Fwd: Project Ideas

[Bryan Bishop]

---------- Forwarded message ----------
From: EJ <ellenjo...@aol.com>
Date: Sun, Mar 29, 2009 at 4:17 PM
Subject: Project Ideas
To: diybio nyc <diybi...@googlegroups.com>

I thought I'd start a separate thread for these. Eric Zhang already
contributed a couple in a previous thread:

I did have project ideas swirling around so here we go:

- constructing a bioreporter i.e. fusing GFP to an organism to detect
presence of a chemical (in ambient air or in food, etc)

- contribute to / participate in a DIY-bio genome sequencing project:

http://groups.google.com/group/diybio/browse_thread/thread/e34e9ab2d9...

- this is quite ambitious, but why not - construct a public version of
Craig
Venter's minimal bacterial genome.

-Eric

My thoughts on these 3 ideas are as follows:

Bioreporter-  this is what a lot of groups are talking about. Not a
bad goal, but I want to look into a rumor from a post on the main
DIYbio about ther being a law against "sensing devices" in New York.

genome sequencing project- this would be a fine thing to do but it is
just contributing $$ to pay a company to do wetwork. So it would not
be a lab project, maybe a fundraising project.

minimal bacterial genome - what are the patent issues associated with
this work?

Russ had an idea to try and engineer a bacteria to make a chemical
product of some kind. This is like the sensor idea. Both are classic
"genetic engineering" projects. We would have to hammer out the
specifics of each in order to determine if they are practical. How
difficult they are will depend on the exact nature of the sensor, or
the product, etc.

[Nathan McCorkle]

so there are a couple guys in town collaborating on this: http://www.simpore.com/applications.html
one is on my campus and I'm trying to get a meeting set up with him, but, my idea is a to use these fine filtering devices, as well as piezoelectric MEMS pumps/valves, and some of the microfluidics we've talked a bit about, build a mechanical cell able to electrically synthesize protein and DNA, as well as sequence DNA. Maybe with these filters, something more DIY (not needing silicon wafer fab) could be done using glass/plastic, and a printer head for pumping, I think it would be more elegant on silicon though, personally.

So how can we copy/simulate those filters? DIY/not-silicon-lithographphy-fab?

--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

[Alec Nielsen]

I think having the DIYbio community contribute to an Open Minimal Organism is a great idea. It would be beneficial for a number of reasons, including being safer to work with, reducing the complexity of engineered biological systems, helping to elucidate the basic features necessary for life, and providing an engineering platform for synthetic biologists.

I'm not sure how heavily guarded Venter's minimal organism is, but ETH Zurich's 2008 iGEM project (http://2008.igem.org/Team:ETH_Zurich) dealt with minimizing E. coli's genome. Over successive generations, they mutated E. coli and selected for genome reductions using nucleotide-limited media in a chemostat (the original strain was a nucleotide auxotroph). At least that was the idea. I don't know how much progress they made, or if they minimized the E. coli genome at all, but it's a cool idea that we could use as a starting point.

Then again, I've brought up the idea of developing an Open Minimal Organism with people before, and responses have been mixed. One reaction has been, "well the minimal organism would be so weak, it would die outside the laboratory." Yes, but that's partly the point. It would pose a smaller threat of being released into the environment and causing harm. If you wanted to deploy your engineered organism in the field (e.g. in a bioreactor, crops, bloodstream, etc.) you would first have to add the requisite genes necessary for survival. 

On the downside, the exotic media and extremely sterile lab conditions needed to keep the organism alive could be prohibitively expensive and unrealistic for DIYbio. It might be frustratingly fragile and finicky, and it wouldn't have decades of research and experience supporting its use. However, if it could prove a safer alternative, or improve the reliability of engineered systems, I still think it's an idea worth pursuing. Maybe there's a healthy middle ground between a completely minimal organism that's difficult to care for and the public-anxiety-causing bugs used currently.

