Diy Bio Brent Listserve

Dear DIY Biology people,
Would be interested in reactions or comments. I don't personally

expect anything bad
to come from DIY bio as it is presently constituted. And I would be
extremely interested
in credible "fun apps" or "useful apps" that offered capabilities or
quantitative levels of
functionality that one could not get otherwise, even if we all
understood that these were
just ideas.
Best,
Roger
----------
Power and responsibility
Roger Brent
Director and President
The Molecular Sciences Institute
Berkeley, California
The introduction
Peter Parker and Uncle Ben are on my mind. The reason is that is
that a month ago I was jumped by Craig Venter. There were TV cameras
around. The live audience was an interesting, edgy mix, on the
interface between "technology", meaning computer technology, and
culture/ media/ journalism; I had just given a closely prepared talk
on the history, promises, and perils of biology, 20 minutes from solar
ignition to origin of life to photosynthesis to agriculture to
Asilomar to now; and I had paid particular attention to the existing
threat from remade and lightly engineered viruses, to the various
technology-empowered approaches that could contribute to a defense
against such unpredictable pathogens. The whole set of ways the
defense strategy needs to shift.
For whatever reasons, Craig came prepared to take the talk as an
attack on himself and his agendas. As if review of human use of
biology in historical context, and talk about real risks, somehow
threatened his ability to mobilize resources toward his goals:
removing nonessential genes from Mycoplasma genitalium, synthesizing
hydrogen and methane, cruising around the world in boats, etc.. The
word "fearmonger" came up, multiple times. "Chicken Little" came up
too, afterwards. And one terrific sound bite, which is that more
people were killed by lightning last year than by anthrax attacks
during the past 50 (see below).
Of course, nobody likes being jumped, but being jumped happens, I
think I held my own, and when it's up on YouTube under Creative
Commons, I hope it at least makes decent television. More to the
point, Craig happens. Complaining that the man can go off half-
cocked, or that he can conflate attempts at analysis with personal
attacks...isn't relevant. Might as well complain that hurricanes are
wet and full of wind. Because Craig is a force of nature, and, what's
more, he's one of those forces that is usually a force for good. It
is very largely due to him that we had large scale shotgun sequencing
as soon as we did. And it's very largely due to his efforts and those
of the extraordinary people he attracted that the fly genome, and then
the human genome, were delivered so fast; had Craig not acted, it
might have taken years more. Craig's sense of scientific celebrity
and his adroit use of it bespeak a deeply intuitive understanding of
our culture. His current work to focus attention on the genomic
analysis of microbial ecologies and energy production is igniting
imaginations and no doubt helping recruit the next generation of
genomic scientists and engineers all over the world. So this isn't
about Craig. Still less about the anomie of the contemporary US
scientific intellectual (misunderstood... yet again... shall we
cry?).
Rather, this is about asking people who identify as members of a
synthetic biology community to take a few next steps toward coming of
age.
The facts on the ground
The first starting point is that certain kinds of biological
engineering, including making pathogens drug resistant, and recovering
live viruses from transfected recombinant DNA, are technically
feasible and have been so for a very long time. The recovery of
poliovirus from cDNA was accomplished by Baltimore and coworkers in
1982. To restate that, a generation ago, a lab (albeit one of the
best virology and recombinant DNA labs in the world at the time) made
infectious virus from DNA. If one needed a demonstration that one
could remake viruses, this was it. Nowadays, remaking viruses is a
matter of making appropriate DNA constructions that encode the viral
genome and that provide any other functions needed to get live virus
out. Polio is one of the simple ones. To remake many other DNA and
RNA viruses requires helper functions-- for example, protein hardware
to make negative RNA strands into positive RNA strands, or to start
viral transcription going. So, to remake viruses, one transfects with
DNA that is the viral genome or (for RNA viruses) directs the
synthesis of the viral genome, together with DNA that directs the
synthesis of the helper functions. You don't need to provide the
helper functions from DNA constructs, you can also co-transfect genome-
encoding DNA into cells co-infected with a related "helper virus" that
you have screwed up so that it cannot replicate. Depending on the
virus one is re-making, the ways one goes about getting live virus
back from DNA used to construct it range from really simple (mix 12
things, wait 24 hours) to relatively gnarly (some classes of viruses
have not even been done yet, so would require new construction work
and troubleshooting). To calibrate "gnarly", I mean "might take one
of the 5,000 most skilled research groups in the world as much as a
year to carry out". For any given family of virus, I (or any of more
than a thousand scientists) can be a great deal more specific about
how one would perform any given construction job, and what technical
hurdles might still exist and how one would overcome them. But given
that this page will be crawled by Google within a week after it goes
up, this is as specific as I'm now going to get.
The second starting point is to imagine two circles in a Venn
diagram. One circle is the set of people who know how to perform
various manipulations and pieces of construction work, who could for
example make the DNA, or troubleshoot what was wrong in a co-
transfection setup as above. The second circle is the set of people
who might be motivated to build and release a self-replicating
organism that hurts people. The number of people in the first circle
has been growing steadily, at a guess at around 10% per year, for many
decades since 1973. At the moment, the number in the second circle is
large, and is affected by international political attitudes (I am
guessing that it has grown significantly in the past 5 years). If we
are in luck, there might now be no people in the intersection of those
two circles. But even if we are lucky now, there is no reason to think
we will stay lucky in the future, because the number of people in the
first circle will continue to grow.
To run the calculation for the first circle, let's ask, if there
are 20,000 undergraduates at UC Berkeley, how many possess the
technical skills and access to labs to make a gram positive organism,
anthrax, resistant to the first line antibiotic fluoroquinilone
antibiotic, ciprofloxin? Let's guess that one tenth of them do. 2,000
UC Berkeley undergraduates. Now, let's try to guess how many have the
DNA manipulative skills needed to construct the plasmids and perform
the transfections needed to follow recipes to recover animal viruses?
Surely, more than 20? Maybe 200? Now, given that techniques keep
getting easier, and more people keep getting trained in their use, how
many past and present UC Berkeley undergraduates will have those
skills in 2016?
How synthetic biology interacts impacts this existing strategic
situation
Now, the group of people who call themselves synthetic biologists
did not make this situation. But up to now, the community of
synthetic biologists has been poorly defined and has staked out
boundaries, that, from outside, seem weird and artificial. To be
provocative, I am going to call the community a self-made ghetto, with
an arbitrary line drawn to wall off a group from a much greater
community of related activities (I am imagining the sacred cord, the
eruv, that the faithful can place at the perimeter of orthodox Jewish
neighborhoods, thus enabling those within the cord to perform certain
activities on the Sabbath). Inside the ghetto, good work on
fabrication, abstraction hierarchies and (in the US but not in Europe
where it is considered to be chemical engineering) on microbe-powered
chemical synthesis. At the same time, the overwhelming majority of
the real genetic engineering work of the world, such as engineering of
crop plants, the applications of genetic engineering to scientific
research, to pharmaceuticals, and to medicine, and most of the complex
applications of recombinant DNA to microbial synthesis of organic
chemicals, has been going on for 3 decades, outside the boundaries and
largely unaware of ghetto activities.
So I would like to stipulate some things. I believe that most
reasonable people can agree with Venter that the applications of
synthetic biology within the current ghetto boundaries pose no
significant risk. Hold a gun to my head, and I say: "zero risk".
Zero, zip, nada, none. To say this again, there is no reason anyone
should fear a minimal Mycoplasma genome, or a bug that makes plastic,
or methane, or artemisinin. Period. Full stop.
But I also submit that most reasonable people can fear drug
resistant anthrax, or smallpox, or a revenant 1918 flu that carries a
point mutation that makes it resistant to the first line antiviral,
tamiflu.
I also submit that the increased attention, capital investment,
and sheer technical ingenuity now being deployed to developed chemical
synthesis of long pieces of double-stranded DNA provides another path
to making DNA constructions. It joins other schemes, ligation in
vitro and PCR and various methods perform homologous ...
read more »
Reply Reply to author Forward Rate this post: Text for clearing space
You must Sign in before you can post messages.

