Publishing Scientific Results

1. Preparing Scien,ﬁc Papers for Publica,on A. Townsend Peterson University of Kansas

2. Overall Publishing Process •  Write the paper •  Edit/proof the manuscript •  Format for the journal •  Submit to the journal •  Editor decides iniAally and sends out to review •  Reviewers provide suggesAons and criAcisms •  Editor decides whether to accept –  … can repeat several Ames •  Author revises •  Final acceptance •  Proofs sent to author •  Author corrects •  Author signs copyright transfer agreement •  PublicaAon

3. WRITING – STRUCTURE AND ORDER

4. Scoping the Paper Short and Sweet •  Advantages –  Easy to write –  Simple message –  “More” publicaAons on your CV •  Disadvantages –  Dilutes the message –  Reader has to search for the whole story across many papers –  Less impact per publicaAon Long and Complete •  Advantages –  Whole story is there in one place –  Greater potenAal impact •  Disadvantages –  More diﬃcult to organize and write –  Message can get complex –  Fewer publicaAons on your CV

6. Picking a Journal •  With advisors and colleagues, decide on the opAmal outlet for your paper •  Aim too high: –  Waste your Ame –  Waste reviewers’ and editors’ Ame •  Aim too low: –  Less credit for you –  Less aUenAon to your work •  Journal characterisAcs –  Subject focus –  Previous papers published –  Impact factor –  Access poliAcs (see the end of this presentaAon)

7. WriAng – Structure and Order •  Suggested order of wriAng: –  Figures / Tables –  Methods / Results –  IntroducAon / Discussion –  Abstract •  Last paragraph of IntroducAon should begin “This paper …” and should state clearly the purpose of the paper •  Length – care not to be overly long in IntroducAon and Discussion •  RepeAAon – no need to repeat parts of IntroducAon in Discussion, or parts of Results in Discussion

8. TECHNOLOGY ASSISTS

9. Technology Assists – Google Docs

10. Technology Assists – Google Groups

11. Technology Assists - EndNote

12. Free Technology Assists - Mendeley Another possibility: hUp://www.zotero.org/ - reference manager, also free

13. WORDS TO AVOID

14. Words to Avoid I •  While: Don’t use this word to mean although, whereas, and, or but, and don’t use it where only a semicolon is necessary. While means “during the Ame that” and should be used to link simultaneous occurrences in instances in which simultaneity is the point. •  E.g., i.e.: The abbreviaAon e.g. means “for example” (exempli gra4a) and introduces an illustraAve instance or a short list of names or other items. The abbreviaAon i.e. means “that is” (id est) and introduces a repeAAon in diﬀerent words of the ideas just discussed •  Compose, comprise: Comprise expresses the relaAon of the larger to the smaller, not the other way around (think of comprise as meaning to embrace or take in). The whole comprises the parts; the whole is composed of its parts. The parts compose the whole and are comprised in it. Do not use comprised of. •  Because, since, as: Because is the most speciﬁc of the conjuncAons used to express reason or cause. It always indicates an unequivocal causal relaAonship. Since is oaen a weak form of because. It also contains a noAon of duraAon over Ame that because does not. Use since when the meaning of what follows it is implied by what precedes it. Using as to mean since or because is always feeble. It makes whatever follows sound trivial. •  Although, though: In most uses these words are interchangeable, but it may be best to begin clauses with although, since it is more emphaAc, and to use though to connect elements within a clause. (Although intelligent, he could not apply himself. She was born of poor though well-educated parents.)

15. Words to Avoid II •  Very: This word is almost always completely unnecessary in sentences. That is, the statements “values of the index were very high” and “values of the index were high” communicate the same informaAon without the hyperbole. •  There is/there are: This sort of construcAon. E.g., “there are thirty birds sicng on the wire” can be replaced by a more direct statement … “thirty birds are sicng on the wire.” •  This/these/those as nouns: “This,” “these,” and “those” are modiﬁers, and should not be used as nouns. •  Passive versus ac,ve verbs: Most (but not all) uses of the passive form of verbs can and should be transformed into acAve forms. For instance “this bird was processed by XJV approaches” can be restated as “we used XJV approaches to process this bird.” •  Et al.: This construcAon is derived from the LaAn et altera for “and others.” It is frequently misused in a variety of uncareful ways: “Johnson et al 2004” (forgecng the abbreviaAon of altera), “Johnson et all 2004,” etc.

