11 ms·

'Artificial life' breakthrough announced by scientists

280 points by blogimus 16y ago

tocomment 16y ago
Here are my questions about this, hope you smart folks don't mind chiming in: How do you physically put DNA into a cell? A very small needle? Or is there something fancier? How were the synthesized pieces of DNA produced? Very tiny robotic hands pushing the molecules together in the right sequence? How did they stitch together the synthesized pieces of DNA? What would say which pieces go with which?
- aheilbut 16y ago
  Bacteria will often take up DNA from their environment, and this ability, called "competence" is widely used in molecular biology. In this case, they treated the cells with a chemical called polyethylene glycol, which increases the efficiency by which the cells can pick up the DNA molecules. The procedure for transplanting genomes was described by the same group in a paper in 2007. It is possible to use a small needle ("DNA microinjection") to inject DNA into cells; one can also use an electric field to disrupt the cell membrane and force DNA into a cell, which is called electroporation. In this case though, the PEG transformation was sufficient (and because these artificial chromosomes were so large, they might not survive being shot through a needle or zapped with electricity too well). The initial pieces of DNA (oligonucleotides) are synthesized chemically - the components are added to a reaction one at a time, and the reaction is controlled so that at each step, only one base gets added. There is a lot of chemistry optimization and QC to be able to make relatively long fragments accurately. They ordered the building block pieces (1080 bases long) from a company called Blue Heron, which specializes in putting together long DNA molecules. The sequences were designed to be partially overlapping, so that the complementary sequences could fit together. Overlapping pieces of DNA can be combined by a process called homologous recombination. There is existing machinery in the yeast cells that they used to join together such complementary sequences. The molecules were assembled hierarchically, so they first made 10kb fragments, then put 10 x 10kb together to make 100kb fragments, and then finally put the 10 100kb fragments together. The overlapping sequences at the ends determined which fragments will stick together.
  - tocomment 16y ago
    Wow thanks. That explains a lot. What's PEG? The electrical method you mentioned? So if the DNA pieces overlapped did that overlapping base pairs somehow get removed when the pieces were joined? Otherwise I'd think the next final DNA sequence would look a lot different from what they were intending to copy.
    - aheilbut 16y ago
      PEG is the abbreviation for PolyEthylene Glycol. Just a chemical they add that makes the transformation work more efficiently. DNA, as you probably know, is a double-stranded molecule, and the strands have complementary sequences. When the overlapping pieces are joined, one strand of one molecule overlaps with its complement on the other piece, and vice versa - the pieces aren't just joined end-to-end. see http://en.wikipedia.org/wiki/Homologous_recombination http://en.wikipedia.org/wiki/Homologous_recombination for all the details.
amichail 16y ago
They just copied the genome of an existing micro-organism. Making changes to the genome to accomplish some task is much harder to do.
- Anon84 16y ago
  Mutants that differ on specific genes are created regularly to study the effects of each mutation.
- raimondious 16y ago
  You say they "just copied the genome" like that's easy to do. This is a landmark because they synthesized the entire genome using nothing but the sequence stored in a computer, much more difficult than replicating a pre-existing piece of DNA.
  - amichail 16y ago
    Even so, calling it artificial life is highly misleading.
    - raimondious 16y ago
      I think it's pretty accurate. There was only information to begin with, and now there is life. It happens that information was gained from a pre-existing cell, but this new cell has nothing to do with the cell it's derived from, it's made completely by the work of humans. That has never happened before. Edit: However, I know what you mean about it not being 100% artificial, as in completely designed by humans: Maybe "synthetic life" is better? Further edit: More than using a pre-existing genome, what makes it not completely artificial is that they had to put their DNA into another cell, basically cloning using synthesized DNA rather than natural DNA.
    - FlorinAndrei 16y ago
      I agree. They wrote a new OS and uploaded it into existing hardware. Still a great feat, but not quite 100% "artificial life" yet.
glymor 16y ago
Better write up: http://arstechnica.com/science/news/2010/05/first-functional-synthetic-bacterial-genome-announced.ars http://arstechnica.com/science/news/2010/05/first-functional...
