How to write a How to write a scientific paperscientific paper

Prof. Dr. Mohamed MokhtarProf. Dr. Mohamed Mokhtar

A scientific experiment is not A scientific experiment is not complete until the results complete until the results have been have been publishedpublished and and understood.understood.

A scientific paper is a written A scientific paper is a written and published report and published report describing describing original research original research results.results.

What is Scientific What is Scientific WritingWriting The purpose of scientific writing is The purpose of scientific writing is

to communicate new scientific to communicate new scientific findings findings

Thus it has to be clear, simple Thus it has to be clear, simple and well ordered communication and well ordered communication to transmit new scientific findingsto transmit new scientific findings

Scientific writing must use proper Scientific writing must use proper English which gives the sense in English which gives the sense in the fewest short wordsthe fewest short words

Origins of Scientific WritingOrigins of Scientific Writing Knowledge is lost without written recordsKnowledge is lost without written records Cave paintings and inscriptions were the first Cave paintings and inscriptions were the first

attempts to leave recordsattempts to leave records About 2000 BC, Papyrus paper was used as a About 2000 BC, Papyrus paper was used as a

medium of communication medium of communication In 190 BC, parchment made from animal skin In 190 BC, parchment made from animal skin

came into usecame into use In 105 AD, the Chinese invented paperIn 105 AD, the Chinese invented paper Knowledge could not be widely circulated with no Knowledge could not be widely circulated with no

effective duplicationeffective duplication In 1100 AD, the Chinese invented movable typeIn 1100 AD, the Chinese invented movable type In 1455 AD, Gutenberg printed his 42-line Bible In 1455 AD, Gutenberg printed his 42-line Bible

from movable type on a printing pressfrom movable type on a printing press By the year 1500 thousands of copies of By the year 1500 thousands of copies of

hundreds of books (called “incunabula”) were hundreds of books (called “incunabula”) were printedprinted

In 1665, the first scientific journals were In 1665, the first scientific journals were publishedpublished

IMRAD StoryIMRAD Story(Introduction, Methods, Results and (Introduction, Methods, Results and

Discussion)Discussion)

Early journals published Early journals published descriptivedescriptive papers (still papers (still used in case reports, geological surveys etc..)used in case reports, geological surveys etc..)

By the second half of the 19By the second half of the 19thth century, century, reproducibility of experimentsreproducibility of experiments became a became a fundamental principle of the philosophy of science.fundamental principle of the philosophy of science.

The The methods sectionmethods section became all important since became all important since Louis Pasteur confirmed the germ theory of diseaseLouis Pasteur confirmed the germ theory of disease

IMRAD organization of a scientific paper started to IMRAD organization of a scientific paper started to develop develop

IMRAD format slowly progressed in the latter half of IMRAD format slowly progressed in the latter half of the 19the 19thth century century

IMRAD FormatIMRAD Format

II = = IntroductionIntroduction, what question , what question (problem) was studied(problem) was studied

MM = = MethodsMethods, how was the problem , how was the problem studiedstudied

RR = = ResultsResults, what are the findings, what are the findings AA = and = and DD = = DiscussionDiscussion, what do these , what do these

findings meanfindings mean

Organization of a Organization of a scientific paperscientific paper

The most common is the IMRADThe most common is the IMRAD If a number of methods were used If a number of methods were used

to achieve directly related results:to achieve directly related results:

M + R = Experimental sectionM + R = Experimental section The results are so complex that they The results are so complex that they

need to be immediately discussed:need to be immediately discussed:

R + D = Results and Discussion R + D = Results and Discussion sectionsection

What is a scientific What is a scientific paperpaper

A scientific paper is a written and A scientific paper is a written and published report describing original published report describing original research results.research results.

