Learning & Writing, Collaboration & Peer Review The "Chemistry Is in the News" Project

Philosophical Background

Chemistry is the Central Science says the American Chemical Society. Chemistry is central indeed and in several ways. Chemistry is central among the sciences and chemistry also is central to the most pertinent issues of modern society.

When thinking about Society and Chemistry, you might reflect on the agricultural growth due to fertilizers and herbicides, you might remember your last bacterial infection and thankfully reflect on the progress chemistry has brought to pharmaceuticals, you might be a space travel enthusiast and contemplate that no shuttle would ever make it back without the new materials developed for the heat shields. On the other hand, you become aware and concerned about the damage caused by chemistry in war and peace time. Chemical warfare has been used in the last century causing unimaginable and extraordinary pain to millions of people. Accidents in chemical plants pose a threat and have exposed many people to potential long term harm. The ozone hole keeps reminding us that atmospheric chemistry might have consequences that we might not even realize.

Newspapers mirror society and newspaper articles allow to construct the important relations between society and chemistry. This is the basic premise of the Chemistry is in the News Project. You begin recognizing these connection first by studying the existing CIITN items. Next, you create new CIITN items yourself. Moreover, your creations will be evaluated not by your teacher but by other students instead. This peer review adds a new layer of complexity as you need to consider the perspectives of others on any given issue. Overall, the CIITN activities serve as a preparation for science communication.

This collaborative group project includes the identification of an important newspaper article, the writing of interpretative comments, the location of pertinent references in a textbook, and the creation of questions with suggested answers including an essay answer to a question about a complex societal issue. The project also includes the peer-evaluation of news items created by three other groups. The first two writing assignments are preparations for the main project.

Assignment 1: Abstract a Newspaper Article

Working as a group,
[1] Read an assigned science-related newspaper article and write an abstract.
[2] Review I: Constructive review by Ms. Kathleen Carson.
[3] Revise your abstract.
[4] Review II: Evaluation & grading by Ms. Kathleen Carson.

Access to electronic journals will be the subject of one collaborative learning session prior to this assignment.

In the "Notice to Authors" of the Journal of the American Chemical Society one is advised that "an abstract should state briefly the reason for the work, the significant results and the conclusions." Hence, the abstract should contain answers to at least three questions: "What question is being asked by the authors?", "How do the authors answer the question?", and "What do the authors think the results mean?" Abstracts should be limited to about 250 words.

Start at URL http://www.chemistry.org, navigate to the Journal of Organic Chemistry and view at least two JOC articles and their abstracts. Such abstracts have a special significance in the way science is communicated. Scientists do not have the time to read entire papers only to find out that they have little or no relevance to their particular interests. A well-written abstract will be the basis on which other scientists will decide whether they should read the paper at all. Hence, the ability to communicate the essential content with clarity and without jargon is an important intellectual skill.

Abstracting also is a wonderful intellectual device to really understand and this technique can be applied to any text. In this assignment you are asked to write an abstract to a science-related newspaper article. Several articles (about 6-8) will be posted on the course web site and you will be assigned one of these. In analogy to the scientific abstract, your abstract should contain answers to the following three questions: "What issue is being addressed by the journalist?", "What information and data are provided by the journalist to inform the issue?", and "What does the journalist report as conclusions to be drawn from the information and data provided?"

Note that the abstract is written by the author of the article. In other words, you should pretend that you are the author of the article and that you need to write an abstract to accompany your article. Note also that quotes are not usually a part of an abstracts. Quotes can be evidence in the article but the abstract would merely refer to "testimony is available to support ..."

