Biodiversity
Achieved
Instructor: Dr. Katayoun Chamany
E-mail: chamanyk@newschool.edu
Telephone: 229-5640
Office: Room 460, 65 West 11th Street
Office Hours: Tuesday:10:45-11:45am, By appointment if
these times do not work with your schedule
Course Description:
As the title of the course states, biodiversity is the focus of this laboratory/seminar
course. We will approach diversity from a genetics standpoint and explore
genetic variance as well as conservation amongst the species of our planet.
We will begin the course by discussing genetic variation in human populations
and the impact that genomic research has had on law, medicine, and politics.
Our investigations will include computer database analysis and PCR analysis.
We will also read Aldous Huxley's Brave New World and explore the technology
and implications of genome projects, genetic testing, gene therapy, and
DNA identification.
We will acquire more laboratory
and investigative skills by completing The Secrets of the Rain Forest
module. During this module you will embark on a bioprospecting adventure
searching for a cancer curing agent in the Andes rain forest. This module
integrates ethnopharmacology, molecular biology, biochemistry and bioethics.
Much like the first part of the course, we will use real life case studies
to examine these issues. You will be expected to come to class prepared
and ready to present your findings during every class session. You must
not miss any LAB sessions, as it will be impossible to make these sessions
up.
Most readings will be conversational, but full of information tangled
with interpretation and opinion. Because this in an intermediate level
course it is imperative that you come to class having read the material
in a thoughtful manner and organizing your methods AHEAD of the lab portions.
This may require that you meet with your partner outside of class time.
After the first few weeks, I will introduce you to the history of biotechnology
and some basic sterile microbiological techniques. Since most of you are
new to laboratory science we will take our time with the modules and make
changes to the syllabus as needed in order to ensure maximal comprehension
of each step. You will receive weekly point by point syllabi throughout
the semester. These will also be on the portal class site and via email
when the portal is not working. So please check this site weekly.
• I will make comments and suggestions on any work that is turned
in late at my convenience, but the work will drop one grade per day (including
all days of the week).
• If you come to the lab sessions unprepared, you will be asked
to leave class that day.
• In order to take this course, you must have a current student
I.D. and working computer account and be comfortable using electronic
databases and the Portal. Therefore, you must complete the information
resources tutorial by February 6 if you have not already done so.
Learning Objectives
• To “try on the hat of a scientist” in designing, executing,
and analyzing laboratory experiments
• To explain the basic principles that underlie biotechnology and
molecular biology
• To analyze the wealth of genetic diversity by studying the genomes
of humans, plants, and microbial populations
• To understand the role of the laboratory scientist in society
• To gain an appreciation for the elegance and utility of the scientific
approach in practice
• To communicate scientific findings to government agencies, public
advocacy groups, and the general populace in a clear and engaging oral
and written format.
Required Texts:
All books are on reserve in the Fogelman Library
Barnes and Noble bookstore will eventually have three books in stock,
but given the broad range of student backgrounds and previously used textbooks,
I have not decided on just one text. Once everyone is registered in the
course I will instruct the class as to the required texts. Until that
time, all readings will be available in the course packet that will be
on reserve in the Fogelman Library.
Susan Barnum. Biotechnology. 1998. Wadsworth Publishing. This text successfully
covers the history of the biotechnology revolution, however the presentations
of the chapters on specific forms of biotechnology are in my opinion a
bit biased. This text has a excellent web page at www.brookscole.com.
Select the genetics and biotechnology link and then click on the text
icon. You will then see flashcards and hyperlinks. The same web site has
the Human Heredity icon and web based learning tools-- very good for research
and review. This text will be referred to as BIO.
This text has been repackaged with an Interactive Concepts of Biology
CD-ROM and can be purchased for about $65.00 using this ISBN number :
0534078206 and this phone number 800.347.7707 .
Sykes Bryan. The Seven Daughters of Eve. (2001). W.W. Norton.
Aldous Huxley. Brave New World. (1965). Harper and Row Publishers.
Chamany, Katayoun. Course Packet. Collection of articles, lab manual,
and book chapters. These readings will be referred to as CP.
PURCHASE a bound or spiral lined notebook from. Avoid graph paper.
Optional Texts:
Most books on reserve in Fogelman , all are avaible in either Bobst or
Fogelman
Bruce Alberts, et al. The Molecular Biology of the Cell. Garland Publishing.
New York, NY. 1996. This is the bible of cell biology, and Essential Cell
Biology, written by the same authors, is a condensed version of this book.
A sophisticated text designed for the very serious cell biology student.
This text will be referred to as Cell.
Balick and Cox. Plants, Peoples and Culture. Scientific American Library.
