BIOL 368: Syllabus

BIOL 368 (NJIT) and 28:120:368 (Rutgers) — Fall 2018

Ecology and Evolution of Disease

Introduction

Ecology and Evolution of Disease addresses those aspects of ecology and evolutionary biology most relevant to understanding the origin, dynamics and treatment of disease (both infectious and hereditary/genetic). It is particularly recommended for pre-health students, including those in the Accelerated Programs, and serves as an introduction to the science behind public health. As well as basic biology, material covered will include aspects of human behavior, as well as some mathematical models.

The course follows a ‘flipped’ model, with class time devoted to discussion as well as group and individual activities intended to reinforce the basic material.

While designated Honors, this course is open to all with the necessary background (see the pre-requisites below). But it is taught at an advanced level, and assumes you have learned and retained knowledge about fundamental evolutionary and ecological processes. Without this background, you will struggle to do well.

Course details

  • Instructor: Gareth J. Russell
  • E-mail: russell@njit.edu
  • Phone: 973 596 6412
  • Office: 428H Central King Building
  • Office Hours: Monday and Wednesday, 11:30 – 12:30 (after class) or by appointment
  • Credits: 3

Prerequisites: Foundations of Ecology and Evolution is required. (General Biology, or Concepts in Biology, are not sufficient.) An upper level ecology or evolution course is recommended. It will also be assumed that you know the basics of cell biology and genetics, so Foundations of Cell and Molecular Biology (or equivalent) is also recommended, as is a basic ability in algebra so that model formulations can be followed. There will be a graded pre-requisite test about 2 weeks into the semester.

Schedule: Class meets Monday and Wednesday, 10:00 to 11:25, in CKB 313 on the NJIT campus. I expect you to attend class and arrive on time.

Class needs: We will often be accessing information in class, and so it will be helpful for as many students as possible to have internet access. So, if you have a laptop or tablet, please bring it. You can use a phone instead, but it won’t be as good. If you don’t have a suitable device, don’t worry: most of this work will occur in groups where devices can be shared.

Learning goals

Content learning goals

After taking this course, students will

  1. Understand the evolutionary factors driving or influencing a variety of non-infectious ailments (such as obesity, heart disease).
  2. Understand the ecological and evolutionary factors driving or influencing infectious diseases (such as cholera, malaria, or HIV).
  3. Understand how failing to take into account evolutionary and ecological principles when addressing disease can have unfortunate consequences (e.g., antibiotic resistance, virulent ‘super-bugs’ etc.).
  4. Understand the basis and evidence for ‘germ theory’, which posits that a number of diseases traditionally thought of as non-infectious may, in fact, be caused by cryptic infectious agents.
  5. Understand the multi-disciplinary teamwork required in the field public health.

Skill learning goals

After taking this course, students will

  1. Be proficient at reading and extracting the important data and conclusions from scientific publications.
  2. Be able to summarize the message of a scientific publication in a few sentences.
  3. Be able to recognize and ‘read’ simple mathematical models of infectious disease.

Grading and exams

There will be two exams, a mid-term and a final, and ten short writing assignments. The grading will be as follows:

Component
Grade percentage
Prerequisite quiz
5
Short writing assignments (total)
20
Participation in class activities
5
Current event postings 5
‘Explainer’ writing assignment 25
Mid-term exam
20
Final exam
20
TOTAL
100

Prerequisite quiz

At the end of the second week or beginning of the third week, there will be a short quiz on various prerequisite topics. You will be given a listing of topics on the first day of class. These are all things which you should recall from Foundations of Ecology and Evolution, and to some extent also Concepts in Biology (or a General Biology course if you are a transfer student) and high school biology. Getting back up to speed on this material right away will let us explore more interesting topics later.

Writing assignments

The idea behind the writing assignments is that you will get better at doing them, and your scores will increase. If you manage to do at least four excellent ones by the end of the semester, you will get the full ‘quality’ score!

Component
Total
2 points for simply doing each assignment ‘adequately.’
12
A quality score for each assignment out of 6, top three scores only count
18
TOTAL
30*

*Scaled to 20% of your final grade

Participation

Please note that this is a flipped course, so participation in class activities is essential. You start with all five participation percentage points. If you start being regularly late to class, or missing classes without an acceptable reason, you will start losing points. I will give you a warning if that is about to happen.

This is not an arbitrary rule: it is the nature of a flipped class that only the students who come to class will succeed. I want you to succeed, and I hope you want to as well!

Current event postings

You will be asked to keep an eye on the news and post any interesting articles related to the course. There will be plenty to find.

‘Explainer’ writing assignment

The class is going to write a ‘Conservation Reader’ — a single document with chapters on certain ‘of the moment’ topics in public health. They will be written in the style of a quality magazine article (think Time).

Textbooks

There are two required textbooks. They are in the NJIT bookstore.

