EGMT1520 - Spring, 2022
When do scientists change their minds?
fasta.bioch.virginia.edu/egmt1520
EGMT1520/109 - Mon/Weds 11:00 – 12:15 AM Bond House 106
EGMT1520/104 - Mon/Weds 2:00 – 3:15 PM Minor Hall 130
Course director: William R. Pearson wrp@virginia.edu
Office hours 9 - 10:30 Weds, Pinn Hall Rm 6-057 or Zoom / email for appt.
Course Description:
Scientists are wrong all the time, sometimes for many decades. This is not surprising, as discovery in science is a process of change. Do scientists change their minds when they get new data, or does the data need to be "special"? In this course, we will trace the processes that caused scientists to change their minds about biological discoveries, beginning with the demonstration that genes are made of DNA, and ending with the controversial role of "junk" DNA in the human genome. By investigating what scientists believed when they were wrong, and then following their arguments for and against the incorrect, and correct explanations, we will both understand better the roles of theory and evidence in scientific discovery, and also develop a process for making sense out of abstract models. In addition to following the process of transition from "wrong" to "right" for settled biological science, we will also examine an unsettled question: "Is 90% of the human genome 'junk'?".
Learning Objectives:
After taking this class students will be able to:
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Read scientific papers, linking claims in the title and abstract to figures and tables in the results section.
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Understand the components of a biological experiment: hypothesis, measurement (assay), and controls
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Use mental models to make predictions of experiments that might confirm or refute hypotheses
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Describe the process and insights that caused scientists to change their minds in about a question.
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Develop a process for "internalizing" abstract scientific concepts into more concrete models that can be used to make predictions (or anti-predictions).
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Identify the limitations, or open-questions, of a new scientific explanation
The Engagements Experience
Ten-percent of your grade in this course will be based on your
participation in the
Engagements Experience. More detailed
instructions for the
Engagements Experience can be
found
here, but briefly, you are
expected to attend attend: (a) one "Scholar Speak" event,
(b) one "self-care" experience and TA-check in, and (c) participate in an "Engaging Grounds"
experience. Please document your participation in each
event by uploading your "ticket" to the assignments page, with the date of the engagement, and the speaker (for Scholar Speak). In addition
(d), you are expected to write 250 word essay drawing parallels between the
perspective changes discussed in this course and the new perspectives you gained through your Engagements Experience.
Course Format:
We will discuss at least one scientific paper each week, after an
introductory lecture that introduces the biology that was known and
the experimental techniques that were available when the experiment
was done. In general, the first session each week will be a lecture
that provdes background to the paper, the second session will be
quizzes and homework discussions in breakout groups. Students will
work in groups to interpret critical results and explore alternative
hypothesis. The course will use two biological examples: the discovery
of DNA as the genetic material and the characterization of the
"functional" (not-junk) fraction of the human genome to explore how
abstract models can make concrete predictions.
Early in the course, students in groups will identify a scientific
phenomenon that "does not make sense." For example, gravity does not
make sense; how can heavy objects fall at the same rate as light
ones? Over the course of the class, each group will explore the
history of the phenomenon, with the goal of identifying the insight
that explains how the phenomenon can make sense.
We will search for these insights by learning how scientists viewed
the problem before their change in perspective, and by exploring how
and why their perspective changed. The course will end with
presentations by each group describing the insight that allows the
phenomenon to "make sense."
Activities and assignments:
During the 7 weeks of the course, progress will be evaluated based on quizzes on assigned readings (20%), individual and group homework (20%), peer evaluation of group contributions (10%), and two project presentations: an intermediate group project presentation (15%) and the final group projects (25%). Group discussions and the group projects will link group members to specific contributions to the discussion and final presentation. The Engagements Experience will count for the final 10% of the grade. While quiz and assignment score will be recorded in gradebook, the final score for the class may differ from the gradebook total and gradebook grade will only be an approximation of the final grade.
Attendance and participation: Students are expected to attend all of
course sessions; unexcused absences will be penalized. Contributions
to group work will be documented in group submissions.
Course Schedule
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Weds 1/19 |
| Introduction/Overview
Lecture PDF
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| Papers: | See Collab Resources Wk1 |
| Tasks: | Read a scientific paper, identify the parts of the paper |
| Assessments: |
(1) (individually -- in class) Take the short quiz on collab (graded for completion, not correctness) to describe your comfort with genome biology;
(2) (individually -- due Friday, Jan. 21, 5:00 PM. See Collab/Assignments. Describe a scientific phenomenon, perhaps one that you learned about in high-school, that seems counter intuitive (does not make sense). Explain why it does not make sense.
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Mon 1/24 |
| The discovery of DNA as the genetic material
Lecture PDF
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| Papers: | Avery, McCarty, MacLeod J. Exp. Med (1944) 79:137 (collab) |
| Tasks: | (1) (in groups) [15 min] Each group will be assigned a paper. Identify the parts of the paper, the claims made in the paper, and the links between claims and results/data. [50 min] lecture on Avery paper |
| Assessments: |
(1) (in groups -- due Fri., Jan. 28) Assignment: reading a scientific paper
(2) (in groups -- due Mon. Jan. 31) 1+ page essay on one figure from Avery et al.
