Team Claims Synthetic Life Feat

gertvs writes "According to the BBC scientists in the US have taken a step towards producing life from scratch in the laboratory by having successfully transplanted an entire genome from one bacterium cell to another. This technique could possibly lead to the creation of 'designer' microbes producing fuel or help cleaning toxic waste. 'The ultimate plan is to stitch together artificial chromosomes, proteins and other building blocks with the aim of jumpstarting their designer microbe to life. But Dr. [Craig] Venter concedes that this may be a long way away, but he says he has taken an important key step towards that goal. His team, essentially, snatched the body of another life-form and invaded it with a new genetic code. This, he says, will be a key tool in testing the artificial chromosomes - or DNA bundles - he plans to make. '"

Comments

Origins Of Life?

[Umbral Blot]

Reminds me of a certain cartoon: http://www.angryflower.com/goinaf.gif

Patents....

[king-manic]

Wait didn't another firm patent artificial life. The gall of these people, working hard to create something new. Thats simply un-American. They should really make vague patents wait for someone else to do the work and sue.

Re:Patents....

[Anonymous Coward]

It was the same firm.

Re:Inteligent design

[stoolpigeon]

I don't see how. They didn't actually create life from scratch - they took a step towards it. They took one form of already living thing and moved it to something else - by design, using their brains. I'm not advocating intelligent design here- or trying to start an argument about it - just pointing out that this development doesn't seem to really 'put a big hole' in that idea.

i am...

[cosmocain]

...almost sure, that we will se a whole lot of paired headlines.

"designed microbe is able to clean water from toxic waste" and a few months/year later: "water-cleaning microbe causes " and some random illness/problem. genetic engineering is full of possibilities, it's the humans that haven't shown responsible behaviour with new technologies.

Imagination needed

[Anonymous Coward]

This technique could possibly lead to the creation of 'designer' microbes producing fuel or help cleaning toxic waste.

Oh come on! Have an imagination! This could make some really killer bioweapons! Or we could mine deer for oil. Convert puppies into kittens. Give George Bush a brain. Think of the implications!

Re:Imagination needed

[Yetihehe]

...Give George Bush a brain. Think of the implications!

George Bush: Braaainnnsss!!

Re:Inteligent design

[Anonymous Coward]

This is going to put a big hole in the whole Inteligent Design crowd. Or will get the religious nuts in a frenzy of protest. We're living interesting times.

What a load of tripe. Did you just pull that one out of your butt? From the summary:

According to the BBC scientists in the US have taken a step towards producing life from scratch in the laboratory by having successfully transplanted an entire genome from one bacterium cell to another.

Notice the words "from one bacterium cell to another"? They didn't exactly create the recipient bacterium cell did they? Or the donor cell for that matter.

Pray tell, how exactly does this "big hole in the whole Inteligent Design crowd"?

Re:Inteligent design

[Anonymous Coward]

it may even strengthen their claim- if we can design something specifically, so can 'He'.

Penrose

[headkase]

If Penrose turns out to be right (The Emperor's New Mind) and quantum-like operations are needed to truly reproduce intelligence then inevitably at some point in the future we will have artificial intelligence even if we have to program some meat to use the same building materials nature used with us.
Other uses could be to adapt humans to non-terran environments. Base-line in brain just tailored to an alternate environment.

Re:Penrose

[king-manic]

If Penrose turns out to be right (The Emperor's New Mind) and quantum-like operations are needed to truly reproduce intelligence then inevitably at some point in the future we will have artificial intelligence even if we have to program some meat to use the same building materials nature used with us.
Other uses could be to adapt humans to non-terran environments. Base-line in brain just tailored to an alternate environment.

What part of that statement was interesting?

If the bum down the street turns out to be right, Bush is the second incarnation of Cleopatra and Kim Jong Il is the reincarnation of Marc Anthony and they will eventually get it on. Both this statement and Penroses are baseless speculations from a flake.

Re:Penrose

[Cyberax]

Penrose was probably smocking crack when he wrote this book.

You definitely don't NEED quantum computers to reproduce intelligence. That's because IF cells contain quantum computers, then they must work in cycles: load initial data, process it, read data. Reading computation results stops quantum computer (collapses it to one state). Even Penrose admits that quantum computers can't work more than a fraction of second in a living cell.

Quantum computers can be simulated by classical computers (they're computationally equivalent), so quantum computers are not NEEDED to simulate human mind.

However, quantum computers might make good accelerators for neural processing (there are several publications on this).

Re:Penrose

[stormeru]

Maybe we should start by adapting humans to live in other Earth places. Since >70% of the Earth surface is water, start populating the oceans. I for one welcome our new Human-With-Gills Overlords.

Re:Penrose

[TheLink]

Well if quantum computing is good at parallel processing, then it would be good for animals to simulate multiple "what if" situations rapidly.

For example a background process considering possible escape routes: "what if I jumped on to (various portions of) that branch or other branches, would they hold my weight, would they lead to better escape routes?". All considered in parallel.

Then the animals start simulating each other (predicting the decisions of a potential competitor/predator is very useful), and then end up (infinitely?) recursively simulating themselves (aka consciousness?).

Not saying it's definitely quantum computing we're using, but I wouldn't be surprised if it is, after all if quantum computing is practical - it'll be a useful thing to have.

Anyway humans (and animals) often don't bother to think about "what if" till too late ;).

Re:Penrose

[Adam Hazzlebank]

Quantum computers can be simulated by classical computers (they're computationally equivalent), so quantum computers are not NEEDED to simulate human mind.

That's not quite true, Quantum computation (perhaps not in the sense your talking about) is more powerful than classical computing in one respect. That is though Quantum randomness a Quantum computer can produce an endless supply of real random numbers. A classical computer can only produce pseudo-random numbers, a way round this is to include a large enough supply of random numbers in the initial configuration. It's not what Penrose was talking about I know but...

