6 ms·

Genetic system performs logic operations and stores data in DNA

58 points by ananyob 14y ago

adobriyan 14y ago
It'd be thrilling to watch if evolution invents cryptographically signed DNA to prevent malicious viruses, plasmids and what not from using cell's reproduction machinery.
- lutusp 14y ago
  > It'd be thrilling to watch if evolution invents cryptographically signed DNA to prevent malicious viruses, plasmids and what not from using cell's reproduction machinery. Here's an example from nature in which evolution came up with an encryption strategy to evade predators. It even uses prime numbers: http://arachnoid.com/prime_numbers/index.html#Mathematical_Locusts http://arachnoid.com/prime_numbers/index.html#Mathematical_L...
  - jules 14y ago
    The cicada simulation on that page is very misleading. You're only seeing prime numbers because you arbitrarily synchronized the cycles of the cicada and the predators at t=0. If you had chosen another starting point at t=0 then you would see that years with many prime factors do better because then the predators consistently miss the cicada cycle. From somebody who criticizes psychology for wrong methodology I'd not have expected a simulation that's nothing more than confirmation bias ;-)
    - lutusp 14y ago
      > The cicada simulation on that page is very misleading. Not at all. > You're only seeing prime numbers because you arbitrarily synchronized the cycles of the cicada and the predators at t=0. Not true. Because of how the math works out, the starting time is irrelevant. Any arbitrary starting times for both the cicadas and predators yields the same outcome over time, because the filtering effect of prime reproductive cycles depends on synchronizing (or not synchronizing) random reproductive periods, not starting points. Just so you won't think this is all rhetoric, and to do your homework for you, here's a short Python program that accepts any starting value and produces the same result regardless of the chosen starting point: https://www.dropbox.com/s/7m8hq9yzcu5nztx/prime_reproduction_test.py https://www.dropbox.com/s/7m8hq9yzcu5nztx/prime_reproduction... Here is a typical output (the output changes in small ways with the chosen starting number, but always favors primes over composites): 2 = 6901 ********************* 3 = 6395 ******************* 4 = 9036 **************************** 5 = 5836 ****************** 6 = 11030 ********************************** 7 = 5468 ***************** 8 = 10410 ******************************** 9 = 7643 *********************** 10 = 9923 ******************************* 11 = 4987 *************** 12 = 14110 ******************************************** 13 = 4810 *************** 14 = 9199 **************************** 15 = 8988 **************************** 16 = 11051 ********************************** 17 = 4528 ************** 18 = 12797 *************************************** 19 = 4414 ************* 20 = 12469 ************************************** 21 = 8273 ************************* 22 = 8251 ************************* 23 = 4219 ************* > If you had chosen another starting point at t=0 ... See above. You're mistaken. If you had tested your idea using actual mathematics, you would have realized your mistake before posting. But this would require a respect for validating one's ideas before posting them. The effect being described counts only synchronization events between two reproductive cycles A and B over a long period of time. In this case, a given prime number A is compared to any number of values for B, and the number of synchronizations is totaled. As it happens, and regardless of the starting times, when a prime number in A is compared to a large range of values in B, and not surprisingly, the number of synchronizations is smallest if A is prime. Another way of saying this is that a prime number has fewer factors than a composite number, hardly a controversial claim, and one that doesn't depend on the starting values for the counters. > From somebody who criticizes psychology for wrong methodology ... Ah, yes, the real reason for your post. I have never criticized psychology for "wrong methodology" anywhere. I criticize the field for not being scientific, as does the sitting director of the NIMH and many, many others. Today's example: Title: "Final Report: Stapel Affair Points to Bigger Problems in Social Psychology" Source: http://news.sciencemag.org/scienceinsider/2012/11/final-report-stapel-affair-point.html http://news.sciencemag.org/scienceinsider/2012/11/final-repo... Quote: "In their exhaustive final report about the fraud affair that rocked social psychology last year, three investigative panels today collectively find fault with the field itself. They paint an image of a "sloppy" research culture in which some scientists don't understand the essentials of statistics, journal-selected article reviewers encourage researchers to leave unwelcome data out of their papers, and even the most prestigious journals print results that are obviously too good to be true. The commissions—one for each of the universities where Stapel has worked—concluded that "from the bottom to the top there was a general neglect of fundamental scientific standards and methodological requirements." That climate made it possible for Stapel's fraud to go undetected for many years, the report says." Somehow people like you think psychology's problems would go away if its critics would simply shut up. But this confuses the messenger with the message.
