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On May 23 2010 12:11 ThunderChunky wrote:Show nested quote +On May 23 2010 11:49 Servolisk wrote:
Such as what?
How do you get from this to designing bacteria doing w/e like converting greenhouse gases (in a new way)? He still wants to create a minimal genome to use as a base for engineering other functions.
What is the point of having a minimal (Mycoplasma) genome if your goal is to engineer novel functions (plus the idea of a minimum genome needs context, and you need to know the majority of gene functions rather than their sequence to be useful as use as a platform IMO)? The is a separate challenge. I am not seeing any reason why this offers a more convenient system than various current systems. I would if, first, the function and role of every gene were known
This will facilitate that because you can delete and add hundreds of genes at once. The techniques could also be used to design and synthesize whole chromosomes to complement an existing cell.
You could already delete hundreds of genes at once. This made no advances in that area.
As for adding... what is the goal? For example the greenhouse gas conversion proposal, people already make transgenic organisms to do that type of thing in the scale of ~10 genes (not greenhouse gases AFAIK but similar concepts). No one is going to take that seriously...to add a genome to do these type of jobs... because it would be equivalent at the very best and counterproductive in all likelihood... -_____-
I am just going by the example put forth in the OP. Is there some other example where it is useful to transplant a whole genome/huge number of genes which you have no idea what they do or how to control?
Obviously, there are still a lot of hurdles to overcome in the field, but converting a large digitized sequence to an actual one is now possible and conceivably will be a powerful tool for synthetic biologists.
Ability to input a large sequence has been improved but that is quite preliminary. It took them many years to copy the genome from mycoplasma, put it back together, and then put it back inside. That just sounds like a large project rather than an improvement of technology. They had unlimited funding and a very large team and a large amount of time, how is that going to be a tool for other biologists?
And that has nothing to do with an organism that has special or novel functionality.
And since the functions of cells he proposes to engineer are a separate project also possible using previously available modified cells I am not seeing what has been added ...
If all scientists were like him when people were able to transplant a pig organ to humans they called it a new species.
Altogether there seems to not be any new science that has been done here aside from the scale. It would be nice if there was but I have not been able to parse it out from the grandiose claims and sci-fi crossovers, or their publication in Science.
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On May 23 2010 13:01 mrproper wrote:Show nested quote +On May 23 2010 11:04 Servolisk wrote:+ Show Spoiler +2008: Craig Venter claims to invent artificial life. And by that he means he took the smallest genome and cut out some things which were unnecessary, and called the remainder man-made artificial life.
2010: Craig Venter claims to invent synthetic life. AFAIK he took the thing from 2008 and rebuilt it using custom nucleotide incorporation, which is a standard technology for a while now on a typically 1/1000 smaller scale.
So I am 99% sure he just redid something which was not artificial life in 2008, and redid it in a pain in the ass way only a large corporation could do, for the sake of claiming they created "synthetic life" and "heralded a new era"? How humble.
It seems funny they try to give off the image you can code a genome like you can write a code when they say they have gone from digital computer information to a functional genome.
Will this artificial organism here do anything itself besides model a large scale gene transplant?
What will the uses be?
What do you learn genetically from this approach?
What will you be able to do with a "artificial organism" better than with the many modified organisms using current approaches? I.e., if someone wants to convert greenhouse gases as this guy does, is there a reason why it would be better to have a chromosome painstakingly derived and created in a time consuming manner from a small parasitic bacteria-which has nothing to do with this proposed function-as opposed to the use of a number of existing bacteria which have can already be manipulated into catalyzing such reactions? Just because he COPIED an existing genome and put it back into a cell in a roundabout way does not mean he has control to make synthetic organisms that do whatever he wants. I just see a preliminary work in the methods addition of very larger than normal genetic elements into cells. Which is good... but what kind of douche who deletes portions of an existing, small genome and claims to create artificial life and even more sickenly boastful things. What I understand is that he wrote the genetic code from parts, he did not copy the whole thing, he created a new unique species from scratch. He basically added meta-information in it (website urls, decoding instructions for easter eggs) and injected this new code in an existing functional donor cell. Next division, the daughter cells are very close to the new species both in function and in structure. It is a man made design, it did not appear in a natural way. What uses? Well he explained we can use them as cheap workers for chemical tasks, like cleaning stuff, creating oil, energy converters, maybe even food, disease inhibitors.... etc...
