Writing a paper

Preparing your results for publication : 

Preparing your results for publication Maximising your chances to get your manuscript rapidly accepted

What to publish? : 

What to publish? Full-length articles are about 5,000 words: a series of experiments making a coherent story Short notes are about 200 words General rule: it is better to publish one solid paper than to split it into two or three short notes Articles in books and reports are less prestigious: publish your primary data in international journals

Where to publish? : 

Where to publish? Carefully select the right journal From which journals do you cite papers in your reference list? Which journals publish on a similar topic? Final decision Prestige (“impact factor”) Time to publish (check time between submission of the manuscript and publication) Your experience with a specific journal (attitude of reviewers and editors) Page charges Charges for colour photos

What exactly is the “impact factor” (IF)? : 

What exactly is the “impact factor” (IF)? Put simply: IF is a rough indicator for the quality of a journal in a narrowly defined discipline, e.g., Agriculture Plant sciences Molecular biology It is silly to compare impact factors between disciplines, e.g., Ecology and Molecular Biology Calculation for journal impact factor: A = 2007 citations of articles published in 2006-07 B = number of articles published in 2006-07 A/B = 2007 impact factor http://www.isinet.com/isi/hot/essays/journalcitationreports/7.html

Plan your experiments in such a way that the data can be published : 

Plan your experiments in such a way that the data can be published Make sure you have a sound question (hypothesis) before you begin your research That hypothesis may not be the same you wish to use when publishing the data Research without a sound hypothesis is hard to write up, but … sometimes there are good reasons to make an “inventory” (no sound hypothesis required) Think twice (three times in Pakistan) before you start your experiments

Data that have not been published do not exist! : 

Data that have not been published do not exist! If you do not publish your data, you might as well not do the experiments Published data can make a lasting impression, like the Great Wall in China Photo Dr Jianbo Shen, CAU, Beijing, PR China

“There are three necessary steps in useful research; the first to begin it, the second to end it and the third to publish it.”Michael Faraday : 

“There are three necessary steps in useful research; the first to begin it, the second to end it and the third to publish it.”Michael Faraday

Slide 10: 

How to start writing How to finish … and in between … A thousand-mile journey starts with the first step. Chinese proverb

The structure of a scientific paper : 

The structure of a scientific paper Title, running title Authors + addresses Abstract Keywords, abbreviations Introduction Materials and methods Results Discussion Acknowledgments References Tables and Figures Lindsay, D. (1984) A guide to scientific writing. Longman, Cheshire.

Begin with the Results section : 

Begin with the Results section Arrange your data in figures and tables Are the data best presented as figures or as tables? Decide which figure/table comes first Decide the order of all other figures/tables Make a structure for your Results Decide what you wish to describe Design the sections in the Results (“dot points”) Then make a structure for each section (dot point) Decide what you wish to describe in each section Then start writing

An example of a structure of your Results section in “dot points” : 

An example of a structure of your Results section in “dot points” Root morphology Specific root length Root thickness Root exudates Carboxylates Phenolics Effect of root exudates on mobilisation of phosphate Effect of carboxylates Effect of phenolics

The style in the Results section : 

The style in the Results section Write your results in the past tense Avoid double negatives The rate of photosynthesis was not very fast. The rate of photosynthesis was slow. Use the active voice Si application increased plant biomass. (active voice) Plant biomass was increased by Si application. (passive voice) This rule does not mean that you should entirely discard the passive voice http://www.bartleby.com/141/strunk5.html

The choice between a Figure or a Table : 

The choice between a Figure or a Table

The choice between a few lines in the text or a Table : 

The choice between a few lines in the text or a Table The yield of rice was 1.232, 2.798, 3.193, 1.009 and 4.272 ton ha-1 for the farms of Dong, Zheng, Cheng, Wong and Shen, respectively These results are easier to take in when presented in a Table

Can we make the table clearer by altering the axes? : 

Can we make the table clearer by altering the axes?

Should we order the data in a different manner? : 

Should we order the data in a different manner? Arrange the farmers alphabetically? No improvement!

Should we order the data in a different manner? : 

Should we order the data in a different manner? Arrange in order of increasing yield? Shen did much better than any of the other farmers!

Do we need this level of precision? : 

Do we need this level of precision? Include as many decimal points as justified by the accuracy of your data

The columns of a table must be labelled appropriately, and the units must be included too : 

The columns of a table must be labelled appropriately, and the units must be included too Farmer Yield (ton ha-1)

We can quickly see why the yield on Zheng’s farm was so high: optimum pH! : 

We can quickly see why the yield on Zheng’s farm was so high: optimum pH!

