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Clinical collaborator has collected samples of different body sites, performed assays using blood samples and collected metadata for all subjects. Our lab and collaborator's lab has PhD students. Our lab student managed logistics for sample transportation, processed the samples of all body sites for DNA extraction, library prep and DNA sequencing. Our lab student then also analyzed the data, created figures, wrote the manuscript. Both students (clinical side and our lab side) had different primary objective but the primary objective of our lab's student is a secondary objective of clinical collaborator's student too. Clinical collaborator wants equal first authorship for their student. There are specific other coauthors involved from clinical side as rightly deserved and are duly attributed (samples collected by clinician, diagnostic facilities).

The paper we wrote is the thesis work of our lab's student and clinical collaborator hasn't given intellectual contribution to the analyses design or the manuscript writing either. We have given into the ask of the collaborator, agreeing that without samples nothing was possible, however our lab student remains heartbroken. How to console the student in our lab or minimize the feeling the student is going through?

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    I don't really have any insight on the authorship culture in biology, but your "true" question seems to be: I/We/Someone had to share first authorship although they do not feel like it was warranted - what can we do? The (unsatisfying) answer here is most likely: It's too late to change anything and sometimes you must bite the bullet to get along with others. Being upfront about this may or may not help depending on the person, but ultimately it is an uncomfortable, but important lesson to learn.
    – tistorm
    Commented Jun 21 at 11:01
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    I don't know how to put this any nicer. Your student needs to suck it up and get over it. An academic career will be judged by the body of work (over a long period of time), not by one paper. Seeing people get so twisted up to the point they make themselves physically ill over truly meaningless authorship details is sad. Sharing lead authorship on a collaborative work does not detract from ones work, it merely shows it was done with a bigger team, and that team felt they should be valued just as yours does. If that's a problem, then find someone else to collaborate with next time.
    – R1NaNo
    Commented Jun 23 at 2:13

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In a sane world the clinical contributor probably deserves authorship, but not first authorship if the paper produced, not the project, was initiated, and driven by the "lab student". Distinguish between the paper and the project, however. Lots of contributions to a project don't have a critical bearing on every paper produced within that project.

I'll note, however, that CERN, who do high energy physics, seems to be very generous about authorship, though not every author (hundreds, perhaps) is a first author.

But in the real world, if this is a first paper by the student then it probably matters little to a career if first authorship is shared or not.

For the future, though, these questions should be worked out in advance, not when a paper is about to be submitted. That is the question that you should be discussing among yourselves.

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