Er, it is difficult to understand "added meta-information in it (website urls, decoding instructions for easter eggs".
I read their paper and they used a modified genome which was 5/6 the Mycoplasma mycoides genome. How is that creating a unique species from scratch..plz.. ?
And what do any of your uses have to do with having a synthetically created ~5/6 Mycoplasma genome. "Creating oil" is a completely separate undertaking which has nothing to do with anything on the Mycoplasma genome.
The person above you posted something similar, Diesel synthesizing bacteria... It did not use genome transfer and it is very, very difficult to imagine how that could be useful.
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On May 23 2010 13:10 Servolisk wrote:Show nested quote +On May 23 2010 12:11 ThunderChunky wrote:On May 23 2010 11:49 Servolisk wrote:
Such as what?
How do you get from this to designing bacteria doing w/e like converting greenhouse gases (in a new way)? He still wants to create a minimal genome to use as a base for engineering other functions. What is the point of having a minimal ( Mycoplasma) genome if your goal is to engineer novel functions (plus the idea of a minimum genome needs context, and you need to know the majority of gene functions rather than their sequence to be useful as use as a platform IMO)? The is a separate challenge. I am not seeing any reason why this offers a more convenient system than various current systems. I would if, first, the function and role of every gene were known [/B]
The point would be to have a minimal life form to start off with that doesn't have any extraneous functions or metabolic pathways to interfere with your design. If the future plan is to design an organism from the ground up, having an idea of the minimal sets of genes will be useful.
You could already delete hundreds of genes at once. This made no advances in that area.
That is not true. It would be very challenging to delete sets of random genes scattered across a genome. Having full genome control allows from much more sophisticated changes than what can be done with standard techniques.
As for adding... what is the goal? For example the greenhouse gas conversion proposal, people already make transgenic organisms to do that type of thing in the scale of ~10 genes (not greenhouse gases AFAIK but similar concepts). No one is going to take that seriously...to add a genome to do these type of jobs... because it would be equivalent at the very best and counterproductive in all likelihood... -_____-
I am just going by the example put forth in the OP. Is there some other example where it is useful to transplant a whole genome/huge number of genes which you have no idea what they do or how to control?
In the future we will have ideas of what the genes do and how to control them.
Ability to input a large sequence has been improved but that is quite preliminary. It took them many years to copy the genome from mycoplasma, put it back together, and then put it back inside. That just sounds like a large project rather than an improvement of technology. They had unlimited funding and a very large team and a large amount of time, how is that going to be a tool for other biologists?
The first human genome sequence cost billions of dollars, now it's only a few thousand dollars and the quality is better. In this work they synthesized a 1Mbp piece of DNA from scratch. The hope is that synthesis technology will improve in cost as it did for sequencing. Future biologists will be able to type out a very long sequence and have it made for them. What they use that sequence for will be up to them.
And that has nothing to do with an organism that has special or novel functionality.
And since the functions of cells he proposes to engineer are a separate project also possible using previously available modified cells I am not seeing what has been added ...
If all scientists were like him when people were able to transplant a pig organ to humans they called it a new species.
Altogether there seems to not be any new science that has been done here aside from the scale. It would be nice if there was but I have not been able to parse it out from the grandiose claims and sci-fi crossovers, or their publication in Science.
You're putting words in his mouth that he never said. He didn't make any grandiose claims in the publication and it explains very clearly what he accomplished with his previous work and how this is an improvement on that. He did say that he calls this a synthetic cell and he explains his rationale for doing so.
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[QUOTE]On May 23 2010 14:04 ThunderChunky wrote:
[QUOTE]On May 23 2010 13:10 Servolisk wrote:
[QUOTE]On May 23 2010 12:11 ThunderChunky wrote:
[QUOTE]On May 23 2010 11:49 Servolisk wrote:
The point would be to have a minimal life form to start off with that doesn't have any extraneous functions or metabolic pathways to interfere with your design.[/QUOTE]
It is possible but it is doubtful that what is minimum for Mycoplasma (under whatever laboratory conditions they had used) is minimum in other contexts. There is a lot of lost beneficial functions in the unknown genes that are removed just because they were not essential to survival.