- rms 16y ago
  Or http://www.sciencemag.org/cgi/content/full/328/5981/958 http://www.sciencemag.org/cgi/content/full/328/5981/958
  - raimondious 16y ago
    My favorite part from that article: So that the assembled genome would be recognizable as synthetic, four of the ordered DNA sequences contained strings of bases that, in code, spell out an e-mail address, the names of many of the people involved in the project, and a few famous quotations.
    - Evgeny 16y ago
      I guess sooner or later the random mutations may make these string "corrupted".
      - Devilboy 16y ago
        I hope they included checkbits!
        zackattack 16y ago
        it may be a misconception but i think that checkbits are a feature of organic dna?
        biotech 16y ago
        Yep! There is some error-checking built into dna-replication. The protein that does the replication is called DNA Polymerase. From its wikipedia article: Error correction is a property of some, but not all, DNA polymerases. This process corrects mistakes in newly-synthesized DNA. When an incorrect base pair is recognized, DNA polymerase reverses its direction by one base pair of DNA. The 3'-5' exonuclease activity of the enzyme allows the incorrect base pair to be excised (this activity is known as proofreading). Following base excision, the polymerase can re-insert the correct base and replication can continue.
orblivion 16y ago
Call me a luddite, genetic engineering gives me the willies.
- macrael 16y ago
  I'm with you, but it is pretty fascinating all the same.
  - orblivion 16y ago
    Yeah it's definitely cool.
- bh42 16y ago
  Luddite. In all seriousness, the dangers brought up in the article can only come from a person lacking significant knowledge of bacteria. Unimaginable numbers of bacteria permeate every part of the world, including miles within the earth, deep sea volcanic vents, radioactive waste, the rain drops falling on our heads, and us, up our noses, in our skin pores, our guts, etc. Those simple bacteria evolve at staggering rates, and swap genes like DJ Danger Mouse mixing tracks. Any new synthetic, or extraterrestrial, or magical, life form would have to compete. And unless you believe in magic it is unlikely to out-compete in a pre-existing niche. The grey goo danger often thrown at nano-tech, is possible only if we violate one or more of the basic laws of thermodynamics. And when it comes to antibiotic resistant bacteria, well we are already doing a great job of breeding those within ourselves. But if you grew a barrel full of MRSA and then poured it down your toilet, the SA wold quickly lose its metabolically expensive MR. Because there is no Methicillin in the sewer, the resistance to Methicillin is a disadvantage. And the only way the Staphylococcus aureus could survive is if it dumped this feature. But luckily you're probably taking antibiotics so you are a niche where MRSA can out-compete and thrive.
  - WilliamLP 16y ago
    > And unless you believe in magic it is unlikely to out-compete in a pre-existing niche. Cars are faster than land animals. Planes are faster than birds. Not being constrained by needing to have come from slow gradual iteration might open some possibilities, some terrifying. Biology doesn't produce the wheel. To consider this as a possibility is not to believe in magic.
MikeCapone 16y ago
This is a huge deal, and I'm not surprised to see that Craig Venter had something to do with it. Kudos!
- joe_the_user 16y ago
  This is a nice step for technology and a really huge deal for human culture and religion. A certain Someone said once "Let the earth put forth vegetation, plants yielding seed, and fruit trees bearing fruit in which is their seed, each according to its kind, upon the earth." That certain Someone later said: "Behold, man has become like one of us..."
  - metamemetics 16y ago
    I can't decipher which English-speaking reader of the New Revised Standard Edition post 1989 you are referring to, how elusive!
  - CamperBob 16y ago
    "Whoa, hold on there. Get your own dirt." - God /card-carrying atheist, but always liked that joke
  - rbanffy 16y ago
    > That certain Someone later said: "Behold, man has become like one of us..." Walt Disney may have had a number of character flaws, but I always found the "if you can dream it, you can do it" quote very inspiring.
sheldonwt 16y ago
Advancements like this make it feel exciting to be young and have so much time ahead of you. The future is bright. Science is key.
- jjs 16y ago
  Advancements like this make it feel exciting to be young and have so much time ahead of you. What, you're still using your original telomeres?
itistoday 16y ago
Oddly enough this makes me feel a bit impotent. Here I am playing with my 1's and 0's... like a caveman. :-p
- Anon84 16y ago