Would a Figure have been better in this example? : 

Would a Figure have been better in this example? I don’t really think so, but it is a matter of opinion

Would lines, connecting the data points have been a good idea? Or perhaps regression lines? : 

Would lines, connecting the data points have been a good idea? Or perhaps regression lines? Never connect data points, if the data on the x-axis are not “scaled” – regression lines would have been a mistake! x

Slide 25: 

Ion concentration, µM Leaching rate, g/h 0 5 10 15 20 25 0 500 1000 1500 2000 2500 LSD0.05 Y = a  X b + X Effective graphs

All figures and tables require appropriate legends : 

All figures and tables require appropriate legends Describe what is shown Do not discuss what is shown Explain abbreviations, if you use any in figures or table Even when you use the same abbreviations throughout text WUE = water-use efficiency Explain errors bars: SE or SD; add n (number of observations) Explain meaning of statistical information *, **, ***

Make sure you use acceptable units, not ones that are “out-of-date” : 

Make sure you use acceptable units, not ones that are “out-of-date” Recommended/preferred SI units For information on SI conventions, the following Web site may be helpful: http://physics.nist.gov/cuu/index.html

The Results : 

The Results Figure 1 Describe what it shows Number figures in order of appearance in the text Table 1 Describe what it shows Lead the reader through your data From one Figure (Table) to the next Arrange a logical flow from section to section

Then continue with writing the Discussion : 

Then continue with writing the Discussion Make a structure for your Discussion Decide what you wish to discuss Design the sections in the Discussion (dot points) Then make a structure for each section (dot points) Decide what you wish to describe in each section Place your results in a wider context Compare your results with those in the literature Then start writing Finish with a paragraph in which you tell the reader what are the main points (“take-home-message”)

The Discussion : 

The Discussion The order in the Discussion may differ from that in Results Figure 1, Table 1etc. Explain what they show Place your results in a wider context How do your data compare with those in the literature? Finish with the “take-home-message”

A bit more about the Discussion : 

A bit more about the Discussion A good researcher is excited about the results Make sure the reader also gets excited Explain why your work is important and exciting

Now the Materials and Methods : 

Now the Materials and Methods Once you know which data you will include, you write up all the Materials and Methods used to acquire the data Methods Check if your methods work (recoveries, standards) Reference, details of all modifications Equipment, chemicals Manufacturer, city, country Growing conditions, treatments Species Latin name Cultivar

Materials and Methods : 

Materials and Methods Include all relevant details Check your chosen journal for “how it is done” Do not use “modified after”, but describe the modifications Describe so that someone else can repeat your experiments Be precise “Room temperature” is not an accurate description

The Introduction is next : 

The Introduction is next Briefly review the literature that is relevant for your manuscript (use your Discussion as a guideline) Do not just write this Introduction for half a dozen colleagues working in exactly the same field, but… Write for a range of interested scientists Finish with the aims of your work and present a clear hypothesis

The Introduction : 

The Introduction Briefly review the literature Address a wider audience than those working in exactly the same field Give the aims of your research and a good hypothesis A good hypothesis is one that can be tested, but it does not need to be “correct”

A bit more about the Introduction : 

A bit more about the Introduction Explain why you did your research The fact that nobody has done it before is not a good reason Your study may follow logically from previous work Your project may have been inspired by a practical problem

References : 

References Cite in a “balanced” manner and do not ignore specific groups Avoid too many references of the work of yourself or your group Cite the primary literature, if referring to a key finding Cite a review, if you wish to refer to a fact that has been found by numerous authors Cite textbooks only when referring to generally accepted knowledge

References : 

References Check the required format for the chosen journal Order (in text and list) Correct abbreviations of journals: http://www.webofscience.com/help/P_abrvjt.html For books: add name of publisher and city (not country) Are all cited references in the list? Have all references in the list been cited?

