Posted by
CmdrTaco
on from the this-is-just-swell dept.
jrrl writes "USAToday is reporting that Craig Venter's research group has synthesized a virus from scratch and that it "became bioactive" (started reproducing). Particularly interesting is that it only took them two weeks to build, rather than several years that previous attempts had taken."
Well, not really terrified I guess, but the whole "We've created life and it's procreating" thing is something that doesn't exactly make me feel warm and fuzzy,. And why did it have to be a virus. Why not a cute little kitten or something?
Worse, they could have created real-life Tribbles but didn't. How can they call themselves scientists yet not pursue the future laid out before us by Gene Roddenberry?
All they actually did was to take commercially available DNA, link it together to duplicate the DNA of an existing bacteriophage, and pop it inside a cell, and watch it go on. They just demonstrated that they have the technology to make a copy of the DNA of an existing virus.
As anyone can tell you, learning how to copy something that already exists doesn't really mean you know that much more about how it works. Just because I could write out a copy of a Chinese story doesn't mean I know anything more about what the story says, just that I can duplicate the writing correctly.
Creating NEW life forms, not just copying existing ones, is still a ways off.
Theoretically, they should be able to do this with a mammal like a feline. Sequence the DNA, build a copy, and replace the DNA in a freshly fertilized egg, and it should grow up just fine. Though the complexity of the animal would add issues that I'm not educated enough to be aware of, certainly.
-- "You know your god is man-made when he hates all the same people you do."
Re:Scared now
by
bubblewrapgrl
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· Score: 3, Interesting
A virus can't self-replicate. It's a bit like a parasite in that it needs a host. Basically, all that composes a virus is a piece of DNA encapsulated by some protein. It can't reproduce because it doesn't contain the necessary organelles, such as ribosomes to make proteins and mitochondria to provide energy, that a cell has. So, when a virus infects a cell, it incorporates itself into the host's DNA. Then, when the host DNA gets replicated, the virus DNA gets replicated along with it. From there, the DNA will either get turned into more DNA (to make new cells that have the virus DNA) or make proteins (which can cause infection by making toxins and more viruses). The virus DNA can also be dormant in the host for awhile by not incoporating itself into the host DNA.
In regards to this synthetic virus, my main question is whether or not the researchers have looked what happens to cells that get infected by the virus. You can't kill a virus like you can a bacterial cell. Basically, your body has to recognize the virus as foreign and make antibodies to kill it, which is why we have to get immunizations. That's a little frightening to me - the possibility that they've created somthing horrible lytic that no one has ever been exposed to.
Technically it's not life. There is still a bit of dispute as to whether virused are alive or not. They contain genetic material, but are not necessarily living organisms. Or that is what some bio major told me once.
Whether virus is life or not depends on the definition of life. There is no consensus on this defintion, so debates on the matter are rather meaningless, it is really disputes over the definition of a word.
What makes viruses controversial is that they cannot reproduce by themselves; they need to infect antoher cell. But then again, many parasites cannot live without some other organism, and they are usuually considered alive.
I still don't really think the benefits (gene expression research, gene therapy in general) are good enough, considering the potential problems.
I'd like to know who's funding them. Is it civilian or military?
As if there weren't enough virii on the planet already, we have to go making more. Fantastic academic achievement, but wish they hadn't done it. A bit like a nuclear bomb, in its own way...
Simon.
-- Physicists get Hadrons!
Re:Chilling
by
Space+cowboy
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· Score: 4, Insightful
There is a very very small difference between a cancerous cell and a normal cell. They're identical except the cancerous one keeps on dividing. Just how much did you want that cancer-eating virus ? Given how often virii mutate ?
If they can get it down to seven days then we'll have something;)
--
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All your old jokes are belong to sigs.
Viruses and weapons
by
Fux+the+Penguin
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· Score: 4, Insightful
I think the wonder of any scientific advance should be tempered by a clear-headed analysis of the dangers it might create.
I don't think anybody should be making any new life forms or modifying any existing life forms, at least until we've had a serious societal discussion regarding its possible role and impact on terrorism and biowarfare.
Imagine a scenario where terrorists could alter a disease or organic biological weapon gene by gene to make it immune to current antidotes. Beyond that, I worry that the US itself might use it for its own cache of new-age weapons.
If WE convert it to a weapon, what's the difference? We can claim we're the good guys and we won't use it. But we can look at Nagasaki and Hiroshima.
I hope I'm not fear-mongering here, but, I worry.
Re:Viruses and weapons
by
Sheetrock
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· Score: 4, Insightful
You're not. This is a valid point that is all but ignored by scientists seeking continual funding and rationalizing that if they don't do it someone else will.
However, I think this sort of research is as or more likely to radically benefit society as it is to create catastrophe. Look at the genie released when we first split the atom; I'd argue that the current and future benefits from nuclear power alone outweigh the concern about the misuse of this knowledge. But I feel that ethical concerns must become a stronger part of scientific research and funding, not only because of this breakthrough but because of the ones we're about to make (nanotechnology will present similar worrying potential...)
--
Try not. Do or do not, there is no try. -- Dr. Spock, stardate 2822-3.
Re:Viruses and weapons
by
radish
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· Score: 4, Insightful
You're american right? Doesn't it strike you as kind of an odd coincidence that you come up with the US as the only "responsible" country in the world? Whilst you may be right (you actually missed out an entire continent) I'd hardly call your analysis objective.
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Den ene knappen er powerknapp, den andre er Bender voice knapp "Bite My Shiny Metal Ass"
Re:Viruses and weapons
by
glgraca
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· Score: 4, Insightful
If those countries are so terrible, why do you keep selling them weapons??
Who sold Saddam chemical and biological weapons?
The US insists on a monopoly on WMD technology not for the safety of the world, but for its own economic interests and to maintain its power.
Re:Viruses and weapons
by
TGK
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· Score: 3, Insightful
Gotta clear up a few things here.
1 - Terrorism isn't generaly a R&D effort. The act of terrorism isn't anything new, contrary to what GW Bush Inc. seems to belive. For centuries people have been committing acts of terrorism, but these are not the organizations that develop the new and frightening weapons of war.
