Perhaps (and I'm just tossing out ideas) something small (artificial protein?) that can be 'added' to all normal cells as an enhanced early warning device when something that gets by the white blood cells?
That's how it works now, actually. They're mostly sugar groups, though. HIV is a problem primarily because it steals one of the body's normal tags and coats its virus particles in it, making it look like one of our cells.
White blood cells can do a lot but they need to learn how to identify some invaders better without wiping out their host. It sounds like figuring out how to defend against AIDS is doing better and cancer the same way (ironically using the former's methods).
It would be nice if one could program the current immune system with a broad range identifier would eliminate all but the rarest of virus infections. Then the next step would be to somehow analyze foreign invaders to give scientists advance warning. Then a way to create fixes automatically.
This is where the problems are. In some diseases, there are no distinguishing features for immune cells to lock onto. They can only see what's on the surface, after all; there's no one "broad range identifier" that works. Trying to create one is as problematic as trying to come up with a universal identification for computer malware without an uninfected 'reference' copy: how do you even know if what it's doing is bad? In computers, we always have the "if it's modifying the boot sector, that's bad" excuse, but (a) the human genome is more than 6.2 billion bytes in size, and (b) it changes all the time on its own. There are even things in our bodies that are repurposed viruses, nearly indistinguishable from normal ones except by surface features our immune system already has a handle on. The only really good way to tell if something's diseased is... if it dies.
I promise you I have plenty of imagination! (Try checking out my site!) But I might very well level the same accusation at you, for lingering so much on health problems. Really, though, your probe comes up against some harsh prerequisites: we're still trying to figure out how to deal with cancer and HIV in the lab. When we finally do figure out how to beat them reliably, the most sensible thing to do would be to issue an update to the human genome so it can do the job itself. A symbiont would be a lot riskier.
That being said, I actually did briefly explore the possibility of engineering a pair of symbionts for one of my undergraduate projects. We were looking at the idea of attaching bacteria to the worm C. elegans so that the bacteria could feed the worm a type of gene suppressing-molecule called siRNA. Our main project was making C. elegans easier to engineer, and the bacterium in question (E. coli) is exceedingly well-understood, so we kind of approached the idea as a form of backward compatibility with other engineering projects.
In the end, we abandoned it when we realised that E. coli is one of the major food sources for C. elegans—it was a little like strapping hamburgers to the body of an exceedingly hungry person, in that it was doomed to fail to accomplish anything useful, no matter how delicious it may have been to the worm.
However, if it is symbiotic organisms that get your mind going, one application would be in using siRNA in humans to get around the whole "icky genome patching" issue, which is sure to garner complaints from lots of people. At present, RNA interference experiments in humans typically involve syringes; pills don't work since our digestive systems are much too acidic. siRNA also doesn't last very long. Using so many syringes would be an unpleasant way to keep oneself protected—but having an on-board organism that could release the appropriate RNA under specified times might be highly practical. It does have has its limitations, however, in that it can only turn genes off, not supplement them. Such a guest organism would most likely have to be a genetically population of leukocytes, since there are few ideas in medicine worse than "let's put undetectable bacteria into the bloodstream and watch what happens!" However, this would allow for a "detection –> silencing" cycle for dealing with genetic disorders, cancers, and even particularly vexing viruses like HIV.
There's little in a dead cell that can tell you why or how it died, short of performing huge batches of analyses on every molecule inside of it. If an infectious organism is responsible, it's much more feasible to deal with it in advance—and you can rest assured that the body is already aware of it.
And on that note, good luck outperforming the native biology without causing an immune disorder. We currently work by generating all possible pathogen-detecting receptors that (a) target biological molecules and (b) do not target ourselves. If something that matches is found, we amplify that antibody until the disease goes away. In AIDS, the body generates trillions of disease-fighting cells per day, trying it hardest to outpace the infection. This system is so good that all vaccines have to do is tell the body to prepare certain antibodies in advance by giving it a non-infectious sample to target.
