2023 MAY to JULY: Introduction to Behavioural Research

Instructor

Vic Chiang (they/them)

Course Content

Image source: https://www.newyorker.com/magazine/2021/08/23/why-is-it-so-hard-to-be-rational

Introduction

Some concepts we cover: Observations can be theory-laden, Alternative avenues of knowledge beyond science, Racial & phenotypic bias in science, scientific method, empirical approach, ethnocentricism, hypothesis, multimethod approach

The Scientific Method

Some concepts we cover: Discrimination & ableism in science , Can science determine causality? , Science is embedded in culture and values, Variables , Experiment , Causal inference, Validity, Theory

Ethical Issues in the Conduct of Research

Some concepts we cover: Weaving indigenous views into the scientific method, Arabic contributions to modern science, Is the aim of science to determine ultimate truth?, Risk/benefit ratio, Informed consent, Deception, Debriefing, Plagiarism

Observation

Some concepts we cover: Areas which science chooses to explore, Type of reasoning science achieve, What counts as good scientific explanation? , Naturalistic observation, External validity, Interobserver reliability, Selective survival, Demand characteristics

Survey Research

Some concepts we cover: Problem of exclusive dominance of science, Marginalised minorities in science , Science is pervasive with uncertainties in outcomes and probability , Representativeness, Selection bias, Interviewer bias, Longitudinal design, Spurious relationship

Independent Groups Designs

Some concepts we cover: Essential untested assumptions in science, Problem with reductionism, Rationally admissible belief, Block randomisation, Double-blind procedure, Null hypothesis significance testing, Effect size, Replication

Repeated Measures Designs

Some concepts we cover: Sources of knowledge & justified belief, Scepticisms in the possibility of knowledge , Knowledge-yielding within and outside of psychological states, Repeated measures designs, Sensitivity, Practice effects, Counterbalancing, Differential transfer

Quasi-Experimental Designs and Program Evaluation

Some concepts we cover: knowledge independent and dependent of experience, Beliefs as subjective probabilities , Killing of knowledge systems under systemic oppression , History, Contamination, Program evaluation, Nonequivalent control group design, Maturation

Data Analysis and Interpretation

Some concepts we cover: Indian pramana in modern science , Importance of the collective context, Institutions of science , Stages of data analysis, Measures of central tendency, Measures of dispersion, Confidence interval, Correlation

Guest Speakers

Image source: https://doi.org/10.1093/biosci/biac013

In this class, I hope to present the class with relatable role models from diverse backgrounds, especially those representing a diversity of marginalized identities. I want the class to see them as full people with humanizing information, including their research and their contributions to their field. For this effort, some resources I consulted include:

• 500 Queer Scientists
• DiversifyPlantSci
• 100 inspiring Hispanic/Latinx scientists in America
• Diversify ecologists and evolutionary biologists
• Scientist Spotlights
• Skype a Scientist
• Black in the Ivory
• American Society for Cell Biology (ASCB) Women in Cell Biology and Minority Affairs Committee
• Black Neuroscience PI
• 1,000 inspiring Black scientists in America
• Spark Society's Database of Cognitive Scientists of Color
• Leading Edge Initiative
• The Outlist of Lesbian, Gay, Bisexual, Transgender, Intersex, Queer, and Ally Astronomers!
• Black Women in Biology, Ecology, Evolution, and Marine Science
• Databases of Databases of Diverse Speakers in STEM

Sofía Miñano (June 5th)

Aleen Shakeel (June 5th)

Aleen has completed her Bachelor of Science (Honors) in the Biomedical Science program from Toronto Metropolitan University. She has explored computational methods used in bioinformatics and wet lab techniques while researching the role of kinases in cancer. Aleen currently works in the science communication field to develop the climate science activity program for a national charitable organization called Let's Talk Science. As the Lead Scientist for Savyn, Aleen is learning more about the intersection between translational research and product development. In her free time, she enjoys creating digital art and developing her astrophotography skills!

