DIYbio projects

[Fernando Lindenberg]

Hi guys, I have some questions.

1. Is it possible to get Biobricks from the Registry of Standard parts to use in a DIYbio lab? 

2. On lab reagents label it always says "Only for research use", using it at home or at a community lab would be a research use?

3. Are there any rules for doing DIYbio?

Sorry if these topics have been covered.

Thanks =)

[Avery louie]

1.  It is very difficult.  You would probably have to live near the registry or be a researcher.  But a lot of them dont work anyways!

2.  I am pretty sure that is a CYA move by the companies- it means it cant be used to make anything for people. For instance, they dont want to get sued if someone buys 200 proof ethanol and drinks it, or uses something they sell to make pharmaceuticals, or to self medicate.

3. In the USA, there are no real regulations on "doing" diybio.  There may be restrictions on particular organisms or chemicals, but not on doing biology as a whole.  In europe there are strict regulations on GMOs of any sort, and lab environments.

THAT SAID, the self-imposed rule is to be responsible.  Do research into what is and is not safe.  Talk to people, send out emails to the list, and don't be shady.  Find a responsible way to dispose of your trash, don't grow anything even mildly pathogenic.  Be careful, both of misunderstandings and of the actual hazards of the lab.  Wear gloves.  Don't eat stuff you make (unless you are brewing).

Good luck.  If you are looking for a place to get started, check out my blog/stay on the list- i have an idea brewin'.

blog: www.tequals0.wordpress.com  and the bosslab website www.bosslab.org

--A

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[Nathan McCorkle]

On Fri, May 25, 2012 at 9:26 PM, Fernando Lindenberg
<ff.lin...@gmail.com> wrote:

> Hi guys, I have some questions.
>
> 1. Is it possible to get Biobricks from the Registry of Standard parts to
> use in a DIYbio lab?

I thought only iGem teams got biobrick kits. You can get their text
sequences, and order the DNA online though.

> 2. On lab reagents label it always says "Only for research use", using it at
> home or at a community lab would be a research use?

That's a disclaimer saying its not been prepared in a fashion
warranting approval for human or (medical) diagnostic purposes. This
can range from the type of containers reactions are performed in
(aluminum is out for human end-use) to strictness which the produce
documents their operation. Research grade means its AT LEAST good
enough for chemical reactions, Diagnostic grade means its AT LEAST
good enough for determining human medical health information,
Pharmaceutical grade means its AT LEAST good enough for a human to
eat.

> 3. Are there any rules for doing DIYbio?

Obey zoning laws, pay taxes when due, don't do an experiment unless
you're 99% sure it won't harm yourself, your neighbors, or the natural
environment.

>
> Sorry if these topics have been covered.
>
> Thanks =)
>
>

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[Fernando Lindenberg]

Thanks for answers! =)

[EJ]

I had a disturbing conversation with Randy Rettberg last year at iGEM where he practically put his fingers in his ears and said "La La I can't hear you" when I asked if Genspace could contribute parts to the BioBricks library. Apparently anyone connected with DIYbio is taboo, at least on paper. Which is funny since they know our iGEM team is doing work at Genspace. And we have four years of distributions in our fridge, some salvaged by Genspace members who were on teams where the parts were going to be thrown out after the competition..

But they would probably flip out if we were to officially share them with everyone. This needs to be addressed and rectified, hopefully when the library changes hands.

[Cory Tobin]

> I had a disturbing conversation with Randy Rettberg last year at iGEM where
> he practically put his fingers in his ears and said "La La I can't hear you"
> when I asked if Genspace could contribute parts to the BioBricks library.
> Apparently anyone connected with DIYbio is taboo, at least on paper.

It's funny/sad because on their website they extol concepts like
"sharing" and "freedom" but when confronted about their lack of
sharing they give everyone the silent treatment.

> But they would probably flip out if we were to officially share them with
> everyone. This needs to be addressed and rectified, hopefully when the
> library changes hands.

From what I understand the Foundation has no plans to freely
distribute/sell their distributions to anyone outside the official
iGEM teams or university labs any time soon. The only way DIY people
will be able to get parts is through some unofficial distribution
method.

A couple years ago a few friends and I hashed out a plan to replicate
the iGEM distribution that year. It turned out to be a lot more
tedious and monotonous labor than we had hoped. Transforming and
minipreping in bulk was actually a breeze. The difficult part was the
quality control, which was basically a lot of restriction digests. I
could never come up with a method for rapidly checking the correctness
of the plasmids in parallel.

One could imagine a system where individuals who happen to get their
hands on some parts do quick minipreps in bulk, blot the liquid on
paper and distribute the paper to the recipients with no guarantee
that the parts are correct. The quality control would then be in the
hands of the recipients. It's not the ideal situation but for now
it's probably the only way for outsiders to get parts without any one
person dedicating their life to replicating the parts.


-cory

[Mackenzie Cowell]

Getting 1400 "standardized" biobrick parts is a neat experience, but as others have noted, many do not work or are poorly documented.  It would be great if a team put together an unofficial mini-distribution of the top 48 standard genetic parts: the best of the best.  The ones that are the most commonly used, have the best documentation, and together can be used to create a variety of different systems.

For instance, a library of control elements (promoters, rbs, terminators) with some dynamic range, a plasmid library, some reporter genes, a couple of different biosensors.

Let's start the top-48 list.  What parts would you love to have today that are also well documented and have been show to work?