Re:Penrose

[Cyberax]

AFAIR my university's course, Turing machine with random number generator is computationally equivalent to a common Turing machine.

Re:Penrose

[Cyberax]

Nope, Penrose's quantum computers work on a sub-cellular level.

Thinking about branches requires work of more than one neuron, so quantum computers are not really significant here (they can't talk to each other through cell walls).

Re:Penrose

[Adam Hazzlebank]

AFAIR my university's course, Turing machine with random number generator is computationally equivalent to a common Turing machine.

Your university course is wrong? Here's a problem a common Turing machine can't solve:

Using a program of length n produce n+1 "really" random numbers.

Quantum events are as far as I understand the only source of "really" random numbers we have and are just plain weird. The problem comes in part because we don't have a clear definition of random.

Anyway, I've not read this article yet but it looks like it could be of interest: http://www.nature.com/nature/journal/v318/n6041/ab s/318041a0.html .

Re:Penrose

[TheLink]

Neurons definitely talk to each other and at least some are more sophisticated than you seem to think, even though they may be very specialized.

Some people even have a "Halle Berry" neuron - if they see the name "Halle Berry" or her picture or even a caricature, that neuron will fire.

See: http://www.physorg.com/news4703.html

Maybe that part is a bit like Bingo. Patterns are passed through a huge bunch of neurons, and one of them shouts out and says "Bingo: Halle Berry!", another says "Bingo: Catwoman", and the results are fed back through the neurons.

Whether QC comes into this is debatable. But given the lack of knowledge we have on how it all works, I'm not going to be so certain it doesn't play a role. As I said if QC is possible, it is likely to be advantageous.

Re:Penrose

[Cyberax]

What is 'really random number'? Can you define it?

We can have pseudorandom numbers behaving exactly like real 'random' numbers (though it requires unlimited resources as you get more and more numbers). I.e. you won't be able to distinguish pseudorandom generator and real random source.

Re:Penrose

[Cyberax]

How neurons talk to each other is irrelevant - you can't use classical channels to connect quantum computers. And I can't imagine any quantum channel working across multiple cell walls.

QCs (if they are present inside neurons) are probably advantageous, but it doesn't mean that they will be the fundamental barrier for creating 'artificial brain'. However, it may be practically impossible to build artificial brain without some sort of QC accelerator (i.e. like videocards - you can build games which use only CPU, but it would be prohibitively slow in practice).

Re:Penrose

[Adam Hazzlebank]

What is 'really random number'? Can you define it? A random number source is that which produces a (infinite? or unbound finite) series of numbers which can not be produce by any deterministic algorithm in space less than the size of the number series... Basically the numbers produced by the generator have a high Komolgorov complexity.

We can have pseudorandom numbers behaving exactly like real 'random' numbers (though it requires unlimited resources as you get more and more numbers). I.e. you won't be able to distinguish pseudorandom generator and real random source.

That's not so. The Kolmogorov complexity http://en.wikipedia.org/wiki/Kolmogorov_complexity of a string of pseudo random numbers is very low, by definition I can build a finite length program to produce an infinite string of digits. The digits "look" random with simple tests, that is they have a nice distribution (with I would imagine few periodic features). However they are obviously highly compressible (rather than giving you all the numbers I can just give you a short program to produce them).

This isn't necessarily the case with a Quantum random number generator. The randomness here comes from the inherent probabilistic nature of Quantum events. Now where this randomness comes from is anyones guess the vast majority of modern physicists say that the universe is just inherently probabilistic and the random choice is fundamental. A few physicists few say there are hidden variables which we don't know about and that if/when we know more we'll find that actually it's all deterministic really (but (and please someone correct me) this is kind of way out thinking in phyiscs). Then there are some people who say that actually at every Quantum event ALL possible things happen and multiple universe are created, but we only see one of them (there seems to be little evidence to support this, and to me there appear to be huge holes in the argument logically and I'm not sure if any serious physicists hold this point of view).

Re:Penrose

[Cyberax]

It's true that complexity of any pseudorandom generator is finite.

However, you can't readily tell it from its output. It might well be possible, that the Universe uses a simple formula to determine the outcome of quantum events.

In any case, we can just add hardware-based random number generator to classical computer simulating quantum events.

Re:Penrose

[Adam Hazzlebank]

It's true that complexity of any pseudorandom generator is finite. However, you can't readily tell it from its output

I take a large sample of it's output, I enumerate all possible programs shorter than this output, I run these programs and find the smallest program that outputs this string and then halts.

It might well be possible, that the Universe uses a simple formula to determine the outcome of quantum events.

It's possible, though as I said, it's my understanding that most modern physicist wouldn't agree with you.

In any case, we can just add hardware-based random number generator to classical computer simulating quantum events.

Yes. That's all I'm saying, however such a computer is still in some (perhaps not very useful) sense more powerful than a Turing machine.

Re:Penrose

[Crazy Eight]

Even Penrose admits that quantum computers can't work more than a fraction of second in a living cell.

That point isn't a critique of his hypothesis. IIUC, Penrose's model of the human mind simply includes quantum mechanics as an ingredient in it's operation. You might as well claim that my Athlon isn't really computing because every time its innards clock through an op it shuts down (loses conciousness?) for 1/2,000,000,000th of a second.

You definitely don't NEED quantum computers to reproduce intelligence.

You are assuming that human intelligence can be expressed by a Turing Machine. Even if it can, that doesn't mean such a machine would fit inside a human skull without quantum mechanical assistance.

Re:Penrose

[Crazy Eight]

I doubt my own personal "thinking mechanism" is larger than my nervous system. You claim it can't be smaller than two neurons. Your basis for this lower limit presumes an equivalence between mind and Turing Machine, and that sub-cellular QM effects don't "talk" through synapses.

Mutation

[suv4x4]

"This technique could possibly lead to the creation of 'designer' microbes producing fuel or help cleaning toxic waste."

Well it's perfect that we could just program a microbe to solve all our messy problems just like snapping my fingers.