It is hard to imagine that when you do not know the function of most of these genes you can select which will be optimum as a backbone. Trying to make an optimal backbone is a more difficult task than trying to create designs in existing cells, and I doubt that is done in 50 years barring a completely independent break through. -_- E.g., this "synthetic life" does not have a normal nucleus and the majority of DNA regulating enzymes for the cell won't function properly if it is not in a nucleus and bound to histones.
There are more feasilble ways to handle the problem you mentioned.
[QUOTE]
There are a variety of small and large scale gene silencing methods. If you wanted to delete a large amount of scattered genes which have no pattern then yes it would be hard.
[QUOTE]
In the future we will have ideas of what the genes do and how to control them.[/QUOTE]
Maybe, but that is a very large task not on the horizon.
[QUOTE]
The first human genome sequence cost billions of dollars, now it's only a few thousand dollars and the quality is better. In this work they synthesized a 1Mbp piece of DNA from scratch. The hope is that synthesis technology will improve in cost as it did for sequencing. Future biologists will be able to type out a very long sequence and have it made for them. What they use that sequence for will be up to them.[/QUOTE]
It cost them 15 years and 40 million iirc. In their publication, the methods were standard. I did not see what they have done to improve things. In the genome sequencing case new technology and methods were developed. The publication would be the appropriate place to hear about it, so it seems there was not any innovation, just a end product without convincing uses.
[QUOTE]
You're putting words in his mouth that he never said. He didn't make any grandiose claims in the publication and it explains very clearly what he accomplished with his previous work and how this is an improvement on that. He did say that he calls this a synthetic cell and he explains his rationale for doing so.
[/QUOTE]
Yes, for the journal publication... Outside of that he has been busy heralding a new dawn for mankind? :o Did anyone notice the last dawn in 2008? -_- Let's see if any synthetic biologists who are working on the goals he is interested in actually use his development...
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On May 23 2010 15:53 Servolisk wrote:
It is possible but it is doubtful that what is minimum for Mycoplasma (under whatever laboratory conditions they had used) is minimum in other contexts. There is a lot of lost beneficial functions in the unknown genes that are removed just because they were not essential to survival.
There can be many minimal genomes and we will probably learn more from having many than having only one. It is a worthy goal to pursue for synthetic biologists who would like to be able to create life from scratch.
It is hard to imagine that when you do not know the function of most of these genes you can select which will be optimum as a backbone. Trying to make an optimal backbone is a more difficult task than trying to create designs in existing cells, and I doubt that is done in 50 years barring a completely independent break through. -_- E.g., this "synthetic life" does not have a normal nucleus and the majority of DNA regulating enzymes for the cell won't function properly if it is not in a nucleus and bound to histones.
There are more feasilble ways to handle the problem you mentioned.
The problem of making a minimal genome? The problem of reducing the cost to synthesize long pieces of DNA?
Bacteria do not have a nucleus and they do not have histones, they are much less complex than eukaryotic cells. In some model bacteria we know the functions of a lot of the genes and within out lifetimes will be able to understand all the gene regulation taking place in the cell.
Maybe, but that is a very large task not on the horizon.
Not for a lot of microbiologists.
It cost them 15 years and 40 million iirc. In their publication, the methods were standard. I did not see what they have done to improve things. In the genome sequencing case new technology and methods were developed. The publication would be the appropriate place to hear about it, so it seems there was not any innovation, just a end product without convincing uses.
A lot of that time and money was because of mistakes. They learned things a long the way and developed the technology. They developed new strategies for synthesizing long pieces of DNA. It is same thing that happened with sequencing technology during the genome project.
Yes, for the journal publication... Outside of that he has been busy heralding a new dawn for mankind? :o Did anyone notice the last dawn in 2008? -_- Let's see if any synthetic biologists who are working on the goals he is interested in actually use his development...
Where did he say he created a new species?
When the rest of the synthetic biologists catch up to him they will start to use his technology.
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On May 22 2010 08:09 DallasTx wrote:
I really dislike man playing the role of god :/
I guess you think differently from me. I dislike god playing the roll of man.
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On May 22 2010 02:05 icystorage wrote:
man playing God. i hope man doesnt abuse this if it gets more advanced
Can't play the part of something that doesn't exist.
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Basically we are a long way away from something actually useful.
The engineering exercise was completed, that is all.
