Course Description'''
The goal of the course is to give the students conceptual tools to understand and evaluate critically the philosophical assumptions of different schools of thought in economics. Debates between different approaches in economics may be viewed in part as ontological debates as to the nature of social entities such as prices, markets, economic actors. Hence, the course aims at introducing the core categories that determine the world of economics and exploring how different interpretations of these categories can support different economic claims and systems.


This course provides an introduction to biomedical ontology. It will review how data and information are generated through biological and biomedical experiments and through patient care, and show how ontologies are used in accessing, maintaining and exploiting the results. We will describe how biomedical ontologies are developed and evaluated and provide a comparative critical analysis of the principal current ontology resources. We will also review the major theories, methods and tools for the development of ontologies, and illustrate how these are being used in different areas of biomedical research and healthcare. On completion of this course students will have a thorough understanding of strategies to manage and exploit biomedical data; they will have a knowledge of categorization, of the philosophy of experimentation, of the philosophy of medicine, and of computer-based reasoning with data. The seminar will be highly interactive, featuring debates between Drs Smith and Ceusters and between Smith and Ceusters and the course participants.
Part One of the course introduces topics in social ontology with an eye on economic applications: agency, complexity, information, collectivity, speech acts, claims and obligations.  


All slides and videos will be made available at [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology this link]
Part Two analyzes themes underlying the works of the main contemporary economic schools of thought. Austrian economics will be given special prominence because it is arguably the economic school of thought that makes the most open use of philosophical categories in its theories.


=='''Recommended background reading''' ==
=='''Recommended background reading''' ==
:R. Arp, B. Smith, A. D. Spear, ''[https://mitpress.mit.edu/index.php?q=books/building-ontologies-basic-formal-ontology Building Ontologies with Basic Formal Ontology]''


== '''Recommended background video content''' ==
W. Grassl, and B. Smith (eds.), 2010, Austrian Economics: Historical and Philosophical Background, pp: 1-36, [https://buffalo.box.com/s/9qe3texjo9jwxctoodcu4v66jhrakt20]


Selections from: [http://ncorwiki.buffalo.edu/index.php/Ontological_Engineering_2013]
F. A. Hayek, 1945, "The Use of Knowledge in Society", [https://german.yale.edu/sites/default/files/hayek_-_the_use_of_knowledge_in_society.pdf]
== '''Schedule''' ==


== 8/29/2016 Introduction to Ontology 1: General Overview (BS) ==
G. M. Hodgson, 2007, “Meanings of Methodological Individualism”, [https://www.tandfonline.com/doi/abs/10.1080/13501780701394094]
[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-1.pptx Slides]


Roots of ontology in
C. List & P. Pettit, 2011, "Group Agency: The Possibility, Design, and Status of Corporate Agents", Part I, [https://academic.oup.com/book/3619?login=false]
*artificial intelligence ([https://www.academia.edu/722721/The_second_naive_physics_manifesto Second Naive Physics Manifesto])
*library science ([https://www.nlm.nih.gov/mesh/subhierarchy.html MeSH])
*Semantic Web ([https://en.wikipedia.org/wiki/Web_Ontology_Language OWL])
*Human Genome Project ([http://geneontology.org Gene Ontology])


== 9/12/2016  Ontology of Clinical Practice (WC) ==
== '''Recommended background video content''' ==
[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-2.pptx Slides]


Disease vs. diagnosis; Electronic Health Records and other systems and techniques for modeling, representing and maintaining patient data
Barry Smith, 2023, "Beyond the Goods-Services Continuum", [https://www.youtube.com/watch?v=CZUmhg7vzRs]
*[http://www.slideserve.com/joben/toward-an-ontology-for-general-medical-science Ontology for General Medical Science]
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/ Toward an Ontological Treatment of Disease and Diagnosis]


== 9/19/2016  Ontology of Experiments (WC, BS) ==
== '''Schedule''' ==  


'''Part 1: Ontology of Clinical Practice (continued)''' (WC)
== September 30: Introduction: Economic Agents and Agency ==


[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-3-part1.pptx Slides]
This class introduces the topic of 'agency' from the point of view of social ontology, with a focus on the different kinds of agents that populate the social world. This reflection of agency can make our understanding of core economic notions more sophisticated, including economic actors, markets, government interventions, firms. When reflecting on the assumptions of different economic models, philosophical considerations about society are instrumental. Another very important conceptual distinction is that between 'collectivism' and 'individualism'. Moving from the various levels of this distinction, the class will examine the methodological division between microeconomics and macroeconomics under the lense of individualist-collectivist sprectrum in the socio-ontological literature.


