Scientists Build First Man-Made Genome; Synthetic Life Comes Next

[Apptech]

My cousin Matthew forwarded me this reference.
I was sure that it would just be more of the rubbish that pervades this
topic but decided to have a quick look to confirm my suppositions.

The not quite smiling face of Craig Venter that heads the article told me
immediately that this is, after all, the real thing.
We stand on the bridge at Khazad-dûm. The not distant enough drums sound
their doom-doom call and it's not certain, yet, if Venter is himself the
Balrog or if he is soon to conjure it from the abyss. As he's one of my
select group of (anti?-)heroes I can't complain all too much.

If you can't make head nor tail of that wait a few years and it will be the
only news going :-).

            http://www.wired.com/science/discoveries/news/2008/01/synthetic_genome?currentPage=all




                Russell
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[Matthew Miller-2]

On Fri, Jan 25, 2008 at 05:18:03PM +1300, Apptech wrote:

> My cousin Matthew forwarded me this reference.
> I was sure that it would just be more of the rubbish that pervades this
> topic but decided to have a quick look to confirm my suppositions.
>
> The not quite smiling face of Craig Venter that heads the article told me
> immediately that this is, after all, the real thing.
> We stand on the bridge at Khazad-dûm. The not distant enough drums sound
> their doom-doom call and it's not certain, yet, if Venter is himself the
> Balrog or if he is soon to conjure it from the abyss. As he's one of my
> select group of (anti?-)heroes I can't complain all too much.
>
> If you can't make head nor tail of that wait a few years and it will be the
> only news going :-).
>
>             http://www.wired.com/science/discoveries/news/2008/01/synthetic_genome?currentPage=all

It's likely that in a decade or two (who knows, maybe sooner) that biology
will be a growing, in demand field in about the same way computer science
is/was. I think that it's pretty cool to think about programming genomes
instead of computers. My advice to new freshman: major in biology and minor
in CS. :)

Matt

--
...those who search for, or imagine they have found, the perpetual motion,
are always men to whom the most certain and invariable truths in mechanics
are unknown.  -- Jacques Ozanam (1640-1717)
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[M. Adam Davis-2]

It was/is bound to happen.

I have a hard time believing that scientists are anywhere near
creating (accidently or purposefully) anything that will both survive
in the real world and destroy any animal population or significant
resource (water, oxygen, CO, etc).

My assumption is that nature (evolution & darwin) would be (and has
been) much more efficient at delivering deadly and dangerous microbes
than scientists will be for decades to come.

But I could be wrong.  At least most of this research is happening far
from me so I should have a few days notice.  ;-D

-Adam

On 1/24/08, Apptech <apptech@...> wrote:

> My cousin Matthew forwarded me this reference.
> I was sure that it would just be more of the rubbish that pervades this
> topic but decided to have a quick look to confirm my suppositions.
>
> The not quite smiling face of Craig Venter that heads the article told me
> immediately that this is, after all, the real thing.
> We stand on the bridge at Khazad-dûm. The not distant enough drums sound
> their doom-doom call and it's not certain, yet, if Venter is himself the
> Balrog or if he is soon to conjure it from the abyss. As he's one of my
> select group of (anti?-)heroes I can't complain all too much.
>
> If you can't make head nor tail of that wait a few years and it will be the
> only news going :-).
>
>            http://www.wired.com/science/discoveries/news/2008/01/synthetic_genome?currentPage=all
>
>
>
>
>                Russell
> --
> http://www.piclist.com PIC/SX FAQ & list archive
> View/change your membership options at
> http://mailman.mit.edu/mailman/listinfo/piclist
>

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[Sean Breheny]

While this is amazing and very scary all at the same time, I don't
quite understand how it is close to "creating artificial life". It
sounds like simple genetic engineering to me. They have the ability to
modify the "code" which a cell runs, maybe even replace it completely,
but they still need the "machine" of a cell to "run" the code. They
didn't create or even design that cell, they just borrowed one which
already exists. Furthermore, their "code" will need to be able to
cause the cell to reproduce into a similar enough cell to also "run"
the same "code" again.

The article doesn't say whether the "code" they wrote will actually
execute to do anything useful in the bacterium.

