A story courtesy of our friends at the Associated Press:
This story serves as more evidence of why discussing DIYbio with the
public is such a critical issue. We're doing good so far - we've
explained DIYbio to eachother, even though many of us are computer
scientists, engineers, and beer brewers.
As interest in DIYbio grows, our work with friends, students, parents,
and government officials becomes increasingly important. Through open
discussion with the public community, we will discover greater
applications and uses for our work, and the public will enjoy a
greater understanding of the language of life.
I challenge us all today to make an attempt at explaining DIYbio, or a
DIYbio project, to someone with no biology background. I spoke with my
friend Rob, a glass sculptor, about bioWeatherMaps on Sunday - and got
some great ideas considering he has little experience in biology.
For anybody new to this discussion, we had a bit about it earlier this year-
"just to be clear, just having a central repository is half (or less)
of the battle. The hard part is building a community that sees some
repository as central. Linux is not just a repository of kernel
code... it is THE repository of kernel code, even though there are a
gazillion variations. That's because it has a name, a history and a
group of people who shepherd it and protect it. I think this is what
OS nano and DIYBio need to think about NOW rather than later. It's
great to let a thousand flowers bloom and spread ideas, but open
source innovation dynamics only happen when lots of people feel like
they are contributing to a common cause or project... that's where the
big momentum comes from. "
Anyway, somebody wrote the gel box generator scripts a few months ago,
and now with sites like emachineshop, ponoko and e-oligos almost
everything is ready to go [if it wasn't for the fact that this all
relies on crummy HTTP interfaces instead of something that is slightly
more guaranteed to stay stable over a longer period of time], so as
for the tools of the trade in that sense, things are going well. Also,
the open manufacturing people that I play around with have been
working on open hardware repository formats, and my little bit is some
work on "click to procure" (unptnt's secret weapon it seems) so that
kits can be quickly ordered. Speciality chemicals I'm rather clueless
about- sonoporation and ambient temperature competency is an
interesting alternative of course.
In less biology terms, this can also be described as putting means of
bootstrapping technology into the public (ok, creative) commons. With
biology, it's more evident that there are certain seeds and certain
ways to do agricultural activities that will either succeed or fail.
At a minimum this means that there has to be both the biology and
tool-based infrastructure to allow everyone to use the tools, and
seeds and other lifeforms, if necessary [with their own decision].
Of course, we're already moving on this. ;-)
"The answer is here, in the development of a replicable village
infrastructure, that addresses issues of resource conflict, resource
use equity, environmental regeneration, economic distribution, and,
consequently, legal and financial reform - by advanced
self-sufficiency at unprecedentedly small scales. This is a model of
societal evolution, based on principles of open source, voluntary,
flexible fabrication economies, that start with the infrastructures of
our own backyards - at the same time as they engage in global
collaboration on similar issues.
The point is that the advanced self-sufficiency at unprecedentedly
small scales leads to easy management of survival, a robust working
environment, and, therefore, a voluntary lifestyle that may be
dedicated to addressing pressing world issues."
This is, in turn, why I've been participating in some other projects,
like open manufacturing:
Much of the software infrastructure is being pushed through the iGEM
software teams. It's not enough though. The community lab ideas are a
nice one, as long as they are fully documented -- perhaps even more so
than the fab labs -- and especially if they are using parts and
machinery made from fablabs :-).
That might put in place a serious backbone. I wonder what interesting
ideas can come from combining 'open manufacturing' with 'synthetic
biology' or DIY projects?
I like the example. What more, what if a philanthropist showed up and
started manufacturing via giant vats some ridiculous amount of
artemisinin, which Artemisania relies on for economic livelihood?
After the cost of the initial investment in the hardware is paid for,
the cost of having the organisms grow and such is near-zero, as long
as you continuously have nutrient/input supply. So in this scenario,
not only do you have a country that isn't selling the product, but
nobody's "selling" it at all, yet the demand is being satisfied.
I think it's also important to note that, sadly, there are many bad
"business plans" and many bad "making-a-living plans" out there.
