Ti plasmid web sites, BIO 2020, Baruch College

Web Site Evaluation, BIO 2020, April 2004

John H. Wahlert, Professor of Biology
Baruch College, CUNY
May 12, 2004

Web searches are wonderful tools for discovering resources on the internet, but they merely match key words and do not in any way evaluate the links found. Each of the following sources was cited by a student in the class as being helpful in finding informaton about the Ti plasmid. But not all of the sources are equally good, and there are many questions that should be asked about each web site in order to judge the quality of information presented. Some of them require detective work to figure out.

Any source has to be evaluated. Questions:

Is it a primary source?—the author is the person or group that did the research.
If a primary source, is it published in a journal that has peer review (most scientific journals have this), or is it a direct report on research such as that done by government agencies? Does the journal have a stated purpose that could select for bias through the kinds of papers it accepts for publication?
Is it a secondary source?—a textbook that incorporates the scientific research of others, or a professor supplementing lectures with handouts.
If a secondary source, what is its purpose? is it by a major publisher? is it meant to instruct a college/university class? who is the audience? Sometimes secondary sources are helpful, and primary sources are too technical for you (or me) to understand because their audience is colleagues in a particular branch of science. Some sites are professor's lecture notes or PowerPoint presentations—secondary sources. You may find some excellent scanned figures in the slides, but you probably won't find out the source.

Here are the web sources that class members found. I have arranged them in groups, and explained hou I evaluated them.

Primary sources (great but they may be too technical for you or me to get much out of them):

www.pnas.org/cgi/reprint/95/12/7057.pdf
This is an article (in pdf format) in the Proceedings of the National Academy of Sciences. It is a primary source and difficult reading.

jb.asm.org [the complete link is immense].
This is an article in the Journal of Microbiology. It has the criteria one looks for, a journal heading, an article title, authors and their affiliations: "A New Type IV Secretion System Promotes Conjugal Transfer in Agrobacterium tumefaciens," Lishan Chen, Yuching Chen, Derek W. Wood, and Eugene W. Nester, Department of Microbiology, University of Washington, Seattle, Washington 98195-7242. It has a huge bibliography. This is definitely a primary source—a report on original research. As such, it is probably much more technical than you can understand; don't worry, you aren't the intended audience.

www.plantphysiol.org/cgi/content/full/125/1/9
This web page is a journal article: Plant Physiol, January 2001, Vol. 125, pp. 9-14, "Agrobacterium. A Memoir," Mary-Dell Chilton, Syngenta, P.O. Box 12257, Research Triangle Park, North Carolina 27709. It is a reader-friendly "a foray through the story of Agrobacterium transformation of plant cells." It ranges from history (secondary source) to reporting on current research (primary source).

www.ars.usda.gov/research/projects/projects.htm?ACCN_NO=404300
Agricultural Research Service, the in-house research arm of the U.S. Department of Agriculture. The web address is a give away—whenever you see "*.gov" you are somewhere in the US Government web site. The page gives a summary of the Research Project: "Genetic Engineering Cotton for Enhanced Resistance to Aspergillus Flavus," and tells you the names of the project investigators. If you click on "Research Home" at the left, you will find out the kind of programs that are part of the USDA endeavor. This is a primary source.

www.biochem.wustl.edu/~StrucGen/sec4_what.htm
Here's another .edu, the sign of an educational institution. The page is entitled "Introduction to bacterial type IV secretion systems," and it has an extensive bibliography—a good start on quality. There are also intriguing links across the top. For more information, try clicking on "home" at the bottom of the page. This takes you to a key page: "Structural Genomics Projects at Washington University School of Medicine in St Louis, USA." The page is rich in inforamtion and gives the name of the coordinator at the bottom. It's a primary source web site that you can trust.

www.life.uiuc.edu/farrand/lab/index.html
This is the web page of Stephen Farrand's Microbiology Laboratory. If you click on "Research," you will learn all about Agriobacterium and the Ti plasmid. Form the home page, clicking on "Research" leads to a list of publications by Farrand and co-authors that are on the subject of Agriobacterium. This is a primary source presented by a scientist about his field of research.

books.nap.edu/books/0309034345/html/15.html
This is a different kind of educational institution, The National Academies Press, with over 3000 books that can be read online for free. The link takes you to page 15 of a particular book: Genetic Engineering of Plants: Agricultural Research Opportunities and Policy Concerns (1984) Board on Agriculture (BOA). In the upper right corner of the web page, you can click on "The National Academies" to find out about the parent organization—"Advisers to the Nation on Science, Engineering, and Medicine." This site has primary source material that is clearly attributed.