Yu-Chi Wang (June 7th)

Dr. Yu-Chi Wang (no pronouns) is the School Climate Research Manager at GLSEN. Yu-Chi draws from educational and social psychology, public health, games studies, and learning sciences to conduct research aimed at reducing prejudice against and bettering outcomes for trans and queer youth. In Yu-Chi’s spare time, Yu-Chi enjoys board games, dancing, and karaoke. In the future Yu-Chi hopes to run a board game cafe with research-based programming especially for queer youth of color!

Ufuoma Ovienmhada (June 7th)

Ufuoma Ovienmhada is a third year PhD student at MIT in the Aeronautics and Astronautics Department. She studies applications of satellite remote sensing data for environmental justice. In her dissertation, she employs a multi-method approach to research the distribution of environmental hazards in carceral landscapes and co-design Earth Observation technologies to support environmental justice advocacy. Prior to beginning her PhD, she completed a Masters in the MIT Media Lab. Her Masters Thesis focused on applying remote sensing, low-cost sensors, drone data collection and community-centered design techniques to invasive plant species management in West Africa. Before arriving at MIT, she completed a Bachelor's degree in Mechanical Engineering from Stanford University.

Topic: Satellite Data for Environmental Justice: A Case Study of U.S. Prison Landscapes

Abstract: Over the last few decades, numerous scholars have documented the fact that in general, people of color and other socio-economically marginalized groups in the United States experience a disproportionate burden of environmental challenges - this pattern is referred to as environmental justice (EJ). Satellite Earth Observations (EO) can be used to monitor air quality, water quality, extreme weather and other quantities relevant to Environmental Justice. However the application of this technology in measuring environmental justice, or supporting EJ advocacy efforts has not been widely explored. On a high level, I study technological and methodological interventions in the pursuit of environmental justice and liberatory politics. This is explored through case study research of prison ecology in the United States, an environmental justice issue referring to a pattern of exposure to environmental hazards in carceral landscapes. The first phase of research employs semi-structured interviews with community organizers to understand the potential role and limitations of geospatial data in EJ organizing. Several ethical considerations came up in the design of this research which will be the topic of the presentation to the class. I will share reflections on interview protocol design, recruitment, informed consent and privacy.

Jacob Kodner (June 12th)

Jacob Aaron Kodner is an incoming PhD student in Linguistics at Harvard University. He is interested in the grammatical structure of a variety of East Asian languages, especially those that are endangered and not as well-researched. He has studied verb constructions in Manchu, a critically endangered language of China, and has worked with speakers of this language to develop an online recorded dictionary. He has also conducted fieldwork with speakers of Atayal, an endangered and indigenous language of Taiwan, to research how speakers convey sources of evidence. His presentation will cover fieldwork as a research method, specifically through the lens of his research on Atayal.

Sokha Eng (June 12th)

Dawn Anderson (June 21st)

Dawn is a PhD candidate at the University of Massachusetts Boston in the School for Global Inclusion and Social Development. She has been working to strengthen the cultural and community responsiveness of teachers in K-12 classrooms by centering the local history and contributions of Indigenous and Black communities. By merging her interests in historic preservation, travel, photography, performing arts, and genealogy, she supports teachers in Illinois and Massachusetts who are working to strengthen their cultural and community responsiveness. For her multiple case study, she uses an explanatory sequential mixed-method approach to better understand teacher participants background, practices, and beliefs. The aim of her dissertation project is to explain why local black history has not been taught, challenges teaching it and the impact on students. Professionally, Dawn has worked in the field of International Education at Northeastern University and in Residential Life at MIT. She is a wife, mother and a proud House Head from the suburbs of Chicago.

Dorothy Majewski (June 26th)

Lilly Chin (June 28th)

Jason (Chang) Marvin (July 5th)

Jason C. Marvin, PhD (he/they)

Harvard Medical School Dean’s Postdoctoral Fellow

Massachusetts General Hospital, Musculoskeletal Genetics & Developmental Biology Laboratory (PI: Jenna Galloway, PhD)