As I understand it, there are many major obstacles to being able to
write such "code" which does anything useful:

1) DNA codes for proteins, which is how it gets any work done. We
still have great trouble understanding how even some of the simplest
proteins work. We have trouble predicting how they will fold into
their secondary and tertiary structure, and further trouble
determining how that structure will interact with other molecules.

2) Which proteins get produced when and in what kind of cells depends
on gene expression, which is another whole area which we are just
beginning to get some kind of a hold on.

What is really scary here is that someone will write buggy "code"
which ends up producing a deadly organism.

What is also really scary is the attitude toward life which these
scientists display. There is a LOT of hubris in this article. It has a
lot of potential, but they don't even seem to consider that there
might be downsides to this which make the invention of nuclear weapons
look like child's play.

Sean


On Jan 24, 2008 11:18 PM, Apptech <apptech@...> wrote:

> My cousin Matthew forwarded me this reference.
> I was sure that it would just be more of the rubbish that pervades this
> topic but decided to have a quick look to confirm my suppositions.
>
> The not quite smiling face of Craig Venter that heads the article told me
> immediately that this is, after all, the real thing.
> We stand on the bridge at Khazad-dûm. The not distant enough drums sound
> their doom-doom call and it's not certain, yet, if Venter is himself the
> Balrog or if he is soon to conjure it from the abyss. As he's one of my
> select group of (anti?-)heroes I can't complain all too much.
>
> If you can't make head nor tail of that wait a few years and it will be the
> only news going :-).
>
>             http://www.wired.com/science/discoveries/news/2008/01/synthetic_genome?currentPage=all
>
>
>
>
>                 Russell
> --
> http://www.piclist.com PIC/SX FAQ & list archive
> View/change your membership options at
> http://mailman.mit.edu/mailman/listinfo/piclist
>

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[M. Adam Davis-2]

In a related area:

http://www.phdcomics.com/comics.php

Describes the process of using rat antibodies to detect uranium by
training them against uranium, extracting them, combining them with
cancer cells, and then letting them reproduce in a petri dish for an
infinite supply of biological uranium detectors.

Used to detect uranium in ground water.

-Adam

On 1/25/08, M. Adam Davis <stienman@...> wrote:

> It was/is bound to happen.
>
> I have a hard time believing that scientists are anywhere near
> creating (accidently or purposefully) anything that will both survive
> in the real world and destroy any animal population or significant
> resource (water, oxygen, CO, etc).
>
> My assumption is that nature (evolution & darwin) would be (and has
> been) much more efficient at delivering deadly and dangerous microbes
> than scientists will be for decades to come.
>
> But I could be wrong.  At least most of this research is happening far
> from me so I should have a few days notice.  ;-D
>
> -Adam
>
> On 1/24/08, Apptech <apptech@...> wrote:
> > My cousin Matthew forwarded me this reference.
> > I was sure that it would just be more of the rubbish that pervades this
> > topic but decided to have a quick look to confirm my suppositions.
> >
> > The not quite smiling face of Craig Venter that heads the article told me
> > immediately that this is, after all, the real thing.
> > We stand on the bridge at Khazad-dûm. The not distant enough drums sound
> > their doom-doom call and it's not certain, yet, if Venter is himself the
> > Balrog or if he is soon to conjure it from the abyss. As he's one of my
> > select group of (anti?-)heroes I can't complain all too much.
> >
> > If you can't make head nor tail of that wait a few years and it will be the
> > only news going :-).
> >
> >            http://www.wired.com/science/discoveries/news/2008/01/synthetic_genome?currentPage=all
> >
> >
> >
> >
> >                Russell
> > --
> > http://www.piclist.com PIC/SX FAQ & list archive
> > View/change your membership options at
> > http://mailman.mit.edu/mailman/listinfo/piclist
> >
>
>
> --
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> - - - - - - - - - - - - - - - - - - - - - - - - -
> Moving in southeast Michigan? Buy my house: http://ubasics.com/house/
>
> Interested in electronics? Check out the projects at http://ubasics.com
>
> Building your own house? Check out http://ubasics.com/home/
>

--
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- - - - - - - - - - - - - - - - - - - - - - - - -
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[Mario Mendes Jr.-2]

