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Biotech Science Technology

Open Source, Genetically Engineered Machines From a Kit? 157

An anonymous reader writes "Students in an MIT competition are helping to build a dev-kit for cells. Together with synthetic biologists, they're building a Registry of Standard Biological Parts called BioBricks. They aim to do for cells what open source software has done for computers. 'The competition is a showcase for the burgeoning field of synthetic biology. Knight and his colleagues Randy Rettberg and Drew Endy, who created the contest in 2004, want to make biological systems easy to build by applying the tools of computer science and engineering: using standard parts and modular design to simplify complex systems. The goal is to create "genetic Legos" that could produce any chemical, from ethanol to pharmaceuticals.'"
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Open Source, Genetically Engineered Machines From a Kit?

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  • by rrohbeck ( 944847 ) on Thursday November 15, 2007 @03:25PM (#21369505)
    Sweet. I can think of a few.
  • Ha! I love it (Score:3, Interesting)

    by ByOhTek ( 1181381 ) on Thursday November 15, 2007 @03:25PM (#21369509) Journal
    I had a genetics prof in 2002/2003 some time, that said this kind of thing was at least 40 years off...

    I would love to stick this web page in his face.
  • for 'Shaping 101'?
  • by theRhinoceros ( 201323 ) on Thursday November 15, 2007 @03:31PM (#21369587)
    BioBricks? But 'Plasmid' and 'tonic' have such nicer rings to them...
  • by the_B0fh ( 208483 ) on Thursday November 15, 2007 @03:33PM (#21369619) Homepage
    I just hope that these basic "programming" blocks do not turn out to be Windows.
    • THis is MIT they are talking about.

      They kindof look down on Unix around there. I vaguely remember a friend who went there mentioning they used some OSS variant of Unix that she was fairly sure not to be Linux. She said it developed there and didn't have a huge base.
  • Just what we need (Score:3, Insightful)

    by Xonstantine ( 947614 ) on Thursday November 15, 2007 @03:34PM (#21369643)
    A biowarfare construction kit distributed to the masses.
    • by kars ( 100858 )
      Brings a whole new meaning to the term "root"-kit...
    • by bhima ( 46039 )
      meh... movable type has been around for ages and that's far, far more dangerous.
    • Re: (Score:2, Insightful)

      by dfetter ( 2035 )

      A biowarfare construction kit distributed to the masses.
      Do you realize that you're making the argument for taking away everything from "the masses," which most emphatically includes you, that might conceivably be misused to harm someone. Are you ready to give up your car? Your computer? Your kitchen utensils?
      • Re:Just what we need (Score:5, Interesting)

        by Xonstantine ( 947614 ) on Thursday November 15, 2007 @03:55PM (#21369987)
        My computer, my kitchen utensils, and my car can't kill tens of millions of people.

        This is simply a probability function. The more people that have the ability to create a biowarfare agent, the higher the chances that you'll have one released into the wild.

        Consider this. The DNA sequence for the 1918 avian flu virus is public domain. You can buy base pair sequences online. It's not that difficult to add 1 and 1 to get 2. This isn't really technology you want to democratize to the masses. The number of angst ridden hate the world biochemists is much smaller than the number of angst ridden pimple faced teenagers. Given the ability, sooner or later one of them is going to think it's a cool idea to wipe out half the human species and will try.
        • Re: (Score:3, Insightful)

          by geekoid ( 135745 )
          Here it comes, alarmist without a clue of the field there worried about. At least your on the band wagon early with this one.

          • Re:Just what we need (Score:4, Interesting)

            by Xonstantine ( 947614 ) on Thursday November 15, 2007 @04:48PM (#21370739)

            Here it comes, alarmist without a clue of the field there worried about. At least your on the band wagon early with this one.
            Actually, I majored in biology and have done a fair amount of research into biowarfare agents. So I do, in fact, have a clue about what I'm talking about.

            If I'm being alarmist about this, why not let anyone buy weapons grade plutonium or uranium and publish functional weapons designs along with the CAD/CAM instructions? After all, using your logic it's alarmist to think anyone would actually go to the trouble of actually constructing and using a bomb.

