publishing: where, why, and how. outline why it matters where you publish what journals should you...

Publishing: where, why, and how

Outline

• Why it matters where you publish

• What journals should you try and publish in?

• How to publish in the top tier journals

• An outline for a major article in a top-tier journal

• How the review process works

Why it matters where you publish

• For university faculty jobs, your publication record will likely have a strong impact on your eventual teaching load, and if you get a job at all

• Many publications in top tier journals low teaching load, higher probability of getting a job

• Few publications, and/or publications only in lower tier journals high teaching load, lower probability of getting a job

Why it matters where you publish

• Given that you are going to spend the next few years doing research, it only makes sense to do it in a way that will give you more opportunities and choices in the future

• Ergo, you should write your papers and design your research such that it can be published in top tier journals

Outline

What are “top tier journals”?

• What follows will be my highly subjective opinion (but based partly on hard data and the opinions of many fellow evolutionary biologists and ecologists)

• Varies somewhat between subdisciplines of ecology and evolution

What are top tier journals?

• Best: Nature, Science (duh!)

• Second best: PNAS, PLOS Biology

• Third best: Proceedings of the Royal Society of London/Biology Letters, Current Biology

• (Not clear to me that this third tier is necessarily better than top tier journals within a field…)

What are top tier journals?For Evolutionary Biology (not an exhaustive list)

• Top (in alphabetical order only): American Naturalist, AREES, Evolution, Genetics, Molecular Biology and Evolution, Systematic Biology, TREE

• Uncertain (first or second): Molecular Ecology, Heredity, Journal of Molecular Evolution, BMC Evolutionary Biology

• Second tier: Biological Journal of the Linnean Society, Genetica, Journal of Evolutionary Biology, Journal of Heredity, Molecular Phylogenetics & Evolution

What are top tier journals?

For Ecology (not an exhaustive list)

• Top (in alphabetical order only): American Naturalist, AREES, Ecology, Ecology Letters, Ecological Monographs, TREE

• Uncertain (first or second): Animal Behavior, Conservation Biology, Ecological Applications

• Second tier: Ecography, Journal of Ecology, Journal of Animal/Plant Ecology, Oecologia, Oikos

The bottom line

• You should design your dissertation research such that you will have multiple, first-authored major articles in the best and/or top tier journals

• You can bet that the other people applying for jobs in evolution and ecology will...

Outline

How to get published in the best/top tier journals?

Based primarily on serving as Associate Editor for:

• American Naturalist• Ecology Letters• Evolution• Systematic Biology

• Most important ingredient for publishing in top tier journals = single ingredient lacking in most papers that get rejected

• You generally need to have something to say that is both new and conceptually broad

• From the “Instructions to authors” from the journal Evolution: “Demonstrating a well-established phenomenon in another taxon or context may fall short of being acceptable.”

Examples of what these journals are looking for:

• New hypothesis to explain well known phenomenon

• New way to test old hypothesis (new method, new type of data)

• Show a new phenomenon

• Test a previously untested theory or major assumption of theory

How do I come up with something new to say?

• Subscribe to journals that you want to publish in

• Read the articles; find articles that you like

• Become an expert on a topic

• Once you know a topic, you’ll see that nobody has convincingly demonstrated almost anything, and that most of the really interesting topics are still wide open!

Outline

Outline of a paper in a top-tier journal

• Going to focus on how to publish in a top-tier journal of the type for which I have served as Associate Editor (e.g., Evolution, Am. Nat., Syst. Biol.)

But wait!

• Wouldn’t it be better to know how to get things published in Science or Nature?

But wait!

• No shit.

But wait!

• No shit.

• If you figure out how to do this, please let me know.

Quick Digression:How to get published in Science or Nature

• Work very, very hard on your cover letter; ~90% of papers get rejected without review

• Need to convince the non-specialist editors why the paper is incredibly important and possibly interesting to general public

• After you do that, your chances are rumored to be ~50% (twice as good as Am. Nat.)

