5 ms·

A great article. I suspect the shortest route to atomically-precise manufacturing will be by engineering biology since biology already knows how to do it. And

by jrkelly 13y ago

A great article. I suspect the shortest route to atomically-precise manufacturing will be by engineering biology since biology already knows how to do it. And there is even already a high-school competition as Feynman suggested at the end of that article: http://en.wikipedia.org/wiki/International_Genetically_Engineered_Machine http://en.wikipedia.org/wiki/International_Genetically_Engin...

maaku 13y ago
Biology does not do atomically-precise manufacturing. It does do a lot of sorting and filtering of random interactions, and in a few places (the ribosome), precision alignment of large complex basic units (amino acids). It is very, very unlikely that we will develop Drexlerian nanotech via biological processes.
- dredmorbius 13y ago
  Biology does not do atomically-precise manufacturing. It gets pretty damned close, no? What's gene reading and writing then? If not atomic level, small molecules. Base pairs are 13-15 atom molecules.
  - GFK_of_xmaspast 13y ago
    Transcription is highly specialized, and still makes lots of errors.
    - shawkinaw 13y ago
      ... which are corrected.
      - GFK_of_xmaspast 13y ago
        Through what mechanism?
        dredmorbius 13y ago
        Really not my area of expertise, but, generally, reasonably effective ones. Apparently, DNA polymerase can perform that function: http://www.torna.do/s/Error-correction-during-DNA-replication/ http://www.torna.do/s/Error-correction-during-DNA-replicatio... DNA polymerase (DNAP) is a dual-purpose enzyme that plays two opposite roles in two different situations during DNA replication. It plays its a normal role as a polymerase catalyzing the elongation of a new DNA molecule by adding a monomer. However, it can switch to the role of an exonuclease and shorten the same DNA by cleavage of the last incorporated monomer from the nascent DNA. https://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=4925705&contentType=Conference+Publications https://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=tr... DNA error correcting codes: No crossover. DNA error correcting codes over the edit metric create embeddable markers for sequencing projects that are tolerant of sequencing errors. When a sequence library has multiple sources for its sequences, use of embedded markers permit tracking of sequence origin. Evolutionary algorithms are currently the best known technique for optimizing DNA error correcting codes. In this study we resolve the question of the utility of the crossover operator used in earlier studies on optimizing DNA error correcting codes. The crossover operator in question is found to be substantially counterproductive. A majority of crossover events produce results that violate minimum-distance constraints required for error correction. A new algorithm, a form of modified evolution strategy, is tested and is found to locate codes with record size. The table of best know sizes for DNA-error correcting codes is updated.
        Ergomane 13y ago
        Transcription is the process where RNA is generated from a DNA template. The observed error rate is about 10^-5 per nt. This is the error rate after nucleolytic proofreading.
        dredmorbius 13y ago
        As I said: really not my area of expertise. The point is that at multiple levels, biological functions are operating at the molecular and/or atomic level. The ATP/ADP reaction is another that comes to mind, though it's an energetic transformation involving cleaving/joining of a single atom from a molecule. As for proofing methods: sometimes a transcription is in error. What then? The problem may be caught further upline: a protein is synthesized incorrectly and destroyed, a cell behaves improperly and the body's immune responses remove it, an imperfect embryo is formed and is reabsorbed or stillborn. None of which denies the fundamental fact that biological processes occurring at the molecular/atomic level are in fact commonplace.
    - X4 13y ago
      Biology > Technology I don't know why technologists and physicists underestimate and neglect nature as "not good enough, we can do better" every single time. There is so much ignorance that causes unnecessary friction and hate. To me nature is the most powerful thing in existence and consists of more than our universe, it is responsible for the laws of physics, life and everything. There is so much we will have to discover and what we will discover at the end is that all of what we found out has existed already for aeons and is mostly in use already by nature (if efficient, from it's perspective) somewhere out there. Let me explain that argument by an example why our whole technology evolved only because of bio- or natural mimicry. Physicists who are amongst the most disconnected individuals from nature, were actually those who first learnt by "observing" it. Newton, Galileo, Einstein and many more, have used their incredibly unique perspective and way to observe the nature of the things they wanted to understand. By that, they have evolved or discovered ideas, concepts and later the logic that explains the things they observed.
- deleted 13y ago
  [deleted]
- shawkinaw 13y ago