1.1. It must be the first publication of original It must be the first publication of original research results,research results,

2.2. In a form whereby peers of the author In a form whereby peers of the author can repeat the experiments and test the can repeat the experiments and test the conclusions, andconclusions, and

3.3. In a journal or other source document In a journal or other source document readily available within the scientific readily available within the scientific communitycommunity

Definition of Scientific Definition of Scientific paperpaper

An accepted original scientific publication An accepted original scientific publication containing scientific information to enable containing scientific information to enable peers:peers:

1.1. To assess observationsTo assess observations

2.2. To repeat experimentsTo repeat experiments

3.3. To evaluate intellectual processesTo evaluate intellectual processes

4.4. Must have an impactMust have an impact

5.5. Available to scientific community without Available to scientific community without restrictionrestriction

6.6. Available for regular screening by one or Available for regular screening by one or more of the major recognized secondary more of the major recognized secondary services (Biological abstracts, Index services (Biological abstracts, Index Medicus, Pub Med etc…)Medicus, Pub Med etc…)

Some important Some important LanguageLanguage points:points:

Poor experimentation cannot be Poor experimentation cannot be masked by brilliant writing; masked by brilliant writing; however, however, poor writing can mask poor writing can mask brilliant experimentationbrilliant experimentation

Avoid complex sentence structureAvoid complex sentence structure Use simple and clear EnglishUse simple and clear English Always keep in mind that Always keep in mind that the the

paragraphparagraph is the essential unit of is the essential unit of thoughtthought

Before Starting to Before Starting to Write the PaperWrite the Paper

Record your readings (results)Record your readings (results) Make tablesMake tables Draw graphsDraw graphs Keep file to record summaries of results Keep file to record summaries of results

and any observation however and any observation however insignificantinsignificant

Date the filesDate the files Revise your readings, you may need to Revise your readings, you may need to

repeat an experiment while you still repeat an experiment while you still have the materials.have the materials.

Write ideas when ever they come to youWrite ideas when ever they come to you

Essential Parts of a Scientific Essential Parts of a Scientific paperpaper

TitleTitle: Describe concisely the core contents of the : Describe concisely the core contents of the paperpaper

AbstractAbstract: Summarize the major elements of the : Summarize the major elements of the paperpaper

IntroductionIntroduction: provide context and rationale for : provide context and rationale for the studythe study

MaterialsMaterials: Describe the experimental design so it : Describe the experimental design so it is reproducibleis reproducible

MethodsMethods: Describe the experimental procedures: Describe the experimental procedures ResultsResults: Summarize the findings without : Summarize the findings without

interpretationinterpretation DiscussionDiscussion: Interpret the findings of the study: Interpret the findings of the study SummarySummary: Summarize the findings: Summarize the findings AcknowledgementAcknowledgement: Give credit to those who : Give credit to those who

helped youhelped you ReferencesReferences: List all scientific papers, books and : List all scientific papers, books and

websites that you cited websites that you cited

The TitleThe Title

A good title is defined as the fewest A good title is defined as the fewest possible words that possible words that adequately adequately describedescribe the contents of the paper. the contents of the paper.

The title is extremely important and must The title is extremely important and must be chosen with great care as it will be be chosen with great care as it will be read by thousands, whereas few will read read by thousands, whereas few will read the entire paperthe entire paper

Indexing and abstracting of the paper Indexing and abstracting of the paper depends on the accuracy of the title. An depends on the accuracy of the title. An improperly titled paper will get lost and improperly titled paper will get lost and will never be read.will never be read.

Titles should neither be too short nor too Titles should neither be too short nor too long as to be meaninglesslong as to be meaningless

Waste words (studies on, investigations Waste words (studies on, investigations on, a, an, the etc) should not be used.on, a, an, the etc) should not be used.

Syntax (word order) must be very Syntax (word order) must be very carefully consideredcarefully considered

It should contain the keywords that It should contain the keywords that reflect the contents of the paper.reflect the contents of the paper.

It should be meaningful and not generalIt should be meaningful and not general It should be concise, specific and It should be concise, specific and

informativeinformative It should capture the fundamental nature It should capture the fundamental nature

of the experiments and of the experiments and findingsfindings

ExamplesExamples

1.1. Action of Antibiotics on BacteriaAction of Antibiotics on Bacteria Action: should be definedAction: should be defined Antibiotics: should be listedAntibiotics: should be listed Bacteria: should be listedBacteria: should be listed2.2. Mechanism of Suppression of Mechanism of Suppression of

Nontransmissible Pneumonia in Mice Nontransmissible Pneumonia in Mice Induced by Newcastle Disease VirusInduced by Newcastle Disease Virus

3.3. Evaluation of the methylation status of Evaluation of the methylation status of the promoter of prostate apoptosis par-4 the promoter of prostate apoptosis par-4 gene and its protein expression in gene and its protein expression in Egyptian cancer patientsEgyptian cancer patients

