3 ms·

If I understand correctly, they demonstrated gates in living cells. Which immediately raises further questions, can they also build circuits, where do I get tha

by yk 13y ago

If I understand correctly, they demonstrated gates in living cells. Which immediately raises further questions, can they also build circuits, where do I get that stuff and how does IO work? And to quote Gibson: the future is weird.

anigbrowl 13y ago
Yes, they can build circuits. See the supplementary materials, which also contain all the how-tos (ProTip: although most journal articles are behind paywalls, the materials & methods stuff is often freely accessible, at least for the Nature and Science journal families. It's also often a lot easier to read and understand for the lay person who isn't already familiar with the field in questions, assuming that your interest is more in the engineering than the science end - I see many papers whose theoretical validity I am incompetent to assess, but whose experimental process I am able to understand.) http://www.nature.com/nnano/journal/vaop/ncurrent/extref/nnano.2014.58-s1.pdf http://www.nature.com/nnano/journal/vaop/ncurrent/extref/nna... EDIT: I spoke too soon. Section 6 of the supplementary material, which explores the idea of building more complex circuits and the scaling issues therewith, is unfortunately missing right now. I notified the authors and I'm sure that will be fixed soon. Meanwhile, here's what they say in the paper: The architectures described here are capable of processing two input bits at most. However, the outputs from two 'processors’ can be relayed to a third and increase the processing capacity (limited by the possible number of unique gate-key systems that can be designed). Importantly, the scaling of our design is linear rather than logarithmic, with errors in robot activation propagating in the order of the root sum square of the number of unique robot types in a system (Supplementary Note 6). Figure 4 presents a schematic of a hypothetical 4-input bit architecture for an imaginary task of controlling three therapeutic molecules simultaneously, where only the number of robots comprising the system limits its capacity. The basic concept we describe can be scaled plausibly to exceed the capacity of older 8-bit computers such as a Commodore 64 or Atari 800, which many of us had experience of as children. WTF |8-. Where you get that stuff: the robots are designed with CADnano, which is free software: http://cadnano.org/ http://cadnano.org/ and programmed with Visual DSD, a free project from Microsoft: http://boson.research.microsoft.com/webdna/ http://boson.research.microsoft.com/webdna/ and http://research.microsoft.com/en-us/projects/dna/manual.pdf http://research.microsoft.com/en-us/projects/dna/manual.pdf (isn't it nice that 'webDNA actually means DNA programming on the web' instead of some marketing department BS?) The raw material DNA strands are available from commercial suppliers. IO is currently done by fluorospectroscopy, which is very common in experimental biology - you make compounds that flouresce inside the cell, then pull out some blood/do a biopsy/chop up the host if it's something very primitive and measure the degree of flourescence. So your unit testing is basically probabilistic rather than deterministic.
- Osmium 13y ago
  > Where you get that stuff: the robots are designed with CADnano, which is free software: http://cadnano.org/ http://cadnano.org/ I'm sorry, but there's CAD software for designing DNA structures now?! When did this happen? As someone tragically unaware of recent advances in the biosciences, I'd love to know more about this. I see the structures in screenshots of their CAD software, and then micrographs of the resulting real DNA(?) but how do you go from A to B? Edit: Actually, for anyone reading this: what resources would you recommend for getting up to speed on cell biology, modelling of DNA and the like for someone with a solid science background? (I ask as someone who's done a lot of computer modelling, but more from a solid state physics point of view) I'd just like to be able to read articles like this with a slightly more critical eye...
abecedarius 13y ago
There's course material on this kind of thing at http://www.dna.caltech.edu/courses/cs191/index.html http://www.dna.caltech.edu/courses/cs191/index.html

by yk 13y ago

anigbrowl 13y ago

Yes, they can build circuits. See the supplementary materials, which also contain all the how-tos (ProTip: although most journal articles are behind paywalls, the materials & methods stuff is often freely accessible, at least for the Nature and Science journal families. It's also often a lot easier to read and understand for the lay person who isn't already familiar with the field in questions, assuming that your interest is more in the engineering than the science end - I see many papers whose theoretical validity I am incompetent to assess, but whose experimental process I am able to understand.) http://www.nature.com/nnano/journal/vaop/ncurrent/extref/nnano.2014.58-s1.pdf http://www.nature.com/nnano/journal/vaop/ncurrent/extref/nna... EDIT: I spoke too soon. Section 6 of the supplementary material, which explores the idea of building more complex circuits and the scaling issues therewith, is unfortunately missing right now. I notified the authors and I'm sure that will be fixed soon. Meanwhile, here's what they say in the paper: The architectures described here are capable of processing two input bits at most. However, the outputs from two 'processors’ can be relayed to a third and increase the processing capacity (limited by the possible number of unique gate-key systems that can be designed). Importantly, the scaling of our design is linear rather than logarithmic, with errors in robot activation propagating in the order of the root sum square of the number of unique robot types in a system (Supplementary Note 6). Figure 4 presents a schematic of a hypothetical 4-input bit architecture for an imaginary task of controlling three therapeutic molecules simultaneously, where only the number of robots comprising the system limits its capacity. The basic concept we describe can be scaled plausibly to exceed the capacity of older 8-bit computers such as a Commodore 64 or Atari 800, which many of us had experience of as children. WTF |8-. Where you get that stuff: the robots are designed with CADnano, which is free software: http://cadnano.org/ http://cadnano.org/ and programmed with Visual DSD, a free project from Microsoft: http://boson.research.microsoft.com/webdna/ http://boson.research.microsoft.com/webdna/ and http://research.microsoft.com/en-us/projects/dna/manual.pdf http://research.microsoft.com/en-us/projects/dna/manual.pdf (isn't it nice that 'webDNA actually means DNA programming on the web' instead of some marketing department BS?) The raw material DNA strands are available from commercial suppliers. IO is currently done by fluorospectroscopy, which is very common in experimental biology - you make compounds that flouresce inside the cell, then pull out some blood/do a biopsy/chop up the host if it's something very primitive and measure the degree of flourescence. So your unit testing is basically probabilistic rather than deterministic.

Osmium 13y ago
> Where you get that stuff: the robots are designed with CADnano, which is free software: http://cadnano.org/ http://cadnano.org/ I'm sorry, but there's CAD software for designing DNA structures now?! When did this happen? As someone tragically unaware of recent advances in the biosciences, I'd love to know more about this. I see the structures in screenshots of their CAD software, and then micrographs of the resulting real DNA(?) but how do you go from A to B? Edit: Actually, for anyone reading this: what resources would you recommend for getting up to speed on cell biology, modelling of DNA and the like for someone with a solid science background? (I ask as someone who's done a lot of computer modelling, but more from a solid state physics point of view) I'd just like to be able to read articles like this with a slightly more critical eye...

abecedarius 13y ago

There's course material on this kind of thing at http://www.dna.caltech.edu/courses/cs191/index.html http://www.dna.caltech.edu/courses/cs191/index.html