Terrorism is, by it's very nature, a low budget enterprise. Until Mr and Mrs Smith can grow little Susie a custom built kitten with neon pink fur by hitting some buttons on the Recombinator (tm) you won't see gene level modifications as something available to terrorists.
2 - We've been making viruses resistance to treatment/immunization for years now. Read Ken Alblik's autobiography on his roll in the Soviet Bioweapons program. Until the 1970s the United States was engaged in offensive biological warfare . Today we still research defensive biowarfare, which means that we use developing treatments as an excuse to weaponize deadly organisims.
The former Soviet Union (according to most sources) weaponized the small pox virus. Weaponization, for the unaware, is a process of making a virus resistant to treatment and immunization techniques while increasing it's kill rate.
As was pointed out elsewhere in this thread, if you have something insanely dangerous and you want to it to fall into the wrong hands, the best thing you can do with it it hand it to the Russian Army to guard.
I have the utmost respsect for the scientific community. The work they do is amazing and valuable research, but this isn't something I'm worried about. Somehow, I doubt that a bunch of PhDs in a lab can come up with anything (much) more deadly than billions of years of evolution and 50 years of cold war has produced.
-- Killfile(TGK)
No trees were killed in the creation of this post. However, many electrons were inconvenienced.
Re:Viruses and weapons
by
ishark
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· Score: 4, Insightful
If any country had to be in possession of these things, it should be the US. You don't want it to be the US?
Considering the recent record of the US of bombing and invading countries on purely imaginary perceived threats and very real economic reasons, I'd rather NOT have the US be the only one with such a weapon. I'd like a lot of different people to have it. Balance of terror is bad, but I've come to appreciate the advantages of unstable equilibrium compared to a (albeit very stable) death.
Re:Viruses and weapons
by
bigberk
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· Score: 3, Insightful
Imagine a scenario where terrorists
Oh geez, terrorists, terrorists, terrorists, we're all so afraid of terrorists. You may be a terrorist, your neighbor might be a terrorist, and I'm petrified by fear. I'm so paralyzed by fear that I think we should pull the plug on any project that might be potentially used by terrorists. Whether it's technological, or medical... hell, who cares that we might be coming up with new biological agents to help fight cancer... throw that research out the window! The terrorists might somehow morph the results of the research and create an Osama-superbug that's even wors that SARS and anthrax!!!
Re:Viruses and weapons
by
mesocyclone
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· Score: 3, Informative
In the same light, the US has never created a weapon it has not used.
This is absolutely not true. The US created many chemical weapons which it did not use (I don't know if we used chem weapons in WW-I, but we enver used them since then).
The US has NEVER used biological weapons (even the recorded use of smallpox against Indians was done by the British before the American Revolution).
Thinking on the computer virus side I like this Hawking quote: "I think computer viruses should count as life. I think it says something about human nature that the only form of life we have created so far is purely destructive. We've created life in our own image."
-- Stephen Hawking
-- X(7): A program for managing terminal windows. See also screen(1).
Re:Should we really be doing things like this?
by
Leroy_Brown242
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· Score: 5, Insightful
You would hope that they take great pains to make access to the virii as secure as possible.
But, things like this are very important in the fight to create vaccines to illnesses. Anyone who has taken apart and built a car, computer, or whatever will tell you that thier level of understanding is now MUCH greater than it was before they did it. Knowing how to assemble a virus, will hopefully allow us to defend ourselves against them.
More than a year ago live polio virus was
constructed from component DNA. This is
not a "artificial" virus but a working copy
of phi X bacteriophage. Note that this is
an infringement of God's copyrights and
patents and trade secrets!
(from NY times, July 2002: Scientists construct virus from scratch for first time, synthesizing live polio virus from chemicals and publicly available genetic information; work was conducted by scientists at State University of New York at Stony Brook and financed by Defense Department as part of program to develop biowarfare) countermeasures... )
Not the first time
by
Brahmastra
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· Score: 3, Informative
This story indicates that it was done more than a year ago.
Re:Should we really be doing things like this?
by
oniony
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· Score: 5, Funny
Yeah, I agree -- these people really need to start wearing condoms.
--
Powered by onion juice.
Re:Should we really be doing things like this?
by
f97tosc
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· Score: 5, Insightful
Probably the same as in handling any other virus.
Which is perfectly reasonable. People seem to be exremely afraid of anything made in a lab, but fail to recognize that the greater danger (by far) is from natural evolution of new viruses.
By the same token, the dangers of bio-weapons seem to be greatly excaggerated, when compared to natural pathogens. Some anthrax letters that killed half a dozen people seemed to get more attention and resources than the flu and aids, which kill tens of thousands of people per year in the US alone.
Horsefeathers. Matter is not the essence of a thing. Form and function usually (but not always) are. Transformation into another form may not destroy the mass but it most certainly destroys the thing that existed before.
--
"The legitimate powers of government extend only to such acts as are injurious to others." Thomas Jefferson.
What they did, why it is hard
by
sam_handelman
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· Score: 5, Informative
The human genome (which is DNA), contained in each of your cells, contains the instructions needed to make a cell (much like a computer program.)
However, in order to use these instructions to make a cell, you need a cell of the same kind to read them.
Analogy: You have a computer program that tells you how to manufacture computers but this doesn't do any good unless you already have a computer OF THE SAME KIND on which to execute it.
So, even if I assemble an entire human genome, I can't use it to make a person unless I already have a human cell. Kapish?
A VIRUS, which is what was made here, is NOT A CELL. It is a parasitic piece of DNA that hijacks an existing cell and contains the instructions to make viruses. The DNA that the virus contains is, in the best case, sufficient to hijack the cell all by itself, and convert the cell into a factory for making viruses. Viruses CANNOT make more viruses by themselves. The similarity to a computer virus, I assume, is obvious.
So, if you can make VIRAL DNA, this will be sufficient to make the virus, if you have cells that the virus can infect.
Even making the genome of a virus is very difficult. The "commercially available" DNA mentioned in the article is made chemically. DNA is made up of a chain of monomers; each monomer has a 5' end and a 3' end that can attach together to form a chain. In order to add monomer n+1 to a growing chain, this is what you do (description meant to be accessible to people who don't know a lot of chemistry):...(Monomer n-1) 3' - 5' (Monomer n) 3'(BLOCKED)
-> **add reagent to unblock**
-> wash...(Monomer n) 3'
-> add 5' (Monomer n) 3' {BLOCKED}
-> add reagent to attach 5' and 3' together...(Monomer n) 3' - 5' (Monomer n+1) 3' {BLOCKED} and repeat for Monomer n+2. Recursion is good.