I read the article and had the same thought you did.  But I also thought of
the possibility of not only programming the genomes but interfacing the
genomes to real computers which are them programmed to make them do
something.  Sort of like we use uChip's IDE today to program their cpus to
do something useful.  I can envision a whole group of manufacturers out
there mass producing generic genomes that you can them purchase a few to
program and do whatever it is you need them to do, say a fungus that attacks
the pests that destroy orange crops in Florida.  How cool would that be?
And it'd be green tech too!  There's also the dark side of it, where one
could purchase a few genomes and program them to do some real damage to
large groups of the population, sort of like "green bioterrorism".

-Mario


-----Original Message-----
From: piclist-bounces@... [mailto:piclist-bounces@...] On Behalf Of
Matthew Miller
Sent: Friday, January 25, 2008 6:41 AM
To: Microcontroller discussion list - Public.
Subject: Re: [EE]:: Scientists Build First Man-Made Genome; Synthetic Life
Comes Next


It's likely that in a decade or two (who knows, maybe sooner) that biology
will be a growing, in demand field in about the same way computer science
is/was. I think that it's pretty cool to think about programming genomes
instead of computers. My advice to new freshman: major in biology and minor
in CS. :)

Matt




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[David VanHorn-2]

Well, my experience with software is that most mistakes do not result
in a powerful AI computer that takes over the world.
Usually they just sit in a corner and drool, sometimes with smoke.

So one would hope that the genetic software would be much the same,
"legend" movies notwithstanding.
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[Gerhard Fiedler]

M. Adam Davis wrote:

> My assumption is that nature (evolution & darwin) would be (and has
> been) much more efficient at delivering deadly and dangerous microbes
> than scientists will be for decades to come.

Probably. We just add our planet to the millions of millions of others that
nature (Nature?) has created that are uninhabitable by us -- it's all
natural :)

Gerhard

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[Gerhard Fiedler]

David VanHorn wrote:

> Well, my experience with software is that most mistakes do not result in
> a powerful AI computer that takes over the world. Usually they just sit
> in a corner and drool, sometimes with smoke.
>
> So one would hope that the genetic software would be much the same,
> "legend" movies notwithstanding.

One difference is the "interface" that they have to us. You can switch off
a computer, even if that comes with some kind of temporary chaos for some
of them. You can't switch off a virus on the loose.

Gerhard

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[David VanHorn-2]

> One difference is the "interface" that they have to us. You can switch off
> a computer, even if that comes with some kind of temporary chaos for some
> of them. You can't switch off a virus on the loose.

True. I hope the debugging tools are excellent!  :)
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[Dr Skip]

This thinking avoids the reality of the situation in software as well as the
biology in question. The result may not self-organize into something we could
physically wrestle and which has an inherent understanding of knife usage for
instance. As fairly fragile biological units ourselves, harm can come from lots
of directions. Through evolution, and the separation of continents, we adapted
to 'attacks' from external things such as disease (biological adaptation
through selection over generations) or other agents, such as UV radiation
(melanin production).

Where we are is the joint evolution of everything that's here and now, having
come the same way in the same environment, slowly honed into it's current form
by standing the test of time so to speak, as well as slowly adapting, mutating,
etc over the ages.

Now you create something in the lab that has no relevance to our environment,
and we have no knowledge of it's pending evolution. Most will fail at first,
failure being defined as not acting as expected in controlled cause-effect
relationships. However, failure or not, these introduce combinations of complex
variables into an even more complex system (the ecosystem and us). A system
where we can't even agree on whether it's getting warmer or not, much less the
effect of some new life form on the complex system.

The best analogy would be our system as a nuclear missile and it's control
cabling (an analogy within a reality perhaps...). It presents us with a mass of
control cabling - our interaction with the 'system'. We've studied it and even
sent some signals back and forth, but have nowhere nailed down what everything
and every wire does. This new life form is like a super giant PIC perhaps, or
even a PC, and in introducing it, we connect it to a large group of wires (it's
interaction with the environment or us). What we don't know is if there are
'bugs' in the code, or even how we should structure the code in the computer
such that some combination doesn't launch the missile (and many combinations
could). Who among us would just randomly attach IO lines to these wires and
boot up? Of those that might, there would be big "nothing happened" events, but
not all the time. And as we got cocky, any controls that might have been in
place (put a scope on the line first to see if there's a signal before
connecting) get loosened (use a DVM and just check for voltage perhaps). And,
more people decide to do the same, seeing it might be safe... the danger still
lurks there though...