      - jules 14y ago
        Sorry, but you're wrong. Even though it's fairly intuitively obvious, you can never trust intuition so I had tested it before I posted that. Change the line // are cicadas and predators both present at once? if ((y % py == 0) && (y % cy == 0)) { to // are cicadas and predators both present at once? if ((y % py == 0) && ((y+1) % cy == 0)) { or any other number than +1 to change the initial offset between the cicada and predator cycles, and you'll see that what I said is true. > Ah, yes, the real reason for your post. Not really, I in fact agree with (most of) what you say about psychology. This example just goes to show that one has to be careful with non-rigorous arguments (something that psychology is full of).
        lutusp 14y ago
        > if ((y % py == 0) && ((y+1) % cy == 0)) Wait, hold on. The problem is not with the theory, it's with your code. You're requiring a match between two values n and n+1 at once. That undermines the basic idea. To make your code work and imitate nature, you would need to take separate sums for n and n+1, not together as in your example, just as though there were two organisms, each trying to match up with the cicada's reproductive cycle. BTW my Python program sums values with an arbitrary change of starting point, but separately. Your code above has an obvious bug. > you'll see that what I said is true. Read my edited post with the Python program -- the starting point is irrelevant. > Not really, I in fact agree with (most of) what you say about psychology. Well, I certainly got that wrong. I assumed without evidence that you were one of those who bridles at the thought of someone criticizing psychology.
        jules 14y ago
        Your Python program is incomprehensible to me, probably due to the lack of meaningful variable names and double modulo: for a in range(2,22): total = 0 for b in range(2,25): for c in range(1,1000): cc = c + start_value if(a % ((cc % b)+1) == 0): total += 1 In any case, my point was about the specific simulation on the web page you linked to. See above for my suggestion about how to change the starting offset in the original simulation, which clearly shows that the effect is reversed for different offsets. Response to this edit: > Wait, hold on. The problem is not with the theory, it's with your code. You're requiring a match between two values n and n+1 at once. That undermines the basic idea. To make your code work and imitate nature, you would need to take separate sums for n and n+1, not together as in your example, just as though there were two organisms, each trying to match up with the cicada's reproductive cycle. BTW my Python program sums values with an arbitrary change of starting point, but separately. Your code above has an obvious bug. I am just setting the starting offset (not the starting year as I think you are doing in the Python program) between the cicada and the predators to something other than zero. Lets assume as an example that the cicada cycle is 4 years and the predator cycle is 3 years. At simulation year 0, there can be a variety of situations: at this year the cicada are mating, the next year the cicada are mating, in 2 years the cicada are mating, or in 3 years the cicada are mating. The same goes for the predators: at simulation year 0, the predators are coming, or the next year the predators are coming, or in 2 years the predators are coming. A proper simulation would consider all these possibilities. Your simulation arbitrarily assumes that at simulation year 0 both the cicada are mating and the predators are coming, i.e. the offset between the cicada mating year and the predator arrival year is 0 at the start of the simulation. By increasing the cicada cycle year by a fixed number, I am changing this arbitrary assumption to a different number of years to show that this assumption has a large effect on the outcome of the simulation. So while the change is minimal and perhaps not the most readable way to introduce this offset, the change I made does not introduce a bug. > Well, I certainly got that wrong. I assumed without evidence that you were one of those who bridles at the thought of someone criticizing psychology. No, I even think the problem is more widespread than psychology alone (though in psychology it is particularly severe), having seen first hand and heard second hand how science is conducted in other areas (especially those close to psychology).