I think my all-time favorite part is... bba_r0040.

Mac

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[Simon Quellen Field]

Why not make a business out of it?

A Kickstarter project, and pricing that can support a full-time person to do

the work, including the quality control.

Sell kits to schools, etc.

If you made a lot of blotted paper, then presumably the QC could be distributed

over the whole lot -- test one out of 1,000 postcards, and offer a guarantee --

money back or a new postcard.

An automated web store with outsourced fulfillment leaves the person running it

with lots of time for preparing the parts, writing up web pages that describe how

to use them, and marketing. But if fulfillment is just printing out a label and

sticking it on an envelope from a postage meter, in-house fulfillment is pretty

easy.

Offer to make up special (non-top-48) bricks for a reasonably stiff price, and then

make a few thousand postcards and add them to the catalog.

And if BioCurious wanted to teach classes in how to prepare the parts, and part of

the class was QC and blotting 1,000 postcards, then they could turn that into a

profit center. Charge for the class, and keep a cup of the QC'd part for blotting.

Win twice.

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[Mackenzie Cowell]

Ok.

[Eugen Leitl]

On Fri, Jun 01, 2012 at 06:26:39PM -0700, Mackenzie Cowell wrote:
> Ok.

OK? OK? I think we can do better than that!

[Nathan McCorkle]

Great idea Simon!

[Cathal Garvey]

Patents.

Simon Quellen Field <sfi...@scitoys.com> wrote:

Sent from K-9 Mail on Android

[Pieter]

In the parts registry some parts are labelled with a star, indicating some people liked working with it. If you are lucky they added some text on the "experience" page of that part.

The registry itself is quite awefull in terms of searching and navigating. I feel that I more user-friendly interface would already increase the value of the database. A list of "top biobricks" should be a default feature.

The lack of documentation is the main reason why you hardly see any parts being reused in the next years competition.

Whenever you like to get a biobrick for DIY usage, you might aswell contact the designers of the brick instead of the registry.

[Cathal Garvey]

Academics are devilishly hard to contact. When I was plotting out my plasmid, many if the parts I wanted were used in a different context by the bacillafilla team, so I tried asking.. By email to several folks, twitter, etc. No replies.

I ended up re-synthesizing some parts, couldn't afford others, so had to settle for a simpler system. Thankfully it still worked, no thanks to the incommunicado iGEMmers.

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[Simon Quellen Field]

What about them?

I sell all kinds of things that other people have patents for.

Usually, they don't bother with patents unless they want to sell the thing.

So we help them sell it.

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[Simon Quellen Field]

Here is where this group can make the world a better place.

If the registry is doing a bad job, we can improve access to it ourselves.

We can build a web site that has better documentation, better indexing,

easier navigation, easy user feedback, and some enterprising entrepreneur can 

offer the parts for sale to schools and amateurs.

If someone has a product that needs improving, someone else can make a business

out of improving it. If you know what's wrong with the mousetrap, fixing it can

bring the world to your door.

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[Simon Quellen Field]

It's easy to ignore Twitter and email.

But most people answer the phone.

You may find that people ignore your inquiries because they can't see any personal

benefit from going to the trouble to answer. Giving them a reason to reply can help

that. You are asking someone to do work for you -- give them something in return.

People also respond better to people they know. That is where LinkedIn can help,

and to a lesser extent Facebook and Google+. You may be connected to someone

by a third or fourth distance LinkedIn connection. Asking the person you know to

ask the person they know can get results that a cold call could not. That is the purpose

of the service.

You may also know someone with prestige, renown, fame, or some other attribute

that might get a better response rate than you would. A request from Nature, or the

Citizen's Science Quarterly might get a response that a request from an amateur

biologist might not. Most newspapers have an Action Line column to help readers

get the attention of organizations that ignore individuals without printing presses.

A service like that might be something this group can put together. A letter with a

lot of names and degrees at the bottom might get more attention than a Tweet.

Lastly, you have a lot of friends here who can help. If we are engaged in making a

better parts registry, or an adjunct web site to improve on and add to the existing

work, then getting the attention and help of people who have used particular parts

can be a group endeavor, and the information can be recorded permanently in the

database/web-page for future researchers.

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[Bryan Bishop]

On Sat, Jun 2, 2012 at 11:57 AM, Simon Quellen Field <sfi...@scitoys.com> wrote:
> People also respond better to people they know. That is where LinkedIn can
> help,

But most of us know the biobrick and registry people already. It's not
for lack of knowing them.

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

[Mac Cowell]

Is anyone interested in spending an afternoon cherry-picking the "best" 48 parts with me?

231.313.9062 // @100ideas // sent from my rotary phone

[Cory Tobin]

> Is anyone interested in spending an afternoon cherry-picking the "best" 48
> parts with me?

Count me in. I don't have much experience working with the parts - I
helped advise a team one year but that's it. So I can't really
comment on the reliability of the parts from first-hand experience but
I might be able to help pick parts that _would_ be great, assuming
they work.

Maybe a first step is to assemble a spreadsheet of parts that have
been used successfully in fully-functional projects. There's so much
stuff in the registry with no reviews and the search interface is
really really clunky to say the least. I think it would be good to
have a reduced list of stuff that has been confirmed to work as
described by at least one iGEM team, preferably multiple teams.

Does anyone know of a place that lists the parts used by each iGEM
team? That would save a lot of time digging through the individual
team wikis.