1996.This text is a colorful one and covers the field of ethnopharmacology.
This book is out of print.
Micheal Cummings. Human Heredity. 6th Edition. Wadsworth Publishing. 2002.
This book served as the primary text for the first semester Genetics and
Society/ Genes: the Code of Codes freshman course, a prerequisite for
this lab course. Any edition of the book will do. We will read Chapters
17, 18 and couple of others.
Russo and Cove. Genetic Engineering: Dreams and Nightmares. W. H. Freeman
and Co., NY, NY. 1995. This text will serve as an alternate text for the
course material covering genetics and does not have a "text-book"
feel. This book will be referred to as D &N.
Bazell, Robert.:Her-2 : the making of Herceptin, a revolutionary treatment
for breast cancer. Random House.1998.
Controlling our destinies : historical, philosophical, ethical, and theological
perspectives on the Human Genome Project / edited by Phillip R. Sloan.
2000.University of Notre Dame Press. Notre Dame, Indiana.
W. Bodmar and R. McKie, The Book of Man: The Human Genome Project and
the Quest to Discover our Genetic Heritage, Scribner, New York. 1995.
D.J. Kelves and L. Hood, The Code of Codes: scientific and social issues
in the human genome project, Harvard University Press, Cambridge , Mass.
1992.
D. Suzuki and P. Knudson, Genethics: the Clash Between the New Genetics
and Human Values, Harvard Univeristy Press, Cambridge, MA. 1990.
R. Hubbard and E. Wald, Exploding the Gene Myth, Beacon Press, Boston,
MA.1993.
Council of the National Academy of Sciences, Introduction of Recombinant
DNA-Engineered Organisms into the Environment:Key Issues, National Academy
Press Washington, D.C. 1987.
R. Zilinskas and B. Zimmerman, The Gene-Splicing Wars, Macmillon Publishing
Company, NY, NY. 1986.
E. Bresler, Genetics and Society, Addison-Wesley Company, Reading, MA.
1973.
T. Murray, M. Rothstein, and R. Murray Jr., The Human Genome Project and
the Future of Health Care, Indiana University Press, Bloomington, IN.
S. Cummings, Current Perspectives Genetics, Wadsworth Publishing. 1997.
Course Grading:
Grading Scale
Class participation/notebook: 300 points 100%-93% A
Homework: 250 points 92%-90% A-
Policy Paper (outline) 50 points 89%-87% B+
Policy Paper (final) 100 points 86%-83% B
Brave New World paper: 100 points 82%-80% B-
Exam: Hearing on Patent Breach 200 points 79%-77% C+
1000 point 76%-73% C
72%-70% C-
69%-67% D+
66%-63% D
Deadline Calendar:
Assignments Due
January 30 HW#1 due Biotech article 10' presentation
February 6 Computer tutorials see your email as an attachment.
February 12 Brave New World Paper: Write a final chapter/alternative ending
March 6 HW #2 due: DNA goes to the races and restriction mapping
March 11 Lab Notebooks collected
March 18 HW#3: Ethnopharmacology 10’ Oral Presentations
April 1 HW#4: Lessons 1,2 and 3 for the Secrets of the Rainforest Module
and a conceptual flowchart of the entire 4-week module to be presented
to the class via an overhead or powerpoint
April 8 HW#5: Enzyme Presentations-- Be prepared to give a 5 minute presentation
on your assigned enzyme- don’t forget to consider all the optimal
conditions and outcomes.
April 10 HW#6. Be prepared to share your restriction digest chart with
the rest of the class via overhead. Remember to consider variables and
include controls that would be valuable to the class collaborative effort.
April 15 Lessons 6 and 7
April 22 Lesson 8
May 1 Ethnopharmacology Fast Track Paper or Collection of Letters due
Date/Topic
Jan 23: Introduction/What is Biotech? What is Diversity?
READING: Chapter 1 in Barnum S. Biotechnology. 1998. Wadsworth Publishing.
Jan 30: Examples of biotechnology – videos and student presentations
HW#1: due be ready for 5-10' presentation
Feb 4: Diversity in Populations
READING:
• Chapter 17. Cummings, M. Human Heredity. 2002. Wadsworth Publishing.
• Ridlety, M. “Chromosome 9: disease” in Genome. 1999.
Perennial Publishing.
Feb. 6: Diversity and the Human Genome Project
READING:
• Chapter 18. Cummings, M. Human Heredity. 2002. Wadsworth Publishing.
• Foster, M. W. and W. L. Freeman (1998). "Naming Names in
Human Genetic Variation Research." Genome Res. 8(8): 755-757.