Now.. some mutations have been observed when the microbe was released in the wild. Of course, releasing in the wild means that your creation kinda gets a life on its own. Some mutations have been observed.

Mutation one turns the form of liquid metal that wants to kill John Konnor. Mutation two is a purple mist that's a destroyer of worlds.

But I bet we could engineer a microbe to kill those first microbes.

Re:Mutation

[Aranykai]

I think your confusing real-world mutation with movie/sci-fi mutation. They are hardly the same.
Mutations are almost always:
1.Useless
2.Harmful in some way to the creature
3.Lost in the next generation(assuming the creature can breed)

So, a little more 5 legged frog, and a little less sharks with freakin laser beams.

Re:Mutation

[BiggerIsBetter]

But I bet we could engineer a microbe to kill those first microbes.

"No, that's the beautiful part. When wintertime rolls around, the gorillas simply freeze to death."

Re:Mutation

[suv4x4]

I think your confusing real-world mutation with movie/sci-fi mutation. They are hardly the same.
Mutations are almost always:
1.Useless
2.Harmful in some way to the creature
3.Lost in the next generation(assuming the creature can breed)

So, a little more 5 legged frog, and a little less sharks with freakin laser beams.

You're boring, you know that? But, ok, I'll accept your science ways, and take the 5 legged frog. But only if can laugh in an evil voice and has an army of minions trying to take over the world.

Re:Mutation

[Adam Hazzlebank]

I think your confusing real-world mutation with movie/sci-fi mutation. They are hardly the same. Mutations are almost always: 1.Useless 2.Harmful in some way to the creature 3.Lost in the next generation(assuming the creature can breed)

Yes, but mutations are obviously sometimes beneficial to an organisms survival. I think the point is that if we create a completely artificial gene/set of genes/organism then we don't really know what trajectory it's evolution will follow in the natural world. Organisms engage in coevolution, whereby organisms can slowly adapt to evolutionary changes in others. If you suddenly add a foreign organism in to the ecosystems and this evolves in such a way as to be damaging to other organisms (or completely out performs them) then it is unlikely they will be able to evolve a countermeasure before they are wiped out, the evolutionary distance is just too great. No, that's the beautiful part. When wintertime rolls around, the gorillas simply freeze to death

Re:Mutation

[Anonymous Coward]

"No, that's the beautiful part. When wintertime rolls around, the gorillas simply freeze to death." Is it just me, or does that make a caption perfectly suitable for a Far Side comic when taken out of context? (Somehow picturing one Sabretooth Tiger talking to another.) Too bad Gary Larson retired.

The Venter Institute

[poopdeville]

This is very exciting. I took a class from someone who ended up working at the Venter Institute, so I'm pumped to see that they've made major progress.

On the other hand, the field of Artificial Life is small. Something on the order of a thousand other people are qualified to talk about this intelligently. So my hopes for discussion are pretty much nil.

Re:The Venter Institute

[NeverVotedBush]

But did your professor/teacher tell you how much of an egocentric ass Craig Venter is?

Re:The Venter Institute

[poopdeville]

Yes.

Wolfram still compared negatively to Venter. :-)

Re:The Venter Institute

[NeverVotedBush]

You have to be talking about Stephen Wolfram.

OK, Craig Venter is humble compared to that moron. Smart - but still a moron.

Re:The Venter Institute

[NeverVotedBush]

You know, what happened to the scientist that just did their research and made their contribution to society without all the ego self-masturbation, self promotion, self-written bios that basically compare themselves to God? I understand that a certain amount of self promotion is sometimes necessary when forming companies, etc. But these guys take it to levels that would make Lord Farquar jealous.

Re:The Venter Institute

[poopdeville]

I'm a mathematician, so I'm naturally slightly arrogant. Sort of. I mean, I think I have a fairly reasonable estimate of my skills in mind, hardly ever get "put in my place" by someone with better skills, know when to cede an argument, etc. But I'm confident when I say something with mathematical content.

When I took the class on the Philosophy of Life (focusing specificially on defining life for the purposes of knowing if an artificial creation is "actually" alive, which involved studies in computation, Turing machines, Wittgenstein, first-order logic, experiment design and statistical interpretation, evolution, etc), I joined the ranks of a very small field. Something like a thousand people in the world are qualified to talk about this stuff intelligently. I don't mean to sound arrogant -- artificial life is very multi-disciplinary in scope, so unless one is familiar with all the involved disciplines, it is difficult to not be trivial.

Now, throw someone with a healthy ego into a field like that, where virtually no one they meet is better at it than they are, and you suddenly have an ego explosion. I went through it, and outgrew it (since I know a lot of people better than me at mathematics, my primary interest).

Re:Inteligent design

[Umbral Blot]

If we can design something then you don't need to posit a god as the designer of life on Earth. Thus intelligent design, even if true, would no longer be a argument for the existence of god (if it ever was one), only for some motivated beings who evolved under more favorable conditions to seed life here.

So they pretty much did...

[arakon]

what a Virus already does. They took DNA, and implanted it into another cell and the cell ran the DNA instruction set... Just like cells are wont to do. Seems like a pretty "Cut & Paste" idea to me; hardly "creating Life", or even steps toward it.

We'll have Artificial Intelligence (synthetic life by my standards) I think, long before we're actually engineering proteins and building an original base DNA sequence of our own making and creating the cell to run it from scratch.

At which point our machine overlords will take care of the rest. :P

Re:So they pretty much did...

[poopdeville]

We'll have Artificial Intelligence (synthetic life by my standards) I think, long before we're actually engineering proteins and building an original base DNA sequence of our own making and creating the cell to run it from scratch.

I highly doubt it. Think of the relative complexities of a computer capable of simulating the human brain (and by that I mean capable of running several hundred million threads, each of which runs an interruptable O(2^n) algorithm quickly enough to respond to external stimuli) to the relative simplicity of a single cell. I mean, an artificial species wouldn't have to survive very long to be the first example of artificial life.

