The Vegas Group: bringing quality documentation and longevity science to DIYbio

[Reason]

Good day; my name is Reason, and I manage Fight Aging!, a long-running
science and activism blog that covers a range of topics in research
and biotechnology. ( http://www.fightaging.org for the curious).

As a few of you may know, I recently kicked off work on a new project
called the Vegas Group. This is a volunteer initiative with the
ambitious long-term goal of closing the gap between the longevity
science advocacy and DIYbio communities, the better to encourage work
that will bring demonstrated therapies that enhance longevity in
mammals out of the lab and closer to readiness for humans. If we sit
around doing nothing, waiting for the regulators to get it and stalled
work to emerge into the clinic, nothing will ever get done - but that
can be changed.

While I know that amongst the members of this community stand a number
of supporters of longevity science, Aubrey de Grey's SENS, and near-
future biotechnologies to repair the biochemical changes of aging, the
near-term goals of the Vegas Group are probably of broader interest to
the group.

In short, we intend to build an open, Creative Commons licensed
repository of high quality documentation: how-to guides for the DIYbio
enthusiast and professional life scientist that explain exactly how to
(a) perform longevity-enhancing interventions that have been
demonstrated in mice, and (b) participate in some of the ongoing
investigative research into the repair of age-damaged mammalian
biochemistry.

In the process of building this repository, we will cover a great many
common supporting procedures and techniques in biotechnology and life
science work. These will be documented and made openly available in
the same way as the longevity science guides: it is important to me
that no low rungs on the ladder be missed.

In fact, I will be looking to this community to supply many of the
writers and editors for this process: writing doesn't pay well, even
in specialized fields, and especially for non-profit ventures, but as
we get underway this will be a project that pays its writers. I hope
that some of you will be interested in sharing your knowledge in this
way, and by doing so help to popularize and smooth passage into the
DIYbio community for years to come.

By way of an example, let me outline briefly the present trial run we
are undertaking: to produce quality, comprehensible documentation that
describes how to carry out the process of mitochondrial protofection.

A little background on the biology: as you might know, mitochondria
are the cell's roving herd of mobile power plants, helping to turn
food into ATP, the common fuel chemical used by cellular processes.
Mitochondria contain their own DNA, being the evolved remnants of
symbiotic bacteria. That DNA becomes progressively damaged as a
natural consequence of mitochondrial operation, and this kicks off a
Rube Goldberg chain of consequences that sees cells on the elderly
overtaken by malfunctioning mitochondria, kicking out reactive
pollutant chemicals into their surroundings ... and ultimately
contributing significantly to degenerative aging and many of the
specific diseases of aging.

All this might be averted if we had some way to replace that damaged
mitochondrial DNA - and we do, a technique called protofection that
was demonstrated to work in mice back in 2005. This employs a vector
to introduce replacement mitochondrial DNA into cells throughout the
body, and is fairly well explained (if you are a scientist and up for
reading dense papers) in a selection of scientific publications issued
over the past six years.

At present, Allen, one of the early Vegas Group supporters, is reading
over the research and breaking it down into a list that will act both
as topic headings for documentation writers and steps to recreate the
research for the biotech enthusiast. For my part, I am, as you can
see, hunting for volunteers who can help with this and other aspects
of the project. Further, we are exploring the organization of a non-
profit entity, examining issues relating to the legal web of patents
and IP, and looking over the technical line items of graphic layout
and websites. These are all discussions in progress at the Vegas Group
mailing list, which is open to anyone:

http://groups.google.com/group/the-vegas-group

If you see the merits in this project, I hope that you might think
about volunteering your time and knowledge. Certainly we are in need
of people with experience in the life sciences and practical
biotechnology to assist Allen in setting the groundwork needed for the
writing to begin. Regardless of your background, if you believe that
you can help make the Vegas Group a success, then that is most likely
indeed the case.

For more reading, such as details of the long-term vision for the
Vegas Group, and why I settled on protofection as an initial trial
project, you might look to the following link:

http://groups.google.com/group/the-vegas-group/browse_thread/thread/941d413a6fd5e22b/3389a4601ed87785

And I am happy to answer questions.

[Bryan Bishop]

On Tue, Apr 26, 2011 at 9:09 PM, Reason <rea...@fightaging.org> wrote:

http://groups.google.com/group/the-vegas-group/browse_thread/thread/941d413a6fd5e22b/3389a4601ed87785

I figure some of that is worth quoting:

"""
 The Vegas Group, a Retrospective
-----------------------------------------------------

Looking back from the perspective of 2035, I guess we should all be
surprised that it took so long. The Vegas Group came together formally
sometime in 2016, though the first kick-off meeting was the year prior
at one of the bi-annual conventions for longevity research held in
California. By that time, more than a dozen gene manipulations and
other biotechnologies had been shown to significantly extend life in
mice, but no progress was being made to develop these technologies for
human use. The Vegas Group was a natural outgrowth of a decade of
advocacy and anticipation for human enhancement technologies, coupled
with the frustrating realization that no such technologies would be
meaningfully developed, never mind made available to the public, under
the regulatory regimes then in place in the US and Europe.

There were initial fractures in the Vegas Group around the course of
political change versus direct action - which led to the formation of
another influential movement discussed elsewhere - but by 2017 the
direct action contingent of the Vegas Group consisted of about a
hundred people all told. Their declared objective was a distributed
collaborative effort to (a) develop human versions of the most
successful longevity and metabolic enhancements demonstrated in mice,
and (b) cultivate hospitable medical groups in the Asia-Pacific
countries. When these technologies were developed, the founding
members would cast lots and carefully test upon themselves, in
rotation, and though the agency of medical centers in Asia. In doing
this the hope was to spur change in the public view and greater
progress in the commercialization of these technologies - and of
course to gain access to manipulations that were greatly extending
life in mice. "Pulling the big red lever," as one of the founders
said, a venture where altruism and greed collide to best effect.

By this time, biotechnologies had become cheap enough to enable a
growing amateur development community, akin to the hackers of the
1970s and open source movement of the 1990s and onward, and it is this
community, stirred up and cultivated by the core Vegas Group, that
ensured success. It was a challenge, a middle finger to US authorities
who were at that time attempting to shut down the open biotech
movements, and a tangible way to prove that the "priesthood of the
universities is done and gone." Of course, members of that priesthood
pitched in to help, some to the detriment of their careers, others
clandestinely.

By 2019, the first round of therapies took place amongst the founding
Vegas Group members. This happened to some local fanfare in Singapore,
milked for effect by the sponsoring parties. About half of the
modifications to genes and repair procedures for the damage of aging
were successful, as shown by assays and testing, but no serious side-
effects occurred - a lot of prestige in the broader amateur biotech
community rested on getting that part right at least. So there, in
2019, you have some of the first humans walking around with replaced
mitochondria, cleaned-out cells, manipulated myostatin genes, addition
of bacterial genes to eliminate obesity, and so forth. Strangely, it
met with less interest in the mainstream press than you might expect -
the pop-sci and scientific press release services wouldn't touch it.

Really, that's when the accident should have happened, but with the
benefit of hindsight I think that people became complacent. The
seventeen deaths in 2021 were avoidable - some of the Vegas Group were
emboldened by earlier successes and rushed a new discovery,
underestimating the risk. By that time more than fifty people - a core
of the original Vegas Group, new members, and new offshoots of the
group elsewhere in the world - had been successfully modified in ways
demonstrated to extend life or improve the functioning of biochemistry
in mice, and were leading normal lives. A few of the older group
members had died, but not of any cause linked to their experimental
treatments. The methods for making these modifications to humans were
freely available online, and within the reach of perhaps a few hundred
skilled amateur biotechnologists. They had promptly been outlawed by
most European and the US regulatory authorities.

The commercial outgrowth of the Vegas Group was by this time also
underway. Two companies affiliated with the original founding members
and two more working independently on the science were striding
towards commercial offerings of the technologies. None were based in
the US, of course, and all but one were structured to take advantage
of the trends in medical tourism from America and Europe. Even at
ruinous early-adopter rates, as a luxury good for the wealthy, two of
these companies went on to make their founders fabulously wealthy in a
very short time.

Sadly, it was to be another decade before we came to where we are
today - the first signs that US regulators might finally cease their
prohibition of longevity-inducing and other enhancement technologies
now offered widely in Asia and safely used by ever-increasing numbers
of people.

From the perspective of the mainstream US scientific community, we
still don't know if these alterations work as advertised on human
longevity. The case is pretty much open and closed on calorie
restriction in humans and other primates now, finally, after decades
of debate and new data, but it may be 2055 before researchers are
willing to move beyond measurement of markers and biochemical changes
to acknowledge actual benefits to life expectancy to the procedures
pioneered by the Vegas Group. Meanwhile, people are improving
themselves.

Strangely, the Vegas Group has faded from view, a historical curiosity
of the online cyclopedias that is now supplanted in the "official"
histories by the companies that rose up from their efforts. As a sign
of success, being forgotten in the wake of the vessel you help to
launch has something going for it - burying the daredevils is the
first action of a successful industry setting up for the long term.

 How to Make the Vegas Group a Reality
------------------------------------------------------------

http://www.fightaging.org/archives/2011/03/how-to-make-the-vegas-grou...

Elsewhere, in the land of wishful thinking:

"The Vegas Group came together formally sometime in 2016, though the
first kick-off meeting was the year prior at one of the bi-annual
conventions for longevity research held in California. ... The Vegas
Group was a natural outgrowth of a decade of advocacy and anticipation
for human enhancement technologies, coupled with the frustrating
realization that no such technologies would be meaningfully developed,
never mind made available to the public, under the regulatory regimes
then in place in the US and Europe. ... by 2017 the direct action
contingent of the Vegas Group consisted of about a hundred people all
told. Their declared objective was a distributed collaborative effort
to (a) develop human versions of the most successful longevity and
metabolic enhancements demonstrated in mice, and (b) cultivate
hospitable medical groups in the Asia-Pacific countries."

It is clear to me that this sort of strategy will be (and is) very
necessary as a part of the process of pushing the bounds of medical
technology - which is advancing nowhere near as rapidly as it might
be. Stunning progress in the laboratory doesn't translate into
stunning progress in the clinic, and this is because of the oppressive
shroud of regulation weighing down the entire industry. Can you
imagine a world in which it took ten years and a government agency to
clear the latest innovations in processors and hard drives? We'd still
be stuck with 70s-era computers, and paying ten times the price. Yet
in medicine, this is exactly the situation we find ourselves in; a
worse product, slow progress, and massive expense.

