I'm not sure if stop/start codons would even matter, as it's my understanding that when DNA is used as a computational tool, it is typically rather short, synthesized strands. Keep in mind that a stop/start codon is relevant once the DNA has been transcribed into RNA and the RNA is being translated into proteins - in other words, as far as the DNA is concerned a stop/start codon is just another three base pairs. Also, it's my understanding that besides looking at sequence for the result of the question asked, the ability of the DNA to form a number of 3D confirmations (hairpins, loops, etc) and the resulting thermodynamic properties of the structure are often the "output". As far as the orientation being important, it is -- within a single, given strand. That is what is so elegant about the way DNA works, you only need one strand to convey the necessary info. I meant orientation across strands, not within a single strand. The sequence within a single strand is of course crucial.
I think I already forgot the context;~) Maybe it was this...In computers today there are 1's and 0's, making it a binary system because it has one property or the other. While DNA is composed of 4 bases (with A pairing with T and G pairing with C) you could say it is base 4 because any given base can be a G,C, A, or T, but this is only if you focus on a single strand. If you are looking at both strands, you could consider it a binary system, because across both strands you could only have a pair of A:T or a pair of G:C. So maybe it's better for me to say you can use DNA as a binary system if you use it in the context of both strands. At any rate, I think I've ranted enough...
I think you guys are missing the point. The coding in DNA that we are talking about using is NOT 3 bases coding for a particular amino acid, but using the string of bases, and permutations of those bases, to answer problems that are asked. These types of experiments (and I have read the some of the primary literature) do not rely on the ability of DNA to code for a particular amino acid sequence (and BTW, not all proteins are enzymes), they simply rely on the sequence of the DNA. The DNA isn't transcribed into RNA, and thus no proteins (translated from that RNA) are involved.
What you say is true, but keep in mind that no matter which strand you are looking at (whether the coding strand or the complementary strand) you automatically know the sequence of the other strand. So really, orientation is irrelevant as long as you know which strand you are dealing with. Also keep in mind that we (as in people who don't actually do this research) don't really know how the experiments are carried out, i.e. how the question is asked, and how the answer is obtained, which obviously affects how the results are interpreted.
First off, these ideas have been around and been discussed ever since Watson and Crick cracked the DNA code in the fifties, so there has been a significant amount of literature and thought devoted to the subject. Here's my own thoughts on your questions...
--In the long run, will biology rewrite computing or will modern day technology concepts and theory be integrated into biology? If both are true, which will have the greater effect? I understand long run is ambiguous in this question, but Iâ(TM)m interested in all thoughts using any applicable definition.--
The likelihood that "modern day technology concepts and theory" will be integrated into biology seems unlikely to me, but I think you're really asking the following question-- Will we be able to use technology to design life, based on our ability to manipulate the code? I suspect so, though it will never be possible to escape the reality that what we would be doing was more biology than computer science. For the first part, will biology affect technology? Definitely. Rewrite it completely? I doubt it. It's more likely that biological computing systems will work well for certain tasks but not others (based on factors like complexities or huge numbers of variables).
--Tied to the first question: How will the nature of computing, and how we perceive it, change due to biology integration? More to the point, how much of the theory we learn today may change?--
I don't think anyone can even begin to answer this question, because the possibilites are practically infinite. If I had to guess though, I would say this -- most computer theory (I think not all, but I'm not sure) these days is based solidly on the binary system you mention, things are either one thing or another, a 1 or a 0. I think biological systems may someday be able to solve problems based on "fuzzier" logic, simply because the complexity that could be managed by DNA is very large.
--What will be the biggest issue determining the success of the adoption of biology-integrated computing? Will it be technology factors or will it be societal factors (e.g., rebellion by the Right Wing), or something else? What things must hold true to make the idea succeed?--
Like most things, I think the biggest issue determining the adoption of biology-integrated computing will be the rise of a company that can make a viable product that serves people either better than before or in a new way. Reality has shown that no matter how good an idea is, there are many other factors that can govern what is adopted and what isn't, just look at Betamax vs. VCR. Everybody knows betamax was better, but it didn't matter in the long run.