Re:So they pretty much did...

[joto]

We'll have Artificial Intelligence (synthetic life by my standards) I think, long before we're actually engineering proteins and building an original base DNA sequence of our own making and creating the cell to run it from scratch.

I highly doubt it. Think of the relative complexities of a computer capable of simulating the human brain (and by that I mean capable of running several hundred million threads, each of which runs an interruptable O(2^n) algorithm quickly enough to respond to external stimuli) to the relative simplicity of a single cell.

Two counter-arguments

1. Moore's law is (still) exponential
2. Either field (computing, biotech) is not up to the task (ai, life-from-scratch) at present, and it's hard to judge progress towards something we presently can just hypothesize can be done. It's like asking whether we will first get light-sabers or hooverboards, where we have no idea what exotic physical principles either would use, and no way to be sure any of them will ever exist in a practical form.

Re:So they pretty much did...

[Adam Hazzlebank]

It's even worse than that to be honest. Experiments like this were how we discovered that DNA was the "transforming principle" in organism life. Basically Oswald Avery took a pathogenic (disease causing) strain of bacteria and isolated the DNA then transfered this to a non-pathogenic strain and noted the associated transferal of traits (the non-disease causing strain became disease causing). http://en.wikipedia.org/wiki/Oswald_Avery (this was way back in 1928). This is no huge leap as far as I can see. Even less of a leap toward synthetic life than when Venters team synthesized a virus (http://www.pnas.org/cgi/content/abstract/100/26/1 5440) which I think someone had done before him anyway. Or the time when Celera claimed to out perform the human genome project, when they actually included all the information from the human genome project and even then came out with a lower quality sequence http://www.pnas.org/cgi/content/full/99/7/4143 .

So basically they've not done much interesting. But hay, they got a Science paper out of it and Venter got to jump up and down and say how great he is. I guess that's what matters. :)

Anyway, took me a while to dig out the original Science article, here's the link: http://www.sciencemag.org/cgi/content/abstract/114 4622v1

Re:Inteligent design

[iamacat]

No, it would be an argument that a group of lab researchers are Gods for this particular bacteria.

Forget nuclear weapons

[iamacat]

Imaging Ebola that spreads like a flu. Or mosquitos with black widow spider venom. Genetic engineering is probably essential for our long term survival as a species (for example, modern medicine and cultural values sabotage natural selection). But I am not sure we are ready for it at the moment.

Re:Forget nuclear weapons

[delt0r]

Imaging Ebola that spreads like a flu. It can't, it kills the host to quickly. Turns out there are a lot of limits on these sorts of things. If its real deadly, it won't spread very well because everyone who got sick is dead. If it not that deadly the immune system gets time to adapt. Similar arguments apply to mosquito's.

But I am not sure we are ready for it at the moment. So when will we be ready? Maybe this is as good as it gets.

Re:Forget nuclear weapons

[Colin Smith]

Genetic engineering is probably essential for our long term survival as a species Right because there's no other way we could have survived the last few million years.

(for example, modern medicine and cultural values sabotage natural selection) Or do they just change the selection pressures.

Re:Forget nuclear weapons

[Anonymous Coward]

> Imaging Ebola that spreads like a flu.

> It can't, it kills the host to quickly. Turns out there are a lot of limits on these sorts of things. If its real deadly, it won't spread very well because everyone who got sick is dead. If it not that deadly the immune system gets time to adapt. Similar arguments apply to mosquito's.

So, bad examples, but the principle stands. Imagine an ebola that spreads like flu, but takes 10 years to kill you.

Re:Forget nuclear weapons

[iamacat]

Well, what do you make of plague and smallpox?

Re:Forget nuclear weapons

[iamacat]

Our current selection pressures do not include the ability to be born, live and reproduce without assistance of medicine and technology, let alone forage for food in the wilderness. If technology was suddenly to fail, or if we face an epidemic or political unrest, this could mean the whole humanity going extinct. Even defects we consider benign, like bad teeth or color blindness, would be fatal to a band of survivors trying to form a settlement after a catastrophe.

Re:Forget nuclear weapons

[Kiffer]

Don't be silly. Plenty of people get by with out that much tech.
The human race is not going to go extinct from just the loss of technology, barring massive environmental collapse in which case we would probably need our tech to survive.
Plenty of people around the world get by from day to day using only the level of technology that they themselves, or rather the people in their local area, can support.
Unless by extinction of the human race you meant the extinction of pampered westerners?
Sure we might get knocked back to the stone age, but humanity would survive a sudden "failure" of technology.
Some massive epidemic could wipe us out ...but in all likelihood it wouldn't get every one... and enough isolated populations would survive.

If all High Technology failed we might lose a lot of people and the average life span might drop to 25 but people can have a lot of babies by that age...

Re:Forget nuclear weapons

[delt0r]

Or the Spanish flu. 3% fatality rate IIRC. Plague was spread by hygiene issues as much as anything. The same this could not really happen now. I don't mean they can't be bad. But we have survived. Also we are a lot better at medicine now days. So really big plagues are not likely, and +90% bioweapons are probably imposable.

Re:Forget nuclear weapons

[Anonymous Coward]

A 3% mortality rate spread randomly through an economy would be devastating to that economy.

Any realistic plague would disproportionately kill the old and the very young, most likely obese and anorexic people, most likely urban dwellers and workers, and possibly the poor (who are at greater risk for complications, generally speaking).

While these could be considered less economically productive members of an economy, the demographic shock of losing lots of very young people leads to some awkward actuarial problems with respect to productivity of the entire economy in the future. It is also not free to break up the estates of the old. Finally, disproportionate losses among the working poor increases the risk to the working non-poor if it leads to a decrease in waste handling, janitorial services (toilet and telephone cleaning), safe food handling, and so forth, because of the reduction in labour supply.