Formating Rules:
[1] Give the headline of the article in the first line (or first two lines if needed); give the headline in bold italics and without quotation marks.
[2] Provide the complete reference in the next line; author name (e.g Claudia Dreifus), paper (in italics, e.g. The New York Times), do not miss "The"), publication date in the format Month Day, Year (year in bold).
[3] Since we are working in groups, provide your names on the next line "Abstracted by --your names here separated by commas with "and" before the last name--. The "name" Group." Example: Abstracted by Jason Gentry, Craig Watkins, Anne-Marie Woelbel, and Kristin Rolwes. "The Prime Carbons" Group.
[4] Start your abstract on the next line.
[5] In the next line after the abstract, write "Word Count: N" where N is the number of words in your abstract (no more than 250 words).
[6] In the next lines, suggest two alternative titles for the article and start the titles with "Alternative Title 1:" and "Alternative Title 2:" Give the alternative titles in bold italics and without quotation marks.
[7] Leave an empty line.
[8] List title, authors, and complete reference for each of the two JOC articles of which you read the abstracts. Use ACS format and that means: Provide the title of the paper in italics and without quotation marks. Provide the author names in the format family name first, comma, initials, semicolon, next name ... journal abbreviation in italics ... no comma ... year of publication bold ... comma ... volume number in italics ... comma ... page numbers and a period at the end. Example: The Azine Bridge as a Conjugation Stopper: An NMR Spectroscopic Study of Electron Delocalization in Acetophenone Azines. Lewis, M.; Glaser, R. J. Org. Chem. 2002, 67, 1441-1447.
[9] The assignment needs to be typed double-spaced using Times 12-point font, and 1-inch margins top, bottom, left and right. Submit hardcopy to Dr. Glaser or Ms. Carson.

Sample: A student group in WS04 wrote a perfect abstract on the article Brains and Brawn, One and the Same, by Nicholas Wade, The New York Times, Jan. 25, 2004.

Selection of Articles to Abstract

(1) Filmmakers Examining the 'What Ifs' of Nuclear Power (direct link), Nancy Ramsey, The New York Times, September 8, 2004. [0 groups]
(2) U.S. Hunts for Evidence of Supercoca Plant (direct link), Dan Molinski, The Washinton Times, September 3, 2004. [1 groups]
(3) Toxic waste ship sinks off Turkey (direct link), N.N., The Australian, September 8, 2004. [3 groups]
(4) DNA sequence in hand, dog geneticists aim to build a better pooch (direct link), N.N., The Boston Globe, September 7, 2004. [8 groups]
(5) Spurred by Illness, Indonesians Lash Out at U.S. Mining Giant (direct link), Jane Perlez and Evelyn Rusli, The New York Times, September 8, 2004. [1 groups]
(6) More Cancer Risk Seen in Full-Body CT Scans (direct link), Thomas H. Maugh II and Daniel Costello, The Los Angeles Times, August 31, 2004. [6 groups]

Numbers given in corner brackets behind the articles shows how many groups selected the article.

Categories for Review

(1) Identification of Main Ideas (0-20 points): Did the abstract writer understand the article? Was the abstract writer able to identify the essential responses to the three main questions "What", "Why", and "So What"? Is there any information that is not essential and should not be in the abstract? Is there any information that is essential but is missing in the abstract? Are the suggested alternative headlines "right on"?
(2) Communication of Main Ideas (0-10 points): Is the abstract clear, concise, and coherent? Is the organization logical? Are there any redundencies? Does the abstract stir interest in the article?
(3) Style & Grammar (0-10 points): Is the abstract written in passive voice? Are there many typos? Are there grammatical errors?
(4) Formalities (0-10 points): Is the abstract within the word limit? Are all three required citations in the correct format? Are the citations complete and correct?

Assignment 2: Drawing Structures & Molecular Models

Working as a group,
[1] Select a reaction with at least one substrate, one reagent and one product.
[2] Draw a reaction diagram for this reaction using ChemDraw.
[3] Model the substrate(s) and the product(s) using Chem3D.
[4] Write a Word document that contains a brief verbal description of the reaction, a ChemDraw diagram, and molecular models of substrate(s) and the product(s).
[5] Review I: Constructive review by teaching assistants Ms. Cecelia "Cece" Koetting and Ms. Kathleen Carson..
[6] Revise your assignment.
[7] Review II: Evaluation & grading by Ms. Cecelia "Cece" Koetting and Ms. Kathleen Carson.

Instruction in the use of the programs ChemDraw and Chem3D will be the subject of one collaborative learning session prior to this assignment.

