Economically Republicans today are not Republicans of old. Republicans, initially, favored a minimalist government which spent more time considering reasons NOT to get involved with the affairs of the people.
Hear, hear! Why is this not stressed more often? The philosophical foundation of the Republican party was more laizzes faire, in that they thought that government should be small and unobtrusive, and have minimal interaction in commerce. That has all disentigrated. I originally voted for Bush because he said he'd drop the size of government. That was one of the biggest reasons I was for him. But instead, the government grew more under him than it did under Clinton. Kerry's plans spell out "increased government size", and Bush's record says he'll do the same. Libertarian foreign policy seems like a repeat of the same mistakes we made 100 years ago.
I HATE voting for things I know are bad, but I guess I'll have to figure out who I think will do the least harm. God, this election sucks.
Thank you for pointing out the part about the rights. Although I disagree that the BOR may be harmful (not your assertion, I know) it is certainly not the limit of the rights given. They are highlighted rights. One thing to pick at, though:
The Patriot act was a bald manipulation of public emotion over 9/11 to pass a bill that had been shot down dozens of times over the last few years and decades.
I agree USA-PATRIOT was a manipulation, or at least a knee-jerk (over)reaction. But do you have any references to other serious attempts at such acts being passed?
I think that was kinda the point....The order is unconstitutional. The idea that there was an Excutive Order authorizing something that is that blatantly unconstitutional is scary. To me, at least.
Not sure about the pressing charges part, though. But IANAL.
The University and Researcher own the material, even though both are publicly funded.
I know, I work in a research lab as well. We have patents with the same setup. That's why I referenced the whole thing as a pipe dream. I know it really doesn't (and probably can't) work that way.
Most of the patent stuff here works as individual labs. The PI takes a cut, the department takes a cut, and the U takes a cut. What they all take a cut of is the proceeds and royalties of selling the patent to a major corp. The upside is that these patents are cheaper for the corp, and they (in a perfect world) Pass The Savings On To You! They do, to an extent, but they normally (almost always) don't pass on as much as they could.
If you were, say, hindu, and the majority of people in the USA were, say, christian - would you appreciate it if they decided to 'vote' that the national religion would be christianity and everyone had to go to the same church each sunday? Hey, it's one man one vote and the majority rules.... bullshit.
Not really a valid analogy. The source of the freedom you talk about is the Bill of Rights, and there is no Ammendment to the Constitution affecting the ability of Congress to appropriate funds for exploration.
Why do you assume that I am a single-issue voter? That is a very large, far-reaching and, as far as I can see, unfounded assumption. "People like you" that assume too much do little to advance any sort of discussion (sorry, I'm sarcastic by nature).
Another point, why would you assume that space flight (or any other issue) has no advantage? Why would you say that it is not "the right thing to do", as you put it? It is your *opinion* that it is not the right thing to do, while it is my opinion that it is. I think it is in conformity with the founding pronciples of this country, and that it will help us in the long run. (I know you said that you are personally excited about space flight, I'm just using it to demonstrate broad principle; re-read the above & think really broad)
The fact that we are a representative republic helps alleviate the mob rule aspect of a true democracy. We elect people we think represent our own views, and expect those people to go on and vote accordingly.
The system breaks down, however, when (1) Polticians don't 'go and vote accordingly' and (2) Their constituents don't hold them accountable. Both of which have occured...
To pay for it with tax money, it has to be good enough for other people, not just you.
One man, one vote. To send people into space is the grandparent's vote, and mine echos it. The bulk of your argument seems to deal with the way space is explored under government support, not with the fact that it is supported that way. I agree that there is a lot of waste, way too much waste, in the way NASA does things. But I still think that space exploration needs to be funded on several fronts, including the public front.
Look at biotech as an example. We explore biochemistry to find new ways of doing things. The benefit to mankind is exceptional and obvious. What is better: NIH funding of open projects that are available to all (Human Genome Project) or research done by private companies that are closed or fee based (the Celera genome database)? Biotech is full of similar examples. Would be better or worse off if the cutting edge drugs were discovered and approved in university labs solely funded by NIH, and were open to the public for use (yeah, yeah, a pipe dream for various reasons)?
Perhaps space exploration would be better served if it were under the direction of a body more like the NIH than NASA.