- ananyob 14y ago
  To an extent, engineered bacteria do this already. Though E coli are quite tolerant, I've known instances when they reject foreign DNA that you're trying to get into them (eg to express a protein).
- iwwr 14y ago
  The problem of chain-of-trust still remains. How do you transmit the public keys for verification?
  - adobriyan 14y ago
    Non-trivial sexually reproducible organisms could generate unique keys from parents keys! My understanding is that current detection of unauthorized usage of copying enzymes is limited to "if fits or it doesn't fit".
- wcoenen 14y ago
  I was confused by your comment for a moment. Then I realized that you probably don't know that there already exist natural viruses which hijack bacteria by injecting their own DNA. Wherever you find bacteria, you also find these bacteriophages. They co-evolve with their host in a never-ending arms race of defenses and counters. No asymmetric crypto though :-) http://en.wikipedia.org/wiki/Bacteriophage http://en.wikipedia.org/wiki/Bacteriophage
  - arethuza 14y ago
    And way up there on the creepy/cool scale there are viruses that incorporate themselves into the DNA that is passed from generation to generation: http://en.wikipedia.org/wiki/Endogenous_retrovirus http://en.wikipedia.org/wiki/Endogenous_retrovirus
- spoiler 14y ago
  Soon: Eureka (as seen on SySf).
- CreRecombinase 14y ago
  Not exactly the same, but http://en.wikipedia.org/wiki/RNA_interference#Immunity http://en.wikipedia.org/wiki/RNA_interference#Immunity
steeve 14y ago
DNA as storage, and now DNA as logic gates. But is there any benefit for using DNA for anything non biology related? For instance, one would think works for using atoms themselves as storage would yield a far superior logical/physical size ratio.
- Drakim 14y ago
  I'm guessing that by piggybacking on biology, we can use a lot of preexisting abilities of the living for our organic computers, such as self-repairing.
- ajuc 14y ago
  I don't know if this will ever be possible, I hope it will be: You engineer some harmless bacteria to start glowing if it encounters cancerous cell. You take pill with such bacteria, then you look at your poop. If it glows - you go to doctor. If no - you take such pill half a year later. Most cancers can be cured if detected so early.
  - jfarmer 14y ago
    http://www.nature.com/news/2010/101006/full/467650a.html http://www.nature.com/news/2010/101006/full/467650a.html "For now, most members of the do-it-yourself, or DIY, biology community are hobbyists, rigging up cheap equipment and tackling projects that — although not exactly pushing the boundaries of molecular biology — are creative proof of the hacker principle. Meredith Patterson, a computer programmer based in San Francisco, California, whom some call the 'doyenne of DIYbio', made glow-in-the-dark yogurt by engineering the bacteria within to produce a fluorescent protein. Others hope to learn more about themselves: a group called DIYgenomics has banded together to analyse their genomes, and even conduct and participate in small clinical trials. For those who aspire to change the world, improving biofuel development is a popular draw. And several groups are focused on making standard instruments — such as PCR machines, which amplify segments of DNA — cheaper and easier to use outside the confines of a laboratory, ultimately promising to make DIYbio more accessible."
- epistasis 14y ago
  Using DNA is using "atoms" themselves for storage. DNA is about 50 atoms/bit, and nature has given us machinery for replicating this data and even some types of error correction. And the linear structure and base-pairing action of DNA gives us the capability to perform data retrieval physically. I will be surprised if anybody can come up with a nanotechnology scheme that comes even close to matching DNA's density in the next few decades. Look at the difficulties of even reading DNA, we can stick it through a nanopore, but it's not a trivial task to read off the various shapes of molecules as they poke through. Can you come up with a linear structure that is as stable but also allows for easier readout? If you start with DNA, but then add various modifications, how are you going to read out those modifications to the bases, and how are you going to replicate and copy that data? I'm sure that it will happen that we eventually best DNA's density when it comes to storing information in covalent bonds, but our nanotechnology isn't even close to being able to come up with something like that now. Reusing biology's inventions are our only hope for the near future.
mtp0101 14y ago
wow... doesn't even run CoD... #ignore

