Surveys three major themes of evolutionary biology: adaptation, diversity of life, and the shared characteristics of life. Mechanisms of evolution, speciation, phylogeny, and macroevolutionary processes are discussed.
Prerequisites: BIO 130 - Evolution and Diversity
Robert Williamson - Robert’s schedule
Office: Moench F205
You are assumed to have a working knowledge of basic genetics and phylogenetics for this class. If you need a review you should see Ch 4 and Ch 5 of the main text.
The textbook readings below are optional, but will help clarify and frame topics. The readings of primary source articles are required and expected to be done before they day of class they are associated with.
Here are the times and rooms for each day of the week:
Day 1 - Tuesday 1-2pm, J205 Day 2 - Wednesday 1-2pm, J204 Day 3 - Friday 1-3pm, O103
Week 1
Week 2
Week 3
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Week 4
Week 5
Week 6
Week 7
Week 8
Week 9
Week 10
Finals week
Upon completion of this course, students will be able to:
Freeman, S., & Herron, J. C. (2007). Evolutionary analysis 5th ed.
The chapter numbers in the schedule above refer to this text, readings are meant to supplement the discussions in class.
This book is a collection of essays written by researchers in evolution today. They talk about seminal experiments and ideas, some of these you might recognize from BIO130 or other courses. This is a great resource for jumping deeper into a few key ideas in evolution.
This text is a short volume that enumerates some of the major pieces of evidence for evolutionary thinking. It is a great introduction to evolutionary thought and refutes some of the common ‘criticisms’ of evolution. Jerry Coyne also has a blog of the same name where he reviews scientific articles, discusses evolution, and posts a lot of pictures of cats.
The textbook should be used to help fill in gaps in your knowledge and understanding, or reinforce ideas we discuss in class. Reading it is not strictly necessary, but encouraged.
Other assigned readings provided on moodle will be assumed knowledge for our discussions in class, you should come prepared to discuss these and have questions about them ready each day. These readings might evolve over the course of the quarter to better reflect the interests of the class. You should regularly check the course schedule to ensure you are not missing any key readings.
Each student begins the quarter with two tokens, these are a second chance opportunity. They can be used on any assignment, submission, or activity throughout the quarter. If you are using a token you are expected to inform me within 2 days of the associated assessment item’s normal due date (unless otherwise specified).
You will have several opportunities to gain tokens throughout the quarter. These might be grant for excellent participation, very good performance, or particularly insightful discussion. Robert will inform you of some opportunities to explicitly gain these tokens, but may grant them unannounced. Every interaction and submission should be considered an opportunity to use and gain tokens. A few good ways to earn tokens: send Robert and the class articles relevant to course topics that spark discussion, go above and beyond on analyses for Lab assignments, assist your peers in constructive ways and then have the peer inform the instructor of they ways you helped them learn!
If you end the quarter with at least 2 tokens your final letter grade will receive a half letter-grade boost.
Description
Each Friday, you will receive by email a question relating to course material. You will submit a response to this question by Tuesday at class time on Gradescope. I will return your submission to you ASAP. The question will almost certainly require outside reading or information acquisition; it will definitely require you to practice thinking in the higher levels of Bloom’s taxonomy. Submissions will be scored as per the attached guidelines, using a specifications grading approach. See me in office for clarification of scores or comments. You should indicate how long you spent working on the WA in your submission. All WAs must be submitted using the Overleaf Template found on moodle.
Submissions must be written using the provided Overleaf project template.
Grading
The weekly analysis submissions will be scored using an approach called specifications grading. The specifications are listed below. To earn credit for a submission, all specifications must be met. Some commentary will be provided, although you may always consult me for guidance on improvement or different approaches. During the course of the class, you may re-submit via email a weekly analysis answer, within one week, with the original version included (in the same file as your revised answer) and indicating that you are cashing in a token. I will distribute at least 15 weekly analysis questions (at least one per week) with some weeks having two or even three questions that can be answered. In this way, you will be able to best regulate your effort.
Grading scale
Eight passing submissions 50%
Seven passing submissions 44%
Six passing submissions 37%
Five passing submissions 31%
Four passing submissions 25%
Three or fewer passing submissions 0%
Specifications for a passing submission
Incorporates concepts from class.
Takes a position.
Supports arguments with data or logic.
Identifies constraints, limitations, or alternate perspectives.
Represents a complete, organized, logical response.
Demonstrates Bloom’s taxonomy levels of analysis, synthesis, or evaluation.
Incorporates the primary or secondary literature external to that examined in class.