Representing clinical data
== October 7: Market Equilibrium and Critical Perspectives ==


'''Part 2: Ontology of Scientific Research''' (BS)
This class introduces the main contemporary proposals that have been advanced throughout mainstream economics to overcome some core tenets of classical economics. This will include reflection on the assumptions of neoclassical economics (in particular as represented by Léon Walras' works on general equilibrium models). The core tenets of (neo)classical economics, such as economic rationality, utility maximization, and general equilibrium, are discussed in their deeper philosophical implications by comparing them with notions of social ontology previously introduced in the course. Different perspectives that try to move away from classical economics in these regards are presented, with a major focus on schools of economic thoughts that have critized the core notion of economic equilibrium, from Keynesian economics, to complexity economics, to behavioral economics, to Austrian economics.


[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-3-part2.pptx Slides]
== October 14: FALL BREAK (No class) ==


Background on philosophy of science
== October 21: Economic Goods and Institutions  ==


The generation and dissemination of new knowledge through scientific experiments
Samuelson's classic notions of 'rivalry' and 'excludability' and the subsequent debate around the definition of public goods may be extended to draw a basic ontology of different kinds of economic goods, following the intuitions of Elinor Ostrom and Mancur Olson on the matter. Moreover, the classic spectrum between goods and services can be stretched to further sophisticate our understanding of economic goods. Building an ontology of economic goods is important in the normative domain as well, as institutions can be understood as different systems of rules that are tailored to facilitate the social provision of different kinds of economic goods.


Biomedical research and clinical trials
== October 28: Austrian Economics 1 - Menger, Mises, and Apriorism ==


The Information Artifact Ontology
The class introduces the philosophical presuppositions of the Austrian school of economics, and its program to promote an understanding of economics as a philosophy of human action, or praxeology. This interest begins in the works of the two founding fathers of the school, Carl Menger and Ludwig von Mises, and the course thus introduces the main innovations they proposed: apriorism, the praxeological approach, entrepreneurship as a feature of human action, the subjective theory of value, the re-establishment of methodological individualism.


*[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0154556 Ontology for Biomedical Investigations (OBI)]
== November 4: Austrian Economics 2 - Hayek and the Price System ==
*[http://ceur-ws.org/Vol-1515/regular10.pdf Information Artifact Ontology]
*[http://www.jpathinformatics.org/article.asp?issn=2153-3539;year=2015;volume=6;issue=1;spage=37;epage=37;aulast=Smith Image Ontologies]


Video: [https://www.youtube.com/watch?v=booqxkpvJMg Clinical Trial Data Wants to be Free]
One of the core objections to neoclassical economics made by the representatives of the Austrian school is their nuanced approach toward quantitative mathematical models of the economy. The course tries to present this point with reference to the Austrian's theory of economic equilibrium, represented by Friedrich von Hayek's refinement of the notion of the price system, as the spontaneous order that drives the complex system of the economy toward the correct allocation of resources. This mechanism puts forward an understanding of the economic equilibrium as a process rather than a static state or goal. The course will explore this topic by reflecting especially on its ontological presuppositions, namely the relevance of spontaneous social orders and the communication of price signals through the unintended consequences of the actions of economic agents.


== 9/26/2016  Introduction to Ontology 2: Ontology in Buffalo (BS) ==
== November 11: Austrian Economics 3 - Schumpeter and Kirzner on Entrepreneurship and Creativity in Humans and Beyond ==
[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-4.pdf Slides]


Includes a presentation by [https://scholar.google.com/citations?user=BUcx6agAAAAJ&hl=en Alex Diehl] on the Cell and Protein Ontologies
The last core tenet of Austrian economics that the course finds philosophically important is entrepreneurship as the equilibrating force that drives the process of market equilibrium. The course will present the topic of entrepreneurship through the (sometimes conflicting) ideas of Joseph Schumpeter and Israel Kirzner. The focal point is that entrepreneurship is a fundamental notion in economics that is rarely investigated outside the Austrian school, and this has to do with the Austrian's recognition of the intrinsic complexity of the economy. Entrepreneurship can be further generalized as a feature of all action that has to do with creativity and proactivity, and this will allow to consider the hypothesis of designing AI entrepreneurs out of present-day technologies like stock market prediction systems etc.
*[https://mitpress.mit.edu/index.php?q=books/building-ontologies-basic-formal-ontology Building Ontologies with Basic Formal Ontology]
*[http://obofoundry.org/ Open Biomedical Ontologies (OBO) Foundry]
*[http://obofoundry.org/ontology/iao.html Information Artifact Ontology]
*[http://www.referent-tracking.com/RTU/?page=index Referent Tracking]
*[http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-6 Logical development of the Cell Ontology]
*[http://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0088-7 The Cell Ontology 2016]
*[http://nar.oxfordjournals.org/content/42/D1/D415.long Protein Ontology: a controlled structured network of protein entities]