-cory

[Pieter]

There is a groupparts tag:  http://partsregistry.org/Help:Wiki_Tag_groupparts 

During our iGEM participation we tried to build an iphone app for making browsing the registry more user friendly, unfortunately the API responsiveness was so slow that it was too frustrating. It might have been improved over the past 2 years. Anyone who wants to retry can start out here:  http://partsregistry.org/Registry_API 

When selecting the top 48 biobricks I would start out with the finalist teams. In general they contributed well documented parts. Also, quickly scan the biobrick RFCs for usefull parts http://biobricks.org/programs/technical-standards-framework/

My suggestions would be:

- Enzymes commonly used in the lab that would save a lot of money when produced by yourself, such as DNA restriction and polymerase, some are available on http://partsregistry.org/Protein_coding_sequences/DNA_modification

- Constitutive promotors of the Anderson family:  http://partsregistry.org/wiki/index.php?title=Part:BBa_J23100 

- High copy number plasmid:  http://partsregistry.org/wiki/index.php/Part:pSB1C3 

- Linker domains for isolating proteins: FLAG  http://partsregistry.org/wiki/index.php?title=Part:BBa_K128000, HA  http://partsregistry.org/wiki/index.php?title=Part:BBa_K128001 and HIS  http://partsregistry.org/wiki/index.php?title=Part:BBa_K128005 

[Mac Cowell]

You free on wed afternoon? I'll work on a list, we can go over then.

We could try adding them to the public / open-source JBEI registry (or we could host our own instance) https://public-registry.jbei.org

Cheers mac

231.313.9062 // @100ideas // sent from my rotary phone

[Mac Cowell]

Thanks for the great suggestions, I'll start putting a list together this week.

231.313.9062 // @100ideas // sent from my rotary phone

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[Cory Tobin]

> You free on wed afternoon?  I'll work on a list, we can go over then.

Yeah, Wednesday works for me. I'm free all day.

-cory

[Pieter]

considering the time difference your wednesday afternoon is my wednesday midnight... so I suggest we discuss it when we are in the same timezone next week. I am looking forward to your suggestions

[Cory Tobin]

> My suggestions would be:
> - Enzymes commonly used in the lab that would save a lot of money when
> produced by yourself, such as DNA restriction and polymerase, some are
> available

I like the idea of people being able to produce their own enzymes. It
would be great if we could produce our own Taq, ligase and the four
BioBrick restriction enzymes (EcoRI, XbaI, SpeI, PstI). With those 6
enzymes one could not only work with most BioBrick parts but also
bootstrap their lab and produce any additional enzymes they need.

My main concern with this right now is the lack of inexpensive methods
for purifying the protein. Most column based methods are expensive
(NTA, etc). But I don't have much experience purifying enzymes aside
from using kits. Maybe someone with more experience knows of an
inexpensive method for producing enzymes pure enough to be used for
BioBricks? This project http://2009.igem.org/Team:Washington/Project
looked really promising but it looks like they never really got the
system working and quit working on it.


-cory

[Simon Quellen Field]

That probably has to be one of the first steps, like building a computer

that makes building computers easier. But using the hobby to make the

hobby easier does not widen the appeal to a broader audience, which is

needed for a number of reasons, such as bringing down the cost, getting

more brainpower to work on the problems, and changing the public mindset

to be more favorable to the hobby.

If we could make it easy to create bugs that produce things that lots of people

want, we get a larger audience.  Glowing fish and bunnies are already out there,

but we can add yogurt that glows, yeast with extra vitamins or sweet peptides,

bugs that sequester heavy metals, bugs that produce electricity, or hydrogen,

DNA that folds into metamaterials with negative refraction or cloaking effects,

new antibiotics, cheap DNA barcoding to do biodiversity studies, software for

analyzing personal genomes, designer bacteriophages, home analysis of gut

flora, there are all kinds of things to look into.

How about a bug that has a knockout for a particular vitamin? Spit into a cup

of it and chart the growth curve to see how much of that vitamin was in you.

Maybe we already have something that just needs some marketing to take off.

How many kids would buy yogurt that made their farts smell like bananas?

:-)

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[Cathal Garvey]

I'm working on this. I'd share the idea right away, but I want to
implement it first to guarantee that I've established "prior art" beyond
reasonable doubt.

The problem is, there are great methods out there, but they're patented
to oblivion. Consider Maltose-Binding Protein: You could, in principal,
just use cold (insoluble) potato starch to purify proteins. But, it's
patented in the EU for another few years at least, and possibly in the
US for the time being, too.

I've got something up my sleeve, but I don't want to put it into the
public domain until I'm sure nobody can steal/patent it and prevent it
from being used by the community. I'm sure patent apologists will insist
that this is unreasonable, but history says it's not.

--
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twitter.com/onetruecathal
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PGP Public Key: http://bit.ly/CathalGKey

[Simon Quellen Field]

No one is going to sue you for using cold potato starch to purify proteins.

If you give people irrational fear of litigation, they will self-censor and not

do the wonderful things the group is capable of.

Governments give inventors temporary monopolies (patents) on their inventions

in exchange for publication of the details. This is in the public interest because

otherwise the inventor would try to keep those details secret. The purpose of the

patent system is to disseminate knowledge. We are supposed to read the patents

to understand how things work, so we can use that information to produce new

ideas, inventions, and discoveries.