Is professional in the communication approach, including grammatical and language choices.
Follows the course submission guidelines. [see below]
Description
Each week we will have a lab assignment where we will perform experiments to test evolutionary theory and practice developing our intuition for evolution. These labs will be assigned each Friday and will be due the following Friday.
These assignments will largely use the SLiM simulation framework. You will need to practice interpreting, analyzing, and presenting data. Your submissions must use the provided Overleaf template.
To practice discussing science and interpreting papers some of the required readings will be annotated collaboratively on moodle using the Hypothesis system. These comments are due day 2 of class each week at least 2 hours before class time. Moodle has links to the instructions for the hypothesis system for more detail.
You are required to make at least 2 annotations on each article, and comment on at least one annotation made by someone else.
This will be graded on an all or nothing basis; to earn credit your annotations and comments must meet these criteria:
Some of these articles will be long, and you need to spend serious time reading them to have meaningful conversations. They are all available right now and to practice discussing science together we all need to be engaged at the same time, so there will be no late annotations or tokens accepted for these assignments.
Starting a fruitful discussion and including meaningful outside references in your annotations and comments can earn you tokens for use on other assignments. Note that if you are doing these annotations 2 hours before class, there will be no time for useful discussion. You should check in with your comments and others comments before Day 2 of class each week so you are prepared for the in-class discussions.
You are expected to participate in discussions, activities, and some group work as part of class. This grade will reflect your participation in our live Teams meetings as well as participation through discussion in the Teams group. The “Growing as a Researcher” assignment you will recieve in week 8 contributed heavily to this grade. The prompt for this assignment is here:
“As part of this course you’ve had to find, read, and understand many scientific sources. Explain how you approach to this process has changed during your time as a student. Give specific examples to demonstrate how you have grown as a researcher and what new learning strategies you have developed. Your response should explain at least two learning strategies you have developed or refined. Give at least one example of how you have used each of these strategies during assignments for BIO330.”
This assignment will be graded using the WA specifications outlined below, submit it using the WA template.
Your final project will be writing a literature review about an evolution topic of your choice to be submitted to the journal Rose-Hulman Institute of Technology Evolution Review (RHITER). This is meant to be written as an invited review for evolutionary biologists who are non-experts in the topic you are presenting. You should model your review after papers in the journal Annual Review of Ecology, Evolution, and Systematics. Your formatting for this assignment should follow the guidelines described by the journal. You will use the RHITER template provided on moodle and submit a pdf to gradescope for each milestone.
Invited reviews like this are highly prestigious, highly cited, and can have huge impacts on the direction of a field for years after they are written. The goals of such reviews are to lay out the history of a field, the current state of research, and directions for future investigation. They usually focus on 2-3 specific ideas, methods, or theories and compare and contrast them. These reviews are more than a simple list of relevant references, they do high level synthesis in order to shape the future of research and indicate to new researchers where how the field got to its current state.
We will read several example reviews and discuss them over the quarter to give you a feel for the kind of topics they cover. You can also see example previous issues of RHITER on moodle.
This assignment will have 4 main components:
First draft (10%) You will submit a first draft of your review, this does not need to be completely written. Some sections can be stubs, however the main focus of the review and the stances it should take should be clear. A draft of any figures (hand-drawn approximations are fine) should be included. Additionally, the set of papers your review will rely on should be well fleshed out, and it should be clear how you are using the papers you will be citing. You will submit a pdf and a zip file of your Overleaf project to gradescope for portion of the assignment. You must use the provided Overleaf template for this article.
Submission and Review (20%) You will submit a fully completed article that meets all of the journal’s submission guidelines. This draft will be sent out to reviewers who will assess the appropriateness for your review for publication. Note that “draft” does not mean “unedited”, this should be a complete version of the document. Your submission is required to onclude at least one figure, that figure has to be created by you (not a reused figure from another paper), usually this figure will be made from combining data or findings from several papers you cite. You must own the copyright to this figure, meaning you cannot use one from another journal article.
You will act as an anonymous reviewer for 2 other submissions to RHITER. You are expected to write a review that assesses the quality and appropriateness of the review, and make a decision if the review should be accepted or rejected for publication. I recommend reading Elsevier’s guide to reviewers and in particular look at their sample review before you write your review (they have some very good resources linked at the bottom of the guide too). When you are asked to review a submission the editor (aka Robert) will send you instructions on what to submit.
Your article will be submitted as a pdf to Moodle (not gradescope) for this portion of the assignment.
