A Little List Of Things to Think About When Writing Scientific

Papers

• What is different with scientific papers (in any medium)?

• References (see at the end)

requirements

(1) adhere to the science and the scientific method processes and

testings(2) prepare material for the peer

review process, (3) provide significantly novel

information –some of which could be proprietary and should be protected ,

often due to the contracts with the financiers

requirements

• (4) economize with media space and readers time – media is costly

• (5) position the work presented in the proper past, present and future perspective,

• (6) review the work for accuracy, precision as well as any ethics conflicts etc..

What else

• Overall there is an agreement in the scientific community that papers should be clear, precise and concise, to the best level reasonably achievable. Nevertheless, good papers are expected to be smart and interesting, to a certain level almost entertaining.

Is it easy? No

• Writing scientific papers takes times, objectivity and good organizational skills. The fact that there should be no cluttering with excess wording and that sentences should be rationally crisp is sometimes interpreted as the lack of poetry in the scientific papers. However, the goal here is to guide the reader through often very energy consuming activity –the presentation of novel material - and the excess losses are not welcome.

SciFormat is a friend.

• Indeed, as the reviewer of a scientific paper you will probably have to answer the very common list of questions, including the following: is the work new, is it well communicated, is it accurate and precise, is it of interest to either the journal’s audience or to a larger scientific audience. Novel experimental results or results of theoretical modeling must be not only precise and accurate but should also be communicated in some an acceptable knowledge framework. Scientific paper format helps facilitate organization and uniformity of that communication framework. It is also a check list of need items for different levels of information to go to sometimes even different types of readers with various interests and reading styles.

How to strat ..?

• One should start with a good organization of the material and information that will be presented. Identify main goals. Make the assignment list. Thinking about and writing about the take-home messages is a good start although the writing of conclusion should be the last (as well as the final form of abstract). Outline and the flow diagram are good and helpful tactics. Cracking the tough nuts as soon as possible is also very helpful. Assignment of material you have to the different parts of your paper (introduction, results, methods) is also a good starting point. Think about the tasks you or collaborators need to complete .

• .

So you did something that looks good, what then?

• As you complete this step you may want to ask your real audience to read the draft paper. If you are not sure you may also want to consult a writing stylist to check your sentences and style. You want them to check if your writing has completed sentences and is easily understood. Grammar, spelling , syntax , all come here. As soon as the material goes off your desk you need to make sure that these bases are covered, if not you cannot say that readers understood what you wanted to communicate. Even if your work is novel and ideas great they will be lost. Respect precision and correct choice of words, including scientific terminology. Only if you all understand that terminology you can improve and change it.

After you received those comments..cut it….

• After receiving the comments from your audience you can make decisions on what to change and how far you want to go with your material at hands. In addition, this is the time also to consult the literature –if you have not done that before. The points that did not go through need most attention. Make them more clear and simplifier if they are to complex. Do not sacrifice precision and accuracy , work harder on explaining in more adequate words. On the other hand eliminate the clutter and all that is not necessary. Make sentences shorter and contract the paragraphs-most likely that is what is needed and can be done in a second draft. If you, like many writers write first draft more elaborately, it is time now to make it more concise without forgetting the message. Ask yourself if analogies, phrases, jokes, jargon etc. are really necessary or are they even accurate?

Two communication notes:

• If you are not happy with the outcome of the comments revisit your thinking and facts first then communication. Writing is only the messenger, although important it cannot substitute the substance .

• Remember you can destroy a good material by poor communication, but you cannot make a good scientific paper without a good research work. Also you may be perfect in following the rules you found somewhere but your readers will still not like it. The scientific paper must be interesting and novel to the readers.

Before we go to the format of the SciPaper…

• We will go step by step

…..let us look at some general do-s and do not-s

• You do not have to try to impress people by using words most people have never heard of.

• Do not use colloquial speech, slang, or "childish" words or phrases.

• -Do not use contractions: for example, "don't" must be "do not" and "isn't" must be "is not" etc.