58 points by ananyob 14y ago

It'd be thrilling to watch if evolution invents cryptographically signed DNA to prevent malicious viruses, plasmids and what not from using cell's reproduction machinery.

lutusp 14y ago
> It'd be thrilling to watch if evolution invents cryptographically signed DNA to prevent malicious viruses, plasmids and what not from using cell's reproduction machinery. Here's an example from nature in which evolution came up with an encryption strategy to evade predators. It even uses prime numbers: http://arachnoid.com/prime_numbers/index.html#Mathematical_Locusts http://arachnoid.com/prime_numbers/index.html#Mathematical_L...
- jules 14y ago
  The cicada simulation on that page is very misleading. You're only seeing prime numbers because you arbitrarily synchronized the cycles of the cicada and the predators at t=0. If you had chosen another starting point at t=0 then you would see that years with many prime factors do better because then the predators consistently miss the cicada cycle. From somebody who criticizes psychology for wrong methodology I'd not have expected a simulation that's nothing more than confirmation bias ;-)
  - lutusp 14y ago
    > The cicada simulation on that page is very misleading. Not at all. > You're only seeing prime numbers because you arbitrarily synchronized the cycles of the cicada and the predators at t=0. Not true. Because of how the math works out, the starting time is irrelevant. Any arbitrary starting times for both the cicadas and predators yields the same outcome over time, because the filtering effect of prime reproductive cycles depends on synchronizing (or not synchronizing) random reproductive periods, not starting points. Just so you won't think this is all rhetoric, and to do your homework for you, here's a short Python program that accepts any starting value and produces the same result regardless of the chosen starting point: https://www.dropbox.com/s/7m8hq9yzcu5nztx/prime_reproduction_test.py https://www.dropbox.com/s/7m8hq9yzcu5nztx/prime_reproduction... Here is a typical output (the output changes in small ways with the chosen starting number, but always favors primes over composites): 2 = 6901 ********************* 3 = 6395 ******************* 4 = 9036 **************************** 5 = 5836 ****************** 6 = 11030 ********************************** 7 = 5468 ***************** 8 = 10410 ******************************** 9 = 7643 *********************** 10 = 9923 ******************************* 11 = 4987 *************** 12 = 14110 ******************************************** 13 = 4810 *************** 14 = 9199 **************************** 15 = 8988 **************************** 16 = 11051 ********************************** 17 = 4528 ************** 18 = 12797 *************************************** 19 = 4414 ************* 20 = 12469 ************************************** 21 = 8273 ************************* 22 = 8251 ************************* 23 = 4219 ************* > If you had chosen another starting point at t=0 ... See above. You're mistaken. If you had tested your idea using actual mathematics, you would have realized your mistake before posting. But this would require a respect for validating one's ideas before posting them. The effect being described counts only synchronization events between two reproductive cycles A and B over a long period of time. In this case, a given prime number A is compared to any number of values for B, and the number of synchronizations is totaled. As it happens, and regardless of the starting times, when a prime number in A is compared to a large range of values in B, and not surprisingly, the number of synchronizations is smallest if A is prime. Another way of saying this is that a prime number has fewer factors than a composite number, hardly a controversial claim, and one that doesn't depend on the starting values for the counters. > From somebody who criticizes psychology for wrong methodology ... Ah, yes, the real reason for your post. I have never criticized psychology for "wrong methodology" anywhere. I criticize the field for not being scientific, as does the sitting director of the NIMH and many, many others. Today's example: Title: "Final Report: Stapel Affair Points to Bigger Problems in Social Psychology" Source: http://news.sciencemag.org/scienceinsider/2012/11/final-report-stapel-affair-point.html http://news.sciencemag.org/scienceinsider/2012/11/final-repo... Quote: "In their exhaustive final report about the fraud affair that rocked social psychology last year, three investigative panels today collectively find fault with the field itself. They paint an image of a "sloppy" research culture in which some scientists don't understand the essentials of statistics, journal-selected article reviewers encourage researchers to leave unwelcome data out of their papers, and even the most prestigious journals print results that are obviously too good to be true. The commissions—one for each of the universities where Stapel has worked—concluded that "from the bottom to the top there was a general neglect of fundamental scientific standards and methodological requirements." That climate made it possible for Stapel's fraud to go undetected for many years, the report says." Somehow people like you think psychology's problems would go away if its critics would simply shut up. But this confuses the messenger with the message.
    - jules 14y ago
