Pubwication. Pubwication is what bwings us togethew
today. Pubwication, that bwessed awwangement, that dweam within a
dweam. And authorship, twue authorship, wiww fowwow you fowevah and
evah. So tweasuwe youw authorship.
Last week, our software paper on khmer 2.0 was published on
intend this paper to be a citation marker, but it also represents and
recognizes some significant software engineering work done between
khmer 1.x and khmer 2.0.
As part of the paper process, we offered authorship to everyone who
has contributed to the khmer git repository - anyone who contributed
to the repo was invited to sign on to the paper.
Addendum: I would like to credit Michael Crusoe with the initial
suggestion to offer authorship to all git committers. This is in no
way backing away from my own support for this decision, but I only
realized a few days after writing the post that I had failed to
properly credit Michael. So, kudos, Michael!
This policy has caused some consternation amongst the Twitterati, some (well,
ok, one) of whom recoiled in horror at our author list, pointing at
of (e.g.) the International Committee of Medical Journal Editors.
These recommendations are that authorship be based on (1) design
and/or analysis, AND (2) writing, AND (3) final approval, AND (4)
accountability. While the third and fourth criteria were met by all
of the authors of this paper, the first and second were probably not
met by all authors.
A few points are in order:
our condition for authorship is explicit, verifiable, and
transparent. You can look up contributors in our
release notes and GitHub
repo to find out exactly what
We note that this clarity and verifiability is in contrast to most
authorship has been getting more complicated, and traditional
authorship roles are both ill defined and clearly inadequate for
modern research. There is an ongoing effort to define
authorship roles more clearly and explicitly, and, coincidentally,
GigaScience just announced they're signing on
For those who are curious, the majority of authors on our
F1000Research paper fall under #3 on the CRediT taxonomy.
(We did not talk with F1000Research about their support for this
taxonomy in advance.)
our project is an open source project that is developed by a
community, with contribution requirements
and an extensive process for contributing.
Our author list is an explicit acknowledgement of the role that
the community has played in developing khmer, and the work that
each and every contributor invested in our process.
assuming this paper passes into the peer reviewed literature, there
may be some interesting consequences of our authorship criteria.
For example, since most formal definitions of Conflict of Interest
include shared authorship, Jared Simpson and Lex Nederbragt and I
would now be in conflict and I would be unable to review their
grants or papers. This seems silly to me!
Speaking with my senior author hat on, I hope it's clear that we are
not trying to mock authorship in any way, and this is a serious
publication on a serious project.
That having been said, we are trying out something new - in
particular, we would like to figure out how to acknowledge software
authorship within the scientific literature, both because it's the
right thing to do AND because we'd like to incentivize community
development of software. This is part of an ongoing discussion about
the changing roles of contributorship in research (see first point,
Some note has been made of the presence of what people presume to be
pseudonyms in our author list. There is a long history in science
of choosing a specific name or pseudonym to publish under; see
one example (ht @rgcjk) of
very, very many. We support this tradition.
Respecting peoples' chosen names is also important for many other
reasons. I suggest people read through the Nymwars Wikipedia page, and pay
special attention to the "criticism" section, which raises ethical,
moral, and legal reasons why a "real names" policy is problematic.
Please note that there is a special place in hell reserved for people
who attempt to deanonymize someone's pseudonym on a whim; this is both
unprofessional and potentially harmful to the individual in question.
Yes, I'm talking to you, Lior.
p.s. Please comment responsibly! On this post and all future posts, I
am going to follow the Captain Awkward comments policy - specifically,
"...sometimes comments don't show up because I delete them. This is a
dictatorship, and I can delete any comment at any time for any
There are comments.