December meeting at Harvard Medical School.
Alexander (Sasha) Wait
thanks for subscribing. If you want to change your subscription
settings at any time you can do that through Google or by emailing me:
"await AT genetics.med.harvard.edu".
Thanks also for attending the first meeting! For those of you that
missed it there is a description of the talk here:
* http://non.fiction.org/~await/alife/talks/20041122.walsh.html
As I mentioned, I want ALife Boston to bring together local communities
working on theoretical and experimental approaches to engineering with
biological parts. This work has important social, philosophical and
practical consequences and I believe that approaching it with openness
and a certain spirit of cooperation will pay large dividends.
If you would like to participate, it would help if people began
suggesting topics they would like discussed in future meetings. For now
lets discuss on this list and if necessary we can move to a separate
list if there is too much traffic. One possibility for the next
meeting (Dec 14/15/16/17/20 at Harvard Medical School could work) is to
discuss any new experimental results from the DNA Counter project or any
other experimental effort to compute with biology. Another possibility
is a discussion of experimental progress in manipulating coherent
quantum information in biomolecular systems. Yet another possibility is
to discuss the ethics of "synthetic biology" or economic models for
funding basic research. ALife is a vast interdisciplinary area and if
anyone is interested in volunteering to discuss a journal paper or their
own (related) research, please, post here. If there are certain
dates/times/locations that are better for you, please, post those also.
The group is what we make of it.
Look forward to see everyone in December! Happy Thanksgiving.
--ASW. Cell - 617-642-0623 WWW - http://non.fiction.org/~await
GnuPG (ID 4153C516) 1716 E850 1CE6 6F34 B8B7 50D8 B108 EDF2 4153 C516
val
Sounds good to me, including all the topics mentioned,
in particular, about manipulating quantum info in biosystems -
sounds exciting.
I'd like to share my thoughts about
"Components/parts and their control: synthetic biology and beyond"
and i'll be in touch with Sasha about scheduling.
I like ASW's "The group is what we make of it."
my best,
val
ASW
like to talk in December (at HMS) about my efforts to find new business
models for funding "open" biotechnology:
The escalating cost of developing successful new drugs has spawned a
cabal of lobbyists for new legal restrictions on the distribution of
proprietary ideas. Multi-billion dollar expenditure, so the argument
goes, requires offsetting government intervention on behalf of
investors. The Free Software movement, by contrast, has used the law
to ensure that software and, more recently, software documentation can
be distributed, modified and used without restriction. From my vantage
point-- as a commercial user of Free software since 1993-- I believe
the gap is closing between Free and proprietary software. Government
protectionism--not the action of unfettered market forces--is the main
threat to Free software now. But the success of Free software does
not translate naturally to drug development. Instead, I would like to
consider the explosive growth of certain on-line communities--whose
founders have embraced Free software ideals--as a model for the
biotechnology community. I have taken some initial steps to implement
this idea and would like to report my progress.
---
Irene Chen, a graduate student in Jack Szostak's lab, has kindly
volunteered to speak in January (at MIT, date/time/room to be arranged)
with this abstract:
We are exploring simple mechanisms by which cellular-level traits may
arise in model protocells. The encapsulation of genetic material by a
semipermeable membrane was presumably an important transition during
the origin of cellular life. How might these two components, the
membrane and the genome, combine to produce a unified cellular
'system'? Using vesicles composed of prebiotically plausible
amphiphiles, we first demonstrated that membrane growth causes the
generation of a transmembrane pH gradient, which can be sustained for
several hours under certain conditions. The energy stored in such
gradients would be available for use in cellular processes, such as
genomic replication. This illustrates how the growth of one component,
the membrane, might convey a fitness advantage to the protocell.
Second, we observed the emergence of Darwinian selection between
vesicles encapsulating RNA and empty vesicles. Vesicles containing high
concentrations of RNA experienced substantial osmotic stress, which
drove the uptake of membrane components from unstressed membranes.
Therefore during protocellular evolution, vesicles encapsulating highly
active genomic replicators might grow at the expense of other vesicles,
effectively translating genomic fitness into protocellular fitness.
These results highlight the prospect of building a protocell with
apparently complex behaviors using simple components and
physico-chemical processes.
---
Val, maybe you could speak in February (at NECSI again)? Please send
me an abstract when you have the chance.
What do people think about this plan?
Thanks,
Sasha
Nevin M. Summers
You seem to have some misplaced "attitude" in need of a socially
beneficial direction. What specifically are the "new legal
restrictions on the distribution of proprietary ideas" you mention?
Patents, and their essential role in raising capital for financing
innovation, have been around, and have been highly successful, for
over a century.
I suggest you go to this website http://mitworld.mit.edu/video/223/
and carefully listen to the 3.5 hours of arguments in favor of global
differential pricing of drugs, the relation to sustainable
innovation, patents, capital formation and equitable access - getting
drugs to people in poor developing countries. You might learn
something. I certainly did when I served as the Organizing Committee
Chair for this Forum at MIT last August.
You need to get straight on the big differences between software and
drugs - namely 1) the degree of regulation, 2) the capital required,
3) the time required, 4) the severity of potential adverse events
from a defective product and 5) the ethics of human experimentation.