Disruptive tech that people weren't aware was even possible can easily
change many, many living circumstances. So this is a broader issue
than synthetic biology -- it's a pretty fundamental design problem. I
get kind of annoyed that people think it's a good idea to live without
knowing their "dependency chains", as in, all of the accumulative
technologies that are used to make their life possible -- all of the
infrastructure, all of the materials and all of the information which
are presently restricted by IP, unshareable designs, lack of
collaboration, etc. No, I don't think everyone/anybody should have to
know all of it, but having access, and being able to look at their
community from a technical analytical point of view and find that it's
completely unsustainable, is a good thing.
If you give people these tools they can have some advanced knowledge
before total disruptive disaster strikes, but this is quickly becoming
off-topic. (The dependency chain issues are what openmanufacturing.net
and oscomak.net :-) like to work on.). So that's why I'm still working
on the standardized packaging of open source shared hardware designs,
including synthetic biology via SBML inclusion in the repositories,
and PSL (Process Specification Language) and so on.
> From this angle, the technology is a loss of $1 billion. If it had been
> deployed in a slower fashion over a few years, those workers could gradually
> have shifted their fields to growing something else.
Well, yes, except the math is kinda wrong. Consider the length of time
that it takes to shift the agricultural fields to some new crop. Then
consider the growth rate, the cycles of the seasons; fine, that's
good. Now consider the long tail from the internet and the rest of the
world implementing an increasing number of better solutions using the
new disruptive tech. By the time the farmers are done planting a new
crop, that too could be a disaster waiting to happen.
> What do you all think of this example?
Well, if the cure is open access, published in open access scientific
journals, and the pharma manufacturing infrastructure knowledge is
also shared and the tools and knowledge is available to the Malarians,
what's the deal? :-)
"Hm. This is under IP restrictions in a foreign country. I better not
save my children. Good thing I dodged *that* bullet." <-- unlikely?
Well, what we are really seeing here is a profound transition from
manufacturing being a capital intensive enterprise to one which is
information-driven. Think of the factories as being as easy to
duplicate as the torrent download of your latest movie. Exactly the
same things that are happening today to authors, musicians, film
makers, and artists will be happening in the construction and
manufacturing industries. This is an essential part of the transition
from factory based to self-replication based manufacturing technology.
We don't know how to run an economic system based on abundance rather
than scarcity, but we had best learn rapidly. I hope and trust that
the system that results will be better, not worse for everyone.
There's also some pages on the site about "open money" and "new
monies", but personally I'm not too interested in pursuing that
because if you're going to end up with a post-scarcity model, which I
think would qualify as an advanced civilization, why would you want to
implement money? And if you didn't, is there no longer an economy?
Even though things are still happening?
One issue that is underexplored in this territory are "transistional
issues". You don't just flip a switch and suddenly everything is
post-scarcity; you don't flip a switch and suddenly the Artemisanians
are no longer going hungry, etc. So, I don't know how to address this.
Nathan Cravens has spent some time thinking on this and might comment
(so I'm cc'ing the openmanufacturing list).
No, but there's been talk about creating a Journal of Post-Scarcity
Economics; Joseph Jackson has been running around assembling this and
I'm sure he'll be happy to comment.
> restart the economy. Bernake said he would rain down money from helicopters
> if that happened here. Manufacturing usually uses a fixed cost asset
> approach where capital is expended on many machines. The company doesn't
> actually produce any profit until a certain volume of widgets is sold. As a
> result, manufacturing is especially vulnerable to deflation. Fundamentally
> it becomes one of government planning to prevent harsh repercussions
> from occurring to an abundancy based economy because it flies in the face of
> scarcity which is what most businesses depend on. Believe it or not, the
> government would have to step in and create scarcity to keep the prices from
> falling, which is what they do now in the agricultural sector! It would be
> nice to hear about a better solution than government intervention and
> central planning to solve this issue. What you begin to see is a kind of
> Star Trek kind of economy where money ceases to really mean anything as
> businesses can't survive the rate of innovation. Even if they could, they
> would have to plan so precisely that it would be extremely difficult to say
> at the rate of innovation me must sell x widgets in y timeframe to make x
> profit as the margin would decrease into insolvency by x date.
I'm a big fan of increasing caches of localized functionality over
increasingly broad domains. Anybody who has spent many hours
struggling with his computers because he didn't have bootstrapping
discs will know the importance of this. On the positive side, check
Which I'll quote from below:
The short version: I've realized that I've totally forgotten that I
had access to a lot of Gingery-content via my gingery_machines mailing
list subscription, so here it is:
http://heybryan.org/books/Manufacturing/gingery.zip (warning: 60 MB)
There's also a directory at: /books/Manufacturing/gingery/ where you
can see the files.