• Sankar, P. and M. K. Cho (2002). "GENETICS: Enhanced: Toward
a New Vocabulary of Human Genetic Variation." Science 298(5597):
1337-1338.
• Wade, N. (2002) “ Gene-Mappers Take a New Aim at Diseases.”
The New York Science Times.
• October 29, 2002.
Feb 10 How will DNA Typing Affect Our Sense of Identity
Video- The Lemba of Africa
Review of lab safety and procedures.
Feb 12 Biotechnology and Human Will
Video: Gattaca
READING:
• Aldous Huxley. Brave New World. (1965). Harper and Row Publishers.
Questions to consider for discussion of Brave New World
5. Discussion of Brave New World and sharing of last chapters (which are
due today) Huxley is said to have constructed a “Utopia” in
which science is controlling society. His story is described as prophetic.
Reflect back on the imagery and words to draw up a list of advancements
in biology, psychology, and pharmacology and compare these to current
practices.
6. Huxley uses poetry and prose (Shakespeare) to conjure emotion from
his characters. Why do you think he chooses these forms of art? Does he
use music or visual art, if so when?
7. Towards the end of the book a new character is introduced, Darwin Bonaparte.
Analyze his choice of proper name.
8. Mustapha Mond expresses regret that brilliant science cannot always
be published because it might harm society- do you agree with his sentiment?
Explain your reasoning.
Feb 17 Diversity in the Classroom: PCR on student DNA
This week we will begin a laboratory exercise that employs a technique
called PCR. Each of you will amplify a small region of your DNA and we
will analyze these samples using two detection techniques
• DNA staining and gel electrophoresis (detects the presence or
absence of a 300bp sequence)
• DNA sequencing and gel electrophoresis (analyzes the specific
sequence of a hypervariable mitochondrial DNA sequence
READING:
• Chromosome 8 Gene Amplification Alu-TPA-PCR kit. Read the entire
lab and then pay close attention to lab lesson 1 and 2 which we will complete
during this class session.
• http://www.dnalc.org/resources/BiologyAnimationLibrary.htm Click
on PCR amplification.
• Syke, B. The Seven Daughters of Eve. (2001). W.W. Norton. Great
to read the entire text, but we will focus on Chapters 1-5, 11-14 and
22-23.
HOMEWORK
• Come to class with an objective and a hypothesis based on your
reading. These should be recorded in your lab notebook.
• In addition, be sure that the questions for Lesson 1 are addressed
in the methods portion of your lab notebook in paragraph style. Be sure
that you have made a flow chart or “easy list” for the labs
on Lesson 1 and 2 which will be completed in one lab session. Please note
that we will conduct a second PCR reaction with mitochondrial sequence
primers and this DNA will be amplified and sequenced. In this methods
section consider what type of “controls” you would use to
ensure the technical accuracy in your reagents, techniques, and equipment.
Ask yourself this: If you come in on Thursday and run your gel and there
are no bands, what can you conclude? How sure would you be? Think about
all the possibilities.
• Lastly, complete the questions for Lesson 2 on a separate piece
of paper and submit.
Feb 19 Diversity and Criminal Law: What’s the limit for exclusion?
READING
• http://www.dnalc.org/resources/BiologyAnimationLibrary.htm Click
on DNA Detective icon and follow the links for how to make a fingerprint
and read one of the cases on the home page.
• Lander, E. “ DNA Fingerprinting: Science, Law, and the Ultimate
Identifier,” in The Code of Codes: scientific and social issues
in the human genome project, eds. D.J. Kelves and L. Hood, Harvard University
Press, Cambridge , Mass. 1992.
HOMEWORK
• Review Lesson 3 and 4 in detail. We will run two gels one for
each PCR reaction (intron 8 and mitochondrial DNA). Please note that we
will use ETBR instead of BioSafe DNA stain mentioned in step 8 on page
53 and that the staining will be for 10 minutes and the destaining for
another 10 minutes in water. Again be sure to address the questions in
Lesson 3 in the methods portion of your lab notebook in paragraph style.
Be sure that you have made a flow chart or “easy list” for
the labs in Lesson 3 which will be completed in one lab session.
Feb 24 Hardy Weinberg Revisited
Data sharing from Chromosome 8 lab-Microbiology Sterile Technique Lab
We will add data from previous years and complete the Hardy Weinberg problems
in Lesson 4 of this module. The answer to these questions should be handed
in on a separate piece of paper but the concepts should appear in your
lab notebook discussion.