Now, this is done in parallel in thousands of molecules of DNA (the 5' end of each molecule is fixed to a plate.)
Every time you add the reagent to remove the BLOCKS, it has a percentage chance, which can be very small, of failing.
So, for example, if, on one paritcular molecule, it fails at position 10, then instead of: ACGTACGTACGT you will get, ACGTACGTAGT.
DNA that makes proteins has something called a "reading frame", consisting of codons which are three monomers long. If you shift the reading frame over by 1 monomer, it completely changes the meaning of the message.
So, a single nucleotide deletion, which I describe above, is disastrous - the synthetic DNA becomes useless.
Even if the chance of failing to remove a block is small - typically about 0.1% - if your DNA molecule is thousands of bases long, the chance of successfully adding every base to any individual molecule is slight.
Of course, you can make two different 100-base long molecules by the above technique and then ligate them together (recursion by splitting the task in half) which is, I believe, what's been done here. This has technical difficulties of it's own, of course, but with refinements it woud allow you to make useful DNA of length n*2^m instead of DNA of length n.
This is a frightening prospect because it would allow you to make ebola "from scratch", or just from the the string of letters that represent the genome (which is so short I could write it out by hand on a stack of cocktail napkins.) We're not to that point yet but it is a scary possibility.
-- The good and new comes from no quarter where it is looked for, and is always something different from what is expected.
Re:Should we really be doing things like this?
by
B'Trey
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· Score: 5, Insightful
Assembly is not necessarily the same as synthesis. Designing and building a computer (as oppossed to merely putting together what is essentially a kit created by someone else) certainly implies that you have enough knowledge to make intelligent decisions on how to go about protecting the computer.
--
"The legitimate powers of government extend only to such acts as are injurious to others." Thomas Jefferson.
Morals Schmorals
by
Pedrito
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· Score: 4, Interesting
I don't really care about the morality of this. Frankly, from a scientific point of view: Cool! On the other hand, what does concern me was this quote:
The project was funded in part by the Department of Energy, which hopes to create microbes that would capture carbon dioxide in the atmosphere, produce hydrogen or clean the environment.
Okay, so let's assume we do something like this, with the perfectly innocent intention of cleaning up some level of carbon dioxide. Okay, well you're counting on the virus to reproduce, but what if it gets out of control? It eats up ALL the carbon dioxide. All the trees and plants suffocate and die, but that might not happen before the atmosphere goes up in flames since that carbon dioxide is being turned into hydrogen.
Maybe not a likely event, but my concerns are a bit more on the practical side. Frankly, I'm all for creating new forms of life and bringing back extinct ones, just for the coolness of it. I just hope we don't go doing something foolish, which we always seem to manage to do.
Re:Should we really be doing things like this?
by
Daemonik
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· Score: 4, Insightful
By the same token, the dangers of bio-weapons seem to be greatly excaggerated, when compared to natural pathogens. Some anthrax letters that killed half a dozen people seemed to get more attention and resources than the flu and aids, which kill tens of thousands of people per year in the US alone.
Perhaps bio weapons get more attention than natural viruses simply because if a natural virus kills you, it's an act of [insert deity here] and simply one of the risks of life, like getting hit by a bus.
Bio weapons on the other hand are purposely engineered to maximize the lethality of a disease for the intentional purpose of killing as many people as possible. In other words, it's the intent that matters.
Uh... From scratch?
by
stienman
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· Score: 4, Interesting
Please note that when they say, "From scratch" they mean that they created a synthetic genome (probably from portions of other genomes - I doubt they know enough about the base pair sequences to actually have done it base pair by base pair) and inserted it in a 'living' cell.
The cell then started reproducing. They didn't create the cell. They probably didn't design the genome as much as patch one together from other genomes (though they may have 'created' it - physically manufactured it)
They say it's safe because it only infects batceria. Unfortunately, humans depend on bacteria to survive, so it's not nearly as innocuous as one might like to think.
However, these are nano-machines that might do real work safely (cleaning up chemical toxins, etc) - I'm just worried about mutations and how they will develop. You can't create life and expect it to reproduce itself without change over time. Pretty soon it'll discover that human skin is much more plentiful than the chemical toxins it was eating, and it'll change its diet.
-Adam
human interference....
by
mtrupe
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· Score: 3, Insightful
with nature seems to work so well, why not? I live in Illinois and each fall we are swarmed by millions upon millions of Japanese Lady-Bug-Like Orange Beatles. They were put here to fight Aphids, but they have no predators (birds won't even eat them because they emit this foul stench). They area all over the place and nothing can stop them.
So, what kind of checks and balances will there be on man-made viruses? None- you just cannot introduce anything into nature so quickly. I think the possible outcome is clear. This is downright frightening. I think I'll go rent The Stand this weekend.
Not the first, and is identical to a natural virus
by
Noren
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· Score: 3, Informative
The first reproducing artificial virus was the Polio virus by Wimmer and colleagues.
Ventner's new virus is artificial in the sense that it was created from chemicals- but it is identical to a known natural virus.
Venter's team cobbled together the virus, called phi-X174, following its published genetic sequence.
It's probably not a very effective virus
by
iabervon
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· Score: 4, Insightful
Considering that this virus was synthesized from scratch, it's probably not something very effective. It's a long way from building a virus that works at all to building a virus that targets a particular organism or overcomes natural defenses.
Just because it's man-made doesn't make it more advanced than naturally-occurring viruses. It's been possible for a long time to build viruses from collected stocks, and these are generally much more frightening. What will be scary is when we have some clue as to how to design proteins, and could construct a virus with specific properties. Until then, we're not likely to create anything that doesn't arise in nature.
(Genetically modified foods are a slightly different issue; just because it might arise in nature doesn't mean we'd eat it if it did. Also, most of the organisms involved are much more resistant to mutation and genetic mixing than viruses and bacteria)
Viruses, not virii
by
koreth
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· Score: 4, Informative
This will probably get modded down as flamebait, but someone has to say it: the plural of "virus" is "viruses." It is not "virii" because that isn't an actual English word.