The (active) gingery_machines mailing list is at:
I first learned about Dave Gingery from Kevin Kelly:
(Another article of his worth reading and on topic is re:
civilizations as creatures:
"Recently a guy re-invented the fabric of industrial society in his
garage. The late Dave Gingery was a midnight machinist in Springfield,
Missouri who enjoyed the challenge of making something from nothing,
or perhaps it is more accurate to say, making very much by leveraging
the power of very little. Over years of tinkering, Gingery was able to
bootstrap a full-bore machine shop from alley scraps. He made rough
tools that made better tools, which then made tools good enough to
make real stuff."
But really, if you haven't read that Kevin Kelly article, you really
should. It's about technology dependency trees and networks and why
you might think you see straight into the future of tech, when you're
missing out on all of the actual details. etc. One day when Googling
for that article or Gingery, earlier this year, I met Ben, and
proceeded to complain to him about his server being down or something.
Paul, too, has mentioned a pipedream of buying the publisher who holds
the Gingery books these days. Can't say I blame him (see link below).
It's too bad there's no Gingery Institute, although BFI sounds
conceptually close enough I guess.
Anyway, if we had a bug report system, I'd file "BUG: Gingery machines
[still] not packaged yet". Maybe I'll get some copies of his books and
trudge through it and do the proper packaging soon.
On Thu, Dec 18, 2008 at 3:13 PM, Bryan Bishop <kanz...@gmail.com> wrote:
> I first learned about Dave Gingery from Kevin Kelly:
> (Another article of his worth reading and on topic is re:
> civilizations as creatures:
> http://www.kk.org/thetechnium/archives/2006/03/civilizations_a.php )
> "Recently a guy re-invented the fabric of industrial society in his
> garage. The late Dave Gingery was a midnight machinist in Springfield,
> Missouri who enjoyed the challenge of making something from nothing,
> or perhaps it is more accurate to say, making very much by leveraging
> the power of very little. Over years of tinkering, Gingery was able to
> bootstrap a full-bore machine shop from alley scraps. He made rough
> tools that made better tools, which then made tools good enough to
> make real stuff."
Hm. That second kk.org link, I think, is the wrong one. Let's try this one:
"I've been thinking of civilization (the technium) as a life form, as
a self-replicating structure. I began to wonder what is the smallest
seed into which you could reduce the "genes" of civilization, and have
it unfold again, sufficient that it could also make another seed
again. That is, what is the smallest seed of the technium that is
viable? It must be a seed able to grow to reproduction age and express
itself as a full-fledge civilization and have offspring itself --
another replicating seed.
This seed would most likely be a library full of knowledge and perhaps
tools. Many libraries now contain a lot of what we know about our
culture and technology, and even a little bit of how to recreate it,
but this library would have to accurately capture all the essential
knowledge of cultural self-reproduction. It is important to realize
that this seed library is not the universal library of everything we
know. Rather, it is a kernel that contains that which cannot be
replicated and that which when expanded can recover what we know."
Anyway, somewhere in his bloggings he specifically relates the nucleus
of the civilization creature as the self-replicating library of tools,
information and culture, in the sense of von Neumann probes:
Implementation notes on von Neumann probes
http://heybryan.org/projects/atoms/ (ok, it's old)
"The basic idea of a von Neumann probe is to have a space-probe that
is able to navigate the galaxy and use self-replication (see RepRap
and bio). The probe would contain hundreds of thousands of digital
genomes (sequenced DNA), DNA synthesizers and sequencers, bacteria,
embryos, stem cells, copies of the Internet Archive and a significant
portion of the WWW in general, plus the immediate means and tools to
copy all of the information and create a material embodiment, kind of
like running an unzip utility on top of the thousands of exabytes
predicted to be inexistence today. This would probably include many
people, societies, even entire civilizations if we can collect enough
data and begin to 'debug' civilization. The system might end up using
an ion drive and a hydrogen collector, with on-board nucleosynthesis
to create the biomolecules necessary for life, plus ways to attach to
asteroids and begin replicating and copying the data and
von Neumann replicator award/prize:
So what needs to be done to bring these two things together?