Acknowledgements : 

Acknowledgements Acknowledge the input of people and agencies who allowed you to write this manuscript Your supervisor (if not a co-author) Your technician (if not a co-author) Your colleague, who gave you some bright ideas or critically read your manuscript Someone who helped you with the language Granting agencies Others

The title : 

The title It should cover the main aims and/or message It should appeal to your audience It should not be too long Avoid titles with a numbered subtitle Subtitles may get lost, and hence your paper may not be found in searches

Slide 42: 

Title  It should contain most key words  It should NOT start with a weak word (Effects of.., Influence of.., Contribution to…)  It should hint at the main findings, or conclusions, or both Effect of flooding on pH of rice-producing, acid-sulphate soils in NSW Flooding alters pH of rice-producing, acid-sulphate soils in NSW Flooding increases pH of rice-producing, acid-sulphate soils in NSW

The running title : 

The running title Some journal also require a subtitle It cannot exceed a certain number of characters check instructions for authors of the journal should cover the main aims and/or message It is an abbreviated version of your title It is only printed above some pages of your paper It is not used for literature searches It is therefore less important than a good title Use your actual title as a guideline

The Abstract : 

The Abstract It should contain the aim of your research Do not use references in this part If you must use them, then all details must be there (as in the references list, but without the title) because an abstract must stand on its own Make sure the main results and take-home-message are there

Keywords : 

Keywords Choose a limited number of keywords that adequately cover your research Do not use words that already appear in the title Think of words that you would look for when doing a literature search Arrange alphabetically

Prefer the Active Voice : 

Prefer the Active Voice The project was initiated July 1. The Project began July 1. There has been an increase in the amount of milk consumed by teenagers More milk is being consumed by teenagers. Teenagers are drinking more milk.

Abbreviations : 

Abbreviations All abbreviations must be explained This is commonly done in a section with a separate heading: Abbreviations Sometimes it is better to (also) have a separate Table with all the abbreviations Avoid using abbreviations in the Abstract If you must, these abbreviations must be explained when used the first time

Who are the authors and their addresses? : 

Who are the authors and their addresses? Make sure that all authors have a chance to read your manuscript before you submit it Never add an author, if this person has not had a chance to read the manuscript Include the name of the institute/laboratory where the work was done as the first address If you have moved, also add “present address”

What is the order of the authors of your paper? : 

What is the order of the authors of your paper? The person who did the work and wrote the manuscript should be first (=senior) author Corresponding author is the one that will be the contact for the journal and correspondence that may follow after publication That may be the group leader Senior author and corresponding author can be the same The research-team leader appears as the last author

Frequently made mistakes : 

Frequently made mistakes Invalid statistics e.g., presenting linear regressions when one axis is not scaled (e.g., sites, species, farmers) Units lacking in tables or figures Incorrect units: s (= seconds) instead of S (= Siemens) there should be a unit length in conductivity as well Kg instead of kg Units of time must appear at the end mmol s-1 m-2 should be mmol m-2 s-1 ug, umol and uM, instead of mg, mmol and mM mM m-2 s-1 should be mmol m-2 s-1 mM is short for mmol l-1 No numbers or legends for tables or figures

Frequently made mistakes (cont’d) : 

Frequently made mistakes (cont’d) High, rather than low (very negative), water potential Cited references not given in reference list Incorrect/sloppy style of referencing The data shows … (instead of the data show ….) Too many decimal places 0.239876 (SE = 0.052501) should be 0.23 (SE = 0.05) No space between values and units, or between different units 20m; should be 20 m (but 20% should, indeed, be 20%) 10mmolm-2s-1; should be10 mmol m-2 s-1

Something you must never do : 

Something you must never do Never copy whole sentences or paragraphs without referring to the original text This is called plagiarism It is one of the worst “crimes” in science It will make you look bad, when discovered (which will probably happen) It may ruin your scientific career Just don’t do it!

Slide 53: 

Unnecessary words and phrases Vague emphasis: very, actual, in fact, literally, real, really, true, truly, overall … The overall annual production of ilmenite …. The program Spatial and Temporal Analysis of Crime (STAC) is used very often to detect crime patterns in urban areas. ‘very’ in negative statements is OK: ‘It was not very successful’ is not the same as ‘It was not successful’.

Slide 54: 

Unnecessary words and phrases Quartz veins have been shown to occur in calcitic limestone. (10 words) Quartz veins occur in calcitic limestone. (6 words) It is emphasised that …. It is a fact that …. It is known that ….