Outline of a paper in a top-tier specialist journal (e.g., American Naturalist, Evolution)

The title page

• Authorship

• Another quick digression!!!

Authorship

• As a grad student or postdoc, you need to get multiple first-authored papers

• When you start a collaboration, be clear about authorship up front (don’t expect things to just work out in your favor after the work is done)

• Limit major time investments in junior authored papers (unless you are RAing to pay the bills)

Authorship

• In theory, established researchers should be generous about granting first authorship to more junior people (on the other hand, they will expect you to do more of the work!)

• If you are collaborating with friends at a similar career level as you, you should expect to get (or feel) screwed sometimes--but a little altruism now can pay off later

Abstract

• Most important part of the paper; will determine whether anyone reads it or not

• Introduce the topic, what is lacking in the current approach to it, what you will do, what you found, and the general significance of the results for the field

• Mini-version of introduction and discussion, but not Materials & Methods or Results!

Introduction (each point = separate paragraph[s])

• What the topic is and why the topic is important

• What is lacking in the current approach to the topic

• How the current approach could be improved upon

• What people have done that is similar (and how it is different from what you are doing)

• Introduce what you will do, your study system, and maybe a little about what you will find

Materials and Methods

• Be transparent and concise

• Anticipate every possible criticism of your data and methods (use your imagination) and briefly address it

• Don’t try to sweep weaknesses of your study “under the rug”; mention them and clearly explain why they are not fatal

Results

• Tell people what you found

• Only provide results that are relevant to the main point of your study

• Should be little or no interpretation of the results or comparison to other studies (i.e., no citations); save that for discussion

• Check for same order of analyses in M&M and Results

Discussion (each point = separate paragraph)

• What did your study show (interpret and summarize the results)

• Where does this new approach/new hypothesis take us in understanding the topic?

• How do your results relate to prior work?

• Where do we go next in research on this topic?

Discussion

• Common but very serious flaw in discussion of many papers: discussion is focused solely on the study system and not on the general topic

• Many papers bring up an interesting general question in the Introduction, but never really return to answer it in the Discussion

Literature Cited

• Carefully follow the exact format of the journal

• Make sure that every paper cited in the text is in the Literature Cited and that every paper in the Literature Cited is cited in the text

A comment on sloppiness

• Huge amount of trust involved in review process

• Reviewers routinely assume that you can competently collect data and analyze data

• If you are sloppy and careless in the things that reviewers can see (i.e., manuscript format), why should they trust you for the things that they can’t? (i.e., data collection)

A comment on sloppiness

• Check spelling

• Check “Guide for Authors” of journal and follow very carefully

• Check recent articles in the journal for anything not covered explicitly in the “Guide for Authors”

Figures

• The second most important part of the paper? (after the abstract)

• Should tell the story of the paper and should look great

• Good to be creative (but simple often works fine)

Introduction/Discussion

• The fatal flaw of most papers is that they fail to put their work in the broader context of the field to show the novelty and importance

• Why not? Probably because it is easier and more fun to collect and analyze data than to figure out the broad context of the field and figure out something new to say

Introduction/Discussion--Walking the tightrope

• It is important to show limitations of prior studies

• It is also very important to not piss people off

• Assume that everyone you cite is a potential reviewer

• You need to walk a tightrope of showing prior research to be flawed/limited, without angering authors of that research

• Be very sure to cite all the relevant people in the topic

• If you cite someone, they will have at least some motivation to favor acceptance of your paper, even if your research convincingly demonstrates that they are a complete idiot

• But miss-citing papers can make you look like an idiot

• Important to make it clear that your work is important

• Also very important to not sound pretentious, arrogant, cocky, etc.

• Reviewers can and do complain about the tone of your paper

Being a good (scientific) writer

• Scientific writing is very structured and disciplined

• But there are still good scientific writers and bad scientific writers

• Good writers are clear and understandable, and make the paper interesting and exciting to read (even when the general format is set in stone)

• Try to find papers in your area that you think are well-written and think about what it is that you like about the writing...