  You're using base 2 (0 and 1), they are using base 4 (A, G, C and T)... Not that different, really.
  - deleted 16y ago
    [deleted]
    - crystalis 16y ago
      Yeah, all computers can't recognize jokes.
  - dublinclontarf 16y ago
    Could this mean a step towards biological computers?
eduardoflores 16y ago
Announcement here http://www.jcvi.org/cms/research/projects/first-self-replicating-synthetic-bacterial-cell/overview/ http://www.jcvi.org/cms/research/projects/first-self-replica... with the press release, a FAQ and some fact sheets (and the video is promised to be available soon)
deleted 16y ago
[deleted]
stavrianos 16y ago
they've got root
- haydenchambers 16y ago
  All your base pairs belong to us
danielharan 16y ago
So when do we get dinosaurs?
- deleted 16y ago
  [deleted]
phaedrus 16y ago
This is surprisingly like the first step you'd take if you were about to start hacking the firmware on an embedded board: before you change bits, you upload a known good firmware to prove your programming process is working correctly.
- JeanPierre 16y ago
  But the next steps looks more like software on a computer: You'll have to fix all those compilation-errors on first run, then look out for bugs in the software. Finally, when you ship the software, people use it and report other bugs. And since you can't update running processes at the current moment, you need to terminate and replace it.
- plesn 16y ago
  It's more like a compiler: bootstrapping is not complete yet though, the bacteria produced should be able to produce the rest of the entire cell.
zokier 16y ago
This is awesome. Literally, awe inspiring. We now have a compiler for the code which is DNA. Now we just need a "Hello, world!" app :)
- jacquesm 16y ago
  We'll see if it is awesome, if the compiler is buggy it might turn out to create a 'killall' app instead. This is great news, but with this new power comes also a very large responsibility.
yu 16y ago
Nature article http://www.nature.com/news/2010/100520/full/news.2010.253.html http://www.nature.com/news/2010/100520/full/news.2010.253.ht... Nature asks and eight experts comment on significance http://www.nature.com/news/2010/100520/full/news.2010.255.html http://www.nature.com/news/2010/100520/full/news.2010.255.ht...
mortenjorck 16y ago
DNA: Now jailbroken.
run4yourlives 16y ago
Mandatory: http://www.reddit.com/r/science/comments/c6dea/synthetic_life_breakthrough_announced_by/c0qeydc http://www.reddit.com/r/science/comments/c6dea/synthetic_lif...
- michael_nielsen 16y ago
  That comment can safely be ignored. It makes lots of vague accusations about Venter, and one concrete accusation - that Venter is responsible for patents on genes involved in breast cancer. That accusation is wrong: it's a reference to the BRCA patent by Myriad genetics, which has nothing to do with Venter.
jamesbritt 16y ago
Gripe: "artificial life" already has a somewhat lengthy history of usage, referring to emulating biological activity or traits in software or hardware. It's often shortened to just alife or a-life. It's related to genetic algorithms, genetic programming, and the like. It would be nice if the using-real-chemicals-and-alive-stuff hacking were called "synthetic life", or something to distinguish it from existing terminology.
- nooneelse 16y ago
  That use maybe should have been "simulated life" all along, so as to be more exact. This is a living organism that is artificially made, "artificial life" applies to it just as much as the other subject. Though the more specific terms that capture the way in which their somethings are artificial are good too.
  - jamesbritt 16y ago
    'This is a living organism that is artificially made, "artificial life" applies to it just as much as the other subject.' Maybe. But if you end up with a living organism, then that it's not artificial life; it's life (albeit artificially manufactured) . Whereas the software stuff is never anything but artificial. Long run I'd expect anything that's alive to be called life, regardless of the process that lead to it.
- amalcon 16y ago
  Are we sure that the CS term predates the biological term? I mean, we might not have really succeeded in creating (biological) artificial life in the 1950's, but someone was almost certainly trying.
- aheilbut 16y ago
  The field actually does typically call itself "synthetic biology," rather than "artificial life".
dmn001 16y ago
very informative video on guardian from Craig Venter: http://www.guardian.co.uk/science/2010/may/20/craig-venter-synthetic-life-form http://www.guardian.co.uk/science/2010/may/20/craig-venter-s...
cb18 16y ago
Perspective: http://www.theatlantic.com/science/archive/2010/05/ventners-not-all-that/57046/ http://www.theatlantic.com/science/archive/2010/05/ventners-... (I am not currently well-informed enough in this area to either advocate or not this perspective, just providing it.)