LABORATORY: Streak single pure colonies from microbial cultures
READING :Aseptic Technique and Establishing Pure Cultures Lab
HOMEWORK:Complete the questions in Lesson 4 of the Chromosome 8 kit and
prepare your lab notebook for the entire Aseptic Technique and Establishing
Pure Cultures Lab ( Obj, Hyp, flow chart)
Feb 26 Aseptic Technique Lab- Results, pure cultures, and replica plating
READING: Chapter 4 in Barnum S. Biotechnology. 1998. Wadsworth Publishing.
Focus on p. 49-55.
Collect data from the microbiology lab and reflect on hypotheses and consider
these questions:
1. What do you notice about the shape, smell, number, and color of the
colonies?
2. What do you notice about temperature effects, media effects, and both
combined?
3. How do the yeast and bacteria behave in response to these variables?
4. What happens when you tried to streak to pure culture from the "
Mixed" culture? Were you successful? How can you tell?
5. What would you propose to do next to prove your point?
Watch the Barry Scheck Video on DNA fingerprinting: Innocence Project
and Databases
March 4: Continue the Microbiology Lab
LABORATORY: Replica plating and starting pure cultures lab- consider these
questions:
1. What variable will you be altering in this experiment?
2. Can you imagine a use for such a technique as it applies to increasing
basic scientific knowledge
3. What is a temperature sensitive mutant? What would some genes be cold
sensitive as opposed to heat sensitive? How might having a temperature
sensitive mutant be more useful than a null mutant?
March 6: Genetic Screens and Selections- what's the difference?
LABORATORY: Analyze cultures/ replica plate---- other ideas for experiments?
READING: Discuss Biotechnology Chapter 4
Video: Eloy Rodriguez: Ethnopharmacology and Maurice Iwu from the BDCP
HW #2 due: DNA goes to the races and restriction mapping
March 11: Recombinant DNA: scientific and ethical implications
READING:
• Chapter 2 in Barnum S. Biotechnology. 1998. Wadsworth Publishing.
Review.
• Grobstein C. " Asilomar and the formation of public policy."
in The Gene Splicing Wars edited by Raymond A. Zilinskas and Burke K.
Zimmerman. Macmillan publishing. New York. p3-10
• Zinder N.D. "A personal view of the media's role in the recombinant
DNA war." 1986. The Gene Splicing War. edited by Raymond A. Zilinskas
and Burke K. Zimmerman. Macmillan publishing. New York. p.109-118.
Lab notebooks are collected
March 13: Ethnopharmacology
READING:
•Chapter 1,2 and 6 in Balick and Cox. Plants, Peoples and Culture.
Scientific American Library. 1996. ( about 70 pages of reading)
March 18: Bioconservation
READING:
• Hallowell C. "In Search of the shaman's vanishing wisdom."
Time. Dec. 14, 1998: p.60-73
• Kling J. "Out of Malaysia" Modern Drug Discovery. Nov/Dec
1999:p31-36.
• Dreifus C. "New York's a jungle, and one scientist doesn't
mind." The New York Times. April 6, 1999 F5.
HW#3: due 10' formal presentations on bioprospected drug or product- please
see example in course packet- Willow Drug. Also try visiting
• http://homepage.newschool.edu/~chamanyk/ID%s20Web/0412.html &
click on BDCP homepage http://www.bioresources.org/ and be sure to visit
their conference webpages to get names of people in the field and names
of plants used in traditional medicine.
• http://pubs3.acs.org/acs/journals/hot_article.menu?in_coden=jnprdf
The Journal of Natural Products home page ofr hot articles in the field.
• The Value of Plants, Animals and Microbes to Human Health,”
held on April 17 and 18, 1998 at the American Museum of Natural History.
At this symposium, scientists, environmentalists and policy makers from
around the world discussed the link between conserving biodiversity and
sustaining human health and well-being. http://sciencebulletins.amnh.org/biobulletin/biobulletin/story636.html
and http://sciencebulletins.amnh.org/biobulletin/biobulletin/story631.html
• http://www.columbia.edu/~ftg1/Francesca%20T.%20Grifo.html
March 20: No Class- but you must do work over the break!
April 1: Set-up and review for Secrets of the Rainforest Module
LABORATORY: Plate Plant DNA Library
READING:
• Section on protein chromatography from Alberts et al. Molecular
Biology of the Cell. Garland Publishing 1994. p.166-169.
• LESSONS 1,2,3, to get an idea of what will be doing in the coming
weeks
HW#4: due. Answer all the questions at the end Lessons 1,2,3. Skim the
remainder of the Lessons to design an overarching flowchart of activity
that depict the concepts at work for this module. In addition use the
Chapter 4 reading to determine what type of "library" would
be used to execute this module.
April 2:
LABORATORY: Analyze results of library plating and start overnight LB-AMP/ARA
cultures an cultures between 4:00- 6:00pm- set aside about one and half
hours to analyze these results.