16. Words to Avoid III •  Due to: Most uses of this construcAon should be replaced with “owing to.” “Due to” implies that some quanAty should be paid to or is owed to, whereas the correct meaning is one of causaAon. •  Spaces aPer period and colon: Although tradiAonal typesecng (and probably many of your composiAon classes) required two spaces aaer periods and colons, modern typesecng is not in need of these extra spaces. Most importantly, however, is TO BE CONSISTENT … •  Bri,sh versus US spelling: Perhaps neither is universally correct, but one or the other should be used consistently throughout the enAre document. Ideally, use the style demanded by the journal for which you are wriAng. –  Centre/center Theatre/theater –  Behaviour/behavior –  Acknowledgement/acknowledgment –  Whilst/while Analyse/Analyze •  Hyphenated compound modifiers: Hyphens connect the words of a compound modifier that come before the word being modified. Hyphens are not used this way with compound parts ending in -ly or made up of proper nouns or proper adjecAves. “He is a well-respected man”, “That man is well respected”, “That was a badly punctuated sentence”, and “The South American rain forest is home to hundreds of species of hummingbirds” are correct.

17. Words to Avoid IV •  Where: Where implies a locality, posiAon, or direcAon. Do not use for “in which” or “for which”. “PredaAon on small prey, where many individuals must be captured per dive, is limited to shallow depths.” Replace “where” with “in which”. •  Predate: Predate means to “date in advance”. The verb derived from “predaAon” is “depredate”. •  Monophyle,c clade: A clade is, by definiAon, monophyleAc. Save space and omit this redundancy. •  Data: The word data is plural. The singular is datum. •  The: The is overused. When ediAng, think about whether or not the placement of every “the” is necessary. •  Split infini,ves: To blatantly divide the word “to” from the verb that it accompanies by an adverb is an ugly construcAon. •  Hyphens and dashes: Hyphens are used within text to build compound modifiers (e.g., “early-career professionals), n-dashes are used to indicate ranges of numbers (e.g., 4–5), m-dashes are used within sentences (e.g., “I ate—more than anything—because I was hungry”).

18. FIGURES

19. Figures - Technology •  Save AI version (or GIS original or …) •  Export JPG version for review

20. Color versus Black-and-white •  Color is much beUer for interpretability •  Can use color for review, and subsAtute B&W for publicaAon •  Can use color in electronic publicaAon version, and B&W in hard-copy version (if there is one) •  However, print in B&W to make sure it is interpretable without color, in case reviewers do not print in color … you want them to be able to read the ﬁgure!

22. Figures – Colors and Colorblindness •  hUp://colorbrewer2.org/

23. Structure – Making Readers Refer to CapAons Good Bad

27. Figures – Format •  At end of manuscript •  Figure Legends page •  Then one ﬁgure per page

28. TABLES

29. Tables – Try Not To •  Minimal use of tables is best •  Most informaAon in tables can be expressed beUer in a visual, eyecatching ﬁgure •  Readers tend not to pay much aUenAon to the contents of tables •  Tables take up lots of space •  Consider posAng the full data set as part of the publicaAon, or on a well-documented data site

31. Tables - Format Header informaAon Body of table Table 1. The capAon goes here, immediately above the table itself

32. Tables – Placement •  At end of manuscript •  Aaer ﬁgures •  Pages not numbered •  One table per page

33. PROOFING AND EDITING

34. Proofing and EdiAng - Example Scale effects such as distribuAon amplitude and spaAal resoluAon may also introduce contradictory results when interpreAng LPSR (Rahbeck 2006). For example, in smaller geographic areas, monotonic trends in species richness are usually observed, whereas across larger areas, however, hump-shape paUerns are generally observed (Rahbeck, 2006; Sánchez-Cordero, 2001). SpaAal resoluAon can also affect paUerns of species richness: studies involving too coarse-grained resoluAon may produce misleading results by registering high richness at localiAes where, in fact, low numbers of species occur, averaging over diverse distribuAonal phenomena.