280 points by blogimus 16y ago

Here are my questions about this, hope you smart folks don't mind chiming in: How do you physically put DNA into a cell? A very small needle? Or is there something fancier? How were the synthesized pieces of DNA produced? Very tiny robotic hands pushing the molecules together in the right sequence? How did they stitch together the synthesized pieces of DNA? What would say which pieces go with which?

aheilbut 16y ago
Bacteria will often take up DNA from their environment, and this ability, called "competence" is widely used in molecular biology. In this case, they treated the cells with a chemical called polyethylene glycol, which increases the efficiency by which the cells can pick up the DNA molecules. The procedure for transplanting genomes was described by the same group in a paper in 2007. It is possible to use a small needle ("DNA microinjection") to inject DNA into cells; one can also use an electric field to disrupt the cell membrane and force DNA into a cell, which is called electroporation. In this case though, the PEG transformation was sufficient (and because these artificial chromosomes were so large, they might not survive being shot through a needle or zapped with electricity too well). The initial pieces of DNA (oligonucleotides) are synthesized chemically - the components are added to a reaction one at a time, and the reaction is controlled so that at each step, only one base gets added. There is a lot of chemistry optimization and QC to be able to make relatively long fragments accurately. They ordered the building block pieces (1080 bases long) from a company called Blue Heron, which specializes in putting together long DNA molecules. The sequences were designed to be partially overlapping, so that the complementary sequences could fit together. Overlapping pieces of DNA can be combined by a process called homologous recombination. There is existing machinery in the yeast cells that they used to join together such complementary sequences. The molecules were assembled hierarchically, so they first made 10kb fragments, then put 10 x 10kb together to make 100kb fragments, and then finally put the 10 100kb fragments together. The overlapping sequences at the ends determined which fragments will stick together.
- tocomment 16y ago
  Wow thanks. That explains a lot. What's PEG? The electrical method you mentioned? So if the DNA pieces overlapped did that overlapping base pairs somehow get removed when the pieces were joined? Otherwise I'd think the next final DNA sequence would look a lot different from what they were intending to copy.
  - aheilbut 16y ago
    PEG is the abbreviation for PolyEthylene Glycol. Just a chemical they add that makes the transformation work more efficiently. DNA, as you probably know, is a double-stranded molecule, and the strands have complementary sequences. When the overlapping pieces are joined, one strand of one molecule overlaps with its complement on the other piece, and vice versa - the pieces aren't just joined end-to-end. see http://en.wikipedia.org/wiki/Homologous_recombination http://en.wikipedia.org/wiki/Homologous_recombination for all the details.

amichail 16y ago

They just copied the genome of an existing micro-organism. Making changes to the genome to accomplish some task is much harder to do.

Anon84 16y ago
Mutants that differ on specific genes are created regularly to study the effects of each mutation.
raimondious 16y ago
You say they "just copied the genome" like that's easy to do. This is a landmark because they synthesized the entire genome using nothing but the sequence stored in a computer, much more difficult than replicating a pre-existing piece of DNA.
- amichail 16y ago
  Even so, calling it artificial life is highly misleading.
  - raimondious 16y ago
    I think it's pretty accurate. There was only information to begin with, and now there is life. It happens that information was gained from a pre-existing cell, but this new cell has nothing to do with the cell it's derived from, it's made completely by the work of humans. That has never happened before. Edit: However, I know what you mean about it not being 100% artificial, as in completely designed by humans: Maybe "synthetic life" is better? Further edit: More than using a pre-existing genome, what makes it not completely artificial is that they had to put their DNA into another cell, basically cloning using synthesized DNA rather than natural DNA.
  - FlorinAndrei 16y ago
    I agree. They wrote a new OS and uploaded it into existing hardware. Still a great feat, but not quite 100% "artificial life" yet.

glymor 16y ago

Better write up: http://arstechnica.com/science/news/2010/05/first-functional-synthetic-bacterial-genome-announced.ars http://arstechnica.com/science/news/2010/05/first-functional...