By way of a reminder, it is illegal in the US to commercially develop
and market medical technologies for the purpose of slowing or
reversing aging. I'll stop to let that sink in for a moment, for those
of you who didn't know this. The unelected and largely unaccountable
bureaucrats of the FDA do not recognize aging as a disease, therefore
will not approve any treatment for aging - and so anyone who forges
ahead to try it will be shut down and prosecuted. If you ever wondered
why, in this age of remarkable advances and plummeting costs in
biotechnology, there are not a thousand startup companies striking out
to take on aging itself ... well, this is why.

Pushing change through the FDA is a glacial and very expensive process
of lobbying - a political process, naturally, which must be well
lubricated with money that would be far better spent on research. This
is what it is: essentially corrupt, utterly hostile to progress, a
system in which the incentives are for regulators to cause delay and
obstruction. Absent a revolution, a broken system of governance should
be avoided and worked around, not engaged. When you engage with that
broken system, all you are doing is propping it up and legitimizing
its existence while it has its way with you.

So I have been pondering how best to make the vision of the Vegas
Group a reality: what steps do we take so that we wake up six or seven
years from now to an open source biotech community whose members are
working on enabling the best longevity therapies produced by the
formal research community - and who have the overseas connections to
enable responsible use of resulting therapies in a clinical setting.
The social and regulatory change required to make this happen legally
in the US is so great - and so contrary to the present downward spiral
towards more government and greater regulation in every aspect of life
- that from where I stand, efforts are better directed towards
progress in biotechnology.

So what components are needed to move this from pipe dream to reality?
In no particular order:

- An open repository of technical information: a Wikipedia of
longevity biotechnology and published research, a resource built by a
community into a how-to for specific techniques in longevity science.

- Persuading a sizable segment of the present open biotech community
into finding this grand project interesting enough to support, and
interesting enough to work on.

- Bootstrapping a community of project supporters large enough to
raise funding, hold conferences, and become self-sustaining.

In many ways, I see this sort of thing as the answer to "what comes
next after the SENS Foundation?" When the SENS Foundation is forging
through the waves five years from now, making progress and getting
things done in repairing the biochemical damage of aging, what are the
new and energetic research-focused organizations springing up at that
time? How are they organized? What are their strategies for turning
this growing sea of practical possibilities for repairing aging into
therapies for humans?

I see the SENS Foundation and similarly focused organizations as
covering the mainstream approach to science, which is to say it will
be a slow process moving from working results in the laboratory to
therapies in humans. By the very nature of the Foundation, its
legitimacy in the eyes of people that matter, the ones writing the
checks, depends on going through the established system of research
and regulation, FDA and all. That is their fight.

I don't believe that we can afford to wait for the additional ten
years or however many years it requires to win that fight, however.
Not if there are other options on the table that may enable us to move
faster. The Vegas Group approach is one such option: take the
knowledge and techniques published by the research community into open
biotech communities and overseas laboratories for further development,
work them up to a level at which people are comfortable with the
risks, and try them out. You get things done by getting things done.

After all, these are our lives. Ours. We are not serfs, to be the
property of faceless bureaucrats in the FDA. We can choose our own
risks, just as many open biotech enthusiasts would choose to work on
biotechnologies of rejuvenation that will ultimately benefit all of
humanity. Unless we get this sorted out, the only thing ahead of us is
pain, suffering, and death.

 An Approach to Step One of the Vegas Group: Bootstrapping the Codex
------------------------------------------------------------------------------------------------------------

http://www.fightaging.org/archives/2011/03/an-approach-to-step-one-of...

The Vegas Group: a so far fictional community of the next ten years
that will merge the longevity advocacy and open biotech communities in
order to (a) reverse engineer the most promising life-span-enhancing
techniques demonstrated in the laboratory, (b) translate that work
into human rejuvenation biotechnologies, and (b) make these therapies
available for use via medical tourism to Asia-Pacific region clinics.

"So I have been pondering how best to make the vision of the Vegas
Group a reality: what steps do we take so that we wake up six or seven
years from now to an open source biotech community whose members are
working on enabling the best longevity therapies produced by the
formal research community - and who have the overseas connections to
enable responsible use of resulting therapies in a clinical setting."

The path to this future involves networking and community building in
a whole new and different direction from that taken by much of the
longevity advocacy community - and the construction of a codex of
information, a how-to manual of recipes for replicating specific
products of the formal research community in longevity science.
Networking makes the world go round, and that is the most important
part of any attempt to create the Vegas Group, or indeed any human
endeavor: making relationships and persuading people to join in. But
this is not where I can be the most effective.

So any step one for me will involve considering the codex: what it is,
and how it will be constructed, maintained, and made useful to the
seeds of what will be the Vegas Group - however that organization
ultimately comes about, and whatever form it ultimately takes. It is
very clear to me that open biotechnology will grow into a massive semi-
professional sphere of activity, exactly like the open source software
community today. I want to take advantage of the wave that is coming,
and produce a work that will both aid that wave and in turn be aided
by it.

When thinking about the way in which contributions of content are made
voluntarily to any given community or site - such as Wikipedia, or
blogs such as this one, or the documentation repository at your
workplace - it is self-evident that very, very few people step up to
produce good content. Wikipedia works because a great many people each
contribute just a little, a continual process of polishing, one grain
of sand at a time, applied to the bulk outlines contributed by the
motivated few. But for smaller groups, you don't get polishing, you
just get next to nothing in the way of contributions.

So I'm fairly certain that for the Vegas Group codex, while a wiki
model may be helpful as an adjunct to a motivated community further
down the line, it isn't a way to get things written at the outset -
it's not a way to provide the corpus of work that a community can
later polish. There are few biotechnologists in the world in
comparison to, say, football fans. Look at the number of science
bloggers as compared with other topics, for example. Despite this,
there are still initiatives out there, however, working on pulling
together repositories of techniques and knowledge: OpenWetWare for
example. So the concept of producing an open collection of techniques
and recipies is not a foreign one to the biotechnology community -
it's just not very advanced at this stage, at least not in comparison
to the bodies of knowledge associated with larger communities.

Thus I think that a larger seed, a bigger online repository of freely
available and reliable recipes for longevity-related biotechnology,
would act as an attractor for people willing to tinker and help out.
The same class of supporters and advocates who produced initiatives
like OpenWetWare will contribute to help polish its contents. Overall,
the concept of a codex seems to me to be where a comparatively small
amount of money could be leveraged to good effect. Consider this:

- Creating an initial repository website and content management system
isn't a significant cost given the present state of open source
content management software - it's almost something I could undertake
myself.

- People with significant knowledge of biotechnology are remarkable
cheap to engage at the post-graduate level. Consider that a few
thousand dollars of post-graduate time can net you a long and well-
informed analysis, or detailed explanation of a specific methodology.

- It wouldn't be a good piece of writing of course - no offense is
intended when I say that few post-graduate scientists can write well.
Writing well is hard, and just as much a specialty as is becoming a
scientist; few people have the time and inclination to specialize in
more than a few things, and why should one of them be writing?

- Fortunately, people who can write well are always in supply,
desperate for work, and inexpensive. It is a buyer's market.

So I can envisage a guiding council of advisors putting together a
plan for the hierarchy of topics they would like to see in the Vegas
Group codex, from basic methods in biotechnology through to best
attempt reverse engineering of things we know to be possible and that
have been published: such as Cuervo's work on restoring youthful
levels of autophagy, or protofection to replace mitochondrial DNA. The
end result of that process might look something like a distillation of
Fight Aging! mixed with the very elegant materials produced by the
Science for Life Extension Foundation.

Codex project volunteers would then run an ongoing process of hiring
post-graduates and interested researchers to write, and passing the
results to starving authors who improve the output to a quality
suitable for the open biotechnology community. There would of course
be some back and forth between the post-graduates and the starving
authors in order to reduce the inevitable translation errors, but I
see this as a viable way to produce a body of knowledge that is
sufficiently good to begin with - not perfect, not even necessarily
very good, but sufficient.

Since only a comparatively limited reach of biotechnology is under
consideration, the cost of bootstrapping such a project might be less
than a few hundred thousand dollars. The things I would need to
understand before getting seriously underway on a Vegas Group codex
are largely related to validating that price tag. A few hundred
thousand dollars would mean that it is worth starting with ten
thousand dollars, some volunteers, spare time, and raising funds as we
go based on the quality of work exhibited. That would be true
bootstrapping, but I'd have to give thought in advance to:

- The actual cost of generating the materials - something that I
suspect won't be clear until the project is at least twenty articles
in. I have a fair grasp on the range of costs for writing for hire, in
fields that range from very specialist (pricey) and completely
generalist (a few cents a word), but I've no idea where this market
falls in that spread of values, nor how much management and general
cat-herding of writers would be required.

- The predicted size of a sufficiently large body of information, as
set out by guiding experts. Is it a hundred articles, a hundred
videos, a thousand images, or half that, or ten times that?

- How to make this project attractive to the existing open
biotechnology community even in its earliest stages. There is no such
thing as "build it and they will come" - if anything building in
isolation guarantees that you'll have few visitors.

Which comes right back around to networking and relationships: as I
said, they make the world go round. On that topic, I am sadly lacking
in a knowledge of the current state of the open biotechnology
community - something that will have to change as I give more thought
to the Vegas Group idea. No sense in reinventing the wheel if there is
a wheel out there already ... or even a half-built wheel, a project
where lessons were learned.

 Reverse Engineering Protofection as a First Target for the Vegas Group
--------------------------------------------------------------------------------------------------------

http://www.fightaging.org/archives/2011/04/reversing-engineering-prot...

The Vegas Group is a yet-to-be-built community initiative intended to
bring longevity science to the open biotechnology and DIYbio
communities - and from there reverse engineer and make ready for human
use the most promising longevity-enhancing technologies demonstrated
in mice in the laboratory. We are entering an age of medical tourism,
and the clinics and laboratories of Asia will be happy to accept
business and open source biotechnologies generated by DIYbio work in
the US. At this stage, I'm still thinking through the project:
breaking it down into manageable chunks, and considering what I should
work on first:

"The path to this future involves networking and community building in
a whole new and different direction from that taken by much of the
longevity advocacy community - and the construction of a codex of
information, a how-to manual of recipes for replicating specific
products of the formal research community in longevity science. ...
any step one for me will involve considering the codex: what it is,
and how it will be constructed, maintained, and made useful to the
seeds of what will be the Vegas Group - however that organization
ultimately comes about, and whatever form it ultimately takes."

As the cost of biotechnology falls, so is the door opened to much
wider development and innovation, wherein lab cooperatives host a mix
of hobbyists, moonlighting professionals, and semi-professionals who
collaborate on a range of their own projects. Ultimately, low-cost
desktop biotech toolkits will be developed and a community of tens or
hundreds of thousands of developers will contribute from their homes -
just as is the case for open source software development today. With
computers in mind, a good historical analogy for the present state of
the small DIYbio community is in fact the Homebrew Computer Club in
the mid 1970s, prior to the introduction of the first popular personal
computer kit. Some small but enthusiastic individuals and groups are
designing, building, and selling biotech hardware - such as PCR
machines - that will ultimately be the components of a home
laboratory, but matters are not yet at that stage of take-off that
will see dozens of companies founded and many more people join the
community in a short period of years. That lies ahead. The wave is
coming, in its own time, and I would like to be positioned to take
advantage of it.