Secondary sources (good ones):

www.biologie.uni-hamburg.de/b-online/e34/34.htm
This page is entitled: "Interactions of Plants and Bacteria – Genetic Engineering." "Uni-hamburg.de" tells you that the page is within the University of Hamburg, Germany, web site. It is a little confusing— at the bottom are names of people who might be authors, but that isn't clear. If you click on "Contents," you are taken to a page entitled: "Botany Online - The Internet Hypertextbook" and there are names given at the top; there is a detailed table of contents. You can discover, in German, that someone named Peter v. Sengbusch is responsible for the content. I want to know more, so I shorten the address to www.biologie.uni-hamburg.de, and click on "Teaching Stuff," and there it is. This means that the pages are used in teaching at the University of Hamburg, Germany. Not bad, as a resource. I also clicked on "Highlights of biochemistry" only to find that the pictures do not appear. Maybe you will have better luck; it looks like it might be a great resource. This is mostly a secondary source, but a few pages are by the scientists, themselves. A Google search, with "Peter v. Sengbusch" in quotes, yields interesting pages: International Projects including Botany Online, a current curriculum vitae, and a list of publications. Very impressive stuff.

www.accessexcellence.org/AB/BA/Transforming_Plants.html
The page looks good. It has a clear heading: "Access Excellence, the National Health Museum, About Biotech." The article has a title, "Transforming Plants - Basic Genetic Engineering Techniques," and it is attributed clearly to a published source: Pamela Peters. "Biotechnology: A Guide to Genetic Engineering." Dubuque, IA: Wm. C. Brown Publishers, 1993. If you click on HOME at the bottom of the page, you will see all that this site has to offer. On this page you can click on "Our Board and Supporters" and judge for yourself if this is a diverse community that is probably not promoting a particular product or point of view. The particular article is a quotation from a textbook and may be a mixture of secondary and primary sources.

www.plantphys.net/search.php
Plant Physiology Online is Sinauer Publishers web companion to the textbook Plant Physiology, Third Edition by Lincoln Taiz and Eduardo Zeiger. Since suggestions for the web site are to be forwarded to the authors, they are most likely responsible for the content. This is a very useful, searchable web site and secondary source. Searches on the authors would be interesting to show their particular areas of expertise. Books published by Sinauer and other major scientific publishers have been carefully reviewed by teachers and other researchers.

www.inform.umd.edu/genetics/leafdisc.html
This web page is at the University of Maryland (using a shortened address takes you to the Department of Life Sciences. I had to search the University site to find the faculty web page of Dr. Paul Bottino, the author of this page. He has a good list of recent publications and teaches a course in Modern Molecular Genetics. The web page cited above is entitled "Leaf Disk Method For Agrobacterium Mediated Transformation of Higher Plants" It treats history of the method and shows it in photographs. This is a secondary source but the photos and probably some of the content are a primary source.

Class notes by a professor:

helios.bto.ed.ac.uk/bto/microbes/crown.htm
This site is at the University of Edinburgh, UK; the author of the web page takes credit and acknowledges assistants. It is rich in content and pictures. One would guess that it is a teaching tool. I used Google again to go to the University of Edinburgh; I picked "Staff" and searched on Jim Deacon; there were 961 hits, the first being Jim Deacon's home page. Two selected publications are listed. He is an academic staff member of the Institute of Cell and Molecular Biology. I would like to find out what course these pages are part of; perhaps they are for more general readers. I judge this to be a reliable site—university, transparency of authorship, and thoroughness of content including photographs and diagrams.

www.csun.edu/~hcbio027/biotechnology/lec12/lec12.html
This site is the Biology 470 - Biotechnology course web page of Dr. Stan Metzenberg, Department of Biology, California State University, Northridge. All of this information is available on the same page. This is clearly the web page for a course, but what a web page it is! There are excellent links to diagrams, animations, and photographs of actual infected plants. By backtracking in the address, I found the Department of Biology web page, clicked on Faculty, and then on the link to Stan Metzenberg's personal page. It is clear from his publications, that he is an expert in the area of this course.

www biology.missouri.edu/courses/Bio370_Smith/TiENgineering.doc
"Missouri.edu" tells you that you are at an educational institution, probably the Univeristy of Missouri. The MSWord document, in outline form, is informative, but what is it a part of? If you shorten the address to www biology.missouri.edu/courses/Bio370_Smith/, you will find yourself on the page for "Molecular Biology 370" taught by George Smith. Under "Handouts" you can find MS word documents and power point presentations, but not this one. Perhaps Prof. Smith is not using TiEngineering.doc this semester, but it is still on the college web site. This is a secondary source—Prof. Smith's summary from texts and primary literature (scientific papers). Some back sleuthing on the web address reveals that the school is The University of Missouri-Columbia.

classweb.gmu.edu/achriste/385-Ch17ppt/sld022.htm
I will geuss that the page is in an educational institution and perhaps A. Christe is a professor. This address lands me in the middle of a slide presentation (the ppt in the address suggests PowerPoint), so I am going to back up in the adddress to find out the context: classweb.gmu.edu/achriste/385-Ch17ppt/. This takes me to a page entitled "Chapter 17 Plant Genetic Engineering Methods," so this must be something for a course. I will try a shorter version of the adddress: classweb.gmu.edu/—it gives a list of every page on the classweb site at George Mason University. There are no links back to George Mason University, so I did a Google search on "George Mason University" and landed on the home page. I typed classweb into the search and found a long list of pages that are posted by faculty. I searched again on "A Christe" and found a link to the home page of Alan H. Christensen, Associate Professor in Molecular and Microbiology. He even teaches a course numbered 385, which appears in the web address, and the links are to power point slides; I found the identical slide, but it is at a different web address—that doesn't matter. It's a secondary source, a course lecture presentation. I would like to know about Dr. Christensen's publications, but there is no information on his web page, and a Google search didn't turn up anything helpful.