If we're so susceptible to pandemic like a flu, which is merely a variant of
something our bodies have been through for eons, then so much worse it is for
something entirely new and lethal. Consider it might not kill for 5-10 years,
perhaps by cancer, and it were deemed 'safe' in the lab and released for use in
the 'system'? At least the organisms we live with we have a known
'relationship' with us - avoid plague, keep the antibodies for measles, etc.
Look at the effects of various synthetic chemicals, which are so much simpler
to model and contain the an organism.

The other problem is mutation. It will have very little biological 'experience'
in our environment, so it will be fragile, but HIV is also fragile (it can only
live for a short time outside the body) and look how deadly it is. It will no
doubt mutate. If it doesn't reproduce, it will still be reproducing it's own
cells for growth, unlike a chemical, and perhaps it's own 'cancer' will be the
real problem - found after the fact that it makes it lethal to us.

We are also not the target. Any thing that upsets the balance out there can be
a target. Like a dirty bomb, the destruction isn't the 'bomb', it's the
residual effect. Perhaps the decay of this 'body' creates substances that
radically kill off plankton. No one thinks of that... So, a few dead
cyber-pet-fish get flushed (or many) and we don't notice it until higher orders
of sealife (seafood that is) dwindle and we're stuck with food shortages and a
diseased ocean...

And consider the simple effect of protein molecule twist direction in prions -
the cause of Mad Cow. Something that wasn't even detectable or looked for...
And, they're not destructable.

Lastly, even if one argues their way past all of this and is convincing that
with the right caution and small steps, we can, over a long time, cautiously
develop helpful life forms, from microbes to pets, the reality is that the
industry will be funded by thousands of competitive venture capitalists and
investors, in hundreds or thousands of companies who want immediate big gains
and are in it to rush the latest biological gizmo to market. All in a hundred
different countries who will see it as their way to economic success (or
military success) with various degrees of laxity in whatever controls do happen
to be put into place. In other words, no matter how bad an idea, there will be
money and a place that will be willing to 'risk it' and foist it upon the world
with whatever longer consequences there may be.

-Skip

David VanHorn wrote:
> Well, my experience with software is that most mistakes do not result
> in a powerful AI computer that takes over the world.
> Usually they just sit in a corner and drool, sometimes with smoke.
>
> So one would hope that the genetic software would be much the same,
> "legend" movies notwithstanding.
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[M. Adam Davis-2]

On 1/25/08, Dr Skip <drskip@...> wrote:
> In other words, no matter how bad an idea, there will be
> money and a place that will be willing to 'risk it' and foist it upon the world
> with whatever longer consequences there may be.

People thought the same thing about robots and machines as we started
to move into the electronic age.  At the time it was considered
inevitable that the human brain would be eclipsed by an electronic
brain and soon.  We didn't have enough information then to know how
far away that was, nor how near it was.

Right now we can imagine all sorts of bad scenarios given just this
first tiny foray into biological engineering.

Yes, we don't know how the cells work to the last piece, and to some
degree we are playing with fire.

But while some of the first fires must have gotten out of  control and
killed many people - perhaps populations of people, we got through
that.  The first atomic bomb didn't ignite the atmosphere.  There are
several places in the past where risk wasn't known or understood, and
the benefit has been great.  That's not to say that the ends justify
the means, but that even if human self-destruction is possible using
these methods (and it's not at ALL clear that it's even possible,
nevermind probable) it can still be considered an unlikely outcome.

While some restraint should be shown, I think the fears are greatly
overpowering the discussion here.  It seems like any discussion of the
possible good and useful end product that could result would simply
devolve into, "It's too dangerous."

-Adam
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[Apptech]

> We stand on the bridge at Khazad-dûm. The not distant
> enough drums sound
> their doom-doom call ...