To post a message you must first join this group.
Please update your nickname on the subscription settings page before posting.
You do not have the permission required to post.
Might as w ell pos Feb 4, 3:41 pm Bryan Bishop <ka DIYbio
Bryan View profile

More options Feb 4,
Bishop
3:41 pm
From: Bryan Bishop <kanz...@gmail.com>

Date: Wed, 4 Feb 2009 16:41:02 -0600
Local: Wed, Feb 4 2009 3:41 pm
Subject: Re: Might as well post this for reactions
Reply | Reply to author | Forward | Print | Individual message | Show original | Report this
message | Find messages by this author
On Wed, Feb 4, 2009 at 9:51 AM, Roger Brent <brent.ro...@gmail.com> wrote:
> Dear DIY Biology people,
Weren't you the person who said that you don't trust us?
- Hide quoted text -

- Show quoted text -
How about you just go use a separated habitat/environment if you're

going to be a hypochondriac and hikikomori about viruses?

So, whenever I see people talking about risks, I always refer to the
concise Wikipedia article on SPOFs, or Single Points of Failure. In
any network system, a SPOF is where you have this node spontaneously
fail or do something terrible, which might be a cascading black swan,
completely unpredictable and turns everything upside down. For
instance, if you only have your very important document on one
computer, that's a SPOF, because if that point fails, then all of the
other things that you were going to do with that one document will now
be generally undoable.
http://en.wikipedia.org/wiki/Single_point_of_failure
"""
The strategy to prevent from total systems failure is
1) Reduced Complexity
Complex systems shall be designed according to principles decomposing
complexity to the required level.
2) Redundancy
Redundant systems include a double instance for any critical
component with an automatic and robust switch or handle to turn
control over to the other well functioning unit (failover)
3) Diversity
Diversity design is a special redundancy concept that cares for the
doubling of functionality in completely different design setups of
components to decrease the probability that redundant components might
fail both at the same time under identical conditions.
4) Transparency
Whatever systems design will deliver, long term reliability is based
on transparent and comprehensive documentation.
"""
So, I see DIYbio as implementing a few of these, especially #4 and #1.
But when it comes to risks of total system failure due to viruses, I
see we're completely failing at #3 with having only one single
atmosphere, and thus a possible medium for harmful biological agents.
I mean, it's just a bad idea. It's nice though. I really do like
everything, but I hardly think it's fair to play the blame game and
act like viruses are the cause for how much that possibility sucks-
it's also partly due to just the way that the world has historically
worked.
> The reason the boundaries and self-policing can't work anymore is
> that the multiple and reasonable connotations of the term "synthetic
> biology" naturally mean that anybody not of the ghetto will
> immediately associate it with the entirety of recombinant DNA work in
> general. And this is a time when discussions about recombinant DNA
> powered work are breaking surface again. For all sorts of reasons,
> including the ones above On November 18th, Kofi Annan of the UN
> called for a world discussion about the dangers arising from the
Global problems need global solutions- habitats are one way if you
want to do the environmental isolation from viruses gig. I mean, let's
be honest here. You're looking at the problem of viral infection, so
let's solve *that* problem. Viruses are easy to replicate. Habitats
aren't- that's where the actual effort needs to go into, if you really
are worried about these viral infections.

Because Uncle Ben really isn't a person. Now, if the government wants
to contribute, stay active in these matters, increase infrastructure
for new research and so on, that's fantastic and I am sure many people
on this list would find that a worthwhile use of their time.
> Responsibility to articulate and help bring about positive
> consequences. I suspect that most people who read this will share the
I agree. There is a strong need for clear articulation of topics and

issues. I suspect that there is a problem of 'institutional
boundaries' however- some of us might be articulating thoughts from a
point of view that government bodies simply can't address, such as the
idea of passing university and corporate boundaries for labwork, which
for a while now has been the norm.

...
read more »

Might as w ell pos Feb 4, 4:01 pm Jason Bobe <jaso DIYbio
Jason View profile

More options Feb 4,
Bobe
4:01 pm
From: Jason Bobe <jasonb...@gmail.com>

Date: Wed, 4 Feb 2009 18:01:26 -0500
Another worthwhile article to read and discuss was published by George
Church at SEED:
Safeguarding Biology by George Church • Posted February 2, 2009 11:03 AM
http://www.seedmagazine.com/news/2009/02/safeguarding_biology.php
I like that George offered opinions on practical steps to evaluate safety of
GEOs:
<snip>
But actions speak louder than words. These safety features will be accepted
and used only if they undergo rigorous testing in physical isolation and
review by a diversity of critics. The battery of necessary tests is
formidable, and includes ensuring that GEOs are not toxic to
immunocompromised lab animals, as well as lab examinations of ecological
challenges like unwanted gene transfer and harmful mutations. If we can
construct safety measures that pass all these tests, the door will be opened
to potentially allow more sophisticated biotechnological interventions in
areas like human health.
</snip>
Jason Bobe
...
read more »

Might as w ell pos Feb 4, 4:28 pm Andrew Hessel < DIYbio
View profile
Andrew More options Feb 4,
Hessel 4:28 pm
From: Andrew Hessel <ahes...@gmail.com>

Date: Wed, 4 Feb 2009 18:28:17 -0500
I like that George is thoughtful and looks beyond the immediate outcomes of
a design.
I have to admit to being skeptical of work to reengineer the genetic code,
though. Nature to me is one giant combinatorial engine, leading to
diversity we are just now beginning to comprehend on a molecular/genetic
level. (The macroscopic understanding is pretty weak, too, in many
environments.)
Ever stop to consider why alternative or species-specific genetic codes did
not widely result, after billions of years of evolution?

...
read more »

Might as w ell pos Feb 4, 4:55 pm DIYbio
Meredith View profile

L. More options Feb 4,
Patterson 4:55 pm
From: "Meredith L. Patterson" <clonea...@gmail.com>

Date: Thu, 5 Feb 2009 00:55:21 +0100
On Thu, Feb 5, 2009 at 12:28 AM, Andrew Hessel <ahes...@gmail.com> wrote:
> Ever stop to consider why alternative or species-specific genetic codes did
> not widely result, after billions of years of evolution?
Um, dude, what do you think speciation is?