All journeys start with the first steps, and I'm in favor of
incremental approaches to development. Make something small, a minimum
viable product that is the most elementary building block that can
stand on its own and still contribute to the ultimate goal. Release
it, obtain feedback, and then start on the next building block - and
repeat that process until you have as fully as possible realized your
initial vision. There will be much to learn along the way, and small
building blocks coupled with "release early, release often" make that
learning less painful.

Given a large idea, the challenge is often finding that starting
point. From the broad high level outline of the Vegas Group, I focused
on the codex: the necessary how-to documents and body of knowledge
that will enable people to participate. As a general rule, technical
communities are terrible at documentation - and that lack of
documentation is a real hurdle to recruitment and growth. It could be
argued that the DIYbio community isn't yet at the point where it could
benefit greatly from a codex: there are other tasks to be completed
first relating to hardware. But time is ticking, and progress is being
made. The period of being too early won't last forever, and
establishing even the skeleton of a practical longevity science codex
at hobbyist or non-profit speed will be a process that takes years.

The codex itself is a very large project: something large enough to
found a company on in and of itself. There are any number of
questions: how best to discover the business models that work to
efficiently produce accurate reverse engineering from published papers
on longevity-related biotechnology; how best to structure the
information presented; how to organize writers and researchers; how to
even assemble and prioritize the list of materials needed; and so on
ad infinitum.

Thus a fairly narrow initial project for the codex must be identified,
so that the first group of volunteers to work on it can run into all
the brick walls and fall into all of the potholes without risking a
great deal if it all fails. Small projects are easy to scrap, rework,
and start over if necessary - and that is a tremendous advantage when
you don't yet know the detailed recipe for success. Along the way the
volunteers will come to an understanding of how best to make assembly
of the broader codex work as a process.

What is this first codex project, though? I propose that reverse
engineering and documentation of mitochondrial protofection is a good
candidate. This is a technique by which mitochondrial DNA is replaced
throughout an individual's cells, and was first demonstrated in mice
back in 2005. As you might know, progressively accumulated damage to
mitochondrial DNA is one of the causes of aging, as described by the
mitochondrial free radical theory of aging. Future rejuvenation
biotechnology must include a way to either permanently work around
this form of damage, such as through the methodology advocated by the
SENS Foundation, or periodically repair it - say once every two to
three decades.

Why protofection? In a nutshell:

- It is comparatively easy to explain to a non-technical audience.
- It fits with the SENS vision for rejuvenation biotechnology.
- It has already been demonstrated to work, so at least one group of
researchers knows exactly how to do it.
- It is old enough that this and related knowledge may have spread
somewhat, making it more amenable to reverse engineering.

Protofection works in mice, but since that demonstration six years ago
next to nothing has been heard of it - just a few publications
indicative of a slow exploration in search of possible FDA-approved
applications. The FDA does not consider aging a disease, however, and
therefore its regulators will not approve any treatment that aims to
intervene in aging or achieve rejuvenation. That unfortunate fact is
well known, and thus there is little funding available for attempts to
treat aging: potential technologies are instead subverted into the
development of limited treatments for late stage age-related diseases.
The silence regarding protofection is probably another good example of
the way in which the present regulatory apparatus holds back progress,
as developing protofection for safe general human use is an obvious
course of action based on the weight of evidence linking mitochondrial
DNA damage and aging. Yet it isn't happening.

Given that a number of years have passed since the viability of
protofection was demonstrated, it should be an easier target for
reverse engineering and documentation of processes than more recent
developments. By which I mean that it should be easier to find
researchers and post-graduates unconnected with the work who
nonetheless know enough to write on the topic.

Protofection is also (I hope) narrow enough not to generate a true
mountain of supporting needs in terms of how-to documents. Part of the
process of discovery is to understand how to develop the initial list
of documents required for the codex, starting from a high-level goal
like "let's reverse engineer protofection, make reproducing it
comprehensible to the semi-professional DIYbio volunteer, and release
that documentation under a Creative Commons license" and working all
way down to the brass tacks and petri dishes. Protofection, while
something that can be explained in a few short sentences, stands at
the top of a sizable pyramid of techniques and knowledge in
biotechnology: how to work with DNA, how to manage your own laboratory
equipment, how to keep cell cultures, and so on for a long list of
topics.

If this takes a few years to get right, that's fine by me. It will
provide a blueprint for doing the same to other areas of
biotechnology, and by that time there should be more people interest
in helping out - both for longevity science and for their own areas of
interest.

 An Update on Early Vegas Group Discussions
-----------------------------------------------------------------------

http://www.fightaging.org/archives/2011/04/an-update-on-early-vegas-g...

The Vegas Group is a recently launched initiative that aims to speed
up translation of existing longevity-enhancing biotechnologies from
the laboratory to human therapies. There is little incentive for
commercial entities to work on these technologies in the US because
the FDA does not recognize aging as a disease, and will therefore
never approve a therapy for aging. But if these technologies,
currently documented only in the prickly, dense scientific literature,
can be brought into the open biotechnology arena, explained, and made
accessible, they will be picked up by semi-professionals, developers,
and commercial ventures in less restricted parts of the world.

Protofection, for example, is a technique for introducing replacement
mitochondrial DNA into all the cells of the body - a way to repair the
contribution to aging caused by accumulated defects in mitochondrial
DNA. This was demonstrated in mice back in 2005, but the research
group responsible has since been working on the commercialization of
other aspects of this work. Protofection as a way to repair a
fundamental part of the damage of aging will likely languish
undeveloped in the US for years to come under the present regulatory
regime.

Yet this is an era of medical tourism and near-free transmission of
information - if we take currently esoteric but largely proven
biotechnology and produce good, free, open instruction manuals, then
this knowledge and its application will spread. We can all help to
take advantage of the information age and biotechnology revolution
that we are living through, and we can start to do this by engaging
and persuading the growing open biotechnology and DIYbio community to
pay more attention to longevity science.

The Vegas Group is presently a discussion list of a few active
volunteers and a small crowd of interested folk. We are looking at the
nuts and bolts of organization, focused on a proof of concept
documentation project: take mitochondrial protofection and document it
sufficiently well to make it accessible to the DIYbio community of
enthusiasts and moonlighting biotech professionals who are building
open-access devices and establishing shared laboratories. Along the
way this means finding freelance life science writers, evangelizing
the concept, proofing copy, making diagrams and layouts, and putting
up a website - amongst other line items.

...

If you take a look at the discussion list, you'll see some of the
following threads underway:

- Discussing the details of protofection, and how to proceed with
documenting the procedures involved
- A roving discussion on to-do lists, graphics, and layout
- A list of online resources to learn about the DIYbio community

We are looking for more life science and DIYbio volunteers, writers
and editors, folk with connections that will help move things along,
people with an understanding of the legalities of reverse engineering
and intellectual property, and web developers who can help with the
forthcoming website. Amongst others - if you think you can help make
the Vegas Group a reality, then you probably can. So join the list and
help!
"""

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

[CoryG]

> Good day; my name is Reason, and I manage Fight Aging!, a long-running
> science and activism blog that covers a range of topics in research
> and biotechnology. (http://www.fightaging.orgfor the curious).

You can't pay the respect of using your real name just because you're
hyping a blog with 32 followers?

> As a few of you may know, I recently kicked off work on a new project
> called the Vegas Group. This is a volunteer initiative with the
> ambitious long-term goal of closing the gap between the longevity
> science advocacy and DIYbio communities, the better to encourage work
> that will bring demonstrated therapies that enhance longevity in
> mammals out of the lab and closer to readiness for humans. If we sit
> around doing nothing, waiting for the regulators to get it and stalled
> work to emerge into the clinic, nothing will ever get done - but that
> can be changed.

This might just be my personal viewpoint - but I don't think the
community would benefit from someone aiming to circumvent regulation
for animal and human testing - personal choices are one thing and I'd
be the first to test anything I made, but if you're considering animal
testing without following the proper guidelines you might as well be
advocating that we all start abducting homeless people to experiment
on. For that matter - I personally don't believe that advocacy does
much to progress science in this age - even if it is easier than
actually conducting any form of research and might inspire some
overzealous idiots to perform uncouth acts.

> While I know that amongst the members of this community stand a number
> of supporters of longevity science, Aubrey de Grey's SENS, and near-
> future biotechnologies to repair the biochemical changes of aging, the
> near-term goals of the Vegas Group are probably of broader interest to
> the group.

Don't get me wrong here - I think Aubrey de Grey is a genius and SENS
is a great outline and organization - but they don't exactly need help
provoking people to not want to age/die or with research
capabilities. While I agree all this should be open, I think its safe
to say anything made by the DIYbio community is already very likely to
be integrated into the process if it is of use and anything made by a
group by the SENS foundation (as opposed to the strategy) will
doubtlessly be implemented as a service of some form or another.
strategy - http://en.wikipedia.org/wiki/Strategies_for_Engineered_Negligible_Senescence
organization - http://www.sens.org/

> In short, we intend to build an open, Creative Commons licensed
> repository of high quality documentation: how-to guides for the DIYbio
> enthusiast and professional life scientist that explain exactly how to
> (a) perform longevity-enhancing interventions that have been
> demonstrated in mice, and (b) participate in some of the ongoing
> investigative research into the repair of age-damaged mammalian
> biochemistry.

To me this is kind of like when you start an organization, the first
thing you should ask yourself is "is there someone already doing this,
and if so why not join them" it seems you're trying to get people to
populate your website and shift from all the existing ones
(OpenWetWare in particular comes to mind here) that fulfill these
roles (or perhaps even worse, to waste time trying keeping up multiple
repositories when a nightly backup would work better without confusing
newcomers with multiple instances of the same information - or given
the feel of your post, skewed by your own perceptions of how they
should receive that information).

> In the process of building this repository, we will cover a great many
> common supporting procedures and techniques in biotechnology and life
> science work. These will be documented and made openly available in
> the same way as the longevity science guides: it is important to me
> that no low rungs on the ladder be missed.

Why not apply for an OpenWetWare account and help contribute to it?

> In fact, I will be looking to this community to supply many of the
> writers and editors for this process: writing doesn't pay well, even
> in specialized fields, and especially for non-profit ventures, but as
> we get underway this will be a project that pays its writers. I hope
> that some of you will be interested in sharing your knowledge in this
> way, and by doing so help to popularize and smooth passage into the
> DIYbio community for years to come.