--And perhaps the hottest issue of all: Is there anything inherently wrong with pursuing this avenue? What may be some of the consequences?--
As in all things, there is nothing inherently wrong with pursuing knowledge. It's how we acquire that knowledge and what we do with it that can lead to moral dilemmas.
I wonder if the zoo where the six introduced penguins came from had the same problem? Or if those penguins didn't do it until they got to the new place...maybe they are trying to migrate back to Ohio;~)
Re:No genetic engineering? I don't think so....
on
Shrinking The Watermelon
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· Score: 2, Insightful
I would agree. But let's face it, the average joe on the street (people who have never heard of/. nor care to) is going to have a very different view when you present them with a watermelon produced by mucking about with the DNA in the laboratory versus one whose parents were played with in the greenhouse. Just look at the European Union and their views on GM food. That was my main point.
Re:No genetic engineering? I don't think so....
on
Shrinking The Watermelon
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· Score: 2, Interesting
genetic engineering has a connotation of direct human alteration of a gene, as opposed to just picking which plants get to breed. Semantics I know, but most people make the distinction.
they don't mention "junk" DNA, and I couldn't even find the original article (why in the hell wouldn't the BBC reference it?). What is called junk DNA makes up the vast amount of our 3 billion base pairs, but junk DNA is different than intron DNA (and exon), and there is increasing evidence that Junk DNA may actually be very important. As far as diversity, that usually refers to differences within coding DNA, not junk DNA.
this is off topic, but - it 's fairly well agreed upon by scholars that the greeks mistranslated the hebrew word used to describe Mary (purposefully) into the word virgin, while it actually just meant maiden, or young woman, or something like that.
I hate to state the obvious and spoil all the hilarious comments here (which are undoubtedly meant to ridiculous), but cigarettes from the altered tobacco plants will of course NOT be smoked if you are bitten by a rabid dog. The leaves from the plants will be mushed up and the antibodies will be extracted, yielding a fluid for injection.
This won't do anything for the cigarette industry, but this (and other work in tobacco) could very well help tobacco farmers. Tobacco is used not only because it is easy to introduce DNA into, but because it grows easily, fast, and has big leaves, allowing for high production of the protein of interest.
This one spread through my university like wildfire today! It even seems to fake Norton virus definition updating, such that the computer appears to be updating it's virus definitions but isn't. It seemed to spread via hijacked messages that it attached itself to.
cross-job skill development
on
Chicken Run
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· Score: 1
a potential new job for all those unemployed guys that drive the machines that suck up golf balls...
Can somebody tell me why eBooks are better than audio content? What can possibly be done with electronic text, that cannot be accomplished through audio content? I can understand that audio books are much more expensive to produce, but surely we are nearing the point where synthetic computer voices can "read" the original text, instead of having to employ human voice actors. That being the case, what's the use?
While it will certainly be interesting to learn how many genes there truly are in the human genome, that number will not be very important - what will truly matter is how many proteins are actually expressed (a number that will be much higher than the number of genes, as many genes have multiple mRNA splice variants). It's this "protein" evolution that really makes us what we are (some plants have millions of genes, so higher numbers don't mean crap).
Of course, what this post tells us yet again is that scientists will never pass up a chance to give their opinions, even if it's just a guess at the number of human genes!
How would you suggest that research be funded, if not by the american people? The reason we are the most dominant country in the world scientifically is because we devote so much money to research. If we want to continue leading the world in scientific advances (and hence healthcare advances) we need to continue the funding through taxes. It simply is not possible to conduct the amount of research that is performed in the United States using private money.
As far as the issue of patents -- all universities have scientific patent offices now, so don't be surprised if they try and patent this somehow.
