Paul Yager Teaching Bioengineering Department, Box 355061, University of Washington, Seattle, WA 98195, USA

BIOEN 480B, Senior Capstone Research/Design

Syllabus from Spring ’04,

Paul Yager, Department of Bioengineering

Box 355061

Room 341E AERL

University of Washington

Seattle, WA 98195-2255

206-543-6126

http://faculty.washington.edu/yagerp

yagerp@u.washington.edu

(Please always include “480B” in the subject header for a prompt response)

This is an undergraduate course targeted specifically at juniors in the Department of Bioengineering. There are two goals for this course: the first is to ensure that all students are affiliated with a research laboratory and launched on their senior capstone project (480A) by the end of the quarter. Students will be coached in skills needed to find, enter, and stay in a laboratory, and to accomplish their research projects efficiently. They will also be graded on tasks needed to accomplish this goal. The second aim is to instill in the students the importance of understanding the context of their work with respect to their colleagues, their peers, their society, and their world. This latter aim is accomplished through 1) reading and discussion of science fiction books and stories that include themes related to bioengineering, 2) active monitoring of news media for bioengineering-related stories, and 3) learning about the issues related to professional activity beyond college. They will be graded on their ability to process and communicate ideas on these latter topics.

Communications between students, teacher and TA: There will be a www site established for the course that will contain a copy of the definitive syllabus for the course (see below). Also, homework and projects will be submitted electronically to the TA (with a copy to Yager) via e-mail to be received by 7 PM of the date shown on the syllabus.

Meetings:
Classes will be in a few different formats. The primary format will be the lecture, but students should be aware that the primary lecturer has a tendency to ask lots of non-rhetorical questions of the students. Students should come prepare to participate actively. Extensive question-and-answer sessions are expected for all guest lecturers. In addition, there will be seven formal discussions of topics based on readings of books assigned below. Each discussion will be led by a team of students who will be very familiar with the readings and will present different views of the topics found in the readings.

Student Participation:

Students will be expected to perform several sets of tasks during the course:

I. A one-page self-evaluation with respect to why the student is interested in Bioengineering and Bioengineering research will be submitted in the first week. This will be graded for its completion, not for form or content.

II. Active and informed participation in all discussions during the class, including those on science fiction literature led by other students. Note that everyone is expected to have read all the short stories by the time of the first reading discussion session. Failure to participate or to have read the material beforehand will result in loss of credit.

III. Seven different selected sets of students will be responsible for presenting to the rest of the class as a group. They will present discussions of topics based on readings of the SF books and stories assigned below. The team will be given a grade on the degree to which they create stimulating discussion related to the topics presented in the readings for the session.

IV. For a period during the class students will be asked to keep a log of news items related to bioengineering topics, and hand in this log. It can consist of any form of list, but must include the precise source, and the date for each item.

V. The Hermanns lecture will introduce the class the importance of IP in research and development. To familiarize the students with patents, they will be asked to do a brief patent search using one or more sources (USPTO, for example). In particular, the students will pretend to be inventors in a small biomedically-related company who believe they have invented a new and effective “thing” (but are wrong—it is not novel and has already been patented). This “thing” could be a chemical, a process, or a biomedical device—the nature of the “thing” is the student’s choice, but it should be directly related to the work the student believes her or she will be doing in the capstone project, and it must already exist. The task will be to demonstrate how you found out that the “thing” already exists, how it differs from other similar “things”, who owns the patents and who licensed them, and whether the company that licensed the patent(s) is likely to be able to commercialize that technology, or has already done so. The deliverable will be a 2-page write-up including patent numbers.

VI. One of the goals of the course if for students to fully understand their 480 projects. Students will write and hand in two drafts of their research plan as shown in the syllabus. The paper will contain 4 principal elements:

1) the social and technical background of the research (3 pages)

2) a specific set of experiments to be carried out during the next year (3 pages)

3) a timetable of all work to be done during the next year, including both classes and research, with estimated dates of completion of all steps (1 page)

4) a detailed bibliography for parts 1 and 2, done in numbered format (with in-text citations) and full titles of all references (1 page)

Page limits are both minima and maxima. Writing is to be in 12 point Times or Times New Roman, single spaced. The first draft will be read and graded for content, but not form, as follows.