In what way do you intend to turn this into profit - page hits,
subscription, etc - and if this is to be a community where you are
crowd-sourcing most or all of the contributions how can you possibly
think it is morally acceptable to turn a profit? For that matter the
foundation of your work (based on SENS) isn't even yours.

> And I am happy to answer questions.

Do you smoke a lot of weed, and if not will you share you're actual
name?

[CoryG]

On Apr 26, 10:52 pm, Bryan Bishop <kanz...@gmail.com> wrote:
> On Tue, Apr 26, 2011 at 9:09 PM, Reason <rea...@fightaging.org> wrote:
>

> >http://groups.google.com/group/the-vegas-group/browse_thread/thread/9...

>
> I figure some of that is worth quoting:

Glad you got a copy up of the stuff written in the past-tense around
2016+ - can I get a look at the device you use to speed and slow the
passage of time (assuming it's not under the passenger seat of your
van).

[Reason]

> -----Original Message-----
> From: diy...@googlegroups.com [mailto:diy...@googlegroups.com] On
> Behalf Of CoryG
>
> You can't pay the respect of using your real name just because you're
> hyping a blog with 32 followers?

Ah, the ever polite folk of the internet, so ready to leap into civilized
discourse. Fortunately, the world isn't bounded in its possibilities by your
horizons, and Reason is in fact my real name.

> Why not apply for an OpenWetWare account and help contribute to it?

I think that a distinct initiative to try the production of documentation my
way is a much better option than contributing to that project, especially
given the fairly narrow focus of the Vegas Group on longevity-related
biotech.

> In what way do you intend to turn this into profit - page hits,
> subscription, etc - and if this is to be a community where you are
> crowd-sourcing most or all of the contributions how can you possibly
> think it is morally acceptable to turn a profit?

You pay freelance writers because it is next to impossible to obtain
reliably good work from distributed unpaid volunteers over a project of any
significant length. The Vegas Group isn't intended to make money, nor do I
see it generating revenue; it is intended to do exactly what it says on the
label: build documentation, build relationships, spur meaningful change.

Even if the Vegas Group did generate revenue, there would be nothing wrong
with doing so on the basis of paid labor - and it is certainly the case that
distinct for-profit entities doing something similar might arise to service
other areas of DIYbio-focused biotech documentation that I have no personal
interest in ... but that isn't on the table for me for now. I should close
this line of thought by pointing out that hostility towards profit is not
exactly a sensible attitude when it comes to the growth of any sort of
ongoing, long term ecosystem of relationships and endeavors, this one
included.

Reason

[CoryG]

> Ah, the ever polite folk of the internet, so ready to leap into civilized
> discourse. Fortunately, the world isn't bounded in its possibilities by your
> horizons, and Reason is in fact my real name.

So you're full, legal name, is "Reason" just like "Prince" and without
any sort of underlying intent to implement subliminal messaging of any
kind?

> I think that a distinct initiative to try the production of documentation my
> way is a much better option than contributing to that project, especially
> given the fairly narrow focus of the Vegas Group on longevity-related
> biotech.

What is your way?
How do you aim to have good results disregarding related research that
you screen in some way and deem to be unrelated when you yourself are
not even doing any research?

> You pay freelance writers because it is next to impossible to obtain
> reliably good work from distributed unpaid volunteers over a project of any
> significant length. The Vegas Group isn't intended to make money, nor do I
> see it generating revenue; it is intended to do exactly what it says on the
> label: build documentation, build relationships, spur meaningful change.

You tried to entice people to write for you under the pretense that
people would be paid for their work at a later date when you had
turned a profit - without a mechanism to generate profit how do you
intend to fulfill such a statement? For that matter, without a
mechanism to generate a profit how can you even argue against unpaid
crowd sourcing as being the only thing you intend to employ - or was
the first line in the paragraph above just fluff?

> Even if the Vegas Group did generate revenue, there would be nothing wrong
> with doing so on the basis of paid labor - and it is certainly the case that
> distinct for-profit entities doing something similar might arise to service
> other areas of DIYbio-focused biotech documentation that I have no personal
> interest in ... but that isn't on the table for me for now. I should close
> this line of thought by pointing out that hostility towards profit is not
> exactly a sensible attitude when it comes to the growth of any sort of
> ongoing, long term ecosystem of relationships and endeavors, this one
> included.

I have no hostility toward profit - I have hostility toward:
-People who try to recruit others for projects or work alongside them
without giving out their true identity.
-People who try to entice others with false promises.
-People who utilize subliminal messaging to reach their aims.
-People who spend all their time grandstanding instead of doing
anything while being deluded enough to believe they are making a
difference (trying to proliferate such an attitude amongst people who
do actually at least attempt to research is a particularly new
offensive gesture I'd never actually witnessed before now - though on
this point, I do believe you're from Berkeley).

[mad_casual]

On Apr 27, 12:53 am, CoryG <c...@geesaman.com> wrote:

> I have no hostility toward profit - I have hostility toward:
> -People who try to recruit others for projects or work alongside them
> without giving out their true identity.
> -People who try to entice others with false promises.
> -People who utilize subliminal messaging to reach their aims.
> -People who spend all their time grandstanding instead of doing
> anything while being deluded enough to believe they are making a
> difference (trying to proliferate such an attitude amongst people who
> do actually at least attempt to research is a particularly new
> offensive gesture I'd never actually witnessed before now - though on
> this point, I do believe you're from Berkeley).

+1

I was/am so disappointed in this thread. An out-of-touch elitist
trying to, I dunno, "employ" DIY scientists? Doesn't exactly drive the
'quality', 'documentation', 'longevity', 'science', or 'advocacy'
goals home.

[Jonathan Street]

There seems to be an over-abundance of hostility here a considerable amount of, potentially mis-guided, reading between the lines.

I don't follow fightaging but I've heard of it previously which seems unlikely if it only had 32 followers.  I assume this number was the number of google group members.  Given he says this is a new initiative is this surprising?  For an alternative perspective the site has over 3k pages and 26k inbound links (https://blekko.com/ws/http:%2F%2Ffightaging.org%2F+/domain).  Although I'm personally opposed to the idea of a merger there seems to be some scope for cross-pollination of ideas and effort there.

On the subject of animal testing I saw no reference to that in the text that Bryan posted though I've not looked through the site in more detail.  Have I missed something?

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[Bryan Bishop]

On Wed, Apr 27, 2011 at 5:42 AM, Jonathan Street wrote:

On the subject of animal testing I saw no reference to that in the text that Bryan posted though I've not looked through the site in more detail.  Have I missed something?

I think there was something in those paragraphs about human testing, for what it's worth. "Volunteers needed for a study investigating whether people can distinguish between scientific studies and kidney-harvesting scams."

Regarding the medical tourism industry and DIYbio, I posted a while back about some of the issues:
http://groups.google.com/group/diybio/browse_thread/thread/199021703058b30b

and so did Anselm:
http://groups.google.com/group/diybio/msg/07e7e6f4f7c7e8b4

For stem cell therapies: in the miraculous case that you have good experimental setup, data, verification, working stem cell cultures, etc., then "going rogue" on your stem cell clinic might make sense. But writing unused/untested documentation isn't enough to execute on this (or other molecular therapies, etc.), and in fact, there's a lot to be said for just making its lab/protocol toolchain cleaner and easier to work with right now.

[Reason]

Let me try a shorter, simpler formulation of what I'm looking for by posting
to the DIYbio group:

1) I want to create documentation for a set of life science / biotech
procedures relating to longevity, and ensure it is freely and widely
available for use. The explanation for why I want to do this is in the
longer material that Bryan posted.

2) The project to start work on this launched a couple of weeks ago, and is
presently gathering interested volunteers.

3) Some of the resulting documentation will be useful to the wider DIYbio
community: supporting procedures, common techniques.

4) Many of the members of this group have knowledge that might be useful in
producing this documentation. So it can't hurt to ask.

5) If you see value in this project, please do volunteer. We need additional
life-science folk at this stage to help break down procedures into lists of
topics and activities suitable for handing out to writers.

6) My experience tells me that you can't produce good results on the back of
freelance, online, distributed writing without paying people. Therefore I
will be putting up money to pay people. This goal is important to me.

It really is that simple. I am frankly surprised to be greeted with such
outright hostility.

Reason

[CoryG]

> I don't follow fightaging but I've heard of it previously which seems
> unlikely if it only had 32 followers.  I assume this number was the number
> of google group members.  Given he says this is a new initiative is this
> surprising?  For an alternative perspective the site has over 3k pages and
> 26k inbound links (https://blekko.com/ws/http:%2F%2Ffightaging.org%2F+/domain).  Although I'm
> personally opposed to the idea of a merger there seems to be some scope for
> cross-pollination of ideas and effort there.

SEO ability doesn't equate to real people. Some of the striking
things that irritate me about this page is that there is content
backdated to 2007 or earlier, the domain was itself last changed
ownership in February and all those 3k pages + 26k links seem to be in
large generated by semantic processing techniques (search for
individual blurbs from the site on google to see) and a webring of
spam sites that help eachother attain search ranking and do little
else.

> On the subject of animal testing I saw no reference to that in the text that
> Bryan posted though I've not looked through the site in more detail.  Have I
> missed something?

This was the line I was responding to:

[CoryG]

> It really is that simple. I am frankly surprised to be greeted with such
> outright hostility.
>
> Reason

And yet you can't provide a real name when soliciting help - why
should anyone take you as anything but a scammer looking to crowd
source work?

[J. S. John]

We're very skeptical around here since there were instances of people
pedalling things without much references, names, goals, etc. I don't
understand why you're anonymous if you're running an organization.

[Cathal Garvey]

I for one have no objection to anonymity online so long as money isn't involved. I think it's both normal and prudent to keep your identity online secret until it's foolish to continue doing so.

Of course, given that money might be involved, perhaps that allowance doesn't apply.

Also, although I would generally be against attacking people for soliciting collaboration on something, the spam-ring accusation is a bit suspect.

Also, if someone's actually suggesting animal testing as a DIYbio thing, I'd suggest not doing so or encouraging others to do so. Nothing good lies that way: if you want to do animal testing, go get licensed or work in an established facility.

Sent from my Phone
www.twitter.com/onetruecathal
www.indiebiotech.com

On 27 Apr 2011 15:51, "J. S. John" <phill...@gmail.com> wrote:

On Wed, Apr 27, 2011 at 10:33 AM, CoryG <co...@geesaman.com> wrote:

>> It really is that simple. I am...

We're very skeptical around here since there were instances of people
pedalling things without much references, names, goals, etc. I don't
understand why you're anonymous if you're running an organization.

--
You received this message because you are subscribed to the Google Groups "DIYbio" group.

To po...

[Jonathan Street]

Also, although I would generally be against attacking people for soliciting collaboration on something, the spam-ring accusation is a bit suspect.