Re:Viruses, not virii
by
xinot
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· Score: 3, Informative
No, not flamebait. Just ignorance on your part. You misunderstand how the english language grows and expands. It's not like the French or German or Italian which have their own institutions to determine the specifics of the words that are allowed. With English we expand the vocabulary as it is used. See email. Or many other words. You may not like virii, but if enough people use it, it is a word.
Deal with it.
Re:Viruses, not virii
by
freeweed
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· Score: 5, Funny
Excuseth me, but I have to go visit the Olde Shoppe now.
I'm all for literacy and correct grammar/spelling, but anyone who doesn't think English is a constantly evolving language obviously has never read a book more than 20 years olde.
-- Endless arguments over trivial contradictions in books written by ignorant savages to explain thunder in the dark.
Re:Should we really be doing things like this?
by
diersing
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· Score: 4, Informative
Yesterday, NPR's All Things Considered did a nice piece on it, you can
download it here
Re:Should we really be doing things like this?
by
Waffle+Iron
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· Score: 5, Insightful
People seem to be exremely afraid of anything made in a lab, but fail to recognize that the greater danger (by far) is from natural evolution of new viruses.
Unless somebody figures out how to make an artificial microbe that takes advantage of chemical processes that just aren't found in natural evolution. For example, the human body might not even be capable of attacking a hypothetical microbe that has a teflon or silicone-enhanced outer membrane.
At any rate, natural evolution proceeds at a slow rate, so the defending species has time to adapt. Anthrax, for example, implements a tricky chemical hack to breach animal cells and destroy them. Most animals are pretty defenseless against the special back door that antrax uses, and without it the anthrax bacteria would be no more harmful than a pimple. However, anthrax is a rather obscure organism that mostly lives in the dirt. The reason that animals haven't evolved a defense against its chemical attack is that it just doesn't spread that easily in a natural setting. If anthrax were contagious like a cold, animals would have evolved a defense against it long ago.
Now, people may soon have the knowledge to install anthrax's chemical attack into something like a common cold virus. This short-ciruits the evolutionary process. Instead of just having to resist natural random improvemts in microbes, we may soon also face improvements that take advantage of god-like knowledge of the weaknesses of the defenders.
By simultaneously combining the best parts of various different microbes found in nature, then adding unnatural chemical improvements and using our newly available schematics of human cell defense design, we will certainly be able to create microbes far more dangerous than anything nature is likely to randomly come up with.
I doubt that trying to control this kind of technology is going to do any good, however. Somebody somewhere in the world is going to work on this stuff whether its banned or not. Our only hope is probably to develop means to quickly detect any new microbes, along with adaptive technology to create unnatural defenses to unnatural new organisms in real time.
"Discussion"?
by
AdamHaun
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· Score: 4, Insightful
I don't think anybody should be making any new life forms or modifying any existing life forms, at least until we've had a serious societal discussion regarding its possible role and impact on terrorism and biowarfare.
But the problem is that we're not *going* to have a serious societal discussion because that phrase means nothing. Who's talking with whom? Who makes decisions? Who gets input?
When I hear "societal discussion", I get an image in my head of the entire country sitting at a great big table having a little chat about what to do. But in real life, that sort of thing doesn't happen. You have kooks who think that anything that looks like "playing God" is evil, you have people who think that every new invention must immediately be used to aid/fight terrorism, you have people who don't even understand the basic science behind what's going on(like Slashdot...oops, did I say that out loud?). And in the end, after all of these people have "had their say"(who are they talking to?), who decides what will be done? You want the government to say "Sorry, no more research on microorganisms"? Because that's about all it could do. What right does "society" have to control science? Most people will tell you that they don't even understand what "science" is! Who is qualified to do cost/benefit analysis of this sort of thing? Does anybody even *care* about cost/benefit analysis?
I understand(and sympathize with) your concerns, but no amount of talking is going to do anything about this situation. We can't halt our understanding of the world where it is just because a few people might cause problems with it. Hell, if we had taken that attitude to begin with, we'd be lucky to have fire by now!
-- Visit the
Could help stop biowarfare as well
by
mercuryresearch
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· Score: 3, Interesting
One of the arguments for not destroying the current stock of smallpox is that it might be needed at some future time for research.
With a proven and consistent ability to recreate a virus from its known DNA sequence, the actual viruses themselves could be safely destroyed without impacting the ability to resurrect them in the future. As well, it's probably considerably harder to recreate a virus this way than to steal existing stock.
So while this opens the door to manufacturing viruses for biowarfare, it also makes it possible to destroy current stocks that might be stolen and used for such purposes.
Rainbow Six future scenario?
by
StandardCell
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· Score: 4, Interesting
For those of you who have read Tom Clancy's Rainbow Six, you will know that Tom goes into detail not only about what certain individuals will do to bioengineer fatal viruses. Obviously this particular virus isn't much, but what about the radical elements in humanity? There are individuals willing to kill everything on earth in order to advance their political or religious ideology. If someone can engineer viruses this easily, what will happen when someone disgruntled and who doesn't care about himself, much less others, decide to design and manufacture a virus like this?
Thinking about it in slightly different terms, all societies attempt to limit the proliferation of highly destructive weapons among their populace because the arbitrary nature of people would guarantee their arbitrary misuse. Imagine a world where people could obtain nuclear weapons as easily as a box of ammunition. We'd already all be dead.
This is what makes this particular story quite fear-inducing. When we arrive at the point where we can easily contruct very deadly weapons, particularly with the subtlety of viruses, there should be very strict regulation and government supervision. I can only hope there will be a worldwide treaty to that effect. After all, would you want someone engineering a virulent strain of airborne type 4 Ebola because he or she has a beef with a government's ideology?
Re:Should we really be doing things like this?
by
kiatoa
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· Score: 3, Insightful
There are two kinds of Luddites:
1. The "I don't understand it, we're all gonna die" crowd and...
2. The "I understand it, I don't trust those irresponsible buggers, if we don't do something we're all gonna die" crowd.
Large corporations (and some small ones) have repeated proven themselves to be untrustworthy and irresponsible. Crowd #2 have every reason to fear what they fear.