One way to get the pharmaceutical industry to fund "open" public
domain research is to identify critical "precompetitive" uncharted
areas where no one firm has the resources to go it alone, but where
multiple firms, together with government agencies, would pool
resources in a consortium to fund academic research, the results of
which would be shared by all. For example, such an area would be
"predictive toxicology" or "translational safety" where retrospective
analyses of compounds that failed clinicial trials and prospective
preclinical animal model testing of compound libraries would be
aggregated to establish predictive algorithms of toxicity. Each
company would then use this information in their own proprietary R&D
programs. You might think of other precompetitive areas that you
could research to "de-risk" the highly unpredictable process (let's
face it - the lottery) of bringing a drug to market. The lure of
predictability is the appeal of Systems Biology.... Increase the
probability of success and you lower the cost.
Best wishes,
Nevin
------------------------------
Nevin M. Summers, AIA
Life Sciences Specialist
Corporate Relations
Office of Resource Development
MIT Sloan School of Management
30 Memorial Drive, Suite E60-300
Cambridge, MA 02142-1347 USA
cell: 617-566-3559 or 617-792-0789
fax: 617-253-5584
nsum...@mit.edu
http://mitsloan.mit.edu
https://hstdev.mit.edu
Art is long, life short, judgment difficult, opportunity transient.
-- Goethe (1749-1832)
------------------------------
ASW
> of proprietary ideas" you mention?
>
provisions against reverse engineering, etc. Not so random, headline
from today's New York Times:
Richtel Matt. (2004) Pennsylvania Limits Cities in Offering Net
Access. New York Times; December 2 2004.
In a victory for Verizon Communications, a measure in a new
Pennsylvania law will make it harder for cities to build
high-speed Internet networks that compete with major
telecommunications providers.
http://www.nytimes.com/2004/12/02/technology/02wireless.html
The cities can deploy wireless-- use by everyone-- Internet access for
a fraction of the cost of the telecos closed-- non existent, use by
customers-- network. Cities provide street lamps because its the
economically efficient solution. Why shouldn't the cities deploy
wireless Internet?
> I suggest you go to this website http://mitworld.mit.edu/video/223/
Thanks for the link!
> One way to get the pharmaceutical industry to fund "open" public
> domain research is to identify critical "precompetitive" uncharted
> areas where no one firm has the resources to go it alone, but where
> multiple firms, together with government agencies, would pool
> resources in a consortium to fund academic research, the results of
> which would be shared by all.
One of the things that I love about the Church lab is that, from time
to time, I can work on an idea to fund ideas (biotech ideas, for
example) side by side with people developing proprietary
biotechnologies. The funding idea I'm working on attempts to pool the
resources of large communities of users (aka the people that use the
drugs). In a world where the Internet reaches into every nation,
variants of such a model may prove to be economically more efficient
than existing models.
I hope that government(s) will let the market decide...
Thanks for the thoughtful comments!
Sasha
val
Thanks for thoughtful and stimulating contributions.
You both have interesting and far-reaching ideas/visions of
pharma industry and its R/D and the *open* research and development
process. To me, your thoughts seem to be solid, going in right
directions, and just need further discussions, clarification,
and design-like approach. Waste of ~$1B, ~10 years
per 'successful' drug is *not* a good sign. So, joining R/D
forces in reasonably open environment is an urgent need. That'd
provide a fresh, *in-depth* look at the drug discovery dynamics.
The existing process is an inflexible, shallow, single-dimension
projection of the *fundamental* process of synthesis molecular
structures designed to control behavior of a cell. This kind
of challenge is not for pharma R/D - not due to their people,
just due to their approach/bizmodel. This is why during the
*long decades* we are hearing the same promise - next X years you'll
get the miracle (cancer/whatever) drug. Hardly possibly.
Pooling and redirecting customer's money is right idea and in
right time. An in-depth, fundamental approach to discovery of
necessary molecular structures, understanding underlining mechanisms
is the better guarantee for patients safety (than postfactum/postmortem
data mining). With a challenge of that huge scale, new integration
approaches are necessary, flexible rearrangements in the
Fed/NSF, pharma and other biosci/biotech research headquarters..
Systems biology, synthetic biology, quantum biology, biochemistry,
and biophysics, computational physics, computational cell dynamics,
nanotechnology, and similar 'things' are the components of that
coming Big Integration.
----- Original Message -----
Nevin M. Summers
consumers could share personal genotype/phenotype information,
including drug response (safety, efficacy, tolerability, drug-drug
interaction, etc). They could be aligned with patient advocacy
groups, even investors with a particular therapeutic disease focus.
These online communities could also be early warning systems for bad
batches of unauthenticated pharmaceuticals (ie, counterfeits and
expired drugs) that are increasingly finding their way into the
marketplace. Check out this rather concerning US Senate hearing
http://govt-aff.senate.gov/index.cfm?Fuseaction=Hearings.Detail&HearingID=182
.
When is the next alife-boston meeting?
Nevin
ASW
Does Monday December 20th, 3pm (at Harvard medical school) work for
everyone?
Sasha
David Croll
dhc