      Sorry, but you're wrong. Even though it's fairly intuitively obvious, you can never trust intuition so I had tested it before I posted that. Change the line // are cicadas and predators both present at once? if ((y % py == 0) && (y % cy == 0)) { to // are cicadas and predators both present at once? if ((y % py == 0) && ((y+1) % cy == 0)) { or any other number than +1 to change the initial offset between the cicada and predator cycles, and you'll see that what I said is true. > Ah, yes, the real reason for your post. Not really, I in fact agree with (most of) what you say about psychology. This example just goes to show that one has to be careful with non-rigorous arguments (something that psychology is full of).
      - lutusp 14y ago
        > if ((y % py == 0) && ((y+1) % cy == 0)) Wait, hold on. The problem is not with the theory, it's with your code. You're requiring a match between two values n and n+1 at once. That undermines the basic idea. To make your code work and imitate nature, you would need to take separate sums for n and n+1, not together as in your example, just as though there were two organisms, each trying to match up with the cicada's reproductive cycle. BTW my Python program sums values with an arbitrary change of starting point, but separately. Your code above has an obvious bug. > you'll see that what I said is true. Read my edited post with the Python program -- the starting point is irrelevant. > Not really, I in fact agree with (most of) what you say about psychology. Well, I certainly got that wrong. I assumed without evidence that you were one of those who bridles at the thought of someone criticizing psychology.
        jules 14y ago
        Your Python program is incomprehensible to me, probably due to the lack of meaningful variable names and double modulo: for a in range(2,22): total = 0 for b in range(2,25): for c in range(1,1000): cc = c + start_value if(a % ((cc % b)+1) == 0): total += 1 In any case, my point was about the specific simulation on the web page you linked to. See above for my suggestion about how to change the starting offset in the original simulation, which clearly shows that the effect is reversed for different offsets. Response to this edit: > Wait, hold on. The problem is not with the theory, it's with your code. You're requiring a match between two values n and n+1 at once. That undermines the basic idea. To make your code work and imitate nature, you would need to take separate sums for n and n+1, not together as in your example, just as though there were two organisms, each trying to match up with the cicada's reproductive cycle. BTW my Python program sums values with an arbitrary change of starting point, but separately. Your code above has an obvious bug. I am just setting the starting offset (not the starting year as I think you are doing in the Python program) between the cicada and the predators to something other than zero. Lets assume as an example that the cicada cycle is 4 years and the predator cycle is 3 years. At simulation year 0, there can be a variety of situations: at this year the cicada are mating, the next year the cicada are mating, in 2 years the cicada are mating, or in 3 years the cicada are mating. The same goes for the predators: at simulation year 0, the predators are coming, or the next year the predators are coming, or in 2 years the predators are coming. A proper simulation would consider all these possibilities. Your simulation arbitrarily assumes that at simulation year 0 both the cicada are mating and the predators are coming, i.e. the offset between the cicada mating year and the predator arrival year is 0 at the start of the simulation. By increasing the cicada cycle year by a fixed number, I am changing this arbitrary assumption to a different number of years to show that this assumption has a large effect on the outcome of the simulation. So while the change is minimal and perhaps not the most readable way to introduce this offset, the change I made does not introduce a bug. > Well, I certainly got that wrong. I assumed without evidence that you were one of those who bridles at the thought of someone criticizing psychology. No, I even think the problem is more widespread than psychology alone (though in psychology it is particularly severe), having seen first hand and heard second hand how science is conducted in other areas (especially those close to psychology).
ananyob 14y ago
To an extent, engineered bacteria do this already. Though E coli are quite tolerant, I've known instances when they reject foreign DNA that you're trying to get into them (eg to express a protein).
iwwr 14y ago
The problem of chain-of-trust still remains. How do you transmit the public keys for verification?
- adobriyan 14y ago
  Non-trivial sexually reproducible organisms could generate unique keys from parents keys! My understanding is that current detection of unauthorized usage of copying enzymes is limited to "if fits or it doesn't fit".
wcoenen 14y ago
I was confused by your comment for a moment. Then I realized that you probably don't know that there already exist natural viruses which hijack bacteria by injecting their own DNA. Wherever you find bacteria, you also find these bacteriophages. They co-evolve with their host in a never-ending arms race of defenses and counters. No asymmetric crypto though :-) http://en.wikipedia.org/wiki/Bacteriophage http://en.wikipedia.org/wiki/Bacteriophage
- arethuza 14y ago
  And way up there on the creepy/cool scale there are viruses that incorporate themselves into the DNA that is passed from generation to generation: http://en.wikipedia.org/wiki/Endogenous_retrovirus http://en.wikipedia.org/wiki/Endogenous_retrovirus
spoiler 14y ago
Soon: Eureka (as seen on SySf).
CreRecombinase 14y ago
Not exactly the same, but http://en.wikipedia.org/wiki/RNA_interference#Immunity http://en.wikipedia.org/wiki/RNA_interference#Immunity

