5 ms·

Cambridge scientists create living organism with redesigned DNA

116 points by okket 7y ago

atemerev 7y ago
What about Mycoplasma laboratorium?
- korm 7y ago
  It's partially synthetic according to Google
- deleted 7y ago
  [deleted]
ElijahLynn 7y ago
That is some scary stuff, actually. Got the same feeling as watching some of Boston Robotics' videos.
gen220 7y ago
The latest WIRED magazine had some truly mind-boggling articles in this vein. https://www.wired.com/story/synthetic-biology-vaccines-viruses-horsepox/ https://www.wired.com/story/synthetic-biology-vaccines-virus... This guy (a renowned smallpox researcher) was able to synthesize a cousin of smallpox (horsepox) using commercially/publicly-accessible tools and resources. He did this to try and create a new/better smallpox vaccine, because he believes that motivated actors will be able to synthesize smallpox in the next 20 years, and that the world needs to be ready with better vaccines for the same. His team's resulting publication ("we made smallpox, this is the gist of how") was met with strongly negative responses. The gist of these articles is that while synthesizing functioning viruses/microorganisms was possible in the past (TFA says the first "synthetic" organism was made in 2010), it's much easier/faster/cheaper to do so today, when crispr techniques/tools are more generally wielded and better-understood. Cool/scary stuff!
- godelski 7y ago
  I'd be curious as to what the actual critics said. I would gather that it is (significantly) more nuanced than "you demonstrated that something dangerous can be created. You shouldn't be attempting to make dangerous things."
- inciampati 7y ago
  How is CRISPR used for genome synthesis? I thought it was all driven by synthesis, and overlapping homology of sticky ended fragments, and ligase, but maybe that's the old days.
  - folli 7y ago
    It's not used for synthesis. It's very helpful for modifications of existing genomes, but it has no relevance in commercial DNA synthesis (which is a purely chemical process).
- pulse7 7y ago
  "...because he believes that motivated actors will be able to synthesize smallpox in the next 20 years, and that the world needs to be ready..." So the essence is "we are doing it first, becuase otherwise others will be doing it first"... So the race who will come first there continues... No (further) comment...
hsikka 7y ago
What are the design tools that synthetic biology researchers use to create genomes? Is it some sort of EDA environment like Cello or Asimov, or is it done manually?
- daijobu 7y ago
  Mostly its just manipulating text files w/ bash, R, python. The tools used by this particular study: https://github.com/TiongSun/GenomeRecoding https://github.com/TiongSun/GenomeRecoding https://github.com/TiongSun/iSeq https://github.com/TiongSun/iSeq
  - hsikka 7y ago
    Thank you!
- 100ideas 7y ago
  That’s a good question! I wouldn’t be surprised if the academic team in this case developed something relatively simple. Let’s try to find out how they dispatched the synthesis orders they made over the two years. Was it excel or csv at the end of the day? If they were an enterprise biotech I would bet the would have a much more elaborate in-house data & design toolchain + Lims. But academic teams rarely have the resources or drive necessary to engineer digital tools approaching that level of sophistication. Other software academics might use - benching - teselagen - maaaaybe antha-lang - ??? Alternatively, perhaps the synthesis vendor supplied their own optimized design and inventory tool. Who did they buy from - gen9?
- udibai 7y ago
  Plenty of excellent open and closed source tools are available. For example check out clc genomics workbench
gpvos 7y ago
> Known as Syn61, the bug is a little longer than normal, and grows more slowly, but survives nonetheless. Why is this? If AGC is identical in function to TCG, and the same holds for the other replacements, shouldn't the new organism function exactly the same?
- jfarlow 7y ago
  Nothing in biology is exactly the same - or said another way, biology is optimized at many different scales - from basic (even quantum) physics, all the way up to social adaptations. So screwing with codons could have very subtle effects that have nothing to do with the physical design of the organism, but nonetheless affect its size and growth rate. Off the top of my head, to give some random examples - the locations on the genome of two metabolic enzymes have been shifted by what amounts to a few nanometers, and that affects metabolic flux, or the DNA now has more purines in a row than before and that causes some charge buildup that calls in DNA repair mechanisms slightly more often and disables transcription slightly more, or the genome when folded up is slightly more rounded than oblong because of strange sterics, or any number of very weird optimizations all the way down the physical causal ladder.
- deleted 7y ago
  [deleted]
- 781 7y ago
  Not an expert, but for example maybe decoding the TCG instruction (in the ribosome) is slower or uses more energy.
  - Amygaz 7y ago
    I doubt that's the only reason but according to this table [0], AGC triplets are 2x more prevalent than UGC in that bacteria. Edit: this the frequency of that codon being used o the genome sequence. But the assumption could be that it is also preferably produced as a t-RNA so it can replicate its genome efficiently. It's more likely that they have introduced errors, or non-preferred patterns, which affect the number of replication forks and stall the replication machinery. [0] https://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=83333 https://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species...