35. Proofing and EdiAng - Example Scale effects such as range size distribuAon amplitude and spaAal resoluAon may also introduce contradictory results when interpreAng LPSR (Rahbeck, 2006). For example, in smaller geographic extentsareas, monotonic trends in species richness are usually observed, whereas; across larger areas, however, hump-shape paUerns are generally observed (Rahbeck, 2006; Sánchez-Cordero, 2001). SpaAal resoluAon can also affect species richness paUerns of species richness: studies at overly involving too coarse- grained resoluAon may produce misleading results by finding registering high richness at ‘localiAes’ where, in fact, lower numbers of species occur., The difference results from averaging over diverse distribuAonal phenomena.

41. CITING OTHER AUTHORS

42. GeneraliAes •  Cite other studies to place your work in the context of work already done •  Avoid self-citaAons, unless your work is the key and best citaAon for the point being made •  Cite others’ work broadly and fairly: – Cover what is ‘out there’ in the literature – Don’t play favorites – Try not to have enemies, or at least try to “cite thy enemy” •  CitaAons are not rewards or symbols of friendship or alliance

43. LITERATURE CITED

44. GeneraliAes •  Literature Cited. This sector of scienAﬁc wriAng is almost universally rife with errors and inconsistencies. Here are a few: – CapitalizaAon aaer a colon in journal Atles – either way is acceptable and journals vary in their preferences, BUT pick one style and be consistent – Spaces between iniAals in authors’ names – again, journals vary in their preferences, but be consistent – Inclusion of issue number – be consistent

45. •  BIRDLIFE INTERNATIONAL. 2012. IUCN Red List for birds. Downloaded from hUp://www.birdlife.org on 03/07/2012. •  BROWN, R. M., AND A.C. DIESMOS. 2002. ApplicaAon of lineage-based species concept to oceanic island frog populaAons: The effects of differing taxonomic philosophies on the esAmaAon of Philippine biodiversity. Silliman Journal 42, 133–162. •  CLEMENT, M., POSADA, D., AND K.A. CRANDALL. 2000. TCS: a computer program to esAmate gene genealogies. Molecular Ecology 9:1657–1659. •  COLLAR, N.J. 2006. A parAal revision of the Asian babblers, Timaliidae. Forktail 22:85–112. •  COLLAR, N. J. AND C. ROBSON. 2007. Family Timaliidae (babblers). 70–291. In Handbook of the birds of the world. Volume 12. Picathartes to 4ts and chickadees. Del Hoyo, J., A. EllioU, and D. A. ChrisAe. Editors. Lynx Edicions. Barcelona, Spain. •  COYNE, J.A. AND T.D. PRICE. 2000. LiUle evidence for sympatric speciaAon in island birds. Evolu4on, 54, 2166– 2171. •  DE ROEVER, J. 1990. Notes on the Luzon Wren-Babbler. Bull. Oriental Bird Club 12:33-–34. •  DIAMOND, J.M. 1977. ConAnental and insular speciaAon in Pacific landbirds. Systema4c Zoology, 26, 263– 268. •  DUPONT, J.E. 1971. Notes on Philippine birds (No. 1). Nemouria 3. •  DUPONT, J.E. 1971. Philippine birds. Delaware Museum of Natural History Monographs Series 2. •  HEANEY, L. R., 1986. Biogeography of mammals in SE Asia: esAmates of rates of colonizaAon, exAncAon and speciaAon. Biological Journal of the Linnean Society 28: 127–165. •  HIJMANS, R.J., CAMERON, S.E., PARRA, J.L., JONES, P.G., AND A. JARVIS. 2005. Very high resoluAon interpolated climate surfaces for global land areas. InternaAonal Journal of Climatology 25:1965–1978. •  IUCN STANDARDS AND PETITIONS SUBCOMMITTEE. 2010. Guidelines for Using the IUCN Red List Categories and Criteria. Version 8.1. Prepared by the Standards and PeAAons SubcommiUee in March 2010. Downloadable from hUp://intranet.iucn.org/webfiles/doc/SSC/RedList/RedListGuidelines.pdf •  LAMBERT, F.L. 1993. Some key sights and significant records of bird from the Philippines and Sabah. Bird ConservaAon InternaAonal 3:281–297. •  GONZÁLEZ, L.A.S., OLIVEROS, C., PUNA, N. AND R.G. MOYLE. 2010. Nests, Nest Placement, and Eggs of Three Philippine Endemic Birds. Wilson Journal of Ornithology 122:587–591. •  GOODMAN, S. M. AND P. C. GONZALES. 1990. The birds of Mt Isarog NaAonal Park, southern Luzon, Philippines, with parAcular reference to alAtudinal distribuAon. Fieldiana Zoology 60:1–39.