Your review must include a summary of the article and its main arguments, you must suggest at least one new reference that should be included in the article, and you should include a discussion of the figures and their captions. Your review should refer to specific line numbers and sections of the original source. Your review will be submitted as a pdf to Moodle.
Response to Reviewers (10%) Based on the feedback from your reviewers and the editor you will make changes to your submission and write a response to the reviewers. Here is another Elsevier article and here is a PLoS article about responding to reviewers, you should read these before starting your response. You will be assessed by how well you incorporate and respond to reviewer feedback. Remember: you do not have to make every change reviewers propose, but you must make a reasonable argument about why you are not making their proposed changes in your response.
Your response to reviewers will be submitted as a pdf to gradescope.
Final submission (60%) Your final submission will be your fully formatted and edited article along with the response to reviewers you have written. It will be graded based on how it improved over the corse of the peer-review process, its professionalism, and how well it demonstrates your depth of thought and understanding on topics in evolution.
Your final submission will be submitted as a pdf and a zip file of your Overleaf project to gradescope.
RHITER Article 30%
In-class participation 10%
Hypothesis Annotations 10%
Weekly analyses 30%
Lab assignments 20%
The grades on moodle do not necessarily reflect your actual grade. You can use the provided “What’s my grade?” excel sheet on moodle to estimate your grade.
Assignments will be submitted and returned via gradescope or moodle, the link and instructions for our gradescope page can be found on moodle. In general, assignments should be submitted as a pdf, using the Overleaf templates provided. We will be practicing out LaTeX skills throughout the course, you can reference this guide on basic LaTeX as you work through things. In general, do not get stuck on formatting problems. The core idea behind LaTeX is to separate the formatting from the content. For each assignment just write the text and worry about the formatting later. If you have a problem getting a file to compile into a pdf come see me, I will be generous with extensions related to these problems, but only if I see that your text is complete if you ask for help after an assignment is due.
This class will be highly interactive, I expect you to have read and assigned material before class and come prepared to discuss, ask questions, and think deeply about the topics of the day. If you miss more than 3 days of class you will automatically fail the course. However, if you are sick or otherwise indisposed please do not come to class. Also, we are a small campus with high connectivity, which is the perfect case for spread of infection disease. Therefore, I highly encourage you to get flu vaccines as soon as you can!
Collaboration is encouraged on homework, quizzes, and laboratories. When you collaborate, you must properly credit your collaborators and clearly indicate the extent of the collaboration. In all cases, each individual is responsible for understanding and writing out the entire solution. For example, on weekly analyses, this means that once a group solution has been achieved, each collaborator must rework the problem and write up the solution independently. Copying is not collaboration.
Any kind of plagiarism or cheating will result in a severe penalty in the course and Student Affairs will be notified. See this page for details.
Most importantly, any actions that reduce your ability or your opportunity to learn can be considered academic misconduct. Make sure you learn!
It is expected that any work submitted for assessment represents the intellectual work of the individual(s) submitting the work. Any attempt to pass off the intellectual work of another (including the work generated by Large Language Models, LLMs, like ChatGPT) as their own or without proper attribution is an example of academic misconduct and is subject to the penalties described in the Rose-Hulman Academic Rules and Procedures and Student Handbook documents. However, I believe that LLMs and other AI tools will become standard aids in most fields in our near future. So, I will not ban the use of these tools in this class. Before you use these tools you need to ask yourself:
If you use any LLM or any other AI as part of an assignment, I require you to attach the resulting inputs and outputs from the use to your assignments. This serves a few purposes. 1) I can see how you are using it, to make sure you aren’t missing something important in what you are supposed to be doing. 2) You are more protected from claims of academic dishonesty. 3) I can verify that the tool is not lying to you. 4) We can learn how to better use these tools together. If I discover that you have used an LLM without attribution you will receive a grade penalty appropriate to the severity of the use and I will submit a notice of academic dishonesty to the Dean of Faculty and Dean of Students, per the guidelines in the student handbook. Particularly ingenuitive and appropriate uses of AI in this class can earn you tokens, if they meet the guidelines above.
I strongly encourage students to document special academic needs with staff at the Office of Student Affairs and/or the Counseling Center, and then to contact me as soon as possible so that we can work together to provide recommended academic accommodations while protecting your privacy.
If you have any concerns about any course matters, you should tell someone. You can email your instructor, speak to your instructor, or leave anonymous feedback in Moodle. You can also contact the department head, Student Affairs, or another Rose employee you feel comfortable with.
This syllabus is subject to revision with prompt notification of enrolled students.
