Bi 1 Syllabus: Principles of Biology

Spring Quarter / 2018

Division of Biology and Biological Engineering, California Institute of Technology

 

Course Description

There are three overarching theories in biology, the theory of the cell, the theory of the gene, and the theory of evolution.  Each of them has had major impacts on our lives – for example the concept of the gene has led to treatments for inherited diseases, personalized and genomic medicine, forensic DNA testing, and modern agriculture.  Each theory will be discussed from its 19th century origin to its standing in the 21st century, and the scientific understanding and societal impact of each will sampled. The course will also ask if there is yet a theory of the brain, and if not, how one might be framed.  The course is designed to teach what technically adept members of society should know about biology.

Learning Outcomes

By the end of this course, students will be able to read and understand the scientific basis of news stories relating to biology, the environment and human disease, and be able to assess the actual significance of the claims made.  Students also should be able to read any Wikipedia or other encyclopedia article on a biological subject and understand it and its implications for research and society.

Problem Sets

There will be 8 problem sets to assess understanding and progress with the course material, each worth 100 total points if answered perfectly.  The grade on the lowest-scoring problem set will be excluded from the final grade except for seniors, as their grades are due to the registrar before the due date for the final problem set, so they will need to be scored on the first seven problem sets.  Late problem sets will not be accepted unless there is a validated medical excuse, and the instructors are given prior notice by email.

Exams

There will be a midterm exam and a final, both take home with a 3-hour time limit.  Each exam will count for 150 points for a perfect score.  Exams late by 30 minutes will get half credit, late by more than 30 minutes will receive no credit unless there is a validated medical excuse.

Clickers

Each student will have a clicker issued for the duration of the course, and it will be used during lectures to answer multiple choice questions presented by the lecturer to assess the level of previous understanding, and the efficacy of knowledge transfer during the lectures.  Extra credit (2 problem set points) will be given for each lecture that a student attends and in which they answer the clicker questions. 

Foldscopes

Each student will have the use of a Foldscope [https://www.foldscope.com/ ], a single-lens 17th-century style microscope with up to 140x magnification.  Everyone will be expected to construct the microscope from the supplied kit, and student exercises and challenges that use the microscope will be presented for a hands-on experience.  Photographs (the microscope is cell-phone camera compatible) of specimens known and unknown, taken by class students, will be put on the lab web site.  On some weeks foldscope activities will be required and a total of 50 points for participation and performance will be given. In addition extra credit will be given for improvements to the microscopes or for particularly informative photographs taken with the microscope and sent in for the class web page.

Website

The class web site will be the source of problem sets, exams, problem answers, and class communication with TAs, instructors, and other students. The URL is http://www.zinnkbio.caltech.edu/

Assessment Rubric

There will be 8 problem sets, contributing a total possible 700 points to the final grade.  There will be two exams, a midterm and a final, each contributing as much as 150 points.  Foldscope activities that are graded will contribute up to 50 points to the grade, so that the total grade will be 67% Problem Sets, 29% Exams, and 5% Foldscope (all rounded up).  Extra credit from answering clicker questions and special foldscope photos and recitation attendance (see below) will be added to the score, making it possible to have over 1,050 points. 

 

Honor Code

No member of the Caltech community shall take unfair advantage of any other member of the Caltech community.

Collaboration Policy

Collaboration on homework assignments is encouraged. You may consult outside reference materials, other students, the TA, or the instructor. The problem sets you hand in, however, must be your own and not copied from others or from the blackboard in Recitation. You are encouraged to work on the problems with others and to seek additional help if you find that useful, but the write-up must be your own. Also, you may not consult any prepared solutions for the problems, whether they are this years or from previous years, or from Caltech or external sources. As a guideline for the collaboration policy, you should be able to reproduce any solution you hand in without help from anyone else. It is possible to achieve high scores on the problem sets but still fail the midterm and final exams. This indicates poor adherence to the collaboration policy: the object of the HW problems and the collaboration policy is to help you learn the material.

Attendance

Students are expected to attend lectures, and all who do and answer clicker questions (see below) during the class will receive extra credit.

Lecture Conflicts

Course policy is not to sign Time Conflict Cards for non-seniors: students are expected to be free to attend lectures, and conflicts with classes that prevent this need to be resolved by avoiding the conflict (for example by taking Bi 8 and 9 or Bi1x instead of Bi 1, or by postponing the other class to a later year).  Seniors with conflicts can discuss the conflict with the instructors.

Accessibility

We hope that this course is accessible for all students, and any student with a issue for which we can try to make accommodation should contact the instructors  as early in the term as possible.  In the case of a documented disability, please contact Dr. Barbara Green, Associate Dean of Students, x.6351 to coordinate any special accommodations.

Lecture Schedule

Lecture schedules including topics, associated readings and homework.

Week	Date	Lecture Topic	Lecturer	Homework handed out	Homework Due
1	Tue, 4/3	The living world – what is out there?	EM
1	Thurs, 4/5	The Theory of the Gene: Mendel and Morgan to gene control, DNA sequencing and genomics 1	EM
2	Tue, 4/10	The Theory of the Gene: Mendel and Morgan to gene control, DNA sequencing and genomics 2	EM	PS1
2	Thurs, 4/12	Forensic DNA testing	EM
3	Tue, 4/17	Ancient DNA and human archaeology and migrations	EM	PS2	PS1 due
3	Thurs, 4/19	Inherited diseases, the human genome project and personalized medicine	EM
3	Sat, 4/21	ADD DAY
4	Tue, 4/24	Plant breeding: ancient farmers to GMOs	EM	PS3	PS2 due
4	Thurs, 4/26	The Theory of the Cell: history? What is a cell?  Prokaryotic cells and their components.	KZ
5	Tue, 5/1	The cell as a factory for converting information (in the genes) into actions (mediated by proteins). This would include transcription, translation, protein localization (including secretion), and protein degradation.	KZ
5	Thurs, 5/3	How do proteins work?  Reverse information flow from protein conformations and its relationship to diseases.	KZ	MIDTERM HANDED OUT	PS3 due
6	5/8	MIDTERMS DUE			MIDTERMS DUE
6	Tue, 5/8	The eukaryotic cell. Capture of mitochondria and chloroplasts. Compartmentalization within eukaryotic cells and protein trafficking.	KZ	PS4
6	Thurs, 5/10	Viruses (Pamela Bjorkman)	PJB
7	Tue, 5/15	Development of multicellular animals	KZ	PS5	PS4 due
7	Thurs, 5/17	Developmental Biology, Regulatory Genes, and Gene Regulatory Networks: Flower Development	EM
8	Tue, 5/22	Systems Biology (Lior Pachter)	LP	PS6
8	Thurs, 5/24	The Theory of Evolution: Darwin to population genetics to cladistics 1	EM		PS5 due
8	Thurs, 5/24	DROP DAY
9	Tue, 5/29	The Theory of Evolution: Darwin to population genetics to cladistics 2	EM	PS7
9	Thurs, 5/31	How predictable is evolutionary change? (Joseph Parker)	JP	SENIOR FINAL HANDED OUT	PS6 due
10	Tue, 6/5	Neurobiology: neuronal wiring, neuronal computation, brain function 1	KZ	PS8 (Seniors not responsible)
10	Thurs, 6/7	Neurobiology: neuronal wiring, neuronal computation, brain function 2	KZ	FINAL EXAM HANDED OUT	PS7 due
10	6/8	SENIOR FINALS DUE			SENIOR FINALS DUE
11	Tues, 6/12
11	Thurs, 6/14				PS8 due
11	Fri, 6/15	FINAL EXAMS - EXAM DUE 6/15