Course Info

Title: MAT 690: Combinatorics of Genome Rearrangements
Semester: Spring 2022
Credits: 3
Section: 1
Time: 11:30-12:20PM MWF
Location: AMB 207

Instructor Info

  Dana C. Ernst, PhD
  AMB 176
  10-11:15AM MWF, 11:30-1PM Th
  dana.ernst@nau.edu
  928.523.6852
  danaernst.com

What is This Course All About?

When comparing two genomes, the content of the DNA molecules is often similar, but the way in which it is arranged may differ substantially. The mutations that led to these differences are called genome rearrangements, and the structural differences between two genomes motivates the study of their combinatorics. In this course, we will study several combinatorial optimization problems that arise out of the evolutionary events that lead to genome rearrangements. In addition, we will study related permutation sorting problems that are independent of biology.

The mathematician does not study pure mathematics because it is useful; he studies it because he delights in it, and he delights in it because it is beautiful.

Course Materials

There is no textbook for this course. All course content will be covered via lectures and homework.

An ounce of practice is worth more than tons of preaching.

Rights of the Learner

As a student in this class, you have the right:

  1. to be confused,
  2. to make a mistake and to revise your thinking,
  3. to speak, listen, and be heard, and
  4. to enjoy doing mathematics.

You may encounter many defeats, but you must not be defeated.

Commitment to the Learning Community

In our classroom, diversity and individual differences are respected, appreciated, and recognized as a source of strength. Students in this class are encouraged and expected to speak up and participate during class and to carefully and respectfully listen to each other. Every member of this class must show respect for every other member of this class. Any attitudes or actions that are destructive to the sense of community that we strive to create are not welcome and will not be tolerated. In summary: Be good to each other. I would appreciate private responses to the following question: Are there aspects of your identity that you would like me to attend to when forming groups, and if so, how?

Students are also expected to minimize distracting behaviors. In particular, every attempt should be made to arrive to class on time. If you must arrive late or leave early, please do not disrupt class. Please turn off the ringer on your cell phone. I do not have a strict policy on the use of laptops, tablets, and cell phones. You are expected to be paying attention and engaging in class discussions. If your cell phone, etc. is interfering with your ability (or that of another student) to do this, then put it away, or I will ask you to put it away.

Don’t fear failure. Not failure, but low aim, is the crime. In great attempts it is glorious even to fail.

Rules of the Game

Reviewing material from previous courses and looking up definitions and theorems you may have forgotten is fair game. However, when it comes to completing assignments for this course, you should not look to resources outside the context of this course for help. That is, you should not be consulting the web, other texts, other faculty, or students outside of our course in an attempt to find solutions to the problems you are assigned. This includes Chegg and Course Hero. On the other hand, you may use each other, the textbook, me, and your own intuition. If you feel you need additional resources, please come talk to me and we will come up with an appropriate plan of action. Please read NAU’s Academic Integrity Policy.

You will become clever through your mistakes.

Homework

You are allowed and encouraged to work together on homework. However, each student is expected to turn in their own work. Unless stated otherwise, homework will be due at the begining of class on the day it is due. In general, late homework will not be accepted. However, you are allowed to turn in up to two late homework assignments with no questions asked. When doing your homework, I encourage you to consult the Elements of Style for Proofs. On each homework assignment, please write (i) your name, (ii) name of course, and (iii) Homework number. You can find the list of assignments on the homework page. I reserve the right to modify the homework assignments as I see necessary.

Generally, the written homework assignments will be due on Wednesdays, but I will always tell you when a given homework assignment is due. Your homework will always be graded for completion and some subset of the problems will be graded for correctness. Problems that are graded for completeness will be worth 1 point. Problems that are graded for correctness will either be worth 2 points or 4 points depending on the level of difficulty. Generally, computational problems will be worth 2 points while problems requiring a formal proof will be worth 4 points. Each 4-point problem is subject to the following rubric:

Grade Criteria
4 This is correct and well-written mathematics!
3 This is a good piece of work, yet there are some mathematical errors or some writing errors that need addressing.
2 There is some good intuition here, but there is at least one serious flaw.
1 I don't understand this, but I see that you have worked on it; come see me!
0 I believe that you have not worked on this problem enough or you didn't submit any work.

To compute your score on a given homework assignment, I will divide your total points by the total possible points to obtain a percent score. Each homework assignment has the same weight. Your overall homework grade will be worth 50% of your final grade.

I write one page of masterpiece to ninety-one pages of shit.

Exams

There will be one midterm exam and a cumulative final exam. Each exam will consist of an in-class portion and a take-home portion. The in-class portion of the midterm exam is tentatively scheduled for Friday, March 4 (week 8) and is worth 25% of your overall grade in the course. The in-class portion of the final exam will be on Monday, May 2 at 12:30-2:30PM and is worth 25% of your overall grade. Make-up exams will only be given under extreme circumstances, as judged by me. In general, it will be best to communicate conflicts ahead of time.