4.4. Effect of sunlight on leaf morphologyEffect of sunlight on leaf morphology

How to Prepare the How to Prepare the TitleTitle

Make a list of the most important keywordsMake a list of the most important keywords Think of a title that contains these wordsThink of a title that contains these words The title could state the conclusion of the The title could state the conclusion of the

paperpaper The title The title NEVER NEVER contains abbreviations, contains abbreviations,

chemical formulas, proprietary names or chemical formulas, proprietary names or jargon (terms or Terminology)jargon (terms or Terminology)

Think, rethink of the title before submitting Think, rethink of the title before submitting the paperthe paper

Be very careful of the grammatical errors Be very careful of the grammatical errors due to faulty word orderdue to faulty word order

Avoid the use of the word “using” Avoid the use of the word “using”

The AbstractThe Abstract An abstract can be defined as a summary of An abstract can be defined as a summary of

the information in a document the information in a document It is of fundamental importance that the It is of fundamental importance that the

abstract be written clearly and simply, as it is abstract be written clearly and simply, as it is the first and sometimes the only part of the the first and sometimes the only part of the manuscript read.manuscript read.

It should provide a brief summary of each of It should provide a brief summary of each of the main sections (IMRAD) of the paper:the main sections (IMRAD) of the paper:

1.1. State the principal objective and scope of the State the principal objective and scope of the investigationinvestigation

2.2. Describe the methods usedDescribe the methods used3.3. Summarize the results, and Summarize the results, and 4.4. State the principal conclusionsState the principal conclusions It is easier to write the abstract after It is easier to write the abstract after

completion of the papercompletion of the paper

Criteria of the AbstractCriteria of the Abstract It should not exceed 250 wordsIt should not exceed 250 words It should be written in one paragraph.It should be written in one paragraph. It should be written in the past tense as it It should be written in the past tense as it

refers to work done.refers to work done. Long words should be followed by its Long words should be followed by its

abbreviation which would be used through abbreviation which would be used through out the abstract and paper.out the abstract and paper.

It should not cite any references (except in It should not cite any references (except in rare cases)rare cases)

It should never give any information or It should never give any information or conclusion that is not stated in the paperconclusion that is not stated in the paper

Must be accurate with respect to figures Must be accurate with respect to figures quoted in the main text.quoted in the main text.

The IntroductionThe Introduction

The introduction should answer the The introduction should answer the following questions:following questions:

1.1. What was I studying?What was I studying?2.2. Why was this an important question?Why was this an important question?3.3. What did I know about this topic What did I know about this topic

before I did this study?before I did this study?4.4. What model was I testing? andWhat model was I testing? and5.5. What approach did I take in this What approach did I take in this

study?study?

Suggested rules for a Suggested rules for a good introduction:good introduction: It should present the nature and It should present the nature and

scope of the problem investigatedscope of the problem investigated Review the pertinent literatureReview the pertinent literature State the method of investigationState the method of investigation State the principal results of the State the principal results of the

investigationinvestigation State the principal conclusion(s) State the principal conclusion(s)

suggested by the resultssuggested by the results

General rulesGeneral rules

Use the present tense when referring to work Use the present tense when referring to work that has already been published, but past that has already been published, but past tense when referring to your own study.tense when referring to your own study.

Use the active voice as much as possibleUse the active voice as much as possible Avoid lengthy or unfocused reviews of Avoid lengthy or unfocused reviews of

previous research. previous research. Cite peer-reviewed scientific literature or Cite peer-reviewed scientific literature or

scholarly reviews. Avoid general reference scholarly reviews. Avoid general reference works such as textbooks.works such as textbooks.

Define any specialized terms or abbreviations Define any specialized terms or abbreviations

How to write the How to write the Materials and Methods Materials and Methods sectionsection

Provide full details so that the experiments are Provide full details so that the experiments are reproducible reproducible

If the peer reviewer has doubts that the If the peer reviewer has doubts that the experiments could be repeated, the manuscript will experiments could be repeated, the manuscript will be rejected.be rejected.

Organize the methods under subheadings, with Organize the methods under subheadings, with related methods described together (e.g. subjects, related methods described together (e.g. subjects, experimental design, Measurement of…, Hormonal experimental design, Measurement of…, Hormonal assays etc…).assays etc…).