Humans don't need augmentation to help them fight disease. That's what they've evolved to do, and they do it pretty well as long as they're healthy. If you want to play with tech like that, focus on improving our lives beyond what they already have the ability to be. Go back to Douglas Engelbart's ideas of intellect augmentation. Brain-computer interfaces are much more useful for creating two-way communication to control and access external information systems.
This is a notice to inform you that your geek card has been revoked. Here is your missing reference. Please study this carefully before you reapply for your card.
No. The real reason Oracle is doing all the Evil in the world now because Bill Dead Gates said so. This is just another shill post on Oracle here, one of many I have seen in last few days.
Sarcasm. Such e-mails are presumably not just 50 characters. I was making a joke about typical office e-mails, which are severely top-posting and content-free, like some kind of IM system gone wrong.
The solution is referential quoting. Instead of letting e-mails bulk up with huge morraines of backlogs, use reference numbers to refer to the message in the mailbox that this message most likely was a reply to. Then, trim out the extra data. Voila, now each e-mail is guaranteed to be an average of 50 bytes—guess your co-workers didn't have that much to say!
Knowing E. coli? Probably somewhere between a day and a week. Bacterial DNA replication is really lousy. Anything that doesn't contribute to keeping the cell alive tends to get a little messed up when it's allowed to reproduce freely.
The primary application of this kind of biological computing tends to revolve around the negligible energy requirements: just throw some sugar water on it, and you're done for the next while; no electricity required. Other than that, there's a lot of theoretical interest in these systems for their comparability to neurons, but to be honest they're comparatively useless. We have great respect for DNA computing (which is very different from turning bacteria into transistors) and the potential of exploiting enzyme kinetics for computing applications, but projects like this are relatively fluffy and conceptual.
None of those functions would do very well in a symbiont. An organism tasked with repairing your tissue would have to be made out of your stem cells. An organism tasked with receiving signals from, or affecting, the nervous system would have to be capable of interacting with nerve endings. Unless you were thinking of manual endocrine signalling (releasing a hormone in response to a thought), which is inherently slow, and would still require a great deal of engineering the human side of things to produce the desired effect.
E. coli is the best-studied bacterium. It's a lot more convenient to work with them.
If it's any consolation, students in past years at iGEM have figured out how to make it smell like mint or bananas with some genetic engineering, if you add the right chemical precursor to the plate. You can even silence the foul-smelling metabolic pathways (which are part of, but not all of, the awful smell of feces) if you're really determined to, but most of the time it's not worth it.
There are two categories, I'd say, in which genetic engineering could be undetectable with present technology:
1. A very small mutation or alteration, especially one produced by selective exposure to a chemical mutagen such as EMS. This has been a common technique in biology for many, many years to produce defective organisms; the idea being that if it's broken, you can figure out what it was supposed to do by examining what is no longer working. A mutation like this would just resemble a random event; it would be indistinguishable from background noise. That being said, they're basically impossible to control, and they never add things, only damage genes, so you wouldn't get a unicorn out of them.
2. A naturally-induced mutation engineered not directly, but through selective pressure. If you've been near biology for very long, you've probably heard of a company called Monsanto. Their most notorious business is selling herbicides and complementary herbicide-resistant crops. These crops weren't actually spliced in the lab, just selectively bred through plant eugenics until the right immunity developed. This is similar to how we domesticated plants and animals for agriculture in the first place.
To produce anything truly exciting, you'd have to be doing some splicing or rewriting. Hypothetically if you knew all of the statistical properties of DNA and could make your constructs look like plausible members of related genes family, and had the power to synthesize an entire mammalian chromosome (or insert into one without evidence, which is fairly easy with PCR, but you still have to get it into the nucleus), then you could produce something that looked natural and authentic—but the benefits of doing so would be extremely questionable. Even after all that, you'd still have the original horse kicking around, and just by comparing the two, you'd be able to see that the modifications all seemed to come in one nice, neat package, and furthermore that they didn't have any ancestors that gave them an alibi as to where they came from.
Faking life on this level is equivalent to faking an entire branch in a source repo, except the source repo has no code formatting standards, and code can only be contributed in tiny little bits by copying functions and then altering them one line at a time. Do you have the previous revisions? Does the code look like it was written all at once? Are the comments written all by one person? Are there inconsistencies in indentation style? Are there typos all over the place? Do all the other devs have the previous version on their computers still? What about the guy we fired last month; does his machine have the version before that on it? If not, it's fake.