The impediment to action advances action. What stands in the way becomes the way.

Attendance and Participation

Regular attendance is expected and is vital to success in this course, but you will not explicitly be graded on attendance. Students can find more information about NAU’s attendance policy on the Academic Policies page. You are also expected to respectfully participate and contribute to class discussions. This includes asking relevant and meaningful questions to both the instructor and your peers in class and on our Discord server.

I must not fear.
Fear is the mind-killer.
Fear is the little-death that brings total obliteration.
I will face my fear.
I will permit it to pass over me and through me.
And when it has gone past I will turn the inner eye to see its path.
Where the fear has gone there will be nothing.
Only I will remain.

Extra Credit

The only thing I will award extra credit for is finding typos on course materials (e.g., textbook, exams, syllabus, webpage). This includes broken links on the webpage. However, it does not include the placement of commas and such. If you find a typo, I will add one percentage point to your next exam. You can earn at most five percentage points over the course of the semester. They’re is a typo right here.

Basis for Evaluation

In summary, your final grade will be determined by your scores in the following categories.

Category Weight Notes
Homework 50% See above for requirements
Midterm Exam 25% In-class portion on Friday, March 4
Final Exam 25% Monday, May 2 at 12:30-2:30PM

It is not the critic who counts; not the man who points out how the strong man stumbles, or where the doer of deeds could have done them better. The credit belongs to the man who is actually in the arena, whose face is marred by dust and sweat and blood; who strives valiantly; who errs, who comes short again and again, because there is no effort without error and shortcoming; but who does actually strive to do the deeds; who knows great enthusiasms, the great devotions; who spends himself in a worthy cause; who at the best knows in the end the triumph of high achievement, and who at the worst, if he fails, at least fails while daring greatly, so that his place shall never be with those cold and timid souls who neither know victory nor defeat.

Department and University Policies

You are responsible for knowing and following the Department of Mathematics and Statistics Policies (PDF) and other University policies listed here (PDF). More policies can be found in other university documents, especially the NAU Student Handbook (see appendices) and the website of the Student Outreach and Support (SOS).

As per Department Policy, cell phones, MP3 players and portable electronic communication devices, including but not limited to smart phones, cameras and recording devices, must be turned off and inaccessible during in-class tests. Any violation of this policy will be treated as academic dishonesty.

Important Dates

Here are some important dates:

  • January 17: MLK Day (no classes)
  • January 20: Last day to add a course
  • January 20: Last day to Drop/Delete (without “W”)
  • March 14-18: Spring Break (no classes)
  • March 21: Last day to withdraw from individual courses without a petition (with “W”)
  • May 2: Final Exam (12:20-2:30PM)

Getting Help

There are many resources available to get help. First, you are allowed and encouraged to work together on homework. However, each student is expected to turn in their own work. You are strongly encouraged to ask questions in our Discord discussion group, as I (and hopefully other members of the class) will post comments there for all to benefit from. You are also encouraged to stop by during my office hours and you can always email me. I am always happy to help you. If my office hours don’t work for you, then we can probably find another time to meet. It is your responsibility to be aware of how well you understand the material. Don’t wait until it is too late if you need help. Ask questions!

Tell me and I forget, teach me and I may remember, involve me and I learn.

Changes to the Syllabus

Any changes to this syllabus made during the term will be properly communicated to the class.

If you want to sharpen a sword, you have to remove a little metal.


Dana C. Ernst

Mathematics & Teaching

  Northern Arizona University
  Flagstaff, AZ
  Website
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Current Courses

  MAT 411: Abstract Algebra
  MAT 690: Genome Combinatorics

About This Site

  This website was created using GitHub Pages and Jekyll together with Twitter Bootstrap.

  Unless stated otherwise, content on this site is licensed under a Creative Commons Attribution-Share Alike 4.0 International License.

  The views expressed on this site are my own and are not necessarily shared by my employer Northern Arizona University.

  The source code is on GitHub.

Land Acknowledgement

  Flagstaff and NAU sit at the base of the San Francisco Peaks, on homelands sacred to Native Americans throughout the region. The Peaks, which includes Humphreys Peak (12,633 feet), the highest point in Arizona, have religious significance to several Native American tribes. In particular, the Peaks form the Diné (Navajo) sacred mountain of the west, called Dook'o'oosłííd, which means "the summit that never melts". The Hopi name for the Peaks is Nuva'tukya'ovi, which translates to "place-of-snow-on-the-very-top". The land in the the area surrounding Flagstaff is the ancestral homeland of the Hopi, Ndee/Nnēē (Western Apache), Yavapai, A:shiwi (Zuni Pueblo), and Diné (Navajo). We honor their past, present, and future generations, who have lived here for millennia and will forever call this place home.