First Self-Replicating Synthetic Bacterial Cell

[gary]

For those who missed arguably the biggest news story of the day -
http://www.jcvi.org/cms/research/pro...cell/overview/

Press release -
http://www.jcvi.org/cms/fileadmin/si...ease-final.pdf

As mentioned in the press release, inserted in the genome of the artificial bacteria
are encoded watermarks that includes a web address to send emails to if you can
successfully decode it, the names of 46 key contributors to the bacteria's creation
and three quotations, including one by James Joyce that is said to read -
"TO LIVE,TO ERR.TO FALL,TO TRIUMPH TO RECREATE LIFE OUT OF LIFE".

[Robh (Rob)]

Absolutely amazing!
The implications of being able to produce a living organism from a synthetic genome cannot be underestimated.

Regards, Rob.

[JimmyH155]

That's real scary stuff. What will they make next?? A Darlek???

[Ric]

Quite an amazing article Gary with a lot of fantastic implications.

At the same time it's also a tad scary.

[multiweb (Marc)]

Originally Posted by Ric

Quite an amazing article Gary with a lot of fantastic implications.

At the same time it's also a tad scary.

It is amazing and bloody scary at the same time. Doesn't the chaos theory say something along the lines that very complicated and uncontrollable systems birth in combinations of very simple elements to start with? How we're going to contol those little guys when they take over the world. Attack of the Yeast. Ok I've watched resident evil too many times.

[marki]

Nothing too suprising in this achievement, scientists have been inserting great lumps of DNA into bacteria cells for a long time, hell we even did it to make ampicillian resistant bacteria (super bugs) when I was at uni and it is not too difficult to do. No one has ever managed to replace an entire genome and have it replicate though, not to my knowledge anyway. Still a few more steps for the big one though.

Mark

[avandonk]

This is just the start. We have been cloning stuff for nearly thirty years in our lab. I see this more as a proof of concept. To build a living organism no matter how simple was the challenge. The anti evolutionists used to proclaim this was impossible! When did the scientists stick in the soul?

Bert

[renormalised (Carl)]

Very big...the possibilities are endless and also, like anything else, fraught with danger. However, it doesn't mean that it shouldn't be done. It will be very interesting to follow where this technology will go in the next 50 or so years.

[PeterM]

OMG (not literally) Implications are well .... astronomical.
PeterM.

[dugnsuz (Doug)]

Perhaps I'm being cynical, but this seems to be touted as "artificial life produced" in the media - but as far as I can ascertain, the whole thing needs an already living entity as the precursor for this new artificial lifeform.
So, in fact 'life' can't really be made without pre-existing "life" in the equation.
I'm not trying to undermine this amazing discovery - I just don't think our manipulation of the building blocks of life really gets any closer to the elemental spark that mobilizes the elements that constitute DNA.*
What makes GCTA want to dance reproductively!?

ps...I'm sure the medical implications are enormous - just being philosophical (aka a PITA!)

*EDIT: on re-read, obviously these kind of breakthroughs DO bring us closer

[renormalised (Carl)]

You're right, Doug. It's not life from first principles, so to speak. But it's a long way down the road towards that.

[Lee]

I hope that they have inserted specific genes to allow this little bug to be knocked over by our basic antibiotics, or more to the point, have they worked out a way to prevent it picking up resistance genes?? Does this little sucker grow well at 37 degrees, ie will it grow in your tissues?? I think stem cell research is great, but making self-replicating bacteria sounds fraught with danger.....

[StephenM (Stephen)]

Originally Posted by renormalised

You're right, Doug. It's not life from first principles, so to speak. But it's a long way down the road towards that.

That's right Carl. The key point here is that its a synthetic genome, rather than "synthetic life". The success here relects both our understanding of bacterial genomes, and also the revolution that has taken place in DNA synthesis (and sequencing) technologies in the last few years. The cost of synthesizing genes has now reached a point where, for many applications, it is cheaper and faster to get your gene of interest synthesized rather than cloning it yourself. We have completely redesigned and ordered quite a few synthetic genes in my lab in the last 18 months, at less than $800 per gene! But this demonstration is gene synthesis on a whole new scale!

