New Lifeforms Are Go!

R

redarmy11

Registered Senior Member
I am creating artificial life, declares US gene pioneer
http://www.guardian.co.uk/science/2007/oct/06/genetics.climatechange
Sat. 6th October 2007

Craig Venter, the controversial DNA researcher involved in the race to decipher the human genetic code, has built a synthetic chromosome out of laboratory chemicals and is poised to announce the creation of the first new artificial life form on Earth.

The announcement, which is expected within weeks and could come as early as Monday at the annual meeting of his scientific institute in San Diego, California, will herald a giant leap forward in the development of designer genomes. It is certain to provoke heated debate about the ethics of creating new species and could unlock the door to new energy sources and techniques to combat global warming.

Mr Venter told the Guardian he thought this landmark would be "a very important philosophical step in the history of our species. We are going from reading our genetic code to the ability to write it. That gives us the hypothetical ability to do things never contemplated before".

The Guardian can reveal that a team of 20 top scientists assembled by Mr Venter, led by the Nobel laureate Hamilton Smith, has already constructed a synthetic chromosome, a feat of virtuoso bio-engineering never previously achieved. Using lab-made chemicals, they have painstakingly stitched together a chromosome that is 381 genes long and contains 580,000 base pairs of genetic code.

The DNA sequence is based on the bacterium Mycoplasma genitalium which the team pared down to the bare essentials needed to support life, removing a fifth of its genetic make-up. The wholly synthetically reconstructed chromosome, which the team have christened Mycoplasma laboratorium, has been watermarked with inks for easy recognition.

It is then transplanted into a living bacterial cell and in the final stage of the process it is expected to take control of the cell and in effect become a new life form. The team of scientists has already successfully transplanted the genome of one type of bacterium into the cell of another, effectively changing the cell's species. Mr Venter said he was "100% confident" the same technique would work for the artificially created chromosome.

The new life form will depend for its ability to replicate itself and metabolise on the molecular machinery of the cell into which it has been injected, and in that sense it will not be a wholly synthetic life form. However, its DNA will be artificial, and it is the DNA that controls the cell and is credited with being the building block of life.

Mr Venter said he had carried out an ethical review before completing the experiment. "We feel that this is good science," he said. He has further heightened the controversy surrounding his potential breakthrough by applying for a patent for the synthetic bacterium.

Pat Mooney, director of a Canadian bioethics organisation, ETC group, said the move was an enormous challenge to society to debate the risks involved. "Governments, and society in general, is way behind the ball. This is a wake-up call - what does it mean to create new life forms in a test-tube?"

He said Mr Venter was creating a "chassis on which you could build almost anything. It could be a contribution to humanity such as new drugs or a huge threat to humanity such as bio-weapons".

Mr Venter believes designer genomes have enormous positive potential if properly regulated. In the long-term, he hopes they could lead to alternative energy sources previously unthinkable. Bacteria could be created, he speculates, that could help mop up excessive carbon dioxide, thus contributing to the solution to global warming, or produce fuels such as butane or propane made entirely from sugar.

"We are not afraid to take on things that are important just because they stimulate thinking," he said. "We are dealing in big ideas. We are trying to create a new value system for life. When dealing at this scale, you can't expect everybody to be happy."
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So.. yeah. Frankenstein, here we come. Bacteria are a bit boring, I know, but it's early days so we'll all have to be a bit patient. I just hope they get a move on now though, and we don't have to wait, like, another three million years before we all own six-headed dog-type-things-on-wheels that have a ravenous appetite for litter. What would be really brilliant would be some kind of microbe that eats excess fat so that we could all stuff ourselves on pies and cakes all day long without ever gaining a spare ounce.

Anyway, this whole thing is really brilliant ethically-speaking because there are no yoomans involved, it's just, like, invented lifeforms and I don't believe we have any 'rules' covering those so we can probably just make up the 'rules' as we go along. We could even breed all kinds of sensitivity out of them to make creatures that don't mind too much if you set them on fire or beat them up. Biological inventions of no intrinsic value, that exist only to serve our every pleasure and do our bidding. God, it'll be brilliant - I can't wait!!!