116 points by okket 7y ago

atemerev 7y ago

What about Mycoplasma laboratorium?

korm 7y ago
It's partially synthetic according to Google
deleted 7y ago
[deleted]

ElijahLynn 7y ago

That is some scary stuff, actually. Got the same feeling as watching some of Boston Robotics' videos.

gen220 7y ago

The latest WIRED magazine had some truly mind-boggling articles in this vein. https://www.wired.com/story/synthetic-biology-vaccines-viruses-horsepox/ https://www.wired.com/story/synthetic-biology-vaccines-virus... This guy (a renowned smallpox researcher) was able to synthesize a cousin of smallpox (horsepox) using commercially/publicly-accessible tools and resources. He did this to try and create a new/better smallpox vaccine, because he believes that motivated actors will be able to synthesize smallpox in the next 20 years, and that the world needs to be ready with better vaccines for the same. His team's resulting publication ("we made smallpox, this is the gist of how") was met with strongly negative responses. The gist of these articles is that while synthesizing functioning viruses/microorganisms was possible in the past (TFA says the first "synthetic" organism was made in 2010), it's much easier/faster/cheaper to do so today, when crispr techniques/tools are more generally wielded and better-understood. Cool/scary stuff!

godelski 7y ago
I'd be curious as to what the actual critics said. I would gather that it is (significantly) more nuanced than "you demonstrated that something dangerous can be created. You shouldn't be attempting to make dangerous things."
inciampati 7y ago
How is CRISPR used for genome synthesis? I thought it was all driven by synthesis, and overlapping homology of sticky ended fragments, and ligase, but maybe that's the old days.
- folli 7y ago
  It's not used for synthesis. It's very helpful for modifications of existing genomes, but it has no relevance in commercial DNA synthesis (which is a purely chemical process).
pulse7 7y ago
"...because he believes that motivated actors will be able to synthesize smallpox in the next 20 years, and that the world needs to be ready..." So the essence is "we are doing it first, becuase otherwise others will be doing it first"... So the race who will come first there continues... No (further) comment...

hsikka 7y ago

What are the design tools that synthetic biology researchers use to create genomes? Is it some sort of EDA environment like Cello or Asimov, or is it done manually?

daijobu 7y ago
Mostly its just manipulating text files w/ bash, R, python. The tools used by this particular study: https://github.com/TiongSun/GenomeRecoding https://github.com/TiongSun/GenomeRecoding https://github.com/TiongSun/iSeq https://github.com/TiongSun/iSeq
- hsikka 7y ago
  Thank you!
100ideas 7y ago
That’s a good question! I wouldn’t be surprised if the academic team in this case developed something relatively simple. Let’s try to find out how they dispatched the synthesis orders they made over the two years. Was it excel or csv at the end of the day? If they were an enterprise biotech I would bet the would have a much more elaborate in-house data & design toolchain + Lims. But academic teams rarely have the resources or drive necessary to engineer digital tools approaching that level of sophistication. Other software academics might use - benching - teselagen - maaaaybe antha-lang - ??? Alternatively, perhaps the synthesis vendor supplied their own optimized design and inventory tool. Who did they buy from - gen9?
udibai 7y ago
Plenty of excellent open and closed source tools are available. For example check out clc genomics workbench

gpvos 7y ago

> Known as Syn61, the bug is a little longer than normal, and grows more slowly, but survives nonetheless. Why is this? If AGC is identical in function to TCG, and the same holds for the other replacements, shouldn't the new organism function exactly the same?

jfarlow 7y ago
Nothing in biology is exactly the same - or said another way, biology is optimized at many different scales - from basic (even quantum) physics, all the way up to social adaptations. So screwing with codons could have very subtle effects that have nothing to do with the physical design of the organism, but nonetheless affect its size and growth rate. Off the top of my head, to give some random examples - the locations on the genome of two metabolic enzymes have been shifted by what amounts to a few nanometers, and that affects metabolic flux, or the DNA now has more purines in a row than before and that causes some charge buildup that calls in DNA repair mechanisms slightly more often and disables transcription slightly more, or the genome when folded up is slightly more rounded than oblong because of strange sterics, or any number of very weird optimizations all the way down the physical causal ladder.
deleted 7y ago
[deleted]
781 7y ago
Not an expert, but for example maybe decoding the TCG instruction (in the ribosome) is slower or uses more energy.
- Amygaz 7y ago
  I doubt that's the only reason but according to this table [0], AGC triplets are 2x more prevalent than UGC in that bacteria. Edit: this the frequency of that codon being used o the genome sequence. But the assumption could be that it is also preferably produced as a t-RNA so it can replicate its genome efficiently. It's more likely that they have introduced errors, or non-preferred patterns, which affect the number of replication forks and stall the replication machinery. [0] https://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=83333 https://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species...