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Author Topic:   Digital Life Design—What a concept!
Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 1 of 13 (450996)
01-25-2008 12:56 PM


Craig Venter's lab succeeds in Digital Life Design (DLD). It announces the first synthesis of a bacterial genome and the development of DLD synthetic life:
quote:
...In June 2007 another major advance was achieved when JCVI researchers led by Carole Lartigue, Ph.D., announced the results of work on genome transplantation methods allowing them to transform one type of bacteria into another type dictated by the transplanted chromosome. The work was published in the journal Science, and outlined the methods and techniques used to change one bacterial species, Mycoplasma capricolum, into another, Mycoplasma mycoides Large Colony (LC), by replacing one organism’s genome with the other one’s genome.
Genome transplantation was the first essential enabling step in the field of synthetic genomics as it is a key mechanism by which chemically synthesized chromosomes can be activated into viable living cells. Today’s announcement of the successful synthesis of the M. genitalium genome is the second step leading to the next experiments to transplant a fully synthetic bacterial chromosome into a living organism and “boot up” the cell.
This connects to the Life! What a concept! thread (where a discussion of the EDGE book is ongoing) because that book addresses claims that life is digital. As such, for all of the deniers of digital life, here is an interesting EDGE discussion between Richard Dawkins and Craig Venter, under the subtitle, LIFE: A GENE-CENTRIC VIEW:
quote:
DAWKINS: It’s more than just saying you can pick up a chromosome and put it in somewhere else. It is pure information. You could put it into a printed book. You could send it over the Internet. You could store it on a magnetic disk for a thousand years, and then in a thousand years’ time, with the technology that they’ll have then, it would be possible to reconstruct whatever living organism was here now. What has happened is that genetics has become a branch of information technology. It is pure information; it’s digital information; it’s precisely the kind of information that can be translated digit-for-digit, byte-for-byte into any other kind of information.
~
VENTER: Biology is the ultimate nanotechnology and it can now be digitally designed and reconstructed.
Seems to me that Venter has made good on his claims.
Questions: Will DLD end at bacteria? Will it be a new evolutionary forces to deal with?
”HM

Replies to this message:
 Message 3 by Wounded King, posted 01-26-2008 8:18 PM Fosdick has replied

  
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Message 2 of 13 (451000)
01-25-2008 1:39 PM


Thread moved here from the Proposed New Topics forum.

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 3 of 13 (451225)
01-26-2008 8:18 PM
Reply to: Message 1 by Fosdick
01-25-2008 12:56 PM


Its a pretty cool bit of research, and an impressive achievement to synthesis the whole thing. I wouldn't say Venter has quite made good on his claims though, its not so much that the new genome has been digitally designed as plagiarised after all.
Will DLD end at bacteria?
I doubt that designing fully artificial genomes, especially larger scale ones, is ever going to be a particularly worthwhile endeavour practically, although they might represent significant technical achievements. It is simply too easy to modify genomes using much simpler extant technologies if one wants a specific feature, or set of features, introduced.
Perhaps in concert with research on non standard chiral biological molecules one could eventually make a mirror image system of life, but I'm not sure why you would want to or if we could even understand the sterochemistry sufficiently to make it work.
It still pretty cool though.
TTFN,
WK

This message is a reply to:
 Message 1 by Fosdick, posted 01-25-2008 12:56 PM Fosdick has replied

Replies to this message:
 Message 4 by molbiogirl, posted 01-26-2008 9:41 PM Wounded King has not replied
 Message 6 by Fosdick, posted 01-26-2008 10:08 PM Wounded King has not replied

  
molbiogirl
Member (Idle past 2642 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 4 of 13 (451241)
01-26-2008 9:41 PM
Reply to: Message 3 by Wounded King
01-26-2008 8:18 PM


I wouldn't say Venter has quite made good on his claims though, its not so much that the new genome has been digitally designed as plagiarised after all.
Fair enough. Even Venter admits that.
But while we can create and develop new species, we're not creating life from scratch.
P. 51, Life: What a Concept!.
But these are important notions that get lost in the over-simplified interpretation of what we are doing. I don't think we are creating life. We're coming up with new modified life forms, and we should be able to go from the digital world right to the analog world in the computer, and we have a team working on a program to do that, designing a species in the computer.
P. 53, Life: What a Concept!.
He also makes a point of calling his genome "synthetic", not "artificial".
Still and all. Pretty spiffy. And synthetic chromosomes + genome transfer ...
A short while ago we published a paper in Science on genome transportation, where we took a purified chromosome from one species, made sure it was totally devoid of any protein, and put that chromosome into another bacterial species, and it's the ultimate identity theft because the new chromosome we put in completely took over the cell, and the cell converted completely into the cell dictated by the new chromosome. the new chromosome dictated everything. All the proteins changed over to that. The phenotype of the cell, everything changed, converted from the old species into the new species.
P. 48, Life: What a Concept!.
... = extra spiffy.