Companies that own the patents will try to game the system to get the benefit of

the monopoly when the benefit to society would have happened anyway. Prior art

is one way that government decides whether the idea is already public. The courts

are there to protect the interests of society, not to protect the corporations, despite

the uneven playing field caused by corporate wealth.

But consider the case of a company with a patent on potato starch purification of

proteins and a DIYBio member using that method to purify her own proteins. Several

hurdles must be overcome before the DIY biologist is harmed:

• The company must become aware that someone is using their patented process.
• They must decide that suing her is the best use of their resources.
• They must prove in court that they have been harmed.
• They must collect the damages awarded, which are limited to the damage done plus a punitive amount designed to prevent further harm.

Given that the 'damage' is that the DIY biologist did not pay a few dollars for the

potato starch the corporation sells to be used for this purpose, the likelihood of the

lawsuit ever happening is small. Patent lawsuits are about people selling other

people's intellectual property, not using it.

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[Cathal Garvey]

It's not concern of litigation, it's a matter of source derivation.

Yes, I can "DIY" my own proteins at home for lulz, and nobody will care
if I'm breaking patents.

What about if I give away/sell the plasmids, allowing everyone to break
the patents, and undercut the companies that currently live on
artificial scarcity, imposed by the patents?

Then I get sued. Not only that, their attention turns to derivatives of
the method, to cut off other problems before they appear.

Instead, we come up with "Free-Libre Open Source" DNA and methods, which
can be infinitely derivatised without fear of patent-trolling. It's
elementary, and obvious: this is where we're headed, and distractions
down patent-trollable dead-ends will only waste a lot of our time and
money as a community.

> - The company must become aware that someone is using their patented
> process.
> - They must decide that suing her is the best use of their resources.
> - They must prove in court that they have been harmed.
> - They must collect the damages awarded, which are limited to the damage

> done plus a punitive amount designed to prevent further harm.
>
> Given that the 'damage' is that the DIY biologist did not pay a few dollars
> for the
> potato starch the corporation sells to be used for this purpose,
> the likelihood of the

> lawsuit ever happening is small. Patent lawsuits are about people *selling *
> other
> people's intellectual property, not *using *it.

[cameron]

This is an interesting thread. At Biocurious, we've been trying to work with Registry parts for a couple months, not much success for a host of reasons.  Personally, I have been pushing for Bioc members to develop our own completely open source library of parts that will be freely available (no IP restrictions) for all to post into and obtain parts from.  We should all work on this together.  The lack of availability of parts is clearly hampering the growth of DIYBio in general.  At Bioc we have people in the lab who (with some training) can work to vet parts and probably maintain them.  I'm not sure about the distribution piece of the puzzle, but building a better web interface and completely and freely available bioparts would be of greater interest to this community than the Registry - as I see it.  I've been willing to spearhead this effort at Bioc, but unfortunately am heading out of the country for a few months so I can't do much (other than have phone conversations) until I return in August.  Mac,  let's try to work on something together leveraging the resources we have at Biocurious.  There is big interest from folks there to get up to speed with working with parts, stepping beyond playing with GFP.

Cameron

>> diybio+unsubscribe@googlegroups.com.

[cameron]

One more thing.  Omry gave a nice presentation on Sunday at Biocurious on his Gene Compiler software.  It would be great to integrate any database design efforts with his software because it will make designing a snap.  And, he has the interest to help this community.  He clearly understands and supports us.  We need that from the vendors, and integrating with Gene Compiler would mean that we may not need to re-invent the wheel. I'm happy to contact him about this.

Cameron 

[John Griessen]

Simon wrote: Patent lawsuits are about people selling other
people's intellectual property, not using it.

On 06/05/2012 10:21 AM, Cathal Garvey wrote:
> Yes, I can "DIY" my own proteins at home for lulz, and nobody will care
> if I'm breaking patents.
>
> What about if I give away/sell the plasmids, allowing everyone to break
> the patents, and undercut the companies that currently live on
> artificial scarcity, imposed by the patents?
>
> Then I get sued. Not only that, their attention turns to derivatives of
> the method, to cut off other problems before they appear.




>
> Instead, we come up with "Free-Libre Open Source" DNA and methods, which
> can be infinitely derivatised without fear of patent-trolling. It's
> elementary, and obvious: this is where we're headed, and distractions
> down patent-trollable dead-ends will only waste a lot of our time and
> money as a community.

Yes, finding "just as good" non-patented methods, then locking them open
somehow, (publishing solid prior art), would be a better test
of open/free-licensing than for manufactured things,
since it is in the process patent realm. I've not heard any talk of
that in the open hardware crowd.

What kind of prior art documenting do you have in mind, Cathal?

John Griessen

[Meredith L. Patterson]

On Tue, Jun 5, 2012 at 8:41 PM, John Griessen <jo...@industromatic.com> wrote:
>> Instead, we come up with "Free-Libre Open Source" DNA and methods, which
>> can be infinitely derivatised without fear of patent-trolling. It's
>> elementary, and obvious: this is where we're headed, and distractions
>> down patent-trollable dead-ends will only waste a lot of our time and
>> money as a community.
>
> Yes, finding "just as good" non-patented methods, then locking them open
> somehow, (publishing solid prior art), would be a better test
> of open/free-licensing than for manufactured things,
> since it is in the process patent realm.  I've not heard any talk of
> that in the open hardware crowd.

"Locking them open" in Europe is simply a matter of disclosing, full
stop. Published material cannot be patented if the application is
filed after publication date.