Interestingly when they first introduced this synthetic genome it failed to replicate, and in just 3 months they were able to identify a single nucleotide error that prevented replication!

This report is definately a significant event in the history of biology and biotechnology.

Cheers,
Stephen

[OneOfOne (Trevor)]

Originally Posted by dugnsuz

...
What makes GCTA want to dance reproductively!?

I seem to recall something a few years ago about artificial DNA research where the active molecules were not GCTA and suggested that there were other possibilities, all life on Earth just happens to use this permutation....perhaps the best evidence that we all share a common heritage. Alien life forms may use other amino acids to build their code, or even something other than a DNA like structure. I can't wait for some "other" sort of life form to be found elsewhere....Mars, Europa...even more exciting would be non GCTA base Earth life.

[renormalised (Carl)]

Originally Posted by StephenM

That's right Carl. The key point here is that its a synthetic genome, rather than "synthetic life". The success here relects both our understanding of bacterial genomes, and also the revolution that has taken place in DNA synthesis (and sequencing) technologies in the last few years. The cost of synthesizing genes has now reached a point where, for many applications, it is cheaper and faster to get your gene of interest synthesized rather than cloning it yourself. We have completely redesigned and ordered quite a few synthetic genes in my lab in the last 18 months, at less than $800 per gene! But this demonstration is gene synthesis on a whole new scale!

Interestingly when they first introduced this synthetic genome it failed to replicate, and in just 3 months they were able to identify a single nucleotide error that prevented replication!

This report is definately a significant event in the history of biology and biotechnology.

Cheers,
Stephen

Can you imagine what it would take to produce a completely artificial lifeform from first principles. You'd have to make the amino acids, join them together in base pairs in an artificial DNA, code however many base pairs you needed to create an entire set of genes for the organism, wrap them into chromosomes and then create an entire suite of proteins to make up all the organelles and such for a cell...it would be one hell of a job and something that's a wee bit beyond us for the present. Then you'd have to find some way of giving life to it all, otherwise it'd be just a bag of proteins and nucleic acids wrapped up in funny little structures.

It's like saying what's the difference between a dead cell and a living one....nothing, except one cell is alive, the other isn't. All the chemistry and such is still there in the dead cell, it's just not working. That's what they don't know...what is it that makes it work.

[gary]

Originally Posted by StephenM

Interestingly when they first introduced this synthetic genome it failed to replicate, and in just 3 months they were able to identify a single nucleotide error that prevented replication!

Stephen,

When I read the Press Release about the original error that made the cell fail
to replicate, it instantly reminded me of a similar problem that anyone who
has attempted to write a compiler for a programming language is likely to have faced.
I am sure anyone who has done an undergraduate course in compiler design where
one of the tasks was to write your own compiler will relate to this.

When you create a compiler for some programming language, historically
you first wrote it in some other high level language or even assembly language
first. You then wrote another version of the complier in its own language.
So for example, if you were creating a C compiler for a particular CPU
architecture, you might first write a C compiler in assembler and then a C
compiler in C. What you would then do is compile your C compiler written
in C using your C compiler written in assembler. This would then result in
a new executable. Using this executable, you would then attempt to compile
the C complier written in C with itself. At this point you might typically encounter
a bug and need to correct it. Once you finally got the C compiler to compile itself,
as a final test you would then make sure that the binary executable image created
as a result of compiling itself would be identical to the binary executable image
that was used to compile it. You would thus reach a stable executable
analogous to a bug free self replicating DNA sequence.

Best regards

Gary

[gary]

Originally Posted by Lee

I hope that they have inserted specific genes to allow this little bug to be knocked over by our basic antibiotics, or more to the point, have they worked out a way to prevent it picking up resistance genes??

Hi Lee,

According to a paragraph in the Press Release, the researchers are now mostly
interested in, as they put it "whittling away at the synthetic genome and repeating
transplantation experiments until no more genes can be disrupted and the genome is
as small as possible. This minimal cell will be a platform for analyzing the function
of every essential gene in a cell."