Sounds familiar. My wife & I technically live a bare scratch from the poverty line. If we had another kid, we'd qualify for welfare. When our daughter was born, we could have gotten WIC. But we paid less in taxes this year than last (same number of dependents each year), even though I got a cost of living "raise" last year. And yes, I mean actual net taxes paid after refund, not just the size of the refund we got, or witholdings, or anything else stupid like that.
Damn, if I'm among the wealthiest 2% of US families, how in the hell do the bottom 98% survive?
It's not so much that he didn't break the law. He did break the law, no question. The MPAA was well within their rights to pursue him for copyright infringement. Based on the dates on the video archive and the date of the raid he talks about, his hosting of the videos most likely triggered the raid. Perfectly legit, as far as what the MPAA did.
But that's not what got my attention here. What got my attention was the use of the Patriot act to get eveidence on him. We were told over and over again that it wouldn't be used for anythying except investigations into terrorist acts, but here it is being used to acquire evidence for copyright infringement.
Copyright infringement.
It wouldn't matter to me if it was a murder investigation, it's still precisely what we were assured, over and over again, would never happen, under any circumstances. There is a reason that our legal and investigative arms of the government are set up the way they are. The law enforcement arm is limited in what it can do, for very good reason. This act allows law enforcement to do things they otherwise could not, and should not, be able to do.
Good point on technology, but I think it's really a case of degrees.
Technology is really just advanced tool use. Using a chainsaw is at least fundamentally similar to using a stone axe, it's just more complex and advanced. From this standpoint, technology does not make us unique among Earth's animals. Elephants and apes both use tools, and I think other animals do as well. It's just that we do it to a greater extent.
I don't think there is a single thing that sets us apart. It's probably set of things that all finally happened in one organism. Maybe the combination of complex communication, social structures, tool use, and rudimentary mathematics. I don't know any other animal that has all of those characteristics.
But what relevance does this have to intelligence, anyway? Recall in the opening of HHGTG :
...Man had always assumed that he was more intelligent than dolphins because he had achieved so much... the wheel, New York, wars, and so on, whilst all the dolphins had ever done was muck about in the water having a good time. But conversely the dolphins believed themselves to be more intelligent than man for precisely the same reasons.
I can see how this would be a problem for ethics-based vegans (as opposed to health-based vegans), but why would it pose a problem for anti-GMO types? It's not a GM product. Ferritin, or something like it, is found in a lot of animals.
Actually, there is a possible solution for the vegans. I'll have to check, but I'm pretty sure there's a microbial version of this protein. Hindus can be easily taken care of, they can use ferritin from pigs. Jews & Muslims can use the cow stuff. The rest of us can use whichever is cheaper.
Now I await the deluge of virus and bug jokes for the microbe comment....
This doesn't use molecular biology to store the data, just to make the infrastructure. There is an iron-carrying protein in blood called ferritin. It can hold single atoms of iron quite tightly, and keep it coordinated in a specific location, and in a (kind of) specific way. I'm guessing these guys make an array of conjugated ferritin (which would be fairly easy and cheap to do, especially on a large scale) and then use some mechanism to alter the oxidation state of the iron in the protein and assiging each either a 1 or a 0. It still uses standard magnetic reading, it's just the medium that's changed. Or at least as far as I can tell from the article.
Pribram? Kind of dating yourself there;) My wife used to work as a tech in the neuro department here. His name got tossed about a little bit.
I oughtta try that out on a grant proposal. "Impact? What do you mean 'impact'? It's to figure things out!"
It's funny, the real reason we do stuff is just because it's cool, and we're curious. The real world applications are just a perk that gets us the money. Well, maybe that's not all they are. They do give us fame and fortune, right?
Mostly, I just want to know stuff. It's why I became a scientist.
Reminds me of a fortune I saw once. "As an adolescent I aspired to lasting fame, I craved factual certainty, and I thirsted for a meaningful vision of human life - so I became a scientist. This is like becoming an archbishop so you can meet girls."
It rings so true for a grad student in the doldrums of the 4th year.....
But I still just want to know. It's a curse. If my PI would let me pursue all the tangents I want to pursue, I'd be here for 15 years with no coherent project. He once told me that science is like a hydra; if you answer one question, two more pop up in it's place. The nad news is that you can never kill the hydra, but there is some good news. Being a scientist does not mean you have to kill the hydra. Being a scientist just means you have to fight it. The Zen of biochemistry. Heh.