April 3: Pharmacopia
LABORATORY: Complete cell lysis and plasmid DNA miniprep purification
protocol/ Lab 4A and 5A
READING:
• LESSONS 4A and 5A to prepare for plasmid DNA extraction
• Thiel K. “Combinatorial Biology: Can Science Create Enough
Biodiversity? Bioventure View. Vol 13 (9);September 1998. ( 8 pages)
• Root -Bernstein R and M. "Conclusion: From Folk Wisdom to
Pharmacopia." Honey, Mud & Maggots. First Mariner Books. 1998.
p. 245-258.
• Visit this website as well “Natural Product Pharmaceuticals:
A diverse approach to drug discovery” January 6, 2001. http://www.pjbpubs.com/cms.asp?pageid=287&reportid=168
• Root-Bernstein. " The Development and Dissemination of Non-patentable
Therapies." Perspectives in Biology and Medicine .(38) I Autumn 1995:
110-17.
April 8: Enzymes- finicky proteins
HW#5 due: Enzyme Presentations-- Be prepared to give a 5 minute presentation
on your assigned enzyme- don’t forget to consider all the optimal
conditions and outcomes.
April 10: Plasmid DNA restriction digest planning- confirmation of the
GFP encoding DNA clone
READING: Review the plasmid restriction maps
HW#6: due. Be prepared to share your restriction digest chart with the
rest of the class. Remember to consider variables and include controls
that would be valuable to the collaborative effort of the class.
April 15: DNA restriction digest
LABORATORY: Conducting Lab 5B- the restriction digest.
HW#7 due: Lessons 6 and 7
April 17: Analysis of DNA and Protein
LABORATORY:Lesson 5C- Analysis of Digest: Gel Electrophoresis
Lesson 4B Protein Purification Phase 2—Bacterial Lysis, Lesson 4C
Protein Purification Phase 3—Protein Chromatography
April 22: Review the results of the Rain Forest Module
Please come to class prepared to present your results in the context of
the overall and specific goals of the module. This should be a 5-7 minute
presentation with your partner. You should outline your original objective,
hypothesis, methods, and conclusions.
LABORATORY: Confirming your genotype and phenotype: Lesson 9, Bacterial
Transformation
HW# 8 due: Lesson 8
April 24: Wrap Up
LABORATORY: Collect results of bacterial transformation
Reading: Stearns, T. The Green Revolution. Current Biology 1995, 5:262-264.
1221-1264.
http://journals.bmn.com/journals/list/browse?uid=JCUB.bb5314&node=TOC%40%40JCUB%4005%40t03%4005_t03April
29: Catch Up Day
May 1: Fast Track Papers Due
• Visit http://homepage.newschool.edu/~chamanyk/seminarseries/ID_Web/0308.html
for more information on clinical trials – lots of links
• http://www.accessdata.fda.gov/scripts/cder/onctools/Accel.cfm#FastTrack
Lots of links to info on fast track
• FDA. FDA Consumer: From Test Tube To Patient: New Drug Development
in the United States. January,1995;2002(July 8). http://www.fda.gov/fdac/special/newdrug/ndd_toc.html
or more recnet version (1999) http://www.fda.gov/cder/about/whatwedo/testtube.pdf
• http://www.cancer.gov/clinicaltrials This is a great site to understand
the clinical trial process and drug development.
• This paper does a great job of reviewing the fast track process.
Schulman and Brown. “The Food and Drug Administration’s Early
Access and Fast-Track Approval Initiatives: How Have They Worked?”
(1995) Food and Drug Law Journal. 50: 503-517.
• An old but interesting article on HIV/AIDS drugs. Gieringer D.
“Compassion Vs Control: FDA Investigational-Drug Regulation.”
(May 20, 1986) Cato Policy Analysis 72: http://www.cato.org/cgi-bin/scripts/printtech.cgi/pubs/pas/pa072.html
• http://www.fdli.org/pubs/Journal%20Online/50_4/art4.pdf
• Visit The International Conference on Traditional Medicine in
HIV/AIDs and Malaria 2000 http://www.intercedd.com./events.htm and click
on the link that takes you to the downloadable report from that conference
http://www.intercedd.com/downloads/bdcp-interceddconf.pdf
• Sunderland T. “Benefit Sharing and the Botanic Garden,”
Biological Resources : Symposium on Benefit Sharing and Botanic Gardens
was held after the Convention of Biodiversity's (CBD) Subsidiary Body
on Scientific, Technical and Technological Advise (SBSTTA) meeting of
the 2-6 September, 1996 in Montreal, Canada 1996.(2003) < http://www.bioresources.org/pub37.htm
>
• Visit http://www.worldbank.org/globallinks/english/environment.html
to view Nature’s Pharmacy video and images.