Alec

[Dan]

I'd also be curious to know about how that iGEM team did on the genome
reduction. I know there's a commercially available strain out there:
http://www.scarabgenomics.com/default.aspx

Getting use license is fairly inexpensive. There's another license
that allows you do to your own tweaking to the genome but the price
isn't listed. I suspect it's not cheap but I can them an inquiry if
there's interest.

[Bryan Bishop]

On Sun, Mar 29, 2009 at 8:17 PM, <ellenjo...@aol.com> wrote:
> I'm not sure i understand you, Eric. You bought a copy of the patent or you
> bought  a license for the technology? If Ventner has patented the sequence
> of his genome, normally we would not be able to duplicate it without paying
> whoever owns the patent a licensing  fee.

No, I'm fairly certain that duplication does not require paying fees-
that's only when you do any sort of commercialization. For amateur
projects, it's a different story.

I found this interesting-

"Four out of five innovations originate in user suggestions"
http://groups.google.com/group/openmanufacturing/browse_frm/thread/31c7e9bc94f7954c

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

[Cory Tobin]

> No, I'm fairly certain that duplication does not require paying fees-
> that's only when you do any sort of commercialization. For amateur
> projects, it's a different story.

I'm no lawyer but according to Wikipedia, US patents exclude one from
making the invention regardless of whether or not you are going to
sell it.

"For example, in the United States, a patent covers research, except
"purely philosophical" inquiry. A U.S. patent is infringed by any
"making" of the invention, even a making that goes toward development
of a new invention — which may itself become subject of a patent."
[ http://en.wikipedia.org/wiki/Patent ]

-Cory

[Bryan Bishop]

If this is true, then why am I not being sued for harboring bacteria
that are making "makings of the invention" when it comes to particular
DNA sequences? Anyway, you're right- I didn't check the documentation,
and IANAL etc. etc. "Make at your own risk."

[Jake]

A lot of patents aren't worth the paper they're printed on (for a
variety of reasons). Most educational/institutional/research licenses
allow you to do anything you want with the organisim short of selling
it or giving it away to others.

Standard practice in industry is to simply infringe patents and wait
to be sued. Likewise standard practice for patent holders is to let
people infringe your patents until they've made enough money to make
it worthwhile to sue them for royalties.

It takes a lot of money to defend a patent and it simply isn't
worthwhile to sue someone to recover a few thousand in royalties.
Likewise there is little incentive to start paying royalties for
something that may never produce much money or may never be discovered
or may never be persued by the patent holder.

If you get sued for infringement you just end up having to pay
royalties on what you produced and you may then either negotiate a
license/royalties or may be ordered to stop production. It's a civil
matter and it's not like you're facing jail time.

A couple exceptions exist... If you're hurting their business some
way, or if they want to make an example and drive you out of
business. However, most of the time they keep their bottom line in
mind and if you're not hurting them they'd like to see you make as
much money as possible so that they can collect royalties from you.

Although the wikipedia language sounds strong there is no real
recourse or enforcement for most of it. Suppose you make an invention
in order to improve upon it. Usually the patent holder would be all
for this. Anything you make that is an improvement upon their
invention you will have to pay them royalties on if anything ever
comes of it. On the other hand if they want to sue you they're going
to end up in court saying you made a dozen of their inventions in
order to improve on it and never sold any of it for any money. You
also have no profits to show for it. How much do you think the judge
is going to order you to pay in royalties? Exactly, very little.
Meanwhile the patent holder has spent a lot of legal fees and court
costs to obtain a tiny judgement. Also, especially with small timers,
if they were to obtain a large judgement the defendent simply wouldn't
be able to pay and they would never even recover the judgement they
got. For that reason patent suits almost always are against someone
with deep pockets.

So unless you're causing them so much trouble that they are willing to
pony up a bunch of cash for lawyers just to squash you, you really
don't have anything to worry about. BTW patent cases are almost
always really messy with a poor payoff. They usually tend to drag on
for years and cost a fortune to get finished.


-Jake

[Chris]

Idea: sent activated bio luminescent
Description: a device that changes color based on smells.