            After all, the technical and monetary investment needed to build a nuclear bomb is several orders of magnitude greater than what is required to build a biological agent. If we don't have anything to worry about with biological agents, then obviously our nuke fears are overblown as well.
            • the tools used for terrorism are not the problem, the underlying cause of terrorism in the first place *is* the problem and its consistently ignored in favor of restricting the advances of technology for "safety" and it's absolute bs.
              • the tools used for terrorism are not the problem, the underlying cause of terrorism in the first place *is* the problem and its consistently ignored in favor of restricting the advances of technology for "safety" and it's absolute bs.

                Sure. Whatever.

                Look, society has no problem over reacting to low probability, low impact events like school shootings. So now we have a proliferation of "zero tolerance" policies in schools that result in suspensions and even expulsions over things like cake knives being seen in a locked car in the student parking lot or being in possession of aspirin (drugs are bad). The reason why these are low impact events is the destructive ability of a deranged school shooter is limited. The reason why it's lo

                • I understand your point but I'm curious as to what you suggest we do about it. hide under a rock? ban the technology? forbid the creation of the technology in the first place? or should we take advantage of the technology to prevent these same kind of weapons from being effective?
                  • I'm not sure there is anything we CAN do about it. Hence my original comment "just what we need..."

                    It is what it is, and to some extent the genie is already out of the bottle.
                    • indeed, my concern about the whole thing is that although we can probably stop the spread of these diseases using the same technology that created them, many people would die in the mean time. Even worse is that such a powerful technology is probably going to be abused as much as it will be for doing good which is a shame.
        • Comment removed based on user account deletion
          • I'm not saying there's no threat, but we need a lethal combination of angry biologists and a design for an unbelievably successful virus. The success of conventional warfare as opposed to chemical on both the battlefield and the terrorist's cities suggests that few attempts would ever be made to use such a technique.

            You don't really need a combination of angry biologists, and you don't need an unbelievably successful virus or bacterial agent. You just need a modestly successful one. Non-weapons grade anthrax may not kill you as fast or in as small doses as weapons grade anthrax, but it'll still kill you. And live bacteria and viral agents are the gift that keeps on giving.

        • by dfetter ( 2035 )

          My computer, my kitchen utensils, and my car can't kill tens of millions of people.

          If you're going to say that someone could create a nasty biological strain with this that they couldn't have constructed without it, you'll have to provide some evidence. For example, if you simply take a stack of petri dishes, expose the first one to air, pick the fastest-growing strain, then lather, rinse and repeat 20 times, the resulting strain will be lethal.

          What really bugs me is the automatic assumption that anything people can use their curiosity on will be so misused that we have to ban it in adv

          • What really bugs me is the automatic assumption that anything people can use their curiosity on will be so misused that we have to ban it in advance of any evidence that it will actually cause any harm.

            Sigh ... we used to say that about computer software. Now we'll *really* need to keep our antivirus signatures up to date.

            • so your having to worry about antivirus signatures is due to people having the freedom to explore and couldn't possibly be due to running Microsoft's bloated, poor quality crapware for which pre-teens can write malware, rather than a real OS?
              • Ahh, the grand assumption that I'm in Microsoft's pocket, combined with a bandwagon ad-hominem that attempts to tie me to your perception of a common enemy.

                You're a tool.

        • Your being paranoid. It is easy to add 1 and 1 to get 2. It is not currently possible to order the entire genome of Influenzavirus, strain H1N1, and create an epidemic. You don't really know what your talking about. Just for giggles say you could mastermind such an endevour and order your virus "to go". You could order a giant 200-base oligo from IDT [idtdna.com] and it would cost you about $5,435.20(US) and it would come in about 68 chucks that you would then have to reconstruct into its original multipartite genome. T
        • You want to kill tens of millions of people? Pick up a bunch of poisonous crap from random home depots around the country, gather it all up in some vans, and dump it all in a bunch of $RANDOM_SMALL_CITY water supplies across the country at the same time, the small cities who don't have budget or infrastructure go guard those supplies. There you go - millions dead from common household materials, and all you have to know how to do is drive a truck and not be an idiot. You don't have to have genetically engin
  • by dotancohen ( 1015143 ) on Thursday November 15, 2007 @03:35PM (#21369645) Homepage
    Now that they've released it under open source, God is going to sue them for copyright infringement.
  • Imagine creating toothpaste that when combined with mashed up peanuts (salted) becomes an explosive?