1) Show that 90 % of a self assembling robotic system can be
fabricated using a rapid prototyping system that can also self
2 )Show that 90 % of the assembly from parts of a rapid prototyping
system can be done by a robotic system that can also self assemble."
**but** Freitas clearly outlines the issue of closure engineering that
shouldn't be ignored in his KSRM book and AASM report:
Which I'll quote from again:
Fundamental to the problem of designing self-replicating systems is
the issue of closure.
In its broadest sense, this issue reduces to the following question:
Does system function (e.g., factory output) equal or exceed system
structure (e.g., factory components or input needs)? If the answer is
negative, the system cannot independently fully replicate itself; if
positive, such replication may be possible.
Consider, for example, the problem of parts closure. Imagine that the
entire factory and all of its machines are broken down into their
component parts. If the original factory cannot fabricate every one of
these items, then parts closure does not exist and the system is not
fully self-replicating .
In an arbitrary system there are three basic requirements to achieve closure:
Matter closure - can the system manipulate matter in all ways
necessary for complete self-construction?
Energy closure - can the system generate sufficient energy and in the
proper format to power the processes of self-construction?
Information closure can the system successfully command and control
all processes required for complete self-construction?
Partial closure results in a system which is only partially
self-replicating. Some vital matter, energy, or information must be
provided from the outside or the machine system will fail to
reproduce. For instance, various preliminary studies of the matter
closure problem in connection with the possibility of "bootstrapping"
in space manufacturing have concluded that 90-96% closure is
attainable in specific nonreplicating production applications (Bock,
1979; Miller and Smith, 1979; O'Neill et al., 1980). The 4-10% that
still must be supplied sometimes are called "vitamin parts." These
might include hard-to-manufacture but lightweight items such as
microelectronics components, ball bearings, precision instruments and
others which may not be cost-effective to produce via automation
off-Earth except in the longer term. To take another example, partial
information closure would imply that factory-directive control or
supervision is provided from the outside, perhaps (in the case of a
lunar facility) from Earth-based computers programmed with
human-supervised expert systems or from manned remote teleoperation
control stations on Earth or in low Earth orbit.
The fraction of total necessary resources that must be supplied by
some external agency has been dubbed the "Tukey Ratio" (Heer, 1980).
Originally intended simply as an informal measure of basic materials
closure, the most logical form of the Tukey Ratio is computed by
dividing the mass of the external supplies per unit time interval by
the total mass of all inputs necessary to achieve self-replication.
(This is actually the inverse of the original version of the ratio.)
In a fully self-replicating system with no external inputs, the Tukey
Ratio thus would be zero (0%).
It has been pointed out that if a system is "truly isolated in the
thermodynamic sense and also perhaps in a more absolute sense (no
exchange of information with the environment) then it cannot be
self-replicating without violating the laws of thermodynamics"
(Heer,1980). While this is true, it should be noted that a system
which achieves complete "closure" is not "closed" or "isolated" in the
classical sense. Materials, energy, and information still flow into
the system which is thermodynamically "open"; these flows are of
indigenous origin and may be managed autonomously by the SRS itself
without need for direct human intervention.
Closure theory. For replicating machine systems, complete closure is
theoretically quite plausible; no fundamental or logical
impossibilities have yet been identified. Indeed, in many areas
automata theory already provides relatively unambiguous conclusions.
For example, the theoretical capability of machines to perform
"universal computation" and "universal construction" can be
demonstrated with mathematical rigor (Turing, 1936; von Neumann, 1966;
see also sec. 5.2), so parts assembly closure is certainly
An approach to the problem of closure in real engineering-systems is
to begin with the issue of parts closure by asking the question: can a
set of machines produce all of its elements? If the manufacture of
each part requires, on average, the addition of >1 new parts to
product it, then an infinite number of parts are required in the
initial system and complete closure cannot be achieved. On the other
hand, if the mean number of new parts per original part is <1, then
the design sequence converges to some finite ensemble of elements and
bounded replication becomes possible.
The central theoretical issue is: can a real machine system itself
produce and assemble all the kinds of parts of which it is comprised?