This message is a reply to:
 Message 3 by Wounded King, posted 01-26-2008 8:18 PM Wounded King has not replied

Replies to this message:
 Message 5 by Fosdick, posted 01-26-2008 9:59 PM molbiogirl has replied

  
Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 5 of 13 (451246)
01-26-2008 9:59 PM
Reply to: Message 4 by molbiogirl
01-26-2008 9:41 PM


Spiffy!
molbiogirl writes:
... = extra spiffy.
Yeah, it sure is, mbg. Makes me want to go places where Ringo would like to step in and kick my ass around. I'm probable off the map with my reasoning on this, but I can't apprehend what the digital part of life really means. Should I assume then that the functional core of biological life is digital, rather than analog?
Go ahead and beat me up over this. But I can't help thinking these stupid thoughts.
”HM

This message is a reply to:
 Message 4 by molbiogirl, posted 01-26-2008 9:41 PM molbiogirl has replied

Replies to this message:
 Message 7 by molbiogirl, posted 01-26-2008 11:27 PM Fosdick has replied

  
Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 6 of 13 (451247)
01-26-2008 10:08 PM
Reply to: Message 3 by Wounded King
01-26-2008 8:18 PM


Counter-chiral life
WK writes:
...non standard chiral biological molecules one could eventually make a mirror image system of life, but I'm not sure why you would want to or if we could even understand the sterochemistry sufficiently to make it work.
Careful, Wounded. You put a meme like that out there and the tabloids will run with it. Who's to say that counter-chiral life wouldn't take us back to the Garden of Eden? Cure all our problems!
”HM

This message is a reply to:
 Message 3 by Wounded King, posted 01-26-2008 8:18 PM Wounded King has not replied

  
molbiogirl
Member (Idle past 2642 days)
Posts: 1909
From: MO
Joined: 06-06-2007


Message 7 of 13 (451262)
01-26-2008 11:27 PM
Reply to: Message 5 by Fosdick
01-26-2008 9:59 PM


Re: Spiffy!
Should I assume then that the functional core of biological life is digital, rather than analog?
To the extent that it relies on DNA (or RNA), yes.
Do you honestly not understand the digital nature of DNA or are you trolling again?

This message is a reply to:
 Message 5 by Fosdick, posted 01-26-2008 9:59 PM Fosdick has replied

Replies to this message:
 Message 8 by Fosdick, posted 01-27-2008 11:38 AM molbiogirl has not replied

  
Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 8 of 13 (451346)
01-27-2008 11:38 AM
Reply to: Message 7 by molbiogirl
01-26-2008 11:27 PM


Re: Spiffy!
mbg writes:
Do you honestly not understand the digital nature of DNA or are you trolling again?
Look who's trolling now.
Ever since the 2008 Admin Massacre I've been trying to mend my ways, using the example set by Nem Jug. But, oh no! I gotta put up with more of your petty plinking. The fact is, madame molecular biologist, I've been debating digital life for some time now. For example, please see Message 26 of the The "Digital Code" of DNA.
So why don't you just lighten up a little and take Nem Jug's advice, along with a handful of Midol.
”HM

This message is a reply to:
 Message 7 by molbiogirl, posted 01-26-2008 11:27 PM molbiogirl has not replied

  
AshsZ
Member (Idle past 5400 days)
Posts: 35
From: Edgewater, FL USA
Joined: 05-17-2008


Message 9 of 13 (469870)
06-08-2008 5:31 AM


Pretty neat-o stuff. In an analogous sense, and by no means meant to devalue the work, it reminds me of pulling the stock non-turbo engine out of my Nissan Z and transplanting a twinturbo engine in its place. Once that conversion was complete, the car behaved like a twinturbo Z.
It would be interesting to know how this effect would take place, timewise. Say, hypothetically, if this technology were highly refined, that it be used to "convert" one human's genome to a replica of another. How long would it take for the subject's appearance to "morph"? If this were the trend, would this process ever complete or to what bound?
Perhaps a brain-dead patient could undergo this process to produce (a) compatible organ(s) for transplant to another individual? (and not just "compatible", but rather, a genetic match for the recipient..)
Interesting stuff. Please forgive my ignorance....