There are thousands, perhaps millions of species-specific proteins and
metabolic pathways out there. Countless more existed in species that
are now extinct. Certainly there's a laundry-list of machinery that's
common across species -- heritability and parallel evolution at work
(thanks, selection pressure!) -- but the innumerable variation already
extant in nature is precisely the result of species-specific genes.
Even common functionality has subtle differences from one species to
another, DNA-wise.
Cheers,
--mlp
Might as w ell pos Feb 4, 5:16 pm Guido D. Núñez-M DIYbio
Guido View profile

D.
More options Feb 4,
Núñez-
5:16 pm
Mujica
From: Guido D. Núñez-Mujica <noalaignoran...@gmail.com>

Date: Thu, 5 Feb 2009 19:46:25 +1930
Meredith, as I see it, Andrew means the code for translating
nucleotides to protein.
AAA codes for lysine pretty much in every animal, plant and fungus.
There are exceptions, however. Our Mithocondria uses a slightly
different code. But the exceptions are not that different from the
standard and there are only two extra aminoacids from literally
thousands of possibilities.
Here there is more about the variations:
http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
On Thu, Feb 5, 2009 at 7:25 PM, Meredith L. Patterson


Might as w ell pos Feb 4, 5:23 pm William Heath <w DIYbio
View profile
William More options Feb 4,
Heath 5:23 pm
From: William Heath <wghe...@gmail.com>

Date: Wed, 4 Feb 2009 16:23:43 -0800
Why does mitochonrdria have dna? Does it use it somehow?
-Tim
On Wed, Feb 4, 2009 at 4:16 PM, Guido D. Núñez-Mujica <


Might as w ell pos Feb 4, 5:27 pm Guido D. Núñez-M DIYbio
Guido View profile

D.
More options Feb 4,
Núñez-
5:27 pm
Mujica
From: Guido D. Núñez-Mujica <noalaignoran...@gmail.com>

Date: Thu, 5 Feb 2009 19:57:53 +1930
Yes. Mitochondria have a set of their own genes that are transcribed
and expressed there and fulfill functions on cellular metabolism.
However, why is a different question of which I ignore the answer.


Might as w ell pos Feb 4, 5:29 pm Bryan Bishop <ka DIYbio
Bryan View profile

More options Feb 4,
Bishop
5:29 pm

Date: Wed, 4 Feb 2009 18:29:41 -0600
On Wed, Feb 4, 2009 at 6:23 PM, William Heath <wghe...@gmail.com> wrote:
> Why does mitochonrdria have dna? Does it use it somehow?
Yes, in humans it encodes the use of 13 proteins which have caused

Aubrey quite a headache. There have been some who have suggested
attempting to port the proteins into the nucleic DNA instead of
mitochondrial DNA.
http://www.mfoundation.org/research/adgpubs#allo
http://www.mfoundation.org/research/adgpubs#mtmut
See also MitoSENS. I'm sure there's other more interesting
mitochondrial DNA research out there that I am failing to remember to
cite.
- Bryan
http://heybryan.org/
1 512 203 0507

Might as w ell pos Feb 4, 5:33 pm Ingrid Sw anson < DIYbio
Ingrid View profile

More options Feb 4,
Swanson
5:33 pm
From: Ingrid Swanson <iswan...@u.washington.edu>

Date: Wed, 4 Feb 2009 16:33:47 -0800
The why: Mitochondria have DNA by virtue of being derived from
bacteria. Some mitochondrial proteins are made from this DNA (they
have their own ribosomes too) while others are encoded in the
chromosomal DNA (or the "extracellular plasmid" from the point of view
of the mitochondria, as coined by mitochondrial expert Dr. Douglas
Wallace). These proteins are imported into the mitochondria from the
cytoplasm.
Ingrid
On Feb 4, 2009, at 16:23, William Heath <wghe...@gmail.com> wrote:


Might as w ell pos Feb 4, 6:10 pm Lora <lmcamer...@ DIYbio
View profile
Lora More options Feb 4,
6:10 pm
From: Lora <lmcamer...@verizon.net>

Date: Wed, 4 Feb 2009 17:10:20 -0800 (PST)
I think Roger is perhaps missing the basic point that when it comes to
restricting *either* knowledge of how-to *or* access to cooties *or*
having lots of angry disenfranchised people, Elvis has left the
building.
So far all the approaches to biohazard control I have seen are sort of
built on the precedent set by the nuclear industry: The same basic
premise that uranium is hard to come across, that manipulating it into
things that go boom is a difficult skill to master, that the knowledge
is arcane and mysterious.
This is just not the case w/ biology. Limiting access to nasty
pathogens? What are you going to do, quarantine every squirrel and
prairie dog in the Southwest US and Pacific coast? Ban sheep farming?
For that matter, you better start paying nursing aides in the old
folks' homes a LOT better and putting them through serious background
checks--nursing homes are prime breeding grounds for antibiotic-
resistant pathogens of all sorts.
Limit access to the knowledge? How? Burn every undergrad text and open
access article on transfection techniques published since 1950? Close
every public library? Good luck with that.
I'm probably dating myself here, but when I was an undergrad, the
first step in setting up a blot was going to the grocery store to buy
Brillo pads. The first step in making a DNA gel was boiling potatoes
and cutting up strips of blotter paper. (Yes, I am a dinosaur,
thanks.) Kits and Invitrogen toys don't actually enable anyone to do
anything they couldn't do before, they just make it faster and more
efficient. *waves cane at Roger* You whipper-snappers don't know how
good you have it!
Look, when it comes to the issue of Horrible Pathogens That Will Kill
Us All, synthetic bio is about the LAST thing I worry about. I'm more
worried about idiots who run factory farms that drown entire towns in
several feet of raw sewage, feedlot operations that use massive
amounts of antibiotics and hormones in food, lack of infection control
in hospitals / schools / workplaces that don't give sufficient sick
days, prion diseases, farm labor pooping Salmonella in the spinach
fields for lack of toilets, dumping raw sewage into rivers and lakes
used as drinking water and recreation, lack of public health
infrastructure, poor vaccination rates due to fear-mongering, and
using halogen-based disinfection in water systems when we know just
about every water bug is chlorine-resistant at this point. Those are
things which are proven, over and over, to create disease and death,
*and which we already know how to fix*. It should tell you something
when we know without debate that those things are hazardous to life
and humanity, and we have the technology in hand to fix those things,
*yet we don't fix them anyway*. I'd suggest that when it comes to
making the world safer, we work on things we already are sure of,
before going off half-cocked on the WhatIfs. We got enough problems,
let's not go imagining more.
On Feb 4, 7:33 pm, Ingrid Swanson <iswan...@u.washington.edu> wrote:


Might as w ell pos Feb 4, 6:28 pm Len Sassaman <L DIYbio
Len View profile

More options Feb 4,
Sassaman
6:28 pm
From: Len Sassaman <Len.Sassa...@esat.kuleuven.be>

Date: Thu, 5 Feb 2009 02:28:33 +0100 (CET)
Hmmm. Your common sense smackdowns are intriguing to me and I wish to
subscribe to your newsletter.

Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

Might as w ell pos Feb 4, 6:35 pm Mackenzie Cow e DIYbio
View profile
Mackenzie More options Feb 4,
Cowell 6:35 pm
From: Mackenzie Cowell <m...@diybio.org>

Date: Wed, 4 Feb 2009 20:35:44 -0500
In response to Lora's comments:
I think Roger would agree with you about the difficulty of biological
material control. As he wrote, it is unlike the nuclear situation,
which is amenable to material and process control. Instead, it is:
"the "Maginot line problem", that an attacker will want to outflank
fixed defenses, means that we will need to move to agile detection and
response to pathogens we cannot now predict."
I do not think Roger is necessarily advocating a ban of synthesizer or
a stockpiling of hepa gas masks, but rather that synthetic biologists,
and larger society in general, are not devoting enough effort to
developing strategic defenses to biological disaster. Roger argues
that the intersecting area of the venn diagram of expertise + ill-will
is increasing, and hence the chance of disaster is as well. As people
who are contributing to that increase by developing the first circle
in that diagram, it is our responsibility to also spend effort
developing the safeguards and defenses.
A practical step forward would be for iGEM (igem.org) to launch a
biological defense track for the 2009 competition. In this way, at
least some of the newest echelon of synthetic biologists would be
devoted to inventing the defenses Roger is wishing for.
Mac


Might as w ell pos Feb 4, 6:46 pm Julie Norville <julie DIYbio
Julie View profile