• Rohter, L. “Brazil Moves to Protect Jungle Plants From Foreign
Biopiracy.” New York Times, December 23, 2001:4. http://query.nytimes.com/gst/abstract.html?res=FA0616FC3C550C708EDDAB0994D9404482
• Center for Ethnobotanical Research http://www.cieer.org/ebdirectory/educat.html
• Read the “Fast Track News Release by the BDCP “ in
course packet and on the portal
May 6: Introduction to Interactive Final Exam
You will each role play an expert witness for a particular molecular biological
technique and present the significance of the data with respect to a patent
infringement hearing involving two see companies. You will not know which
seed company you will be representing until the day of the interactive
exam. I will serve as arbitrator.
May8: Work in seed company groups to plan your strategy for the hearing
May 13: Work in seed company groups to plan your strategy for the hearing
May 15: Patent Dispute Hearing
Important places and resources to know:
• Fogelman Library, 65 Fifth Avenue for books and CD-ROMs on reserve.
• Bobst Library, Washington Square South East Corner, 9th floor
is for science.
• Gimble Library, 2 West 13th Street for video viewing and the Avery
Fisher Video Library at Bobst.
• The UCC, 3rd floor, 66 West 13th Street for computer access.
• The ACC, 2nd floor, 65 Fifth Avenue for computer access.
• The STS journals, books, video, and CD-ROM collection for on location
use, Room 459, 65 West 11th Street.
The Fogelman, Bobst, and NY Public Library Web pages for access to electronic
databases.
• http://www.newschool.edu (click on the libraries and Fogelman)
• http://www.nypl.org
• http://www.nyu.edu/libray/bobst
• The Writing Center, basement of 65 West 11th Street.
Useful Web Sites:
http://homepage.newschool.edu/~chamanyk/seminarseries/SeminarSeries.htm
this is the STS home page and has links to Genomics Seminar Series
http://www.brookscole.com ******
this site is associated with your textbook and has a wealth of resources
including flash cards and links to tutorials. Click on the Human Heredity
Icon and follow the links.
http://www.freemedicaljournals.com/#fmj
asite with free full text links to journals
http://vector.cshl.org/ *******
this site is maintained by Cold Spring Harbor and has many resources,
" DNA form the Beginning" http://vector.cshl.org/dnaftb/ , a
great interactive primer for classical and molecular genetics-I encourage
you to click on the "problems" buttons on the bottom of each
section. The site main site also has links to news, videos and on-line
textbooks and much more.
http://www.fathom.com/special/biodiversity/
An entire site dedicated to issues of biodiversity.
http://www.dnalc.org/resources/BiologyAnimationLibrary.htm
The DNA Learning Center’s home page for animations of many biotechnological
techniques.
http://globetrotter.berkeley.edu/people/Harris/harris-con0.html
This site review my colleague Eva Harris’s work on PCR technology
transfer to Latin America and how this technology can address the rising
infectious diseases threats.
http://biology.arizona.edu *****
this site has tutorials and images of genetics and cells. Very good for
the first few weeks of class.
http://ehrweb.aaas.org/ehr/books/contents.html *****
this site an ON-LINE book about the Human Genome Project ( Your genes
, your choices) is published by the American Association for the Advancement
of Science
http://www.pbs.org/wgbh/nova/genome/program.html
The NOVA program Cracking the Code of Life website. Has video clips, interactives
and useful commentaries to understand genetics, genetic engineering, mutations,
and diseases.
http://news.bmn.com/hmsbeagle/ *****
This site requires free registration and is one of the best sites for
news, headlines and evaluated Medline (an electronic database) and evaluated
web links. It also has an on-line journal called HMS Beagle as well as
full text access to Trends in Cell Biology.
http://www.spacenet.eybe.eduon.ca/sciencewriting/
This site contains a tutorial for science writing. It was developed by
a science writer, Lydia Dotto. Please review this before starting your
first writing assignment.
http://www.the-scientist.com
This site requires registration for full text articles in the journal
The Scientist.
The journal also has a list of guidelines for all science writers: http://www.newscientist.com/about/style.html
http://www.nmsu.edu/~molbio/cell/CellLinks.html
This site contains links to summaries about cell function, organelles,
images, movies, and more.
http://www.accessexcellence.org/AB/GG/garland_PDFs/gar?PDF_indx.html
This site contains model images of cell structure and research techniques
from the MBOC/ECB text.