Personally I can't find evidence to support that accusation.  The posts on fightaging aren't each unique but it's no worse than any major news site.  Some of the posts are syndicated elsewhere but from my experience that happens with or without input from the author, it seems to be a common affliction on the web these days.

Most of the links will be from junk sites but there are also links from some high profile sites including wikipedia, msnbc, huffington post, etc.

the domain was itself last changed ownership in February

I see that the whois record was last updated in February.  I don't have access to the record prior to the change.  Cory, do you have access to the record prior to February?  If so then I would be interested in seeing what the change was.  If not then I don't see how you can support this statement.

 

[CoryG]

> Personally I can't find evidence to support that accusation.  The posts on
> fightaging aren't each unique but it's no worse than any major news site.
> Some of the posts are syndicated elsewhere but from my experience that
> happens with or without input from the author, it seems to be a common
> affliction on the web these days.
>
> Most of the links will be from junk sites but there are also links from some
> high profile sites including wikipedia, msnbc, huffington post, etc.

Bots don't move that quickly without being provoked to do so -
spammers are dirty but their not typically wealthy enough to afford
the computing power. The affliction itself isn't from 3rd party bot
makers seeking web traffic, it's a pretty standard SEO tactic which is
why you see those things in mainstream news sites beyond just having
3rd parties quote them. Typical SEO behavior is to setup multiple
sites that interconnect with a general theme between the sites (each
geared to target a specific keyword or finite set of them) then
interlink them, the number of interconnected references will function
to drive up the rank in algorithms like google's pagerank and when
there is a verbatim copy of text (typically between a paragraph and a
full page) it gets around most of the spam filters that try to check
for actual content rather than just links. Another method is that
long list of links on the right side of his page to mainstream sites,
which work on a similar principle to pagerank but for algorithms
checking the links in more than a referencing site sense.

> the domain was itself last changed ownership in February
>
>
>
> I see that the whois record was last updated in February.  I don't have
> access to the record prior to the change.  Cory, do you have access to the
> record prior to February?  If so then I would be interested in seeing what
> the change was.  If not then I don't see how you can support this statement.

I can't support this statement publicly - the most I'll say is it
involved social engineering to determine.

[Phil]

On Apr 26, 10:09 pm, Reason <rea...@fightaging.org> wrote:

> All this might be averted if we had some way to replace that damaged
> mitochondrial DNA - and we do, a technique called protofection that
> was demonstrated to work in mice back in 2005. This employs a vector
> to introduce replacement mitochondrial DNA into cells throughout the
> body, and is fairly well explained (if you are a scientist and up for
> reading dense papers) in a selection of scientific publications issued
> over the past six years.

AFAIK there are only two papers on protofection, and they
are both too vague to enable anyone to reproduce it.
Numerous people have tried; no one has been able to replicate the
results.

Can you post all your protofection references?

Thanks,
Phil

[Phil]

Scammers do things to make money.
This doesn't have any obvious potential for making money.

I don' understand Cory's hostility.
My best theory is that he's categorized Reason
as a bad and dangerous person because he wants
to circumvent federal regulation, and is thus
projecting all sorts of other negative things bad
and dangerous people do onto Reason,
without evidence. In just a few sentences Cory
made three baseless accusations: that Reason is
making "false promises", using "subliminal messaging",
and "grandstanding".

I agree with Reason that we will all die of old age
if we do things the way the FDA wants them to be done.
Reason should perhaps think about moving to Asia or India,
or finding collaborators there.

Cory wrote:
>I think its safe to say anything made by the DIYbio community
>is already very likely to
>be integrated into the process if it is of use and anything made by a
>group by the SENS foundation (as opposed to the strategy) will
>doubtlessly be implemented as a service of some form or another.

It is naive to imagine that cures would be used if they existed.
We have, for example, numerous partial cures for Duchenne's
muscular dystrophy that have been sitting on the shelf for
about 6 years while going through the approval process -
even though you could in some cases just pick up the syringe you
used on a mouse and apply it to a child and save his life
(the myostatin gene is identical in humans and mice).
In the meantime, thousands of boys have died of this disease,
allegedly because trying out cures that might save
their lives would be "too dangerous". This despite the fact
that some of these cures do not have any serious
known or theoretical risks. (The only serious risk in
some cases is that they may stop working after a few months.)

[CoryG]

> I don' understand Cory's hostility.
> My best theory is that he's categorized Reason
> as a bad and dangerous person because he wants
> to circumvent federal regulation, and is thus
> projecting all sorts of other negative things bad
> and dangerous people do onto Reason,
> without evidence.  In just a few sentences Cory
> made three baseless accusations: that Reason is
> making "false promises", using "subliminal messaging",
> and "grandstanding".

I've given explicit citations above, however to reiterate:
"false promises" = he attempted to entice help from others on the
promise of later payment with, as you say, no potential to actually
make money - whether this is incompetence or deception I can't say for
certain.
"subliminal messaging" = look at his name, he's so self-righteous he
believes the name "reason" is fitting - he's making deliberate
attempts to manipulate people by stating it is his real name.
"grandstanding" = read his writings

> Cory wrote:
> >I think its safe to say anything made by the DIYbio community
> >is already very likely to
> >be integrated into the process if it is of use and anything made by a
> >group by the SENS foundation (as opposed to the strategy) will
> >doubtlessly be implemented as a service of some form or another.
>
> It is naive to imagine that cures would be used if they existed.
> We have, for example, numerous partial cures for Duchenne's
> muscular dystrophy that have been sitting on the shelf for
> about 6 years while going through the approval process -
> even though you could in some cases just pick up the syringe you
> used on a mouse and apply it to a child and save his life
> (the myostatin gene is identical in humans and mice).
> In the meantime, thousands of boys have died of this disease,
> allegedly because trying out cures that might save
> their lives would be "too dangerous".  This despite the fact
> that some of these cures do not have any serious
> known or theoretical risks.  (The only serious risk in
> some cases is that they may stop working after a few months.)

Thats actually a pretty serious risk if you're speaking of trying to
cure another person. There is no direct method of imposing a lack of
liability (the first person to suffer a side-effect from something if
you're going around the FDA process WILL land you in jail) without
allowing for all kinds of nasty loopholes to emerge. The proper thing
to do is to work with the system, not to waste so much time fighting
it you never actually produce anything.

[Nathan McCorkle]

On Wed, Apr 27, 2011 at 2:04 PM, CoryG <co...@geesaman.com> wrote:
>> I don' understand Cory's hostility.

I agree, I think you came on a little quick here CoryG... I would have
offered constructive criticism first, then if things kept sounding
unrealistic, I would have brought out the more severe criticisms. That
said, maybe you know what he's talking about quite well, enough to
skip to the harsh criticisms.

If I was faced with a life threatening or really debilitating disease,
I would certainly be pressed to weigh the options had.... but I might
not be opposed to self-treating (injecting myself with the mouse cure)
depending on my options. It sucks that in the U.S. we don't have those
options in the hospital.... but I really don't know the whole story
with the ins and outs of regulation, and I hope there is a logical
reason behind not having this option.

> --
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>
>

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

[J. S. John]

Reading this again, all I see is that he wants to build some kind of
article depository. He's also asking for writers to write about some
topics in life extension. The payments mentioned seem to be for the
articles. I don't see anything about running experiments although the
documents will give anyone a how-to on that. Is that the gist of it?

[Cathal Garvey]

As unlikely as a payment scheme may seem at this point, it seems that all that he's asking is for writers for open access content. I imagine if it's written under a Creative Commons license or similar, it's as good there as anywhere, as it can be reposted as needed or desired on other sites. Redundancy can't hurt, after all.

I don't like the idea of encouraging experimentation DIYbio-style that doesn't really fit the bill for "Hobby Biotech", and animal experiments and self-medication are the sort of categories that can get DIYbio into trouble and could result in harm to people or animals which is easily avoided. If we're being asked to write articles on "how-to vivisection" I'd encourage refusal. If it's more "How-to protect yourself against protein misfolding" or "How-to raise intracellular levels of glutathione", that's all cool provided it doesn't involve anything potentially hazardous to the unwary reader.

Because, we should all be aware that there are unwary/overly credulous readers out there by now.

letters.cunningprojects.com
twitter.com/onetruecathal
http://www.indiebiotech.com

[Reason]

> -----Original Message-----
> From: diy...@googlegroups.com [mailto:diy...@googlegroups.com] On

> Behalf Of Cathal Garvey
> Sent: Wednesday, April 27, 2011 1:44 PM
>
> I don't like the idea of encouraging experimentation DIYbio-style that
> doesn't really fit the bill for "Hobby Biotech", and animal experiments
> and self-medication are the sort of categories that can get DIYbio into
> trouble and could result in harm to people or animals which is easily
> avoided. If we're being asked to write articles on "how-to vivisection"
> I'd encourage refusal. If it's more "How-to protect yourself against
> protein misfolding" or "How-to raise intracellular levels of
> glutathione", that's all cool provided it doesn't involve anything
> potentially hazardous to the unwary reader.

My own take on animal experimentation is that the only thing worse than it
is its absence. I look forward to the foreseeable future in which
experiments in silico become cheap enough to naturally displace the vast
majority of in vivo work, and loathe the fact that our human condition
pushes us toward the unpleasant utilitarian decision to conduct animal
studies.

That said: the measure of a scientist is whether they adhere to the
scientific method, not whether they are formally associated with a major
institution. There is a modest range of people out there who are running and
have run animal experiments that fall within the financial range of a
citizen scientist. For example, the fellow who ran a series of fly life span
experiences back a decade or so ago on the Extropy list, or the fellow
presently engaged through volunteer fundraising from Longecity in order to
test laser ablation of lipofuscin on long-lived breeds of nematode.

And that said: the purpose of the Vegas Group project, the long-term
purpose, is to build a bridge between on one side the work demonstrated in
the laboratory but which will never be developed well under the present US
regulatory regime, and on the other side development communities in
Asia-Pacific regions with more permissive medical regulations (e.g. any of
them at this present time, China included, which is a sad statement to be
able to make). My view of the future is that the DIYbio and surround
communities will play a large role in building this bridge - you are too
small and too few to do so well now, but the future of DIYbio looks very
much like the present of the open source software and open hardware
communities. A lot of people, many passionate causes, a vast number of
semi-professional workers and distributed projects.

It doesn't hurt to be too early to the party.

This bridge building starts with documentation; that's the very first step.
How it proceeds from there to relationship building and the final result of
technologies liberated for development in other parts of the world is up to
the participants. I can't imagine that there will be some mad rush of
citizen scientists slavering over their lab rats as a result of falling
costs or growing documentation from all sources - that's just silly fiction.
Some people will try out some steps of the biotech, some people will only
write or edit, or build relationships, or build equipment. Work will be
done, progress will be made.