== 10/3/2016  Ontology of Social Entities (BS) ==
== November 18: Market Socialism, AI, and Economic Planning ==
[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-5.pdf Slides]


Ontology of obligations
The class will explore the 'calculation debate' sparked by Mises' and Hayek's objections to economic planning. The two main socialist replies will be introduced: the objectivity of economic value through the labor theory of value, and market socialism. Soon, the calculation debate has been flooded by proposals to harness the successes of AI technology for planning the economy. The class will thus present and discuss the most promising models that attempt to plan the economy through AI intervention, starting from Salvador Allende's CyberSyn project in Chile: the Lange-Lerner model, the Cockshott-Cottrell model, Nieto's model, and Saros' democratic economic planning model.


Speech act theory
== November 25: Student Presentations ==


Patient consent
== December 2: Student Presentations ==


Healthcare organizations
== '''Student Learning Outcomes''' ==
*[http://ontology.buffalo.edu/document_ontology/ Document Acts]
         
*[http://www.ontobee.org/ontology/d-acts d-acts Ontology]
{| class="wikitable"
|-
! Program Outcomes/Competencies 
! Instructional Method(s)
! Assessment Method(s)
|-
| The student will acquire a knowledge of the philosophy of the social sciences in general  and of economics in particular.
| 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 of philosophical argument, in formulating complex propositions pertaining to economic matters


== 10/10/2016 How to Build an Ontology (BS/WC/[http://www.jneilotte.com/ NO])==
| Participation in practical experiments
| Review of results
|-
| The student will acquire experience in formulating ideas using powerful persuasive prose.  
| Creation of documentation and youtube presentations
| Review of results
|}


Principles of ontology building (BS) [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-6-part1.pptx Slides]
=='''How to Write an Essay'''==


Further principles of ontology building (WC) [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-6-part2.pptx Slides]
:Steven Pinker, ''The Sense of Style'', Penguin Books, 2014
:Strunk and White, ''[http://www.jlakes.org/ch/web/The-elements-of-style.pdf The Elements of Style]''
:[https://philosophy.fas.harvard.edu/files/phildept/files/brief_guide_to_writing_philosophy_paper.pdf Harvard's guide to writing philosophy]
:[http://www.jimpryor.net/teaching/guidelines/writing.html Jim Pryor's guide to writing philosophy]
:[https://web.archive.org/web/20191209181112/https://jordanbpeterson.com/wp-content/uploads/2018/02/Essay_Writing_Guide.docx Jordan Peterson's Essay Writing Guide]
:[https://buffalo.box.com/s/xku6jc38cx7u1dgm5lteus5qbq7909i9 How to Use ChatGPT to write an essay]


First look at [http://protege.stanford.edu/ Protégé] (NO)
=='''Suggested Additional Reading'''==


Interactive session (WC/NO/BS)
W. B. Arthur, 2021, “Foundations of Complexity Economics”, [https://www.nature.com/articles/s42254-020-00273-3]


Target text for interactive session:
S. Bostaph, 2019, “Schumpeter vs Kirzner on Entrepreneurs”, [https://mises.org/wire/schumpeter-vs-kirzner-entrepreneurs]
:Mary Ceusters, a 54 year old non-smoking female, arrives at a Buffalo General Hospital on August 12th, 2007 and Nurse Smith takes her blood pressure and records 160/90mmHg. Based on this reading, Nurse Smith concludes Mary has high blood pressure and prescribes the drug Bumetanide. On July 11, 2009, Mary Ceusters arrives at Erie County Medical Center complaining of sudden chest pains and Doctor Searle conducts an external examination and concludes Mary has suffered a heart-attack, which he suspects is likely the result of coronary artery disease exacerbated by hypertension.