Earlier in the same document they mention, "We can now begin on our ultimate
objective of synthesizing a minimal cell containing only the genes necessary
to sustain life in its simplest form. This will help us better understand how cells
work."

I noted one of the three chosen quotations they embedded in the genome
was by Richard Feynman and it says "What I cannot build, I cannot understand".
This choice of quotation appears to match the stated goals of the researchers.

So in a nutshell, I think rather than adding stuff, the focus currently is in stripping
out as much stuff as possible as long as it keeps on working. That little
minimalist machine would then be the starting point for reverse engineering
how the cells really work. I would then envisage that beyond that a goal would
then be able to code and engineer these things from scratch with the same depth
of understanding as if we had originally created them ourselves.

One might speculate that self-checking repair mechanisms during replication
will be a key focus for many researchers in the future.

[wavelandscott (Scott)]

"Any sufficiently advanced technology is indistinguishable from magic..."
Arthur C. Clarke, "Profiles of The Future", 1961 (Clarke's third law)
English physicist & science fiction author

Exciting stuff and getting closer to magic all of the time...

[renormalised (Carl)]

Originally Posted by kinetic

Carl,
I woke up this morning and looked out over my dew covered lawn
at 5am, the kookaburras starting to stir, the whole house still asleep.
Pure heaven, these hours before dawn.
I saw Jupiter, shining beautifully through some thin, high cloud.
I thought: what a truly wonderful thing we are, a collection of cells which
are mostly water, but assembled in a way that I could stand there and
take in the light from Jupiter, know what it is, read about it in a book,
live in an age where the smartest few of our species had sent a spacecraft
across the gulf of space between it and sent back photographs of it.
What an amazing assembly of these cells we call life, we are.
Then I thought of this thread, that I have been following a while.

I hope this research can one day find what it is in our make up,
maybe right down to the cells and genome etc, what it is that
also makes us want to kill each other, destroy animal habitats, cause
us to make whole species extinct .....where does that great evil come
from...

Steve

Yep, mate, it makes you wonder, doesn't it. Although, the thought of getting up at 5am for some people is tantamount to crazy, so you could say in those terms what you wrote there is "prozac-ick"

Science is great at discovering the mechanics behind the reasoning for something's existence, but when it boils down to the why of it all, it falls very short. In most cases it fails, especially when it comes to the big questions. Scientists can pontificate all they like about "the natural order of things", "random chance" and "as a consequence of the physical laws of nature", but they know themselves deep down, even if they don't want to admit it to themselves because of their training and mindset, that there's a whole lot more to the meaning of existence than just pure, randomly contrived, physical laws which just happen to pop into existence in an event which they have little real understanding about. There's a lot more going on here and they don't want to admit it, or would rather see it go away, so they can get back to working within their limited paradigm of knowledge.

Science is limited by its own way of doing things, in how it sees and measures the reality of this world. Yes, we will discover a great many things using science as our tool for discovery, but there are other things in reality which no matter how well we understand the mechanics of their workings and how they came to being, we will always be grasping for the why of their existence. To understand will require an intuitive reasoning that is beyond the boundaries of how science operates at present. It may even require something that science abhors in every sense...faith. Not faith in a religious sense, but faith in our abilities to look past the obvious, the "scientific", and see the meaning behind the why of things. To feel that what we have deduced from our reasoning and our insight is correct...even if only approximately. We will never know exactly why, because that would require us to have perfect knowledge of everything, and despite what many scientists may say or think, that is something we can never achieve. We may have access to all the knowledge, but we could never assimilate it all at once. That would mean we would be God (in the strictest definition) and that is something we are not.

[marki]

Ahh philosophy, the art of moving in ever decreasing spirals until one disappears up ones own fundernetal orriface . This stuff is far more interesting then it is scary. The possible implications are huge both for the cure of disease /making super humans and the scope of absolute chaos we can create when used for the wrong reasons or simply stuff up. Ethics smethics I say, I can't wait for evolution to do the job, bring it on .

Mark