More options Feb 4,
Norville
6:46 pm
From: Julie Norville <julie.e.norvi...@gmail.com>

Date: Wed, 4 Feb 2009 20:46:38 -0500
Hi Roger Brent, If you will be in Boston, we would like to invite you to
give a lecture or lead a discussion at a Synthetic Biology Working Group
lunch (at MIT) for the local synthetic biology and DIYbio community to
discuss these issues further. If you are interested, we can continue this
conversation (about setting up a SBWG lunch) offline.
http://openwetware.org/wiki/SynBERC:MIT
Best,
Julie Norville
-----------------------------------------------------------------------------------------
Mackenzie Cowell to diybio
show details 8:38 PM (3 minutes ago)
Reply
Yes, I would definitely be up for that. I'm sure Jason B would as well.
When can we introduce Roger Brent?
Mac
On Wed, Feb 4, 2009 at 8:32 PM, Julie Norville

...
read more »

Might as w ell pos Feb 4, 10:34 pm JonathanCline <jn DIYbio
View profile
JonathanClin More options Feb 4,
e 10:34 pm
From: JonathanCline <jncl...@gmail.com>

Date: Wed, 4 Feb 2009 21:34:19 -0800 (PST)
On Feb 4, 9:51 am, Roger <brent.ro...@gmail.com> wrote:
> Dear DIY Biology people,
> Would be interested in reactions or comments. I don't personally
> expect anything bad
> to come from DIY bio as it is presently constituted. And I would be
> extremely interested
> in credible "fun apps" or "useful apps" that offered capabilities or
> quantitative levels of
> functionality that one could not get otherwise, even if we all
> understood that these were
> just ideas.
> Best,
> Roger
Your quote: "I am going to call the community a self-made ghetto,

with an arbitrary line drawn to wall off a group from a much greater
community of related activities (I am imagining the sacred cord, the
eruv, that the faithful can place at the perimeter of orthodox Jewish
neighborhoods, thus enabling those within the cord to perform certain
activities on the Sabbath)."
It's not necessary to use libel. Did you just say "ghetto"?
ghetto |ˈgetō|
noun ( pl. -tos or -toes)
a part of a city, esp. a slum area, occupied by a minority group or
groups.
Why would you want to allude that "the group of people who call
themselves synthetic biologists" is a slum?
slum |sləm|
noun
a squalid and overcrowded urban street or district inhabited by very
poor people.
• a house or building unfit for human habitation.
(And then you ask for the opinion of this list? That's so bizarre!)
## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################


Might as w ell pos Feb 5, 5:57 am Nick Taylor <nick1 DIYbio
Nick View profile

More options Feb 5,
Taylor
5:57 am
From: Nick Taylor <nick1...@googlemail.com>

Date: Fri, 6 Feb 2009 01:57:47 +1300
Local: Thurs, Feb 5 2009 5:57 am
This post gives me a fairly massive sense of relief tbh - someone actually
attempting to address the risk at a systemic level rather than just trying
to downplay it.
I think I'd add something to that list... something that Jason's
microbial-birdwatching addresses I think - I haven't quite put my finger on
it yet, but it's got something to do with an network-based, over-arching
awareness of what's going on. Everywhere.
I mean transparency is one thing, but you've still got to have people who
can read - and having networks of on-the-ground trend/change-spotters would
create a lot of resilience in the system overall - with regards early
warnings etc.
That algal bloom up the road from me for example wasn't dealt with until it
had gone really toxic and was leaching ammonia everywhere. I think informed
bio-citizen-journalists are probably fairly crucial if Craig Ventor's
predictions of a Cambrian-era style explosion of species hit anywhere near
the truth.


Might as w ell pos Feb 5, 6:28 am Nick Taylor <nick1 DIYbio
Nick View profile

More options Feb 5,
Taylor
6:28 am

Date: Fri, 6 Feb 2009 02:28:32 +1300
> Look, when it comes to the issue of Horrible Pathogens That Will Kill
> Us All, synthetic bio is about the LAST thing I worry about.
Yea, well personally I'm more worried about upsetting the balance of
ecosystems by introducing new species that can out-compete the existing ones
than I am about human diseases. You can persuade humans line up for
vaccinations. Honey bees not so much.
> It should tell you something when we know without debate that those
> things are hazardous to life and humanity, and we have the technology
> in hand to fix those things, *yet we don't fix them anyway*.
Fair point, but when you're talking about replicating organisms, you're into
profoundly, qualitatively different ground. It's like comparing software
bugs with botnet viruses. It's linear vs exponential.
> I'd suggest that when it comes to making the world safer, we work on
> things we already are sure of, before going off half-cocked on the
> WhatIfs. We got enough problems, let's not go imagining more.
It's not a question of imagining more, it's a question of making more.

Might as w ell pos Feb 5, 7:09 am Bryan Bishop <ka DIYbio
Bryan View profile

More options Feb 5,
Bishop
7:09 am
Date: Thu, 5 Feb 2009 08:09:01 -0600

Thank you. :-) Strategies for preventing total system failure are
important, and another aspect of it is a constructive or
creation-based approach. Anyway, check out this too:
http://constructal.org/ "According to the Constructal law, every
system is destined to remain imperfect, i.e. with flow resistances.
The natural constructal tendency then is to distribute the
imperfections of the system, and this distribution of imperfection
generates the shape and structure of the system."
http://en.wikipedia.org/wiki/Systemantics
"""
* The Primal Scenario or Basic Datum of Experience: Systems in general
work poorly or not at all. (Complicated systems seldom exceed five
percent efficiency.)
* The Fundamental Theorem: New systems generate new problems.
* The Law of Conservation of Anergy [sic]: The total amount of anergy
in the universe is constant. ("Anergy" = 'human energy')
* Laws of Growth: Systems tend to grow, and as they grow, they encroach.
* The Generalized Uncertainty Principle: Systems display antics.
(Complicated systems produce unexpected outcomes. The total behavior
of large systems cannot be predicted.)
* Le Chatelier's Principle: Complex systems tend to oppose their own
proper function. As systems grow in complexity, they tend to oppose
their stated function.
* Functionary's Falsity: People in systems do not actually do what the
system says they are doing.
* The Operational Fallacy: The system itself does not actually do what
it says it is doing.
* The Fundamental Law of Administrative Workings (F.L.A.W.): Things
are what they are reported to be. The real world is what it is
reported to be. (That is, the system takes as given that things are as
reported, regardless of the true state of affairs.)
* Systems attract systems-people. (For every human system, there is a
type of person adapted to thrive on it or in it.)
* The bigger the system, the narrower and more specialized the
interface with individuals.
* A complex system cannot be "made" to work. It either works or it doesn't.
* A simple system, designed from scratch, sometimes works.
* Some complex systems actually work.
* A complex system that works is invariably found to have evolved from
a simple system that works.
* A complex system designed from scratch never works and cannot be
patched up to make it work. You have to start over, beginning with a
working simple system.
* The Functional Indeterminacy Theorem (F.I.T.): In complex systems,
malfunction and even total non-function may not be detectable for long
periods, if ever.
* The Newtonian Law of Systems Inertia: A system that performs a
certain way will continue to operate in that way regardless of the
need or of changed conditions.
* Systems develop goals of their own the instant they come into being.
* Intrasystem [sic] goals come first.
* The Fundamental Failure-Mode Theorem (F.F.T.): Complex systems
usually operate in failure mode.
* A complex system can fail in an infinite number of ways. (If
anything can go wrong, it will.) (See Murphy's law.)
* The mode of failure of a complex system cannot ordinarily be
predicted from its structure.
* The crucial variables are discovered by accident.
* The larger the system, the greater the probability of unexpected failure.
* "Success" or "Function" in any system may be failure in the larger
or smaller systems to which the system is connected.
* The Fail-Safe Theorem: When a Fail-Safe system fails, it fails by
failing to fail safe.
* Complex systems tend to produce complex responses (not solutions) to problems.
* Great advances are not produced by systems designed to produce great advances.
* The Vector Theory of Systems: Systems run better when designed to
run downhill.
* Loose systems last longer and work better. (Efficient systems are
dangerous to themselves and to others.)
* As systems grow in size, they tend to lose basic functions.
* The larger the system, the less the variety in the product.
* Control of a system is exercised by the element with the greatest
variety of behavioral responses.
* Colossal systems foster colossal errors.
* Choose your systems with care.
"""
> I think I'd add something to that list... something that Jason's
> microbial-birdwatching addresses I think - I haven't quite put my finger on
> it yet, but it's got something to do with an network-based, over-arching
> awareness of what's going on. Everywhere.
That's interesting, could you elaborate some more on this over-arching

