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Corso di comunicazione scientifica 2008/2009

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Scuola di DottoratoScienze della Terra

Corso di comunicazione scientificaaa 2008-2009

How to write a scientific paper

G. ArtioliUNIPD


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Scientific research demands precision. Scientific writing should reflect this precision in the form

of clarity.

fuzzy writing reflects fuzzy thinking

The first task to accomplish as you begin the process ofwriting is to order and organize the information you wish to present.

• why do I wish to write a paper (purpose)• what do I want to communicate?

ideas/models (new ways of looking at objects)techniques/methods (object measurement)facts/results (object manipulation)


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• A well-written scientific paper explains

• the scientist's motivation for doing an experiment• the experimental design and execution• the meaning of the results

• Their purpose is to inform an audience of other scientists about an important issue and to documentthe particular approach they used to investigate that issue.


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Types of documents

abstracts (meetings)thesisscientific papers in journalsscientific reviews / books / chapters of multi-authored booksreportsresearch proposals for

funding personnel instrument beamtime allocation


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Scientific Research

The purpose of science is to get paid for doing fun stuff (Schulman et al. 1991).Nominally, science involves discovering something new about the Universe, but this isn't really necessary. What is really necessary is a grant. In order to obtain a grant, your application must state that the research will discover something incredibly fundamental. The grant agency must also believe that you are the best person to do this particular research, so you should cite yourself both early and often. Feel free to cite other papers as well so long as you are on the author list.

Once you get the grant, your university, company, or government agency will immediately take 30 to 70% of it so that they can heat the building, pay for Internetconnections, and purchase large yachts.

Now it's time for the actual research. You will quickly find out that (a) your project is not as simple as you thought it would be and (b) you can't actually solve the problem.However -- and this is very important -- you must publish anyway.

E.R. Schulman (1996) “How to write a scientific paper”Annals of Improbable Research, 2 (5), pp 8.

http://improbable.com/airchives/paperair/volume2/v2i5/v2i5-toc.html


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Scientific Writing

You've spent years on a project and have finally discovered that you can't solve the problem you set out to solve. Nonetheless, you have a responsibility to present your research to the scientific community. Be aware that negative resultscan be just as important as positive results, and also that if you don't publish enough you'll never be able to stay in science.




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information content

communication skillsand style

language


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Checklist BEFORE writing the paper:

who will be reading the paper ? (relevant community)peers / refereesstudentsevaluating committee / paneltype and diffusion of the journal

selection of the information to include (content) [list of major points, checklist of topics, list of figures, …)

organization of the materials (structure)

selection of the style / level / depth / background

choice of the journal (IP, citations, …)


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Choice of the journal may be influenced by severalparameters:

• quality and impact• diffusion in the community• tradition• editorial board• review system• page charges• technical requirements (including space)• language


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Why God Will Never Get Tenure

1. He published only one book.2. It was in Hebrew.3. It had no references.4. He did not publish it in referenced journals.5. Some doubt He even wrote it Himself.6. He is not known for His cooperative work7. Sure, He created the world, but what has He done lately?8. He did not get permission from any review board to work with human subjects.9. When one experiment went awry, He tried to cover it up by drowning all the subjects.10. When sample subjects do not behave as predicted, He deletes the whole sample.11. He rarely comes to class - and just tells His students to read the Book.12. It is rumored that He sometimes lets His Son teach the class.13. Although He only has 10 requirements, students often fail His tests.14. He expelled His first two students for learning.15. His office hours were infrequent and usually held on a mountain top.


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Scientific papers are written in a style that is exceedingly clear and concise.

• Your writing should be in complete sentences and easily understood

• Make sure that every paragraph has a clear topic sentence and that theparagraph content supports the topic

• It should conform to the conventions of standard written English(sentence form, grammar, spelling, etc.)

• Remember always that scientific terminology very often has precisemeaning. Be certain you choose your words correctly and wisely. Use them appropriately and consistently.