-- 90% of the wealth is in 2% of the pockets. Bummer to be in the majority.
i, for one, would like to *welcome* our virus-creating overlords...
/me looks around nervously, and dons a N100 mask.
-- Just raise the taxes on crack.
The bizzare genome of Phi X 174
by
MagnaMark
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· Score: 4, Interesting
The specific virus that Venter et al synthesized is called Bacteriophage phiX174. They probably chose it because it has such a short genome.
In fact, it's genome is so short that at first it confused researchers. It's genome is shorter than it should be. That is, there are fewer codons in the genome than there are amino acids in the virus's proteins. Normally, there would need to be a 1:1 codon:amino-acid ratio.
This lead researchers to the amazing discovery that phiX174 contains "genes within genes" and "overlapping genes". (Link to Genetic Map of phiX174) In several instances, one gene is entirely contained within another gene. In another, there are two genes (A and A*) that overlap with "reading frames" that are off by one.
This discovery challenges notions of what a gene is. With this knowledge, you can't say that a gene is simply a particular region of DNA.
These overlapping genes also call attention to the improbability of the evolution of phiX174. Commonly when a genetic mutation occurs, one base changes. This could affect one amino-acid in the protein for which the gene codes. In phiX174's case, a single base mutation could change 2 amino-acids in 2 proteins. This means that the evolution of these proteins is interdependent. That two functional proteins evolved in this manner is absolutely extraordinary.
Of course, now that it has evolved that way, it gives phiX174 an advantage of genetic economy. It takes less energy to maintain and reproduce a shorter genome. So phiX174 gets more bang for it's genetic buck by overlapping genes in this way.
Re:Should we really be doing things like this?
by
f97tosc
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· Score: 4, Interesting
At any rate, natural evolution proceeds at a slow rate, so the defending species has time to adapt.
Natural evolution is not slow for viruses; their genetic code does not have the copy-protection mechanisms of say mammals. That is why we have a new flu pop up every other year, or a SARS for that matter.
Anthrax, for example, implements a tricky chemical hack to breach animal cells and destroy them. Most animals are pretty defenseless against the special back door that antrax uses, and without it the anthrax bacteria would be no more harmful than a pimple. However, anthrax is a rather obscure organism that mostly lives in the dirt. The reason that animals haven't evolved a defense against its chemical attack is that it just doesn't spread that easily in a natural setting. If anthrax were contagious like a cold, animals would have evolved a defense against it long ago.
With all due respect I think you are contradicting yourself. When a patheogen spreads for natural or not so natural reasons, people may die. Some survive, the resistant genes thus become more common. There may even be mutations of strong resistance that start to spread.
When this process happens for natural reasons, you label it "evolving a defense", or "defending species having time to adapt". When it happens by an act of man, you think of it as man being caught "defenseless". Of course, in both cases the species start out as (relatively) defenseless, and end up with a better defense.
My whole point was that there seem to be no lab-made pahtogen worse than anything evolved in nature. As for spreading it by man, well, anthrax did get an assist by man. But the extent of that "outbreak" was miniscule next to the natural outbreaks that happen every year.
Unless somebody figures out how to make an artificial microbe that takes advantage of chemical processes that just aren't found in natural evolution. For example, the human body might not even be capable of attacking a hypothetical microbe that has a teflon or silicone-enhanced outer membrane.
Possibly. But then again, if such mechanisms were very successful, why did they not evolve for 4 billion years on a planet surface covered in silicon compounds. In general, it is very difficult for people in labs to compete with the lab which is our planet, and time-scales of millions or billions of years.
Tor
Re:Should we really be doing things like this?
by
jimsum
·
· Score: 5, Funny
Let's hope they use some sort of copy protection on these viruses so that they can only reproduce with the permission of the owner. That's DRM I have no trouble with.
-- --
Pot is safer than Beer
Re:Should we really be doing things like this?
by
2short
·
· Score: 3, Interesting
I agree that bio weapons get more attention than natural viruses because they involve someone doing something intentionally. But I don't think it makes sense. The way I see it the downside of my getting killed by an intentional attack is that I'm dead. The downside of my getting killed by a natural virus is that I'm dead. Whether or not anyone intended me to be dead doesn't modify that downside at all for me. If society is going to try to do some stuff to prevent me (and others) from becoming prematurely dead, it seems to me it would make sense to allocate more resources to things that are more likely to kill people.
Re:Should we really be doing things like this?
by
4of12
·
· Score: 3, Insightful
Knowing how to assemble a virus, will hopefully allow us to defend ourselves against them.
As long as the rate at which the virus reproduces and the level of devastation it causes is not too fast or too irreversible.
Consider the effects of some natural virus and other life forms that have been unleased.
A fungus from the Eastern hemisphere pretty well wiped out the American chestnut tree in short order.
Russian thistle, introduced to North America in the 19th century has likewise become endemic, to the point where tumbleweeds are considered an essential ingredient in any Western film set.
Rabbits in Australia, etc., provide some indication of how rapidly reproducing organisms can spread and how much change they can cause.
Do we trust our knowledge of virus mechanics enough to believe that an inadvertent release of "grey goo" can be undone?
To put it another way:
Even if I'm extremely knowledgeable about cars, have built them from scratch, repaired them, etc., is that sufficient assurance I will be able to stop a speeding car running straight at me in time?
-- "Provided by the management for your protection."
Slashdot Mirror
Well, not really terrified I guess, but the whole "We've created life and it's procreating" thing is something that doesn't exactly make me feel warm and fuzzy,. And why did it have to be a virus. Why not a cute little kitten or something?
I want the fire back.
Yeah I know. Luddite reaction. Yadda yadda yadda.
I still don't really think the benefits (gene expression research, gene therapy in general) are good enough, considering the potential problems.
I'd like to know who's funding them. Is it civilian or military?
As if there weren't enough virii on the planet already, we have to go making more. Fantastic academic achievement, but wish they hadn't done it. A bit like a nuclear bomb, in its own way...
Simon.
Physicists get Hadrons!
Quick! Lets blacken the skies, they won't be able to live without light!
