BDE 702 Fundamentals of Biological Design II
Spring, 2011
Course Information
Schedule line number 20341, 3 credit hours
Description: The second semester of the Biological Design core course will emphasize the
integrative areas of bioinformatics, systems biology and synthetic biology, and their application in
biomedical research. The course also includes discussion of ethical and regulatory issues concerning
the responsible conduct of research and the larger societal context of science and technology.
Instructors: JoAnn Williams, jwilliams@asu.edu, BD-A320E, office hours by appointment
Karin Ellison
Ira Bennett
Class Meeting Times
Monday, Wednesday, Friday 9:00 AM – 10:30 AM
Room BD-A250
Course readings and assignments will be available online through a MyASU/Blackboard website.
Assignments and Evaluation
Assignments
Homework Assignments on Papers
Projects
Research Ethics
Total
100 points
100
100
300
Grades are calculated as follows:
A–, A, A+
90 – 100%
B–, B, B+
80 – 89%
C, C+
70 – 79%
D
60 – 69%
E
Less than 60%
It is essential that assignments be completed and submitted on time. Late assignments will only be
accepted without penalty in rare circumstances. These include professional conflicts, major and
documented illnesses, personal or family crises, etc. It is the responsibility of the student to inform
the instructor if such an event occurs before a deadline passes.
Academic Integrity
The Biological Design Graduate Program, the Graduate College, and Arizona State University
expect the highest standards of academic integrity from students in this course. The University
Academic Integrity Policy and the Graduate Policies and Procedures regarding Academic Integrity
can be found at http://provost.asu.edu/academicintegrity and
http://graduate.asu.edu/academic_policies.html. Violations of the ASU Student Academic Integrity
Policy include but are not limited to cheating on an academic evaluation or assignment, plagiarizing,
academic deceit such as fabricating data or information, aiding Academic Integrity Policy violations,
and falsifying academic records. An appropriate sanction will be determined for violations of the
academic integrity policy. For some assignments, students may work together. The collaboration
conditions will be specified for those assignments. Please let the instructors know if you have any
questions regarding academic integrity or the standards of academic scholarship.
Schedule
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
Jan 19
Jan 21
Jan 24
Jan 26
Weds
Fri
Mon
Weds
Jan 28
Fri
Jan 31
Feb 2
Feb 4
Feb 7
Feb 9
Feb 11
Feb 14
Feb 16
Feb 18
Feb 21
Feb 23
Feb 25
Feb 28
Mar 2
Mar 4
Mar 7
Mar 9
Mar 11
Mar 14-19
Mar 21
Mar 23
Mar 25
Mar 28
Mar 30
Mon
Weds
Fri
Mon
Weds
Fri
Mon
Weds
Fri
Mon
Weds
Fri
Mon
Weds
Fri
Mon
Weds
Fri
Apr 1
Fri
Apr 4
Apr 6
Apr 8
Apr 11
Apr 13
Apr 15
Apr 18
Apr 20
Apr 22
Apr 25
Apr 27
Apr 29
May 2
Mon
Weds
Fri
Mon
Weds
Fri
Mon
Weds
Fri
Mon
Weds
Fri
Mon
Mon
Wed
Fri
Mon
Weds
Review
Research Ethics: Introduction, Pre-test – Karin Ellison
Introduction to Yeast Systems Biology
Systems Biology Group Project
Research Ethics: Approaches to the Ethics of Scientific Research –
Karin Ellison
Guest Speaker – Tim Karr, Systems Biology of Sperm
Discussion of Papers 1, 2, and 3
Research Ethics: Misconduct, Responding to Problems – Karin Ellison
Discussion of Papers 1, 2, and 3
Discussion of Papers 1, 2, and 3
Recruitment Weekend - No Class
Systems Biology Group Project
Guest Speaker – Tim Karr, Systems Biology of Sperm
Research Ethics: Data Management – Karin Ellison
Discussion of Papers 4, 5, and 6
Discussion of Papers 4, 5, and 6
Research Ethics: Authorship, Peer Review – Karin Ellison
Discussion of Papers 4, 5, and 6
Systems Biology Group Project
Research Ethics: Sustainability, Funding Science – Ira Bennett
Group Project Presentations
Group Project Presentations
Research Ethics: Mentors and Trainees – Karin Ellison
Spring Break – No Class
Guest Speaker – Xiao Wang
Discussion of Papers 7 and 8
Research Ethics: Science and the Military – Karin Ellison
Discussion of Papers 7 and 8
Discussion of Papers 7 and 8
Research Ethics: Conflicts of Interest, Collaboration in Research –
Karin Ellison
Guest Speaker – Neal Woodbury
Guest Speaker – Neal Woodbury
Research Ethics: Animal Subjects – Karin Ellison
Synthetic Biology Group Project
Discussion of Papers 9, 10, and 11
Research Ethics: Human Subjects – Karin Ellison
Discussion of Papers 9, 10, and 11
Discussion of Papers 9, 10, and 11
Research Ethics Post-test 1
Synthetic Biology Group Project
Group Project Presentations
Research Ethics Post-test 2
Group Project Presentations
Readings
Paper 1
Giaever, G., Chu, A. M., ..., Davis, R. W., and Johnston, M. (2002) Functional profiling of the
Saccharomyces cerevisiae genome, Nature 418:387-391.