steeve 14y ago

DNA as storage, and now DNA as logic gates. But is there any benefit for using DNA for anything non biology related? For instance, one would think works for using atoms themselves as storage would yield a far superior logical/physical size ratio.

Drakim 14y ago
I'm guessing that by piggybacking on biology, we can use a lot of preexisting abilities of the living for our organic computers, such as self-repairing.
ajuc 14y ago
I don't know if this will ever be possible, I hope it will be: You engineer some harmless bacteria to start glowing if it encounters cancerous cell. You take pill with such bacteria, then you look at your poop. If it glows - you go to doctor. If no - you take such pill half a year later. Most cancers can be cured if detected so early.
- jfarmer 14y ago
  http://www.nature.com/news/2010/101006/full/467650a.html http://www.nature.com/news/2010/101006/full/467650a.html "For now, most members of the do-it-yourself, or DIY, biology community are hobbyists, rigging up cheap equipment and tackling projects that — although not exactly pushing the boundaries of molecular biology — are creative proof of the hacker principle. Meredith Patterson, a computer programmer based in San Francisco, California, whom some call the 'doyenne of DIYbio', made glow-in-the-dark yogurt by engineering the bacteria within to produce a fluorescent protein. Others hope to learn more about themselves: a group called DIYgenomics has banded together to analyse their genomes, and even conduct and participate in small clinical trials. For those who aspire to change the world, improving biofuel development is a popular draw. And several groups are focused on making standard instruments — such as PCR machines, which amplify segments of DNA — cheaper and easier to use outside the confines of a laboratory, ultimately promising to make DIYbio more accessible."
epistasis 14y ago
Using DNA is using "atoms" themselves for storage. DNA is about 50 atoms/bit, and nature has given us machinery for replicating this data and even some types of error correction. And the linear structure and base-pairing action of DNA gives us the capability to perform data retrieval physically. I will be surprised if anybody can come up with a nanotechnology scheme that comes even close to matching DNA's density in the next few decades. Look at the difficulties of even reading DNA, we can stick it through a nanopore, but it's not a trivial task to read off the various shapes of molecules as they poke through. Can you come up with a linear structure that is as stable but also allows for easier readout? If you start with DNA, but then add various modifications, how are you going to read out those modifications to the bases, and how are you going to replicate and copy that data? I'm sure that it will happen that we eventually best DNA's density when it comes to storing information in covalent bonds, but our nanotechnology isn't even close to being able to come up with something like that now. Reusing biology's inventions are our only hope for the near future.

mtp0101 14y ago

wow... doesn't even run CoD... #ignore