awareness?
> I mean transparency is one thing, but you've still got to have people who
> can read - and having networks of on-the-ground trend/change-spotters would
> create a lot of resilience in the system overall - with regards early
> warnings etc.
Neil Gershenfeld has mentioned that there is a new type of literacy,

which largely surpasses the basics of reading/writing and is more in
tune with microcontroller programming, or basic stuffhacking.
"From this combination of passion and inventiveness I began to get a
sense that what these students are really doing is reinventing
literacy. Literacy in the modern sense emerged in the Renaissance as
mastery of the liberal arts. This is liberal in the sense of
liberation, not politically liberal. The trivium and the quadrivium
represented the available means of expression. Since then we've boiled
that down to just reading and writing, but the means have changed
quite a bit since the Renaissance. In a very real sense post-digital
literacy now includes 3D machining and microcontroller programming.
I've even been taking my twins, now 6, in to use MIT's workshops; they
talk about going to MIT to make things they think of rather than going
to a toy store to buy what someone else has designed. The World Bank
is trying to close the digital divide by bringing IT to the masses.
The message coming back for the fab labs is that rather than IT for
the masses the real story is IT development for the masses. Rather
than the digital divide, the real story is that there's a fabrication
and an instrumentation divide. Computing for the rest of the world
only secondarily means browsing the Web; it demands rich means of
input and output to interface computing to their worlds. There was an
amazing moment as I was talking to these Army generals about how the
most profound implication of emerging technology for them might not
lie in designing a better weapon to win a war, but rather in giving
more people something else to do. So we're now at a cusp where
personal fabrication is poised to reinvent literacy in the developed
world, and to engage the intellectual capacity of the rest of the
world."
- Bryan
1 512 203 0507

Might as w ell pos Feb 5, 11:41 am Roger <brent.ro.. DIYbio
View profile
Roger More options Feb 5,
11:41 am
From: Roger <brent.ro...@gmail.com>

Date: Thu, 5 Feb 2009 10:41:00 -0800 (PST)
Dear All,
Brian requested a reply to some of the thoughtful comments
on this question, and that's more than fair. Right now,
I can't do them justice, so will be brief. Might have done
this better earlier, but will welcome further guidance as
to what might be appropriate etiquette on discussion
forums of this type.
In no particular order.
Am impressed with the many eyes arguments and
of course with the brio and idealism of this community.
We all understand that controls of material and knowledge
here are impossible. I suspect that everybody also would
agree that the spread is a good thing.
The use of the word "ghetto" was, as said, deliberately
intended to provoke. Not the meaning of "slum"
but rather the earlier meaning, but neighborhood
full of weirdly religious people. Who might
for example have run a string
around the boundaries of the neighborhood and
nobody not of the neighborhood can possibly
take the string seriously. I did not mean to be too
sharp. In the essay, however, I did mean to
try to push for intellectually defensible boundaries
(in Europe, the 100s of people making bugs to
make materials call themselves microbial
chemical engineers). And I especially wanted
to see if it was possible to diminish the drumbeat
of false claims of novelty. None of the above
is at issue here in the DIY community.
Would love to talk with people about the security
issues in person on a trip to Boston or wherever.
Am not sure I will be able to participate consistently
in this, but I will try, and am grateful to Brian and others
for past or future pointers for proper behavior.
Roger

...
read more »

Might as w ell pos Feb 5, 5:10 pm Lora <lmcamer...@ DIYbio
View profile
5:10 pm

Date: Thu, 5 Feb 2009 16:10:52 -0800 (PST)
Local: Thurs, Feb 5 2009 5:10 pm
>Fair point, but when you're talking about replicating organisms, you're into
profoundly, qualitatively different ground.

I *am* talking about replicating organisms though. Bacteria and human
pathogens definitely replicate. For sure, they acquire fitness from
the selective pressures in their environments (antibiotics, heavy
metals, etc.). I agree that there's a HUGE difference between a
naturally occurring antibiotic-resistant Clostridium that happens to
live in a biofilm in garden soil with Acinetobacter neighbors, vs. a
Clostridium that has specifically adapted to life in a Zithromax-
saturated hospital, and that the latter is much more hazardous, having
already acquired other pathogenic characteristics from its
environment, but I don't see that cloning antibiotic resistance is
necessarily more hazardous or worse than the hospital pathogen
adaptation. If anything, the nosocomial infection adaptations should
be worse--able to acquire Staph toxin genes, already selected for
pathogenicity in humans (as opposed to mice or whatever the Evildoers
are using), already surviving every precaution and treatment humanity
can throw at it in the bestest of medical facilities. Cloning that
sort of thing is technically much more challenging and likely to
result in many disappointing failures.
Well, OK, it's only the Evildoers who would be disappointed. But you
know what I mean.
> >You can persuade humans line up for
> vaccinations. Honey bees not so much.
Feh, humans not so much. We have that problem right now--measles

outbreaks all over the Western world due to that Wakefield fool who
couldn't do math (or immunology, but that's another rant), polio all
over Nigeria and north African countries because of the politics of
the war in Iraq, and so on and so forth.
> It's not a question of imagining more, it's a question of making more.
How is the Boy Scout Code Of Honor working out for Hwang Woo-suk, Jan
Henrik Schoen, Malcolm Pearce, Thereza Imanishi-Kari, Charles Dawson,
Luk van Parijs, Pons & Fleischmann...?
We've got the Geneva Convention of course, which already forbids
bioweapons, although I hear that's not working out so hot these days
either. I mean, if international treaties don't do the trick, what
other ideas did you have?
I'm sorry you're scared, but honestly, I don't know what to do for
you--I don't see that there's a whole lot more to be done. I already
vote for the "diplomacy first" hippie politicians when I can. I could
make you a nice cup of tea and give you a hug, that's about it.