In the US it's a bit tricker, since a patent can be filed up to 12
months from the date of first disclosure. One thing that might work is
filing a provisional patent application ($125), then just letting that
naturally expire (it's only valid for a year) and not following up on
it. But I am not a lawyer and it has been several years since I've had
anything personally to do with patent law, so anyone who wants to try
that sort of thing should consult an actual lawyer.

Fun fact: BitTorrent is not patented. Bram Cohen disclosed the
algorithm publicly (on a mailing list), and never bothered to file a
patent, plus no one else patented it out from under him within the
12-month window.

Cheers,
--mlp

[Avery louie]

Iirc, you cant "patent things out from under people".  If *anyone* publishes or discloses enabling infornation, it is prior art, and the discloser has a few months to start to filing process.

[John Griessen]

On 06/05/2012 02:39 PM, Meredith L. Patterson wrote:
> One thing that might work is
> filing a provisional patent application ($125), then just letting that
> naturally expire

I've heard of that for design patents, but with the careful legal writing needed to get
a fundamental or derivative process patent at all, just filing may not be enough.
It's probably necessary to learn a little about patent writing to
properly "expire a patent app to public domain".

What are the guidelines for publishing prior art in Europe so as to preclude patentability?

John Griessen

[Ravi]

Interesting conversation on IP. While as far as DIYbio, one person, doing a patented protocol at home is not going to be sued, someone selling kits do the same protocol opens themselves up to risk. Ultimately, to spread biology and DIYbio we need low cost, intuitive "kits" for people to get started. These will have to be completely based upon expired or non-patented methods. 

Its unfortunate the amount of IP in the biology field. For example, tests using LAMP could easily be implemented for DIYbio - users can accurately, easily test for a gene/disease/virus isothermally and detect the results of the test visibly. Unfortunately patents block anyone from   providing easy kits to do so (which is what it will take to spread to "masses").

As far as DNA "parts" how can these be patented - especially if there from organisms e.g. unaltered Taq enzyme, GFP, promoters, terminators etc.? These should be open domain?

Ravi

[Cathal Garvey]

One of the idiocies of patent law is that yes, you can patent unaltered,
wild DNA.

And Avery: Indeed, technically if you publish something, then that
establishes a form of "prior art", which in the US means you'd have the
right to patent and someone else would be barred from stealing your work.

In practise, can you afford better lawyers than them? Don't, ever, rely
on patent office people to properly establish whether prior art exists.
A patent lawyer (in Australia, I believe/recall) once patented the wheel
to prove how easily exploited the system is.

There are patents on the most stunningly obvious or
obviously-preexisting things. There are patents on things invented by
others, not invented at all, or simply scribbled idly into the margins
of a mass-patent application. There are patents on hundreds of unrelated
DNA sequences at once, when technically a patent would be required for each.

Don't assume common sense, don't assume the rules will be followed, and
don't think you can win against a patent troll, because they have patent
law (a system set up to establish unreasonable monopolies by nature) on
their side from the moment they file first.

So, I always assume that it's a predatory system to be carefully
skirted. Instead of relying on publishing of an idea, if possible I'll
implement it first to fully establish a realised "prior art". I wish I
didn't feel this was necessary, because I'd far rather work out in the
open from the get-go.

[John Griessen]

On 06/05/2012 04:24 PM, Cathal Garvey wrote:
> Instead of relying on publishing of an idea, if possible I'll
> implement it first to fully establish a realised "prior art". I wish I
> didn't feel this was necessary, because I'd far rather work out in the
> open from the get-go.

So, you think a trade secret implementation is necessary before publishing,
and maybe publish with patent attorney help if it is a good one with
conceptually nearby patented competition?

It seems much open hardware is less competitive than that, but you can see
how genetically engineered chem/drug factories-in-a-bug are the ultimate
in multiplication of a monopolist's effort, so it must have attracted droves of
them in guise of biologists. Perhaps herds of biologists are also managed by monopolist bosses
with those familiar tech job IP agreements where the company owns all your output.

[Giovanni Lostumbo]

Addendum: if anyone wants to develop low cost laboratory equipment such as vaccine refrigerators/ tuberculosis medication for the developing world, MIT's media lab recently hacked a cooler and fitted it with electronic temperature sensors that relay it to a central monitoring station: http://www.patexia.com/feed/redesigned-cooler-reinvents-tuberculosis-treatment-20120601
This perhaps could help with the mass/global appeal of being able to buy and store low-cost registry parts in a free-and-open source development and distribution system.

[Giovanni Lostumbo]

Additionally, regardless of the cost of making the reagent or plasmid, having a rack of compartmentalized freezers with a dispenser rather than a big door would help with storing individual high-volume and high-frequency accessed reagents. To be notified if in a warehouse of freezers/fridges, any individual units have lost electricity/temperature levels, tweets, something like Tweet-a-watt http://makeprojects.com/Project/Tweet-A-Watt-Power-Monitor/470/1 along with other statistics customized could also help.

[Simon Quellen Field]

If it costs a million dollars to defend a patent, then if follows that it would be

economically unwise to spend money on a patent if you don't expect to make

more than a million dollars from the product.

If you make your idea public, and some large corporation patents it anyway,

where are you going to get the million dollars to overturn the patent?

In court, it is not a simple matter to show that your published idea was the same

as that in the patent. It takes lawyers and money.

