
I was wrong (part 2) - adenadel
https://liorpachter.wordpress.com/2017/08/03/i-was-wrong-part-2/
======
glangdale
Good to see this change, but I wish people wouldn't go down this road to begin
with.

Speaking as someone who sits in industry now, I have found it almost
_impossible_ to successfully conclude negotiations between not-very-interested
academics who don't really understand how licensing works (and the staff who
supposedly help them) and a big, paranoid company.

When you put some rando commercial license or complicated terms on your
(likely tax-payer funded) data or software, what it essentially requires from
big companies is a extremely expensive legal review to see what we would be
signing up for. This review might be considerably more expensive than the
amount being asked for the data/software. What's more, if a small company
signs up for this, and ever wants to be _acquired_ by a big company, the
review may not happen (small companies and startups are usually more relaxed
about this stuff) but will have to take place during acquisition.

Bonus points for when the academics or their representatives wander away mid-
discussion.

As a final bonus, I have seen our commercial competitors in this area just
essentially fund university researchers to do thinly veiled advertising by
accessing the same dataset for an "academic" paper. Meanwhile I sit on my
hands respecting "the latter and spirit" of the law.

~~~
folli
As someone also on the industry side of things, what would be your recommended
solution to the problem? On the one hand we don't want the legal mess that
licensing entails, on the other hand I'm absolutely in favor of reimbursing
the academics in some way. But how?

Some new, standardized, industry accepted commercial license (who will invest
the required legal effort to come up with such a license that's accepted by
both sides?)? A concept based on voluntary donations (good luck getting that
by the finance department)?

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anjc
I don't understand why you think you were wrong, based on the article. Surely
it depends upon your objectives. If your goal is for researchers to use the
software then one license might be preferable, if your goal is
commercialisation then another license might be.

In the same way that some researchers wont use software which doesn't have
permissive licenses, some companies wont use software which does.

I don't get it. I also don't get why you expected license agreements to be
signed and completed in a single day by commercial entities. You couldn't sign
and complete a 5 minute coffee date with most company's IP staff within a
single day, nevermind have licensing arrangements agreed upon.

~~~
ubernostrum
The wrongness I read from it is a certain level of arrogance, that there can't
really be anything too complex in licensing and copyright issues, and all
those lawyers just must be posturing or engaging in pointless make-work. The
discovery that well-understood standard license terms are preferred for a
reason, and that there are very real issues lurking in non-standard license
agreements, and corresponding realization that maybe all the people saying
"you're wrong" had a point... is a step toward correcting that arrogance.

~~~
anjc
That makes total sense but it sounds as if his realisation tended towards open
licenses being preferable in all academic scenarios, due to a now-more firmly
held belief that lawyers etc are a waste of time. This obviously isn't a rule
which applies generally, and I'm not sure why it even applies here when his
goal was to commercialise, not to please researchers.

------
dankohn1
I'd like to commend the author for realizing that a commercial license was not
achieving the goals he had for his software and being willing to own up
publicly about why and how he changed directions.

However, while I have used MIT/BSD-style licenses in the past, I can no longer
recommend them, as they potentially open up software users to malicious
submarine patent attacks. That is, a contributor can intentionally contribute
code that (purports to) read on a (not-even-issued-yet) patent, and then later
threaten to sue users of the software.

That's why I instead recommend Apache-2.0. My arguments are more fully
described here: [https://www.cncf.io/blog/2017/02/01/cncf-recommends-
aslv2/](https://www.cncf.io/blog/2017/02/01/cncf-recommends-aslv2/)

~~~
paulgb
Interesting, has this actually happened?

~~~
dankohn1
Yes, a patent-owning entity has tried to contribute code reading on that
patent. Apologies that I can't give the details.

------
hprotagonist
I've been about half a block down this road. Thank God, the university office
determined it wasn't worth the universities time to invite the lawyers -- and
my project is happily open source.

~~~
mbreese
One of my least favorite experiences in grad school was dealing with our
school's tech transfer office. They fought hard to avoid using the GPL for
licensing anything. Just getting them to agree that a simple (to be published)
tool should have an open source license was difficult. (And took many
meetings)

Fast forward to two different Bay area universities and it was a completely
different experience. Open source licenses were agreed upon over a quick
email.

~~~
hprotagonist
I had a fun time with the library copyright office. 6 months before my thesis
defense I emailed them with "hi what's policy and procedure for creative
commons licenses on theses". Nobody had ever asked before...

edit: my thesis is cc-by licensed.