== 10/17/2016 Ontology, Logic and Software (WC/AR)==
P. Boettke & R. Candela, 2022, "On the Feasibility of Technosocialism", [https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4219398]


[https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0098-5 Diagnosis, misdiagnosis, lucky guess, hearsay, and more] (WC)
A. Cottrell & P. Cockshott, 1993, "Calculation, Complexity and Planning: The Socialist Calculation Debate Once Again", [https://users.wfu.edu/cottrell/socialism_book/calculation_debate.pdf]


[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-7-part1.pptx Slides]
J. Fernández-Villaverde, 2020, "Simple Rules for a Complex World with Artificial Intelligence", [https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3559378]


Language vs. Ontology ([https://scholar.google.com/citations?user=tIcr1AkAAAAJ&hl=en AR])
F. A. Hayek, 2012, "Law, Legislation and Liberty. A New Statement of the Liberal Principles of Justice and Political Economy", pp: 35-54, [https://www.taylorfrancis.com/books/mono/10.4324/9780203103814/law-legislation-liberty-hayek-paul-kelly]


What is a ((Health)Care) Process? We have the words. But they are used casually and ambiguously. How do we sort this out? (AR)
O. Lange, 1936, “On the Economic Theory of Socialism”, [https://academic.oup.com/restud/article-abstract/4/1/53/1547969?redirectedFrom=fulltext]


The Web Ontology Language (OWL): What it is and how to relate it to Ontology. A quick introduction to OWL including problems when OWL is used to build ontologies (AR)
M. Olson, 1971, "The Logic of Collective Action. Public Goods and the Theory of Groups", Part I, [https://www.hup.harvard.edu/catalog.php?isbn=9780674537514]


[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-7-part2.pdf Slides]
S. Phelan, 2020, "Can Entrepreneurship Be Learned by Intelligent Machines", [https://duckduckgo.com/?q=phelan+ai+entrepreneurs&atb=v342-1&ia=web]


== 10/24/2016 Representing Types and Representing Instances (WC) ==
F. Schmitt, 2003, "Joint Action: From Individualism to Supraindividualism", [https://philpapers.org/rec/SCHJAF]


Introduction to [http://www.referent-tracking.com/RTU/?page=reftrackparadigm.phtml Referent Tracking] (WC)
B. Smith, 1997, "The Connectionist Mind: A Study of Hayekian Psychology", [https://philarchive.org/rec/SMITCM]


Application of Referent Tracking to deal with Errors in Databases (WC)
S. Thurner et al., 2018, "Introduction to the Theory of Complex Systems", [https://global.oup.com/academic/product/introduction-to-the-theory-of-complex-systems-9780198821939]


[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-8.pptx Slides]
A. Quinton, 1976, “Social Objects”, [https://philpapers.org/rec/QUISO]


== 10/31/2016 Overview of Ontology: BFO, GO, OBO Foundry (BS) ==
=='''Important Dates'''==
History and current theoretical foundations for the development of effective biomedical ontologies
{| class = wikitable
|  Sep 11 || - submit book review choice, and start to discuss the content of your essay with Dr Smith
|-
|  Sep 25 || - submit proposed title and abstract of your essay
|-
|  Oct 2|| - last day to ''present'' book summary
|-
|  Oct 23 || - submit a table of contents of your essay and 300 word summary plus draft of associated ppt slides
|-
|  Oct 30 || - submit first draft of essay (~1000 words) and associated powerpoint (~10 slides)
|-
|  Nov 13 || - submit second draft of essay (~2000 words) and associated powerpoint (~10 slides)
|-
|  Nov 20 || - class presentation
|-
|  Dec 10 || - submit final version of essay and powerpoint slides and upload final version of video to youtube
|}


[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-9.pptx Slides]
=='''Grading'''==


*[http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration]
Grading will be based on two factors:  
*[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3104413/ Ontological Realism as a Methodology for Coordinated Evolution of Scientific Ontologies]


== 11/7/2016 Ontology and Terminology (WC / AR)==
I: understanding and criticism of the material presented in classes 1-13


The Ontology for Oral Health and Disease ([http://www2.unb.ca/csas/data/ws/icbo2013/papers/ec/icbo2013_submission_63.pdf OHD]) (AR)
All students are required to take an active part in class (and where relevant on-line) discussions throughout the semester.  


Ontology and Terminology: An Introduction (WC)
II: preparation of an essay, and associated powerpoint slides and recorded presentation.