> Because, we should all be aware that there are unwary/overly credulous
> readers out there by now.

Which is never a sufficient excuse to hold back from doing one's best to put
out good work and push forward the state of a particular field. Hammers and
knifes have this problem, and every technology since has had it too. The
balance of good is always to forge ahead sensibly.

Reason

[Reason]

> -----Original Message-----
> From: diy...@googlegroups.com [mailto:diy...@googlegroups.com] On

> Behalf Of Phil
> Sent: Wednesday, April 27, 2011 10:43 AM
>
> I agree with Reason that we will all die of old age
> if we do things the way the FDA wants them to be done.
> Reason should perhaps think about moving to Asia or India,
> or finding collaborators there.

That would be step two in the grand bootstrapping, not step one. See my
previous email about the bridge: there are people able to develop over
there, and there are locked-up technologies that are unknown or
underappreciated here. Joining the two is a big grand long-term exercise
that can only really grow in lock-step with the growth of open/DIYbio.

> It is naive to imagine that cures would be used if they existed.
> We have, for example, numerous partial cures for Duchenne's
> muscular dystrophy that have been sitting on the shelf for
> about 6 years while going through the approval process -
> even though you could in some cases just pick up the syringe you
> used on a mouse and apply it to a child and save his life
> (the myostatin gene is identical in humans and mice).

This is exactly the sort of thing that should (a strong word, should, but
that's what I mean) be worked around by any ethical means possible - by
making it more attractive for groups in other regions of the world, beyond
the reach of the FDA and the equivalents in Europe, to pick up this work,
for example. This would be (eventually) through building a process and a
community that can lower their costs of entry, give them a better starting
portfolio of leads to follow, and so forth.

Again, grand visions - but they have to start at the bottom, with validation
of each step. Can you reverse engineer useful techniques from published
papers, can you break it down into sufficiently good documentation that adds
value to the DIYbio community and helps make people more interested, can you
parlay that into connections in Asia and a bigger volunteer community. And
so forth. Each stage, each small step has to add value for someone,
somewhere, who will build on that and help to construct the bridge.

Reason

[Reason]

> -----Original Message-----
> From: diy...@googlegroups.com [mailto:diy...@googlegroups.com] On
> Behalf Of Phil

> Sent: Wednesday, April 27, 2011 10:05 AM
>
> > All this might be averted if we had some way to replace that damaged
> > mitochondrial DNA - and we do, a technique called protofection that
> > was demonstrated to work in mice back in 2005. This employs a vector
> > to introduce replacement mitochondrial DNA into cells throughout the
> > body, and is fairly well explained (if you are a scientist and up for
> > reading dense papers) in a selection of scientific publications
> issued
> > over the past six years.
>
> AFAIK there are only two papers on protofection, and they
> are both too vague to enable anyone to reproduce it.
> Numerous people have tried; no one has been able to replicate the
> results.

I would be very interested if you could point me to those numerous people
and any publications showing failure. I'm not talking much to Gencia folk at
the moment because trying to do this without asking for their help is a good
proof of principle. As you point out, there are few published papers, but so
far it looks like that should be enough. See these discussion threads for
the latest:

https://groups.google.com/group/the-vegas-group/browse_thread/thread/4861096
67ad350e1
https://groups.google.com/group/the-vegas-group/browse_thread/thread/2d48c64
4114f8a38

It will not concern me overly if it turns out that protofection can only be
documented to 90% - it is one of many bricks in the bridge and many possibly
early projects. All can be revisited later, and even a partial result can
still lead to a range of good, complete documentation on supporting
procedures, use of equipment, and the like. Or I could go and see if the
Gencia folk are interested in filling in the gaps; it can't hurt to ask.
They are, after all, largely focused at the moment on the mitochondrial
biogenesis aspect of their technology rather than the mitochondrial DNA
transfer - it's their evaluation that the money is in biogenesis, and I'm in
no position to dispute that assessment.

Whether or not protofection comes to a satisfactory conclusion, I have a
possible list of other interesting things for volunteers to work on
documenting, such as work on LysoSENS - which isn't a therapy, but rather a
chance for DIYbio people to actually do some meaningful amateur research.
Synthesize your own lipofuscin components, get some graveyard soil, culture
some bacteria, and see what you come up with. It's a numbers game, but
someone somewhere will find a bug and its enzymes that can break down the
major components of lipofuscin; there's no reason that someone has to be in
an institutional setting.

(As an aside on that topic, I see that the SENS Foundation is presently
hiring a research project lead for LysoSENS work in the Bay Area:
http://www.sens.org/node/2002 - I'm sure there are folk on this list who
would be well suited.)

> Can you post all your protofection references?

These are the two worth looking at:

1) the biogenesis side of the house
http://dx.doi.org/10.1016/j.mito.2010.08.004

2) the 2009 open access paper which makes more sense in the context of the
biogenesis paper above:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829286/

And you can dig up the rest of the older stuff by searching PubMed for
Shaharyar M. Khan, who's the lead. There will probably be a small flood of
publications as and when Gencia sorts out big number funding/a business
relationship/whatever it is they are going to do, but I understand that most
of that is going to be biogenesis-related.

Reason

[Reason]

> -----Original Message-----
> From: diy...@googlegroups.com [mailto:diy...@googlegroups.com] On

> Behalf Of J. S. John
> Sent: Wednesday, April 27, 2011 7:51 AM
>
> We're very skeptical around here since there were instances of people
> pedalling things without much references, names, goals, etc. I don't
> understand why you're anonymous if you're running an organization.

I'll say this once more and once more only: my real name is Reason. The way
this works offline is as follows:

Rude Person: You're called Reason? Really? Really?

Me: Yes.

Rude Person: Oh.

And that's where it stops. So I'd appreciate it if that's where it stops
here too.

Further, I think it behooves everyone to carefully disentangle whatever
associations they have reflexively built up between (a) the form of a name,
(b) anonymity, and (c) abuse of anonymity. These are three completely
different, separate, and distinct things.

Reason

[JonathanCline]

On Apr 27, 6:04 pm, "Reason" <rea...@fightaging.org> wrote:
>[stuff]

Actually, no one is being rude for requesting your true identity. It
is quite common on the internet in serious venues to prefer full
names. I've seen it dozens of times in different formats, a couple
times on this group and many times elsewhere over the years. It's
your choice to use a short name, especially if it looks like an alias,
and the mistrust of others comes with that. If at some point in the
future you prefer to gain more trust, then you might consider using
your real name. The ancient Usenet Nettiquette FAQ (written before
FAQs were called FAQs) specifically stated such. The conclusion is:
you're actually the one who's being rude by stepping into a forum
where names are traditional and expected. Science culture also
recognizes names in order to sift the wheat from the chaff, leading to
that trust. If you'd like to continue to argue against it, well, have
fun spending effort, because human nature which demands trust doesn't
change that much and it won't change much online either. Didn't I
just post a message about naive unemployed visa-holders trying to get
jobs with long, nonsensical-to-everyone names which confuse their
hiring process? If it adds confusion to your cause, here or in
person, then why are you doing it? Fix it. Otherwise you'll be
behooving people until the end of time.

The whois for your web site lists an invalid physical address. So it
would seem more like a purposeful alias is the agenda in this case.

Secondly it would seem very simple to use an existing book forum to
accomplish your goals without a new site. Everyone always wants to re-
invent the wheel. Wikipedia and Wikibooks are very successful
projects with an extremely wide audience and that would likely help
the goal. Whereas, a new site, with a new gateway and a new
gatekeeping system won't have such wide exposure. Openwetware is also
very stable and gets significant use regardless of who owns it. Not
sure why you'd claim that unpaid authors and/or other hosts don't
create results, when clearly they have and will continue to do so.
Wikipedia has destroyed real, paper, encyclopedia publishers in terms
of productive capacity, and hasn't paid out money to its authors, and
yes, most of the content is better than the commercial competition.
Wikipedia is continually gaining in popularity when beginning research
on a topic by the average bio/med student, regardless of the eye-
rolling opinions by the faculty. They work.

These are two process-oriented bugs, it seems the project could be
much more successful if these bugs were fixed.


## Jonathan Cline
## jcl...@ieee.org
## Mobile: +1-805-617-0223
########################

[Cathal Garvey]

For the record on the animal-research angle:

I'm personally in favour of carefully conducted animal research where necessary. I don't believe that animals can be replaced by in-vitro studies, and that hardly obviates the cruelty element in any case (fetal calf serum, anyone?). Eventually, as you say, we won't need to use animals and I'd hope that the scientific community would rapidly adopt alternatives as they arrive. Given the exorbitant cost of animal research, I expect that they will.

However, I don't think that animal research belongs under the heading of DIYbio, any more than I believe pathogen research or embryo experimentation belongs. There are places and institutions where animal research is controlled and managed properly, and if those don't suit your needs you can always establish a proper facility in full compliance with standards of ethics and care for animal research in your country. But at that point, it's hardly "DIYbio" anymore, and rightly so.

DIYbio is the hobby-to-small-startup end of biology, and naturally there are things that don't fit in that heading, because there are things that require much greater infrastructure than DIYbio is likely to encompass. The other term, "Garage Biotech", seems to cover larger ventures, and perhaps at this end of the pond you're discussing people who can establish reliable and standardised enclosures for animal research..

It's not just about cruelty, I should add. It's about the hallmark of good science; reproducibility. Animals that are under stress (not given proper living conditions with stimulation and appropriate socialisation if required by the species, bedding disturbed too often) will give differing results in experiments and screw things up. Rooms that aren't carefully made ready will have unforeseeable complications; on this list in the past we've discussed (hotly, as I recall) the effects of ultrasound on mouse breeding and maternal care.

Finally, even if an individual can carefully conduct animal research to a high scientific and ethical standard... perhaps it's still best not to call it "DIYbio", because we have enough press issues to deal with already without having people picket a headlining "DIYbio Cruelty Research Lab In Your Suburbs", as I'm certain they would.

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[mad_casual]

On Apr 27, 12:42 pm, Phil <philgo...@gmail.com> wrote:
> My best theory is that he's categorized Reason
> as a bad and dangerous person because he wants
> to circumvent federal regulation, and is thus
> projecting all sorts of other negative things bad
> and dangerous people do onto Reason,
> without evidence.  In just a few sentences Cory
> made three baseless accusations: that Reason is
> making "false promises", using "subliminal messaging",
> and "grandstanding".

I don't want to speak on behalf of CoryG, but reasons why I agree with
him:
1. I tend not to assume understanding or expertise. I can't do a
literature or Google search for "Reason" and see what biology (DIY or
not) 'Reason' has done. The best I find are vague sketches that don't
constitute a full project plan or gantt chart. Stuff that doesn't even
constitute a rightful 'cocktail napkin'.