GUIDELINES FOR PAPER/PRESENTATIONS
Requirements
You will write one paper which will address four perspectives: FDA ; Patient
Advocacy Groups—Ramon and Other Cancer Patients, American Cancer
Society; Indigenous Peoples Advocacy groups.; and Biotex Employees. The
paper can be a proposal that best satisfies all four groups or it can
be a collection of letters sent by members of each organization that address
their specific concerns but do offer up a compromise. Should you decide
to write a creative nonfiction piece for this assignment, developing characters
and such, you must allow yourself enough time to do the research as well
as the creative writing process. Whatever approach you choose, straight
up research paper or a version of a creative paper. The final product
must be typed, 10 pages maximum, double-spaced, minimum 12 point font,
and 1” margins. You must include citations and references (even
if creative). The papers are due, in class on May 1st. You may turn your
paper in earlier if you'd like to obtain feedback. I strongly suggest
using the writing center.
Recommendations
For the paper, regardless of the approach you choose, I expect an introduction
to the subject. This introduction should be presented such that given
this introduction, anyone would be able to follow the remainder of the
paper. Within the introduction, the relevance of the topic should be clearly
stated and historical background should be presented to support this view.
The best source of information with which to start are your own texts
and those on reserve in the library. The next source of material which
will provide a great background (both social and biological) will be secondary
literature, such as Scientific American , the New Yorker, Newsweek, Time,
NYTimes, or Discover articles. I suggest you browse the literature and
start with review articles and work your way up to the primary literature.
I do not expect you to understand all of the primary scientific sources,
but I do expect you to come to me with questions so that I may clarify
or guide you. Also check out the http://homepage.newschool.edu/~chamanyk/ID%20Web/0308.html
site.
The style and organization of this paper will depend heavily on the nature
of your topic. For instance, the field of drug discovery, regulation,
and its applications has an incredibly rich history and societal impact.
Rather than present all the information about this topic, I would present
only a few aspects focusing on one that I find particularly interesting,
such as the FDA retractions of drugs on the market or the way that genetic
engineering has shaped preventive medicine.
With regard to the science, the background may also include examples from
other researchers, or a contradictory result that you will through your
presentation now eliminate. Ideally, your paper should attempt to apply
the science to the social impact, including a best case compromise that
would satisfy all fours groups ( FDA, Patients, social conscience, and
pharma). To accomplish this melding, you may mention society’s response
to past and current applications concerning the scientific basis of your
topic. The last portion of the paper, will again, vary, depending on the
approach, but ultimately, present the future direction of the field. Remember
that this is a proposal. Here is your chance to be creative--feel free
to finish with a bit of your own opinion for a method of continuing or
discontinuing this research in FDA FAST TRACK with an increased level
of understanding, but try to support your argument as best you can with
the facts-as-known (Her2 studies, HIV drug studies) and future experiments.
Sites for the Ethnopharmacology Fast-Track Paper:
• http://homepage.newschool.edu/~chamanyk/ID%20Web/0412.html &
click on BDCP homepage http://www.bioresources.org/ and be sure to visit
their conference webpages to get names of people in the field.
• Visit http://homepage.newschool.edu/~chamanyk/ID%20Web/0308.html
for more information on clinical trials
• Visit The International Conference on Traditional Medicine in
HIV/AIDs and Malaria 2000 http://www.intercedd.com./events.htm and click
on the link that takes you to the downloadable report from that conference
http://www.intercedd.com/downloads/bdcp-interceddconf.pdf
• Sunderland T. “Benefit Sharing and the Botanic Garden,”
Biological Resources : Symposium on Benefit Sharing and Botanic Gardens
was held after the Convention of Biodiversity's (CBD) Subsidiary Body
on Scientific, Technical and Technological Advise (SBSTTA) meeting of
the 2-6 September, 1996 in Montreal, Canada 1996.(2003) < http://www.bioresources.org/pub37.htm
>
• Visit http://www.worldbank.org/globallinks/english/environment.html
to view Nature’s Pharmacy video and images.
• Read the “Fast Track News Release by the BDCP “ in
course packet and on the portal
• Tiger in the Forest http://research.amnh.org/biodiversity/symposia/tigerintheforest/
The Center for Biodiversity and Conservation’s 2003 spring symposium
will explore the role of nature-based tourism in biodiversity conservation
within mainland Southeast Asia (specifically Cambodia, Lao People’s
Democratic Republic, Myanmar, Thailand, and Vietnam). The region harbors
a significant proportion of the world’s rare and endemic plants
and animals, including several species new to science.