Well, for one—those cats would be at a huge disadvantage. They wouldn't last long in the wild at all.
Two—due to epigenetics, codon bias, Chargaff's second rule, and other sequence biases, it's fairly probable that the sequence itself would be under pressure to mutate regardless of evolutionary pressure, possibly rendering itself inert. The enhanced green fluorescent protein (eGFP) that most labs use is optimized for mammalian expression through things like intron addition, but not at these lower levels. In any case, the cats carrying the gene may not stay glowing green for very long, and that's not counting the possibility of chiasmus cutting it in half.
However, to answer your question, there are several traits that would stand out:
1. To get a mammal to produce a synthetic protein stably, you generally have to build a gene construct and then insert the sequence into the genome using a retrovirus or adenovirus. Depending on the specific delivery virus, the site of integration may be obvious. While viral integration sites don't generally come across as anything remarkable, the genetic construct used by the researchers most likely contains an promoter region (like a file header for genes that defines when and in what tissues a gene should be expressed) that was copied from some other gene. A native promoter inside of a viral integration site would be very unusual and obvious.
2. The payload itself. Green fluorescent protein is only naturally produced by jellyfish. We often combine it with other proteins (in what is called a protein fusion) to make it easy to see where and when the protein is being expressed. It's very much like a debug message.
3. The point of fusion between the promoter and the coding sequence. It's very possible to synthesize the promoter and the protein together as one unit, but often unnecessarily expensive. There are several steps in the protein expression process where it's safe to insert a few extra nucleotides, and often we use a kind of protein called a restriction enzyme to cut up DNA so it can be reassembled into a longer unit. There are thousands of known restriction enzymes, almost all of which cut at very specific and unique sequences. If we spot one of these sequences (called a "ligation scar" because it's left over when you glue the parts back together) between the protein and the promoter, chances are that it was left over by a molecular biologist. Of course, there are many possible such sequences, all very short, but there are only a handful that are really popular, and they're very recognizable.
4. The location of the fusion. Similar genes usually cluster together on chromosomes, because they come from one ancestor that got copied by accident and then slowly drifted apart from each other. The promoter they used is probably from a very different part of the genome than where it was integrated—not to mention the payload, which I've already said is completely alien in several respects.
Hope that's more insightful than not. Let me know if Wikipedia lets you down while looking up any of the terms I've used; I'd be more than happy to help gloss them.
Pointing weaponry of any kind at Creationism is a waste of time. If you want to make a difference, go to the source, and defeat the charismatic leaders by revealing their true intentions to their power base. The rhetoric is not the danger—it's meaningless, irrelevant mudslinging meant to confuse and delay the enemy. It's a power game, and dealing with the symptoms before you fix the source is only going to keep you treading water.
The people who invent Creationist stories don't really believe what they're saying is objectively true; it's just convenient for them to say it is. Carrying out an argument on the grounds of reason only works on their victims' children—who, incidentally, now staff the traditional church. If you want to fight evangelicals and religion-founders, you must take them for what they really are.
I might argue otherwise—if we can visualize the shifts in effect with this much precision, we can use bioinformatics and chemical kinetics to work our way backward and find what's generating the signal, both tasks that are comparatively well-solved.
It would either be short and fat, or dead because there wouldn't be enough room for its organs to grow. Either way, it wouldn't slither very well, and would be at something of a disadvantage.
The use of the word "defect," as you can probably already imagine, is a very biased way of looking at things and will probably do more harm than good. Although, of course, at the time the mutation first appeared, when snakes still had non-vestigial limbs, it probably was at least partially something of an inconvenience.
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I think you need to be deported back to meme joke school. I recommend starting with this batch of actual Yakov Smirnoff jokes and this collection of barely funny "In Soviet Russia" jokes. See if you can spot the pattern, and determine what you did wrong. (HINT: just "is" never works as a verb.)
Your ideas are intriguing to me and I wish to subscribe to your newsletter.
You had me up until "Why?". Alas, computer scientists will never get their full dues.