  I wouldn't call amino acids "large complex basic units" at all, they may be bigger than an atom but 10-20 heavy atoms is hardly complex. Plus many amino acids themselves are synthesized in vivo. Moreover, this misses the point somewhat, namely that the resulting peptide chain folds into a protein with essentially atomically precision. Atoms may not be placed one by one, but an atomically precise structure is created.
  - maaku 13y ago
    When the machinery you want to lay out is composed of carbon atoms placed at sub-nanometer scale, 10-20 heavy atoms is like boxing gloves.
- dkirkman 13y ago
  The whole issue of whether or not nanotech would end up just looking like enzymes was a big part of the famous Drexler/Smalley debate (http://en.wikipedia.org/wiki/Drexler%E2%80%93Smalley_debate_on_molecular_nanotechnology http://en.wikipedia.org/wiki/Drexler%E2%80%93Smalley_debate_...) I always found Smalley's arguments that nanotech would end up looking like biology convincing. Not that I think it matters much: would designing organisms that take the shape of a part and excrete an "exoskeleton" to realize it any less cool than assembling the same thing atom by atom?
- jrl 13y ago
  Enzymes can add hydroxyl groups to molecules in specific locations. A hydroxyl group contains only two atoms. Enzymes can also remove a couple of hydrogen atoms and their electrons in particular places of a molecule. By combining these and similar reactions, cells can do extremely specific remodeling of compounds. For example, a single bond in a fatty acid chain can be turned into a double bond by the dehydrogenation reaction mentioned before, and then hydration and subsequent oxidation yields a keto group. The overall change represent the addition of ONE oxygen to the molecule in the same position. This means that beta oxidation (the metabolic pathway where those reactions take place) of fatty acids involve manipulation of molecules at the atomic level. Drexler describes a path from biochemistry to molecular manufacturing in Engines of Creation. In fact, part of his argument is that biochemistry is similar to a great extent to the molecular machines he envisions.
  - maaku 13y ago
    This is not atomically precise, mechanosynthetic manufacturing. Can you use such a construction to create carbon nanotubes or equivalent and then lay them out in a three dimensional lattice structure with nanometer precision and six-sigma workpiece reliability? Biology does not scale to Drexlarian nanotech. The domains are completely different.
    - jrkelly 13y ago
      Why can't you use biology to do what you want there? Proteins have ~0.05nm precision at placing atoms and are programmable in three dimensions and biology is pretty good at working with carbon. It exceeds our genetic engineering ability today, but we're getting better. Semiconductor Research Corp recently put some money towards this: http://www.src.org/newsroom/press-release/2013/521/ http://www.src.org/newsroom/press-release/2013/521/
    - jrl 13y ago
      "Can you use such a construction to create carbon nanotubes or equivalent and then lay them out in a three dimensional lattice structure with nanometer precision and six-sigma workpiece reliability?" I can use biochemistry to build second-generation machines which might be capable of doing that. We might not have a diamondoid nanomachine but we can eventually synthesize it, since biology gives us atomically precise positioning of atoms. This looks like a feasible way to develop Drexlerian nanotech. An analogy with computer programming could be that biology is like assembly language. Using that you can make a higher-level language such as C, and from there you can develop much more powerful abstractions and technologies (Python, Perl, Lisp, Ruby, etc.) The domains of biochemistry and molecular manufacturing are not completely different because the former could be the foundation of the latter. Also, the science behind biology can inform nanotech. Transforming mechanical energy into chemical processes and viceversa are common processes in cells (e.g., motor proteins.), this is very similar to the type of processes molecular nanotech aspires to make. Another thing is that cells are capable of correcting errors in DNA synthesis to a substantial degree, 1 mistake for every 1 to 10 billion nucleotides. Reliability isn't an insurmountable problem in biology. "This is not atomically precise, mechanosynthetic manufacturing." But we can agree that biology can do atomically precise synthesis. And enzymatic catalysis can sometimes be described in terms of mechanical bending of molecules, such as the ATP synthase. If biochemistry were so irrelevant to molecular manufacturing, Drexler wouldn't have written so many pages talking about it or suggesting it as way to develop nanotech.
lvs 13y ago
I'm pretty sure that's not going to be "the shortest route," J, but it may be "a route" eventually. Samsung already produces a NAND flash chip at 10 nm. The lattice spacing in crystalline Si is about 0.54 nm, so we're talking about a transistor feature size of a bit more than 18 atoms. These are available on the market as we speak, and you might even be using one right now if you have a sweet new Samsung SSD. Proof-of-concept Si FETs have been made down to around 3 nm, last time I checked, or around 6 atoms. Grossly speaking, these are essentially refinements of photolithographic CMOS processes. Soon we'll hit a wall with this, but for now, I think atomically-precise manufacturing is already pretty achievable without engineering biology.