  • Evolutionary Medicine by Stephen C. Stearns and Ruslan Medzhitov. ISBN 978-1-60535-260-2
  • Plague Time by Paul Ewald. ISBN 0385721846. (Note that there are two editions of this book, with different subtitles. The only other difference is in the Foreward — the one subtitled “The New Germ Theory of Disease” has an updated forward that mentions a few case studies that occured after the original version. If you have the other version, don’t worry.)

The following book, which is one of the foundations of the field, you might also find helpful. You can get it for about $10 on Amazon.

  • Why We Get Sick by Randolph M. Nesse and George C. Williams. ISBN 0679746749.

Links

Links to external media are now on their own page.

You will also use Moodle to submit assignments and for other things.

Syllabus

  • Important Note: The syllabus is different every time the course is taught! Some the details may change even as the semester progresses. The reason is that there is usually some emergent infectious disease in the news that we can use as an overall case study. Last year it was zika virus. Before that it was ebola. What is it this year? The syllabus below provides a general outline of topics, but the specifics and timings may still change. Check back here regularly for updates.
  • Textbook readings are identified as “EM” (Evolutionary Medicine) and “PT” (Plague Time). Other readings are provided as PDF files — click on the name to download each one.
  • A week is defined (here and on Moodle) as being from the Thursday prior to the classes, to the Wednesday when the second class meets. That is because you should read the Chapter pertaining to that week’s topic before the first class on Monday.

Week 1 (Wed only): Introduction to the course.

Content: Class introduction and logistics — Prerequisites (importance and quiz) — Discussion of need for the course — Discussion of writing, and writing assignments — The Reader — Discussion of notes, and note-taking.

Class activities: Watch beginning of Dawkins lecture while making notes — In small groups, compare note-taking strategies and discuss — In a group, write 250 word ‘abstract’ summarizing lecture — Discussion of levels of explanation.

Assignments

  1. Get the textbooks.
  2. Read EM Chapter 1 before Monday’s class. Write notes and questions to bring to class.
  3. Find your notes and other materials from Foundations of Ecology and Evolution. Make a study plan for the prerequisite topics.

Week 2: (Re-)introduction to Evolutionary Thinking

Content: Natural selection, neutral evolution, random change, mismatch and adaptation — Styles of thought.

Class activities: Review of EM Chapter 1 — Countering examples of bad evolutionary thinking.

Assignments

  1. Study for pre-requisite quiz.
  2. Read EM Chapter 2. Write notes and questions.

Week 3: Pre-requisite quiz (Monday) and What is a patient?

Content: Pre-requisite quiz — Ancient and recent evolutionary history — The types and origins of human variation — The patient as an ecosystem

Class activities: Review of EM Chapter 1 — Countering examples of bad evolutionary thinking.

Supplemental reading: Jernberg et al. 2010

Week 4: What is a disease?

Preparation (do in advance): Read EM Chapter 3

Supplemental reading:  Medzhitov et al. 2012

Week 5: Defenses

Preparation (do in advance): Read EM Chapter 4

Writing assignment 1 (due Wednesday): Chahroudi and Silvestri 2016

Week 6: Pathogen Evolution

Preparation: Read EM Chapter 5

Writing assignment 4 (due Wednesday): Ewald et al. 1998

Week 7: Review and mid-term exam

Preparation: Study for mid-term. Monday is a review session, with topics determined by you, so study before Monday! Use the review to get clarification on topics you don’t understand — come with questions.

Writing assignment: None.

Important note: There is an unsurprising tendency to take the week after a mid-term exam ‘off.’ Please don’t — there is still prep for next week. It will hurt you in the final exam.

Week 8: Cancer 1

Preparation (do in advance): Read EM Chapter 6

Writing assignment 5 (due Wednesday): Merlo et al. 2006 Cancer as an evolutionary and ecological process. Nature Reviews Cancer 6: 924-935.

Week 9: Cancer 2 — Reproductive medicine

Preparation (do in advance): Read EM Chapter 7

Writing assignment: None.

Week 10: Infectious diseases 1

Preparation (do in advance): None

Writing assignment (for Wednesday): Jones et al. 2008

Week 11: Infectious diseases 2 — Germ Theory 1

Preparation (do in advance): Read Plague Time Chapters 8 through 10 (for Monday), and Plague Time Chapters 3 and 7 (for Wednesday)

Writing assignment (for Wednesday): Worobey et al. 2016

Week 12 (Thanksgiving — Monday class only): Germ Theory 2

Writing assignment (for Wednesday): Woodman et al. 2007

Reading preparation (do in advance):  Plague Time Chapters 8 through 10

Week 13: Antibiotic resistance and microbial ecology

Writing assignment (for Wednesday): Kodaman et al. 2014

Reading preparation (do in advance): Plague Time Chapters 11 through 14

Week 14: Mismatch

Writing assignment (for Wednesday): Koopman et al. 2016

Reading preparation (do in advance): EM Chapter 8

Week 15: Open Questions and Review

Optional writing assignment (for Wednesday):

Reading preparation (do in advance): EM Chapter 11

Final exam: TBD (but do not plan vacation travel until you know when the exam is).

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