You said it yourself: "it's an issue of "where" did it happen again"
. What are the necessities for life? Is there only one set of circumstances that allow it to arise, or can it have alternative chemistry? What are the other possible biochemistries of life? What are alternatives to information storage? What are the alternatives to structure, energy storage, signaling, or synthesis?
These are just a few of the scientifically important questions that can be answered, at least in part, by the discovery of other life. That is why it is important to find out where it developed, so we can take a closer look at it. Finding the model is an early step in good research. You even brought up a good question yourself:
We also know that if there was life it's doubtful it went beyond the microscopic range as not only is there no evidence of that, but life existed on this planet for eons w/o going past the microscopic range.
First, we don't know that it didn't develop past microbial stage on Mars. We don't even know it got that far. To use the cliche, "Absence of evidence is not evidence of absence." Besides, the question remains : What made life on Earth suddenly explode into complexity? We were nothing but simple Archea for a few billion years. Then, suddenly, complex organisms exploded into view. Why? What spurred this on? Seeing an environment where it didn't happen could further understanding of our own origins.
In my experience, most scientists don't give a rat's ass about disproving religion (IIAS, and I work with scores of other scientists). BTW, I'm a Christian, too. And life on other planets presents no crisis to my faith. I think the assumption that it does is a bit overstated. Frankly, I don't even know anyone that has a problem with there being life on other planets.
Well, re-reading that, it's a bit of a ramble, but I don't have time to rewrite it now, so sorry....
Just wanted you to know I haven't forgotten about the references for the folding simulation. I sent my friend an email last week, but as it turns out, she is on vacation through this weekend. I'll let you know when I hear from her.
That's arguable. The flipside is that if shown images of graphic imitaion violence over and over, will someone become desensitized to it, so that when/if they see it for real, it won't affect them as harshly?
I don't know, and I don't know if it's even known. I grew up on A-Team type violence, and the first time I saw a guy get seriously injured (he almost lost an arm in a car crash) it had a huge impact on me; the sight snapped everything into focus really quickly. It helped me react to the situation better, and more quickly than I think I otherwise would have. Could the same be said for someone who has been exposed to highly realistic images of the same kind of thing? I don't know.
You're right, though. It should be horrifying. Would continuous exposure reduce how horrific it appears? I think it would, but I don't know.
You have to take into account the interactions between the single modules, which is vastly more complicated.
Damn, you'd need to know a lot more than THAT;).
I'm not so concerned with some superbug as I am with an idiot that causes some localized problem (some bacterium that outcompetes local soil bugs due to some immunity and causes drops in crop yeilds, for instance). This could be damaging not so much from an actual direct impact as it would be from the Frankenstein effect.
I am a biochemist, and work with a lot of (too much, IMHO) molecular biology, so this kind of technology looks very, very cool to me. So don't get me wrong, I'm not opposed to it at all. I just think it should be controlled, so that idiots don't get their hands on it to make the next round of GM wheat or corn, and then screws it up with poor containment and bad experimental design. Make a system even an idiot can use, and idiots will use it.
I'll send her an e-mail today. As for the QM effects, I'd be interested in learning a bit more about it. I'm more interested in interactions within and with the lipid bilayer, but the same principles would apply. Do you have any good review articles I could start with?
1) Folding predictions sometimes can work - but these are mostly on the basis of sequence homologies - so no real ab initio methods, as the grandparent stated. Even in the case of homology based modelling the accuracy is rather low.
These do exsist. They are thermodynamically based, and not based on sequence homolgy. And the accuracy is getting a lot better. Like I said, this girl just presented a few weeks ago that her predicted sturcture (based on thermodynamic modeling, not seqence homolgy) was very close to the crystallography that came out. She says she has done modeling on other structures as well to test the validity of the model, but didn't show all the data. These modeling systems are out there and they do work. They need improvement, and for the time being they need crystallography to verify them, but they do work.
As for additional forces (electrostatic, etc), that is what I was referring to when I mentioned "more than one force". As for dielectrics on proteins, this is just another example of large systems. It's easy to figure it out for an alkene with a single hydroxyl on it, but add in a couple of hundred partially charged groups on a peptide backbone and it gets really tough.
I don't know much about how quantum mechanics come into biochemistry; I've never read anything discussing it's effects on folding or activity, other than bond formation. Can QM interactions act over distances beyond the electron shell? I do know that most ligand-protein, protein-protein, etc interactions are mostly governed by electrostatics, though. And charge densities can be predicted once the structure is known.