Describe the experimental design in detailDescribe the experimental design in detail Do Do not not mix some of the Results in this section Write in the past tenseWrite in the past tense

MaterialsMaterials Must identify accurately experimental animals, Must identify accurately experimental animals,

plants, and microorganisms used by genus, plants, and microorganisms used by genus, species and strainspecies and strain

The source of subjects studied, number of The source of subjects studied, number of individuals in each group used, their sex, age, and individuals in each group used, their sex, age, and weight must be clearly statedweight must be clearly stated

If human subjects are used, the criteria for If human subjects are used, the criteria for selection should be described, and consentselection should be described, and consent

For chemicals used, include exact technical For chemicals used, include exact technical specifications and source or method of specifications and source or method of preparation.preparation.

Avoid the use of trade names of chemicals, generic Avoid the use of trade names of chemicals, generic or chemical names are preferred.or chemical names are preferred.

MethodsMethods This part of the manuscript must be clear, precise This part of the manuscript must be clear, precise

and concise so that it can be reproducibleand concise so that it can be reproducible If the method is new, If the method is new, all all details must be provided If the method has been previously published in a

scientific journal, only the reference should be given with some identification:

e.g. “cells were broken by ultrasonic treatment as previously described by …”. Preferable than “cells were broken as previously described by …. “

Questions such as “how” or “how much” must be answered and not left to be puzzled over

Methods used for statistical analyses must be mentioned; ordinary ones without comments, but advanced or unusual ones require literature citation

How to write the How to write the ResultsResults Results section is written in the past tenseResults section is written in the past tense

It is the core or heart of the paperIt is the core or heart of the paper It needs to be clearly and simply stated It needs to be clearly and simply stated

since it constitutes the new knowledge since it constitutes the new knowledge contributed to the worldcontributed to the world

The purpose of this section is to summarize The purpose of this section is to summarize and illustrate the findings in an orderly and and illustrate the findings in an orderly and logical sequence, without interpretationlogical sequence, without interpretation

The text should guide the reader through The text should guide the reader through the findings, stressing the major pointsthe findings, stressing the major points

Do not describe methods that have already Do not describe methods that have already been described in the M&M section or that been described in the M&M section or that have been inadvertently omittedhave been inadvertently omitted

Methods of presenting Methods of presenting the datathe data

1.1. Directly in the textDirectly in the text2.2. In a tableIn a table3.3. In a figureIn a figure All figures and tables All figures and tables mustmust be be

accompanied by a textual accompanied by a textual presentation of the key findingspresentation of the key findings

Never have a table or figure that is Never have a table or figure that is not mentioned in the textnot mentioned in the text

Tables and figuresTables and figures Tables are appropriate for large or Tables are appropriate for large or

complicated data sets that would be complicated data sets that would be difficult to explain clearly in text.difficult to explain clearly in text.

Figures are appropriate for data sets that Figures are appropriate for data sets that exhibit trends, patterns, or relationships exhibit trends, patterns, or relationships that are best conveyed visually.that are best conveyed visually.

Any table or figure must be sufficiently Any table or figure must be sufficiently described by its title and caption or legend, described by its title and caption or legend, to be understandable without reading the to be understandable without reading the main text of the results section.main text of the results section.

Do not include both a table and a figure Do not include both a table and a figure showing the same informationshowing the same information

How to write the How to write the DiscussionDiscussion It is the hardest section to write.It is the hardest section to write. Its primary purpose is to show the Its primary purpose is to show the

relationships among observed relationships among observed factsfacts

It should end with a short It should end with a short summary or conclusion regarding summary or conclusion regarding the significance of the work.the significance of the work.

Components of the Components of the discussiondiscussion

Try to present the principles, relationships, Try to present the principles, relationships, and generalizations shown by the Resultsand generalizations shown by the Results

Point out any exceptions or any lack of Point out any exceptions or any lack of correlation and define unsettled pointscorrelation and define unsettled points

Show how your results and interpretations Show how your results and interpretations agree or contrast with previously published agree or contrast with previously published workwork

Discuss the theoretical implications of your Discuss the theoretical implications of your work, and any possible practical applications.work, and any possible practical applications.