I was impressed and pleased at the range of responses to
that post. Many of the implications have been nicely
unearthed.

>
> http://www.wired.com/science/discoveries/news/2008/01/synthetic_genome?currentPage=all

Nobody gave the Balrog or the bridge a second mention though
:-).

FWIW it needs to be realised that Craig Venter is arguably
the most capable person on earth to produce results in this
field, bust because of his person knowledge and experience
and capabilities and also because of his demonstrated
ability to put together competent teams of people who
achieve world class results. he was the person who single
handedly upstaged the human genome project, lead to his
efforts and theirs being merged in a shotgun-wedding when it
became obvious that he would beat them by years if they
didn't join with him (his success, their funding :-) ), and
fwiw it's quite possibly his personal genome that was
sequenced by the project, although nobody will ever tell
you.

He above all others is well aware of how little we know
about the complexities of the arcane machinery that we are
playing with (His quote some time after the successful end
of the HG project done his way " "We don't know shit") in a
world  where many think that we have it all under control.
He is among the most aware of the dangers that can be
unleashed and of our inability to protect against them. And
he is the one most liable to do it.

All the various possibilities that people mentioned are "on
the menu" with varying degrees of likelihood. From the
drooling pile in the corner to the humanity destroying super
scum. My exemplar would be something that combines the
characteristics of Ebola, HIV and the common cold. It
travels the world at just below the speed of sound (thanks
to Mr Borings fine products), is largely undetectable, has a
decade long incubation period so that everyone on earth
contracts it before the payload delivers and then attacks
with the efficacy of Ebola (speed and short term impact) so
that attempts to manage it are overwhelmed. With a bit of
care and 'luck' it should be able to take out the whole
human race. If Venter and co don't manage this by mistake
somebody (some of the more extreme people from eg F.O.T.E.
seem good candidates) should be able to engineer it to order
in the next decade or so.

Venter is not creating life, and doesn't claim to be. He is
using the protein folding 101 super arcane magic making
utterly complex beyond our understanding tool-kit to splice
together bits and pieces to order. He has only the very very
very vaguest idea of the more complex interactions that will
occur between most of the portions of his creation - and he,
unlike most others, is well aware of this. He is the
pre-eminent expert in understanding in depth and with
insight the vastly complex nature of what he is doing. The
last two sentences are not mutually contradictory. Tremble.

Venter is head of the race to destroy the race. And he knows
it. And he is running well at the front of the field and
with skill and stamina. I read the other day that most of
the top management of NATO are arguing for the need to have
pre-emptive nuclear strike capability to combat major
terrorist threats. Perhaps they'll have that ability any
week now and ... ;-).

We stand on the bridge at Khazad-dûm. The not distant enough
drums sound their doom-doom call ...
Don't any of you watch fine NZ movies? :-)



            Russell

>
> http://www.wired.com/science/discoveries/news/2008/01/synthetic_genome?currentPage=all

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[Apptech]

The intention of this response is sympathised with, but the
subject is of an entirely different nature to the
comparisons offered..

>> In other words, no matter how bad an idea, there will be
>> money and a place that will be willing to 'risk it' and
>> foist it upon the world
>> with whatever longer consequences there may be.

Aye.

> At the time it was considered inevitable that the human
> brain
> would be eclipsed by an electronic brain and soon.
> We didn't have enough information then to know how
> far away that was, nor how near it was.

BUT the beliefs were based on hubris  - on what we thought
WE would be able to do.
The new beliefs are based also on hubris. We have pried open
a toolbox and a glistening array of mystical and magic
machinery beyond our remotest understandings 9as assessed by
the man who knows more than any of us about them). And we
are pushing the buttons and pulling the levers and crying
with glee at the wonderful resyults that the magic machines
can achieve.  We did not make them. We did not design them.
We know what they can do but not what they will do.

> Right now we can imagine all sorts of bad scenarios given
> just this
> first tiny foray into biological engineering.

And they can be demonstrated with certainty, even given our
minute amount of knowledge,  to be entrirely reasonable
possibilities. Real world proof of concept demonstrations of
about the worst possible outcomes exist, arrived at entirely
by experimental accident,  - fortunately in crippled form.