• -- Do not use abbreviations in the text except for units of measure and those that are referenced

Referencing facts and work in time:

• - Research papers reflect work that has been completed, therefore use the past tense throughout your paper (including the Introduction) when referring to the actual work that you did, including statements about your expectations or hypotheses. Use the past tense, as well, when referring to the work of others that you may cite.

Style

• - If there is one stylistic area where scientific disciplines and journals vary widely, it is the use of first vs. third person constructions. Some disciplines and their journals (e.g., organismal biology and ecology) have moved away from a very strict adherence to the third person construction, and permit limited use of the first person in published papers. Other disciplines, especially the biomedical fields, still prefer the third person constrcution. Limit your use of first person construction (i.e., " I (or we) undertook this study ....): usually it is most acceptable in the Introduction and Discussion sections, and then only to a limited extent. Use first person in the methods sparingly if at all, and avoid its use in the results.

Verbs

• Use active verbs whenever possible; writing that overly uses passive verbs (is, was, has, have, had) is deadly to read and almost always results in more words than necessary to say the same thing.

• ACTIVE: "the reaction consumed oxygen at a higher rate..."

• PASSIVE: "oxygen was consumed by the mouse at a higher rate.."

What not to do ever

• -Plagiarism (use of others words, ideas, images, etc. without citation) is not to be tolerated and can be easily avoided by adequately referencing any and all information you use from other sources. In the strictest sense, plagiarism is representation of the work of others as being your work. Paraphrasing other's words too closely may be construed as plagiarism in some circumstances. In journal style papers there is virtually no circumstance in which the findings of someone else cannot be expressed in your own words with a proper citation of the source. Refer to LSU documents about it. If you are unclear about what constitutes plagiarism, please confer with your instructor.

Tense (a suggestion)

• Past, present, and future tense. Results described in your paper should be described in past tense (you’ve done these experiments, but your results are not yet accepted “facts”). Results from published papers should be described in the present tense (based upon the assumption that published results are “facts”). Only experiments that you plan to do in the future should be described in the future tense.

3 vs 1, and One

• Third vs first person. It is OK to use first person in scientific writing, but it should be used

• sparingly – reserve the use of first person for things that you want to emphasize that “you” uniquely did (i.e. not things that many others have done as well). Most text should be written in the third person to avoid sounding like an autobiographical account penned by a narcissistic author. However, it is better to say “It is possible to ..” than to say “One could ...”. Writing that uses the impersonal pronoun “one” often seems noncommittal and dry. In addition, inanimate objects (like genes, proteins, etc) should be described in third person, not with anthropomorphic or possessive terms (e.g., instead of saying “its att site”, say “the chromosomal att site”).

No substance…….

• Empty phrases. Avoid using phrases that do not contribute to understanding. For example, the following phrases could be shortened (or completely deleted) without altering the meaning of a sentence: “the fact that ...” (delete); “In order to ...” (shorten to simply “To ...”). Likewise, the title of a table of results does not benefit from the preface “Results of ...”. In short, don’t use more words than you need to make your point.

Always Specify

• Specify. If several expressions modify the same word, they should be arranged so that it is explicit which word they modify. It is common to use a pronoun such as “it” or “they” to refer to a concept from the previous sentence. This is OK as long as there is only one concept that “it” or “they” means. However, if there are more than one concepts it is easy for the reader to get confused about what the pronoun is meant to specify (even if you know which one you mean). It is better to error on the side of redundancy by repeating the concept in subsequent sentences, than to take the chance of confusing the reader. Don’t make the reader guess what you mean.

“ “• Parentheses. Avoid them

Check again and again..

• Proofreading: Always spellcheck your paper and carefully proofread your paper before submission. In addition to checking for errors and typos, read your paper to yourself as if you were reading it out loud to ensure that the wording and sentence construction is not clumsy.