Dr. Jason (Chang) Marvin is a Dean’s Postdoctoral Fellow in the Center for Regenerative Medicine at Massachusetts General Hospital (MGH) and the Department of Genetics at Harvard Medical School. He received his B.S. and Ph.D. in biomedical engineering from the University of Texas at Dallas and Cornell University, respectively. Their research leverages naturally regenerative animal models to study the biological mechanisms underlying effective musculoskeletal tissue repair and develop tailored therapeutic strategies. As a genderqueer and gay scientist, Dr. Marvin has received numerous accolades for championing institutional and national efforts (e.g., Out in STEM, Biomedical Engineering Society, Orthopaedic Research Society, BME Organizations Leading Diversity) focused on inclusive pedagogy, mentorship, and advocating for the support and retention of historically marginalized and minoritized communities in STEM. Their presentation will cover best practices in hypothesis testing, experimental design, and data analysis & visualization with an emphasis on the biological sciences and bioengineering research.

Sexual diversity examples to contextualise the concepts learnt

Image source: https://doi.org/10.1038/s41559-019-1019-7

Some of these examples were obtained from Evolution's Rainbow: A Queer Species Database Of 200+ Organisms https://www.genderinclusivebiology.com/newsletter/evolutions-rainbow-a-queer-species-database-of-200-organisms

J F McLaughlin and others, Multivariate Models of Animal Sex: Breaking Binaries Leads to a Better Understanding of Ecology and Evolution, Integrative and Comparative Biology, 2023;, icad027, https://doi.org/10.1093/icb/icad027

Funnell, T. R., Fialkowski, R. J., & Dijkstra, P. D. (2022). Social dominance does not increase oxidative stress in a female dominance hierarchy of an African cichlid fish. Ethology, 128, 15– 25. https://doi.org/10.1111/eth.13232

Álvarez, B., Koene, J.M., Hollis, K.L. et al. Learning to anticipate mate presence shapes individual sex roles in the hermaphroditic pond snail, Lymnaea stagnalis. Anim Cogn (2022). https://doi.org/10.1007/s10071-022-01623-7

da Silva Jack and Drysdale Victoria L. 2018Isogamy in large and complex volvocine algae is consistent with the gamete competition theory of the evolution of anisogamy. Proc. R. Soc. B.2852018195420181954 http://doi.org/10.1098/rspb.2018.1954

Diamant Eleanor S., Falk Jay J. and Rubenstein Dustin R. 2021Male-like female morphs in hummingbirds: the evolution of a widespread sex-limited plumage polymorphism. Proc. R. Soc. B.2882020300420203004 http://doi.org/10.1098/rspb.2020.3004

Dieter Lukas, Tim Clutton-Brock, Monotocy and the evolution of plural breeding in mammals, Behavioral Ecology, Volume 31, Issue 4, July/August 2020, Pages 943–949, https://doi.org/10.1093/beheco/araa039

Heredero Saura, L., Jáñez-Escalada, L., López Navas, J. et al. Nest-site selection influences offspring sex ratio in green turtles, a species with temperature-dependent sex determination. Climatic Change 170, 39 (2022). https://doi.org/10.1007/s10584-022-03325-y

Nobuaki Mizumoto, Thomas Bourguignon, Nathan W. Bailey, Ancestral sex-role plasticity facilitates the evolution of same-sex sexual behaviour, bioRxiv 2022.06.20.496918; doi: https://doi.org/10.1101/2022.06.20.496918

Rosenwohl-Mack A, Tamar-Mattis S, Baratz AB, Dalke KB, Ittelson A, Zieselman K, et al. (2020) A national study on the physical and mental health of intersex adults in the U.S. PLoS ONE 15(10): e0240088. https://doi.org/10.1371/journal.pone.0240088

Han H, Yang S, Li J, Zhao J, Wei H, Ha S, Li W, Li C, Quan K. Intersex goats show different gene expression levels in the hypothalamus and pituitary compared with non-intersex goats based on RNA-Seq. Vet Med Sci. 2022 Jan;8(1):367-376. https://doi.org/10.1002/vms3.672

Arnoldussen M, van der Miesen AIR, Elzinga WS, Alberse AE, Popma A, Steensma TD, de Vries ALC. Self-Perception of Transgender Adolescents After Gender-Affirming Treatment: A Follow-Up Study into Young Adulthood. LGBT Health. 2022 May-Jun;9(4):238-246. https://doi.org/10.1089/lgbt.2020.0494