Even when the patent office knows about your published idea, the lawyers for the

corporation can make convincing arguments why the new patent is different, even

when it is not. And with no opposing lawyers arguing the other side of the case, the

patent office can be persuaded.

Keeping your ideas secret out of fear that some company will steal them and patent

them is exactly what the patent system is there to prevent. It is not good for society

to have people keeping inventions and ideas secret. It is not good for the person keeping

the secret either, as it means she has no help from the broader community.

Don't worry about patents. Publish your ideas early and often, and freely. Society will

benefit earlier, the ideas will be expanded upon earlier and by more people, and we

all benefit. There will still be patents filed. You won't prevent that. But when corporations

have wanted to produce products from my own published designs, they have come to me

for licenses, because they don't know whether I have started the patent process already.

I give them the license, and take their money. Everybody wins.

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[David Murphy]

million dollars to defend a patent?

 

Lots of companies engage in speculative invoicing. it doesn't even matter if it's somthing trivial.
once they have a patent they've got the high ground legally and it's very hard to get one overturned.

For example Lodsys patented the spectacularly obvious idea of having a "buy now" button in the demo of an app.

they don't sue google or microsoft. they sue the little guys. if you don't have a legal team but do have a few thousand in cash then you're exactly who they love going after.

http://techcrunch.com/2011/05/17/patent-troll-sells-licenses-for-in-app-buy-buttons-then-tries-to-explain-itself/

Cathals approach isn't the best for society but it's utterly rational if he has anything to lose or is thinking of setting up a small buisness. the fact that it's utterly rational is an indictment of the patent system.

[John Griessen]

On 06/06/2012 11:12 AM, Simon Quellen Field wrote:
> Don't worry about patents. Publish your ideas early and often, and freely. Society will
> benefit earlier

But only as much as corps want in the course of their normal business.

Kinda leaves out all chance of some indie bio breakthroughs or getting any limelight.

Can we all just shuffle along and be of service to the universe and
be content that "the big money" gets all the glory?

And can we be content at the speed of change by monopolists acting to extract the most money
per time unit rather than effect the greatest change?

How about this:

Your goal is not to defend one patent, but a range of innovations, some closely related, some not.
You start making money and get a reputation on some free-published processes, materials, chemistry,
DNA chunks, etc.

Since defending one patent is so ridiculously expensive, start a savings account for generally
making it a pain to attack most of your innovations and spend it directly and along with
crowd funded matching funds on patent apps done with the help of a open hardware friendly attorney
in a ratio of maybe 1% of sales income on kits, machines, trainings, etc. For every $100K you didn't
spend on a single defense, you could buy 800 self filed patent apps.
If you paid your attorney $250 for handling
every boilerplate app over time and also a few carefully crafted ones for the same rate, that would
be 267 patent apps for the same money.

Sure, it needs some actual money flow to do, but why just give up on independent bio work?

[Simon Quellen Field]

Spending time and money worrying about patents leaves you less time and money

for doing science.

This is the first time I have heard anyone in the group saying that they were doing

the work to get glory.

Cathal seems to be worried that someone will get a patent that prevents him from

working with some organism, molecule, or method. I think he can work with patented

organisms, molecules, and methods without worry.

John seems to be worried that someone with money can steal his glory if he publishes

first and does not patent. I get enough ego satisfaction from publishing that I don't

worry a lot about people who copy my work, even when they make money doing so. You

can see a lot of my designs being sold in scientific toy catalogs and museum gift shops.

I don't worry a lot about that -- it doesn't seem to affect my sales, and certainly doesn't

affect my ego, which is pretty saturated at the high end already. :-)

What I am concerned about is that members of the group will self-censor, and not work

on things because they think someone else will sue them for infringing a patent. If I

steal a circuit for intermittent windshield wipers from a patent and install it in my car,

and then crow about it in Make magazine, I don't think GM and Ford are going to sue me.

Or win much if they do.

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[John Griessen]

On 06/06/2012 06:03 PM, Simon Quellen Field wrote:
> Spending time and money worrying about patents leaves you less time and money
> for doing science.

but... it could help for doing business that also lets you do
some engineering or science for pure fun. If you're too poor, you have time for nothing.
You've spent plenty of time on merchandising to create your selling web sites.
You chose less time for pure-fun-doing-science when you created your sites.
Maybe you have oodles of free time now, but I don't. Cathal has a time window
of opportunity aided by his wife. You can't expect him to waste any of that.

>
> This is the first time I have heard anyone in the group saying that they were doing
> the work to get glory.

Lots of scientists and ordinary people do things for recognition. glory <==> exaggerated form(recognition)

>
> Cathal seems to be worried that someone will get a patent that prevents him from
> working with some organism, molecule, or method. I think he can work with patented
> organisms, molecules, and methods without worry.

I've heard Cathal say he has business plans to do with kit manufacturing for diybio
and he said just yesterday "distractions

down patent-trollable dead-ends will only waste a lot of our time and
money as a community."

> What I am concerned about is that members of the group will self-censor

They may. It's not your call what they do about what they know.

I don't think talking about anti patent strategies is a waste at all.
As an engineering employee, it often came up and was ordered to stop by bosses,
put down by some peers pressure, and mostly because being more aware of business
mechanics usually makes more employees quit or complain, so seen as negative from employer perspective.

Bio seems so patent saturated, it's hard to not talk about it.