All they did was create a copy of an existing "wild type" bacteria. They still don't understand how to alter the DNA to create something.
What they're trying to develop is chromosomes for bacteria that could produce a useful vaccine perhaps, or maybe produce some type of fuel.
When they manage to design a NEW bacterial cell that actually does something, that will be the major step.
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On May 23 2010 18:02 Shrewmy wrote:Show nested quote +On May 22 2010 02:05 icystorage wrote:
man playing God. i hope man doesnt abuse this if it gets more advanced Can't play the part of something that doesn't exist.
stop throwing the topic discussion into another religious tangent.
I think this is really interesting. This is just the beginning into this new field, but I'm not sure whether i'm supportive of it or not. There may be dangers to it that we can never be aware of until some time after use, could be bad..
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The first computer was called the ENIAC (Electronic Numerical Integrator And Computer). The contract to make it was signed on June 5, 1943, and the first one manufactured was on February 14, 1946. It was designed by John Mauchly and J. Presper Eckert of the University of Pennsylvania. For the very earliest computer, see the related link to the Antikythera Mechanism. It was also made to help humans to be better at spelling
We are way less than a century past the first pathetic excuse for a computer....
The shit they are doing is absolutely impressive. Beyond impressive.
We are decoding the program that writes life and beginning to tinker with it.
So what if we are not the masters of it yet?
Achieving what we have in the timescale we have is absolutely insane, I don't understand those who do not seem to appreciate that.
I would rather hail this man as a prophet than attempt to downplay his and his teams successes.
On the subject of man playing god.... hell yes!
Watching the 2008 talk made me feel proud to be part of the human race.
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interesting how they created a cell out of synthetic DNA
i dont find it too useful though since organs can already be grown to save lives  but its another field that can be explored with almost unlimited possibilities.
^^Why are you talking about computers?
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This is quite rediculous ;/ wanna reproduce? Its called SEX  its much easier, free, and much less risky, not to mention both parties have a great time ;p
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On May 23 2010 21:46 ReachTheSky wrote:This is quite rediculous ;/ wanna reproduce? Its called SEX its much easier, free, and much less risky, not to mention both parties have a great time ;p
not all the time :O
i really cant comprehend this stuff but it seems really interesting. i have no idea what civilization will be like in the next century
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On May 23 2010 21:13 Mykill wrote:interesting how they created a cell out of synthetic DNA i dont find it too useful though since organs can already be grown to save lives but its another field that can be explored with almost unlimited possibilities.
Contradict much?
From OP:
The researchers copied an existing bacterial genome. They sequenced its genetic code and then used "synthesis machines" to chemically construct a copy.
On May 23 2010 21:13 Mykill wrote:
^^Why are you talking about computers?
LOL I HAVE NO IDEA 
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On May 23 2010 23:08 Reason wrote:
From OP:
The researchers copied an existing bacterial genome. They sequenced its genetic code and then used "synthesis machines" to chemically construct a copy.
Actually, no...
The researchers constructed a bacterium's "genetic software" and transplanted it into a host cell.
They copied a genome 3 years ago. Now they created a brand new genome, from existing parts, but the species they created does not exist in nature, and has been created in a single generation. That is the topic title.
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On May 23 2010 23:33 mrproper wrote:Show nested quote +On May 23 2010 23:08 Reason wrote:
From OP:
The researchers copied an existing bacterial genome. They sequenced its genetic code and then used "synthesis machines" to chemically construct a copy.
Actually, no... The researchers constructed a bacterium's "genetic software" and transplanted it into a host cell.They copied a genome 3 years ago. Now they created a brand new genome, from existing parts, but the species they created does not exist in nature, and has been created in a single generation. That is the topic title.
Actually, yes...
I wasn't making a comment on this directly or saying that this was the most recent stage of development, I was pointing out that computers play a central role in these experiments, citing this as evidence.
In future make sure you read a post thoroughly before attempting to refute it and patronize the poster.
For anyone making comments along the lines of this :On May 22 2010 02:19 Keniji wrote:
(don't get me wrong, it's huge and pretty impressive but not as big of a milestone as Venter like to present it.)
I'll quote Venter's own description of this breakthrough from the video:
A "baby step".
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On May 23 2010 21:13 Mykill wrote:interesting how they created a cell out of synthetic DNA i dont find it too useful though since organs can already be grown to save lives but its another field that can be explored with almost unlimited possibilities. ^^Why are you talking about computers?