I'll talk to my friend, and find out when she plans to publish. If it's soon, I'll post a link to the abstract when it comes out.
designing the sequence so that this oligo carries the information you want and ultimately leads to a certain phenotype is quite difficult
Certainly, in cases where neither is known. But if your take a CMV promoter, put it in front of GFP, and slap into HEK293, what happens? Granted, that's a simple example, but as these things are discovered they are published.
If I understand correctly, the idea behind this technology is to go ahead and do the characterization & sequencing steps, giving parts that have known activities & regulation. That takes away the difficult part. To use the tired computer metaphor, you don't need to know how to design a hard drive to build a computer. Right now, you have to know how to characterize genes & bash promoters to build a construct. This technology seeks to remove that difficulty. This is a good thing, it's a great tool. It just needs to be kept from the wrong people.
We probably do. My opinion is that the GM technology is quite good and safe (though improvement is always good), it's just too bad that it's being impletmented by people that are jerks.
Ah, so you're talking about business practice and not direct GM effects. I assumed (my apologies) that you were talking about the mixing of GM grains. According to that link, you were talking about industrial waste.
This does not surprise me. I have always been of the opinion that Monsato is not run honestly (again, being nice). I just hate it that they are to be the first into the GM business. It's good technology, and good science. Monsato is applying bad business to it, though.
The AA sequence maps to a protein or peptide. Right there, we're screwed. There is no ab initio method which accurately predicts protein folding. There are no reliable empirical methods either.
The tools are actually getting quite good. I just went to a seminar last week where a student here had found that her folding prediction based on these worked out very similar to the X-ray crystalography that was later done. The changes were not very significant, and very close to the tolerances that were in the crystal.
There are ways to determine the function and regulation of a protein, though. None are in silico, and few are simple, but they do exsist. They are done all the time.
I think you're wrong when you say that 'Biology does NOT follow any simple rules of logic'. It does, and we know what most of them are. The problem is that it is a n-body problem. Give an astrophysicist a 200-body gravitational problem and he'll give yo a blank stare. A cell is a billion+ body problem, and there is more than just one interacting force. We know the rules, the system is just too complex to look at effectively. But I agree that the comparison to computers is a weak one. Biological systems are infinitely more complex than computers. Just to take the brain into consideration, there are 6 orders of magnitude more connections in the human brain than in a P4*. And that's just looking at a simple structure (synapse) as a single functional unit; within each synapse are dozens, if not hundreds of different kinds of players. With 100s to 100000s of copies of each player. And beyond that, you have long term regulatory effects,
*avg of 2000 synapses at each CNS neuron, and ~10^11 neurons in the human brain. Gives 10^13 connections total.
It's pretty well known how to analyze the stuff, and synthesis is (normally) quite easily done in various biological systems. It's just that the whole process is very labor intensive, and difficult to automate. The structure and function of individual proteins are analyzed and important regions are identified in silico, then mutated to see if they are required. If they are, they try to find out if there is anyway that the organism can compensate for its loss. If not, they try a vaccine made from it. Historically, each time one has been thought to have been found, it is tested and it fails in culture. Others have proven to be unstable, and others have proven to just be ineffective antigens for some reason or another.
Some have proposed systematically introducing single base pair changes (SSNPs) into each base pair and screening for nonviables. The trouble with this is that it's a dangerous fishing expedition that many scientists are loathe to do. I wouldn't do it; too much risk involved.
HIV is a particullarly bad bug because it infects the very cell that would be the crucial link in the viruses destruction. It's a very strategic mechanism. Furthermore, HIV is more mutation prone than most viruses, and it has therefore developed very good redundancy. We are left with the task of finding the small number of redundancies that natural selection has missed.
Immunization against HIV is most certainly not out of the question. It mutates a lot, but there are conserved portions of the virus that do not, and cannot change and still have an infectious virus. We hope to make effective antigens from these portions.
Each HIV has dozens of antigens, each with potentially scores, or even humdreds, of epitopes. Some of these epitopes can only be altered so much before the function they happen to serve is lost (loss of one function of one gene in a bug as streamlined as HIV would make it ineffective). If we can target the small number of functional variations of that antigen or epitope, we could have an effective vaccine. It's just that we haven't found one yet, and people are quite reluctant to be guinea pigs for an HIV vaccine.