Perhaps (and I'm just tossing out ideas) something small (artificial protein?) that can be 'added' to all normal cells as an enhanced early warning device when something that gets by the white blood cells?
That's how it works now, actually. They're mostly sugar groups, though. HIV is a problem primarily because it steals one of the body's normal tags and coats its virus particles in it, making it look like one of our cells.
White blood cells can do a lot but they need to learn how to identify some invaders better without wiping out their host. It sounds like figuring out how to defend against AIDS is doing better and cancer the same way (ironically using the former's methods).
It would be nice if one could program the current immune system with a broad range identifier would eliminate all but the rarest of virus infections. Then the next step would be to somehow analyze foreign invaders to give scientists advance warning. Then a way to create fixes automatically.
This is where the problems are. In some diseases, there are no distinguishing features for immune cells to lock onto. They can only see what's on the surface, after all; there's no one "broad range identifier" that works. Trying to create one is as problematic as trying to come up with a universal identification for computer malware without an uninfected 'reference' copy: how do you even know if what it's doing is bad? In computers, we always have the "if it's modifying the boot sector, that's bad" excuse, but (a) the human genome is more than 6.2 billion bytes in size, and (b) it changes all the time on its own. There are even things in our bodies that are repurposed viruses, nearly indistinguishable from normal ones except by surface features our immune system already has a handle on. The only really good way to tell if something's diseased is... if it dies.
Do you work for Chief Quimby?
That works—but I don't think bullwhips do all that well in space. May want to pack a tricorder instead.
I promise you I have plenty of imagination! (Try checking out my site!) But I might very well level the same accusation at you, for lingering so much on health problems. Really, though, your probe comes up against some harsh prerequisites: we're still trying to figure out how to deal with cancer and HIV in the lab. When we finally do figure out how to beat them reliably, the most sensible thing to do would be to issue an update to the human genome so it can do the job itself. A symbiont would be a lot riskier.
That being said, I actually did briefly explore the possibility of engineering a pair of symbionts for one of my undergraduate projects. We were looking at the idea of attaching bacteria to the worm C. elegans so that the bacteria could feed the worm a type of gene suppressing-molecule called siRNA. Our main project was making C. elegans easier to engineer, and the bacterium in question (E. coli) is exceedingly well-understood, so we kind of approached the idea as a form of backward compatibility with other engineering projects.
In the end, we abandoned it when we realised that E. coli is one of the major food sources for C. elegans—it was a little like strapping hamburgers to the body of an exceedingly hungry person, in that it was doomed to fail to accomplish anything useful, no matter how delicious it may have been to the worm.
However, if it is symbiotic organisms that get your mind going, one application would be in using siRNA in humans to get around the whole "icky genome patching" issue, which is sure to garner complaints from lots of people. At present, RNA interference experiments in humans typically involve syringes; pills don't work since our digestive systems are much too acidic. siRNA also doesn't last very long. Using so many syringes would be an unpleasant way to keep oneself protected—but having an on-board organism that could release the appropriate RNA under specified times might be highly practical. It does have has its limitations, however, in that it can only turn genes off, not supplement them. Such a guest organism would most likely have to be a genetically population of leukocytes, since there are few ideas in medicine worse than "let's put undetectable bacteria into the bloodstream and watch what happens!" However, this would allow for a "detection –> silencing" cycle for dealing with genetic disorders, cancers, and even particularly vexing viruses like HIV.
Nah. We'll probably all be artists and scientists, or something.
There's little in a dead cell that can tell you why or how it died, short of performing huge batches of analyses on every molecule inside of it. If an infectious organism is responsible, it's much more feasible to deal with it in advance—and you can rest assured that the body is already aware of it.
And on that note, good luck outperforming the native biology without causing an immune disorder. We currently work by generating all possible pathogen-detecting receptors that (a) target biological molecules and (b) do not target ourselves. If something that matches is found, we amplify that antibody until the disease goes away. In AIDS, the body generates trillions of disease-fighting cells per day, trying it hardest to outpace the infection. This system is so good that all vaccines have to do is tell the body to prepare certain antibodies in advance by giving it a non-infectious sample to target.