• http://www.columbia.edu/~ftg1/Francesca%20T.%20Grifo.html
The Value of Plants, Animals and Microbes to Human Health,” held
on April 17 and 18, 1998 at the American Museum of Natural History. At
this symposium, scientists, environmentalists and policy makers from around
the world discussed the link between conserving biodiversity and sustaining
human health and well-being. http://sciencebulletins.amnh.org/biobulletin/biobulletin/story636.html
and http://sciencebulletins.amnh.org/biobulletin/biobulletin/story631.html
Plagiarism and Quoting
Plagiarism is the most serious academic crime. Ignorance of the
rules is not an excuse to commit plagiarism, and therefore you must understand
it. In science writing people often think that they must cite every sentence
and this is the case if you look at primary literature in the field. When
writing for the lay audience (secondary literature), you can use sources
to construct your own story. Remember that the readers want to hear your
interpretation of the science. If they wanted to hear the most accurate
story they would read the primary source. So how do you cite sources in
this latter scenario?
A. Paraphrasing-Changing a few words around in a sentence of a source
without citing the source is still plagiarism. You must take the concept
and place into your own words. Try to explain it to yourself and then
write that down as a start. If this takes a few sentences, you can cite
the whole paragraph by citing the source for the last sentence only. If
can be understood by the flow of the paragraph, that all of the information
came from one source. One way to make this clear is to mention the author's
name in the sentences that precede the last sentence of the paragraph.
B. Quoting-Quoting is rarely used in science. Again, the readers are interested
in your ideas and how they fit into the context of your written essay.
Quotes often disrupt the flow and style of your paper causing readers
to make unnecessary leaps of faith or understanding. Reserve quotes for
those times when the vocabulary is so unique that the meaning, tone, or
impact would be lost if summarized in any other way. Lastly, excessive
use of quotes tips readers off that you, the author, do not understand
what you are writing. DO NOT USE QUOTES because you can't think of a better
way to say it- be creative and explain the information. Citations and
Bibliography
Acknowledge the source of all material that is not your own. Citation
formats vary form from one academic field to another. Unlike writers in
the humanities, for example, scientists rarely use footnotes or endnotes
to acknowledge sources. Instead they insert citations directly in the
text, by giving the last name of the author and the publication date(name-
year system)or by a number (number system). Complete bibliographic information
is listed for each cited reference in the References section of the paper.
All citations go at the end of a sentence in the text of your paper. If
there is more than one citation per sentence, place them in chronological
order.
Work by one author:
In Chamany’s study of microtubule dynamics.... was established (Chamany,
1994).
Work by two authors:
Other researchers have suggested ...about dynamics (Barnes and Drubin,
1995).
Work by three or more authors:
Other researchers have suggested ...about dynamics (Barnes et al., 1995).
Two or more works by one author in the same year:
Other researchers have suggested ...about dynamics (Barnes et al., 1995a;
Barnes, 1995b).
Direct quotation
The microtubules “ are intertwined and splayed in right angles”
(Chamany, 1993, p 4).
Works you have not Consulted Directly
Avoid referring to sources you have not read yourself. Occasionally, however,
you may need to cite an important source that is not accessible to you.
If so, specify where you acquired your secondhand knowledge of this source.
Arcari reported that ..... with regard to dynamics (Arcari, 1982, as cited
in Castrodale, 1985).
In this example Arcari was cited in a review article by Castrodale and
therefore only the Castrodale work would appear in the bibliography.
References/Bibliography:
List your citations in alphabetical order in this format:
Articles
Authors. Title of article. Name of journal year. volume (number): pages.
Barnes GB, Drubin D, Stearns T. The Yeast Cytoskeleton. Cell Motility
and the Cytoskeleton. 1995. 50(2):310-324.
Books: Follow the MLA guidelines
For a chapter in an edited book
1) For the citation use the author of the chapter NOT the editor
2) For the reference, list the author of the chapter, the title of the
chapter as found in the title of the book and the editor and then follow
the MLA as if for a book.
Web Sites
Read the information on these websites and I want to see the search engine
used as well.
• http://www.bio.davidson.edu/Biology/macampbell/evaluate.html :Tells
you how to evaluate sites
• http://www.smpcollege.com/online-4styles~help/: This site gives
you all the info you need to cite a Web site.
• http://www.bedfordstmartins.com/online/cite5.html#1 : Here is
the direct link for how to do a URL in the references or bibliography
• here is an example from my own work. Notice how the date for development
of the web site is placed before the date that you accessed the information.
Terry T. (2000)."Botulinum Toxin Mechanism of Action" as found
in Biology 102: Lecture Notes: The Nervous System. University of Connecticut.
November 13, 2000. 2002 (May15) http://www.microvet.arizona.edu/Courses/MIC420/lecture_notes/clostridia/clostridia_neurotox/movie/botulinum_movie.html