[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-10.pptx Slides]
Content and structure of the essay should be discussed with Dr Smith.  


*[http://www.openclinical.org/medicalterminologies.html Medical Terminologies]
'''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:


== 11/14/2016 Introduction to SNOMED  (WC/NO)==
Weighting Assignment
:20%    - class discussions  
:15%    - youtube video presentation
:15%    - powerpoint slides
:50%    - essay


SNOMED: Systematized Nomenclature for Medicine (WC)
'''Final Grades'''


[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-11-part1.pptx Slides]
Percentages refer to sum of assignment grades as listed above


Using [http://protege.stanford.edu/ Protégé] ([http://www.jneilotte.com/ Neil Otte])
Grade Quality Percentage
{| class = wikitable
|  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
|}


[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-11-part2.pptx Slides]
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.


== 11/21/2016 Internet of Things / Concluding Summary (WC/BS)==
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.


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


The Internet of Things (Biomedical Applications (WC) [http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-12-part1.pptx Slides]
=='''Related Policies and Services'''==


*[http://www.referent-tracking.com/RTU/sendfile/?file=CeustersBonaParis2016ReadyForPublication.pdf Tracking Data Quality through the Internet of Things] [http://www.referent-tracking.com/RTU/sendfile/?file=STC2016-Slides.pptx Slides]
'''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.  


Concluding Summary -- What you should have learned from this class (BS)
'''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].
[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-12-part2.pptx Slides]


Coda on SNOMED (WC)
'''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.
[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/slide-12-part3.pdf Slides]


== 11/28/2016  Student presentations ==
'''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.
*4:00 James Schuler: '''The Ontology of Diabetes Camp'''
:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Schuler.pptx Slides]
:[https://www.youtube.com/watch?v=URMWuBZd-4A Video]
*4:20 Jonathan Blaisure: '''OMOP'''
:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Blaisure.pptx Slides]
:[https://youtu.be/23K3_FOXVjA Video]
*4:40 Sarah Mullin: '''The Ontology of Biological and Clinical Statistics'''
:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Mullin.pdf Slides]
:[https://youtu.be/y9LTbsYlGBY Video]
*5:00 Francesco Franda: '''Organizations: An Ontological Approach'''
:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Franda.pptx Slides]
:[https://youtu.be/smyTVlkY_QI Video]
*5:20 Fernanda Farinelli: '''Ontology of Document Templates'''
:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Farinelli.pptx Slides]
:[https://www.youtube.com/watch?v=X3FVwSqZhag Video]
*5:40 Cameron Bosinski: '''The Origin of Information'''
:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Bosinski.pptx Slides]
:[https://youtu.be/QNYJCip79FI Video]
*6:00 Uriah Burke: '''The Zika Virus'''
:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Burke.pptx Slides]
:[https://www.youtube.com/watch?v=C5PDE02nEPw Video]


== 12/5/2016  Student presentations ==
'''Counselling 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:  
*4:00 Qiuyi Zhang: '''Understanding Accessibility in Healthcare Facilities'''
:Counseling Services: 120 Richmond Quad (North Campus), phone 716-645-2720
:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/QZhang.pptx Slides]
:Health Services: Michael Hall (South Campus), phone: 716-829-3316
:[https://youtu.be/oz0bmykt820 Video]
:Health Promotion: 114 Student Union (North Campus), phone: 716- 645-2837
*4:20 Scott Luan: '''On the Ontology of (Biomedical) Artifacts'''
:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Luan.pptx Slides]
*4:40 Matthew Hudson: '''Disease surveillance through the lens of ontology'''
:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Hudson.pptx Slides]
*5:00 Ruoyu Yang and Binbin Zhang: '''Ontology of Materials'''
:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Ruoyu.pptx Slides]
:[https://youtu.be/ufAVzxSlHTU Video]
*5:20 Munira Binti Mohd Ali: '''Additive Manufacturing in Dentistry'''
:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Ali.pptx Slides]
:[https://www.youtube.com/watch?v=-tq0TKUtMIc Video]
*5:40 Federico Borsotti: '''Ontologies and Relational Databases'''
:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Borsotti.pptx Slides]
:[https://www.youtube.com/watch?v=DobwIniiFFY Video]
*6:00 Evan Murphy: '''Ontology of Mental Illness'''
:[http://ontology.buffalo.edu/smith/courses16/Biomedical_Ontology/Presentations/Murphy.pptx Slides]