Plague was spread by hygiene issues as much as anything

Hygiene was one important factor. People are cleaner now, but they are also more likely to come into close contact with many more people than even the most urbanized people in the early 1900s would.

But we have survived

Mere survival of the species is not as comfortable as continuing economic growth.

Shades of "Zodiac".

[Glytch]

When the movie of the same name was announced, I was deeply disappointed that it wasn't based on Neal Stephenson's novel.

Sounds Good, But....

[arollo]

When do I get to start playing God from the comfort of my own home?

Re:Sounds Good, But....

[eggman9713]

I think that is what ant farms are for. Cause famine, flood, fire, and the apocalypse (aka, the ol flusheroo), right in your own home!

Re:Sounds Good, But....

[deetsay]

When do I get to start playing God from the comfort of my own home?

1989

Re:Sounds Good, But....

[The Only Druid]

I think Spore was delayed until 2008.

Synthetic Life Feat

[niceone]

And one of these days those feet are gonna walk all over you.

Oh feat, right. As you were.

Definition of life

[eggman9713]

I don't really know if I buy their "synthetic life" term. IMHO, life is not something that can be made by man. All they are doing in TFA is a bunch of fancy chemistry. True life is not made by one of life's own evolutionary steps, which is all that man is. All we are doing is showing that we can do what mother nature and father time (or whatever you believe in) did.

Re:Definition of life

[tukkayoot]

IMHO, life is not something that can be made by man. All they are doing in TFA is a bunch of fancy chemistry.

When you come right down to it, life is fancy chemistry and nothing more. Life could also be described as "really fancy physics," if you wanted to. There is no clear line between when chemistry stops and biology begins, hence the term
biochemistry.

True life is not made by one of life's own evolutionary steps, which is all that man is.

On the contrary, all life is made by one of life's own evolutionary steps. That's a pretty vital component of how and why evolution works.

Re:Definition of life

[Anonymous Coward]

I would not be sure about that. When a person connected to a heart-lung machine dies during an operation, the chemistry is still there and working, but the person is _dead_. They had a case in Germany where they kept a pregnant woman on the support machine for several weeks. She was brain dead but her body and the whole "chemistry" was still there.

Re:Definition of life

[Alchemist253]

No, only part of the chemistry was "there."

The brain is basically an enormous collection of cells performing primary metabolism (which presumably was functioning) but that also has loads of secondary metabolic pathways in the form of electrochemical communication.

This is why drugs exist (LSD, ritalin, halothane, take your pick) that can have a profound effect on consciousness: they change the chemistry of the brain.

Re:Definition of life

[tukkayoot]

I would not be sure about that. When a person connected to a heart-lung machine dies during an operation, the chemistry is still there and working, but the person is _dead_. They had a case in Germany where they kept a pregnant woman on the support machine for several weeks. She was brain dead but her body and the whole "chemistry" was still there.

If anything, that just serves to illustrate my point. Life is not always simple, binary function. If you lack a heartbeat, you're said to be clinically dead, but your body is still composed of billions of living cells. If you're in a persistent vegetative state ("brain dead"), your existence as a conscious entity may be at a definitive end, but a lot of the chemistry that's going on your body is still life, unless you're going to define life as requiring consciousness. If you do that, bacteria, plants, fungi, etc. no longer qualify as living organisms.

Wow, that's amazing

[jollyreaper]

I suppose the synthetic life has got to walk around on something. But when are they going to do the rest of the body?

They did something very different from a virus

[wisebabo]

A virus (DNA or RNA) when injected into a cell utilizes the existing cellular machinery to make mass copies of its own genetic code, encase them in proteins that its genetic code has transcribed and explodes the cell to allow the newly created viral particles out. In a few cases (retroviruses) the virus becomes reverse transcripted into the cell's DNA and can stay there hidden (like HIV) for a long time, sometimes even reproducing with the cell (a possible source of "junk" DNA or even some cancers). Notice that a virus has far less than the minimum number of genes to create the cellular mechanisms for life let alone reproduction.

Venter's group has taken a cell and replaced ALL of the original DNA with the newly introduced DNA. (I believe a virus replaces nothing, it merely adds its own genetic code). While the newly introduced DNA comes from another bacterium, there is no reason to think that the DNA from a completely "man-made" source couldn't be introduced instead. By introducing fewer and fewer genes, Venter (and others) hope to find the "minimum" number of genes needed to make a living creature.

Once this minimal life is created is new, possibly never before seen in nature, genes can be introduced one at a time. Because these genes are added to a "clean" slate, their functionality and efficiency can be controlled and optimized. Kinda like a much more powerful version of the transgenic mice they use in research where they selectively eliminate just ONE gene from the mouse strain to see what its effect is. I believe they have strains for all/almost all the thousands of genes in mice so they can evaluate them for various genetic ailments, disease resistance and whatnot. (Harvard was the first to get a patent on the genetic code of one of these mice: the first patented life. Go Harvard!)

Here instead of removing one gene from the entire set (to an admittedly MUCH more complex organism), Venter will be able to control ALL the genes in his bacteria. This will greatly reduce/eliminate unwanted interactions (because the "unneeded" genes have been eliminated) allowing R&D to go much more quickly. Thus the optimism on creating oil producing bacteria. (Please note that "unneeded" refers to our needs not the bacteria, we can make a bacteria that is alive but is utterly dependent on vital nutrients that "wild" bacteria make themselves. Since our bacteria is simpler, we will use it not the wild version.)

Re:They did something very different from a virus

[plunge]

Speigelman's monster was already pretty damn small: the smallest reproducing/evolving version had, what, like 48 base pairs TOTAL or something? True, it needed to live in an environment where it's enzyme and raw materials already existed, but still, I don't see an "organism" getting much smaller than THAT.

Re:They did something very different from a virus

[eli pabst]

Here instead of removing one gene from the entire set (to an admittedly MUCH more complex organism), Venter will be able to control ALL the genes in his bacteria. This will greatly reduce/eliminate unwanted interactions (because the "unneeded" genes have been eliminated) allowing R&D to go much more quickly.