More than other disciplines, chemistry heavily relies on symbolic notations and modeling. The notations are precisely defined, they allow for powerful condensation, and mastering this symbolic language is a fundamental skill in chemistry. In science modeling is inextricably bound to the generation of new ideas and the development of theories. Linus Pauling described modeling as a unique way of thinking. Instead of model sets, we can now use more accurate computer generated models. Precise models represent precise thinking.

Give the name of the reaction in line 1 in bold type (e.g. The Fischer Esterification) and your names and the group name on the next line(s). Leave an empty line. Start your brief description of the reaction on the next line. The reaction diagram should follow as Scheme 1 and the scheme should have a scheme legend (e.g. Scheme 1. Reaction diagram of the Fischer esterification.). The molecular models should be shown as Figure 1 and the figure should have a figure legend (e.g. Figure 1. Molecular models of the tetrahedral intermediate and of the ester.). Your reaction description must include references to the scheme and the figure. Also include a sentence about the significance of the reaction. The assignment needs to be typed wikth "at least 24 points" using Times 12-point font, and 1-inch margins top, bottom, left and right. The ChemDraw scheme needs to be prepared according to the guidelines issued by the American Chemical Society (discussed during ChemDraw instruction) and used after enlargement to 125 percent. Chem3D models should be cylindrical bonds (atom size 20%), depth ratio 60, shadowed color or pattern by element, element symbols as atom labels. There is a strict 2-page limit in portrait format. Submit color hardcopy to Dr. Glaser or one of the teaching assistants as announced on the online Schedule. A sample assignment is available.

Categories for Teaching Assistant Review

(1.1) Reaction Description (0-5 points): Describe a specific reaction as an example. Include statements regarding the scope of the reaction. What is the significance of the specific reaction and what is the significance of this type of reaction in general?
(1.2) Nomenclature (0-5 points): Are all compounds referred to by name (or just by number)? Are the names correct or at least reasonable? Have abbreviations been defined?
(1.3) Reference to Scheme & Figure and Legends (0-5 points): Have references to scheme and figure been included in the reaction description? Have legends been provided for scheme and figure? Are the legends descriptive and "headline-like" (e.g. incomplete sentences allowed)?
(2.1) Drawings of Substrate(s) and Product(s) (0-5 points): Are the molecule complete? Are functional groups correct? Are substituents missing? Are all heteroatoms shown? Are all bonds shown? Are important lone pairs indicated? Are unpaired electrons indicated? Are charges and formal charges properly shown? Are stereochemical issues properly indicated?
(2.2) Arrows & Reagents (0-5 points): Is the reaction arrow of the correct type? Is the reaction reversible? Is this an equilibrium reaction? Is the reagent given on top of the arrow? Are the reaction conditions indicated (pressure and temperature)? Is the solvent indicated? Is it clear whether the reagent is stoichiometric or catalytic? Are catalysts specified?
(2.3) Alignments (0-5 points): Are the "crucial" bonds either vertical or horizontal? Are the orientations of the molecules on both sides of the arrow the same? Are substrate(s) and product(s) in proper horizontal alignment? Are substrate(s), product(s) and arrow items clearly separated (non-overlapping boxes criterion).
(2.4) Fonts & Sizes (0-5 points): Have ACS requirements been met (bond and font settings)? Has the magnification to 125 percent been performed?
(3.1) Modelling (0-5 points): Do the models look right? Are all atoms where they should be? Are the conformations right (as much staggered as possible)? Are the configurations correct (at double bonds, at chiral centers)?
(3.2) Model Display (0-5 points): Are the models displayed with the requested settings? Are labels visible and inside the atoms? Have important structure parameters been included in the Figure?
(3.3) Alignment & Size (0-5 points): Are the models aligned in a reasonable fashion? Are they aligned (more or less) in reasonable agreement with the drawings of the Lewis structures in the scheme? Have the models been rotated in a reasonable manner to best feature the most important structural issue? Are the sizes of the substrate and product models consistent? Is the figure layout reasonable (e.g. substrate on the left, product on the right).

