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BioE 502 Professionalism. Spring 2014 Prof. Brad Sutton Slides adapted from Brian Cunningham. Schedule. 1/24 Intro and Authorship (Sutton) 1/31 Human Subjects and Animals in Research (Sutton) 2/7 Writing and Speaking ( Bhargava )

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bioe 502 professionalism

BioE 502Professionalism

Spring 2014

Prof. Brad Sutton

Slides adapted from Brian Cunningham


1/24 Intro and Authorship (Sutton)

1/31 Human Subjects and Animals in Research (Sutton)

2/7 Writing and Speaking (Bhargava)

2/14 Ethical Behavior in Scientific Research (Loui)

2/21 Grant Proposals (Boppart)

2/28 Intellectual Property (Wille)

3/7 Conflict of Interest (Bashir)

3/14 Final Exam (Leckband)

ready to write your first paper who should be the first author
Ready to write your first paper?Who should be the first author?
  • It is your thesis work
  • First author is generally the person who did most of the experimental work and data analysis
  • First author takes responsibility for writing the first draft of the manuscript and incorporating others’ contributions
who should be a co author
Who should be a co-author?
  • Your thesis advisor
    • Discussion and development of ideas and overall research direction
    • Obtained external funding for the research and other resources used for the work
    • Listed as the last author
  • Others in the lab who helped you
    • (older) Students who offered SUBSTANTIAL advice, ideas, experiment planning
    • (newer) students who helped perform some of the “gruntwork” in the lab or data analysis
    • Students from another research group who you collaborated with
      • Must include their advisor also
      • Next-to-last author
    • Someone from another lab, where you used a specialized device or other equipment
who should be a co author1
Who should be a co-author?
  • Special device used in another lab(students helped)
  • Key reagents were supplied from outside lab (intellectual contribution to reaction design and use)
  • Research agreement with a company that enabled access to critical insights and tools

Grad Student in Hwu Lab

Post-doc in Sutton Lab

Grad Student in Liang Lab

Grad Student in Sutton Lab


Computation Co-PI

Algorithm Co-PI

criteria for authorship
Criteria for Authorship
  • Multi-authored papers are the norm
  • All authors must be able to defend the work
  • Authorship gives credit but also demands responsibility
  • Key metric: Intellectual contribution
    • Performs key experiment, critical interpretation
    • Usually technicians are not listed as authors, if person just followed instructions blindly
  • Grey areas require careful judgment
    • Good to establish expectations before the collaboration starts
criteria for authorship1
Criteria for authorship
  • From Science:

Authorship: All authors must agree to be so listed and must have seen and approved the manuscript, its content, and its submission to Science. Science will send an email to all authors to confirm receipt of each paper. Submission of a paper that has not been approved by all authors may result in immediate rejection without appeal. Any changes in authorship must be approved in writing by all the original authors. All authors of accepted manuscripts are required to affirm and explain their contribution to the manuscript, agree to the conditions of publication including the availability of data and materials, and declare any conflicts of interest. The senior author from each group is required to have examined the raw data their group has produced. Specific information will be sent to most authors at the time of manuscript revision.

what does it hurt to be all inclusive
What does it hurt to be all-inclusive?
  • All people on the paper are responsible for its contents, accuracy, ethics.
  • Your paper will end up on other people’s CV’s as they are co-author. Their reputation is impacted.
  • Scientific community trusts that if that person has co-authored papers in that area, they know what they are doing in that area.
    • They will review other papers and grants
    • They will get jobs and promotions
    • They will hire and promote others
    • They will determine future research directions for YOUR field
author order
Author Order
  • First
    • Major contributor and writes first draft
  • Last
    • Corresponding author
    • Head of lab or major professor
    • Shares responsibility for accuracy and quality
    • Ensures acknowledgements are complete
    • Works with first author to decide on coauthors
  • Co-authors
    • Listed in order of contribution
  • It is possible to indicate when two authors shared equal responsibility for first authorship
  • If you used key technology (reagents, systems) from an outside company, but did not buy them commercially
    • If a particular person was involved substantially, they may rise to the level of co-author.
    • It is a good policy to discuss the issue with them personally
  • Sponsor of research (NSF, NIH, Company)
  • Program manager, if the person had some involvement in the project
    • This person may also be a co-author, so it is a good idea to ask if they would like to be listed as one
what are the products of academia
What are the “products” of academia
  • New Knowledge
    • Journal papers
    • Conference presentations & posters
    • Books
    • Patents
  • Knowledgeable Workforce
    • Postdocs, graduate students, undergraduates