    On a lighter note, do you think they can turn lead into gold? I hear Ron Paul would like to have some more of it to back the dollar?
    • On a lighter note, do you think they can turn lead into gold?

      Lead can be turned into gold. It's just prohibitively expensive.
      • That would completely crash the world economy.
        • by geekoid ( 135745 )
          no it wouldn't. mThe current economy is based on faith in little pieces of paper.

          The store says milk is worth 2 pieces of paper, you pay two pieces of paper, you say from you employer, I need 2000 piece of paper to do work, your landlord says you can stay for 200 pieces of paper.

          Gold isn't needed. Yes, it's based on a non tangible. So what?
  • So the old 2 horny boys and a chemistry set scenario can finally come to pass.
  • New License on Life (Score:4, Interesting)

    by Doc Ruby ( 173196 ) on Thursday November 15, 2007 @03:38PM (#21369729) Homepage Journal

    A consortium of universities will release the first draft of the BioBrick Public License in 2008. It will allow anyone to use the biological parts -- essentially a cellular dev kit -- for free.

    What is this crap about a license taking months to produce and release? They should just release it with a license saying everything made with the kit is in the public domain, with the single exception to that disclaimer of all rights that any derivative must also come with that license. Why would it take more than 5 minutes to agree to release that license, and release it?

    When some university comes after me for metabolizing glucose as part of my job (moving a muscle during business hours, just like you sometimes do), I don't want to have to argue about some license they've got on some DNA they synthesized.

    All these patents on discovered genes are the purest BS violation of prior art. Any complexity in this BioBrick Public License will create more problems than it could ever solve.
    • What is this crap about a license taking months to produce and release? They should just release it with a license saying everything made with the kit is in the public domain, with the single exception to that disclaimer of all rights that any derivative must also come with that license. Why would it take more than 5 minutes to agree to release that license, and release it?

      You know, you'd think it should be that simple. But to actually build legal code that would implement those protections in enough jurisd

      • Nah, the CC licenses are complex. There's no reason the license can't read "this software/dataset/whatever is hereby released from any rights or obligations by either the recipient or anyone from whom they receive it, except the obligation to include this notice is required".

        Even if that needs tweaking by a lawyer, any lawyer who can't make that sound, given all the knowledge of existing contracts, isn't worth their own license.

        Besides, that contract isn't even necessary. They can just release it with "this
        • Besides, that contract isn't even necessary. They can just release it with "this thing is hereby placed in the public domain". If they want to ensure that any changes or derivations are forced to be published, which I don't see as necessary, they can publish it under the GPL, which is easier to defend precisely because it's not new. If it's content, not code, they can publish it under an existing CC.

          Ah, but are the various biobrick items content, or code? I would guess they're neither, but something differe

          • Public domain still covers everything. And with a simple statement of perpetuity for derivatives, it really covers everything, every way, forever. We're talking under an hour for a competent IP lawyer, not months for teams of them.

            Unless they're protecting more than the freedom of what they release, like some of their own private interests in its not-so-free perpetuation.
  • upside: any elicit drug, or pharmaceutical intellect property drugs, can be made

    downside: hello nerve gas

    results: all of the pluses and minuses of free computer code manipulations we are familiar with (intellectual property meltdown, hackers, etc.), replicated in the world of biochemistry. except this time, the script kiddies are playing with petri dishes

    what took an entire universy research department, with all the pcr machines, southern blots, grad students, etc. 10 years ago, will 10 years from now be on the workbench of high school students

    i'm all one for the relentless march of technology, and there is no putting pandora back in the box, but this leaves me feeling queasy

    maybe it's just the GM wasabi in my sushi
    • Re: (Score:3, Informative)

      by LionMage ( 318500 )
      Wow... Normally, I'd let this stuff slide, but...

      upside: any elicit drug [...]

      Emphasis added. The word you want to use here is "illicit," as in illegal. "Elicit" is a homophone, but means something entirely different.