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Hear, hear! Why is this not stressed more often? The philosophical foundation of the Republican party was more laizzes faire, in that they thought that government should be small and unobtrusive, and have minimal interaction in commerce. That has all disentigrated. I originally voted for Bush because he said he'd drop the size of government. That was one of the biggest reasons I was for him. But instead, the government grew more under him than it did under Clinton. Kerry's plans spell out "increased government size", and Bush's record says he'll do the same. Libertarian foreign policy seems like a repeat of the same mistakes we made 100 years ago.
I HATE voting for things I know are bad, but I guess I'll have to figure out who I think will do the least harm. God, this election sucks.
Not sure about the pressing charges part, though. But IANAL.
I know, I work in a research lab as well. We have patents with the same setup. That's why I referenced the whole thing as a pipe dream. I know it really doesn't (and probably can't) work that way.
Most of the patent stuff here works as individual labs. The PI takes a cut, the department takes a cut, and the U takes a cut. What they all take a cut of is the proceeds and royalties of selling the patent to a major corp. The upside is that these patents are cheaper for the corp, and they (in a perfect world) Pass The Savings On To You! They do, to an extent, but they normally (almost always) don't pass on as much as they could.
Not really a valid analogy. The source of the freedom you talk about is the Bill of Rights, and there is no Ammendment to the Constitution affecting the ability of Congress to appropriate funds for exploration.
Why do you assume that I am a single-issue voter? That is a very large, far-reaching and, as far as I can see, unfounded assumption. "People like you" that assume too much do little to advance any sort of discussion (sorry, I'm sarcastic by nature).
Another point, why would you assume that space flight (or any other issue) has no advantage? Why would you say that it is not "the right thing to do", as you put it? It is your *opinion* that it is not the right thing to do, while it is my opinion that it is. I think it is in conformity with the founding pronciples of this country, and that it will help us in the long run. (I know you said that you are personally excited about space flight, I'm just using it to demonstrate broad principle; re-read the above & think really broad)
The fact that we are a representative republic helps alleviate the mob rule aspect of a true democracy. We elect people we think represent our own views, and expect those people to go on and vote accordingly.
The system breaks down, however, when (1) Polticians don't 'go and vote accordingly' and (2) Their constituents don't hold them accountable. Both of which have occured...
One man, one vote. To send people into space is the grandparent's vote, and mine echos it. The bulk of your argument seems to deal with the way space is explored under government support, not with the fact that it is supported that way. I agree that there is a lot of waste, way too much waste, in the way NASA does things. But I still think that space exploration needs to be funded on several fronts, including the public front.
Look at biotech as an example. We explore biochemistry to find new ways of doing things. The benefit to mankind is exceptional and obvious. What is better: NIH funding of open projects that are available to all (Human Genome Project) or research done by private companies that are closed or fee based (the Celera genome database)? Biotech is full of similar examples. Would be better or worse off if the cutting edge drugs were discovered and approved in university labs solely funded by NIH, and were open to the public for use (yeah, yeah, a pipe dream for various reasons)?
Perhaps space exploration would be better served if it were under the direction of a body more like the NIH than NASA.
Damn, if I'm among the wealthiest 2% of US families, how in the hell do the bottom 98% survive?
But that's not what got my attention here. What got my attention was the use of the Patriot act to get eveidence on him. We were told over and over again that it wouldn't be used for anythying except investigations into terrorist acts, but here it is being used to acquire evidence for copyright infringement.
Copyright infringement.
It wouldn't matter to me if it was a murder investigation, it's still precisely what we were assured, over and over again, would never happen, under any circumstances. There is a reason that our legal and investigative arms of the government are set up the way they are. The law enforcement arm is limited in what it can do, for very good reason. This act allows law enforcement to do things they otherwise could not, and should not, be able to do.
Technology is really just advanced tool use. Using a chainsaw is at least fundamentally similar to using a stone axe, it's just more complex and advanced. From this standpoint, technology does not make us unique among Earth's animals. Elephants and apes both use tools, and I think other animals do as well. It's just that we do it to a greater extent.
I don't think there is a single thing that sets us apart. It's probably set of things that all finally happened in one organism. Maybe the combination of complex communication, social structures, tool use, and rudimentary mathematics. I don't know any other animal that has all of those characteristics.
But what relevance does this have to intelligence, anyway? Recall in the opening of HHGTG :
Actually, there is a possible solution for the vegans. I'll have to check, but I'm pretty sure there's a microbial version of this protein. Hindus can be easily taken care of, they can use ferritin from pigs. Jews & Muslims can use the cow stuff. The rest of us can use whichever is cheaper.