Anyway: once all the misery gutses have had a jolly good moan at this - "Ooh, you can't do that, it's playing God, etc., ffs, stfu" - and done their best to spoil our fun, let's all have a big debate about what the best designer microbe would be and what brilliant features you would want it to have!!! eg pisses vodka and has a built-in drinks cabinet.

Go!!!
 
First patent claimed on man-made life form, and challenged
http://www.world-science.net/othernews/070607_mycoplasma.htm

June 7, 2007


A research institute has applied for a pat­ent on what could be the first largely ar­ti­fi­cial or­gan­ism. And peo­ple should be al­armed, claims an ad­vo­ca­cy group that is try­ing to shoot down the bid.

The idea of own­ing a spe­cies breaches “a so­ci­e­tal bound­ary,” said Pat Mooney of the Ot­ta­wa, Canada-based ETC Group, which is asking the pat­ent ap­pli­cants to drop their claim. Creat­ing and own­ing an or­gan­ism, he added, means that “for the first time, God has com­pe­ti­tion.”

More...
 
They've actually only created a DNA sequence, for injection into pre-existing cells. A breakthrough from 'mere' reading to writing.

But to develop your analogy - I think the idea is that the copies of the barebones machine, to which they own the patent, can be purchased and fitted with any custom harddrive you like. As one commentator has remarked it seems like Venter's institute is aiming to become the Microsoft of genomics.
 
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As I understand from the article in the first post, they "read" the genome of a bacteria, and then recreated it artificially? In its current form, it is hardly anything that could be considered artificial life. It does create a basis for further and deeper work on the subject though, which will in my opinion be a lot more complicated. We now have a "script editor" and a lot of extremely complicated "programs" from which to learn, but due to the complexity of the interactions between genes and proteins synthesized, it will be an enormous task to actually create something fundamentally new, instead of trial-and-error modifying existing bacteria to fit the purpose necessary. I would expect that creating a completely artificial chromosome, as opposed to copying an existing one artificially, would take another 3 or more years, and when entered into a "blank" cell, it would probably be little more than a life-support system for the cell. Creating more complex genomes artificially, that could actually perform more tasks than saying alive and reproducing would be another step further. In the same time, progress will probably be done in the field of creating new and functional proteins from ground up, and although it is hard to say without being actually involved in the front-line research, I would assume that it will be an even harder task to accomplish, given that we can hardly predict a proteins higher level structure and its function from its amino acid order now.
 
As I understand from the article in the first post, they "read" the genome of a bacteria, and then recreated it artificially?
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Not even that. They used the chromosome of an parasitic bacterium that already had a reduced genome and simply knocked everything non-essential out.
Technically, it is nothing new.
If I recall it correctly they then reinserted the modified chromosome into a "normal" bacterium. During cell division they simply hoped that one of the daughter cells eventually only carries the modified chromosome instead of the original one.
I'd rather call it a mutant strain than artificial live (but then Venter was always great on marketing).
 
Nope, it still leaves me the impression, that they took an existing chromosome and removed everything unnecessary, to reduce the amount of DNA they would need to put together artificially. The chromosome they created was still build from ground-up. That is the part that is actually new, as it is different form simply modifying an existing genome.
 
Ok, they used a new technique to modify something that already exists. Still didn't create an artificial life form any more than any modified organism used in biological research is an artificial life form.
 
The artificial life claim, I agree, is a promotional trick. However, as I already said, I understand the article as saying that they didn't modify anything, but put together a copy of the existing DNA from single nucleotides artificially.

To continue the discussion, I would like to ask how would one define a completely artificial life? If we need to use an existing cell to support the artificial DNA, can it be considered artificial life at all? Would it be an example of artificial life, if I somehow put together an entire cell from single atoms, but used an existing cell as a blueprint? If not, how much would the blueprint have to be modified in order to qualify as an artificial life? Can we call anything that uses the same biochemical mechanisms we have copied from nature, artificial life?
I would argue that there is no solid barrier between artificial life and natural life, unless we manage to perform a complete abiogenesis from anorganic substances, that would not include any copying at all.
 
What about designing a gene from scratch that has no relationship to anything out there in the library of life and has a novel function, as in it produces a protein unlike anything in nature, with a specific function.

That would be one step towards something artificial.

Another one would be to design a cell that works with something else than DNA as the genetic code.
 