by jrkelly 13y ago

maaku 13y ago

Biology does not do atomically-precise manufacturing. It does do a lot of sorting and filtering of random interactions, and in a few places (the ribosome), precision alignment of large complex basic units (amino acids). It is very, very unlikely that we will develop Drexlerian nanotech via biological processes.

dredmorbius 13y ago
Biology does not do atomically-precise manufacturing. It gets pretty damned close, no? What's gene reading and writing then? If not atomic level, small molecules. Base pairs are 13-15 atom molecules.
- GFK_of_xmaspast 13y ago
  Transcription is highly specialized, and still makes lots of errors.
  - shawkinaw 13y ago
    ... which are corrected.
    - GFK_of_xmaspast 13y ago
      Through what mechanism?
      - dredmorbius 13y ago
        Really not my area of expertise, but, generally, reasonably effective ones. Apparently, DNA polymerase can perform that function: http://www.torna.do/s/Error-correction-during-DNA-replication/ http://www.torna.do/s/Error-correction-during-DNA-replicatio... DNA polymerase (DNAP) is a dual-purpose enzyme that plays two opposite roles in two different situations during DNA replication. It plays its a normal role as a polymerase catalyzing the elongation of a new DNA molecule by adding a monomer. However, it can switch to the role of an exonuclease and shorten the same DNA by cleavage of the last incorporated monomer from the nascent DNA. https://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=4925705&contentType=Conference+Publications https://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=tr... DNA error correcting codes: No crossover. DNA error correcting codes over the edit metric create embeddable markers for sequencing projects that are tolerant of sequencing errors. When a sequence library has multiple sources for its sequences, use of embedded markers permit tracking of sequence origin. Evolutionary algorithms are currently the best known technique for optimizing DNA error correcting codes. In this study we resolve the question of the utility of the crossover operator used in earlier studies on optimizing DNA error correcting codes. The crossover operator in question is found to be substantially counterproductive. A majority of crossover events produce results that violate minimum-distance constraints required for error correction. A new algorithm, a form of modified evolution strategy, is tested and is found to locate codes with record size. The table of best know sizes for DNA-error correcting codes is updated.
        Ergomane 13y ago
        Transcription is the process where RNA is generated from a DNA template. The observed error rate is about 10^-5 per nt. This is the error rate after nucleolytic proofreading.
        dredmorbius 13y ago
        As I said: really not my area of expertise. The point is that at multiple levels, biological functions are operating at the molecular and/or atomic level. The ATP/ADP reaction is another that comes to mind, though it's an energetic transformation involving cleaving/joining of a single atom from a molecule. As for proofing methods: sometimes a transcription is in error. What then? The problem may be caught further upline: a protein is synthesized incorrectly and destroyed, a cell behaves improperly and the body's immune responses remove it, an imperfect embryo is formed and is reabsorbed or stillborn. None of which denies the fundamental fact that biological processes occurring at the molecular/atomic level are in fact commonplace.
  - X4 13y ago
    Biology > Technology I don't know why technologists and physicists underestimate and neglect nature as "not good enough, we can do better" every single time. There is so much ignorance that causes unnecessary friction and hate. To me nature is the most powerful thing in existence and consists of more than our universe, it is responsible for the laws of physics, life and everything. There is so much we will have to discover and what we will discover at the end is that all of what we found out has existed already for aeons and is mostly in use already by nature (if efficient, from it's perspective) somewhere out there. Let me explain that argument by an example why our whole technology evolved only because of bio- or natural mimicry. Physicists who are amongst the most disconnected individuals from nature, were actually those who first learnt by "observing" it. Newton, Galileo, Einstein and many more, have used their incredibly unique perspective and way to observe the nature of the things they wanted to understand. By that, they have evolved or discovered ideas, concepts and later the logic that explains the things they observed.
deleted 13y ago
[deleted]
shawkinaw 13y ago
I wouldn't call amino acids "large complex basic units" at all, they may be bigger than an atom but 10-20 heavy atoms is hardly complex. Plus many amino acids themselves are synthesized in vivo. Moreover, this misses the point somewhat, namely that the resulting peptide chain folds into a protein with essentially atomically precision. Atoms may not be placed one by one, but an atomically precise structure is created.