Now I await the deluge of virus and bug jokes for the microbe comment....
This doesn't use molecular biology to store the data, just to make the infrastructure. There is an iron-carrying protein in blood called ferritin. It can hold single atoms of iron quite tightly, and keep it coordinated in a specific location, and in a (kind of) specific way. I'm guessing these guys make an array of conjugated ferritin (which would be fairly easy and cheap to do, especially on a large scale) and then use some mechanism to alter the oxidation state of the iron in the protein and assiging each either a 1 or a 0. It still uses standard magnetic reading, it's just the medium that's changed. Or at least as far as I can tell from the article.
I oughtta try that out on a grant proposal. "Impact? What do you mean 'impact'? It's to figure things out!"
It's funny, the real reason we do stuff is just because it's cool, and we're curious. The real world applications are just a perk that gets us the money. Well, maybe that's not all they are. They do give us fame and fortune, right?
Right?
Reminds me of a fortune I saw once. "As an adolescent I aspired to lasting fame, I craved factual certainty, and I thirsted for a meaningful vision of human life - so I became a scientist. This is like becoming an archbishop so you can meet girls."
It rings so true for a grad student in the doldrums of the 4th year.....
But I still just want to know. It's a curse. If my PI would let me pursue all the tangents I want to pursue, I'd be here for 15 years with no coherent project. He once told me that science is like a hydra; if you answer one question, two more pop up in it's place. The nad news is that you can never kill the hydra, but there is some good news. Being a scientist does not mean you have to kill the hydra. Being a scientist just means you have to fight it. The Zen of biochemistry. Heh.
. What are the necessities for life? Is there only one set of circumstances that allow it to arise, or can it have alternative chemistry? What are the other possible biochemistries of life? What are alternatives to information storage? What are the alternatives to structure, energy storage, signaling, or synthesis?
These are just a few of the scientifically important questions that can be answered, at least in part, by the discovery of other life. That is why it is important to find out where it developed, so we can take a closer look at it. Finding the model is an early step in good research. You even brought up a good question yourself:
We also know that if there was life it's doubtful it went beyond the microscopic range as not only is there no evidence of that, but life existed on this planet for eons w/o going past the microscopic range.
First, we don't know that it didn't develop past microbial stage on Mars. We don't even know it got that far. To use the cliche, "Absence of evidence is not evidence of absence." Besides, the question remains : What made life on Earth suddenly explode into complexity? We were nothing but simple Archea for a few billion years. Then, suddenly, complex organisms exploded into view. Why? What spurred this on? Seeing an environment where it didn't happen could further understanding of our own origins.
In my experience, most scientists don't give a rat's ass about disproving religion (IIAS, and I work with scores of other scientists). BTW, I'm a Christian, too. And life on other planets presents no crisis to my faith. I think the assumption that it does is a bit overstated. Frankly, I don't even know anyone that has a problem with there being life on other planets.
Well, re-reading that, it's a bit of a ramble, but I don't have time to rewrite it now, so sorry....
Just wanted you to know I haven't forgotten about the references for the folding simulation. I sent my friend an email last week, but as it turns out, she is on vacation through this weekend. I'll let you know when I hear from her.
I don't know, and I don't know if it's even known. I grew up on A-Team type violence, and the first time I saw a guy get seriously injured (he almost lost an arm in a car crash) it had a huge impact on me; the sight snapped everything into focus really quickly. It helped me react to the situation better, and more quickly than I think I otherwise would have. Could the same be said for someone who has been exposed to highly realistic images of the same kind of thing? I don't know.
You're right, though. It should be horrifying. Would continuous exposure reduce how horrific it appears? I think it would, but I don't know.
Damn, you'd need to know a lot more than THAT ;).
I'm not so concerned with some superbug as I am with an idiot that causes some localized problem (some bacterium that outcompetes local soil bugs due to some immunity and causes drops in crop yeilds, for instance). This could be damaging not so much from an actual direct impact as it would be from the Frankenstein effect.
I am a biochemist, and work with a lot of (too much, IMHO) molecular biology, so this kind of technology looks very, very cool to me. So don't get me wrong, I'm not opposed to it at all. I just think it should be controlled, so that idiots don't get their hands on it to make the next round of GM wheat or corn, and then screws it up with poor containment and bad experimental design. Make a system even an idiot can use, and idiots will use it.