In our generalized terrestrial industrial economy manned by humans the
answer clearly is yes, since "the set of machines which make all other
machines is a subset of the set of all machines" (Freitas et
al.,1981). In space a few percent of total system mass could feasibly
be supplied from Earth-based manufacturers as "vitamin parts."
Alternatively, the system could be designed with components of very
limited complexity (Heer, 1980). The minimum size of a self-sufficient
"machine economy" remains unknown.
According to the NASA study final report : "In actual practice, the
achievement of full closure will be a highly complicated, iterative
engineering design process.* Every factory system, subsystem,
component structure, and input requirement must be carefully matched
against known factory output capabilities. Any gaps in the
manufacturing flow must be filled by the introduction of additional
machines, whose own construction and operation may create new gaps
requiring the introduction of still more machines. The team developed
a simple iterative procedure for generating designs for engineering
systems which display complete closure. The procedure must be
cumulatively iterated, first to achieve closure starting from some
initial design, then again to eliminate overclosure to obtain an
optimized design. Each cycle is broken down into a succession of
subiterations which ensure qualitative, quantitative, and throughput
closure. In addition, each subiteration is further decomposed into
design cycles for each factory subsystem or component." A few
subsequent attempts to apply closure analysis have concentrated
largely on qualitative materials closure in machine replicator systems
while de-emphasizing quantitative and nonmaterials closure issues
, or have considered closure issues only in the more limited
context of autocatalytic chemical networks [2367, 2686]. However, Suh
 has presented a systematic approach to manufacturing system
design wherein a hierarchy of functional requirements and design
parameters can be evaluated, yielding a "functionality matrix" (Figure
3.61) that can be used to compare structures, components, or features
of a design with the functions they perform, with a view to achieving
* To get a sense of the complex iterative nature of closure
engineering, the reader should ponder the design process that he or
she might undertake in order to generate the following full-closure
self-referential "pangram"  (a sentence using all 26 letters at
least once), written by Lee Sallows and reported provided by
Hofstadter : "Only the fool would take trouble to verify that his
sentence was composed of ten a's, three b's, four c's, four d's,
forty-six e's, sixteen f's, four g's, thirteen h's, fifteen i's, two
k's, nine l's, four m's, twenty-five n's, twenty-four o's, five p's,
sixteen r's, forty-one s's, thirty-seven t's, ten u's, eight v's, four
x's, eleven y's, twenty-seven commas, twenty-three apostrophes, seven
hyphens, and, last but not least, a single !" Self-enumerating
sentences like these are also called "Sallowsgrams"  and have
been generated in English, French, Dutch, and Japanese languages using
iterative computer programs.
Partial closure results in a system that is only partially
self-replicating. With partial closure, the machine system will fail
to self-replicate if some vital matter, energy, or information input
is not provided from the outside. For instance, various preliminary
studies [2688-2690] of the materials closure problem in connection
with the possibility of macroscale "bootstrapping" in space
manufacturing have concluded that 90-96% closure is attainable in
specific nonreplicating manufacturing applications. The 4-10% that
still must be supplied are sometimes called "vitamin parts." (The
classic example of self-replication without complete materials
closure: Humans self-reproduce but must but take in vitamin C, whereas
most other self-reproducing vertebrates can make their own vitamin C
.) In the case of macroscale replicators, vitamin parts might
include hard-to-manufacture but lightweight items such as
microelectronics components, ball bearings, precision instruments, and
other parts which might not be cost-effective to produce via
automation off-Earth except in the longer term. To take another
example, partial information closure might imply that factory control
or supervision is provided from the outside, perhaps (in the case of a
lunar facility) from Earth-based computers programmed with
human-supervised expert systems or from manned remote teleoperation
control stations located on Earth or in low Earth orbit.
Regarding closure engineering, Friedman  observes that "if 96%
closure can really be attained for the lunar solar cell example, it
would represent a factor of 25 less material that must be expensively
transported to the moon. However, ...a key factor ... which deserves
more emphasis [is] the ratio of the weight of a producing assembly to
the product assembly. For example, the many tons of microchip
manufacturing equipment required to produce a few ounces of microchips
makes this choice a poor one – at least early in the evolution – for
self-replication, thus making microelectronics the top of everyone's
list of 'vitamin parts'."
Here's to cramming everything into as small a space as possible.