  
Stephen
Junior Member (Idle past 5769 days)
Posts: 7
From: Charleston, SC, USA
Joined: 06-11-2008


Message 10 of 13 (470420)
06-11-2008 5:51 AM


That's a pretty interesting piece of research and I can't wait what else could be done to the genoms.

  
Lwilliams
Junior Member (Idle past 5768 days)
Posts: 2
Joined: 05-27-2008


Message 11 of 13 (470784)
06-12-2008 4:58 PM


by reading this thread I get very curious about the future & how far science is going to take us.
I guess my kids, kids will be living in a whole nother world.

oolong tea

Replies to this message:
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AshsZ
Member (Idle past 5400 days)
Posts: 35
From: Edgewater, FL USA
Joined: 05-17-2008


Message 12 of 13 (471219)
06-15-2008 3:45 PM
Reply to: Message 11 by Lwilliams
06-12-2008 4:58 PM


I must re-reply to this - please forgive me.
I read through the links provided in the original post and it has raised a concern.... It is pointed out that this kind of technology, while certainly amazing and having great potential, could also be a sort of pandora's box leading to unexpected and possibly catastrophic outcomes if used.
I am by all means an optimist and discussions like this thoroughly excite me. The potential this technology has also excites me in ways I can't express and I would love nothing more than to see this knowledge actually doing something beneficial. But at the same time, and against my "optimistic" nature, I am surprisingly (to myself) skeptical about this technology being further refined and put into use.
For the most part we humans learn from mistakes more than from positive outcomes. It is fortunate that we dont appear to have made any mistakes big enough to compromise our existence - we have the technology but haven't blow ourselves up - yet. But this new technology is a bit scary... Genetics and the success of "life" here go hand in hand - both are intimately tied to each other just as much as all life on this planet is tied in some way or another to other life. There apears to be a dynamic balance in the organisms and the biosphere which are conducive to life. I am sure everyone here has made decisions in their lives expecting positive results only to find that while the original idea seemed promising, changing the various aspects of one's life in the direction necessary to accomplish said goal(s) proved to affect other areas in their life in an undesired way which was not originally anticipated.
I liken this to the tinkering of genetic code. Even if the processes involved can be shown to produce predicted results in whatever organism being manipulated within a laboratory, there will undoubtedly be unpredictable results arising once said organism is placed into the environment. I dont personally like the idea of using the planet as an experiment with technology we are just breaking the ice on.
I am sure the concerns I have are nothing new. These concerns would be the foundation for laying the framework of process/direction of this technology. There are brilliant minds at work as well as other brilliant minds looking over their shoulders. Although my internal devil's advocate is telling me that these scientists aren't going to run off and start experimenting in the environment with reckless abandon, it is the concern arising from the fact that probability of some mistake being made where one of these bugs do make it out into the wild cannot be zero. Although the probability that one of these bugs getting out in the environment could cause some catastrophic effect is even lower, we might want to ask ourselves how much longer are we going to be "lucky?" The concept of "MAD", or Mutual Assured Destruction, was one which played a huge role in preventing the cold war from going hot. What's the point if we are all dead? "Dont push the button!"
It is interesting that "Digital Life Design" is the wordage being used - this technology, in a refined version, would be analogous to writing a computer program. While that description fits really well to the technology, wouldn't that mean that these "programs" would need to be made in such a way so as to remain static in design to maintain control over said program? If genetic evolution is allowed to function, the programs are going to change over time and lead to results which may or may not be known. DNA has a knack at evolving into potently effective structures in ways we dont fully understand - not to mention, some of the mechanisms we do know of that create evolution already reveal how little control we have over it and how feeble any attempt to predict it would be. I wonder if it is possible to remove the "evolution" action from DNA. Are there any life forms which its DNA has always been the same?
I know there are environmental forces causing change to DNA code but perhaps there is some organism which keeps a "backup", if you will, to prevent any change to DNA ever?
I'm not so sure evolution can be prevented in DNA though - I'm not an expert on these things. If there is no way to prevent evolution, wouldn't that mean the programs we create inherently are subject to a degree of control that is out of our hands? (Not saying they "control" themselves, but rather, that we dont have 100% control)
Maybe we dont want to make their genetic code static - maybe we want these creations to have evolutionary ability. Afterall, the world does change and so too will our need for our machines to change. So why not just program them to evolve to our needs? <<-- that question is asked entirely sarcastically with intention to show where a limitation exists with this technology at a fundamental level. Even if we can build genetic code to make any "designed" organism we wish, it will be designed for some purpose for our needs that fits the times, like a machine. How can an organism be both designed to meet some particular need and also possess the "coding" required for it to understand our changing needs and adapt accordingly? Wouldn't that mean we would need to somehow write human history into the code to provide the organism with the information necessary to make such adaptation decisions? (parcially sarcastic there) The ability to effectively write genetic code tramples all over evolution as being a non-intelligent, non-conscious "thing" when looking at evolution from a "human" perspective. We are life and with this technology, life would be consciously evolving itself. Or will we state that evolution comes in two forms - that which we do with our minds and then that which is done by natural selection? I know we already do this, but what isn't natural about artificial evolution? What is the difference, or is there one? No difference between the two would mean that there is "mind" to all evolution - something is "thinking" about it, which really doesn't appear all that crazy - evolution does appear to be very "thought" out. What would some intelligent alien stumbling across this planet see it as? Artificial selection? Or would they see it just as "evolution?"
Fortunately the machines we humans manufacture do not possess the ability to reproduce themselves nor are they capable of running forever. They break down and require maintenance - not to mention the inability of these machines to seek and obtain their own "food" to drive their functions. These are just a few attributes we do see in life amongst many others which our machines do not possess. While I never forsee any automobile to take on traits like that in "The Cars", "Herbie", "Christine", or "Maximum Overdrive", a biological "machine" we create will have the ability to repair itself, feed itself, reproduce itselt, it is "alive". - will it also possess the characteristic of evolution or be subject to environmentally-induced reprogramming in unexpected ways out of our control?
With the application of many inventions in society there appears to be both benefit as well as drawback associated with them. Setting that into motion, it is as if we invent one technology, put it into use, and then find we have to invent another technology to counter the negative effects of the original, which then becomes a cascade of such where we have to pedal harder and harder to keep up. Is this really what was meant in the warning of eating the proverbial apple of knowledge? Or is my perspective too pessimistic, or jaded? All parts of my adrenaline-junkie say go for it - develop the technology and lets make awesome things happen. Even if we are digging a deeper hole in our pursuit of knowledge, we've already scarfed the apple - no turning back now - let's eat the rest of the batch and get on with evolution.