photoscience.la.asu.edu/photosyn/courses/BIO_343/lecture/geneng.html
The page entitled "Plant Genetic Engineering: Methodology" consists of text for a course in Genetic Engineering and Society at Arizona State University. The table of contents states that "Most of the material at this website has been compiled over the years by Wim Vermaas, a Professor in the School of Life Sciences." The next task is to visit the ASU web site and find out about the Professor. Prof. Willem F. J. Vermaas is a faculty member in the School of Life Sciences. Publication titles show his research to be in the area of photosynthesis. The web pages for the course should be a good source of inforamtion—a secondary source.

www.pssc.ttu.edu/pss3421/genetic%engineering.htm
The link doesn't lead anywhere. Using only part of the address ending in PSS3421/ takes on to a Principles of Genetics course numbered PSS 3421 [Plant and Soil Science] at Texas Tech University. The page may have contained useful information, but it is another course web page.

Secondary source, but what is the purpose?

www.i-sis.org.uk/Agrobacterium.php\
This web page, entitled "Common Plant Vector Injects Genes into Human Cells" in which " Prof. Joe Cummins warns of hazards to laboratory and farm workers." Questions come to mind: Professor of what discipline and at what institution. A Google search leads to a paper by "Prof. Joe Cummins / Department of Biology / University of Western Ontario" [Professor Emeritus], and he has a web page. His article is on the web site of The Institute of Science in Society, and it is important to discover if this society has a particular viewpoint on genetic engineering. If you point to the top right link "more" you can click on "About Isis." After reading the descripiton, I believe the site contains mainly voices that question the rapid progress of genetic modification or organisms; its concerns go beyone science into politics. I would expect questions about technology to be presented here.

Secondary source, but by whom?

www.engg.ksu.edu/KSE/features/genengg.htm
The page is an article in a web site entitled "Kansas State Engineer." It has none of the criteria to be assessed as a peer-reviewed journal, but it is within a web address at the University of Kansas. Using just the beginning of the address, www.engg.ksu.edu, leads to the home page of Kansas State University Engineering. Click on "About the College" in the links at the left, and a drop down menu lists "Publications: K-State Engineer Magazine." The link doesn't work, but at least there is evidence that the College is the publisher. The site gains credibility, but it lacks evidence of being a true journal. It is a secondary source.

Weak sources (student papers, though that doesn't really mean they must be mediocre):

http://cseserv.engr.scu.edu/NQuinn/ENGR300Winter2001/WeeklyTechnologyAssessment/Doblack-GeneticallyModifiedFood.pdf
The web address takes you to page within the Santa Clara University School of Engineering where Neill R. Quinn Jr. is a faculty member. The page shows that he taught ENGR300 in the winter of 2001. The Weekly Technology Assessment web pages are clearly papers submitted by students in the course. Would you consider a paper written by the student sitting next to you as proper source material in your own research? The correct answer is NO.

www.ppws.vt.edu/~sforza/prokaryote/ti_map.html
This is a colorful diagram of a Ti plasmid, and you can click on parts to see what they do. If you shorten the address to www.ppws.vt.edu/~sforza, you will learn that Peter Sforza is an M. S. student in Plant Pathology at Virginia Tech at Blacksburg. This is a fun source but not particularly informative.

www.newton.dep.anl.gov/askasci/bio99/bio99765.htm
The Newton BBS is a wonderful website where teachers and students K-12 can ask questions of scientists. The particular page cited is a response to a 15 year old high school student. The scientist's last name is given, but who is it. This might be a good starting place to find out about a subject, but it is aimed too low to qualify as something you can site in a research paper. It's a secondary, secondary source.

info.bio.cmu.edu/Courses/03441/TermPapers/99TermPapers/Quorum/taraproks.htm
The web page is within the Carnegie Melon University site and has a link at the bottom to a "Table of Contents." At the bottom of this page is a link "Back to 1999 Term Papers." This is clearly a multi-authored student term paper.

Poor sources:

wwww.ento.vt.edu/HyperNews/get/forums/ent2004dlsum102arc/83.html
This website has moved, and I can not find the page. This is apparently the Entomology Department of Virginia Tech University, Blacksburg. When Entomology 2004 is offered in the summer, it is a distance learning course. The word "forum" in the title suggests this is a discussion site—probably not even a secondary source.

www.ba-education.demon.co.uk/for/science/gm.html. This site impressed one student as a journal published on the web, but is it really like a scientific print journal? In a printed journal, I expect to find articles attributed to authors, there should be a board of editors, an associated society or agency, and rules for authors. If you click on "main index" or "this index" (whatever that means), you will find none of this information. This site, no matter what it says, ranks low in the hierarchy of trustworthyness. It is clearly a secondary source, if that.