•  

..Back to Sci Format

• T,A, I, R, D ,C,R

Title, Authors' Names, and Institutional Affiliations

• Your paper should begin with a Title that describes the contents of the paper. Use descriptive words that you would associate strongly with the content of your paper: the molecule studied, the organism used or studied, the treatment, the location of a field site, the response measured, etc. A majority of readers will find your paper via electronic database searches and those search engines key on words found in the title.

Title

• The title should be centered at the top of page 1 (DO NOT use a title page - it is a waste of paper for our purposes); the title is NOT underlined or italicized.

• the authors' names (PI or primary author first) and institutional affiliation are double-spaced from and centered below the title. When more then two authors, the names are separated by commas except for the last which is separated from the previous name by the word "and".

ABSTRACT ( a definition)

• Abstract: An abstract is a short and to the point (one paragraph) summary of the entire paper. The abstract should briefly describe the question posed in the paper, the methods used to answer this question the results obtained, and the conclusions. It should be possible to determine the major points of a paper by reading the abstract. Although it is located at the beginning of the paper, it is easiest to write the abstract after the paper is completed.

• An abstract summarizes, in one paragraph (usually), the major aspects of the entire paper in the following prescribed sequence:

• the question(s) you investigated (or purpose), (from Introduction)

– state the purpose very clearly in the first or second sentence.

• the experimental design and methods used, (from Methods)

– clearly express the basic design of the study.

– Name or briefly describe the basic methodology used without going into excessive detail-be sure to indicate the key techniques used.

• the major findings including key quantitative results, or trends (from Results)

– report those results which answer the questions you were asking

– identify trends, relative change or differences, etc.

• a brief summary of your interpetations and conclusions. (from Discussion)

– clearly state the implications of the answers your results gave you.

Simple rule

• How do you know when you have enough information in your Abstract? A simple rule-of-thumb is to imagine that you are another researcher doing an study similar to the one you are reporting. If your Abstract was the only part of the paper you could access, would you be happy with the information presented there?

Not to do

• The Abstract SHOULD NOT contain:

• lengthy background information,

• references to other literature,

• elliptical (i.e., ending with ...) or incomplete sentences,

• abbreviations or terms that may be confusing to readers,

• any sort of illustration, figure, or table, or references to them.

INTRO

• Introduction: The Introduction should (i) describe the question tested by the experiments described in the paper, (ii) explain why this is an interesting or important question, (iii) describe the approach used in sufficient detail that a reader who is not familiar with the technique will understand what was done and why, and (iv) very briefly mention the conclusion of the paper.

• Establish the context of the work being reported. This is accomplished by discussing the relevant literature (with credit/references) and summarizing our current understanding of the problem you are investigating;

• State the purpose of the work in the form of the hypothesis, question, or problem you investigated; and,

• Briefly explain your rationale and approach and, whenever possible, the possible outcomes your study can reveal

INTRO

• Quite literally, the Introduction must answer the questions, "What was I studying? Why was it an important question? What did we know about it before I did this study? How will this study advance our knowledge?"

• Begin your Introduction by clearly identifying the subject area of interest.

• Establish the context by providing a brief and balanced review of the pertinent published literature that is available on the subject.

• What literature should you look for in your review of what we know about the problem?

• Be sure to clearly state the purpose and /or hypothesis that you investigated.

• Provide a clear statement of the rationale for your approach to the problem studied.

• Materials and Methods: The Materials and Methods section should s describe what was actually done. It should include description of the techniques used so someone could figure out what experiments were actually done. The details of a published protocol do not need to be reproduced in the text but an appropriate reference should be cited

M&M

• the the physical objects (s) studied if a field study

• the experimental OR sampling design

• the protocols, i.e., how the experimental procedures were carried out, and,

• how the data were analyzed (qualitiative analyses and/or statistical procedures used) modeled and what computer programs used

Style

• Style: The style in this section should read as if you were verbally describing the conduct of the experiment. You may use the active voice to a certain extent, although this section requires more use of third person, passive constructions than others. Avoid use of the first person in this section. Remember to use the past tense throughout - the work being reported is done, and was performed in the past, not the future. The Methods section is not a step-by-step, directive, protocol as you might see in your lab manual.