If they can get it down to seven days then we'll have something ;)
---
All your old jokes are belong to sigs.
I think the wonder of any scientific advance should be tempered by a clear-headed analysis of the dangers it might create.
I don't think anybody should be making any new life forms or modifying any existing life forms, at least until we've had a serious societal discussion regarding its possible role and impact on terrorism and biowarfare.
Imagine a scenario where terrorists could alter a disease or organic biological weapon gene by gene to make it immune to current antidotes. Beyond that, I worry that the US itself might use it for its own cache of new-age weapons.
If WE convert it to a weapon, what's the difference? We can claim we're the good guys and we won't use it. But we can look at Nagasaki and Hiroshima.
I hope I'm not fear-mongering here, but, I worry.
Thinking on the computer virus side I like this Hawking quote:
"I think computer viruses should count as life. I think it says something about human nature that the only form of life we have created so far is purely destructive. We've created life in our own image."
-- Stephen Hawking
X(7): A program for managing terminal windows. See also screen(1).
You would hope that they take great pains to make access to the virii as secure as possible.
But, things like this are very important in the fight to create vaccines to illnesses. Anyone who has taken apart and built a car, computer, or whatever will tell you that thier level of understanding is now MUCH greater than it was before they did it. Knowing how to assemble a virus, will hopefully allow us to defend ourselves against them.
Pretty Pictures!
More than a year ago live polio virus was constructed from component DNA. This is not a "artificial" virus but a working copy of phi X bacteriophage. Note that this is an infringement of God's copyrights and patents and trade secrets!
... )
(from NY times, July 2002: Scientists construct virus from scratch for first time, synthesizing live polio virus from chemicals and publicly available genetic information; work was conducted by scientists at State University of New York at Stony Brook and financed by Defense Department as part of program to develop biowarfare) countermeasures
This story indicates that it was done more than a year ago.
Yeah, I agree -- these people really need to start wearing condoms.
Powered by onion juice.
Probably the same as in handling any other virus.
Which is perfectly reasonable. People seem to be exremely afraid of anything made in a lab, but fail to recognize that the greater danger (by far) is from natural evolution of new viruses.
By the same token, the dangers of bio-weapons seem to be greatly excaggerated, when compared to natural pathogens. Some anthrax letters that killed half a dozen people seemed to get more attention and resources than the flu and aids, which kill tens of thousands of people per year in the US alone.
Tor
Horsefeathers. Matter is not the essence of a thing. Form and function usually (but not always) are. Transformation into another form may not destroy the mass but it most certainly destroys the thing that existed before.
"The legitimate powers of government extend only to such acts as are injurious to others." Thomas Jefferson.
The human genome (which is DNA), contained in each of your cells, contains the instructions needed to make a cell (much like a computer program.)
...(Monomer n-1) 3' - 5' (Monomer n) 3'(BLOCKED) ...(Monomer n) 3' ...(Monomer n) 3' - 5' (Monomer n+1) 3' {BLOCKED}
However, in order to use these instructions to make a cell, you need a cell of the same kind to read them.
Analogy: You have a computer program that tells you how to manufacture computers but this doesn't do any good unless you already have a computer OF THE SAME KIND on which to execute it.
So, even if I assemble an entire human genome, I can't use it to make a person unless I already have a human cell. Kapish?
A VIRUS, which is what was made here, is NOT A CELL. It is a parasitic piece of DNA that hijacks an existing cell and contains the instructions to make viruses. The DNA that the virus contains is, in the best case, sufficient to hijack the cell all by itself, and convert the cell into a factory for making viruses. Viruses CANNOT make more viruses by themselves. The similarity to a computer virus, I assume, is obvious.
So, if you can make VIRAL DNA, this will be sufficient to make the virus, if you have cells that the virus can infect.
Even making the genome of a virus is very difficult. The "commercially available" DNA mentioned in the article is made chemically. DNA is made up of a chain of monomers; each monomer has a 5' end and a 3' end that can attach together to form a chain. In order to add monomer n+1 to a growing chain, this is what you do (description meant to be accessible to people who don't know a lot of chemistry):
-> **add reagent to unblock**
-> wash
-> add 5' (Monomer n) 3' {BLOCKED}
-> add reagent to attach 5' and 3' together
and repeat for Monomer n+2. Recursion is good.
Now, this is done in parallel in thousands of molecules of DNA (the 5' end of each molecule is fixed to a plate.)
Every time you add the reagent to remove the BLOCKS, it has a percentage chance, which can be very small, of failing.
So, for example, if, on one paritcular molecule, it fails at position 10, then instead of:
ACGTACGTACGT
you will get,
ACGTACGTAGT.
DNA that makes proteins has something called a "reading frame", consisting of codons which are three monomers long. If you shift the reading frame over by 1 monomer, it completely changes the meaning of the message.
So, a single nucleotide deletion, which I describe above, is disastrous - the synthetic DNA becomes useless.
Even if the chance of failing to remove a block is small - typically about 0.1% - if your DNA molecule is thousands of bases long, the chance of successfully adding every base to any individual molecule is slight.
Of course, you can make two different 100-base long molecules by the above technique and then ligate them together (recursion by splitting the task in half) which is, I believe, what's been done here. This has technical difficulties of it's own, of course, but with refinements it woud allow you to make useful DNA of length n*2^m instead of DNA of length n.
This is a frightening prospect because it would allow you to make ebola "from scratch", or just from the the string of letters that represent the genome (which is so short I could write it out by hand on a stack of cocktail napkins.) We're not to that point yet but it is a scary possibility.
The good and new comes from no quarter where it is looked for, and is always something different from what is expected.
Assembly is not necessarily the same as synthesis. Designing and building a computer (as oppossed to merely putting together what is essentially a kit created by someone else) certainly implies that you have enough knowledge to make intelligent decisions on how to go about protecting the computer.
"The legitimate powers of government extend only to such acts as are injurious to others." Thomas Jefferson.
I don't really care about the morality of this. Frankly, from a scientific point of view: Cool! On the other hand, what does concern me was this quote:
The project was funded in part by the Department of Energy, which hopes to create microbes that would capture carbon dioxide in the atmosphere, produce hydrogen or clean the environment.