Exactly. You could do the same thing that Venter is doing using a virus to infect bacteria, but the real goal is to be able to strip out all the excess cellular processes that would otherwise be consuming energy. That way the bulk of your input energy (in the form of nutrients) is going almost exclusively to whatever the bacteria is engineered to do (such as make hydrocarbon fuels) rather than "wasteful" cellular processes. People are freaking out over this idea and in reality it isn't really that different from much of what is going on today in labs across the country. In fact by its very nature of having a stripped down genome, you are inherently creating a "weaker" life form that can't live on it's own in the wild.

Re:They did something very different from a virus

[VisceralLogic]

So, basically, they cloned a bacterium?

Seriously

[McNihil]

I read the headline as if they had made Silicon based life... synthetic oil being silicon and all.

Horror Movie

[Joebert]

"That chromosome was transplanted, inserted through the cell walls, the cell membrane of a second species and, after several days of growth and cell division, the original chromosome in the cell disappears and we have cells containing only the transplanted chromosome."

Sounds like somthing out of a science-fiction horror movie.

Hardly...

[Anonymous Coward]

They didn't create life from scratch; they used existing genetic material!

God and a genetic engineer had a contest to create life. The genetic engineer started by picking up a lump of earth. God looked over and says, "Hold on there! You've got to get your own dirt.".

creating life in the laboratory is rather frequent

[Anonymous Coward]

It only requires (at least) one female lab assistant and one (or more) male lab assistant(s), a bit of boredom or stress, then life is created in the lab. Nine months later the life is introduced to the rest of us. One can argue about the from scratch business. However, regardless of which way life in the lab is created, the researchers had to be there! On the other hand, the researchers don't need to be there if you start with a couple of rabbits (at one male and one female for you nit-pickers).

Patent tomfoolery

[GovCheese]

Something tells me that patenting life forms is going to make the code world's problems look rational in comparison.

Slashdot the Nerds National Enquirer

[truckaxle]

Slashdot title --> "Team Claims Synthetic Life Feat"

No they don't. From the article....

"What's in this paper is the result of taking a native chromosome from one species," Dr Venter explained.

"That chromosome was transplanted, inserted through the cell walls, the cell membrane of a second species and, after several days of growth and cell division, the original chromosome in the cell disappears and we have cells containing only the transplanted chromosome."

The took genetic material from one species and inserted into another and this genetic material achieved a position in the germline.

OK but certainly not "Synthetic"

Re:Slashdot the Nerds National Enquirer

[plunge]

You missed the part about how this was the last big hurdle for implanting a man-sequenced code into a cell. Which is what they are going to do next. So, yes, this IS a big feat in the field of creating synthetic life: according to them, it's pretty much the last piece of the puzzle prior to actually doing it.

What is the big deal?

[mapkinase]

Technologically: transfer of genome from one cell to another has been done on much more complex level: Dolly the sheep anyone (I claim that complexity of eukyotic cell beats the addtional complexity of inserting DNA vs injecting the nucleus)? True, this is the first time I here about researchers that have induced a bacterium to take up the entire genome of another, related bacterium. But it leaves me in utter bewilderment of how that is "transforming"? Bacterias are much less epigenetic compared to higher forms (one obvious result is that bacteria cells are not capable of differentiation), in other words, there genome defines pretty much what they are doing and how do they look. It is amazing of course, how old intracellular proteome of the host (including protein synthesis machinery) coexisted with the new DNA and its products, but the degree of that amazement is seriously dependent on how "related" are the host and the bacteria which DNA was injected. I cannot read Science right now, those idiots require subscription even for News...

Interesting, but...

[ChrisMounce]

...I won't be terribly impressed until they start cobbling together custom genetic material, instead of just copy-paste from one microbe to another. No disrespect to the scientists - I'm sure even copy-paste's hard to do - but don't call it synthetic life if you didn't create anything original, know what I mean?

Also, be warned that I will be as scared as I will be impressed when they do write their own software for the hardware.

IT'S ALIVE

[Tekoneiric]

IT'S ALIVE! Wahahahahaha

Update Re:What is the big deal?

[mapkinase]

In the study, the researchers removed intact DNA from Mycoplasma mycoides and inserted it into Mycoplasma capricolum. That is the same genus. If you compare 16S RNAs of those two species they have 1515 identical nucleotides (one of them has in total 1524, another - 1527 nucleotides). 16S ribosomal RNAs are a standard marker for comparison of species, since ribosomal RNAs are the most universal component of any independently living organsim (that is every single life form except viruses).

In other terms this is quite similar to getting DNA from one cell and transfering it to another cell (transformation). First happened in 1928. Venter has done it in a technologically more impressive way, but scientifically - no big deal.

About practical implications: is not it much more practical to transform existing bacteria to produce whatever is necessary by adding required features into the genome?

Re:Update Re:What is the big deal?

[eli pabst]

About practical implications: is not it much more practical to transform existing bacteria to produce whatever is necessary by adding required features into the genome?

Depends on what you mean by practical. If you mean easier for us to do, then yes. However, the point is to create a synthetic organism that is engineered to make a single product. So it makes more sense to strip out all of the extraneous genes/processes that are not necessary for production of that compound. As an example, in a standard bacteria with an inserted gene, you'd have 95% of energy being used for cellular processes (making structural genes, cell movement, cell signaling, etc) and 5% going to making the target compound*. Now if you strip out all of the unnecessary processes you could get down to 50% cellular processes and 50% compound production. So you can see how that would be extremely useful for commercial applications.

*Note: These are arbitrary numbers, but you get the idea

Re:Update Re:What is the big deal?

[mapkinase]

At the same logic we can make 18 wheelers out of the carton. 95% of the genome is not necessary to produce the target but are necessary to sustain the bacterial colony.

Re:Update Re:What is the big deal?