Fry KM, Grzanka PR, Miles JR, DeVore EN. Is Essentialism Essential? Reducing Homonegative Prejudice by Targeting Diverse Sexual Orientation Beliefs. Arch Sex Behav. 2020 Jul;49(5):1725-1739. https://doi.org/10.1007/s10508-020-01706-x

Delclos PJ, Forero SA, Rosenthal GG. Divergent neurogenomic responses shape social learning of both personality and mate preference. J Exp Biol. 2020 Mar 16;223(Pt 6):jeb220707. doi: 10.1242/jeb.220707. PMID: 32054683. https://doi.org/10.1242/jeb.220707

Ambler, J. K., Lee, E. M., Klement, K. R., Loewald, T., Comber, E. M., Hanson, S. A., Cutler, B., Cutler, N., & Sagarin, B. J. (2017). Consensual BDSM facilitates role-specific altered states of consciousness: A preliminary study. Psychology of Consciousness: Theory, Research, and Practice, 4(1), 75–91. https://doi.org/10.1037/cns0000097

Gil-Llario, M.D., Fernández-García, O., Huedo-Medina, T.B. et al. Analysis of the Differential Efficacy of the Reduced Version Over the Extended Version of an Affective-Sexual Education Program for Adults with Intellectual Disabilities. Arch Sex Behav (2022). https://doi.org/10.1007/s10508-022-02407-3

Group debating using primary research articles to support arguments (20% of final grade)

Image source: https://www.currentaffairs.org/2021/10/why-we-should-teach-kids-to-debate

Debate Motion	Starting Vote: PRO	Starting Vote: OPP	Closing Vote: PRO	Closing Vote: OPP
Your partner escapes without you during an emergency, you should forgive them.	Practice Only	Practice Only	Practice Only	Practice Only
If superheroes existed, the world would be a better place.	20%	80%	33%	67%
Right before we die, we would read a poem rather than seeing our family.	50%	50%	75%	25%
If we could have the power of telepathy, we should accept it.	67%	33%	50%	50%
If we could write our own destiny, we should do it.	29%	71%	13%	88%
After a complete loss of memory, we should be responsible for our crimes committed before that.	71%	29%	86%	14%

Group Projects using DeepLabCut on animals (20% of final grade)

Image source: http://www.mackenziemathislab.org/deeplabcut

All things DeepLabCut

Get help with DeepLabCut

Installation: how to install DeepLabCut

Labelling using DeepLabCut GUI

DeepLabCut neural network training and analysis on Google Colab

Outputs for your DeepLabCut data e.g. bodypart trajectories

Project submissions using Github and Jupyter Notebook

Masai giraffe (Giraffa camelopardalis tippelskirchi)

DeepLabCut Tutors & Mentors

Shruti Varade

Shruti Varade is a graduate student at the University of Massachusetts, Boston currently pursuing Master's in Computer Science. She completed her undergraduate degree from the University of Mumbai, India. After completing Bachelor of Engineering in Computer Engineering she worked at a multi-national Company, TATA Consultancy Services as a Software Engineer for 2 years. She also gained professional expertise in analytics while working as an intern with Stepoutplay while analyzing football tournaments and player performance. She believes that her contribution to assisting students at DeepLab Cut will enable students with the requisite skills and knowledge boosted by their hardworking and dedication to propel them towards achieving their goals and help them make a significant contribution to the field of Data Analysis.

Hiral Lunkad

Hiral is a graduate student at the University of Massachusetts Boston with a major in Business Analytics. She holds a BE in Computer Science from RGPV University India. Throughout her early career, she has explored and utilized different technological skillset for web development and, application development. Having 2 years of professional experience as a Software engineer where she has experience working with Python, Jupyter,and data visualizations tools. She has contributed significantly to team projects, collaborative efforts and achievements through her collaboration and communication abilities which will be helpful to me for the position of DeepLabCut tutor as well. She is a strong believer in providing value and creating impact through her work and want her efforts to reach and change lives of larger groups of end users for a good.