2. Not everything the FDA does is entirely baseless. Animal testing is
standardized and controlled for the benefit of the regulators, policy
makers, practitioners, and researchers. I, personally believe we
should be free to put into our bodies whatever we want to put into our
bodies and the FDA should make sure that what we put in our bodies and
what we think we're putting in are the same thing. Unfortunately, the
only people I find saying 'I hate the FDA it should be subverted or
abolished' are people who either, A) don't interact with the FDA in
any professional capacity or B) unwittingly commit fraud or C)
knowingly commit fraud or D) permutatoins of the above.

3. The lack of actual "Reason", publish under creative commons? Why
would I do it under the guise of the Vegas Group and not as a DIY
Biologist, especially if there's no pay involved? The Vegas Group can
feel free to aggregate my protocols any way they wish (which they
don't appear to have a problem doing), so what is the "Reason" this is
being asked?

>
> I agree with Reason that we will all die of old age
> if we do things the way the FDA wants them to be done.

I hate to break it to you, but Methusela is dead. The only people that
will never die of old age will be killed or die young.

> It is naive to imagine that cures would be used if they existed.
> We have, for example, numerous partial cures for Duchenne's
> muscular dystrophy that have been sitting on the shelf for
> about 6 years while going through the approval process -
> even though you could in some cases just pick up the syringe you
> used on a mouse and apply it to a child and save his life
> (the myostatin gene is identical in humans and mice).

Steroids and hormone therapy have existed for much longer, are much
more understood and much cheaper. The FDA regulates steroids at the
behest of congress and the American Public.

> In the meantime, thousands of boys have died of this disease,
> allegedly because trying out cures that might save
> their lives would be "too dangerous".  This despite the fact
> that some of these cures do not have any serious
> known or theoretical risks.  (The only serious risk in
> some cases is that they may stop working after a few months.)

Much like you assert CoryG is jumping to conclusions, you're ascribing
qualities to myostatin inhibitors that they aren't known to have and
you're assuming there's no risk. Theoretical risk is easily generated
and pretty much every pharma class I sat in had a mantra of every drug
has at least two effects, the intended one and the unintended one. A
physician seeking to "Do no harm" is responsible for his patients'
lives, it's his choice to offer a treatment even without the FDA (off-
label).

[Forrest Flanagan]

My own take on animal experimentation is that the only thing worse than it

is its absence. I look forward to the foreseeable future in which
experiments in silico become cheap enough to naturally displace the vast

majority of in vivo work..

DIYbiologists could Double Norn Lifespan! It's low-hanging fruit.

[Reason]

"In silico" here meaning to conduct studies using simulations of animals or
animal tissues, as opposed to working in the silicon-based life that seems
so commonplace in our science fiction. The progression of computing power
will make simulated animal models viable fairly soon.

Reason

[Russell Whitaker]

On Thu, Apr 28, 2011 at 9:53 AM, Reason <rea...@fightaging.org> wrote:
>
> "In silico" here meaning to conduct studies using simulations of animals or
> animal tissues, as opposed to working in the silicon-based life that seems
> so commonplace in our science fiction. The progression of computing power
> will make simulated animal models viable fairly soon.
>

This statement wrongly assumes that all the interesting pathways have been
fully characterized. This is clearly not true. It doesn't matter how much crunch
you throw at a modeling problem, if your model is incomplete.

--
Russell Whitaker
http://twitter.com/OrthoNormalRuss
http://orthonormalruss.blogspot.com/

[Reason]

On Thu, 28 Apr 2011 11:24:20 -0700, Russell Whitaker
<russell....@gmail.com> wrote:
> On Thu, Apr 28, 2011 at 9:53 AM, Reason <rea...@fightaging.org> wrote:
>>
>> "In silico" here meaning to conduct studies using simulations of animals
> or
>> animal tissues, as opposed to working in the silicon-based life that
> seems
>> so commonplace in our science fiction. The progression of computing
> power
>> will make simulated animal models viable fairly soon.
>>
>
> This statement wrongly assumes that all the interesting pathways have
been
> fully characterized. This is clearly not true. It doesn't matter how much
> crunch
> you throw at a modeling problem, if your model is incomplete.

No such assumption was made. The pace at which the remaining needed
knowledge is uncovered is itself a function of computing power, and the
present state of the art isn't too shabby. e.g.:

http://news.illinois.edu/news/11/0330cell_ZaidaLuthey-Schulten_ElijahRoberts.html

So fairly soon - by which I meant twenty years. I'm happy to handwave
things over this sort of timescale for fields wherein this is a very large
community of people working on the challenges and established trends in
increased capabilities with no end in sight. This is good enough for me to
base my long-term plans on; your mileage may of course vary.

Reason

[CoryG]

> No such assumption was made. The pace at which the remaining needed
> knowledge is uncovered is itself a function of computing power, and the
> present state of the art isn't too shabby. e.g.:
>

> http://news.illinois.edu/news/11/0330cell_ZaidaLuthey-Schulten_Elijah...

>
> So fairly soon - by which I meant twenty years. I'm happy to handwave
> things over this sort of timescale for fields wherein this is a very large
> community of people working on the challenges and established trends in
> increased capabilities with no end in sight. This is good enough for me to
> base my long-term plans on; your mileage may of course vary.
>
> Reason

I'm really trying hard not to feed a troll more than I have already,
but as someone who codes at an expert level in 23 languages and has
explored every computing technique presently available, I can
definitely state that you are wrong.

As Russell stated, the pathways have not been fully characterized and
there is no perfect model out right now. I'm working toward acquiring
the data with an automated organic micro lab and the appropriate
software to operate a semantically based artificial neural network
driven synthesis process - but even the basic chemical processes are
very involved and lacking in complete documentation (for example my
recent post to the group looking for a phase diagram database is
DIRECTLY related to this - phase diagrams are more or less a required
dataset to base the models on for such automation and direct feedback
from computing into chemical reactions [amongst many other metrics]
simply to let the computer know what to put into which reaction
vessels - and even the diagrams for mapped compounds and solutions
tend to exist in temperature-pressure relations disregarding volume
[which becomes increasingly important at small scales - adding the
shape/composition of the container, only increasing in importance when
you get into a cellular scale - all aside from actually putting the
equipment together]). Even when the data is complete in all chemical
aspects, you have to account for a model of the human body's
functional groups to simply design in silica and call it complete - if
the technology and research in all areas involved followed Moore's law
to keep pace with the computing power (which is does not even come
close), I wouldn't inject myself with something a computer designed
within my natural lifetime without significant testing outside that
simulation.

[J. S. John]

On Thu, Apr 28, 2011 at 3:31 PM, Reason <rea...@fightaging.org> wrote:

> No such assumption was made. The pace at which the remaining needed
> knowledge is uncovered is itself a function of computing power, and the
> present state of the art isn't too shabby. e.g.:
>
> http://news.illinois.edu/news/11/0330cell_ZaidaLuthey-Schulten_ElijahRoberts.html
>
> So fairly soon - by which I meant twenty years. I'm happy to handwave
> things over this sort of timescale for fields wherein this is a very large
> community of people working on the challenges and established trends in
> increased capabilities with no end in sight. This is good enough for me to
> base my long-term plans on; your mileage may of course vary.
>
> Reason

I agree with Cory and Russel on this. You can't model if you don't
know what is actually happening. No amount of computing power could
help you. From my brief experience with comp. chem simulations, my
project and that of the professors in the department all used existing
data. If you don't have data of how the molecules behave, how can I
run experiments. In the same way, for biology, the data must be there
and with the data you can create models, alter parameters and run
in-silico experiments. Computational chemistry/biology will not exist
without the data to run the calculations. And how can you run
calculations without a function. You can't have a modeling function
without understanding how things work.

[Reason]

> -----Original Message-----
> From: diy...@googlegroups.com [mailto:diy...@googlegroups.com] On

> Behalf Of J. S. John
> Sent: Thursday, April 28, 2011 1:55 PM
> To: diy...@googlegroups.com
> Subject: Re: The Vegas Group: bringing quality documentation
> andlongevityscience to DIYbio
>
> I agree with Cory and Russel on this. You can't model if you don't
> know what is actually happening. No amount of computing power could
> help you.

I think I understand where you're going wrong; you're ascribing no value to
simulations that do not reflect reality. Nothing could be further from the
case: simulation/modeling of partially understood complex systems is a
fundamental tool by which those systems can be better understood. That
describes pretty much the entirety of astrophysics, for example.

You can't completely eliminate the need to work with animals and cells: you
need data against which you can to calibrate simulations, for example. But
as the cost of running simulations falls, and the complexity rises, the
utility of using best-present-knowledge simulations to discover new
biochemistry rises. It will displace the bulk of in vivo investigations,
which will remain only to absolutely verify end results. So that's one way
in which things will progress towards ever better simulations, capable of
replacing arbitrary in vivo work.

In terms of obtaining data outside of simulational-deductive methodologies,
is it your believe that twenty years from now, there will not be something
approaching a complete catalogue of pathways for all the most important
areas of mouse and human biochemistry? That would seem unlikely, given
present trends.

Reason

[Reason]

>-----Original Message-----
> From: diy...@googlegroups.com [mailto:diy...@googlegroups.com] On

> Behalf Of JonathanCline
> Sent: Wednesday, April 27, 2011 10:14 PM
>
> Openwetware is also
> very stable and gets significant use regardless of who owns it.

Given that I plan to publish the Vegas Group results as Creative Commons, if
you feel they should be on OpenWetWare, you could always put them there
yourself.

> Not sure why you'd claim that unpaid authors and/or other hosts don't
> create results, when clearly they have and will continue to do so.

Because it is absolutely the case that volunteer projects trying for
specific end goals have a terrible track record. You see the few successes,
but not the innumerable failures. I've been involved in volunteer efforts of
all sorts for more than a decade, and all suffer from the essential problem
that unpaid volunteers have a very high turnover and low productivity. If
you have a specific set of goals in mind and a long term need to keep
volunteers engaged, you can't beat paying people.

Reason

[Gavin Scott]

On Thursday, April 28, 2011 5:06:35 PM UTC-7, Reason wrote:

> I agree with Cory and Russel on this. You can't model if you don't
> know what is actually happening. No amount of computing power could
> help you.

I think I understand where you're going wrong; you're ascribing no value to
simulations that do not reflect reality. Nothing could be further from the
case: simulation/modeling of partially understood complex systems is a
fundamental tool by which those systems can be better understood. That
describes pretty much the entirety of astrophysics, for example.

Simulations in Astrophysics make sense for things like galaxy formation because the fundamental physics of how particles behave is well understood, and the complexity comes from having effing great numbers of them, not from any lack of information about how they individually behave or interact. As a fluid dynamics problem, we can tell you everything about how one molecule will behave, but can't say much (if anything) about how all of them are going to behave together. There's nothing subtle about simulation at this level. It exposes higher-level aggregate statistical behavior without producing any information on lower-level details.