[eli pabst]

95% of the genome is not necessary to produce the target but are necessary to sustain the bacterial colony.

Not really. If you are designing an organism for a specific purpose then you only need a minimal set for critical life processes and for producing the target compound. Most bacteria have a wide variety of metabolic genes for utilizing various macromolecule nutrients for energy, which are largely unnecessary if you are going to be feeding it a specific nutrient broth, so you can chuck out a bunch of genes that are involved in metabolism of other compounds than what you are feeding it. You can also throw out things like genes for motility, congugation, recombination, as well. The patent was for an organism with 381 genes, so in the case of mycoplasma genetalium it obviously wasn't a huge amount as it has ~470 genes naturally. Still that's roughly 20% of the genome.

Re:Update Re:What is the big deal?

[mapkinase]

I would wait until they will go down on living model organism with such small number of genes, because proving that this gene is involved in that pathway does not prove that it is not involved in other pathways.

And, again, why is it necessary to strip it down to "minimal" amount of genes?

Re:Update Re:What is the big deal?

[eli pabst]

proving that this gene is involved in that pathway does not prove that it is not involved in other pathways.

The number of pathways known (or unknown) that a given gene is involved in is irrelevant from their point of view. If they can knock out a particular gene and have the organism still grow at the same level and produce compound X, then that gene is unnecessary for their purposes.

And, again, why is it necessary to strip it down to "minimal" amount of genes?

Primarily because production of "unnecessary" genes is wasting energy. Things like RNA transcription, protein translation, and protein degradation all have real (albeit small) energy costs. When you ramp production up to a level where you are producing hydrocarbon fuels to power an economy, then those trivial energy costs become significant. You can right that off as minor, but it clearly is important otherwise there wouldn't be several groups actively trying to accomplish the same goal, though some are using other model organisms like yeast.

Re:Update Re:What is the big deal?

[mapkinase]

I do not buy this argument. Bacteria well know for the effective usage of really junk energetic resources. Instead of feeding touchy feely warm and fuzzy stripper bacteria it makes more sense to me to add necessary genes to some tough badass bacteria that can it dirt and make a living on it.

Re:Update Re:What is the big deal?

[eli pabst]

Bacteria well know for the effective usage of really junk energetic resources

Which is exactly why they have genes that are unnecessary for the purposes that Venter's group is targeting it for. In fact part of the patent application describes the medium that they plan on using:

The inventors have identified 101 protein-coding genes that are non-essential for sustaining the growth of an organism, such as a bacterium, in a rich bacterial culture medium, such as SP4. Such a culture medium contains all of the salts, growth factors, nutrients etc. required for bacterial growth under laboratory conditions. A minimal set of genes required for sustaining the viability of a free-living organism under laboratory conditions is extrapolated from the identification of these non-essential genes. By a "minimal gene set" is meant the minimal set of genes whose expression allows the viability (e.g., survival, growth, replication, proliferation, etc.) of a free-living organism in a particular rich bacterial medium as discussed above.
it makes more sense to me to add necessary genes to some tough badass bacteria that can it dirt and make a living on it.
I disagree. The more self-sufficient your bacterium is, the higher the likelihood of it surviving outside of the lab. Plus by that very definition it will produce less output of the target compound than a bacteria which is engineered to be a specialist.

Re:Update Re:What is the big deal?

[mapkinase]

The more self-sufficient your bacterium is, the higher the likelihood of it surviving outside of the lab. Plus by that very definition it will produce less output of the target compound than a bacteria which is engineered to be a specialist.

This is utter nonsense, which I do not consider necessary to consider for answer.

Re:Update Re:What is the big deal?

[eli pabst]

This is utter nonsense, which I do not consider necessary to consider for answer

LOL, so you apparently know of some strain of bacteria that is capable of violating the laws of thermodynamics? If you have X amount of input energy in the form of nutrients and Y is the amount of energy consumed by the cell for life, then X-Y will equal the amount left over for other things like reproduction or in this case biosynthesis of a compound. In an organism that has extraneous cellular processes such as the ability to metabolize a wide array of input macromolecules, that Y will be larger than in an organism that has a stripped down genome, as it has to produce the enzymes to metabolize those compounds and replicate those added genes during cell division. The very reason that they even chose mycoplasma genetalium is that it is a obligate parasite and has become specialized to living in a restricted environment thereby allowing it to undergo a massive genome reduction.

Re:Update Re:What is the big deal?

[mapkinase]

I have just got a chance to read the popular rendition of the article in Science. Seems to me, that my skepticism is shared by Church (no pun intended):

Regardless, George Church of Harvard University questions the need for genome transplantation; instead of starting with a minimal genome, he's making useful chemicals by simply adding customized genes to existing species' genomes.

Call me an extremist, but this looks like Venter's ego trip...

more quotes Re:Update Re:What is the big deal?

[mapkinase]

"In a sheep, what you're doing is nuclear transfer -- sending in all the machinery ready to roll," he said. "Here, you just send in the blueprint." Well, Dr. Ellington, that is quite a bit of exhaggeration. "All the machinery ready to roll"? Like ribosomes, which are "bound to endoplasmic reticulum or freely floating in the cytoplasm"? Give me a break. I think every scientists that talks to media should be banned from government grants for ever (analog of disbarring)

Re:Inteligent design

[The_Wilschon]

Even if they did make a new cell from scratch (random atoms lying around, I suppose), that would not put a hole in ID at all. ID claims that life is too complex to have arisen out of the primordial soup by chance alone, so it must have been designed by some intelligence. Showing that it is possible for an intelligence (scientists in a lab) to design life (make a new cell from scratch) would in some indirect and not very useful sense support ID (by demonstrating that it was possible for ID to have taken place) although not to the exclusion of anything else, and would certainly not damage the idea.

Note: I am not a proponent of ID.