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• You do not have to try to impress people by using words most people have never heard of. Many published articles are like this, and they are poor paperson account of it.• 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.• Specific formats, such as abbreviations, acronyms, units, etc. are usually specified by each journal’s “instruction for authors”• Research papers reflect work that has been completed, therefore use the past tense throughout your paper (including the Introduction) when referring to theactual work that you did, including statements about your expectations orhypotheses. Use the past tense, as well, when referring to the work of others that you may cite.• Limit your use of first person construction• 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 morewords than necessary to say the same thing.


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… The task of gathering relevant information is being constantly frustrated by the disproportion between the flood of information and the little time available to sorting it out. Our conclusion is that it is the writer’s duty to do his best to help the potential readers extract the relevant information from his paper. The writer should spend much time in writing the paper so that the potential readers can spend much lesstime in the process of extracting the information relevant to them out of the paper. …

O. Goldreich (2004) “How to write a paper”http://www.wisdom.weizmann.ac.il/~oded/writing.html

How to serve the reader’s needs:

• Focusing on the readers’ needs rather than on the writer’s desires• Awareness to the knowledge level of the reader• Balancing between contradictory requirements• Making reading a non-painful experience

… we urge the writers to try to imagine the difficulties they would have had if they had tried to read the paper, just being written, half a year ago ...


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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 ofothers 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 whichthe findings of someone else cannot be expressed in your own words with a proper citation of the source.

scientific fraud, examples


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A scientific paper is a written report describing original research results whose format has been defined by centuries of developing tradition, editorial practice, scientific ethics and the interplay with printing and publishing services. The result of this process is that virtually every scientific paper has:

• title• list of authors and affiliations• (keywords)• abstract• introduction• materials and methods• results• discussion• (conclusions)• acknowledgements• references• annexes (appendixes, deposited data)


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TitleA title should be the fewest possible words that accurately describe thecontent of the paper. Omit all waste words such as "A study of ...", "Investigations of ...", "Observations on ...", etc.

Indexing and abstracting services depend on the accuracy of the title,extracting from it keywords useful in cross-referencing and computersearching.

An improperly titled paper may never reach the audience for which it was intended, so be specific. If the study is of a particular species or chemical,name it in the title. If the study has been limited to a particular region or system, and the inferences it contains are similarly limited, then name theregion or system in the title.

Do not be afraid to be grammatically creative.


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Here are some variations on a theme, all suitable as titles:

THE EFFECT OF TEMPERATURE ON GERMINATION OF CORN

DOES TEMPERATURE AFFECT GERMINATION OF CORN?

TEMPERATURE AND CORN GERMINATION: IMPLICATIONS FOR AGRICULTURE

Sometimes it is possible to include the principal result or conclusion in thetitle:

HIGH TEMPERATURES REDUCE GERMINATION OF CORN


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List of authors

Use the same name to avoid mis-referencing and mis-counting in citations.

The common tradition in some communities is to list authors in alphabetical order. This tradition seems linked to the typical situation in which each author has made a fair (if not significant) contribution to the work.In other disciplines main autorship may be dictated by hierarchy in laboratory managments, funding, etc.

Minor contributors and technical assistants may be inserted in the acknowledgement section.


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AbstractThe abstract should be as informative as possible and yet not too cumbersomeor too long. Given the limited space, typically, one cannot (and should not)provide a rigorous definition and detailed statement of results in the abstract.Instead, one should provide a high-level description of the contents of thepaper. One should bear in mind that, for a variety of reasons, some people willonly read the abstract and it should enable these people with as much information as possible. A well-prepared abstract enables the reader to identifythe basic content of a document quickly and accurately, to determine its relevance to their interests, and thus to decide whether to read the document inits entirety. The abstract should be a self-contained unit capable of being understood without the benefit of the text. The abstract concisely states the principal objectives and scope of the investigation where these are not obvious from thetitle. More important, it concisely summarises the results and principal conclusions. Do not include details of the methods used unless the study is methodological, i.e. primarily concerned with methods.