rms 16y ago
Or http://www.sciencemag.org/cgi/content/full/328/5981/958 http://www.sciencemag.org/cgi/content/full/328/5981/958
- raimondious 16y ago
  My favorite part from that article: So that the assembled genome would be recognizable as synthetic, four of the ordered DNA sequences contained strings of bases that, in code, spell out an e-mail address, the names of many of the people involved in the project, and a few famous quotations.
  - Evgeny 16y ago
    I guess sooner or later the random mutations may make these string "corrupted".
    - Devilboy 16y ago
      I hope they included checkbits!
      - zackattack 16y ago
        it may be a misconception but i think that checkbits are a feature of organic dna?
        biotech 16y ago
        Yep! There is some error-checking built into dna-replication. The protein that does the replication is called DNA Polymerase. From its wikipedia article: Error correction is a property of some, but not all, DNA polymerases. This process corrects mistakes in newly-synthesized DNA. When an incorrect base pair is recognized, DNA polymerase reverses its direction by one base pair of DNA. The 3'-5' exonuclease activity of the enzyme allows the incorrect base pair to be excised (this activity is known as proofreading). Following base excision, the polymerase can re-insert the correct base and replication can continue.

orblivion 16y ago

Call me a luddite, genetic engineering gives me the willies.

macrael 16y ago
I'm with you, but it is pretty fascinating all the same.
- orblivion 16y ago
  Yeah it's definitely cool.
bh42 16y ago
Luddite. In all seriousness, the dangers brought up in the article can only come from a person lacking significant knowledge of bacteria. Unimaginable numbers of bacteria permeate every part of the world, including miles within the earth, deep sea volcanic vents, radioactive waste, the rain drops falling on our heads, and us, up our noses, in our skin pores, our guts, etc. Those simple bacteria evolve at staggering rates, and swap genes like DJ Danger Mouse mixing tracks. Any new synthetic, or extraterrestrial, or magical, life form would have to compete. And unless you believe in magic it is unlikely to out-compete in a pre-existing niche. The grey goo danger often thrown at nano-tech, is possible only if we violate one or more of the basic laws of thermodynamics. And when it comes to antibiotic resistant bacteria, well we are already doing a great job of breeding those within ourselves. But if you grew a barrel full of MRSA and then poured it down your toilet, the SA wold quickly lose its metabolically expensive MR. Because there is no Methicillin in the sewer, the resistance to Methicillin is a disadvantage. And the only way the Staphylococcus aureus could survive is if it dumped this feature. But luckily you're probably taking antibiotics so you are a niche where MRSA can out-compete and thrive.
- WilliamLP 16y ago
  > And unless you believe in magic it is unlikely to out-compete in a pre-existing niche. Cars are faster than land animals. Planes are faster than birds. Not being constrained by needing to have come from slow gradual iteration might open some possibilities, some terrifying. Biology doesn't produce the wheel. To consider this as a possibility is not to believe in magic.

MikeCapone 16y ago

This is a huge deal, and I'm not surprised to see that Craig Venter had something to do with it. Kudos!

joe_the_user 16y ago
This is a nice step for technology and a really huge deal for human culture and religion. A certain Someone said once "Let the earth put forth vegetation, plants yielding seed, and fruit trees bearing fruit in which is their seed, each according to its kind, upon the earth." That certain Someone later said: "Behold, man has become like one of us..."
- metamemetics 16y ago
  I can't decipher which English-speaking reader of the New Revised Standard Edition post 1989 you are referring to, how elusive!
- CamperBob 16y ago
  "Whoa, hold on there. Get your own dirt." - God /card-carrying atheist, but always liked that joke
- rbanffy 16y ago
  > That certain Someone later said: "Behold, man has become like one of us..." Walt Disney may have had a number of character flaws, but I always found the "if you can dream it, you can do it" quote very inspiring.

sheldonwt 16y ago

Advancements like this make it feel exciting to be young and have so much time ahead of you. The future is bright. Science is key.

jjs 16y ago
Advancements like this make it feel exciting to be young and have so much time ahead of you. What, you're still using your original telomeres?

itistoday 16y ago

Oddly enough this makes me feel a bit impotent. Here I am playing with my 1's and 0's... like a caveman. :-p

Anon84 16y ago
You're using base 2 (0 and 1), they are using base 4 (A, G, C and T)... Not that different, really.
- deleted 16y ago
  [deleted]
  - crystalis 16y ago
    Yeah, all computers can't recognize jokes.
- dublinclontarf 16y ago
  Could this mean a step towards biological computers?