This message is a reply to:
 Message 11 by Lwilliams, posted 06-12-2008 4:58 PM Lwilliams has not replied

Replies to this message:
 Message 13 by Fosdick, posted 06-16-2008 11:17 AM AshsZ has not replied

  
Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 13 of 13 (471359)
06-16-2008 11:17 AM
Reply to: Message 12 by AshsZ
06-15-2008 3:45 PM


Digital tampering
AshsZ writes:
It is interesting that "Digital Life Design" is the wordage being used - this technology, in a refined version, would be analogous to writing a computer program. While that description fits really well to the technology, wouldn't that mean that these "programs" would need to be made in such a way so as to remain static in design to maintain control over said program? If genetic evolution is allowed to function, the programs are going to change over time and lead to results which may or may not be known. DNA has a knack at evolving into potently effective structures in ways we dont fully understand - not to mention, some of the mechanisms we do know of that create evolution already reveal how little control we have over it and how feeble any attempt to predict it would be. I wonder if it is possible to remove the "evolution" action from DNA. Are there any life forms which its DNA has always been the same?
All life has the same DNA. Chemically, it's the same molecule. The only difference that matters is the arrangement of its nucleotides. And therein lies the digital code. By discovering it, and by manipulating it, you know damn well that the future will be full of genetic tampering. I don't think our imaginations are broad enough to comprehend the consequences.
”HM

This message is a reply to:
 Message 12 by AshsZ, posted 06-15-2008 3:45 PM AshsZ has not replied

  
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