Paper 2
Hillenmeyer, M. E., Fung, E., ..., Nislow, C., and Giaever G. (2008) The chemical genomic
portrait of yeast: uncovering a phenotype for all genes, Science 320:362-365.
Paper 3
Costanzo, M., Baryshnikova, A., ..., Andrews, B. J., and Boone, C. (2010) The genetic landscape
of a cell, Science 327:425-431.
Paper 4
Gavin, A. C., Bösche, M., ..., Neubauer, G, and Superti-Furga, G. (2002) Functional organization
of the yeast proteome by systematic analysis of protein complexes, Nature 415:141-147.
Paper 5
Acar, M., Mettetal, J. T., and van Oudenaarden, A. (2008) Stochastic switching as a survival
strategy in fluctuating environments, Nature Genet. 40:471-475.
Paper 6
King, R. D., Whelan, K. E., …, Kell, D. B., and Oliver, S. G. (2004) Functional genomic
hypothesis generation and experimentation by a robot scientist, Nature 427:247-252.
Paper 7
Kelly, J. R., Rubin, A. J., … Monie, D. D., and Endy, D. (2009) Measuring the activity of
BioBrick promoters using an in vivo reference standard, J. Biol. Eng. 3:4.
Paper 8
Sinha, J., Reyes, S.J., and Gallivan, J.P. (2010) Reprogramming bacteria to seek and destroy an
herbicide, Nature Chem. Biol. 6:464-470.
Paper 9
Danino, T., Mondragón-Palomino, O., Tsimring, L., and Hasty, J. (2010) A synchronized
quorum of genetic clocks, Nature 463:326-330.
Paper 10
Steen, E. J., Kang, Y., Bokinsky, G., Hu, Z., Schirmer, A., McClure, A., del Cardayre, S. B., and
Keasling, J. D. (2010) Microbial production of fatty-acid-derived fuels and chemicals from plant
biomass, Nature 463:559-562.
Paper 11
Paegel, B. M. and Joyce, G. R. (2008) Darwinian evolution on a chip, PLoS Biol. 6:900-906.
Yeast systems biology review
Vemuri, G. and Nielsen, J. (2009) Yeast as a prototype for systems biology, in Systems Biology and
Synthetic Biology, Fu, P. and Panke, S., eds., John Wiley and Sons, Inc., pp. 287-353.
Synthetic biology review
Heinemann, M. and Panke, S. (2009) Synthetic biology: putting engineering into bioengineering, , in
Systems Biology and Synthetic Biology, Fu, P. and Panke, S., eds., John Wiley and Sons, Inc., pp.
387-409.
Reference Textbook Chapters
Lesk, A. M. (2008) Introduction to Bioinformatics, 3rd edition, Oxford University Press.
Chapter 2 Genome organization and evolution, pp. 69-131.
Chapter 7 Proteomics and systems biology, pp. 389-456.
Tim Karr: Systems Biology of Sperm
Vibranovski, M.D., Lopes, H. F., Karr, T. L., and Long, M. (2009) Stage-specific expression
profiling of Drosophila spermatogenesis suggests that meiotic sex chromosome inactivation drives
genomic relocation of testis-expressed genes, PLoS Genetics, 5:e1000731.
Wasbrough, E. R., Dorus, S., Hester, S., Howard-Murkin, J., Lilley, K., Wilkin, E., Polpitiya, A.,
Petritis, K., and Karr, T. L. (2010) The Drosophila melanogaster sperm proteome-II (DmSP-II), J.
Proteomics 73:2171-2185.
Xiao Wang
Ellis, T., Wang, X. and James J Collins, J. J. (2009) Diversity-based, model-guided construction of
synthetic gene networks with predicted functions, Nature Biotechnology 27:465 – 471.