I'll send her an e-mail today. As for the QM effects, I'd be interested in learning a bit more about it. I'm more interested in interactions within and with the lipid bilayer, but the same principles would apply. Do you have any good review articles I could start with?
These do exsist. They are thermodynamically based, and not based on sequence homolgy. And the accuracy is getting a lot better. Like I said, this girl just presented a few weeks ago that her predicted sturcture (based on thermodynamic modeling, not seqence homolgy) was very close to the crystallography that came out. She says she has done modeling on other structures as well to test the validity of the model, but didn't show all the data. These modeling systems are out there and they do work. They need improvement, and for the time being they need crystallography to verify them, but they do work.
As for additional forces (electrostatic, etc), that is what I was referring to when I mentioned "more than one force". As for dielectrics on proteins, this is just another example of large systems. It's easy to figure it out for an alkene with a single hydroxyl on it, but add in a couple of hundred partially charged groups on a peptide backbone and it gets really tough.
I don't know much about how quantum mechanics come into biochemistry; I've never read anything discussing it's effects on folding or activity, other than bond formation. Can QM interactions act over distances beyond the electron shell? I do know that most ligand-protein, protein-protein, etc interactions are mostly governed by electrostatics, though. And charge densities can be predicted once the structure is known.
I'll talk to my friend, and find out when she plans to publish. If it's soon, I'll post a link to the abstract when it comes out.
Certainly, in cases where neither is known. But if your take a CMV promoter, put it in front of GFP, and slap into HEK293, what happens? Granted, that's a simple example, but as these things are discovered they are published.
If I understand correctly, the idea behind this technology is to go ahead and do the characterization & sequencing steps, giving parts that have known activities & regulation. That takes away the difficult part. To use the tired computer metaphor, you don't need to know how to design a hard drive to build a computer. Right now, you have to know how to characterize genes & bash promoters to build a construct. This technology seeks to remove that difficulty. This is a good thing, it's a great tool. It just needs to be kept from the wrong people.
We probably do. My opinion is that the GM technology is quite good and safe (though improvement is always good), it's just too bad that it's being impletmented by people that are jerks.
This does not surprise me. I have always been of the opinion that Monsato is not run honestly (again, being nice). I just hate it that they are to be the first into the GM business. It's good technology, and good science. Monsato is applying bad business to it, though.
The tools are actually getting quite good. I just went to a seminar last week where a student here had found that her folding prediction based on these worked out very similar to the X-ray crystalography that was later done. The changes were not very significant, and very close to the tolerances that were in the crystal.
There are ways to determine the function and regulation of a protein, though. None are in silico, and few are simple, but they do exsist. They are done all the time.
I think you're wrong when you say that 'Biology does NOT follow any simple rules of logic'. It does, and we know what most of them are. The problem is that it is a n-body problem. Give an astrophysicist a 200-body gravitational problem and he'll give yo a blank stare. A cell is a billion+ body problem, and there is more than just one interacting force. We know the rules, the system is just too complex to look at effectively. But I agree that the comparison to computers is a weak one. Biological systems are infinitely more complex than computers. Just to take the brain into consideration, there are 6 orders of magnitude more connections in the human brain than in a P4*. And that's just looking at a simple structure (synapse) as a single functional unit; within each synapse are dozens, if not hundreds of different kinds of players. With 100s to 100000s of copies of each player. And beyond that, you have long term regulatory effects,
*avg of 2000 synapses at each CNS neuron, and ~10^11 neurons in the human brain. Gives 10^13 connections total.
Some have proposed systematically introducing single base pair changes (SSNPs) into each base pair and screening for nonviables. The trouble with this is that it's a dangerous fishing expedition that many scientists are loathe to do. I wouldn't do it; too much risk involved.
HIV is a particullarly bad bug because it infects the very cell that would be the crucial link in the viruses destruction. It's a very strategic mechanism. Furthermore, HIV is more mutation prone than most viruses, and it has therefore developed very good redundancy. We are left with the task of finding the small number of redundancies that natural selection has missed.
Each HIV has dozens of antigens, each with potentially scores, or even humdreds, of epitopes. Some of these epitopes can only be altered so much before the function they happen to serve is lost (loss of one function of one gene in a bug as streamlined as HIV would make it ineffective). If we can target the small number of functional variations of that antigen or epitope, we could have an effective vaccine. It's just that we haven't found one yet, and people are quite reluctant to be guinea pigs for an HIV vaccine.