Anth 197 MS:  Introduction to Biomarkers and Lab Techniques for the Social Sciences
​UCSB Winter 2023
Lecture: HSSB 2001a
M 9:30-12
Lab sections: BioEngineering Rm 0202, Bldg 512, meet here, lab phone 805-893-5988
M or W 3 - 5 pm (section sign up)
Instructor: Prof. Nicole Thompson González, natg @ ucsb.edu, office hours: Tues 2 - 3 pm
Teaching Assistant: Emily Cobb, emilycobb @ ucsb.edu, office hours: Thurs 11 am -1 pm
Office hours sign up.
Welcome!
  Biomarkers are increasingly used in the social sciences because they are windows into physiological processes. They give us clues about individual condition and the impact of social and physical environments on health and Darwinian fitness. Biomarkers also play a strong role in our behavior, as behavior is an emergent aspect of our phenotype. This course spans a broad range of theory and methods involved in using biomarkers in the social sciences.  Theory comes from areas of behavioral research that center on or make use of biomarker data, e.g. behavioral endocrinology, behavioral ecology, evolutionary medicine, and public health. Methods focus on but are not limited to non-invasive sampling (saliva, urine, feces), quality concerns for their timing, storage, and processing, and the principles of immunoassays used to measure biomarker concentrations.

By the end of this course, you will be able to 
  • differentiate several physiological processes important for health and fitness
  • describe these processes as pathways by which the environment impacts health and fitness
  • identify biomarkers that are representative of these processes
  • design a study to evaluate the role of a given pathway and biomarker(s) in linking physiology, behavior, and health​

In this class, ​respect for one another is our highest priority. We will actively listen to one another's interests, thoughts, and perspectives and maintain respectful curiosity for perspectives that we do not understand. These perspectives include but are not limited to religion, sexual orientation, gender expression,  and racial identity. Disagreement and debate is good, don't shy away from it. Try though to use "I" statements during disagreements and make reference to your understanding of specific readings and your personal experience. Avoid making over-generalized statements, e.g. "everyone knows" or "it is a fact that". We will also prioritize impact over intention, i.e. if you pissed someone off but didn't intend to, you still need to say sorry. Please write or speak to me in private if you would like help to address or moderate any issue.

*Before the first day of class*
  1. If not already on UC Learning Center, request that I create an account for you.
  2. Complete "UC Laboratory Safety Fundamentals Initial"
  3. Simply forward certificate of completion email from SumTotal to natg@ucsb.edu.
  4. ​Schedule a blood draw in the student health portal for any day between 2/14 and 2/25. Appointment type: "Lab SHS provider". More instructions to follow in class.​      ​​Note: the appointment calendar automatically shows the next 21 days, however you can insert your own custom date to create an appointment.
  5. Due latest 2/27: complete "Bloodborne Pathogens for Labs and Researchers Initial" and forward completion email to emilycobb@ucsb.edu. 

Your major assignments for class:
  • daily participation*
  • discussion leading
  • lab reports
  • team research proposal presentation
  • team research proposal written
(* if public speaking is difficult for you, speak with me about special assignments in lieu of participation)
​
Opportunities for 6 pt extra credit: précis ​

Jan 9 : Introductions
Time to introduce the themes of the course, the lab, and ourselves to one another.
Readings for day of class: Discussion in class: Due: Lab Safety Fundamental certificate + Brainstorm area of interest for research proposal.
Lab work: Lab safety tour,  pipetting and dilutions exercise.


Jan 16: Martin Luther King Jr. Day: No class
Due Jan 17: 3 candidate topics for research proposal + 2 citations per topic (1 paragraph each, 2 pages max).


Jan 23: Social determinants of health (SDOH)
How do our social environments relate to our physiology, health, and biological fitness? This topic covers a lot of ground. The first reading takes a comparative lens on SDOH, which examines the relationship of the social environment, health, and fitness across animals. The second reading includes the idea of "embodiment" (Gravlee),  which emphasizes that our physiology develops in dynamic interaction with our environment . Approach the readings in whatever order you choose.
Lecture recording
Readings for day of class: Discussion in class:
  • Sociality and health in humans and other animals
  • Embodiment theory
  • (slides)
Due:  Annotated bibliography for research proposal (9 refs minimum, 2 max from from previous readings).
Lab work:  Basic colorimetric assay - Creatinine.