State your conclusions as clearly as possibleState your conclusions as clearly as possible Summarize your evidence for each conclusion Summarize your evidence for each conclusion

How to State the How to State the AcknowledgmentsAcknowledgments You should acknowledge: You should acknowledge:

1.1. Any significant technical help that you Any significant technical help that you have received from any individual in your have received from any individual in your lab or elsewherelab or elsewhere

2.2. The source of special equipment, The source of special equipment, cultures, or any other materialcultures, or any other material

3.3. Any outside financial assistance, such as Any outside financial assistance, such as grants, contractsgrants, contracts or fellowships or fellowships

Do not use the word “wish”, simply write “I Do not use the word “wish”, simply write “I thank …..” and not “I wish to thank…”thank …..” and not “I wish to thank…”

Show the proposed wording of the Show the proposed wording of the Acknowledgement to the person whose Acknowledgement to the person whose help you are acknowledging help you are acknowledging

ReferencesReferencesWhat is referencing? Referencing is a standardized way of

acknowledging the sources of information and ideas that you have used in your document.

A list of ALL the references used in the text must A list of ALL the references used in the text must be written.be written.

Reference format varies widely: Reference format varies widely: – Harvard formatHarvard format (the name and year system) is (the name and year system) is

the most widely usedthe most widely used– Alphabet-Number system is a modification of

name and year system– Citation order system

In-text citations In name and year system: Citation in the text is followed by the author’s last Citation in the text is followed by the author’s last

name and year of publication between parentheses. name and year of publication between parentheses. – If they were two authors then both last names are written. If they were two authors then both last names are written. – If more than two then the only first author’s name is If more than two then the only first author’s name is

written followed by the abbreviation written followed by the abbreviation et alet al If a single statement requires more than one If a single statement requires more than one

citation then the references are arranged citation then the references are arranged chronologically from oldest to more recent, chronologically from oldest to more recent, separated by semicolons.separated by semicolons.– If more than one reference share the same year then they If more than one reference share the same year then they

are arranged alphabetically within the year.are arranged alphabetically within the year.

In alphabet-number system:In alphabet-number system: Citation by number from an alphabetically arranged Citation by number from an alphabetically arranged

numbered reference list.numbered reference list.In Citation order system:In Citation order system: The references are numbered in the order they are The references are numbered in the order they are

mentioned in the textmentioned in the text

Reference ListReference List Any papers not cited in the text should not be Any papers not cited in the text should not be

included.included. Reference lists allow readers to investigate the Reference lists allow readers to investigate the

subject in greater depth. subject in greater depth. A reference list contains only the books, articles, and

web pages etc that are cited in the text of the document. A bibliography includes all sources consulted for background or further reading.

In name and year system: The reference list is arranged alphabetically by author.

If an item has no author, it is cited by title, and included in the alphabetical list using the first significant word of the title.

If more than one item has the same author, list the items chronologically, starting with the earliest publication.

Each reference appears on a new line. There is no indentation of the references There is no numbering of the references

In alphabet-number system:In alphabet-number system:It the same as above in addition each reference is given a

number

In Citation order system:In Citation order system:The reference list is arranged by the number given to the

citation by the order that it were mentioned in the text

BookBook– 1.  Okuda M, Okuda D. 1.  Okuda M, Okuda D. Star Trek Chronology: Star Trek Chronology:

The History of the Future.The History of the Future.  New York: Pocket  New York: Pocket Books; 1993. Books; 1993.

Journal or Magazine ArticleJournal or Magazine Article (with volume numbers) (with volume numbers)– 2.  Wilcox RV. Shifting roles and synthetic 2.  Wilcox RV. Shifting roles and synthetic

women in Star trek: the next generation. women in Star trek: the next generation. Stud Stud Pop Culture.Pop Culture. 1991;13:53-65. 1991;13:53-65.

Newspaper, Magazine or Journal ArticleNewspaper, Magazine or Journal Article (without (without volume numbers)volume numbers)– 3.  Di Rado A. Trekking through college: 3.  Di Rado A. Trekking through college:

classes explore modern society using the classes explore modern society using the world of Star trek. world of Star trek. Los Angeles TimesLos Angeles Times. March . March 15, 1995:A3.      15, 1995:A3.      