Re:Inteligent design

[plunge]

I agree that ID really doesn't have much to lose by this, but certainly a lot of the theological and philosophical ideas that undergird creationism in general do. For starters, it's pretty much the final death-knell to the idea of vitalism or that there's something special about "life" outside of having the right physical and chemical components.

In fact that latter idea is pretty critical to a lot of the less nuanced creationist arguments against a natural origin of life: there have been plenty of claims that "scientists can't even create a cell, how could it have happened in nature." Well, says science, shrug, okay, I guess we'll get on that.

Change chimp to man

[raman3007]

How about this:

- Take chimp single celled embryo right after fertilization
- Chimp gene is 99% similar to human, so change the genes that differ in the embryo and make it look exactly like a human embryo (make it look like Dubya's genome.. he won't be convinced otherwise)
- Will we get a Dubya clone from that embryo ??

More improtantly, does this mean that any animal can be turned into a human (or any other animal, for that matter ) ?

Re:Change chimp to man

[joto]

If by "animal", you mean "any life-form that as a zygote look sufficiently similar to what you started with, as a zygote", and if you by "turned into" means "(through a hypothesized theoretical process) replace genetic code inside zygote with genetic code from zygote of wanted result", then the answer is obviously "yes". If you mean in practical terms, the answer is "no". And if you believe that you theoretically can change the zygote of a flatworm into one of Tyrannosaurus Rex, I doubt that it can be done, even theoretically, as the Tyrannosaurus has bigger egg-cells than the flatworm (and probably some other important differences as well (such as internal micro-structure to support a different number of chromosomes, etc), apart from the purely genetic difference)

Good thing I read the headline twice ...

[ScrewMaster]

I thought it said, "Teen Claims Synthetic Life Feast".

I need another beer.

Intelligent Design

[turgid]

Well, what more proof do you need?

/me ducks.

Re:Inteligent design

[Anonymous Coward]

Sure it would, because ID is ALWAYS about the Christian God in the USA in a political context. Sure, aliens could have designed us, but that's not what they really mean in a practical sense. ID was invented by the Discovery Institute, more or less, a religious political group with specific aims to "invent the controversy".

If us lowly humans can make totally artificial life, life that has the ability to evolve theoretically, it will be a blow to ID in every practical sense.

That is not synthetic life!

[Anonymous Coward]

That is just a cloning analog, but with bacteria, taking the DNA from one and inserting it into another, with the original DNA removed.

They didn't create anything. This is closer to grafting than anything else.

stubborn?

[jadin]

For the time being it is my belief (personal opinion) that a) life from scratch and b) artificial intelligence are impossible to create. I've never seen any "step toward" those goals even come close to breaking those barriers. Now if something happens I will have to rethink said beliefs. But until then I personally see all the attempts as people wasting their time striving for the impossible. I'm not sure why but it seems like going faster than the speed of light would be an easier goal to me.

Again just my opinions.

Re:stubborn?

[Anonymous Coward]

You stated that you don't believe it will happen, yet posit no reasons whatsoever? What are your credentials? Are you a micro-biologist, a geneticist, a bio-physicist? Until you become an expert in a given field you probably should just keep uninformed opinions to yourself, because no one will really care.

Re:Inteligent design

[Bjarke Roune]

I don't follow - I don't think anyone are arguing that an omnipotent being might not be able to create cells like the ones on earth today.

Paging Mary Shelley...

[CptNerd]

On the other hand, the field of Artificial Life is small. Something on the order of a thousand other people are qualified to talk about this intelligently. So my hopes for discussion are pretty much nil.

Especially since one of the best thinkers about it isn't around anymore, except for her words...

Re:Inteligent design

[looseSpark]

The only thing that would really put a hole in the ID argument be for someone to demonstrate that a living organism evolved through a process that did not require any kind of intelligent input. That is most certainly not what has happened in this case. I don't think it does any damage to the ID argument at all really.

Teen Claims Synthetic Life Feat

[pseudosero]

_____ .

Stop the B.S. Gee Whiz headlines

[Samarian Hillbilly]

Transplanting a genome is a great feat but hardly "synthetic life". I suggest toning down the National Enquirer style headlines.

Re:Inteligent design

[UncleTogie]

Sure it would, because ID is ALWAYS about the Christian God in the USA in a political context.
Says who? I live in the US as well, and have never restricted the ID debate to a guy with a white beard and robe. I vote.

Sure, aliens could have designed us, but that's not what they really mean in a practical sense.

"They" who? Mighty dangerous to lump ANY group of people together like that... and who are you to tell us that we've not already allowed for that possibility? Here, I'll take ya one further... What if [and I don't personally believe this is the case] Jesus was sent along by those same scientists as a "litmus" test of our development? Did we flunk?

Jus' some thought fodder... {or cannon fodder, one of the two...}

Re:Inteligent design

[The_Wilschon]

You still don't get it, do you? My ability to shoot a basketball through a hoop in no way implies that the basketball could just drift through the hoop by chance. A human scientist's ability to create an artificial cell in no way implies that that cell could have come together spontaneously in the primordial soup. Sure, ID is a Christian idea. But, I claim that the ability of scientists to create artificial life does not blow a hole in an entire class of ideas which resemble ID in that they claim that life could not have spontaneously appeared in the primordial soup.

Now, if we were to add more information, and claim that the scientist's mechanism for creating artificial life is to make a replica of primordial soup and then wait (which isn't the case with this experiment), and also that this mechanism actually works, then we would have a hole in that entire class of ideas, as well as ID. But we don't.

merely synthetic DNA; 30K other chemicals

[peter303]

OK they've synthesized a couple of the 30K+ chemicals in a cell, albeit one of the more complicated and important. But I dont conisder true synthtic life and the final refutation of "vitalism" until all the chemicals are synthesized.
Vitalism contends there is some important constitute to life outside of known chemistry and physics. Some "neo-vitalists" claim life can only come from existing life, or some pattern thereof. Others claim mysterious new phsice like quantum microtubes, etc.