> Yes, we don't know how the cells work to the last piece,
> and to some
> degree we are playing with fire.

We know only a very very very small fraction of the whole
story. Venter knows this well. Most don't. We do however
know how severely we are playing with fire.

> But while some of the first fires must have gotten out of
> control and
> killed many people - perhaps populations of people, we got
> through
> that.

Straw man. Totally incomparable.
Best (albeit feeble) comparison would be that fire might
somehow ignite incipient fie in every living being and once
unleashed spread from organism to organism across the
planet. eg "ice 9" would be a far better analogy than fire.

> The first atomic bomb didn't ignite the atmosphere.

And the first water pistol didn't dissolve the person shot
with it.
And there was never any prospect that it would. Or that the
A bomb would cause air to undergo fission or fusion
reactions. AND the engineers who were developing it had an
extremely good idea of how likely it was that it would, even
at their level of knowledge at the time. Any peson can make
a suggestiion of a possible danger and people will then
proclaim sagely on it. The difference with what is being
done with GMO in general is that almost any doomsday
scenario has the genuine possibility to be credible. eg it
is CERTAIn that it would be possible to make an 'organism'
that combined the caharcteristics of HIV, the common cold
and Ebola and that would have a very very very very good
chance of destroying the whole human race while leaving most
other species untouched. this is not a doomsday ignite the
atmosphere idea but rather a certain possibility - the only
question is - 'how would we achieve it, given that we can't
yet drive the toolbox to more than a few percent of its
capacity?'.

> There are
> several places in the past where risk wasn't known or
> understood,

Whereas in this area it is utterly undoubted what the risks
can be. How we go about unlocking the risks is the only
question.

> the benefit has been great.

The benefits and potential capabilities are undoubted.
Pohl's "Day Million" http://dmznyc.com/html/daymil.01.html 
does a good job of painting some of them - if you consider
his Eutopian future benefit filled :-).

> That's not to say that the ends justify
> the means,

More extreme F.O.T.E.' ers would be sure it did - go to.

>  but that even if human self-destruction is possible using
> these methods (and it's not at ALL clear that it's even
> possible,
> nevermind probable) it can still be considered an unlikely
> outcome.

What part of "certainly possible" don't you understand?
What part of "possibly certain" don't you understand?
:-)


> While some restraint should be shown,

:-)
:-) :-)
:-) :-) :-)
:-) :-) :-) :-)
:-) :-) :-) :-) :-) :-)
:-) :-) :-) :-) :-) :-) :-) :-)
:-) :-) :-) :-) :-) :-) :-) :-) :-) :-) :-)
:-) :-) :-) :-) :-) :-) :-) :-) :-) :-) :-) :-) :-) :-) :-)
:-)
:-) :-) :-) :-) :-) :-) :-) :-) :-) :-) :-) :-) :-) :-) :-)
:-) :-) :-) :-) :-) :-) :-) :-)
:-) :-) :-) :-) :-) :-) :-)  ... err - stack overflow -
printer on fire ...

> I think the fears are greatly
> overpowering the discussion here.  It seems like any
> discussion of the
> possible good and useful end product that could result
> would simply
> devolve into, "It's too dangerous."

This is where I came in :-)

> We stand on the bridge at Khazad-dûm. The not distant
> enough drums sound their doom-doom call ...



                Russell

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[Apptech]

> Well, my experience with software is that most mistakes do
> not result
> in a powerful AI computer that takes over the world.
> Usually they just sit in a corner and drool, sometimes
> with smoke.

> So one would hope that the genetic software would be much
> the same,
> "legend" movies notwithstanding.

Software is written from scratch with a moderately full idea
of the capabilities of the beast.

Genetic Engineering is done by hacking into an arcane device
with capabilities beyond our (even Craig Venters) wildest
dreams, identifying some core functionality and then pushing
buttons to see what happens.

Usually we will manage to make it drool, but it is already
capable of much more than that, and one day we may 'get it
right'.

One large danger is that there are parts of the system that
have been ring-fenced to take them out of operation when
they proved lethal for some reason. Those with the
successful ring-fence survived, those without didn't. We are
in the business of hacking through ring-fences or leaping
over them. It's only a matter of time ... .



        Russell


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