Assignment 3: CIITN Group Project

Working as a group,
[1] Read online newspapers and search for articles whose content in some way is connected to organic chemistry. Consider only top-notch well recognized newspapers to assure the highest quality.
[2] Identify one article that illustrates an important consequence of organic chemistry well. Identify the key organic chemistry topic the article touches upon and identify the chapter in a textbook that is most relevant. Identify keywords that best describe the issues raised by the article. Identify keywords that best describe the most relevant chemistry topics related to the article.
[3] Create editorial comments with links to useful online resources, pertinent references section, and questions & answers in CIITN web tool.
[4] Peer Review I: Constructive intergroup peer review.
[5] Revise your item considering the commentary and recommendations made in the constructive peer review.
[6] Peer Review II: Evaluation & grading by intergroup peer review.
[7] Peer Review III: Intragroup peer review.

Instruction in online searching of news media, using the CIITN webtool, and preparations for the peer review will be the subjects of instructions in lectures and another several collaborative learning sessions prior to this assignment. The session "Revise, revise, revise!" will be taught by Dr. Martha Patton of the MU Campus Writing Program; there will be a handout on Revising Scientific Prose and an example about Genetically Modified Corn.

Guidelines for Newspaper Article Selection

A key feature of online publishing is access to national and global information. To be able to access national and global information, one needs to develop an awareness of the extraordinarily increased accessibility. You can only find new things if you are looking for new things. But how does one look for new things? Well, looking around in a curious manner helps. To make your searches of "new" sources of information more interesting, here is a little incentive. The instructor will award 10 extra points to every member of three groups with "novel" source selection.

You are not limited to any particular online news services, you can use any online newspaper that you can find on the WWW. Let's restrict ourselves, however, to English language newspapers for now. So, where to look? The New York Times and the Washington Post make a good start. Get the West Coast view from the Los Angeles Times. But then again, don't limit yourself to the US, take a look across the Pacific and browse the Japan Times. Why not. In fact, let's think global and find a newspaper by way of an online directory service, e.g. Online Newspaper Directory, World Newspaper Directory, NewsDirectory, NewsLink, ScienceDaily, PressDisplay, ... You might also want to visit the newswise web site, a search tool for reporters, or WurekAlert!, the media advisory service of the American Association for the Advancement of Science.

Your selection of topic and of its connectedness to chemistry will be judged by your peers. To further increase the quality of your selections of topic, the instructor will award 10 extra points to each member of three groups that, in his view, have done excellent jobs in article topic selection.

The URLs of newspaper article sometimes change and that can be a problem. Some online providers use a different link for their current editions and their archives. Use an online provider that does not change the URL. Also, use only an online provider that is accessible free of charge.

The MU Library has subscriptions to many electronic journals and newspapers. For example, The New York Times is available through the Nexis - Lexis Academic Database. The databases have powerful search facilities you might find useful. To determine whether MU has electronic access to specific magazines and journals, use the "Electronic Journals" link on the Library's gateway page: http://mulibraries.missouri.edu.

Make sure you have the text of the article stored in electronic form. If there are problems with the direct link, we can always make the article available via a local link. If that becomes necessary, please upload the html file of the news and name it as group#_article.html. A local link needs to contain href="../2004001/group#_article.html". The absolute URL of the article is http://ciitn.missouri.edu/testsite/www/2004001/group#_article.html.

Every news item should be connected to one of the book chapters covered in the course. As much as possible, let's try to get an equal distribution.

There will be three top project awards; these awards give 20 extra points to each member of these groups. Two of these awards will be made by the instructor. One of the awards goes to that project that wins the highest peer review score.

Guidelines for Interpretative Comments and Links

There are many approaches you may take in writing the 8interpretative comments. Make sure that you realize at all times for what audience you are writing.

Embedded Link Requirements and Construction. The interpretative comments should contain between 4 - 8 links to sites that provide information that deepen the understanding of the subject matter of the newspapers article and provide the best possible context definition. Several issues need to be considered in selecting these links. [a] Quality. Is the information provided by this link pertinent? Is the information presented well? Are layout, graphics, and animations used in the best possible way? How much can one learn from this site? [b] Credibility. Is the information provided by this link credible? Who wrote the link and what is the authors' agenda? A link written by the tobacco industry telling you that smoking is good for you might be suspicious. [c] Stability. Will this link exist in future? This question is much related to the quality issue. You should only use links that are likely to be stable.