Praedor - thanks for correcting my error (too early in the morning!). Although unleashing humanity on outerspace would undoubtedly result in some detrimental effects (numerous sci-fi books where humans spread through the galaxy like a plague come to mind), it would still be preferable to the disappearance of our species.
I'd just be happy to see Homo Sapiens someplace other than Earth.
I agree. Let's face it, our future here is too delicate. Who wants 15 billion years of evolution destroyed by a single errant asteroid? We need to get out there in space whatever it takes, and if the chinese are the first to do it, so be it.
Slashdot Mirror
I'm not sure if stop/start codons would even matter, as it's my understanding that when DNA is used as a computational tool, it is typically rather short, synthesized strands. Keep in mind that a stop/start codon is relevant once the DNA has been transcribed into RNA and the RNA is being translated into proteins - in other words, as far as the DNA is concerned a stop/start codon is just another three base pairs. Also, it's my understanding that besides looking at sequence for the result of the question asked, the ability of the DNA to form a number of 3D confirmations (hairpins, loops, etc) and the resulting thermodynamic properties of the structure are often the "output". As far as the orientation being important, it is -- within a single, given strand. That is what is so elegant about the way DNA works, you only need one strand to convey the necessary info. I meant orientation across strands, not within a single strand. The sequence within a single strand is of course crucial.
I think I already forgot the context ;~) Maybe it was this...In computers today there are 1's and 0's, making it a binary system because it has one property or the other. While DNA is composed of 4 bases (with A pairing with T and G pairing with C) you could say it is base 4 because any given base can be a G,C, A, or T, but this is only if you focus on a single strand. If you are looking at both strands, you could consider it a binary system, because across both strands you could only have a pair of A:T or a pair of G:C. So maybe it's better for me to say you can use DNA as a binary system if you use it in the context of both strands. At any rate, I think I've ranted enough...
I think you guys are missing the point. The coding in DNA that we are talking about using is NOT 3 bases coding for a particular amino acid, but using the string of bases, and permutations of those bases, to answer problems that are asked. These types of experiments (and I have read the some of the primary literature) do not rely on the ability of DNA to code for a particular amino acid sequence (and BTW, not all proteins are enzymes), they simply rely on the sequence of the DNA. The DNA isn't transcribed into RNA, and thus no proteins (translated from that RNA) are involved.
What you say is true, but keep in mind that no matter which strand you are looking at (whether the coding strand or the complementary strand) you automatically know the sequence of the other strand. So really, orientation is irrelevant as long as you know which strand you are dealing with. Also keep in mind that we (as in people who don't actually do this research) don't really know how the experiments are carried out, i.e. how the question is asked, and how the answer is obtained, which obviously affects how the results are interpreted.
DNA can be thought of as a binary system because it either comes in a G:C pair or an A:T pair.
RNA seems to only copy DNA, but there are some theories that RNA actually came first.
--In the long run, will biology rewrite computing or will modern day technology concepts and theory be integrated into biology? If both are true, which will have the greater effect? I understand long run is ambiguous in this question, but Iâ(TM)m interested in all thoughts using any applicable definition.--
The likelihood that "modern day technology concepts and theory" will be integrated into biology seems unlikely to me, but I think you're really asking the following question-- Will we be able to use technology to design life, based on our ability to manipulate the code? I suspect so, though it will never be possible to escape the reality that what we would be doing was more biology than computer science. For the first part, will biology affect technology? Definitely. Rewrite it completely? I doubt it. It's more likely that biological computing systems will work well for certain tasks but not others (based on factors like complexities or huge numbers of variables).
--Tied to the first question: How will the nature of computing, and how we perceive it, change due to biology integration? More to the point, how much of the theory we learn today may change?--
I don't think anyone can even begin to answer this question, because the possibilites are practically infinite. If I had to guess though, I would say this -- most computer theory (I think not all, but I'm not sure) these days is based solidly on the binary system you mention, things are either one thing or another, a 1 or a 0. I think biological systems may someday be able to solve problems based on "fuzzier" logic, simply because the complexity that could be managed by DNA is very large.