~~~
ensignavenger
Is it traditional for students to sign away copyright to their thesis to the
University? That seems outrageous to me, but perhaps I am missing something?

~~~
hprotagonist
traditionally you register a personal copyright. it's implicit if you register
nothing.

some students may choose to request an embargo on their thesis, in those cases
where their thesis work will be published elsewhere (in a peer reviewed
journal, usually), or if their thesis would constitute disclosure of something
for which a patent application is underway.

my thesis was boring enough to avoid those cases.

~~~
ensignavenger
If you retained the copyright personally, why would you need permission from
the university to publish your work under a creative commons license? Was it
just a courtesy email to let them know your plans?

~~~
horsawlarway
I can't speak for OP, but in my experience it's very rare for a thesis to be
_just_ your work.

It's based on data and research often paid for by the university, and includes
the work of many different people. indirectly: advisors, lab partners,
professors, other students. Directly: Co-authors of papers, research
assistants, and other contributors.

It's a messy bundle of work.

~~~
ensignavenger
But copyright isn't based on ideas and doesn't cover raw data/facts- it covers
the expression of those ideas and the compilation of the data.

------
sevensor
I was an onlooker -- for four months -- as a university IP office struggled to
license source code developed at the university, to one of its own
researchers. When the drama was concluded, the IP office couldn't find the
source code.

------
nnutter
BSD does not have a patent license clause so if Lior, et al. have a patent on
any part of the algorithm then won’t commercial use will still be ambiguous?
And even if they don’t it could still be using (infringing) on a patent of a
third party. Basically software patents make using any software a risk but
possibly more so when you’re using something based on novel ideas.

Edit: GPL and ASL have explicit patent clauses (obviously only applies to
patents the software licensor has authority to license).

------
dm319
Here's the license for stampy, a popular read aligner from Oxford:

12\. License ===========

This is a release version. Permission is granted for the normal use of the
program and its output in an academic setting, including in publications. If
the program is used to generate data for a publication, please cite this
paper:

G. Lunter and M. Goodson. Stampy: A statistical algorithm for sensitive and
fast mapping of Illumina sequence reads. Genome Res. 2011 21:936-939.

The program itself may not be modified in any way, and may not be reverse-
engineered.

This license does not allow the use of this program for any commercial
purpose. If you wish to use this program for commercial purposes, please
contact the author.

No guarantees are given as to the program's correctness, or the accuracy or
completeness of its output. The author accepts no liability for damage or
otherwise following from using and interpreting the output of this program.
The software is supplied "as is", without obligation by the author to provide
any services or support.

[http://www.well.ox.ac.uk/~gerton/README.txt](http://www.well.ox.ac.uk/~gerton/README.txt)

------
Gatsky
Some context:

The blog author just wrote another post which was essentially a hatchet job on
a 'rival' software package. One of the major differences between his software
kallisto and the rival Salmon was the license - Salmon has a GNU General
Public License.

~~~
dm319
'I was wrong' part 1 was a really a discussion about how wrong / fraudulent
some authors were who published in Nature in 2004. It looks like it turned
into a bit of flame-fest[1], with the original authors chipping in.

[1] [https://liorpachter.wordpress.com/2015/05/26/pachters-p-
valu...](https://liorpachter.wordpress.com/2015/05/26/pachters-p-value-
prize/#comment-4436)

~~~
Gatsky
No I mean this blog post: [https://liorpachter.wordpress.com/2017/08/02/how-
not-to-perf...](https://liorpachter.wordpress.com/2017/08/02/how-not-to-
perform-a-differential-expression-analysis-or-science/)

------
dsjoerg
Thanks for sharing your painful journey!

~~~
adenadel
I can't take credit, I just follow Lior's blog :)

------
drefgert
There won't be too many comments on this post cause the internet ain't
interested when someone says they are wrong. The internet wants to TELL them
they are wrong, when they think they're right.

~~~
csydas
I'm not sure that's so true. Everyone enjoys a good argument over what license
the author should have used. )

I do get what you're saying but I think people discuss positive things all the
time on even the worst sites. Admitting you're wrong isn't all that novel, but
the changing of license is.

~~~
drefgert
So you're saying I'm wrong?

~~~
mort96
What are you trying to argue? Can't people on the Internet both enjoy telling
someone they're wrong, _and_ be interested in someone saying they were wrong,
at the same time?