In a cell, the problem is that you don't have the information you need to do a full simulation, and no amount of simulation of the stuff you know will lead to great insights about stuff you don't know. You may discover fascinating aggregate behavior about the stuff you think you already understand, but it will not magically produce anything from a lower (more detailed, closer to reality) level, and where the simulated behavior is affected by the stuff you don't know, the simulation will be wrong (with no hint or a problem until you try to rely on the results and things go all pear-shaped on you).

In regard to your proposal, I think the goal of documenting, clarifying, and explaining is a worthy one almost regardless of the subject or the motivation.

However, when I read what you're trying to do, I get the feeling that perhaps you're not really interested in mice, but want to make it possible for anyone moderately skilled to be able to follow your procedure to perform an experimental life-extension procedure on themselves or other humans (once a few more details are worked out). You may feel that there is some government conspiracy to withhold the promise of this treatment from the public.

Such a procedure as the one that you're interested in, when applied to humans or even mice, will involve many of the sorts of things that are likely to scare the crap out of people, such as a virus-based (or similar) delivery mechanism for direct modification of cells in a living mammalian host.

I personally think it's probably not a good idea for the DIYbio movement to get associated with projects like this.

I'm sure that further research along the lines you're interested in is going to take place, and as soon as someone comes up with a reproducible  reliable, technique that holds the promise of significant benefits to the life extension of humans, then Congress will be pretty quick to nudge the FDA or whoever to change their stance on this (the fact that Congress is mostly comprised of aging white guys is often a benefit to the rest of us :)

G.

 

[Bryan Bishop]

On Thu, Apr 28, 2011 at 10:09 PM, Gavin Scott <ga...@allegro.com> wrote:

Such a procedure as the one that you're interested in, when applied to humans or even mice, will involve many of the sorts of things that are likely to scare the crap out of people, such as a virus-based (or similar) delivery mechanism for direct modification of cells in a living mammalian host.

I personally think it's probably not a good idea for the DIYbio movement to get associated with projects like this.

Is this because of the scare factor (a sort of meta phobiophobia), or did something else lead you to that opinion? Just wondering.

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

[Gavin Scott]

On Thursday, April 28, 2011 8:40:56 PM UTC-7, Bryan Bishop wrote:

Is this because of the scare factor (a sort of meta phobiophobia), or did something else lead you to that opinion? Just wondering.

Heh, "phobiophobia" is already meta enough :)

I guess I just worry that people will get the idea that everyone's primary interest is in experimenting on themselves with "gene therapy" etc. just as soon as they can (i.e. in some irresponsible fashion) and that this will result in negative publicity (at the point that anyone actually notices) and presents a danger of knee-jerk reactions from regulators etc.

G.

[CoryG]

> I'm sure that further research along the lines you're interested in is going
> to take place, and as soon as someone comes up with a reproducible
> reliable, technique that holds the promise of significant benefits to the
> life extension of humans, then Congress will be pretty quick to nudge the
> FDA or whoever to change their stance on this (the fact that Congress is
> mostly comprised of aging white guys is often a benefit to the rest of us :)

Indeed it is in this field. Take a look at HGSI (a stock I made a
decent profit on a couple years ago after news of their retro-virus
based therapy for AIDS). The company hadn't even started phase 1
trials in Humans, was rated around 60 cents a share, broke news of a
revolutionary treatment for AIDS with potential in many areas of
disease treatment and even genetic modification (though this doesn't
appear to be pursued in full just yet, still too sketchy) and jumped
to right around $30 per share in a couple months time, got rushed
through the FDA process and has some treatments in the market now -
still being watched because its so new, but more importantly being
rushed to market.

> I guess I just worry that people will get the idea that *everyone's* primary

> interest is in experimenting on themselves with "gene therapy" etc. just as
> soon as they can (i.e. in some irresponsible fashion) and that this will
> result in negative publicity (at the point that anyone actually notices) and
> presents a danger of knee-jerk reactions from regulators etc.

I kinda get this feeling too, the last thing we need is the FBI
breaking down our doors and butt-stroking us in the heads over a slime
mold because we're associated with someone touting retrovirus testing
in Humans without FDA approval.

[rwst]

On Apr 28, 9:31 pm, Reason <rea...@fightaging.org> wrote:
> http://news.illinois.edu/news/11/0330cell_ZaidaLuthey-Schulten_Elijah...

>
> So fairly soon - by which I meant twenty years. I'm happy to handwave
> things over this sort of timescale for fields wherein this is a very large
> community of people working on the challenges and established trends in
> increased capabilities with no end in sight. This is good enough for me to
> base my long-term plans on; your mileage may of course vary.

I have reason to be pessimist in this regard: that paper does NOT
simulate a whole cell with its pathways. Rather, it simulates a single
pathway and assumes realistic stochastic behaviour for the rest. I
have tried in the last year to help with bioinfo efforts on human
pathways to complete existing databases from the literature, and I can
say that it appears that noone cares about such completeness. An
example is ubiquinone biosynthesis, something you would think was well
known: a prototype was researched in yeast but even that lacks one or
two reactions; for humans, half of the enzymes are missing. What's
more, it assumes a molecule as start material which we don't even know
how it's produced exactly--we simply don't know if and how humans
would produce 4-hydroxybenzoate! Assuming it's catabolized from
tyrosine is a good guess made in the 60s and if true would falsify all
books.

The point is doing such detective work isn't sexy for the usual lab
rat, and neither for companies. So it isn't done. Refute me.

Regards,
rwst

[Gavin Scott]

On Thursday, April 28, 2011 9:53:29 PM UTC-7, CoryG wrote: 

I kinda get this feeling too, the last thing we need is the FBI
breaking down our doors and butt-stroking us in the heads over a slime
mold because we're associated with someone touting retrovirus testing
in Humans without FDA approval.

There's this "rock and a hard-place" thing where on the one hand you have "artists" and fantasy/science-fiction people talking about life-extension, growing tails (not that that wouldn't be cool), etc. who are likely to provide ammunition to the "we need to protect the public from these crazy people" crowd, yet on the other hand you have rational realistic people who think they can ultimately make a positive difference who are perhaps going to scare the commercial biology companies into pushing for regulation that imposes requirements just onerous enough that nobody but a commercial company with a dozen Phd's can live up to them, i.e. requiring protocols that the hobbyist just can't afford to meet.

I grew up during the computer revolution, and have spent the past couple years learning about biology. A nerd with a computer disturbs nobody, but a nerd with recombinant DNA and retro-virus technology is quite likely to freak out lots of people. I hope for the best, but history demonstrates lots of justification for pessimism :)

I sort of waffle back and forth between worrying about the risks and being convinced that this is all pretty harmless. I had a discussion recently with someone who was of the "ZOMG! someone's going to create a killer virus and we're all going to die!" school of thought. My argument was the same one as with the LHC and the concern that it would create a black-hole that would swallow the earth, namely that nature has been doing these same experiments for millions of years and yet we're still here.

G.

[JonathanCline]

On Apr 28, 8:07 pm, Gavin Scott <ga...@allegro.com> wrote:
>
> I personally think it's probably not a good idea for the DIYbio movement to
> get associated with projects like this.

It's about on par with asking people to eat two sticks of butter or 2
cups of coconut oil every day, long term, to measure their cognitive
abilities -- something that's clearly guesstimated by current medicine
to be bad for the health. Compare differing projects with equal
weighting.

[Cathal Garvey]

Astrophysics might be a bad example of modelling.. they've had to invent at least three effects for which there is scant-to-no evidence just to preserve the integrity of theory versus model versus reality. Every time I hear about "Dark matter" or "Dark Energy" all I hear is "invisible dragon".

I am somewhere between Reason and the rest. While I know our current models are awful and computation won't immediately solve things, we've only been using the word 'proteome' for two or three decades. Extrapolation of future knowledge based on current rates of research is a bit short sighted, because we don't know what might come around the technological corner.

What if there emerged tomorrow a means to real-time-scan a single cell, down to the macromolecular scale? We'd have the ability to watch everything from protein interactions to transcription to production of stuff like the above mentioned ubiquitination precursors. And with enough computing power, we bould record it, parse it for significant interactions, and probably have a decent model in no time.

It may seem silly to imagine it now but in twenty years we really could have this problem solved and a simulated animal model in the bag.

..although, if your model is faithful enough to reality, is There any difference between cruelty to animals and cruelty to models? :)

Sent from my Phone
www.twitter.com/onetruecathal
www.indiebiotech.com

On 29 Apr 2011 04:30, "Gavin Scott" <ga...@allegro.com> wrote:

On Thursday, April 28, 2011 5:06:35 PM UTC-7, Reason wrote:
>

> > I agree with Cory and Russel on th...

Simulations in Astrophysics make sense for things like galaxy formation because the fundamental physics of how particles behave is well understood, and the complexity comes from having effing great numbers of them, not from any lack of information about how they individually behave or interact. As a fluid dynamics problem, we can tell you everything about how one molecule will behave, but can't say much (if anything) about how all of them are going to behave together. There's nothing subtle about simulation at this level. It exposes higher-level aggregate statistical behavior without producing any information on lower-level details.

In a cell, the problem is that you don't have the information you need to do a full simulation, and no amount of simulation of the stuff you know will lead to great insights about stuff you don't know. You may discover fascinating aggregate behavior about the stuff you think you already understand, but it will not magically produce anything from a lower (more detailed, closer to reality) level, and where the simulated behavior is affected by the stuff you don't know, the simulation will be wrong (with no hint or a problem until you try to rely on the results and things go all pear-shaped on you).

In regard to your proposal, I think the goal of documenting, clarifying, and explaining is a worthy one almost regardless of the subject or the motivation.

However, when I read what you're trying to do, I get the feeling that perhaps you're not really interested in mice, but want to make it possible for anyone moderately skilled to be able to follow your procedure to perform an experimental life-extension procedure on themselves or other humans (once a few more details are worked out). You may feel that there is some government conspiracy to withhold the promise of this treatment from the public.

Such a procedure as the one that you're interested in, when applied to humans or even mice, will involve many of the sorts of things that are likely to scare the crap out of people, such as a virus-based (or similar) delivery mechanism for direct modification of cells in a living mammalian host.

I personally think it's probably not a good idea for the DIYbio movement to get associated with projects like this.

I'm sure that further research along the lines you're interested in is going to take place, and as soon as someone comes up with a reproducible  reliable, technique that holds the promise of significant benefits to the life extension of humans, then Congress will be pretty quick to nudge the FDA or whoever to change their stance on this (the fact that Congress is mostly comprised of aging white guys is often a benefit to the rest of us :)

G.

 

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