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Monday, December 14, 2009

Talk: Writing a manuscript for bio-medical publication - Ian E.P. Taylor (Professor emeritus of Botany, UBC)

I was asked to blog this by a colleague. I haven't caught up with the other talks from last week, but since I'm here, and I found an outlet, I figured I could just dump my notes to the web. So here they are. I've left in a few comments of my own, but really, the lecture stands on it's own. Most of the notes are derived directly from the talk - but they mirror the distributed hand outs pretty closely. And frankly, the talk was full of examples and anecdotes that really helped illustrate the point. If you get a chance to see Dr. Taylor speak, I highly suggest it. Any mistakes, as always, are mine, and you shouldn't take my advice on publishing...

[I will clean up the (HORRIBLY BAD) HTML that was caused by dumping in an open office document. (Update: I've now removed the bad HTML - and I won't be cutting and pasting from open office again. That was brutal.)]

Writing a manuscript for bio-medical publication

By Ian E.P. Taylor (Professor emeritus of Botany)

Started with an anecdote: When you publish a paper, the people you have to impress are 2 reviewers and an editor. They are harder to impress, and you have to worry about first impressions, or they will be hostile. Don't be negative about your work. For things that are missing: keep them for your next experiment.

Peer review: An independent but generic tool that allows an editor to
  • Determine originality
  • operationally competence
  • coherent reports of research
  1. Unpublished research may as well not have been done.
  2. Unread publications may as well not have been written.
Four steps to understand: (Plan for the lecture.)
  1. Plan and plan for your journal
  2. Real and credible authorship. (Those who are listed have done something... names have been put on cheques for authorships.)
  3. Peer review. (The web hasn't changed this much – people still want to see peer review.)
  4. Responses to review.

Picking a journal:
Polling the audience – lots of usual reasons. [Joke about having your professor on the editorial board....]
His reasons:

  1. indexed
  2. best in field
  3. appropriate readership
  4. i read it a lot
  5. timeliness
  6. costs
  7. profile of other authors
  8. professor-choice

Impact factor:

  • Kind of a fake idea.... the papers have impact factors, not journals. Several examples of high impact papers in low impact factor journals.

The plan:

Know the giants upon who's shoulders you stand. What are their backgrounds, and where do they publish?

  1. Know your goals, hypothesis
  2. If you can't write what you discovered in 20 words, you haven't discovered it.
  3. How did you discover it
  4. prepare the outcomes (text, figs, tables, supplementary)
  5. what do they mean?
  6. Keep your references as you write. (Missing references piss off reviewers!)
[The only decent cheese in the world is cheshire cheese – and yes, that's where he grew up.]

Planning abstract:
  • State what you discovered in the first line, and your conclusion in the second line
  • As you write, challenge each sentence against your plan.
  • If necessary, change plan

“We have discovered...” Everything you write should fit this goal.

Elements of a paper:
  • Results – no results, no paper
  • Methods – how you got the results
  • Discussion – why the methods. (May or may not be the choppy approach....)
  • Introduction – direct the reader
  • Conclusions – not repeat of results
  • Aside on abstract: can be structured – explains order of what you're discussing, or can be intro: explain significance.
How to read a paper:
  • Introduction -> Methods -> Discussion.
  • Introduction should lead you straight to discussion.... should be able to skip results and methods.
  • Writing author (always singular) – You should try to write it out yourself, as this is key. You don't want to mix styles.
  • Co-authors
  • senior author (first)
  • senior author (PI)
  • corresponding author.
In case it's not obvious, first is the person who did the work, last is the PI. (for Biomedical) Some places do alphabetical, but it depends on your field.

Writing Author:
  • Get the instructions to authors from the journal
  • write the first draft, which is a record of your work
  • unify style
  • share draft with all co-authors
  • Responsible for ensuring the record of ethical performance.
  • It's key that you get the style correct for your journal.

Before you write – make sure you know which journal.

[Great advice to me: Journals do not publish the truth! They publish results, written truthfully!]

Wonderful anecdote about how they used to write papers by putting everyone into a room and not leaving till the 2nd draft was done.

Who are the authors?
  • Only the people who should be on there. Eg, supervisors who wrote the grant, didn't actually supervise.
  • Data providers
  • Analysis data (e.g. statisticians)
  • political.... yeah, it happens
  • All who contributed to an essential part of the actual research reported
  • No one who is there for contributing a gift of ANY sort
  • check the journal for the criteria.
  • All authors must agree to the authorship list
  • All authors must agree to submission.
People who create libraries should not be included. Eg, if they supply you with a DNA library or something of that nature – if they didn't do the work, they don't belong on the paper. Just as a acknowledgement. See American Journal of Medicine – they have a form for this. (=

Fabrication, Falsification, Publication: they are criminal offenses in the scholarly community. Most time detection is by accident.

Author obligations - everyone on the paper takes responsibility for the whole paper.
  • inform editor of related works
  • refer to instructions to authors for details
  • covering letter should context of other published work. Make sure each paper is an original idea.
  • Inform editors of financial or other conflicts of interest
  • Identify (un)acceptable bias
  • Full justification of 'representative results'
  • Negative results???
  • The stuff you'd expect
  • list of suitable reviewers! Don't just pick the people who are best in the field - give others too. Don't just pick editorial board either. Give some reason why you picked them.
Remember: You are the world expert on the subject you're writing on.

Reviewer Obligations:
  • Treat as you would wish a stranger to treat you
  • Follow directions from editor
  • Consult editor before consulting others
  • group reviews must adhere to confidentially
  • One person must sign off on it.
  • Refuse, rather than delay: 2 weeks max. Do not delay!
  • if you're waiting for journals, don't put up with delay, get on the phone and call!
  • If asked for recommendation, follow criteria.
  • Annotate manuscript, but AVOID being rude.
If you're reviewing, Track changes is acceptable
  • Don't steal ideas or use their ideas for your gain
  • Do not break confidentially
  • Avoid becoming investigator. - don't tell the research how to do the research.
Disclose potential conflict of interests - let the editor decide if it's a problem
and yeah, don't talk to the author unless the editor says it's ok (explicitly)
  • Reviewer conflicts:
  • Recent collaborations
  • intellectual conflicts
  • scientific bias or personal animosity
  • parallel research activity, research work on a competing project
  • potential financial benefit
  • AND potential benefit from advanced knowledge of new work
Responding to reviewers:

  • In the end, the editors decide what's in the journal - not the reviewer
  • It is not an election - the editor can ignore the recommendations
  • Take all the comments - particularly the editors - seriously
  • The editor can say "your paper is accepted subject to the actions of the reviewers...." It has not yet been accepted.
  • Vent about negative comments - but only for 10 minutes.
  • Mark every point on a copy of the manuscript
  • Fix all typos and mechanics IMMEDIATELY. (within 24 hours.)
  • Fix the criticisms, THEN and ONLY THEN worry about the rebut.
  • The comment expressed by reviewer 1 is incorrect because...
  • We have addressed....
  • Don't delay!

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Blogger -M said...

Thanks so much for this, I found it very helpful!

December 20, 2009 3:51:00 PM PST  

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