57. COVER LETTERS

58. Minimalist Version To The Editor: Please ﬁnd aUached to this leUer a manuscript enAtled This Is The Title of My Manuscript, for consideraAon for publicaAon in Your Journal. This manuscript is the intellectual product only of myself and my coauthors, and is not currently submiUed for publicaAon with any other journal. I hope that this manuscript will prove acceptable for publicaAon in your journal. Please do not hesitate to contact me should you need any further informaAon. Sincerely,

59. Should You Argue For Your MS In Cover LeUer? •  For high-end journals (Science, Nature, PNAS), it is necessary … pre-review editorial decisions may depend on it! •  For ‘normal’ journals, it is a maUer of choice … many people do include a paragraph of why the paper is important; I do not •  Be VERY careful not to overstate the importance of the paper or the impact of the results

60. CHOOSING AND RECOMMENDING REVIEWERS

61. Reviewers •  Many journals permit suggesAons regarding appropriate reviewers for a manuscript •  These suggesAons may be opAonal or may be required, depending on the journal •  The editor may or may not follow your suggesAons

62. Suggested Reviewers •  Ideally, reviewers will have experAse and experience in the area of the paper •  Reviewers should not have any conﬂict of interest with any of the authors •  Do not suggest reviewers who are close associates, friends, relaAves (!), or involved in the project … quite simply, it is not appropriate, and it is unfair to the editors to make them have to discover these connecAons without the authors’ honesty

63. Non-suggested Reviewers •  Occasionally, conﬂicts of opinion, personal disagreements, nonfuncAonal personaliAes, and other issues can cloud the objecAvity of peer review •  Authors can request editors to remove such individuals from consideraAon as reviewers—either in the cover leUer or via lists on web pages: –  In cover leUer: “Based on past experiences, in which XXXXX showed lack of objecAvity in peer review of manuscripts by myself and my coauthors, I would respec{ully that XXXXX not be considered as a reviewer for this manuscript.” •  Editors may nonetheless request reviews from such individuals, but may consider the resulAng review in light of the knowledge that a conﬂict is at least perceived to exist

64. AUTHORSHIP

68. Reasons For Authorship •  Wrote the paper •  Provided criAcal intellectual input to ideas or methods •  Worked hard gathering or analyzing data •  Led the lab group •  Your advisor •  In sum, should be people who made signiﬁcant contribuAons to the overall eﬀort

69. RESPONSES TO REVIEWS

71. First – Understand the Response Thank you very much for submicng your manuscript "Uses and misuses of bioclimaAc envelope modelling" for review by Ecology. The reviewers and I appreciate the work you have accomplished. Based on the reviews, we will not be able to accept this manuscript for publicaAon at this Ame. We would be willing to consider a much- revised version, based on the review comments. Indeed conceptual papers, as this one, are diﬃcult to write. Here both reviewers stressed that the arguments and balance view of the debate should be beUer presented (not as vague). Both reviewers were very generous in their construcAve comments and a revised version could make a great contribuAon.

72. In General •  Whenever possible, say “OK” •  When not possible to say OK, then be reasonable, make some changes •  When you really disagree, then state a clear reasoning as to WHY •  Finding reviewers is a hard task for editors •  Your objecAve … the editor accepts the paper without further review

73. Ideal Responses Line 28. "Oﬀer a bridge across scales". Statement is not explained or supported in any way. Should be removed. •  Done. Line 563. "microscopic" is obviously incorrect. Do you mean "small areas" •  Changed. I ﬁnd that the paper is very long relaAve to the points it makes. Many of the secAons could be shorthened considerably. This secAon could be much shorter. •  The manuscript has indeed been shortened quite a bit, with 2 major sec4ons either removed en4rely or shortened massively.