Slide 55: 

Unnecessary words and phrases After a careful analysis of the results, we determined ... The experimental field was located near Kojonup. Before the advent of computers, it was difficult to carry out statistical analysis. (13 words) 10

Slide 56: 

Unnecessary words and phrases Obvious repetition Selection intensities were selected to give an overall selection intensity of approximately 25%. (13 words) Overall selection intensities were about 25%. (6 words) Additionally, the crop’s root diameters were measured to determine maximum root diameter in each sample at the mid-December sampling to further examine the influence of seedling rate on root growth. (31 words) We measured the maximum root diameter of each sample taken in mid-December to further examine the influence of seedling rate on root growth. (24 words)

Slide 57: 

Unnecessary words and phrases Tautologies (ie. repeating the concept without clarifying it) … in close proximity to … (near, or close to) … forward planning … (ever heard of ‘backward planning’?) … general consensus … (consensus is a general agreement) … necessary prerequisite … (prerequisite means required beforehand) … vast expanse … (expanse is a wide extent) … slightly (very) unique … (unique is one of a kind) … is comprised of … (comprise means to include, to contain) This rock is comprised of four minerals. This rock comprises four minerals.

Slide 58: 

…over… …more than… Avoid Use …lower… …less than… or …fewer… …following… …after… or …in… Unnecessary words and phrases …feel… …think… or …believe…

Slide 59: 

Leave only what is ESSENTIAL to the subject of the paper. Sentences and words that are MERELY RELEVANT need to be deleted. Make it short Surgeon needs to cut through perfectly good skin to get at a medical problem. In surgery, the bottom line is the patient’s health. In writing, the bottom line is essential information. A good place to begin with is your first sentence; throw it away. After a few revision there may be nothing really bad in your paper, but there probably is too much of a good thing.

Slide 60: 

The bench on which the trial was conducted was moved periodically around the glasshouse (it was on wheels) so that plants were not influenced by a position factor with regard to growth, mainly due to differential shading by the beams in the glasshouse roof. (44 words) From an Honours thesis The position of pots in the glasshouse was changed periodically to minimise influence of any potential gradients in environmental parameters. (20 words) Pots were re-randomised periodically to minimise influence of gradients in environmental parameters. (12 words) Make it short

Slide 61: 

Increasing phosphorus applications increased shoot phosphorus concentration 3-fold (Fig. 2). (10 words) Phosphorus application to the growth medium had a significant effect on shoot phosphorus concentrations in both pho2 mutant and the wild type (Fig. 2). With increasing phosphorus application, phosphorus concentration in shoots also increased markedly. (35 words) Make it short

Slide 62: 

Make it short They should be replaced with an ecosystem analysis approach that includes both the biotic and abiotic components of the ecosystem. (20 words) 16

Slide 63: 

Statistical analysis (ANOVA) of results showed that the response to potassium treatment was significantly different among varieties for grain yield (p<0.001). (21 words) Make it short The interaction between varieties and potassium treatment was significant for grain yield (p<0.001). (13 words) Statistical analysis (ANOVA) of results showed that the grain yield response to potassium treatment was significantly different among varieties (p<0.001). (20 words)

Fraud in science : 

Fraud in science Publication of results that you have not really acquired is considered fraud There are examples where “scientists” have published results that were copied from other journals Other “scientists” have published results that were not really based on actual experiments It is one of the worst “crimes” in science You are bound to get caught: Just don’t do it!

Finally, a few comments on language and the structure of sentences and paragraphs : 

Finally, a few comments on language and the structure of sentences and paragraphs

A few hints : 

A few hints Avoid complicated sentences Do not use words that you think you understand, but have not really checked carefully Too easy to do when using your computer program, without checking in a dictionary Do not make sentences that are too long Use a spelling checker, and use either UK English, or US English, but not a mixture of both

Spelling checkers pick up some mistakes, but not all : 

Spelling checkers pick up some mistakes, but not all Sauna Barber Ball Guest

More about spelling checkers : 

More about spelling checkers Eye have a spelling chequer. It came with my pea sea. It plainly marques four my revue. Miss steaks eye kin knot sea.

“The information that begins a sentence establishes for the reader a perspective for viewing the sentence as a unit.” : 

“The information that begins a sentence establishes for the reader a perspective for viewing the sentence as a unit.” Gopen, G.D. & Swan, J.A. 1990. American Scientist 78: 550-558.

An example of how (not) to begin a sentence : 

An example of how (not) to begin a sentence 2. The P concentrations in root halves supplied with 1 μM P were invariably low, regardless of the P concentration supplied to the other root half. 1. Regardless of the P concentration supplied to the other root half, the P concentrations in root halves supplied with 1 μM P were invariably low. In 2., the important part is placed at the beginning. Therefore, that is the sentence order that you should use!