Humans don't need augmentation to help them fight disease. That's what they've evolved to do, and they do it pretty well as long as they're healthy. If you want to play with tech like that, focus on improving our lives beyond what they already have the ability to be. Go back to Douglas Engelbart's ideas of intellect augmentation. Brain-computer interfaces are much more useful for creating two-way communication to control and access external information systems.
This is a notice to inform you that your geek card has been revoked. Here is your missing reference. Please study this carefully before you reapply for your card.
No. The real reason Oracle is doing all the Evil in the world now because Bill Dead Gates said so. This is just another shill post on Oracle here, one of many I have seen in last few days.
Sarcasm. Such e-mails are presumably not just 50 characters. I was making a joke about typical office e-mails, which are severely top-posting and content-free, like some kind of IM system gone wrong.
The solution is referential quoting. Instead of letting e-mails bulk up with huge morraines of backlogs, use reference numbers to refer to the message in the mailbox that this message most likely was a reply to. Then, trim out the extra data. Voila, now each e-mail is guaranteed to be an average of 50 bytes—guess your co-workers didn't have that much to say!
Knowing E. coli? Probably somewhere between a day and a week. Bacterial DNA replication is really lousy. Anything that doesn't contribute to keeping the cell alive tends to get a little messed up when it's allowed to reproduce freely.
You may enjoy reading The evolution of the past tense - how verbs change over time by Ed Yong.
The primary application of this kind of biological computing tends to revolve around the negligible energy requirements: just throw some sugar water on it, and you're done for the next while; no electricity required. Other than that, there's a lot of theoretical interest in these systems for their comparability to neurons, but to be honest they're comparatively useless. We have great respect for DNA computing (which is very different from turning bacteria into transistors) and the potential of exploiting enzyme kinetics for computing applications, but projects like this are relatively fluffy and conceptual.
None of those functions would do very well in a symbiont. An organism tasked with repairing your tissue would have to be made out of your stem cells. An organism tasked with receiving signals from, or affecting, the nervous system would have to be capable of interacting with nerve endings. Unless you were thinking of manual endocrine signalling (releasing a hormone in response to a thought), which is inherently slow, and would still require a great deal of engineering the human side of things to produce the desired effect.
E. coli is the best-studied bacterium. It's a lot more convenient to work with them.
If it's any consolation, students in past years at iGEM have figured out how to make it smell like mint or bananas with some genetic engineering, if you add the right chemical precursor to the plate. You can even silence the foul-smelling metabolic pathways (which are part of, but not all of, the awful smell of feces) if you're really determined to, but most of the time it's not worth it.
Personally I prefer the irony of the Genesis Device for my apocalyptic non sequiturs, but to each her own.
There are two categories, I'd say, in which genetic engineering could be undetectable with present technology:
1. A very small mutation or alteration, especially one produced by selective exposure to a chemical mutagen such as EMS. This has been a common technique in biology for many, many years to produce defective organisms; the idea being that if it's broken, you can figure out what it was supposed to do by examining what is no longer working. A mutation like this would just resemble a random event; it would be indistinguishable from background noise. That being said, they're basically impossible to control, and they never add things, only damage genes, so you wouldn't get a unicorn out of them.
2. A naturally-induced mutation engineered not directly, but through selective pressure. If you've been near biology for very long, you've probably heard of a company called Monsanto. Their most notorious business is selling herbicides and complementary herbicide-resistant crops. These crops weren't actually spliced in the lab, just selectively bred through plant eugenics until the right immunity developed. This is similar to how we domesticated plants and animals for agriculture in the first place.
To produce anything truly exciting, you'd have to be doing some splicing or rewriting. Hypothetically if you knew all of the statistical properties of DNA and could make your constructs look like plausible members of related genes family, and had the power to synthesize an entire mammalian chromosome (or insert into one without evidence, which is fairly easy with PCR, but you still have to get it into the nucleus), then you could produce something that looked natural and authentic—but the benefits of doing so would be extremely questionable. Even after all that, you'd still have the original horse kicking around, and just by comparing the two, you'd be able to see that the modifications all seemed to come in one nice, neat package, and furthermore that they didn't have any ancestors that gave them an alibi as to where they came from.