74. When You Disagree

75. When You Disagree

76. CHECKING PROOFS

77. “Proof” Reading •  Last check before publicaAon •  What problems and errors are not detected are your fault, not the journal’s •  Must check enAre proof in minute detail •  Special aUenAon to equaAons, tables, literature cited … anywhere that concentraAon is hard •  Some people even read backward … !

83. COPYRIGHT TRANSFER AGREEMENTS AND OPEN ACCESS

84. Copyright is A Bundle of Rights 84 Rights are held by the OWNER of the work (not necessarily the creator/author). Owners may: • Reproduce - make copies of their works publicly or privately. • Adapt - prepare addiAonal works derived from their copyrighted work, (aka, derivaAve works). • Distribute - Disseminate copies of their works, to the public by sale or other transfer of ownership, or by rental, lease, lending. • Perform - Perform their work publicly (at locaAon open to the public or to persons other than close family and social acquaintances). • Display - Display their work publicly (applies to all works except sound recordings and architectural works). From, SecAon 106 of 1976 Copyright Act and see, hUp://www.copyright.gov/circs/circ1.pdf

89. Why Open Access???

91. Conceive Research Idea Submit Paper Write Paper Do Research Secure Research Funding Paper Published Editor Accepts Reviewers Consider Editor Receives Subscrip,on Fees Access Charges Page Charges

93. How Big is the Access Problem? An Experiment for EEB Scholarship •  Take 10 EEB papers, each from a diﬀerent journal •  Send full bibliographic record for each to 50 colleagues around the world •  Ask each colleague to go to his/her oﬃce, and to aUempt to obtain access to the enAre text of the publicaAon

94. How Big is the Access Problem? An Experiment for EEB Scholarship •  Michael J. Farabee, Edith L. Taylor, Thomas N. Taylor, CorrelaAon of permian and triassic palynomorph assemblages from the central TransantarcAc Mountains, AntarcAca, Review of Palaeobotany and Palynology, 65:257-265. •  Claire Horner-Devine, M., Leibold, M. A., Smith, V. H., Bohannan, B. J. M. 2003. Bacterial diversity paUerns along a gradient of primary producAvity. Ecology LeUers 6:613-622. •  Rafe M. Brown, Jimmy A. McGuire and Arvin C. Diesmos. 2000. Status of some Philippine frogs referred to Rana evereY (Anura: Ranidae), descripAon of a new species, and resurrecAon of Rana igorota Taylor 1922. Herpetologica 56:81-104. •  Billings, S. A. 2008. Biogeochemistry: Nitrous oxide in flux. Nature 456:888-889. •  Harald Schneider, Alan R. Smith, Raymond Cranfill, Terri J. Hildebrand, Christopher H. Haufler, Tom A. Ranker. 2004. Unraveling the phylogeny of polygrammoid ferns (Polypodiaceae and GrammiAdaceae): exploring aspects of the diversificaAon of epiphyAc plants. Molecular PhylogeneAcs and EvoluAon 31:1041-1063. •  Neal Woodman, Robert M. Timm, Norman A. Slade and Terry J. Doonan. 1996. Comparison of traps and baits for censusing small mammals in Neotropical lowlands. Journal of Mammalogy 77:274-281. •  Leonard Krishtalka and Philip S. Humphrey. 2000. Can natural history museums capture the future? BioScience 50:611–617. •  Bryan L. Foster, Timothy L. Dickson. 2004. Grassland diversity and producAvity: The interplay of resource availability and propagule pools. Ecology 85:1541-1547. •  Paul O. Lewis, Mark T. Holder, and Kent E. Holsinger. 2005. Polytomies and Bayesian phylogeneAc inference. SystemaAc Biology 54:241-253. •  Lena C. Hileman, Jens F. Sundstrom, Amy LiU, Meiqin Chen, Takudzwa Shumba, and Vivian F. Irish. 2006. Molecular and phylogeneAc analyses of the MADS-box gene family in tomato. Molecular Biology and EvoluAon 23:2245-2258.