To construct an embedded link you need to supply the URL of the site to which you want to link. This information is provided in a so-called "a-tag". The "a-tag" starts with <a> and ends with </a> and the word that will serve as the link will be between these tags. The URL is provided as part of the <a> tag in the "href" qualifier in the format <a href="URL">link-to-this-text</a>. The web site of CNN for example is located at http://www.cnn.com and a link to this web site could be provided by the statement <a href="http://www.cnn.com">CNN</a>. When you enter the text of your project in the online database, please do provide such "a-tags" whenever you want to embed a link.

Inclusion of Reaction Diagram Requirement. The interpretive comments section should contain one reaction diagram. Prepare the reaction diagram with the program ChemDraw and save the picture as a "gif" file. Name your gif file group#_rxn.gif or group#_pic#.gif (e.g. for group 9 the filename should be group9_rxn.gif or group9_pic1.gif) and upload your gif file to the CIITN web site. You should include the instruction <BR> <BR> <CENTER> <img src="../2004001/group#_rxn.gif"> <CENTER> <BR> <BR> in your interpretive comments at the place where the structure diagram should be inserted.

You can insert other images as well, e.g. other structure drawings, pictures of molecular models generated with Chem3D, sketches as part of Q & A, ... If you have several images, insert the others in the same fashion and again use a name of the type group#_whatever.gif.

Inclusion of 3D Molecular Model. (Not Required.) If you want to be really cool, include a molecular model in 3D (e.g. as in the visualization centers). Create the model in Chem3D and store it as a PDB file and name it for example group30_ASPIRIN.pdb. Upload this PDB file to the web site. Then create the file group30_ASPIRIN.html as follows and upload that file to us as well. Change the name of the PDB file, adjust the height and width percentages (percent of display screen covered by model window), play with the other qualifiers as you wish.

Include this link:

<a href="../212w03%%PR/group30_ASPIRIN.html">Model of Aspirin</a>

<html>
<body bgcolor=white>
<embed src="group30_ASPIRIN.pdb" frank=no name="molecule" 
startspin=no height=100% width=100% display3D="ball&stick" bgcolor=white
palette="foreground" script="zoom 150; set specular on; set ambient 40;
select *.h; color atoms [196,209,146];
select *.c; color atoms [26,80,70];
select *.n; color atoms [92,180,220];
select *.o; color atoms [220,37,110]; select all">
</html>

Guidelines for Questions and Answers

Asking good questions is not a simple task. In fact, to ask a good question about a problem leads halfway toward its solution. Asking questions is a key problem-solving skill and schools critical thinking.

You need to write 5 interesting questions. The questions should include as many of the following types as possible and question 5 has to be of the PSP type. You should identify the type of each of your questions by providing the type abbreviation in parentheses after the question.

You also need to provide answers to your questions. Answers to questions 1 - 4 will be rather factual and should be given as brief and concise as possible. Question 5 should be answered by a 1-page essay and this essay should be the result of a collaborative effort. There is no one correct answer to PSP questions and instead the quality of the essay will be decided by the depth of the analysis and the number and quality of arguments in favor and against the thesis. Note that you are answering your own question and you are in the wonderful position where you might consider improving the question as you work on finding an answer.

Identification of Components and Relationships (ICR) Questions in this category seek to emphasize pertinent pieces of information in the assignment. Questions of this type require the reader to identify essential pieces of information and identify their logical value (hypothesis, assumption, deduction, rationale, ...).
Seeking Clarification (SCL) Questions that fall in this category seek closer definition of material or clarifying background information.
Reasoning Using Quantitative Data (RQD) Questions in this category require the interpretation of graphs, tables, and figures or the manipulation of data therein.
Evaluation Process (EVL) Questions in this category require judgment as to whether the conclusions are justified by the evidence and whether the given interpretation is the only one interpretation possible. Questions in this category assess credibility.
Flexibility and Adaptability of Scientific Reasoning (FAR) Questions in this category require the extension of concepts and information presented to unfamiliar situations. Questions of this sort often are useful to assess whether "the point really came across".
Reasoning about Philosophical, Societal and Political Implications (PSP) Questions in this category usually will be open-ended and subjective. Questions in this category are meant to create discussion and not necessarily to lead to an immediate answer. Answers to questions of this type might be subject to ideology. Every news items is required to contain one such question as the last question.