...Not impressive because we can do something completely different by other means?
-_-
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On May 23 2010 20:21 Reason wrote:
The first computer was called the ENIAC (Electronic Numerical Integrator And Computer). The contract to make it was signed on June 5, 1943, and the first one manufactured was on February 14, 1946. It was designed by John Mauchly and J. Presper Eckert of the University of Pennsylvania. For the very earliest computer, see the related link to the Antikythera Mechanism. It was also made to help humans to be better at spelling
We are way less than a century past the first pathetic excuse for a computer....
The shit they are doing is absolutely impressive. Beyond impressive.
We are decoding the program that writes life and beginning to tinker with it.
So what if we are not the masters of it yet?
Achieving what we have in the timescale we have is absolutely insane, I don't understand those who do not seem to appreciate that.
I would rather hail this man as a prophet than attempt to downplay his and his teams successes.
On the subject of man playing god.... hell yes!
Watching the 2008 talk made me feel proud to be part of the human race.
I agree.
But I like to call the Z3 the first computer 
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On May 23 2010 13:10 Servolisk wrote:Show nested quote +On May 23 2010 12:11 ThunderChunky wrote:On May 23 2010 11:49 Servolisk wrote:
Such as what?
How do you get from this to designing bacteria doing w/e like converting greenhouse gases (in a new way)? He still wants to create a minimal genome to use as a base for engineering other functions. What is the point of having a minimal ( Mycoplasma) genome if your goal is to engineer novel functions (plus the idea of a minimum genome needs context, and you need to know the majority of gene functions rather than their sequence to be useful as use as a platform IMO)? The is a separate challenge. I am not seeing any reason why this offers a more convenient system than various current systems. I would if, first, the function and role of every gene were known Show nested quote +
This will facilitate that because you can delete and add hundreds of genes at once. The techniques could also be used to design and synthesize whole chromosomes to complement an existing cell.
You could already delete hundreds of genes at once. This made no advances in that area. As for adding... what is the goal? For example the greenhouse gas conversion proposal, people already make transgenic organisms to do that type of thing in the scale of ~10 genes (not greenhouse gases AFAIK but similar concepts). No one is going to take that seriously...to add a genome to do these type of jobs... because it would be equivalent at the very best and counterproductive in all likelihood... -_____- I am just going by the example put forth in the OP. Is there some other example where it is useful to transplant a whole genome/huge number of genes which you have no idea what they do or how to control? Show nested quote +
Obviously, there are still a lot of hurdles to overcome in the field, but converting a large digitized sequence to an actual one is now possible and conceivably will be a powerful tool for synthetic biologists.
Ability to input a large sequence has been improved but that is quite preliminary. It took them many years to copy the genome from mycoplasma, put it back together, and then put it back inside. That just sounds like a large project rather than an improvement of technology. They had unlimited funding and a very large team and a large amount of time, how is that going to be a tool for other biologists? And that has nothing to do with an organism that has special or novel functionality. And since the functions of cells he proposes to engineer are a separate project also possible using previously available modified cells I am not seeing what has been added ... If all scientists were like him when people were able to transplant a pig organ to humans they called it a new species. Altogether there seems to not be any new science that has been done here aside from the scale. It would be nice if there was but I have not been able to parse it out from the grandiose claims and sci-fi crossovers, or their publication in Science.
Why are you blabbering about science you clearly have no understanding of?
A minimal genome is advantageous in that it is far simpler to build off of and reliably predict what will develop without interference. Starting with a more advanced genome means that your introduced material has to compete with everything else that has been evolved for irrelevant purposes to your research. The cell might not even live because of these conflicts, which was one of the major hurdles overcome in this breakthrough - the majority of Ventur's press statement is devoted to describing the years of work and techniques involved in transforming their reduced ("synthetic") genome into a self-replicating cellular species. They literally hijacked a mycoplasma genitalium cell by forcing in their DNA and tossed out 100% of what was already there, a nuclear coup d'etat - research since 2008 was focused on getting their introduced genome to "boot up" in the cell.
That is why it is called synthetic "life" and not just genetically engineered life. They now have a species to base future work off of that is far simpler, more expressible, and better understood than anything else in nature.
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EPT