Okay, so let's assume we do something like this, with the perfectly innocent intention of cleaning up some level of carbon dioxide. Okay, well you're counting on the virus to reproduce, but what if it gets out of control? It eats up ALL the carbon dioxide. All the trees and plants suffocate and die, but that might not happen before the atmosphere goes up in flames since that carbon dioxide is being turned into hydrogen.
Maybe not a likely event, but my concerns are a bit more on the practical side. Frankly, I'm all for creating new forms of life and bringing back extinct ones, just for the coolness of it. I just hope we don't go doing something foolish, which we always seem to manage to do.
Perhaps bio weapons get more attention than natural viruses simply because if a natural virus kills you, it's an act of [insert deity here] and simply one of the risks of life, like getting hit by a bus.
Bio weapons on the other hand are purposely engineered to maximize the lethality of a disease for the intentional purpose of killing as many people as possible. In other words, it's the intent that matters.
Please note that when they say, "From scratch" they mean that they created a synthetic genome (probably from portions of other genomes - I doubt they know enough about the base pair sequences to actually have done it base pair by base pair) and inserted it in a 'living' cell.
The cell then started reproducing. They didn't create the cell. They probably didn't design the genome as much as patch one together from other genomes (though they may have 'created' it - physically manufactured it)
They say it's safe because it only infects batceria. Unfortunately, humans depend on bacteria to survive, so it's not nearly as innocuous as one might like to think.
However, these are nano-machines that might do real work safely (cleaning up chemical toxins, etc) - I'm just worried about mutations and how they will develop. You can't create life and expect it to reproduce itself without change over time. Pretty soon it'll discover that human skin is much more plentiful than the chemical toxins it was eating, and it'll change its diet.
-Adam
with nature seems to work so well, why not? I live in Illinois and each fall we are swarmed by millions upon millions of Japanese Lady-Bug-Like Orange Beatles. They were put here to fight Aphids, but they have no predators (birds won't even eat them because they emit this foul stench). They area all over the place and nothing can stop them.
So, what kind of checks and balances will there be on man-made viruses? None- you just cannot introduce anything into nature so quickly. I think the possible outcome is clear. This is downright frightening. I think I'll go rent The Stand this weekend.
[FromTheMorning]
Ventner's new virus is artificial in the sense that it was created from chemicals- but it is identical to a known natural virus.
Considering that this virus was synthesized from scratch, it's probably not something very effective. It's a long way from building a virus that works at all to building a virus that targets a particular organism or overcomes natural defenses.
Just because it's man-made doesn't make it more advanced than naturally-occurring viruses. It's been possible for a long time to build viruses from collected stocks, and these are generally much more frightening. What will be scary is when we have some clue as to how to design proteins, and could construct a virus with specific properties. Until then, we're not likely to create anything that doesn't arise in nature.
(Genetically modified foods are a slightly different issue; just because it might arise in nature doesn't mean we'd eat it if it did. Also, most of the organisms involved are much more resistant to mutation and genetic mixing than viruses and bacteria)
This will probably get modded down as flamebait, but someone has to say it: the plural of "virus" is "viruses." It is not "virii" because that isn't an actual English word.
Yesterday, NPR's All Things Considered did a nice piece on it, you can download it here
Unless somebody figures out how to make an artificial microbe that takes advantage of chemical processes that just aren't found in natural evolution. For example, the human body might not even be capable of attacking a hypothetical microbe that has a teflon or silicone-enhanced outer membrane.
At any rate, natural evolution proceeds at a slow rate, so the defending species has time to adapt. Anthrax, for example, implements a tricky chemical hack to breach animal cells and destroy them. Most animals are pretty defenseless against the special back door that antrax uses, and without it the anthrax bacteria would be no more harmful than a pimple. However, anthrax is a rather obscure organism that mostly lives in the dirt. The reason that animals haven't evolved a defense against its chemical attack is that it just doesn't spread that easily in a natural setting. If anthrax were contagious like a cold, animals would have evolved a defense against it long ago.
Now, people may soon have the knowledge to install anthrax's chemical attack into something like a common cold virus. This short-ciruits the evolutionary process. Instead of just having to resist natural random improvemts in microbes, we may soon also face improvements that take advantage of god-like knowledge of the weaknesses of the defenders.
By simultaneously combining the best parts of various different microbes found in nature, then adding unnatural chemical improvements and using our newly available schematics of human cell defense design, we will certainly be able to create microbes far more dangerous than anything nature is likely to randomly come up with.
I doubt that trying to control this kind of technology is going to do any good, however. Somebody somewhere in the world is going to work on this stuff whether its banned or not. Our only hope is probably to develop means to quickly detect any new microbes, along with adaptive technology to create unnatural defenses to unnatural new organisms in real time.
I don't think anybody should be making any new life forms or modifying any existing life forms, at least until we've had a serious societal discussion regarding its possible role and impact on terrorism and biowarfare.
But the problem is that we're not *going* to have a serious societal discussion because that phrase means nothing. Who's talking with whom? Who makes decisions? Who gets input?
When I hear "societal discussion", I get an image in my head of the entire country sitting at a great big table having a little chat about what to do. But in real life, that sort of thing doesn't happen. You have kooks who think that anything that looks like "playing God" is evil, you have people who think that every new invention must immediately be used to aid/fight terrorism, you have people who don't even understand the basic science behind what's going on(like Slashdot...oops, did I say that out loud?). And in the end, after all of these people have "had their say"(who are they talking to?), who decides what will be done? You want the government to say "Sorry, no more research on microorganisms"? Because that's about all it could do. What right does "society" have to control science? Most people will tell you that they don't even understand what "science" is! Who is qualified to do cost/benefit analysis of this sort of thing? Does anybody even *care* about cost/benefit analysis?
I understand(and sympathize with) your concerns, but no amount of talking is going to do anything about this situation. We can't halt our understanding of the world where it is just because a few people might cause problems with it. Hell, if we had taken that attitude to begin with, we'd be lucky to have fire by now!
Visit the
One of the arguments for not destroying the current stock of smallpox is that it might be needed at some future time for research.
With a proven and consistent ability to recreate a virus from its known DNA sequence, the actual viruses themselves could be safely destroyed without impacting the ability to resurrect them in the future. As well, it's probably considerably harder to recreate a virus this way than to steal existing stock.