Latest revision as of 17:05, 15 April 2024

PHI 637 (seminar, 2 credits). Registration number: [1]

Time: 1:00-3:50pm, selected Mondays (TBD), Fall Semester 2024

Room: Park 141, UB North Campus

Instructors: Barry Smith (Philosophy) and Emanuele Martinelli (Philosophy, University of Zurich)

Office hours: BS: by appointment via email; EM: by appointment via email

Course Description

The goal of the course is to give the students conceptual tools to understand and evaluate critically the philosophical assumptions of different schools of thought in economics. Debates between different approaches in economics may be viewed in part as ontological debates as to the nature of social entities such as prices, markets, economic actors. Hence, the course aims at introducing the core categories that determine the world of economics and exploring how different interpretations of these categories can support different economic claims and systems.

Part One of the course introduces topics in social ontology with an eye on economic applications: agency, complexity, information, collectivity, speech acts, claims and obligations.

Part Two analyzes themes underlying the works of the main contemporary economic schools of thought. Austrian economics will be given special prominence because it is arguably the economic school of thought that makes the most open use of philosophical categories in its theories.

Recommended background reading

W. Grassl, and B. Smith (eds.), 2010, Austrian Economics: Historical and Philosophical Background, pp: 1-36, [2]

F. A. Hayek, 1945, "The Use of Knowledge in Society", [3]

G. M. Hodgson, 2007, “Meanings of Methodological Individualism”, [4]

C. List & P. Pettit, 2011, "Group Agency: The Possibility, Design, and Status of Corporate Agents", Part I, [5]

Recommended background video content

Barry Smith, 2023, "Beyond the Goods-Services Continuum", [6]

Schedule

September 30: Introduction: Economic Agents and Agency

This class introduces the topic of 'agency' from the point of view of social ontology, with a focus on the different kinds of agents that populate the social world. This reflection of agency can make our understanding of core economic notions more sophisticated, including economic actors, markets, government interventions, firms. When reflecting on the assumptions of different economic models, philosophical considerations about society are instrumental. Another very important conceptual distinction is that between 'collectivism' and 'individualism'. Moving from the various levels of this distinction, the class will examine the methodological division between microeconomics and macroeconomics under the lense of individualist-collectivist sprectrum in the socio-ontological literature.

October 7: Market Equilibrium and Critical Perspectives

This class introduces the main contemporary proposals that have been advanced throughout mainstream economics to overcome some core tenets of classical economics. This will include reflection on the assumptions of neoclassical economics (in particular as represented by Léon Walras' works on general equilibrium models). The core tenets of (neo)classical economics, such as economic rationality, utility maximization, and general equilibrium, are discussed in their deeper philosophical implications by comparing them with notions of social ontology previously introduced in the course. Different perspectives that try to move away from classical economics in these regards are presented, with a major focus on schools of economic thoughts that have critized the core notion of economic equilibrium, from Keynesian economics, to complexity economics, to behavioral economics, to Austrian economics.

October 14: FALL BREAK (No class)

October 21: Economic Goods and Institutions

Samuelson's classic notions of 'rivalry' and 'excludability' and the subsequent debate around the definition of public goods may be extended to draw a basic ontology of different kinds of economic goods, following the intuitions of Elinor Ostrom and Mancur Olson on the matter. Moreover, the classic spectrum between goods and services can be stretched to further sophisticate our understanding of economic goods. Building an ontology of economic goods is important in the normative domain as well, as institutions can be understood as different systems of rules that are tailored to facilitate the social provision of different kinds of economic goods.

October 28: Austrian Economics 1 - Menger, Mises, and Apriorism

The class introduces the philosophical presuppositions of the Austrian school of economics, and its program to promote an understanding of economics as a philosophy of human action, or praxeology. This interest begins in the works of the two founding fathers of the school, Carl Menger and Ludwig von Mises, and the course thus introduces the main innovations they proposed: apriorism, the praxeological approach, entrepreneurship as a feature of human action, the subjective theory of value, the re-establishment of methodological individualism.

November 4: Austrian Economics 2 - Hayek and the Price System

One of the core objections to neoclassical economics made by the representatives of the Austrian school is their nuanced approach toward quantitative mathematical models of the economy. The course tries to present this point with reference to the Austrian's theory of economic equilibrium, represented by Friedrich von Hayek's refinement of the notion of the price system, as the spontaneous order that drives the complex system of the economy toward the correct allocation of resources. This mechanism puts forward an understanding of the economic equilibrium as a process rather than a static state or goal. The course will explore this topic by reflecting especially on its ontological presuppositions, namely the relevance of spontaneous social orders and the communication of price signals through the unintended consequences of the actions of economic agents.