John Griessen

[John Griessen]

On 06/06/2012 02:44 PM, John Griessen wrote:
> On 06/06/2012 11:12 AM, Simon Quellen Field wrote:
>> Don't worry about patents. Publish your ideas early and often, and freely. Society will
>> benefit earlier

In this talk at minute 19 Sangiovanni Vincentelli expounds an what drives people and companies
to innovate, create value--
http://www.youtube.com/watch?v=GW4WrEI4-IY

He sums it up as innovation's impact is the driver -- something to brag about -- in society, not alone,
in an ecosystem like he matured in: Silicon Valley/Berkeley. So he probably sees mostly good in patents,
but would also be open to free-publishing's value, coming from Berkeley. Starting out as a professor,
his work caught Intel's attention and he became a founder of Cadence, so has plenty of money and is a VC
now.

All I say, is it's perfectly OK to not give all your work away in this world, and instead demand
some income from it to enable more work/play/exploring. Probably secret developments and then
expiring patent apps are the best anti-patent device we have at present.

Especially if your work has broad appeal. My work is all niche market now so I can get myself
enough money to operate well, but later, with some workable anti-patent strategy, some
work on big public issues would be nice without having to go to venture capitalists and without a
stock company to fund it.


John Griessen

[Simon Quellen Field]

Why not get a patent and then offer DIY-friendly cheap licensing?

I don't think patents are evil. They encourage people with money to invest that

money helping people with patents bring their ideas to the market.

I just think they aren't for me. They are a license to sue, and it costs money to

defend them. The people who are investing lots of money can defend them. Those

of us who choose not to solicit large amounts of money from those people, and

end up effectively working for them, can bootstrap our businesses, using the web

as both a marketing platform and as a distribution channel.

Taking money from investors in exchange for stock means that growth is the main

objective in your business. It also means that you no longer own your business, and

you can get fired if you don't grow it fast enough.

A fine furniture maker might want to spend his time hand-crafting art. He might be

content to have the business make only enough money for his family, if he gets his

satisfaction from admiring customers. Writers, artists, and performers might also

have this kind of motivation, and they tend not to be patent holders.

None of these people benefit from keeping their work secret.

I am not aware of anyone in this group getting sued for patent infringement. Nor have

I seen any evidence that someone in the group has had their ideas stolen from them and

then patented. But somehow there is a lot of fear that this will happen, and people are

spending time worrying about it, and keeping secrets from the rest of the group in fear

of it. That is harmful.

Put your ideas out there right away. The rest of the group can help, with comments,

sourcing of materials, helping you find problems, or pointing out opportunities and

corollaries you didn't think of.

Fear being what it is, I am not going to convince anyone they are not in some kind of

danger. To those people, I offer this: File a provisional patent application. It costs

between $110 and $220. You just describe your invention, perhaps adding some drawings.

You don't need legalese or lawyers. Now you can say "Patent pending" for a year.

Now you can talk about it for a year, and decide if you want to pay a patent fee (starting

at $545). That fee gets the patent office to look at your description and tell you why it

isn't patentable. Keep their refusal letter. If some company then later patents your idea,

and then sues you, you can present that letter in your defense, as evidence of prior art.

You might pay your court costs with a Kickstarter campaign. But you won't have to, since

you will never be sued.

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[Cathal Garvey]

On 8 June 2012 16:25, Simon Quellen Field <sfi...@scitoys.com> wrote:

Why not get a patent and then offer DIY-friendly cheap licensing?

Have hashed over the rest already, but this one comes up a lot.

If we were only discussing a single innovation, the idea of offering "fair licensing" would be fine; no big deal. But, we're not. We're talking about 2012, where innovations come fast and are quickly the basis for new derivatives, often in combination with many other innovations.

The effect of even fair licensing upon innovation is pretty obvious in areas like computer science (in America, where software patents are permissible) and telecoms, where hundreds or thousands of patents exist, covering everything under the sun. If I try to create a new phone tomorrow, even if it has no "novel" elements, how many "fair licenses" will I need to negotiate?

Even in a fair ecosystem where we're not all out to sue one another: say we decide that asking for 0.5% of a derivative's profits is reasonable. What about derivatives that come packaged with elements of >100 other precursors? Not unreasonable to consider in the 10-20yr future, when we may be discussing whole genome assembly from community parts created in the next 5 years.

So what then? 50% of profits divided among 100 recipients? You'd spend longer on paperwork than you'd ever spend doing the science.

It may sound like laziness, but the net effect of knowing that you'll have to beg permission from perhaps hundreds of people before your invention can reach the world, and that even one denial could break the whole idea, is to stifle innovation. It makes it too difficult to get anything done at any level above "fun tinkering at home".. and while we all love fun, some of us have to eat.

 

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[David Murphy]

It's not crazy to think that in a decade or so DIYbio enthusiasts will be able to create things on a par with golden rice but look at what happened to that.

 

it was almost killed entirely due to patents and only after a media firestorm did the patent holders even grudgingly let it be used. Even then they essentially had to hand over the rights to it to companies which hadn't done any work at all towards actually creating golden rice.

Biotech used to be more like the car industry, high cost, highly centralised and slow. a good fit for patents.
Now it's becoming more and more like the software industry. low cost, highly decentralised and fast. a ver bad fit for patents.

it's also becoming more and more popular for patent trolls who make their buisness out of lots of small lawsuits and the kinds of small buisnesses people on here are setting up are prime targets. no legal team, just enough assets to make it not worth their while to fight.