This. Nor do you just flip a switch and an entire country loses its
economy, either -- it takes time and money for new manufacturing
processes to get up to speed, new distribution channels to get laid
down, &c, &c.
For that matter, name one country whose *entire* economy rests on one
commodity. Hint: there's not one. The closest example I can think of
is Zimbabwe, which was once the breadbasket of Africa but which
systematically destroyed its entire farming infrastructure over a
matter of months thanks to policies implemented by the Mugabe
administration. The result has, of course, been economic catastrophe,
but that's generally what happens when you legally deny an entire
class of (historically extremely productive) people *the right to own
property*. Agricultural economies which no longer have a world market
for their products can still feed themselves; it's when you destroy
the means of production that you're fucked.
Another, less pure example might be Ukraine during the Holomodor.
Farming conditions in 1932-33 were no better or worse than they had
been in previous years, but boneheaded central planning policies
(which may or may not have been politically motivated -- but that's
actually irrelevant, as the bottom line is that *you cannot distribute
more of a commodity than you can produce*) killed somewhere between
2.2 million and 3.5 million people. Don't do that.
Emerging technologies take a while to emerge, longer to take hold, and
longer still to become dominant. Whether you're on the rising side or
the falling side of a technology, you can take advantage of this time
lag to get up to speed as needed.
Surfing close to 'The Diamond Age' philosophy here now aren't we :)
|| Dan || dan[at]dreadportal.com || http://dreadportal.com/ ||
"Reality is that which, when you stop believing in it, doesn't go away."
(Philip K. Dick - How to Build a Universe)
Yes, but I thought we were talking about the people in the fictional
country that get screwed? I'd be more concerned about people not being
able to meet basic needs in these scenarios at first, in the case of
sudden economic collapse and such, rather than be concerned about the
People who structure their lives around a single job are relying on
that "one commodity" (their job), and when it goes away in a puff of
smoke, that's what I'm talking about for 'transitional issues'.
"Welcome, you have now become unemployed. We regret to inform you that
there aren't many openings for jobs, and the alternative to working to
live hasn't been able to fully scale and deploy at this time. Good
luck." <- That's kind of what I mean. :-/
Amorphous computing/fabrication isn't quite what everyone expects.
It's not the same as traditional engineering. I'm preaching to the
choir, everyone around here knows this. Insert notes here on the
packaging of projects, blah blah blah wouldn't it be optimal to have a
lot of tiny little tools that we could combine into a synthetic
biology compiler, etc. :-) (I've said this all before, nothing new, or
so it seems.)
On a more serious of a note, a few months ago I started talking about
the concept of a bioreactor or some type of tank that could be fed
nutrients and such and be a fully contained, self-replicating toolkit
for do-it-yourself bio. One of the major hurdles is the construction
of a completely biological DNA synthesizer (another major hurdle is
specialty purified chemicals for specific protocols/recipes). There's
a set of ideas that I worked on, with some others, for a "retarded
polymerase" that would probably take an entire lab to develop over
many years, which would respond to some wavelength of light to attach
a certain nucleotide to a batch of DNA; issues with this idea is that
it's slow, slow and still slow. A "writozyme" if you will. Also the
experimental methodology to construct it requires something like a
triple-tiered directed selection experiment, aptamers, and a number of
other things that make me increasingly less optimistic.
Another issue to consider is that the majority of lab tech is
manufactured using giant bulky milling machines, CNC machines and so
on as you mention, Tom. So the dependency requirements on lab stuff is
already requiring some industrial ecology. I don't know about
specialty chemical factories that Dow, Sigma-Aldrich and friends are
using, Meredith might know something about IDT that she could
elaborate on though? Lab instrumentation is also another issue.
Growing perfect pipettes doesn't seem likely, but I can guess that
there are alternatives that we will have to grow from the ground up.
What may end up happening anyway is the mutual and gradual growth of
both the toolkits for the do-it-yourself synthetic biology platforms
in conjunction with fablabs and open manufacturing. I'm kind of
jealous of you Boston folk, since this is already happening up where
Any ideas on completely biologically manufactured biolabware (esp.
synthesizers) always welcome though.
Alert: you must have a level-nine clearance to bare children. Hrm. I
don't know if that's going to fly. Actually, what I'd be interested in
exploring is deploying something akin to debian's "social contract"
but for diybioists. Excessive regulation will be met with the "route