Slide 71: 

“Beginning with the exciting material and ending with a lack of luster often leaves us disappointed and destroys our sense of momentum.” Gopen, G.D. & Swan, J.A. 1990. American Scientist 78: 550-558.

Therefore, the structure of the Discussion should be both logical and exciting : 

Therefore, the structure of the Discussion should be both logical and exciting Begin with what needs to be addressed first and continue to explain the rest Hide what must be included, but is not really exciting This can be done by presenting it in a Table in Results, without further discussing in Discussion Finish with the most important and exciting aspects No need to use exactly the same order as in Results

The structure of a paragraph : 

The structure of a paragraph Text is organised in paragraphs Paragraphs have a distinct structure They are not arranged so as to have a certain number of sentences or lines Paragraphs deal with one topic Paragraphs begin with a sentence that “sets the scene” An introduction to what the paragraph is about Paragraphs finish with a conclusion A sentence that refers back to the first sentence http://www.bartleby.com/141/strunk5.html

Websites very useful for rules where (not) to place commas, for synonyms, and for explanations of words : 

Websites very useful for rules where (not) to place commas, for synonyms, and for explanations of words Website for Strunk & White’s  “Elements of Style” is: http://www.bartleby.com/141/strunk.html#1 Website for Roget’s “Thesaurus” is:http://www.bartleby.com/62/ Web Site for Fowler's “Dictionary” is:http://www.bartleby.com/116/ (great to read about mistakes made in the Times, the Daily Telegraph, and Dickens)

Slide 75: 

Reading aloud forces you OUT of the writer mode and INTO the reader mode. Revise your paper several times Read your paper aloud Ask someone else to read your paper.

Slide 76: 

During revising, keep asking yourself questions of substance Will this be clear to the reader? Do I need to expand on this point? Am I including appropriate information? What am I trying to say?

A final check : 

A final check Check the instructions for authors again Did you follow all instructions properly? Remember: it is not the task of the reviewers or the editor to take care of details you should have checked yourself Your manuscript may be sent back without review, if you have not addressed these items 

Before you submit your manuscript to a journal : 

Before you submit your manuscript to a journal Ask a colleague, friend or a discussion group to “review” your manuscript Their suggestions may lead to elimination of small mistakes and improve the readability of your manuscript

Send it off, and wait for the editorial decision : 

Send it off, and wait for the editorial decision

What next? : 

What next? You should receive a note from the journal that your manuscript has been received If this does not happen, check with the journal After several weeks you will receive the editorial decision If this does not happen in a reasonable time, check with the journal This decision can be: Accepted without revision (extremely rare) Accepted with minor/major revision Rejected with(out) an invitation to resubmit your manuscript

How do you respond when minor/major revision is required? : 

How do you respond when minor/major revision is required? Carefully consider all the points raised by the reviewers and the editor They have spent time on your manuscript, and you must give all their points careful attention Make the requested changes if you consider that these changes are appropriate Explain in a letter to the editor why you did not make the changes You will need good reasons! Return the revised manuscript as soon as possible

How to respond when a manuscript has been rejected, with(out) an invitation to resubmit? : 

How to respond when a manuscript has been rejected, with(out) an invitation to resubmit? Carefully consider the critical points Use the critical points to improve your manuscript You may need to read more literature More experiments may be required Revise your manuscript Resubmit your manuscript to the same journal (if invited to do so) Choose an alternative journal (if not invited to resubmit to the same journal) Never submit your manuscript to an alternative journal without appropriate revision Your revised manuscript may end up in the hands of the same reviewer

Send it off again, and wait for the final editorial decision : 

Send it off again, and wait for the final editorial decision

What makes life 100 %? : 

What makes life 100 %? If. A B C D E F G H I ……………X Y Z Is equal to 1 2 3 4 5 6 ………. 24 25 26 Then H+A+R+D+W+O+R+K 8+1+18+ 4+23+15+18+11 = 98 % ONLY K+N+O+W+L+E+D+G+E 11+14+15+23+12+5+4+7+5 = 96 % ONLY But. A+T+T+I+T+U+D+E 1+20+20+9+20+21+4+5 = 100% So a person with the right ATTITUDE is always a WINNER

Slide 85: 

Thank You

Slide 86: 

With the right aptitude, it is just a matter of learning a few tricks