So while this opens the door to manufacturing viruses for biowarfare, it also makes it possible to destroy current stocks that might be stolen and used for such purposes.
For those of you who have read Tom Clancy's Rainbow Six, you will know that Tom goes into detail not only about what certain individuals will do to bioengineer fatal viruses. Obviously this particular virus isn't much, but what about the radical elements in humanity? There are individuals willing to kill everything on earth in order to advance their political or religious ideology. If someone can engineer viruses this easily, what will happen when someone disgruntled and who doesn't care about himself, much less others, decide to design and manufacture a virus like this?
Thinking about it in slightly different terms, all societies attempt to limit the proliferation of highly destructive weapons among their populace because the arbitrary nature of people would guarantee their arbitrary misuse. Imagine a world where people could obtain nuclear weapons as easily as a box of ammunition. We'd already all be dead.
This is what makes this particular story quite fear-inducing. When we arrive at the point where we can easily contruct very deadly weapons, particularly with the subtlety of viruses, there should be very strict regulation and government supervision. I can only hope there will be a worldwide treaty to that effect. After all, would you want someone engineering a virulent strain of airborne type 4 Ebola because he or she has a beef with a government's ideology?
There are two kinds of Luddites:
1. The "I don't understand it, we're all gonna die" crowd and...
2. The "I understand it, I don't trust those irresponsible buggers, if we don't do something we're all gonna die" crowd.
Large corporations (and some small ones) have repeated proven themselves to be untrustworthy and irresponsible. Crowd #2 have every reason to fear what they fear.
90% of the wealth is in 2% of the pockets. Bummer to be in the majority.
Just raise the taxes on crack.
The specific virus that Venter et al synthesized is called Bacteriophage phiX174. They probably chose it because it has such a short genome.
In fact, it's genome is so short that at first it confused researchers. It's genome is shorter than it should be. That is, there are fewer codons in the genome than there are amino acids in the virus's proteins. Normally, there would need to be a 1:1 codon:amino-acid ratio.
This lead researchers to the amazing discovery that phiX174 contains "genes within genes" and "overlapping genes". (Link to Genetic Map of phiX174) In several instances, one gene is entirely contained within another gene. In another, there are two genes (A and A*) that overlap with "reading frames" that are off by one.
This discovery challenges notions of what a gene is. With this knowledge, you can't say that a gene is simply a particular region of DNA.
These overlapping genes also call attention to the improbability of the evolution of phiX174. Commonly when a genetic mutation occurs, one base changes. This could affect one amino-acid in the protein for which the gene codes. In phiX174's case, a single base mutation could change 2 amino-acids in 2 proteins. This means that the evolution of these proteins is interdependent. That two functional proteins evolved in this manner is absolutely extraordinary.
Of course, now that it has evolved that way, it gives phiX174 an advantage of genetic economy. It takes less energy to maintain and reproduce a shorter genome. So phiX174 gets more bang for it's genetic buck by overlapping genes in this way.
At any rate, natural evolution proceeds at a slow rate, so the defending species has time to adapt.
Natural evolution is not slow for viruses; their genetic code does not have the copy-protection mechanisms of say mammals. That is why we have a new flu pop up every other year, or a SARS for that matter.
Anthrax, for example, implements a tricky chemical hack to breach animal cells and destroy them. Most animals are pretty defenseless against the special back door that antrax uses, and without it the anthrax bacteria would be no more harmful than a pimple. However, anthrax is a rather obscure organism that mostly lives in the dirt. The reason that animals haven't evolved a defense against its chemical attack is that it just doesn't spread that easily in a natural setting. If anthrax were contagious like a cold, animals would have evolved a defense against it long ago.
With all due respect I think you are contradicting yourself. When a patheogen spreads for natural or not so natural reasons, people may die. Some survive, the resistant genes thus become more common. There may even be mutations of strong resistance that start to spread.
When this process happens for natural reasons, you label it "evolving a defense", or "defending species having time to adapt". When it happens by an act of man, you think of it as man being caught "defenseless". Of course, in both cases the species start out as (relatively) defenseless, and end up with a better defense.
My whole point was that there seem to be no lab-made pahtogen worse than anything evolved in nature. As for spreading it by man, well, anthrax did get an assist by man. But the extent of that "outbreak" was miniscule next to the natural outbreaks that happen every year.
Unless somebody figures out how to make an artificial microbe that takes advantage of chemical processes that just aren't found in natural evolution. For example, the human body might not even be capable of attacking a hypothetical microbe that has a teflon or silicone-enhanced outer membrane.
Possibly. But then again, if such mechanisms were very successful, why did they not evolve for 4 billion years on a planet surface covered in silicon compounds. In general, it is very difficult for people in labs to compete with the lab which is our planet, and time-scales of millions or billions of years.
Tor
Let's hope they use some sort of copy protection on these viruses so that they can only reproduce with the permission of the owner. That's DRM I have no trouble with.
-- Pot is safer than Beer
I agree that bio weapons get more attention than natural viruses because they involve someone doing something intentionally. But I don't think it makes sense. The way I see it the downside of my getting killed by an intentional attack is that I'm dead. The downside of my getting killed by a natural virus is that I'm dead. Whether or not anyone intended me to be dead doesn't modify that downside at all for me. If society is going to try to do some stuff to prevent me (and others) from becoming prematurely dead, it seems to me it would make sense to allocate more resources to things that are more likely to kill people.
Knowing how to assemble a virus, will hopefully allow us to defend ourselves against them.
As long as the rate at which the virus reproduces and the level of devastation it causes is not too fast or too irreversible.
Consider the effects of some natural virus and other life forms that have been unleased.
A fungus from the Eastern hemisphere pretty well wiped out the American chestnut tree in short order.
Russian thistle, introduced to North America in the 19th century has likewise become endemic, to the point where tumbleweeds are considered an essential ingredient in any Western film set.
Rabbits in Australia, etc., provide some indication of how rapidly reproducing organisms can spread and how much change they can cause.
Do we trust our knowledge of virus mechanics enough to believe that an inadvertent release of "grey goo" can be undone?
To put it another way:
"Provided by the management for your protection."