RESULTS• /Results: Begin each paragraph with an opening sentence that tells the

reader what question is being tested in the experiments described in that paragraph. Write the opening sentence in bold font for emphasis. (Sometimes a complete sentence is used and sometimes a short phrase is used

• – either style is OK but the style should be used consistently throughout the manuscript.) Any results that include multiple data points that are critical for the reader to evaluate the experiment should be shown in tables or figures. However, the results should be summarized in ccompanying text. When referring to a particular table or figure, they should be capitalized (e.g., Table 1, Figure 6, etc.) The text of the Results section should be succinct but should provide the reader with a summary of the results of each table or figure. Not all results deserve a separate table or figure. As a rule of thumb, if there are only a few numerical results or a simple conclusion describe the results in the text instead of in a table or figure. Your paper should focus on what worked, not things that did not work (unless they didn’t work for reasons that are interesting and provide biological insights).

• Style: Write the text of the Results section concisely and objectively. The passive voice will likely dominate here, but use the active voice as much as possible. Use the past tense. Avoid repetitive paragraph structures. Do not interpret the data here. The transition into interpretive language can be a slippery slope. Consider the following two examples:

Organization

• Organize the results section based on the sequence of Table and Figures you'll include. Prepare the Tables and Figures as soon as all the data are analyzed and arrange them in the sequence that best presents your findings in a logical way. A good strategy is to note, on a draft of each Table or Figure, the one or two key results you want to addess in the text portion of the

What not to do

• Do not reiterate each value from a Figure or Table - only the key result or trends that each conveys.

• Do not present the same data in both a Table and Figure - this is considered redundant and a waste of space and energy. Decide which format best shows the result and go with it.

• Do not report raw data values when they can be summarized as means, percents, etc

IMPORTANT

• Present the results of your experiment(s) in a sequence that will logically support (or provide evidence against) the hypothesis, or answer the question, stated in the

There is a difference between NO results and NEGATIVE results

• Report negative results - they are important! If you did not get the anticipated results, it may mean your hypothesis was incorrect and needs to be reformulated, or perhaps you have stumbled onto something unexpected that warrants further study. In either case, your results may be of importance to others even though they did not support your hypothesis. Do not fall into the trap of thinking that results contrary to what you expected are necessarily "bad data". If you carried out the work well, they are simply your results and need interpretation. Many important discoveries can be traced to "bad data".

Discussion

• Discussion: Do not simply restate the results — explain your conclusions and interpretations of the Results section. How did your results compare with the expected results? What further predictions can be gleaned from the results?

DISCUSSION

• The function of the Discussion is to interpret your results in light of what was already known about the subject of the investigation, and to explain our new understanding of the problem after taking your results into consideration. The Discussion will always connect to the Introduction by way of the question(s) or hypotheses you posed and the literature you cited, but it does not simply repeat or rearrange the Introduction. Instead, it tells how your study has moved us forward from the place you left us at the end of the Introduction.

ASK

• Do your results provide answers to your testable hypotheses? If so, how do you interpret your findings?

• Do your findings agree with what others have shown? If not, do they suggest an alternative explanation or perhaps a unforseen design flaw in your experiment (or theirs?)

• Given your conclusions, what is our new understanding of the problem you investigated and outlined in the Introduction?

• If warranted, what would be the next step in your study, e.g., what experiments would you do next?

STYLE

• Style: Use the active voice whenever possible in this section. Watch out for wordy phrases; be concise and make your points clearly. Use of the first person is okay, but too much use of the first person may actually distract the reader from the main points.

HOW

• Approach: Organize the Discussion to address each of the experiments or studies for which you presented results; discuss each in the same sequence as presented in the Results, providing your interpretation of what they mean in the larger context of the problem. Do not waste entire sentences restating your results; if you need to remind the reader of the result to be discussed, use "bridge sentences" that relate the result to the interpretation:

• You must relate your work to the findings of other studies - including previous studies you may have done and those of other investigators.

• Do not introduce new results in the Discussion.

End