Neal Woodbury
Benner, S. and Sismour, A. M. (2005) Synthetic biology, Nature Rev. Genet. 6:533-543.
Assignments
Homework Assignments on Papers (10 points each)
Eleven papers have been assigned as readings. Approximately one week before the class
discussion of each set of papers, students will be given an assignment with a set of questions for
each paper. The expectation is that students will have read the paper carefully before class and
will turn in the assignment at the start of class on the day each paper is discussed. Assignments
turned in after the start of class will be considered to be late. Students are encouraged to discuss
the papers among themselves and with the TAs but the written assignments are to be done
individually.
One assignment will be dropped in the final point total. Homework assignments on papers
turned in after the due date will received at most 75% of the points available, if they are received
within one week of the due date. No assignments will be accepted more than one week after the
due date.
Group Projects
Systems Biology Group Project (50 points)
A fundamental problem in systems biology is in understanding how the components of a cell
interact to produce the phenotype. In this project, students will work in groups to explore
what is involved in predicting the phenotype of a cell.
Synthetic Biology Group Project (50 points)
Integrated biosensing systems have mechanisms for specific recognition and signal
transduction that produce characteristics of selectivity, sensitivity, and robustness. Students
will work in groups to design a biosensor using similar properties found in biological
systems.
BDE 702 Biological Design II
Research Ethics Section
Spring 2011
Dr. Karin Ellison
LSC 270, 727-7111
karin.ellison@asu.edu
Office hours: by appointment
Have you wondered whether scientists who conduct research with animals should discuss their work
with animal rights activists? Or, whether terrorists might benefit from your publications? This section
introduces students to the ethical and regulatory issues in the conduct of research. It covers the nine core
areas of responsible conduct of research (RCR), as identified by the National Institutes of Health. The
areas are:
1.
2.
3.
4.
5.
6.
7.
8.
9.
Animal welfare
Collaborative science
Conflict of interest and commitment
Data acquisition, management, sharing, and ownership
Human subjects
Mentor/trainee responsibilities
Peer review
Publication practices and responsible authorship
Research misconduct
In addition, students will explore the two topics that highlight the moral dilemmas and issues that
collectively confront the scientific enterprise—military funding of university research and sustainability.
Discussion of real and hypothetical cases will tie broad ethical considerations to current concerns of
scientists.
Student Learning Objectives
Students will develop their capacities in:



Identifying ethical dilemmas in research
Identifying norms, policies, and regulations that speak to those ethical dilemmas
Using problem solving skills to generate and select options for action in the face of such
dilemmas
Assignments
The assignments for this section are reading, short weekly writing assignments, and presenting a case for
one class session.
Readings
Reading assignments are given in the schedule below. Reading must be completed before each class so
that discussion can draw on your knowledge of the readings. Readings will be posted in the BlackBoard
site for the course. Each session we will have readings from
Steneck, Nicholas H. ORI Introduction to the Responsible Conduct of Research, Revised ed.
Washington, DC: Health and Human Services Dept., Office of Research Integrity, 2004.
This text is available electronically for free or in paper for a modest price at:
http://ori.dhhs.gov/publications/ori_intro_text.shtml. You may wish to download or purchase it.
Weekly writing assignments
For most sessions, students will write a brief essay—1 page—in response to a writing prompt posted in
BlackBoard. The essays generally concern a reading assignment or case study. The writing prompt will
be posted to BlackBoard a week before the assignment is due, or earlier. Students should submit their
one-page essays via BlackBoard before the class session in which the assignment is due.
Case presentations
Most sessions, individual or pairs of students will present an actual ethics case for discussion. See Case
Presentations handout for details.
Have fun with this assignment! The goal is to discuss items of interest to people in the group.
Evaluation and the Fine Print
Grades for this section will generally be calculated as follows:
a. Attendance, demonstrated knowledge of assigned readings, and thoughtful contributions to
discussion: 30 pts (3 pts for each of 10 content sessions)
b. Weekly writing assignments: 50 pts (5 pts for each of 10 short essays)
c. Case presentation: 20 pts
Section Schedule
Jan 21 - Introduction, Pretest
Jan 28 - Approaches to the Ethics of Scientific Research
Steneck. "Ch. 1 Rules of the Road." In ORI Introduction to the Responsible Conduct of Research.
Greenwood, Ernest. "Attributes of a Profession." In Ethical Issues in Engineering, ed. Deborah G.
Johnson (Upper Saddle River, NJ: Prentice Hall, 1991): 67-77.