 

DIYbio hits the same problem as FOSS: any licensing fee, fair or not is too much because once you have to pay a dollar to someone else to distribute your makerbot template for some piece of equipment you can't give it away for free and heaven help you if you want to create something that uses lots and lots of little dollar priced patented methods.

[Simon Quellen Field]

This is why patents expire.

But it does not apply to you.

Your licensing fee is zero.

But you are still talking about home tinkerers being worried about patents.

They shouldn't be. No one is going to sue them for patent infringement.

You only get sued when you are making money that someone else wants, or

you are preventing someone else from making enough money to make it worth

suing you.

Publish all the ideas you want to give away for free.

If someone tries to patent one of your published ideas, and then sues to prevent you

from using it, THEN worry about how to convince a court that your idea was prior art.

That way your insurance company pays for your lawyer, and they have enough money

to defend you.

Your argument that telecom patents are preventing innovation in phones does not

seem to pass the sniff test. I see new phones come on the market every week.

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[Simon Quellen Field]

You have set up a straw man argument -- it is no surprise you can so easily knock

it down.

The question is whether to keep your ideas a secret so that no one else patents

them, or to publish them right away so that no one else can patent them.

That there have been patent snafus in the past when people tried to solve problems

via patents is not the question.

If you create a gene sequence for a rice plant that produces extra vitamins, and no one

has patented that, if you then publish it, it would not be difficult to show that as prior

art when someone tried to patent it later. If someone then took that information and

actually created the rice plant, they may have to invent methods that are novel and

patentable to do that.

But if someone uses methods that are out of patent to apply your gene to rice, they

could defend themselves against that patent.

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[John Griessen]

On 06/08/2012 12:58 PM, Simon Quellen Field wrote:
> you are still talking about home tinkerers

NOT

[Simon Quellen Field]

I was replying to Cathal.

:-)

I understand that we are all coming from slightly different directions, which is why

this looks like an argument when we probably are in much more agreement than it

appears.

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[John Griessen]

On 06/08/2012 05:37 PM, Simon Quellen Field wrote:
> I was replying to Cathal.
> :-)
> I understand that we are all coming from slightly different directions, which is why
> this looks like an argument when we probably are in much more agreement than it
> appears.

I doubt he's talking hobbyists either. Just clarifying, not ranting.

John Griessen

[Mega [Andreas Stuermer]]

Just wondering, 

If this is written in the patent "Deemed to be withdrawn" - this means the patent is expired?? Can you use it for open source projects? 

As an example this patent 

http://www.google.com/patents/EP1422711A4?cl=en

LEGAL EVENTS

Date	Code	Event	Description
Aug 31, 2011	18D	Deemed to be withdrawn	Effective date: 20110303
Jan 5, 2011	A4	Supplementary search report	Effective date: 20101206

[Mega [Andreas Stuermer]]

Just changed the title again

[John Griessen]

On 11/21/2014 05:21 AM, Mega [Andreas Stuermer] wrote:
> this is written in the patent "Deemed to be withdrawn" - this means the patent is expired??

Sounds very much like it is. Once any fees go unpaid on a patent, it goes public domain immediately.

[Brian Degger]

Also alsing my local IP place(they arent layers) .

They are also not pro+ Patents, but are interested in expired ones.

cheers

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[John Griessen]

On 11/21/2014 07:56 AM, Brian Degger wrote:
> Also asking my local IP place, (they aren't lawyers).

>
> They are also not pro+ Patents, but are interested in expired ones.

I corrected your texting.

Please tell us more... ?
I want to know about such IP places, even if not local.

[Brian Degger]

Website and blurb

http://www.bipcnewcastle.co.uk
Business & IP Centre, Newcastle

The Business & IP Centre Newcastle supports entrepreneurs, inventors and small businesses in the North East, from that very first spark of inspiration to successfully launching and developing a business.

At the Centre, you can learn the skills to start and grow your own business, research your market, learn how to protect your ideas (intellectual property) and make money from them, gain confidence and inspiration and meet fellow entrepreneurs.

You’ll find us on the third floor of Newcastle City Library, where our trained staff can help you find the specialist information you need.

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[Mega [Andreas Stuermer]]

Where have they been all my life? :D

[Brian Degger]

Surely uk isn't the only place that has that sort of business support?

On 21 Nov 2014 16:50, "Mega [Andreas Stuermer]" <masters...@gmail.com> wrote:

Where have they been all my life? :D

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[John Griessen]

On 11/21/2014 12:34 PM, Brian Degger wrote:
> Surely uk isn't the only place that has that sort of business support?

We have some volunteer organizations staffed by retirees, but it's mostly
for vanilla styles of business. IP is pretty expensive here in the US.
Lawyer fees are far more than patent office, and there is hardly anyone
to ask about forcing something open by patent and abandon to public
domain strategies. We hear a little talk about patent pools with
an open hardware purpose, but see no action.

[Mega [Andreas Stuermer]]

If there were one in Austria I would have knowen. In fact there is the Wirtschaftskammer where I went, but they said they couldn't help me with that (non-gmo) project. In fact I got the impression that if I wanted to do a lipstick factory they would help, but real innovation is not wanted here. Plus you seem to have a lot of start capital, so you'd better be born a rich man's son.

[Mega [Andreas Stuermer]]

In fact the last start-up in Austria that successfully "was noted on ~Wallstreet" (went public) was ~1995 IIRC. We are pretty much the country that is the least enterpreneur-friendly, only big corporations get real support...