Jan 30:  Sample collection and Principles of immunoassays
Lecture recording 
Readings: Discussion in class: 
  • Sampling media (slides), key physiological functions to be measured, and logistical considerations
  • Principles of ELISA (slides) 
  • ELISA equipment
  • The standard curve
Due: NA.
Lab work:  Mock plate of competitive ELISA.
Précis for extra credit: Video lecture on principles of immunoassays.
This video does a good job at explaining and visualizing the principles of immunoassays, and enzyme-linked immunosorbent assays (ELISAs) in particular.
There are several different strategies that researchers (and manufacturers) use to design ELISAs. The narrator goes over the 4 common strategies:
  • Direct
  • Indirect
  • Sandwich
  • Competitive
The narrator refers to the analyte (or antigen) of interest consistently as a "protein"... we are not always looking for proteins with immunoassays. Sometimes, yes, we want to detect a protein or peptide (e.g. insulin, oxytocin, immunoglobulins, thyroid hormones), other times we want to detect a  steroid (e.g. cortisol, estradiol, testosterone). Here is optional information that highlights the different structures of different hormones. Immunoassays work the same way to detect any analyte - specific antibodies are developed for the analyte/antigen and are used to capture and detect it. Of course, there are lots of other methods to detect other things... flow cytometry and differential centrifugation for cell types, liquid chromotography  - mass spectrometry (LC-MS) for almost any type of molecule, and polymerase chain reaction (PCR) in part to detect particular regions of genetic code. With the exception of differential centrifugation, we will not be covering them in this class.


Feb 6: Energetics, life history, and reproduction
Today is the first class that we get into one of our major physiological domains - energy allocation. This topic is central and foundational to an evolutionary perspective of human biology and behavior, including life history theory. We tie in female menstrual cycles, reproduction, and the logistics of their measurements, because it is so closely tied to energetic status and is a major area of energetic investment.
Lecture Recording
Readings for day of class: Discussion in class: Due: Outline of background for research proposal. 2 urine samples and 2 saliva samples​
​Lab work: Aliquoting, labeling, & measuring specific gravity of urine.


Feb 13: The stress response and glucocorticoids
The hypothalamic-pituitary-adrenal (HPA) axis plays a powerful and fundamental role in regulating homeostasis and governs a large part of our physiological stress response.  The end products of HPA activity are glucocorticoids, which mobilize energy and have a multitude of effects across different physiological systems. These effects vary by the intensity and duration of glucocorticoid exposure. Short-term exposure is typically adaptive. However, long-term exposure can lead to deleterious consequences for digestion, reproduction, cognition, and immunity.

Readings for day of class: Discussion in class: (lecture slides)
  • Homeostasis, HPA axis, and the logic of the stress response (pp. 409-418)
  • System-specific stress effects and related disease - good girl gone bad (pp. 418 - 425, 435
  • Psychosocial stress (pp. 436 - 448)
  • (slides)
  • What to expect for cortisol lab.
Due: NA.
Lab work:

Feb 20: Presidents' Day: No class
Discussion for week: Schedule any 1-on-1 meeting times for support on proposal writing.
Due Feb 21: Outline of methods for research proposal.


Feb 27: Inflammation and immunity
​Readings for day of class: Discussion in class: (lecture slides)
  •  Intro to immunity
  • GCs and Immunity
  • (slides both)
Lab work:  Blood differentials with QBC star: QBC protocol, QBC Star analysis overview
Due Tuesday 2/28: Cortisol lab report 


Mar 6: Social Hierarchies and Health
Readings for day of class: Discussion in class: 
  • What are hierarchies in the non-human animal world?
  • How are they similar/different to social class/status in humans?
  • What are primary pathways of status effects on health?
  • What are the outcomes?
  • Are all hierarchies the same?​
Due:  QBC star lab report
Additional/optional reading: these highlight the endocrinological bases of several types of behavior related to competition, hierarchies, in-group out-group dynamics.
​
March 13: Student presentations
See "Oral Presentation" section here


Full research proposals due Friday March 16th, emailed to natg@ucsb.edu by 5 pm PT. 

Grading: (200 pts total)
​Discussion leading and participation (60 pt) 
  • Lead 2 discussions - guidelines linked above  (9 points each)
  • Participate in all 7 other discussions (6 points each)  
  • Discussion leader schedule
Lab reports (20 pt x 2)
Team research proposal (100 pt) 
  • 3 ideas for research proposal (9 pt) [4 pt peer-graded]
  • Research question and annotated bibliography for proposal (12 pt) [6 pt peer-graded]
  • Assigned team roles doc (3 pt)
  • Outline of background section, hypothesis, and predictions (12 pt) [6 ptspeer-graded]
  • Outline of methods for proposal (12 pt) [6 pt peer-graded]
  • Oral presentation (28 pt) [10 pt peer-graded]
  • Written proposal (24 pt) [10 pt peer-graded]
Extra credit: précis (6 pt each)

Submission instructions:
Turn in assignments as a word doc attachment to my email address (natg @ ucsb.edu) with Emily Cobb cc'd (emilycobb @ ucsb.edu)
Include ANTH 197 in the subject line of the submission email.
Put your team name at the start of the doc title (means you have to make up a team name).
All lab reports and proposal related assignments are due by midnight PT on the due date.
Written proposals are due Fri 3/16 at 5 pm.
Extra credit can be turned in any time before the written proposal is due.

​Late submissions: For each day late, 10% of points (rounded) are subtracted from your grades for the next 5 days, after which homework is assigned zero points except in circumstances that entail a doctor's note

​
Possible references for projects:
Resources here
Nelson Chapter 1 What is behavioral endocrinology
Nelson Chapter 2 The endocrine system
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