Background material	2.5
Research Plan	2.5
Timeline	2.5
References	2.5
Total	10

VII. The second draft will be read and graded for both form and content. In it, writing must be in good formal (not colloquial) English, with attention paid to punctuation, reference formatting, grammar, etc. The formal list of the references at the end must be related to in-text citations. Plagiarism (and if you don’t know the definition, ASK) will be rewarded by a grade of 0 on that piece of work and all subsequent work for the class.

Grading on the second paper will be as follows:

English writing and proofreading	5
Background material	5
Research Plan	5
Timeline	5
References	5
Total	25

VIII. A 3-minute oral presentation of the research plan will be made to the entire class during the time of the final exam as a test of oral presentation skills. Grading will be as follows

Content	10
Quality of visual materials	5
Oral communication	5
Keeping to time allotted (all or nothing)	5
Total	25

Course Grading:

Task	Points
Attendance: 18 x (1 points)	18
Self-Evaluation	3
Active Participation	4
Leading reading discussion session	7
News Log	4
Patent search	4
First Draft of Research Plan	10
Second Draft of Research Plan	25
Oral Presentation of Research Plan:	25
Total	100

Course Syllabus

Wk	Day	Speaker	Topics	In-Class Activity	Task Assigned	Assignment Due
1	W Mar 31	Yager	Course Intro Introducing your teacher Class Mission Statement Class Deliverables Science Fiction Opening statement What are the aims of scientific research? Personal Inventory-what makes you want to do Science/ Engineering??	Introducing People Fill out forms on who has a lab and at what stage is their thinking about a project.	Self-evaluation: your research interests
	F Apr 2	No Class	All must attend Rushmer Lecture, poster contest, and reception
2	W Apr 7	Vicini Yager	What is engineering design? What is a Professor? Who are OUR professors, and how to find out about their labs Process for finding a lab that matches your interests; resources		Pick SF story discussion groups	1-page self-evaluation of research interests
	F Apr 9	Yager	The capstone project: steps, deliverables, standards Interview Protocols Working with peers Lab etiquette Working with an advisor-- Communication with supervisor Staying in a lab		Pick Laboratories with which to interview Read SF	SF stories and books chosen
3	W Apr 14	Yager	Science/Engineering entanglement with Politics/Religion Keeping up on current events Continuing technical education Design/Management of open-ended project	Modeling the lab interview process Discussing The Wizards of Pung's Corners	Progress check: finding lab Read SF	Turn in list of labs to be interviewed
	F Apr 16	Yager, Chris Neils	Getting your work into print Searching the Literature Introduction to Neils and what he does (second half of class) Setting up your capstone project final paper		Begin current events journal tracking science/ engineering stories in newspapers, magazines NPR, TV, web news Read SF
4	W Apr 21	Yager	Lab Notebooks and keeping track of what you’re doing. Interpersonal lab ethics Managing your time Project Management software	Discussion of progress on finding laboratories	Read SF
	F Apr 23	Yager	PY and his practicum in grant-writing and team formation	First in-class SciFi reading discussion Group A. Gil Hamilton and Organlegging vs Tissue Engineering	Begin background (literature) research for project description Read SF	Lab for capstone research chosen and identified in writing. (countersigned by lab PI).
5	W Apr 28	Yager	How research is funded: Government Foundation Industry Big Industry Venture Capital The military and technology, the military and Sci-Fi Technology and War (Defense vs. Offense) Robocop, The Borg, Cyborg issues	Group B. The Long Twilight and Extending Life Indefinitely	Read SF
	F Apr 30	No Class	Volunteer for Open House!		Read SF
6	W May 5	Karl Hermanns	Intellectual Property Lab notebooks as a tool in avoiding IP problems as a student		Patent search
	F May 7	Yongmin Kim	Tech Transfer—the Academic’s Perspective		Read SF
7	W May 12	Karen Hedine	The Small BioTech-based Business, Venture Capital, etc.	Group C. Neuromancer, virtual reality and conscious machines	Read SF	Hand in patent search
	F May 14	Yager	Building your career (in industry, government labs, and academic organizations) Typical trajectories The most important factors for success A bit on myths	Group D. Lord of Light and reincarnation and growing humans (or their organs) for that purpose	Read SF	Written research plan, prepared for content critique only
8	W May 19	Tam	Global Health PATH http://www.path.org/programs/healthtech.htm		Read SF
	F May 21	No Class	Attend Undergraduate Meeting with Dr. Kim		Read SF
9	W May 26	Beach	Research Ethics in the Lab Authorship Human Subjects Ethics Animal Testing Ethics	Group E. Cyteen and human cloning and the Brave New World scenario	Read SF	Hand in current events journal
	F May 28	Yager	Working out Bioengineering ethics for ourselves	Group F. Downbelow Station Sculpting the human into a tool of sabotage—today and in the future.	Read SF
10	W Jun 2	Yager	CIDR Evaluation of program References and Plagiarism		Read SF	Written research plan, prepared for content and form
	F Jun 4	Yager	When disaster strikes—how to cope with a project/advisor that does not work out. Oral presentation tools and skills and encapsulating your thoughts in small packages. Demonstration of a (hopefully) good 3-minute presentation of a research plan The elevator pitch and final talk. Class evaluation	Group G. The Snow Queen and experimentation with animals, the morality of prolonging life	Prepare 3-slide presentations of research plans
Finals	Th Jun 10, 2:30 PM		3- Minute Oral Presentation of Research Plan