95. Percent Success Note that: - only 2 colleagues achieve 100% success - no US colleague had 100% success - access can be quite unsaAsfactory, even in the US

96. How Available are Diﬀerent Journals? i.e., percent success of colleagues in accessing papers Journal Success rate Systematic Biology 91.18 Molecular Biology and Evolution 91.18 Ecology 73.53 Nature 70.59 Ecology Letters 64.71 BioScience 64.71 Molecular Phylogenetics and Evolution 55.88 Journal of Mammalogy 44.12 Review of Palaeobotany and Palynology 41.18 Herpetologica 41.18

97. ATP Opinion Academic publishing has been “bought out” by an opportunis4c commercial publishing world, and is fast becoming inaccessible to the academic community, and par4cularly to the global scholarly community.

100. What Is Open Access (from Peter Suber)? •  Open-access (OA) literature is digital, online, free of charge, and free of most copyright and licensing restricAons. •  OA is possible thanks to the internet and consent of the copyright-holder. •  Scholarly journals do not generally pay authors, who can therefore consent to OA without losing revenue. •  OA is compaAble with peer review; all major OA iniAaAves for scienAﬁc and scholarly literature insist on its importance. •  OA literature is not free to produce; the goal is to make scholarly literature costless … are there are beUer ways to pay the bills than by charging readers and creaAng access barriers.

101. SOLUTION #1 – PUBLISH IN OPEN ACCESS JOURNALS

102. Open Access Journals •  Open access journals have removed the “subscripAon barrier” to access to journal scholarship •  As with closed-access journals, they vary in quality and editorial policies •  Open access journals have the same potenAal to provide peer review •  Many open access journals now with high circulaAon and impact

103. SoluAon #1 – OA Journals

105. SOLUTION #2 - JOURNAL SELECTION … WORK WITHIN THE LIMITS

106. SoluAon #2 – Work Within the Limits

109. SOLUTION #3 – CHANGE THE LIMITS: THE OA@KU EXAMPLE

110. KU Example: write on the copyright agreement: “Subject to aeached addendum”

111. Addendum to PublicaAon Agreement

112. Addendum to PublicaAon Agreement

113. Or Simply Edit the CTA: If the publisher looks at your edits and says “NO!” … you can: – Sign the original agreement and the paper is published – Debate/negoAate with the publisher about terms – Withdraw the paper(!)

114. Copyright Transfer Summary •  Access is a major problem for scholarship •  Open access journals are building, but are not suﬃciently abundant or high-enough impact to sustain scholarly publishing •  Scholars can “select” journals based on access, if they choose •  InsAtuAons can pass policies regarding open access •  Scholars can amend and debate the copyright transfer agreements

115. OA Key Internet Resources •  SHERPA/RoMEO – summary of OA policies for each journal and publisher: hUp://www.sherpa.ac.uk/romeo/ •  ROARMAP – summary of OA policies at insAtuAons and funding agencies: hUp://www.eprints.org/openaccess/policysignup/ •  KU ScholarWorks – KU’s OA repository: hUp://kuscholarworks.ku.edu/ •  Harvard Oﬃce of Scholarly Communica,on – hUp://osc.hul.harvard.edu/osc.php

116. Overall Publishing Process •  Write the paper •  Edit/proof the manuscript •  Format for the journal •  Submit to the journal •  Editor decides iniAally and sends out to review •  Reviewers provide suggesAons and criAcisms •  Editor decides whether to accept –  … can repeat several Ames •  Author revises •  Final acceptance •  Proofs sent to author •  Author corrects •  Author signs copyright transfer agreement •  PublicaAon

117. TOWN@KU.EDU

Publishing Scientific Results

Recommended

Recommended

More Related Content

What's hot

What's hot (20)

Similar to Publishing Scientific Results

Similar to Publishing Scientific Results (20)

More from Town Peterson

More from Town Peterson (20)

Recently uploaded

Recently uploaded (20)

Publishing Scientific Results