Case: "Making the Grade" Online Ethics Center for Engineering 4/24/2006 National Academy of
Engineering Accessed: Wednesday, January 12, 2011
<www.onlineethics.org/Resources/Cases/grade.aspx>
Feb 4 - Misconduct, Responding to Problems
Steneck. "Ch. 2 Research Misconduct." In ORI Introduction to the Responsible Conduct of Research.
Gunsalus, C. K. "How to Blow the Whistle and Still have a Career Afterwards." Science and
Engineering Ethics 4 (1998): 51-64.
Feb 11 - No class
Feb 18 - Data Management
Steneck. "Ch. 6 Data Management Practices." In ORI Introduction to the Responsible Conduct of
Research.
Case: "Who Framed Roger's Data" Online Ethics Center for Engineering 4/4/2006 National Academy of
Engineering Accessed: Wednesday, January 12, 2011
<www.onlineethics.org/Resources/Cases/roger.aspx>
Feb 25 - Authorship, Peer Review
Steneck. "Ch. 9 Authorship and Publication." In ORI Introduction to the Responsible Conduct of
Research.
Steneck. "Ch. 10 Peer Review." In ORI Introduction to the Responsible Conduct of Research.
Sismondo, Sergio. "Ghosts in the Machine: Publication Planning in the Medical Sciences." Social
Studies of Science 39, no. 2 (April 2009): 171-198.
Mar 4 – Sustainability, Funding Science
Raven, P. H. "Presidential Address. Science, Sustainability, and the Human Prospect." Science 297, no.
5583 (Aug. 9, 2002): 954-958.
Farrell, Alex. "Sustainability and the Design of Knowledge Tools." IEEE Technology & Society
Magazine (1996/1997): 11-15.
Case: "Ethical Issues in the Design of Ultra-Lightweight Vehicles" Online Ethics Center for Engineering
2/27/2006 National Academy of Engineering Accessed: Wednesday, January 12, 2011
<www.onlineethics.org/Resources/Cases/ULV.aspx>
Mar 11 - Mentors and Trainees
Steneck. "Ch. 7 Mentor and Trainee Responsibilities " In ORI Introduction to the Responsible Conduct
of Research.
Evans, Jennifer. "Mentoring Magic." The Scientist 22, no. 12 (December 2008): 70+.
Puljak, Livia. "Career Blocker: Bad Advisors." Science Career Magazine (January 13, 2006),
http://sciencecareers.sciencemag.org.ezproxy1.lib.asu.edu/career_magazine/previous_issues/articles/200
6_01_13/noDOI.9522592743045586763 (accessed August 19, 2009).
Mar 18 – No class, Spring Break
Mar 25 - Science and the Military
Kevles, D. J. "Biotech's Big Chill." Technology Review 106, no. 6 (AUG, 2003): 40-49.
Resnik, David and Adil E. Shamoo. "Bioterrorism and the Responsible Conduct of Biomedical
Research." Drug Development Research 63, no. 3 (2005): 121-133.
Case: Pollack, Andrew. "Scientists Create a Live Polio Virus." New York Times, July 12, 2002.
Apr 1 - Conflicts of Interest, Collaboration in Research
Steneck. "Ch. 5 Conflicts of Interest." In ORI Introduction to the Responsible Conduct of Research.
Steneck. "Ch. 8 Collaborative Research." In ORI Introduction to the Responsible Conduct of Research.
Weinfurt, K. P., D. M. Seils, J. P. Tzeng, L. Lin, K. A. Schulman, and R. M. Califf. "Consistency of
Financial Interest Disclosures in the Biomedical Literature: The Case of Coronary Stents." PloS One 3,
no. 5 (May 7, 2008): e2128.
Apr 8 - Animal Subjects
Steneck. "Ch. 4 The Welfare of Laboratory Animals." In ORI Introduction to the Responsible Conduct
of Research.
Case: "Animals (RCR Role Plays)" Online Ethics Center for Engineering 9/23/2009 National Academy
of Engineering Accessed: Wednesday, January 12, 2011
<www.onlineethics.org/Resources/Cases/21317.aspx>
Apr 15 - Human Subjects
Steneck. "Ch. 3 The Protection of Human Subjects." In ORI Introduction to the Responsible Conduct of
Research.
Elliot, Carl. “Guinea-Pigging: Healthy Human Subjects for Drug-Safety Trials are in Demand. But is it a
living?” The New Yorker 83,42 (January 7, 2008): 36+
Apr 22 - Posttest 1
Apr 29 - Posttest 2