Designing proteins is an interesting topic, but as far as I know we are having troubles with predicting the proteins higher level structure from its amino acid sequence, so that anything else besides the most common structure elements are more or less out of reach. Designing proteins by anything else but trial and error would require enough computational power to predict the structure of the protein with very high accuracy. After that is achieved, we can use the knowledge about natural proteins to use elements from them to produce new proteins with predetermined function.
Although by today, we are a long long away from accomplishing that, I nevertheless believe that progress made in both computation and biochemistry will allow us to get there eventually. My prediction would be in the time range of 5-15 years or so.
 
fo3 said:
Designing proteins by anything else but trial and error would require enough computational power to predict the structure of the protein with very high accuracy. My prediction would be in the time range of 5-15 years or so.
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it took nature a bit longer! ;)
 
it did evolve evolvability. Not quite planning ahead, but acquiring the means of speeding ahead into new directions. :confused: obligatory smiley
 
The artificial life claim, I agree, is a promotional trick. However, as I already said, I understand the article as saying that they didn't modify anything, but put together a copy of the existing DNA from single nucleotides artificially.
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From what I read it appears rather clear to me that they merely cured the Mycoplasma chromosome. They did create an genome from scratch, earlier. However, it was only a viral genome with merely 5,386 bps.
The "artificial" bacterial genome was around 580,000 bps and it wouldn't be feasible to synthesize a chromosome of this size de novo with current techniques (at least not in the given time frame).
If they had created such a technique, they would've published it much earlier. I might be wrong, but frankly I wouldn't see the point to synthesize whole chromosomes artificially only to create a reduced a copy of the original if you can merely mutate that one with conventional techniques.
Similar approaches were made to curate quasi-essential megaplasmids in some bacteria, btw.

At this stage I am pretty confident that either the media got it wrong or it was deliberately phrased in a confusing way.
The novelty thing they did, however is to replace a normal chromosome with the mutated one with a technique that was published earlier this year.

I would probably classify an organism an artificial one, if they manage first to create a cell from scratch (instead of using an already existing one) and maybe have a truly artificial chromosome in which at least 50% of genes code for metabolic activities not previously found in the organism from which the backbone of the DNA was taken. Technically such a fusion is possible (and together with a chromosome exchange one can actually try to get such an organism viable). Tweaking the regulation to get it right would be a nightmare, though.
Also note that to date they need the original organism to reinsert the chromosome. It does not work with a different cell (and we are still generations away from artificial cells).
 
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CharonZ said:
From what I read it appears rather clear to me that they merely cured the Mycoplasma chromosome.
Click to expand...

Using lab-made chemicals, they have painstakingly stitched together a chromosome that is 381 genes long and contains 580,000 base pairs of genetic code.

The DNA sequence is based on the bacterium Mycoplasma genitalium which the team pared down to the bare essentials needed to support life, removing a fifth of its genetic make-up. The wholly synthetically reconstructed chromosome, which the team have christened Mycoplasma laboratorium, has been watermarked with inks for easy recognition.
Click to expand...
Lab-made chemicals seems to indicate that they used single nucleotides and put together a chromosome manually. The nucleotide order they put together was the same as a Mycoplasma bacterium genome, with unnecessary parts removed. If not, I am still missing something.
 
Well, the problem is that the "stitiched together" part was not a quote but a phrase obviously made up by the author. I read other articles which formulated it different.
In this field (or most sciences for that matter) one has to be careful about what was said and how it was interpreted. Especially as synthesizing half a megabase de novo is technically far more challenging than pruning down the existing chromosome.

However, in the end we have to wait for the publication to be 100% sure. I would be surprised to find an existing half megabase DNA synthsizer somewhere, though as normal DNA synthesizer have a maximum synthesis length of ~100 bps.

Edit: I just noticed that the original chromosome was already 580,000 (and 525 ORFs). Hence the article was also wrong on this account (where it stated that the reduced chromosome was 580 kb). If the reduced chromosome carries 381 genes one would expect a genome size of ~380,000, or a 200 kb deletion.

But as to steer a bit back to the topic, I do not see how this organisms qualifies as artificial life form. I would have termed it a mega-mutant, but as only ~200kb is missing I'd have to call it a kilo-mutant. Doesn't sound as grand, though.
 
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