- maaku 13y ago
  When the machinery you want to lay out is composed of carbon atoms placed at sub-nanometer scale, 10-20 heavy atoms is like boxing gloves.
dkirkman 13y ago
The whole issue of whether or not nanotech would end up just looking like enzymes was a big part of the famous Drexler/Smalley debate (http://en.wikipedia.org/wiki/Drexler%E2%80%93Smalley_debate_on_molecular_nanotechnology http://en.wikipedia.org/wiki/Drexler%E2%80%93Smalley_debate_...) I always found Smalley's arguments that nanotech would end up looking like biology convincing. Not that I think it matters much: would designing organisms that take the shape of a part and excrete an "exoskeleton" to realize it any less cool than assembling the same thing atom by atom?
jrl 13y ago
Enzymes can add hydroxyl groups to molecules in specific locations. A hydroxyl group contains only two atoms. Enzymes can also remove a couple of hydrogen atoms and their electrons in particular places of a molecule. By combining these and similar reactions, cells can do extremely specific remodeling of compounds. For example, a single bond in a fatty acid chain can be turned into a double bond by the dehydrogenation reaction mentioned before, and then hydration and subsequent oxidation yields a keto group. The overall change represent the addition of ONE oxygen to the molecule in the same position. This means that beta oxidation (the metabolic pathway where those reactions take place) of fatty acids involve manipulation of molecules at the atomic level. Drexler describes a path from biochemistry to molecular manufacturing in Engines of Creation. In fact, part of his argument is that biochemistry is similar to a great extent to the molecular machines he envisions.
- maaku 13y ago
  This is not atomically precise, mechanosynthetic manufacturing. Can you use such a construction to create carbon nanotubes or equivalent and then lay them out in a three dimensional lattice structure with nanometer precision and six-sigma workpiece reliability? Biology does not scale to Drexlarian nanotech. The domains are completely different.
  - jrkelly 13y ago
    Why can't you use biology to do what you want there? Proteins have ~0.05nm precision at placing atoms and are programmable in three dimensions and biology is pretty good at working with carbon. It exceeds our genetic engineering ability today, but we're getting better. Semiconductor Research Corp recently put some money towards this: http://www.src.org/newsroom/press-release/2013/521/ http://www.src.org/newsroom/press-release/2013/521/
  - jrl 13y ago
    "Can you use such a construction to create carbon nanotubes or equivalent and then lay them out in a three dimensional lattice structure with nanometer precision and six-sigma workpiece reliability?" I can use biochemistry to build second-generation machines which might be capable of doing that. We might not have a diamondoid nanomachine but we can eventually synthesize it, since biology gives us atomically precise positioning of atoms. This looks like a feasible way to develop Drexlerian nanotech. An analogy with computer programming could be that biology is like assembly language. Using that you can make a higher-level language such as C, and from there you can develop much more powerful abstractions and technologies (Python, Perl, Lisp, Ruby, etc.) The domains of biochemistry and molecular manufacturing are not completely different because the former could be the foundation of the latter. Also, the science behind biology can inform nanotech. Transforming mechanical energy into chemical processes and viceversa are common processes in cells (e.g., motor proteins.), this is very similar to the type of processes molecular nanotech aspires to make. Another thing is that cells are capable of correcting errors in DNA synthesis to a substantial degree, 1 mistake for every 1 to 10 billion nucleotides. Reliability isn't an insurmountable problem in biology. "This is not atomically precise, mechanosynthetic manufacturing." But we can agree that biology can do atomically precise synthesis. And enzymatic catalysis can sometimes be described in terms of mechanical bending of molecules, such as the ATP synthase. If biochemistry were so irrelevant to molecular manufacturing, Drexler wouldn't have written so many pages talking about it or suggesting it as way to develop nanotech.

lvs 13y ago

I'm pretty sure that's not going to be "the shortest route," J, but it may be "a route" eventually. Samsung already produces a NAND flash chip at 10 nm. The lattice spacing in crystalline Si is about 0.54 nm, so we're talking about a transistor feature size of a bit more than 18 atoms. These are available on the market as we speak, and you might even be using one right now if you have a sweet new Samsung SSD. Proof-of-concept Si FETs have been made down to around 3 nm, last time I checked, or around 6 atoms. Grossly speaking, these are essentially refinements of photolithographic CMOS processes. Soon we'll hit a wall with this, but for now, I think atomically-precise manufacturing is already pretty achievable without engineering biology.