Readings:
There is no text for this course. There will eventually be a set of PowerPoint lecture notes by the professor and guest lecturers. These notes will be available on a class-dedicated WWW site. Login name and password are "XXXX" and "XXXX", (case sensitive). Do NOT distribute the passwords or lecture notes to anyone not in the class! These lecture notes will be available as PDF documents. Note that lecture notes will probably be put online after the lectures this year, and may be updated during the course, so it is suggested that the students NOT print material from the site more than 3 days in advance. If there IS something on the site relevant to an upcoming class, please BRING A COPY of that week's lecture notes TO CLASS, since there will be no other lecture notes distributed.

In addition, a requirement of the class is reading and interpretation of science fiction stories and books as listed below. Not all of the items must be read by all students, as explained below the list. However, all of the stories are worth reading (at least 2-3 times over a few decades). The books and most of the short story collections, even though out of print, can be purchased from commercial sources. Without suggesting such a source, the professor notes that everything was available for sale (either used or new) on Amazon.com for very reasonable prices and with 1-3 day delivery. The short stories will be made available in paper form as a packet for purchase a few days after the beginning of class. If students have less than perfect memories, they should bring copies of the stories and books to classes during the weeks in which they are to be discussed.

Bioengineering 480B Reading List

#	Story Title	Book Title	Author	Publisher	Year of pub., (orig. pub.)	# of Pages	Bioengineering Themes	Issues	PY’s Naughtiness and PC Rating
1		The Snow Queen	Joan D. Vinge	Dell	1984 (1980)	536	Integration of humans with information systems, ethics of farming animals for pharmaceuticals	First of a 3-book series. Good story with female protagonists. Hugo winner	PG-13 for some sex
2		Downbelow Station	C.J. Cherryh (female author)	Warner Books	1981 (1981)	477	Training of humans for covert activity, human cloning	Beginning of Merchanter series and Hugo winner. Suggest Cyteen next.	PG. For moderate violence. A great female villainess.
3		Cyteen(first book)	C.J. Cherryh (female author)	Warner Books	1988 (1988)	359	Government-controlled human cloning, and breeding the clones for specific capabilities,	Nature vs nurture? First of a trilogy, Part of Merchanter universe. Should read Downbelow Station first!	PG-13. Nothing explicit, but some disturbing sexual kinkiness implied
4		Lord of Light	Roger Zelazny	Avon	1972 (1967)	319	Life extension by transfer of personality from body to body, and fanciful consequences of extreme longevity in strange places	Painless introduction to Hinduism and Buddhism. Hugo winner.	PG for mild violence and one extremely bad pun
5		Neuromancer	William Gibson	Ace	1986 (1984)	270	Human-internet interfaces, virtual reality	Gibson invents virtual reality. No real heroes here. Hugo, Nebula and Dick awards	PG-13 for rare sex, and frequent violence
6		The Long Twilight	Keith Laumer	Berkley	1970 (1969)	222	Consequences of enhancing tissue regeneration.	Some dated issues about transmitted power—or are they?	PG for some violence
7		The Long arm of Gil Hamilton	Larry Niven	Ballantine Books	1976 (1976)	182	Social consequences of extremely good organ transplantation technology. It could never happen—or has it already?	3 stories with the same TK detective protagonist. Rare example of good SciFi mystery stories	PG-13 for some violent creepiness
8	Home is the Hangman	My Name is Legion	Roger Zelazny	Ballantine Books	1976 (1976)	80	Robotics and ethics	Excellent example of complex short story writing. Last of a 3-story series about the same protagonist.	PG for mild violence. Nobody is hanged