The abstract may be the last section to be written


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Introduction

The function of an introduction is to present the question being asked and place it in the context of what is already known about the topic. Backgroundinformation that suggests why the topic is of interest and related findings by other scientists are usually mentioned here. In other words, this section should contain:1. a description of the nature of the problem and current state of knowledge orunderstanding at the beginning of the investigation (background);2. a statement of the purpose, scope, and general method of investigation inyour study;3. hypothesis/hypotheses and predictions

The Introduction is meant to introduce the reader to your research, not summarize and evaluate all past literature on the subject (which is the purposeof a review paper). An important function of the introduction is to establish thesignificance of your current work: Why was there a need to conduct thestudy? Having introduced the pertinent literature and demonstrated the need forthe current study, you should state clearly the scope and objectives


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Introduction

Scientific papers (e.g., ……) are an important--though poorly understood--method ofpublication. They are important because without them scientists cannot get money fromthe government or from universities. They are poorly understood because they are not written very well (see, for example, … and selected references therein). An excellent example of the latter phenomenon occurs in most introductions, which are supposed tointroduce the reader to the subject so that the paper will be comprehensible even if thereader has not done any work in the field.

The real purpose of introductions, of course, is to cite your own work (e.g., ….), the work of your advisor (e.g., …), the work of your spouse (e.g., …), the work of a friendfrom college (e.g., …), or even the work of someone you've never met, as long as your name happens to be on the paper (e.g., …). Note that these citations should not be limited to refereed journal articles (e.g., …), but should also include conference proceedings (e.g., …), and other published or unpublished work (e.g…).




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Materials and methods

The main purpose of the 'Materials and Methods' section is to provide enough detail for a competent worker to repeat your study and reproduce theresults. The scientific method requires that your results be reproducible, andyou must provide a basis for repetition of the study by others.

Be precise in describing measurements and include errors of measurement. Ordinary statistical methods should be used without comment; advanced orunusual methods may require a literature citation. Show your materials andmethods section to a colleague. Ask if they would have difficulty in repeating your study.


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Results

The section provides data in tables, figures and text format. The function of this section is to summarize general trends in the data without comment, bias, orinterpretation. Statistical tests applied to your data are reported in this section although conclusions about your original hypotheses are saved for the Discussion section. Do NOT interpret the data in this section.Data may be presented in figures and tables, but this may not substitute for averbal summary of the findings. The text should be understandable by someone who has not seen your figures and tables.

The results should be short and sweet. Do not say "It is clearly evident from Fig. x that crystal chemical complexity increases during the process". Say instead“The process increased the crystal chemical complexity (Fig. x)". However, do not be too concise. Readers cannot be expected to extract important trends from the data unaided.


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DiscussionInterpretation of the results is the focus: You should discuss what principles have been established or reinforced; what generalisations can be drawn; how your findings compare to the findings of others or to expectations based onprevious work; and whether there are any theoretical/practical implications ofyour work.

When you address these questions, it is crucial that your discussion rests firmlyon the evidence presented in the results section. Refer briefly to your results to support your discussion statements. Do not extend your conclusions beyond those that are directly supported by your results.

A brief paragraph of speculation about what your results may mean in a general sense is usually acceptable, but should not form the bulk of the discussion. Be sure to address the objectives of the study in the discussion and to discuss thesignificance of the results. Don't leave the reader thinking "So what?" End thediscussion with a short summary or conclusion regarding the significance of the work.

Do NOT ignore negative or apparently uninterpretable results !!


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The Discussion should contain at least:

1. the relationship between the results and the original hypothesis, i.e., whether they support the hypothesis, or cause it to be rejected or modified.

2. an integration of your results with those of previous studiesin order to arrive at explanations for the observed phenomena.

3. possible explanations for unexpected results andobservations, phrased as hypotheses that can be tested be realistic experimental procedures, which you should describe.


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Conclusions

Some people tend to think that each paper should end with conclusions and/orsuggestions for further work. We strongly disagree with this opinion, and seelittle use in a “conclusion section” that merely re-iterates things said in the abstract and/or in the introduction. Similarly, we see no point in listing well-known open problems or re-iterating questions that were already raised in the introduction. On the other hand, we do value a conclusion section that contains high-levelmaterial that better fits after the main part of the paper (and thus is not placed in the introduction). Similarly, for raising important questions that are moreappealing after reading the technical part (even if they were raised already in the technical part but not in the introduction).

