Open Source Licenses for publishing sequences?

[Jarrad]

Hey Guys,

There seems to be alot of interest around open science and how to go about that,

Has anyone looked at Creative Commons (http://creativecommons.org/licenses/)  or Open source licenses such as Apache 2.0, MIT, GPL
Has anyone thought about creating a more specific license for biology (sequences/protocols/etc) ?

For example it's unclear what license/terms the parts in iGEM use http://parts.igem.org

[Marc Juul]

Hi Jarrad. It is generally accepted that copyright does not apply to DNA as it does not constitute a creative work. This may change in the future as increasingly complex DNA is designed by humans. There are some legal arguments available for why copyright may already apply to certain DNA sequences. For now DNA is in the regime of patents. iGEM parts use the Biobrick Public Agreement (BPA): https://biobricks.org/bpa/

-- 

marc/juul

[Bryan Bishop]

On Mon, Jul 7, 2014 at 12:08 AM, Marc Juul <ju...@labitat.dk> wrote:

iGEM parts use the Biobrick Public Agreement (BPA): https://biobricks.org/bpa/

only 19 of them:

https://biobricks.org/bpa/find-a-part/

- Bryan
http://heybryan.org/
1 512 203 0507

[Jarrad Hope]

Thanks Marc,

Wow, I had no idea, thanks for the reply. To me, this is clearly going
to change. The analogy here is we goto mars and come across a cache of
books/texts of an alien race, and sure like primitive monkeys we can
only copy, paste & delete parts of alien-Shakespeare - but I don't see
how that's not creative. As you say we will learn how to read & write
in this alien language and make better abstractions (like biobricks)
surely we enter a realm that's clearly copyrightable.

I guess that's why Real Vegan Cheese is exploring patents?

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[Patrik D'haeseleer]

Yeah, so far the Supreme Court in the US has consistently treated DNA as a chemical entity rather than as an information carrier. So patentable, but not copyrightable.

Someone should really write an original piece of poetry, and encode it into DNA along with a copyright notice...

For extra credit: come up with a codon usage table so each codon choice encodes a few bits of information. Then design a functioning enzyme that simultaneously encodes a poem as well. Then patent and copyright the heck out of it, and release it into the wild. Stand back and watch the IP system implode ;-)

Patrik

[Jarrad Hope]

lol - that's not actually a bad idea, would certainly force the topic.

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[Marc Juul]

On Sun, Jul 6, 2014 at 10:51 PM, Patrik D'haeseleer <pat...@gmail.com> wrote:

Yeah, so far the Supreme Court in the US has consistently treated DNA as a chemical entity rather than as an information carrier. So patentable, but not copyrightable.

Someone should really write an original piece of poetry, and encode it into DNA along with a copyright notice...

Related:

  http://henry.simon.net.nz/stories/2011/04/05/james-joyce-quote-in-synthetic-dna-gets-craig-venter-a-cease-and-desist-notice/

 

For extra credit: come up with a codon usage table so each codon choice encodes a few bits of information. Then design a functioning enzyme that simultaneously encodes a poem as well. Then patent and copyright the heck out of it, and release it into the wild. Stand back and watch the IP system implode ;-)

Hehe. Patenting something releases the patent documents into the public domain. I'm not sure if you could patent a novel enzyme without including the DNA sequence in the patent.

-- 

marc/juul

[SC]

Hi Jarrad,

 

To clarify, are you referring to naturally occuring DNA sequences or synthetic sequences?

Genbank has a special division for patented sequence.

 

Stacy

[Jarrad Hope]

Thanks Stacy, well, synthetic sequences, I can see digital
representations of sequences to share alot of similarities of code,
even if it's very low-level (like hexadecimal code or assembler) - the
difference being is that the existing written code is a result of a
massively distributed & massively parallel genetic algorithm that has
been running for billions of years.

This is more of a question for lawyers but I'll ask anyway - how does
patenting sequences work exactly? - like Marc says you'd need to
include the sequence in the patent if it's a discovery - but if
supreme court treats it like a chemical entity - is it then okay to
publish digital representations of that chemical entity (like say a
structure of a chemical compound?) as long as your not publishing the
actual real life sequence? what if the sequence was off by one letter?
is that a new chemical compound and therefore not under the patent (if
the sequence is specifically specified)? What happens if you setup an
entity in say, a place where the patent is not filed, like Ghana, and
have that entity publish the sequence - completely bypassing the US
patent system.

To me, the cost of acquiring a patent (what is it, like $20k?) and
then having to actively defend it just makes me feel like it's a poor
tool to use. Nevermind any litigation process will take years and
probably end in a settlement.

Anyway I'll stop rambling, it's all very confusing stuff for me :)

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[John Griessen]

On 07/07/2014 12:51 AM, Patrik D'haeseleer wrote:
> Someone should really write an original piece of poetry, and encode it into DNA along with a copyright notice...
>
> For extra credit: come up with a codon usage table so each codon choice encodes a few bits of information. Then design a
> functioning enzyme that simultaneously encodes a poem as well. Then patent and copyright the heck out of it, and release it into
> the wild. Stand back and watch the IP system implode ;-)

"But the eagle-eyed Joyce literary estate took exception to the use of the Irish master's quote, Venter revealed, sending him a
cease and desist order."