Might as w ell pos Feb 5, 5:40 pm Nick Taylor <nick1 DIYbio
Nick View profile

More options Feb 5,
Taylor
5:40 pm

Date: Fri, 6 Feb 2009 13:40:39 +1300
>> I think I'd add something to that list... something that Jason's
>> microbial-birdwatching addresses I think - I haven't quite put my finger
on
>> it yet, but it's got something to do with an network-based, over-arching
>> awareness of what's going on. Everywhere.
> That's interesting, could you elaborate some more on this over-arching
> awareness?
What? Like the emergent consciousness of the universal mind? :)

Something like that. Something akin to the web's extraordinary sensitivity
to censorship.
I have a feeling that a type of no-single-person, group-awareness might
actually be an emergent behaviour of networks - not everyone can keep their
eye on everything that concerns them all the time, so everyone keeps an eye
on their little corner of the world... twittering happily to their
neighbours... and if something that concerns the whole network crops up, the
whole network responds.
George Orwell was at least partly wrong... the surveillance society isn't
(generally) a top down thing, it's a bottom up thing. Everyone carries a
camera that can upload into the mass-consciousness. Strangely enough, the
way our govts (especially the British) seem to be reacting to this
network-empowerment is to use 1984 as an instruction manual. Weird.
To (ahem) illustrate: I used to be terrified of being filmed on CCTV drunk
out of my mind in Soho, London. Last time I was there I found myself (as you
invariably do) singing Lost Highway* in the middle of the road at 4am...
being filmed by people with fucking cellphones.
Anyway - the network-response-effect was what I was on about yesterday (in
the point-missing that I apparently did) when I said that Obama's campaign
was about resilience. When attacked by a hierarchy, the response wasn't
hierarchical - instead of saying "oooh, but I'm not a muslim", his entire
base responded by donating money.
This is an observation I've pinched from Umair Haque, who's a genius
(kindof) and who's blog caused me to blurt "holy crap" and to right there
and then read the whole thing from start to finish.
http://discussionleader.hbsp.com/haque/2008/11/obamas_seven_lessons_f...
http://www.bubblegeneration.com/ (though he's mostly on a Harvard blog now)
So. DIYbbio. What I'd like to do... me, personally... (and this is for Jason
if he's listening), is collect algae/pond samples from the various places
that I live, microscopically photograph them and upload them to the web, for
people who know what they're talking about, to identify... so I can learn
how to identify them too.
I also want to do this as an artistic endeavour. I think a series of green
circular plates on a website would look cool.
Every node doesn't need to be a smart node in other words - the thing is to
crowd-source the collection of data, and in a decoupled sort of way,
crowd-source the analysis of it.
There's probably a way of automating this - but it's also a good way of
giving people something to do... or to be more specific, of giving people
value, within an economic system that's geared to reducing their worth.
Sorry. Long post.
Nick
* http://www.youtube.com/watch?v=2PGTEk2ESCU
You can't make an omelette without breaking a few eggs.

Nick View profile

More options Feb 5,
Taylor
5:56 pm

Date: Fri, 6 Feb 2009 13:56:52 +1300
re: http://en.wikipedia.org/wiki/Systemantics
My dad would agree with this one:
* Le Chatelier's Principle: Complex systems tend to oppose their own proper
function. As systems grow in complexity, they tend to oppose their stated
function.
He's a school teacher - and has long held that every new "measure"
instituted within the educational system always has the exact opposite
effect to the one intended.
I'd add one to that list I think :
* Complexity is the fractaline manifestation of flawed assumptions.
A bit like 80s haircuts etc.

Nick View profile

More options Feb 5,
Taylor
6:23 pm

Date: Fri, 6 Feb 2009 14:23:35 +1300
> Would love to talk with people about the security
> issues in person on a trip to Boston or wherever.
I think security is impossible. It's a fear-response, and isn't the issue -

and as someone (who I can't (dear God, please forgive me) help but picture
as looking a bit like the clairvoyance one off Harry Potter*) said
yesterday...
... we already have these problems and we aren't fixing them now.
I think what needs to happen is that we need to become much better at
building resilient ecosystems - we need this regardless of whether 100
million neo-alchemists trying to find the elixir of life (in their potting
sheds) are suddenly unleashed upon the world at once. As an aside, I prefer
the word "quarantine" to"security". The etymological feng-shui of the word
rests a little easier. Security is a state of mind, and is impossible.
Quarantine isn't.
Anyway, maybe solving the problems we've got now will go a long way towards
solving the ones we create.
Nick
* http://www.aceshowbiz.com/images/news/00016210.jpg

Might as w ell pos Feb 7, 6:14 am Lora <lmcamer...@ DIYbio
View profile
6:14 am

Date: Sat, 7 Feb 2009 05:14:38 -0800 (PST)
Local: Sat, Feb 7 2009 6:14 am
> I think security is impossible. It's a fear-response, and isn't the issue -
> and as someone (who I can't (dear God, please forgive me) help but picture
> as looking a bit like the clairvoyance one off Harry Potter*) said
> yesterday...
> ... we already have these problems and we aren't fixing them now.
BWAHAHAHA! I wish I was as pretty as Emma Thompson! Actually, you're

not far off--picture Professor Trelawney in jeans, a t shirt with a
caffeine molecule on it, and a tweed jacket, and that's about right.
And now, my husband, who is reading this over my shoulder, is
sniggering. Thank you...
View profile
9:55 am
Date: Thu, 5 Feb 2009 08:55:37 -0800 (PST)
Subject: Based on reactions, a question
Dear DIY bio people,
Do you think people might be receptive to some measure of absolute
prohibition, along the
lines of "Thou shalt not design, nor build, nor isolate, nor modify,
nor grow, nor release any
self replicating organism, with the intent of causing harm?"
Related
Are their circumstances under which people might agree voluntarily
to a moratorium on projects involving animal viruses, particularly
human ones,
and projects aimed at altering the host range of bacterial pathogens,
or that attempt
to enable bacterial colonization of mammalian organisms, or that
enable invasion
of mammalian cells?
The idea is behind the second question is that the realistic prospect
of such
projects being of interest to and accessible to this community may be
some time
off, and in the interim a community might be able to think through
how or if it wanted to regulate these, whether it should submit such
experiments for review, if so what kinds of review structures if any
might be
appropriate.
Overall thrust. Since so many of us are firmly committed to the idea
that
democratization and dissemination of empowering technologies is
usually A Good
Thing: how, in this particular sphere, with the particular properties
of bio, including
of course that all humans share a similar genome, and an overlapping
set of
microbiological commons, can one try to ensure that this particular
democratization
and dissemination remains a good thing?
Roger

Based on reactio Feb 5, 10:16 am Bryan Bishop <ka DIYbio
Bryan View profile

More options Feb 5,
Bishop
10:16 am

Date: Thu, 5 Feb 2009 11:16:04 -0600
Subject: Re: Based on reactions, a question
On Thu, Feb 5, 2009 at 10:55 AM, Roger Brent wrote:
> Dear DIY bio people,
Roger, would you please reply to the efforts that people put into
replying to your last email before you continue? Otherwise I doubt
people are going to be interested in continuing to reply to you. I'm
kind of hesitant, since it seems my efforts are going nowhere with
you. But I'm willing to give the benefit of a doubt for the moment.
> Do you think people might be receptive to some measure of absolute
> prohibition, along the
What is "absolute prohibition"?

> lines of "Thou shalt not design, nor build, nor isolate, nor modify,
> nor grow, nor release any
I think that happened in my gut this morning. Am I going to prison?

> self replicating organism, with the intent of causing harm?"
Wouldn't it be more useful if people who are actively trying to cause

harm to publicly admit it?
> Are their circumstances under which people might agree voluntarily
> to a moratorium on projects involving animal viruses, particularly
Voluntary to a moratorium ("suspension of activity")? But this is a

basic misunderstanding of both human and non-human biology. The mold
growing on your cheese in the refridgerator does *not* read UN
international backjournals.
> human ones,
Disregarding whether or not people have agreed to a moratorium, how

would you identify whether or not a moratorium is actually implemented
and isn't just some lie you tell yourself to feel better?
> The idea is behind the second question is that the realistic prospect
> of such
> projects being of interest to and accessible to this community may be
> some time
> off, and in the interim a community might be able to think through
> how or if it wanted to regulate these, whether it should submit such
> experiments for review, if so what kinds of review structures if any
> might be
> appropriate.
I would appreciate any recommendations for the formal semantic

structure of submissions of reviews, if you have any. For instance,
I've been thinking of some tools that would take SBML files and other
experiment description formats and generate information and analyses
of materials involved (like for the clinical/molecular biology
protocols), spit out relevant Material Safety Datasheets, etc., so
maybe we can collaborate on this front?
> microbiological commons, can one try to ensure that this particular
> democratization
> and dissemination remains a good thing?
That's too vague though. You can't do that.