9	The Body Builders	Keith Laumer, the Lighter Side, Eric Flint, Ed.	Keith Laumer	BAEN	2001 (1967)	34	Virtual reality plus robotics taken very far	Beware of things that go Bump in the night	PG for bad puns and old-fashioned male chauvinism
10	The Planet Wreckers	Keith Laumer, the Lighter Side, Eric Flint, Ed.	Keith Laumer	BAEN	2001 (1967)	32	Not sure there are any	Beware of things that go Bump in the night	PG for bad puns and old-fashioned male chauvinism
11	The Wizards of Pung’s Corners	Connoisseur’s SF, Tom Boardman, ed.	Frederic Pohl	Penguin	1964 (1959)	31	Technology and the Military-Industrial Complex	Post-apocalyptic world not really necessary to the story	G
12	Cocoon	The Best of Keith Laumer	Keith Laumer	Pocket Books	1976 (1962)	23	End-stage VR (but not quite like The Matrix)	Is this where we want to go?	G
13	Build-up	Connoisseur’s SF, Tom Boardman, ed.	J.G. Ballard	Penguin	1964 (1960)	22	Can engineers solve any problem? Is there such as thing as too much technology	A good intro to one of SF’s darkest writers	G
14	Disappearing Act	Connoisseur’s SF, Tom Boardman, ed.	Alfred Bester	Penguin	1964 (1953)	20	Doctor are not always the best at diagnosis	A great story by a great writer	G
15	Relic of War	The Best of Keith Laumer	Keith Laumer	Pocket Books	1976 (1962)	15	Military robotics	Just a good little story, introduction to Laumer’s Bolo stories	G
16	Learning Theory	Great Science Fiction by Scientists, Groff Conklin, ed.	James McConnell	Collier	1962 (1957)	14	The ethics of experimentation with animals	Let the punishment fit the crime	G
17	Tomorrow and Tomorrow and Tomorrow	Connoisseur’s SF, Tom Boardman, ed.	Kurt Vonnegut, Jr.	Penguin	1964 (1954)	14	Social cost of inexpensive longevity	A good introduction to Vonnegut	G
18	Jigsaw Man	Three Books of Known Space	Larry Niven	Ballantine Books, Del Rey	1996 (1967)	12	Social consequences of extremely good organ transplantation technology	A bit preachy	PG for mild violence
19	Convergent Series	Convergent Series	Larry Niven	Del Rey	1979 (?)	6	Just how smart are you, really?	Just plain fun	PG if you’re very religious

Each student must join one of the following reading groups and complete all the readings by the date shown for the lettered groups shown in the Syllabus. Note that the groups that have shorter reading tasks must finish earlier in the class. The members of the group will briefly outline the plot of the main novel and will lead a group discussion of the Bioengineering themes therein. Groups are limited to the number of students shown below—selection for the groups will be made on a first-come-first-served basis. To apply for membership in one of the groups, you must e-mail the TA for the class with a list of all seven groups in your order of preference. The order in which the e-mails are received (not sent) will determine priority for reading group membership. The performance of the reading group on the date of the discussion will be graded.

Of course everyone is encouraged to read every book as well! Everyone will be expected to participate in the discussions, but it will be better if you have actually read the book ahead of time.

Reading groups:

Reading Group	Primary Story	Book Length	Additional Readings	Total Story Length	Max. # of Students in Group
A)	The Long ARM of Gil Hamilton	(182 pp)	short stories 8-19	(223 pp)	4
B)	The Long Twilight	(222 pp)	short stories 8-19	(223 pp)	4
C)	Neuromancer	(270 pp)	short stories 8-19	(223 pp)	4
D)	Lord of Light	(319 pp)	short stories 8-19	(223 pp)	4
E)	Cyteen (book 1)	(359 pp)	short stories 8-19	(223 pp)	4
F)	Downbelow Station	(477 pp)	short stories 8-19	(223 pp)	4
G)	The Snow Queen	(536 pp)	short stories 8-19	(223 pp)	5

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Updated 08/08/04