Categories for Peer Review

The evaluations of the Collaborative Group Projects will be carried out by public and collaborative peer review. Each group is required to evaluate the projects of three other groups using the CIITN web tool.

Every group can assign up to 100 points to a project. The web tool will request you to assess various aspects of the group projects. For each criterion, you need to supply a number grade and a brief justification. More detailed justifications should be given if the assigned score is either very high or very low.

(1) Is the selected news topic a significant real world issue? (0-10 points): Is the selected topic of interest to broad segments of the audience in their everyday lives? Does the topic have continuing significance?
(2) Is the topic connected in a substantial way to Organic Chemistry? (0-10 points): Was the key organic chemical issue made clear? Was sufficient background provided to understand the chemistry? Have important compounds been described and characterized sufficiently. Is the pertinent reference section complete? If not, what additional references should be given?
(3) Is the news selected from a highly credible news source and is it timely? (0-10 points): Was the newspaper article published in a high quality newspaper? Did the author seem qualified to write on the science? Was the article published within the past year? Is the article too long or too short? Is the article exciting? It it too sensational?
(4) Do the editorial comments provide pertient information? (0-10 points): Do the editorial comments help to place the article in the greater context? Do the comments help to crytallize the key issues in a clear and authoritative manner? Is the reaction shown in the reaction diagram well selected? Is the chemical information provided pertinent?
(5) Are the editorial comments well written and organized? (0-10 points): Is the editorial written in good English (grammar and style) and in a well organized fashion (appropriate number of paragraphs of appropriate lengths and so on). Has a reaction diagram been included? Is the reaction diagram of good quality and chemically correct?
(6) Judge the quality and selection of the links embedded in the editorial? (0-10 points): Do the links satisfy the requirements for relevance, quality and stability? Did you learn something useful while visiting these links? Are the links embedded well into the editorial comments. Is it clear what the function of each link is and why these links were chosen to be included in the editorial comments?
(7) Do the questions address central issues rather than marginal details? (0-10 points): Does the project contain 5 questions? Are the question types specified? Do the questions vary as far as the categories of the questions are concerned. Is the last question a PSP question? Are the questions useful to deepen the connection between chemistry and the real world? Or are the questions bizarre and far-fetched?
(8) Are the questions written in an understandable and clear fashion? (0-10 points): Is it clear what is being inquired? Is it possible to work the problems in a reasonable time?
(9) Are the answers easy to understand and convincing? (0-10 points): Are the answers correct and complete? Could the answers be improved to be more useful? Half of the points in this category should be assigned based on the quality of the essay.
(10) Are all components integrated into an interesting and constructive project as a whole? (0-10 points): Would you consider this problem set fit for publication and use as an educational material by others elsewhere (most points), a useful assignment after some adjustments, or unfit for distribution and general classroom use (few points)?

A detailed rubric is provided on the webtool.

The evaluations from all peer evaluations will be averaged. Do take these evaluations seriously, you are affecting the grade of your fellow students. Try to be fair and objective. You must be comfortable with your judgment and be able to stand by it and defend it in public. Your evaluations have to be made in writing and they will be made public on the web.

The peer review will proceed in two stages. In the constructive peer review, your should focus on pointing out the strengths and making suggestions as to how the project could be improved. The projects will then be revised. The second peer review evaluates the revised and final version of the project. Usually, the scores of this second peer review will be higher than those of the first. Only this final score counts for the course grade.

Inter-Group Peer Review

You will receive via email the numbers of the groups to review. Group Numbers refer to the group numbers used in the CIITN database.

The basic idea is that most groups are reviewed by 3 other groups - the averaging will take the edge off of individual judgements - and that groups never evaluate their own evaluators - revenche is a bad strategy. Some groups will benefit from 4 reviews and some groups will have to prepare 4 reviews.