November 11: Austrian Economics 3 - Schumpeter and Kirzner on Entrepreneurship and Creativity in Humans and Beyond

The last core tenet of Austrian economics that the course finds philosophically important is entrepreneurship as the equilibrating force that drives the process of market equilibrium. The course will present the topic of entrepreneurship through the (sometimes conflicting) ideas of Joseph Schumpeter and Israel Kirzner. The focal point is that entrepreneurship is a fundamental notion in economics that is rarely investigated outside the Austrian school, and this has to do with the Austrian's recognition of the intrinsic complexity of the economy. Entrepreneurship can be further generalized as a feature of all action that has to do with creativity and proactivity, and this will allow to consider the hypothesis of designing AI entrepreneurs out of present-day technologies like stock market prediction systems etc.

November 18: Market Socialism, AI, and Economic Planning

The class will explore the 'calculation debate' sparked by Mises' and Hayek's objections to economic planning. The two main socialist replies will be introduced: the objectivity of economic value through the labor theory of value, and market socialism. Soon, the calculation debate has been flooded by proposals to harness the successes of AI technology for planning the economy. The class will thus present and discuss the most promising models that attempt to plan the economy through AI intervention, starting from Salvador Allende's CyberSyn project in Chile: the Lange-Lerner model, the Cockshott-Cottrell model, Nieto's model, and Saros' democratic economic planning model.

November 25: Student Presentations

December 2: Student Presentations

Student Learning Outcomes

Program Outcomes/Competencies Instructional Method(s) Assessment Method(s)
The student will acquire a knowledge of the philosophy of the social sciences in general and of economics in particular. 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 of philosophical argument, in formulating complex propositions pertaining to economic matters Participation in practical experiments Review of results
The student will acquire experience in formulating ideas using powerful persuasive prose. Creation of documentation and youtube presentations Review of results

How to Write an Essay

Steven Pinker, The Sense of Style, Penguin Books, 2014
Strunk and White, The Elements of Style
Harvard's guide to writing philosophy
Jim Pryor's guide to writing philosophy
Jordan Peterson's Essay Writing Guide
How to Use ChatGPT to write an essay

Suggested Additional Reading

W. B. Arthur, 2021, “Foundations of Complexity Economics”, [7]

S. Bostaph, 2019, “Schumpeter vs Kirzner on Entrepreneurs”, [8]

P. Boettke & R. Candela, 2022, "On the Feasibility of Technosocialism", [9]

A. Cottrell & P. Cockshott, 1993, "Calculation, Complexity and Planning: The Socialist Calculation Debate Once Again", [10]

J. Fernández-Villaverde, 2020, "Simple Rules for a Complex World with Artificial Intelligence", [11]

F. A. Hayek, 2012, "Law, Legislation and Liberty. A New Statement of the Liberal Principles of Justice and Political Economy", pp: 35-54, [12]

O. Lange, 1936, “On the Economic Theory of Socialism”, [13]

M. Olson, 1971, "The Logic of Collective Action. Public Goods and the Theory of Groups", Part I, [14]

S. Phelan, 2020, "Can Entrepreneurship Be Learned by Intelligent Machines", [15]

F. Schmitt, 2003, "Joint Action: From Individualism to Supraindividualism", [16]

B. Smith, 1997, "The Connectionist Mind: A Study of Hayekian Psychology", [17]

S. Thurner et al., 2018, "Introduction to the Theory of Complex Systems", [18]

A. Quinton, 1976, “Social Objects”, [19]

Important Dates

Sep 11 - submit book review choice, and start to discuss the content of your essay with Dr Smith
Sep 25 - submit proposed title and abstract of your essay
Oct 2 - last day to present book summary
Oct 23 - submit a table of contents of your essay and 300 word summary plus draft of associated ppt slides
Oct 30 - submit first draft of essay (~1000 words) and associated powerpoint (~10 slides)
Nov 13 - submit second draft of essay (~2000 words) and associated powerpoint (~10 slides)
Nov 20 - class presentation
Dec 10 - submit final version of essay and powerpoint slides 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.

Grading Policy: Grading follows standard 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 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 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.

Counselling 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