(1) "Good" according to each of our utility functions and valuing functions?
(2) "Good" according to some vague, amorphous grouping of people?
(3) "Good" according to some non-existent community standard?
etc.
I don't think you're making any sense. :-(
- Bryan
1 512 203 0507

Based on reactio Feb 5, 11:48 am Roger <brent.ro.. DIYbio
View profile
11:48 am

Date: Thu, 5 Feb 2009 10:48:16 -0800 (PST)
Brian, you raised questions of how to behave in online
forums and of course a great many intellectual issues.
It could be that I won't be able to participate in open discussions
as much as the thoughtfulness of the community would
merit. Can try, though. For now am grateful for your
thoughts on governance in general. In specific, would
agree that the "semantics" of certain kinds of iffy experimentation
is somewhat limited (see the 7 classes of "experiments of
concern" in the Fink Report) and thus in principle
something that one could approach via a formalized
syntax. It's precisely this kind of thinking that is unlikely
to come from inside the current biomedical establishment
and that can do good for the world. Roger
On Feb 5, 9:16 am, Bryan Bishop <kanz...@gmail.com> wrote:


Based on reactio Feb 5, 12:43 pm Kay Aull <katherin DIYbio

Kay View profile
More options Feb 5,
Aull
12:43 pm
From: Kay Aull <katherine.a...@gmail.com>

Date: Thu, 5 Feb 2009 11:43:37 -0800 (PST)
The people who would agree to "not cause harm" - they aren't the ones
you need to worry about. Pretty words won't stop a criminal. Also,
I'm no lawyer, but I suspect that homebrew bio-weapons are already
illegal.
That said, I think there might be a place for community norms here.
We might reasonably agree that some experiments are off limits; we
can't stop you, but we can refuse to offer technical support and other
resources. Nobody's going to help with an "experiment of concern"
here - my personal line is farther back, around "no pathogens,
period". You can learn a great deal from safe, tractable model
systems, and we should encourage their use.

Based on reactio Feb 5, 4:18 pm Bryan Bishop <ka DIYbio
Bryan View profile

More options Feb 5,
Bishop
4:18 pm

Date: Thu, 5 Feb 2009 17:18:43 -0600
On Thu, Feb 5, 2009 at 12:48 PM, Roger Brent wrote:
> thoughts on governance in general. In specific, would
> agree that the "semantics" of certain kinds of iffy experimentation
> is somewhat limited (see the 7 classes of "experiments of
> concern" in the Fink Report) and thus in principle
> something that one could approach via a formalized
> syntax. It's precisely this kind of thinking that is unlikely
> to come from inside the current biomedical establishment
> and that can do good for the world. Roger
I previously did a quick writeup on XML for clinical protocols:

http://groups.google.com/group/openmanufacturing/msg/1fc4fbbfd4a6fb23
This sort of system could be extended to the representation of amateur
experimentation, such as the specifying materials, protocols, tools
and items of interest, and then a safety analysis tool for lab
protocols would be kind of neat to have. I can see how it might be
architectured.
- Bryan
1 512 203 0507

Based on reactio Feb 5, 4:42 pm Douglas Ridgw ay DIYbio
Douglas View profile

More options Feb 5,
Ridgway
4:42 pm
From: Douglas Ridgway <ridg...@dridgway.com>

Date: Thu, 5 Feb 2009 16:42:51 -0700
Hi Roger,
On Thu, Feb 5, 2009 at 9:55 AM, Roger <brent.ro...@gmail.com> wrote:
Yes, I think you'd find a consensus behind this statement. In fact,

and feel free to correct or augment my understanding, but I believe
this is essentially already in place in the US, under the Bioterrorism
Act of 2002.
> Related
> human ones,
> and projects aimed at altering the host range of bacterial pathogens,
> or that attempt
> to enable bacterial colonization of mammalian organisms, or that
> enable invasion
> of mammalian cells?
Speaking for myself, absolutely. To do such a project in a safe and

acceptable manner requires institutional support. My working
assumption is that the rules which govern my kitchen or basement are
no different than the ones elsewhere. If an experiment would require
review elsewhere, I can't do it in my basement, since there is no IRB
for my basement. Lots of interesting demonstrations and experiments
require no review, however. For example, extracting DNA from pumpkin
seeds can be done with food-grade reagents, and I've done this in my
kitchen. I started with food, I added dish detergent and vodka, and I
ended with food. Recombinant DNA work, however, in my understanding,
if we operate under the NIH guidelines, requires a basic (Level 1)
lab, and my kitchen could never qualify. My basement, on the other
hand, could potentially be made into a Level 1 lab. If I then chose
experiments which would be exempt from review (again, under NIH)
anywhere else, I think I could operate in a manner which would be
generally seen as safe and acceptable. For the moment, though, since
my basement isn't (yet?) a lab, if I want to make bacteria glow, I
have to do it elsewhere.
Still, I think there's a role for some kind of advice and review
process for DIYers. In particular, if an institutional investigator is
uncertain as to whether or not a particular study is in fact exempt,
they have someone to ask. This provides both a check, and a way of
spreading blame. DIYers have no such formal backup... but maybe we
should.
doug.
Based on reactio Feb 5, 9:10 pm Josh Perfetto <j... DIYbio
Josh View profile

More options Feb 5,
Perfetto
9:10 pm
From: Josh Perfetto <j...@snowrise.com>

Date: Thu, 05 Feb 2009 20:10:41 -0800
On 2/5/09 8:55 AM, "Roger" <brent.ro...@gmail.com> wrote:
Comeon, the answer to this question is really basic and has nothing to do
with biology :) A great majority of people would agree to this, and a small
minority won't.

If as you say it is true that such projects would not be a realistic

prospect for the DIY community for some time, then what is the purpose of
trying to create a moratorium on it? Just go ahead and start the thinking
on the second part.
> Overall thrust. Since so many of us are firmly committed to the idea
> that
> democratization and dissemination of empowering technologies is
> usually A Good
> Thing: how, in this particular sphere, with the particular properties
> of bio, including
> of course that all humans share a similar genome, and an overlapping
> set of
> democratization
That is a good and important question; however I'd just point out that the
reason this is an important question is because the
democratization/dissemination you mention is a reality, not just an idea we
are committed to.
-Josh


Based on reactio Feb 5, 9:23 pm DIYbio
View profile
rhdurland@yahoo.co More options Feb 5,
m 9:23 pm
From: "rhdurl...@yahoo.com" <rhdurl...@yahoo.com>

Date: Thu, 5 Feb 2009 20:23:06 -0800 (PST)
Doug,
FWIW, at least some rDNA experiments are officially exempt from NIH
guidelines. See http://oba.od.nih.gov/oba/rac/guidelines_02/NIH_Guidelines_Apr_02.htm...
and http://oba.od.nih.gov/oba/rac/guidelines_02/APPENDIX_C.htm#_Toc7238628.
Moreover, NIH guidelines technically only apply to institutions that
receive NIH funds (http://oba.od.nih.gov/oba/rac/guidelines_02/
NIH_Guidelines_Apr_02.htm#_Toc7261550).
Of coures, you can and should voluntarily choose to follow NIH
guidelines anyway, as a way to ensure safety. But I don't think you're
under a legal requirement to do so.
Ross
On Feb 5, 5:42 pm, Douglas Ridgway <ridg...@dridgway.com> wrote:


Based on reactio Feb 6, 9:34 am JonathanCline <jn DIYbio
View profile
JonathanClin More options Feb 6,
e 9:34 am
From: JonathanCline <jncl...@gmail.com>

Date: Fri, 6 Feb 2009 08:34:55 -0800 (PST)
Local: Fri, Feb 6 2009 9:34 am
Such a prohibition is worthless. Because, very, very few people in

the world do anything with intent to harm; and, if these rare people
(who are psychologically deranged, usually, and also not well
educated) do want to harm people, they will pick an easier way than
spending months on a biology project (like buying a gun). Even your
previous post's argument can be deflated using this reasoning. You
are discussing premeditated acts and very few people act with
premeditation to harm others.
It is far more likely that some unintended harm will occur due to
accident or negligence-- usually stemming from lack of proper
education. Though, you aren't discussing these as possibilities. (Why
not?)
> Related
> human ones,
> and projects aimed at altering the host range of bacterial pathogens,
Yes, however only after proper education (see 1,2,3 below).

> or that attempt
> to enable bacterial colonization of mammalian organisms,
No. Several iGEM projects propose to do this, and probiotic yogurt

already does this.
Do you personally eat genetically modified foods? Why or why not?
> or that
> enable invasion
> of mammalian cells?
No. Although I don't really know what "invasion" means, I assume it's
the same rationale as above. Is that a medical term?
> The idea is behind the second question is that the realistic prospect
> of such
> projects being of interest to and accessible to this community may be
> some time
> off,
Define "some time". I guess 9 months (1Q 2010). Anything iGEM can
do, people here can do better.
> and in the interim a community might be able to think through
> how or if it wanted to regulate these, whether it should submit such
> experiments for review, if so what kinds of review structures if any
> might be
> appropriate.
Does a ghetto typically regulate anything? No. A ghetto behaves

according to mob rules. So why would you ask a ghetto? (Maybe you
should discuss things reasonably, rather than trying to "provoke"
reactions.)
If a community were to regulate projects, then why would "outlaws"
join the community? Individuals who want to do such projects don't
need a DIYBio mailing list. They just need to take 3 semester classes
at a community college in the biotech curriculum. And then the world
is worse off, because those "outlaws" might not be educated on proper
methods to achieve whatever goal they want to achieve (like using
something pathogenic because their prior education didn't cover this
aspect of the technology).
> Overall thrust. Since so many of us are firmly committed to the idea
> that
> democratization and dissemination of empowering technologies is
> usually A Good
> Thing: how, in this particular sphere, with the particular properties
> of bio, including
> of course that all humans share a similar genome, and an overlapping
> set of
> democratization
Three step process:

1. Educate
2. Motivate to work on positive projects. Suggest something.
3. Stop disseminating "fear, uncertainty, and doubt", so that members
can easily separate paranoid-fantasy from fact. (If someone tells
you that your stories are like Chicken Little, then you should pay
close attention to what they are saying, and modify your behavior.)
The above recipe has been experimentally proven to work in other
communities. Graffiti art comes randomly to mind. Rather than
prohibiting cans of spray paint (so that only the outlaws could own
spray paint), community-based organizations realized the reality of
the democratization of spray paint and instead turned towards
funneling motivation into beneficial forms, like public displays of
graffiti art, and community art classes. Prohibition has been tried
many different ways. Guess what; IT FAILS. Outlaws don't care, and
the outlaw element grows bigger under prohibition. So don't suggest
prohibition, and instead follow 1, 2, 3 above. How many other
examples of prohibition do you want? If you want a gateway to bad
behavior, try regulation and prohibition; that's a proven fact.
Among teenagers who want to write computer software viruses ("because
it's cool, man"), these kids can be convinced to work on beneficial
open source software projects (like operating systems) if they are
encouraged with 1,2,3 above. It's relatively easy. You should try
developing this skill.
> Roger
## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################

Diy Bio Brent Listserve

Transféré par

Informations du document

Description originale:

Copyright

Formats disponibles

Partager ce document

Partager ou intégrer le document

Options de partage

Avez-vous trouvé ce document utile ?

Ce contenu est-il inapproprié ?

Droits d'auteur :

Formats disponibles

Diy Bio Brent Listserve

Transféré par

Droits d'auteur :

Formats disponibles

Dear DIY Biology people,

Would be interested in reactions or comments. I don't personally

You must Sign in before you can post messages.

Might as w ell pos Feb 4, 3:41 pm Bryan Bishop <ka DIYbio

Bryan View profile

From: Bryan Bishop <kanz...@gmail.com>

- Hide quoted text -

How about you just go use a separated habitat/environment if you're

- Hide quoted text -

- Hide quoted text -

I agree. There is a strong need for clear articulation of topics and

- Hide quoted text -

You must Sign in before you can post messages.

Might as w ell pos Feb 4, 4:01 pm Jason Bobe <jaso DIYbio

Jason View profile

From: Jason Bobe <jasonb...@gmail.com>

You must Sign in before you can post messages.

Might as w ell pos Feb 4, 4:28 pm Andrew Hessel < DIYbio

From: Andrew Hessel <ahes...@gmail.com>

- Hide quoted text -

You must Sign in before you can post messages.

Might as w ell pos Feb 4, 4:55 pm DIYbio

Meredith View profile

From: "Meredith L. Patterson" <clonea...@gmail.com>

Um, dude, what do you think speciation is?

Might as w ell pos Feb 4, 5:16 pm Guido D. Núñez-M DIYbio

Guido View profile

From: Guido D. Núñez-Mujica <noalaignoran...@gmail.com>

- Hide quoted text -

You must Sign in before you can post messages.

From: William Heath <wghe...@gmail.com>

- Hide quoted text -

You must Sign in before you can post messages.

Might as w ell pos Feb 4, 5:27 pm Guido D. Núñez-M DIYbio

Guido View profile

From: Guido D. Núñez-Mujica <noalaignoran...@gmail.com>

- Hide quoted text -

You must Sign in before you can post messages.

Might as w ell pos Feb 4, 5:29 pm Bryan Bishop <ka DIYbio

Bryan View profile

From: Bryan Bishop <kanz...@gmail.com>

Yes, in humans it encodes the use of 13 proteins which have caused

You must Sign in before you can post messages.

Might as w ell pos Feb 4, 5:33 pm Ingrid Sw anson < DIYbio

Ingrid View profile

From: Ingrid Swanson <iswan...@u.washington.edu>

- Hide quoted text -

You must Sign in before you can post messages.

Might as w ell pos Feb 4, 6:10 pm Lora <lmcamer...@ DIYbio

From: Lora <lmcamer...@verizon.net>

- Hide quoted text -

You must Sign in before you can post messages.

Might as w ell pos Feb 4, 6:28 pm Len Sassaman <L DIYbio

Len View profile

From: Len Sassaman <Len.Sassa...@esat.kuleuven.be>

- Hide quoted text -

You must Sign in before you can post messages.

Might as w ell pos Feb 4, 6:35 pm Mackenzie Cow e DIYbio

From: Mackenzie Cowell <m...@diybio.org>

- Hide quoted text -

You must Sign in before you can post messages.

Might as w ell pos Feb 4, 6:46 pm Julie Norville <julie DIYbio

Julie View profile