Manali Patil

Nansy Hernandez

Razhan Kamal

Marietta Majors

Daniela Hernandez

Hi my name is Daniela Hernandez and I am from Honduras. I studied EE/Physics in undergrad and Im currently pursuing a MEng in Surgery and Intervention at Vanderbilt. I love learning about AI and using DeepLabCut on a daily basis. Feel free to ask me anything and look forward to getting to know you!

Madelyn Smythe

I was born with the “horse bug” and after spending 12 years training and competing young horses I knew I wanted to pursue a career in the equine industry. I went on to finish my B.S. at the University of Minnesota, then I completed a yearlong internship with Kentucky Equine Research which propelled me into my M.S. degree in an equine lab at the University of Florida. There I developed skills in Markerless pose estimation to track locomotor phenotypes in the elite sport horse. My love of horses and my growing passion for teaching led me to my position as a professor at the College of Central Florida. I hope to continue teaching equine science by showing how AI technology, genetics, and physiology can greatly improve the modern-day horse.

Hongbin (Ben) Lin

I'm a 3rd year Ph.D. Student in CUHK majoring in mechanical and automation engineering. I am interested in designing “smart” robot system that allows robots to adapt environment like human. The focus of my current research is A.I. for surgical autonomy.

Martin Migliaro

Ask me where I'm from and I will answer you with a list of places where I have been. Born in Buenos Aires, raised in the Denver, and currently living Mexico City, I'm wrapping up my PhD in Biomedical Science (neuroscience track) at UNAM. I am want to understand the neurophysiological mechanisms that link social status to reward through the lens of computational neuroethology. I’m passionate about harnessing machine learning to study naturalistic behavior and currently using pose estimation to automatize the classification of social interactions.

Jokubas Ausra

Being born in Lithuania and moving to Chicago, Dr. Ausra settled down in the Sunshine State of Arizona. After graduating with his B.S. in Chemical Engineering, Jokubas pursued further education in biofeedback research by studying how animal behavior can guide wireless power transfer to implantable sensors and stimulators for neural and cardiac applications. After receiving his Ph.D. in biomedical engineering, Dr. Ausra is working toward his goal of integrating physiological sensors with automatic control of the environment for people with disabilities. In his free time, he enjoys building breadboard computers, automating home appliances, and playing with pets.

Gia Hepburn

Gia completed her B.Sc. in Biology with a Minor in Chemistry from the University of The Bahamas (2020), after which she pursued a postgraduate diploma in Biomedical Science from Keele University (2021). Then in continued pursuit of higher education, she also completed a master’s degree in Biomedical Science (Blood Science) from Keele University (2022). Her research work consists of using deep neural networks and artificial intelligence for the establishment of a motor skills assessment tool for muscle-wasting conditions. She is currently due to continue her research work at Keele University as a technical assistant this spring. Gia has also been chosen as a 2023 DeepLabCut AI resident fellow and will be improving her artificial intelligence and DeepLabCut skills in Switzerland this coming summer.

Michelle Verhoeven

My name is Michelle Verhoeven, I am Dutch and decided to join the academic world by exchanging my small hometown for the big capital Amsterdam to start studying. There, I graduated from the Research Master in Human Movement Sciences at the Vrije Universiteit Amsterdam. For my master thesis, I conducted a validation study on using DeepLabCut for gait analysis in adults and newly walking toddlers. I recently moved to Belgium to start a PhD at Ghent University. My current research aims to investigate Selective Motor Control during gait (SMCg) in children with Developmental Coordination Disorder (DCD) and cerebral palsy (CP).

Nathan Kirkpatrick

Nathan Kirkpatrick is a biomedical engineering grad student at Georgia Tech & Emory University. He uses DeepLabCut and neuromodulation techniques to study how rats adapt to nerve injury. Specifically, he uses DLC to recognize skeletal landmarks in biplanar high-speed x-ray video to monitor how animals compensate for the loss of peripheral signaling. He has undergraduate degrees in BME and English literature and was a Peace Corps volunteer in the Philippines for two years. After finishing his PhD, he hopes to get a job in industry working for a medical device company.

Recruitment for DeepLabCut Tutors for next semester