To summarize: There are papers that may benefit from a conclusion section, but they are relatively few (say, less than 5% of the papers). Certainly, theinclusion of a conclusion section should not be the default.


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Conclusions

The conclusion section is very easy to write: all you have to do is to take your abstractand change the tense from present to past. It's considered good form to mention at leastone relevant theory only in the abstract and conclusion. By doing this, you don't have to say why your experiment does (or does not) agree with the theory, you merely have tostate that it does (or does not).

We (meaning I) presented observations on the scientific publishing process which(meaning that) are important and timely in that unless I have more published papers soon, I will never get another job. These observations are consistent with the theory that it is difficult to do good science, write good scientific papers, and have enough publications to get future jobs.




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Acknowledgements

You should acknowledge the assistance of those who helped with your study:mentors, financial supporters, teachers, scientists, proofreaders, typists, etc.You should keep this section brief, but be sure to identify major contributions.

Thanks to those who helped or funded the research - be sure to thank everyone that helped you with ideas, collect data in the lab or field, analyze data, creategraphics or prepared the paper-.


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References

When you refer to the work of another scientist in your paper, you mustindicate the source of that information. That way, someone reading your paper will realize that the information comes from another project. Also, the reader may wish to examine other experiments, such as the one you cited. Failure to cite the work of another scientist (that you used in writing your paper) results in a serious offense (plagiarism). We should never mislead the reader by unjustified or inaccurate credits attributed to other works.

The preferred method of citing a reference in text in most scientific papers is the author-date system. All literature cited in the body of your paper must be listed in your Literature Cited section, and all references in the list must be cited in the text. Be sure to include enough information that each sourcecan be identified and located.

Some reviewers appreciate the use of authoritative references (textbooks), rather than short articles and short reports.


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Scientific progress depends on the communication of information that can be trusted, and the peer review process is a vital part ofthat system


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Readers that may be assumed to be critical are reviewers. They typically point out problems and make suggestions. One should not necessarily follow the reviewer’s suggestions, but one must always bear in mind that these suggestions indicate problems in the current write-up. It may be that the reviewer is not suggesting a good solution to these problems (or that the authors has a better a solution), but for sure there is a problem.

That is, the working assumption (which is almost always correct) is that any comment of areviewer indicates a problem in the write-up: Reviewers are typically not idiots, and one canlearn even from idiots!

Scientific Publishing

You've written the paper, and now it's time to submit it to a scientific journal. The journal editor will pick the referee most likely to be offended by your paper, because then at least the referee will read it and get a report back within the lifetime of the editor.Referees who don't care one way or the other about a paper have a tendency to leave manuscripts under a growing pile of paper until the floor collapses, killing the 27 Englishgraduate students who share the office below.




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Technical Rigor: Evaluate whether, or to what extent, the data and methods substantiate the conclusions and interpretations. Ifappropriate, indicate what additional data and information areneeded to validate the conclusions or support the interpretations.

Novelty: Indicate in your review if the conclusions are novel or are too similar to work already published.

The reviewer should be:

• impartial (no conflict of interest)• qualified• independent (no close relation with authors)• timely• anonymous• respect confidentiality


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Useful links:

•http://www.scidev.net/en/science-communication/practical-guides/how-do-i-write-a-scientific-paper-.html

•http://classweb.gmu.edu/biologyresources/writingguide/ScientificPaper.htm

•http://www.pitt.edu/~super1/lecture/lec1331/index.htm

•http://abacus.bates.edu/~ganderso/biology/resources/writing/HTWtoc.html

•http://www.uaf.edu/csem/ashsss/paper_guidelines.html


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And finally the assignments:

(1) Prepare your annual oral presentation (12-14 november) according to Giulio’s guidelines• 1st, 2nd year: 20 minutes (15+5)• 3rd year: 30 minutes (25+5)

(2) Prepare an extended abstract of your activity:• Deadline 15 october 2008 16 [email protected] discussion• 2 written pages (appx. 1000 words)• Including title/abstract (150 words)/references (10 max) /1

figure

(3) Attach a summary of last year’s activity (1 page)

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