Faking life on this level is equivalent to faking an entire branch in a source repo, except the source repo has no code formatting standards, and code can only be contributed in tiny little bits by copying functions and then altering them one line at a time. Do you have the previous revisions? Does the code look like it was written all at once? Are the comments written all by one person? Are there inconsistencies in indentation style? Are there typos all over the place? Do all the other devs have the previous version on their computers still? What about the guy we fired last month; does his machine have the version before that on it? If not, it's fake.
Well, for one—those cats would be at a huge disadvantage. They wouldn't last long in the wild at all.
Two—due to epigenetics, codon bias, Chargaff's second rule, and other sequence biases, it's fairly probable that the sequence itself would be under pressure to mutate regardless of evolutionary pressure, possibly rendering itself inert. The enhanced green fluorescent protein (eGFP) that most labs use is optimized for mammalian expression through things like intron addition, but not at these lower levels. In any case, the cats carrying the gene may not stay glowing green for very long, and that's not counting the possibility of chiasmus cutting it in half.
However, to answer your question, there are several traits that would stand out:
1. To get a mammal to produce a synthetic protein stably, you generally have to build a gene construct and then insert the sequence into the genome using a retrovirus or adenovirus. Depending on the specific delivery virus, the site of integration may be obvious. While viral integration sites don't generally come across as anything remarkable, the genetic construct used by the researchers most likely contains an promoter region (like a file header for genes that defines when and in what tissues a gene should be expressed) that was copied from some other gene. A native promoter inside of a viral integration site would be very unusual and obvious.
2. The payload itself. Green fluorescent protein is only naturally produced by jellyfish. We often combine it with other proteins (in what is called a protein fusion) to make it easy to see where and when the protein is being expressed. It's very much like a debug message.
3. The point of fusion between the promoter and the coding sequence. It's very possible to synthesize the promoter and the protein together as one unit, but often unnecessarily expensive. There are several steps in the protein expression process where it's safe to insert a few extra nucleotides, and often we use a kind of protein called a restriction enzyme to cut up DNA so it can be reassembled into a longer unit. There are thousands of known restriction enzymes, almost all of which cut at very specific and unique sequences. If we spot one of these sequences (called a "ligation scar" because it's left over when you glue the parts back together) between the protein and the promoter, chances are that it was left over by a molecular biologist. Of course, there are many possible such sequences, all very short, but there are only a handful that are really popular, and they're very recognizable.
4. The location of the fusion. Similar genes usually cluster together on chromosomes, because they come from one ancestor that got copied by accident and then slowly drifted apart from each other. The promoter they used is probably from a very different part of the genome than where it was integrated—not to mention the payload, which I've already said is completely alien in several respects.
Hope that's more insightful than not. Let me know if Wikipedia lets you down while looking up any of the terms I've used; I'd be more than happy to help gloss them.
Pointing weaponry of any kind at Creationism is a waste of time. If you want to make a difference, go to the source, and defeat the charismatic leaders by revealing their true intentions to their power base. The rhetoric is not the danger—it's meaningless, irrelevant mudslinging meant to confuse and delay the enemy. It's a power game, and dealing with the symptoms before you fix the source is only going to keep you treading water.
The people who invent Creationist stories don't really believe what they're saying is objectively true; it's just convenient for them to say it is. Carrying out an argument on the grounds of reason only works on their victims' children—who, incidentally, now staff the traditional church. If you want to fight evangelicals and religion-founders, you must take them for what they really are.
I might argue otherwise—if we can visualize the shifts in effect with this much precision, we can use bioinformatics and chemical kinetics to work our way backward and find what's generating the signal, both tasks that are comparatively well-solved.
It would either be short and fat, or dead because there wouldn't be enough room for its organs to grow. Either way, it wouldn't slither very well, and would be at something of a disadvantage.
The use of the word "defect," as you can probably already imagine, is a very biased way of looking at things and will probably do more harm than good. Although, of course, at the time the mutation first appeared, when snakes still had non-vestigial limbs, it probably was at least partially something of an inconvenience.