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Weds 1/26 |
| What did Avery et al. show?
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| Papers: | Avery, McAvery,McCarty,MacLeod J. Exp. Med (1944) 79:137 (Collab Wk2) |
| Tasks: | each group will present one table or result from the Avery paper, and (a) show how the data supports the conclusion; (b) propose an alternative explanation (powerpoint/google slides); (c) group discussions on Gravity presentation) |
| Assessments: |
(in groups -- Due Friday, Jan 28) For the paper your group is assigned, answer the questions outlined in the Reading Scientific Papers assignment
(in groups -- Due Monday, Jan. 31) Assignment - Avery figure essay
(in groups -- Due Weds, Feb. 2) Make a 4-slide Powerpoint/google slide presentation explaining why 'gravity' does not make sense, and the critical insight that resolves the problem
(in groups -- Due Weds, Feb. 2) Write a 750-ish word paper describing the arguments made in the Gravity presentation.
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Mon 1/31 |
| The discovery the structure of DNA
Lecture PDF
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| Papers: | Watson and Crick (1953) Nature 171:737, Watson and Crick (1953) Nature 171:964 (Collab Wk3) |
| Tasks: | for quiz Wednesday, read Deichmann (2004) Hist Stud Phys Biol Sci 34:207 (Collab Wk3) |
| Assessments: |
(1) (Wednesday, Feb. 2) (in groups - Gravity Presentations
(2) short quiz on Deichman paper
(3) (in groups -- due Mon. Feb. 7) As a group, list three possible phenomena/questions, and why they do not make sense.
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Weds 2/2 |
| Implications of the double helix
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| Papers: | Deichmann (2004) Hist Stud Phys Biol Sci 34:207 (Collab Wk3) |
| Tasks: | (1) Group Gravity presentations. (2) Quiz on Deichmann paper. (3) Group discussion -- choice of topic, discussion of topic: Why intuitive is wrong; change in perspective; how perspective makes correct answer intuitive. |
| Assessments: |
(1) (in groups) Assignment: Gravity presentation/essay
(2) Deichman quiz;
(3) (in groups -- Due Monday, Feb. 7) As a group, list three possible phenomena/questions, and why they do not make sense.
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Mon 2/5 |
| The human genome
Lecture PDF
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| Papers: | https://www.genome.gov/human-genome-project
Publically funded project: Nature (2001)
Celera project: Science (2001) 291:1304 (sect. 7) (Collab week 4) |
| Tasks: | visit UCSC Genome browser at http://genome.ucsc.edu |
| Assessments: |
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Weds 2/9 |
| Exploring the human genome
Link
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| Tasks: | (in groups) Answer the questions for the Human Genome lab. |
| Assessments: |
(1) -- Due Friday Feb. 11 (in groups) answer the assignment questions for the gene you examined on Wednesday
(2) -- Due Monday Feb. 14 (individually) repeat the human genome exploration with a new gene, answering questions about the gene and its surroundings
(3) -- Due Weds Feb. 16, individually) -- Peer evaluation assignment
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Mon 2/14 |
| Genome function, ENCODE, and Junk DNA
Lecture PDF
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| Papers: | Nature (2012) 489:57-74, Graur (2013), Eddy (2013) (Collab, Wk 5) |
| Tasks: | (For next Wedsday quiz) - read Graur (2013), Eddy (2013), address reading questions |
| Assessments: |
(next Wednesday) in class quiz
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Weds 2/16 |
| When is junk not junk
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| Papers: | Graur (2013), Eddy (2013) (Collab, Wk 5) |
| Tasks: | (1) group work on final project |
| Assessments: |
(1) In class (individual) quiz on Eddy/Graur criticisms of ENCODE conclusions
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Mon 2/21 |
| Science, statistics, and reproducibility I
Lecture PDF
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| Papers: | Ioannidis (2005) PLoS Med 2:e124 (collab, wk 6) |
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Weds 2/23 |
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| Tasks: | [in groups] (1) [20 min] Describe a hypothesis and a measurement, giving examples of possible false positives and false negatives; discussion of presentation. (2) [30 min] draft presentations |
| Assessments: |
(1) [in groups] Statistics - False positives, false negatives due Friday, Feb. 25
(2) [in groups] Final Project presentation
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Mon 2/28 |
| Science, statistics, and reproducibility II
Lecture PDF
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| Tasks: | [in groups] polishing final project presentations |
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Weds 3/2 |
| Group presentations
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| Tasks: | [one per group] Upload copies of your final presentation and final paper to the Week 7 Project Presentation assignment |
| Assessments: |
(1) [in groups] Final Project presentation
(2) [individually] Peer Evaluation II
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Mon 3/14 |
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Morning EGMT1520 discussion groups
Afternoon EGMT1520 discussion groups
wrp@virginia.edu
Last modified: Mon Feb 28 10:30:57 2022