Sounds like there might be wars between patent rights and copyrights starting already!

[Pieter]

Hi Jarrad,

Thanks for raising this urgent topic again. Last month we had a great meeting on this topic at the Pixelache festival in Helsinki.

I recommend you to read some of the articles in the package that Rudiger assembled in preparation of this:

bioartsociety.fi/archives/2518

It includes the BIOFAB 3.0 report, which is quite open on the ownership issues they were facing.

Also Deibel's article on Open Genetic Code is also a good starting point for you.

Pieter

[Jarrad Hope]

Ah awesome thanks Pieter! There is alot of good material there.

I'll give at least these a read today;
BioBazaar by Janet Hope
Common Genomes by Eric Diebel
BIOFAB 3.0 Open Technology Platforms by Gaymon Bennett

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[SC]

Hi Jarrad,

It costs $280 in the U.S. to file a patent if you do it yourself.  Hiring a lawyer to do the paperwork for you is expensive, but IMHO unnecessary.  You can view other, similar patents online, and I'd say, just cut and paste to make one for yourself, then file.  There is a fairly simple format for DNA sequence patent applications.

Patents for DNA sequence requires making the sequence public, through a public disclosure process.  The USPTO requires synthetic sequences be deposited in Genbank and receive an accession number, which also makes them public and searchable.  This process, like all Genbank processes, is free.

Keep in mind that receiving a patent in the U.S. doesn't mean that someone (in the U.S. or otherwise), won't infringe on it, just that you will have proof that it was your idea first.   Legitimate businesses like pharma or biotech would contact you and negotiate a royalty if they wanted to use your sequence commercially.  Doing this would be cheaper for them than to handle a lawsuit.   Non-legit businesses, and overseas businesses, well, who knows.  Keep in mind how many Disney movies are copied and sold illegally worldwide, I think that's just what happens sometimes no matter what you do.

The USPTO has a special division for handling patents for DNA and other biomolecules.  You may be interested in reading this:

http://www.uspto.gov/web/offices/com/sol/og/con/files/cons099.htm

Best of luck to you!

Stacy

[Jarrad]

Thanks for the input Stacy.

Past week or so I've been reading up on copyright history of software, this is an excellent link for anyone interested;
http://digital-law-online.info/lpdi1.0/treatise17.html

Software choosing to copyright because it's more suitable, after having the same patent vs copyright issue we face today.

Software source-code  is analogous to sequences and it seems inevitable that will be protected under copyright and the most passive way to help enforce this is to bundle a copyright notice with the project.

Here is some relevant highlights from link above;

Copyright Act of 1976, whose Section 102 {FN3: 17 U.S.C. §102(a)}

that “original works of authorship fixed in any tangible medium of expression, now known or later developed, from which they can be perceived, reproduced, or otherwise communicated, either directly or with the aid of a machine or device” are copyrightable.

---------

The Copyright Office concluded that a computer program was like a “how to” book, and therefore protectable by copyright just like that book, if:

(1) The elements of assembling, selecting, arranging, editing, and literary expression that went into the compilation of the program [meaning the creation of the program, not converting it from source code to object code] are sufficient to constitute original authorship. This is essentially a threshold question whether the “de minimis” maxim [that there has to be a minimum amount of originality for copyright protection] applies.

(2) The program has been published, with the required notice [which was a requirement for copyright at the time]; that is, “copies” (i.e. reproductions of the program in a form perceptible or capable of being made perceptible to the human eye) bearing the notice have been distributed or made available to the public.

(3) The copies deposited for registration consist of or include reproductions in a language intelligible to human beings [source code, rather than object code]. If the only publication was in a form that cannot be perceived visually or read [say, on magnetic tape], something more (e.g. a print-out of the entire program) would also have to be deposited. {FN6: Copyright Office Circular No. 61, 1964 version} 


--------

Since then, the copyright of computer programs has been generally accepted, and it became common for computer programs to contain a copyright notice, even if they were not formally registered. This happened more because software developers copied what others had previously done rather than because of a great understanding of copyright law and its relationship to computer software

———

works, other than audiovisual works, expressed in words, numbers, or other verbal or numerical symbols or indicia, regardless of the nature of the material objects, such as books, periodicals, manuscripts, phonorecords, film, tapes, disks, or cards, in which they are embodied. {FN7: 17 U.S.C. §101}


———
the House Report discussing the Act states:
The term “literary works” does not connote any criterion of literary merit or qualitative value: it includes catalogs, directories, and similar factual, reference, or instructional works and compilations of data. It also includes computer data bases, and computer programs to the extent that they incorporate authorship in the programmer’s expression of original ideas, as distinguished from the ideas themselves. {FN8: H.R. Rep. No. 94-1476 at 54}

As you can see there is alot of existing wording here that can easily be applied to sequences. My hope is other people on this list would start applying copyright notices to their projects.