eduardoflores 16y ago

Announcement here http://www.jcvi.org/cms/research/projects/first-self-replicating-synthetic-bacterial-cell/overview/ http://www.jcvi.org/cms/research/projects/first-self-replica... with the press release, a FAQ and some fact sheets (and the video is promised to be available soon)

deleted 16y ago

[deleted]

stavrianos 16y ago

they've got root

haydenchambers 16y ago
All your base pairs belong to us

danielharan 16y ago

So when do we get dinosaurs?

deleted 16y ago
[deleted]

phaedrus 16y ago

This is surprisingly like the first step you'd take if you were about to start hacking the firmware on an embedded board: before you change bits, you upload a known good firmware to prove your programming process is working correctly.

JeanPierre 16y ago
But the next steps looks more like software on a computer: You'll have to fix all those compilation-errors on first run, then look out for bugs in the software. Finally, when you ship the software, people use it and report other bugs. And since you can't update running processes at the current moment, you need to terminate and replace it.
plesn 16y ago
It's more like a compiler: bootstrapping is not complete yet though, the bacteria produced should be able to produce the rest of the entire cell.

zokier 16y ago

This is awesome. Literally, awe inspiring. We now have a compiler for the code which is DNA. Now we just need a "Hello, world!" app :)

jacquesm 16y ago
We'll see if it is awesome, if the compiler is buggy it might turn out to create a 'killall' app instead. This is great news, but with this new power comes also a very large responsibility.

yu 16y ago

Nature article http://www.nature.com/news/2010/100520/full/news.2010.253.html http://www.nature.com/news/2010/100520/full/news.2010.253.ht... Nature asks and eight experts comment on significance http://www.nature.com/news/2010/100520/full/news.2010.255.html http://www.nature.com/news/2010/100520/full/news.2010.255.ht...

mortenjorck 16y ago

DNA: Now jailbroken.

run4yourlives 16y ago

Mandatory: http://www.reddit.com/r/science/comments/c6dea/synthetic_life_breakthrough_announced_by/c0qeydc http://www.reddit.com/r/science/comments/c6dea/synthetic_lif...

michael_nielsen 16y ago
That comment can safely be ignored. It makes lots of vague accusations about Venter, and one concrete accusation - that Venter is responsible for patents on genes involved in breast cancer. That accusation is wrong: it's a reference to the BRCA patent by Myriad genetics, which has nothing to do with Venter.

jamesbritt 16y ago

Gripe: "artificial life" already has a somewhat lengthy history of usage, referring to emulating biological activity or traits in software or hardware. It's often shortened to just alife or a-life. It's related to genetic algorithms, genetic programming, and the like. It would be nice if the using-real-chemicals-and-alive-stuff hacking were called "synthetic life", or something to distinguish it from existing terminology.

nooneelse 16y ago
That use maybe should have been "simulated life" all along, so as to be more exact. This is a living organism that is artificially made, "artificial life" applies to it just as much as the other subject. Though the more specific terms that capture the way in which their somethings are artificial are good too.
- jamesbritt 16y ago
  'This is a living organism that is artificially made, "artificial life" applies to it just as much as the other subject.' Maybe. But if you end up with a living organism, then that it's not artificial life; it's life (albeit artificially manufactured) . Whereas the software stuff is never anything but artificial. Long run I'd expect anything that's alive to be called life, regardless of the process that lead to it.
amalcon 16y ago
Are we sure that the CS term predates the biological term? I mean, we might not have really succeeded in creating (biological) artificial life in the 1950's, but someone was almost certainly trying.
aheilbut 16y ago
The field actually does typically call itself "synthetic biology," rather than "artificial life".

dmn001 16y ago

very informative video on guardian from Craig Venter: http://www.guardian.co.uk/science/2010/may/20/craig-venter-synthetic-life-form http://www.guardian.co.uk/science/2010/may/20/craig-venter-s...

cb18 16y ago

Perspective: http://www.theatlantic.com/science/archive/2010/05/ventners-not-all-that/57046/ http://www.theatlantic.com/science/archive/2010/05/ventners-... (I am not currently well-informed enough in this area to either advocate or not this perspective, just providing it.)