types of publications
Types of Publications
  • Authored books
    • Years of intense work, >500 pages
  • Peer-reviewed journal papers
    • Original submissions
    • Review articles
    • “Correspondences”
  • Edited books
  • Book chapters
  • Conference proceedings
    • Seen as 2nd class compared to journals, since not as strenuously reviewed. Usually 2-4 pages.
  • Others
    • Published abstracts, book reviews
what is expected caveat there are no hard rules
What is expected? Caveat: there are no hard rules.
  • Junior faculty and postdocs
    • 2 first-authored papers/year
    • Several presentations/year
    • Several co-authored publications
    • Senior author on papers with students
  • Graduate students
    • No fixed rule or amount
    • Typical: MS thesis = 1 first-authored paper
    • Typical: PhD thesis = 4-5 first-authored papers
  • Industry
    • Depends on the company. Some actively DISCOURAGE publication
    • If you want to transition to academia, you need to find opportunities to publish
why publish
Why Publish?
  • In academia, your publication list is your “currency” for demonstrating your research accomplishments
    • Promotion
    • Tenure
    • Getting hired
    • Attracting recruits
    • Winning grants
  • Publication archives your work forever, for anyone to access
    • If it is not published, it is almost like it never happened
where to publish
Where to Publish?
  • Get advice from those close to the field, especially your advisor
  • Every field has a hierarchy of journal quality and publication standards
    • Impact factor of journals is a good indicator but should not be only factor considered
  • What journals are providing the references that you are reading?
  • Carefully read “Instructions to Authors” for listing of topics covered by a journal
    • If in doubt, you can write to the editor and ask
  • Your reputation is built by being seen (conferences) and being read (journals), so it is very important to pick the right venue for your work.
impact factor defined
Impact Factor Defined
  • Impact factor = average number of citations received per paper published in the past two years
    • A = # of times articles published in 2006 + 2007 were cited by indexed journals during 2008
    • B = total # of articles published by the journal in 2006 + 2007
    • I.F. for 2008 = A/B
how to publish
How to Publish
  • Slice work into pieces and publish as a series?
    • “Least publishable units”
    • Helps keep your numbers up
  • Quality and content is noticed by your peers, thus affecting your reputation
  • Avoid: “notches in the gun belt” syndrome
  • Avoid: “if it’s not perfect, I’m not publishing”
  • Field moves rapidly: Context for your paper may be evolving. Getting your ideas out there at a reasonable time is important.
    • Captures your contribution
    • Keeps the scientific conversation moving
what is publishable
What is Publishable?
  • Original contribution = First disclosure of results or techniques that enable
    • Demonstrating a capability for the first time
    • Understanding problem and/or observations
    • Someone else to repeat an experiment or derivations
    • Someone to evaluate authors’ intellectual process leading to conclusions
  • Conference Proceeding
    • May be a paper at a preliminary stage, with results that are not entirely complete
    • May be presentation of an aspect of a journal paper that is under review or published recently
    • Guidelines may differ, depending on the conference
peer review process
Peer Review Process
  • Editor
    • Assigns paper to associate editor based on topic
  • Associate Editor
    • Responsible for finding peer reviewers
    • With Editor, responsible for accept/reject/revise decisions
  • Reviewers
    • Faculty, graduate students, postdocs
    • Unpaid (courtesy and honor)
    • Make recommendations based upon significance of the results, accuracy, appropriateness for journal, clarity of presentation, novelty, and cited literature

Example Cover Letter

Correct name and address of Editor

You can suggest potentialjournal cover art

Suggest potential reviewers

with input from advisor

peer review process1
Peer Review Process
  • Reviewers
    • Avoid conflicts of interest
    • Should decline if unable to complete review in 1 month
  • Time frame
    • 3 months for first reviews is typical
    • Wide range (some take more than a year)
  • Outcomes
    • Accept as-is (very rare)
    • Accept with minor revisions
    • Reject but reconsider after revisions
    • Decline
    • Recommend for a different journal
when you get your reviews back
When you get your reviews back
  • First – share them with your co-authors. Usually only the corresponding author is getting email from the journal
  • Read them, then set them down for a day or two
  • Realize that they are not attacking you,
responding to a peer review
Responding to a Peer Review
  • Thank the reviewers for their genius insights
    • If you disagree with the reviewer, need to do it tactfully and constructively
  • Opportunity to clarify confusing issues in the paper for future readers
  • Opportunity to include more data that makes the paper stronger
  • Respond to every point raised by the review INDIVIDUALLY, and state in detail how the paper was changed to reflect your response to the reviewer comment

The reviewers are (in general) intelligent readers. If it was not clear to them, then there is an opportunity to make it more clear for future readers.

and in the revised paper
And in the revised paper

This indicates that the marked region is changed in response to reviewer 2, comment 7

what goes in a response to reviewers
What goes in a response to reviewers?
  • What about figures that directly address the reviewer’s questions? In the response or in the text?
  • Long discussions about the reviewer’s point or a pointer to a clarification paragraph in the Discussion?
  • Reviewers should be pointing out things that other readers would similarly find lacking. Responding directly to them in the response is not an optimal strategy.
    • Although, if you are going to argue the point, then it may be the only strategy.

Reviewer hates our paper!

OUCH! My feelings are hurt!

What an idiot!

Calmly and respectfully disagree

Explain clearly why our work is


  • Do not despair if your paper is not immediately accepted
  • Consider the review comments carefully and write a thorough, thoughtful, respectful reply
    • Address each and every point individually
    • May need to include
      • New discussion or explanation (Words only)
      • New calculations
      • New experiments
      • More clear figures
    • Read editors resubmission directions carefully and submit revision well before the deadline, if possible