Being a good (scientific) writer

Other tips

• When in doubt, write short, simple declarative sentences

• Avoid redundant phrasing and structure “However,…”

• Think about your paper as telling a story, and make sure that everything in the paper helps tell that story and makes it convincing

• Think about the impact that you want your paper to have on the field and write it accordingly

Outline

How does the publication process work?

(most journals)

• Submit to journal office/Editor

• Editor makes initial decision about suitability (some journals reject many papers at this stage)

• Editor assigns an AE (Associate Editor)

• AE picks reviewers

• Reviewers make recommendation to AE AE makes recommendation to Editor Editor makes final decision you get an e-mail from the Editor

How does the publication process work?(most journals)

What are the possible outcomes?

• Accept without revision

• Accept pending minor revision

• Accept pending major revision

• Rejection without prejudice/resubmission possible

• Rejection (no resubmission)

(most journals)

• Reviewers often disagree, and often disagree wildly (e.g., accept pending minor + reject without resubmission)

• Decision typically rests with AE

• AE can also disagree wildly with reviewers (reviewers like it, AE hates it, or vice versa)

How does the publication process work?(most journals)

• In theory, AE protects authors from unfair reviewers (good paper, bad reviews), and protects journal from combination of incompetent authors and incompetent reviewers (bad paper, good reviews)

• BUT: AE typically handle at least some papers outside their area of expertise (can expect AEs to be incompetent also, at least some of the time)

(most journals)

• Will the Editor protect you from an incompetent AE?

• Hardly ever: if the Editor routinely ignores or overrides the AE, the AE can simply quit

• Some Editors have little or no actual input on the decisions

On getting rejected...

• Assume that it will happen sometimes, no matter how important the paper is

• If you have anything important to say, you can assume that someone will find it threatening

• Reviewers and AEs are often lazy, incompetent, and self-serving

• Don’t get too discouraged if you do get rejected, but do pay close attention to the substance of the negative reviews (they’re not always stupid)

Revising your paper

• Most papers require some revision, and for most acceptance hinges upon details of that revision

• You must write a cover letter that accompanies your revision

• Many comments by the reviewers and AE are completely moronic

• May be good idea not to point this out to them explicitly

Revising your paper

• You should assume that every stupid comment made by the reviewers and editors is your fault (i.e., they misunderstood because you didn’t explain things clearly enough)

• In general, you should respond to all or almost all reviewer and AE comments with some change in the manuscript itself

• (Don’t just say that the reviewers and editors are wrong, even if they obviously are)

Manipulating the review process

• You can influence who your paper is sent to or not sent to; many journals ask authors for preferred (or “not preferred”) reviewers and AE

• AEs often appreciate suggestions as to who to send the paper to (especially if paper is outside their area)

• People in the acknowledgements are usually out

• But you can ask them to send it to your friends, collaborators, Aunt Jody, etc.

Manipulating the review process

• You can also ask that they not send it to someone

• They may or may not ask you why

• If you do this, be careful about the “why” (don’t make questionable accusations; you could get sued)

• Too many non-preferred reviewers may also be a “red flag”

• But keep this option in mind...

Final Advice

• Start submitting parts of your dissertation/postdoc research long before you finish

• Get feedback on your manuscripts from your labmates, advisors, and committee members

Final Advice

• Stony Brook E&E students have done great things in the distant and recent past.

• Don’t assume that you can’t do the same.

Some Accomplishments of Recent E&E Graduates/Graduate Students

• Lacey Knowles (graduated 1999; now tenured professor at Univ. Michigan); lead author of most cited paper in Ecology and Evolution in 2003!

• Patrick Stephens (graduated 2005)--interviewed for Assistant Professor position at Yale while still a graduate student here

• Dusty Brisson (graduated 2006)--interviewed and got position as Assistant Professor at Univ. Pennsylvania while still a graduate student here

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