Encyclopedia ArticleEncyclopedia Article– 4.  Sturgeon T. Science fiction. In: Lorimer LT, 4.  Sturgeon T. Science fiction. In: Lorimer LT,

editorial director; Cummings C, ed-in-chief; editorial director; Cummings C, ed-in-chief; Leish KW, managing ed. Leish KW, managing ed. The Encyclopedia The Encyclopedia AmericanaAmericana. Vol 24. International ed. Danbury, . Vol 24. International ed. Danbury, Conn: GrolierConn: Grolier  Incorporated; 1995:390-392.   Incorporated; 1995:390-392.

Book Article or ChapterBook Article or Chapter– 5.  James NE. Two sides of paradise: the Eden 5.  James NE. Two sides of paradise: the Eden

myth according to Kirk and Spock. In: Palumbo D, myth according to Kirk and Spock. In: Palumbo D, ed. ed. Spectrum of the Fantastic.Spectrum of the Fantastic. Westport, Conn: Westport, Conn: Greenwood; 1988:219-223. Greenwood; 1988:219-223.

ERIC DocumentERIC Document– 6.  Fuss-Reineck M. 6.  Fuss-Reineck M. Sibling Communication in Star Sibling Communication in Star

Trek: The Next Generation: Conflicts Between Trek: The Next Generation: Conflicts Between Brothers.Brothers. Miami, Fla: Annual Meeting of the Miami, Fla: Annual Meeting of the Speech Communication Association; 1993. ERIC Speech Communication Association; 1993. ERIC Document Reproduction Service ED364932. Document Reproduction Service ED364932.

WebsiteWebsite– 7.  Lynch T. DSN trials and tribble-ations review. 7.  Lynch T. DSN trials and tribble-ations review.

Psi Phi: Bradley's Science Fiction Club Web site. Psi Phi: Bradley's Science Fiction Club Web site. 1996. Available at:1996. Available at:     http://www.bradley.edu/campusorg/psiphi/DS9/     http://www.bradley.edu/campusorg/psiphi/DS9/epep     /503r.htm. Accessed October 8, 1997.      /503r.htm. Accessed October 8, 1997.

Journal Article on the InternetJournal Article on the Internet– 8.  McCoy LH. Respiratory changes in Vulcans 8.  McCoy LH. Respiratory changes in Vulcans

during pon farr. during pon farr. J Extr MedJ Extr Med [serial online]. [serial online]. 1999;47:237-247. Available at:1999;47:237-247. Available at:     http://infotrac.galegroup.com/itweb/nysl_li_liu.      http://infotrac.galegroup.com/itweb/nysl_li_liu. Accessed April 7, 1999.Accessed April 7, 1999.

How to Write a ThesisHow to Write a Thesis

A PhD thesis in the science is supposed to A PhD thesis in the science is supposed to present the candidate’s original research i.e. it is present the candidate’s original research i.e. it is a scientific papera scientific paper

Unlike the scientific paper, the thesis may Unlike the scientific paper, the thesis may describe more than one topic, and it may describe more than one topic, and it may present more than one approach to some topics.present more than one approach to some topics.

The thesis may present all or most of the data The thesis may present all or most of the data obtained in the student’s thesis related obtained in the student’s thesis related research.research.

Thus it is more involved and longer than a Thus it is more involved and longer than a scientific paper.scientific paper.

Think of a thesis as a good thriller, and write in a Think of a thesis as a good thriller, and write in a logical way so that a reader will find it logical way so that a reader will find it interesting and will not be bored. interesting and will not be bored.

Ethics, Rights and Ethics, Rights and PermissionsPermissions Beware of originality and Beware of originality and

copyrights of others.copyrights of others. Do not copy anything without Do not copy anything without

giving the credit to the owner by giving the credit to the owner by referencing it.referencing it.

In some cases permissions are In some cases permissions are neededneeded

Repetitive publication of the same Repetitive publication of the same data is considered plagiarismdata is considered plagiarism

ReferencesReferences

Robert Day (1995): How to write Robert Day (1995): How to write and publish a scientific paper. 4and publish a scientific paper. 4thth Edition, Cambridge University PressEdition, Cambridge University Press

University of Queensland (2009) University of Queensland (2009) References/Bibliography Harvard Style

http://www.library.uq.edu.au/http://www.library.uq.edu.au/training/citation/harvard_6.pdftraining/citation/harvard_6.pdf