--What will be the biggest issue determining the success of the adoption of biology-integrated computing? Will it be technology factors or will it be societal factors (e.g., rebellion by the Right Wing), or something else? What things must hold true to make the idea succeed?--
Like most things, I think the biggest issue determining the adoption of biology-integrated computing will be the rise of a company that can make a viable product that serves people either better than before or in a new way. Reality has shown that no matter how good an idea is, there are many other factors that can govern what is adopted and what isn't, just look at Betamax vs. VCR. Everybody knows betamax was better, but it didn't matter in the long run.
--And perhaps the hottest issue of all: Is there anything inherently wrong with pursuing this avenue? What may be some of the consequences?--
As in all things, there is nothing inherently wrong with pursuing knowledge. It's how we acquire that knowledge and what we do with it that can lead to moral dilemmas.
I wonder if the zoo where the six introduced penguins came from had the same problem? Or if those penguins didn't do it until they got to the new place...maybe they are trying to migrate back to Ohio ;~)
I would agree. But let's face it, the average joe on the street (people who have never heard of /. nor care to) is going to have a very different view when you present them with a watermelon produced by mucking about with the DNA in the laboratory versus one whose parents were played with in the greenhouse. Just look at the European Union and their views on GM food. That was my main point.
genetic engineering has a connotation of direct human alteration of a gene, as opposed to just picking which plants get to breed. Semantics I know, but most people make the distinction.
they don't mention "junk" DNA, and I couldn't even find the original article (why in the hell wouldn't the BBC reference it?). What is called junk DNA makes up the vast amount of our 3 billion base pairs, but junk DNA is different than intron DNA (and exon), and there is increasing evidence that Junk DNA may actually be very important. As far as diversity, that usually refers to differences within coding DNA, not junk DNA.
this is off topic, but - it 's fairly well agreed upon by scholars that the greeks mistranslated the hebrew word used to describe Mary (purposefully) into the word virgin, while it actually just meant maiden, or young woman, or something like that.
This won't do anything for the cigarette industry, but this (and other work in tobacco) could very well help tobacco farmers. Tobacco is used not only because it is easy to introduce DNA into, but because it grows easily, fast, and has big leaves, allowing for high production of the protein of interest.
This one spread through my university like wildfire today! It even seems to fake Norton virus definition updating, such that the computer appears to be updating it's virus definitions but isn't. It seemed to spread via hijacked messages that it attached itself to.
a potential new job for all those unemployed guys that drive the machines that suck up golf balls...
Can somebody tell me why eBooks are better than audio content? What can possibly be done with electronic text, that cannot be accomplished through audio content? I can understand that audio books are much more expensive to produce, but surely we are nearing the point where synthetic computer voices can "read" the original text, instead of having to employ human voice actors. That being the case, what's the use?
Of course, what this post tells us yet again is that scientists will never pass up a chance to give their opinions, even if it's just a guess at the number of human genes!
How would you suggest that research be funded, if not by the american people? The reason we are the most dominant country in the world scientifically is because we devote so much money to research. If we want to continue leading the world in scientific advances (and hence healthcare advances) we need to continue the funding through taxes. It simply is not possible to conduct the amount of research that is performed in the United States using private money. As far as the issue of patents -- all universities have scientific patent offices now, so don't be surprised if they try and patent this somehow.
Praedor - thanks for correcting my error (too early in the morning!). Although unleashing humanity on outerspace would undoubtedly result in some detrimental effects (numerous sci-fi books where humans spread through the galaxy like a plague come to mind), it would still be preferable to the disappearance of our species.
I'd just be happy to see Homo Sapiens someplace other than Earth. I agree. Let's face it, our future here is too delicate. Who wants 15 billion years of evolution destroyed by a single errant asteroid? We need to get out there in space whatever it takes, and if the chinese are the first to do it, so be it.