      [...] and there is no putting pandora back in the box [...]

      OK, Pandora was never in the box, you dig? The box (actually a jar in better translations) contained a whole host of blessings (at least in some versions), but also many curses besides (from the versions of the myth that have persist

      • why the hell do you think your spelling/ grammar/ greek mythology nazi ways are going to impress me?

        why the hell do you grammar nazis try so hard?
        • You proceed from the false assumption that someone is trying to impress you. This may come across as harsh, but... you're not someone worthy of impressing. I was merely trying to help you out, since you seem to have trouble communicating effectively. That, and I happen to love my language, and my cultural heritage, though you seem to have respect for neither. So, what we have here is an impasse -- you refuse to change your ways, and people like me are not going to stop critiquing you. Either you learn
    • what took an entire universy research department, with all the pcr machines, southern blots, grad students, etc. 10 years ago, will 10 years from now be on the workbench of high school students

      I don't know. Is there any huge reason FOR High School students to be practicing this stuff?

      PCR is surprisingly easy to do (albeit sloppily). Looking back, my high school probably had most of the necessary equipment. However, I can't really think of the educational value of performing a PCR reaction, given that alt

      • there's no reason to make bottle rockets

        there's no reason to make napster

        there's no reason to master electronic sampling in music

        do you really think a teenager finds nothing compelling about a quick and easy way to make any chemical he wants in his gym locker?
    • by Upaut ( 670171 ) on Thursday November 15, 2007 @05:21PM (#21371179) Homepage Journal
      downside: hello nerve gas

      No. No. You are not going to use that argument here. That is the argument that is killing science. You want to stop someone making deadly gas? Here, not even using the classic "Chlorine" form household chemicals one. How about some phosphene gas? Colourless, odorless, tasteless, kills with low concentration. Can be made with urine (collected, aged, and distilled with charcoal to extract phosphorus), and a some natural gas from a line. Want to ban the action of urination?

      Yes, the knowledge and ability to make some deadly compounds have always existed. Its the blight of the scientist; no one trusts us. Scientists are not the heroes, we are always portrayed as either bumbling and accidentally unleashing a horror onto the world, or a megalomaniac bent on global conquest. But the benefit of being able to learn at home far outweighs one or two people that accidently injure themselves. The best way of combatting these accidents? Promoting more science at home. With knowledge instilled at a young age, then its less likely that someone will get hurt, and with learning responsibility at a young age, less likely to hurt others. Its kinda like taking karate, no mater how pissed you get, you don't whip out the years of honed skills for revenge. Its just not polite.

      As a young lad I had seven layers of shit beaten out of me, almost on a daily basis. What did I do? Did I take my gun and shoot everyone? Did I make explosives and take everyone out with me? Did I gas my tormentors? Did I use my historical knowledge of poisons craft a unique death? Nope. Wouldn't. Because all life is important, even the life of the dick that is kicking you in the skull. On the other hand, my former tormentors might have notice they went through tires and cars in general faster then their classmates... Never said I was above all forms of petty vengeance...
  • I'm just thinking of the applications for household pets...

    Dwarf elephants the size of kittens. Basselopes. Maybe even unicorns...

    • Snipes... Don't forget snipes.
    • by geekoid ( 135745 )
      OMG, if my daughter reads that I'm doomed.
      "Daddy can I have a Unicorn"

      OTOH, it would be a great test of her virginity in a bunch of years.

      "Sweatheart, Why won't Uni let you pet him? nN an unrelated note, I will need to find my gun before your boyfriend arrives to pick you up...and my shovel."

  • by Mr.Ned ( 79679 ) on Thursday November 15, 2007 @03:46PM (#21369835)
    I saw a talk by Tom Knight recently about BioBricks. It's a cool concept.

    Some interesting points I remember from the talk:

    - His lab and others like it are trying to take the craft out of manipulating cells and make it an engineering discipline.

    - They've got ready-made kits of cell building blocks that you can piece together like Legos, and are adding thousands of new ones each year.

    - Cells are enormously more efficient at storing information that we can in silicon - 5 or 6 orders of magnitude more dense - but most cells aren't good at writing new data, just reading it.

    - Cells are really good at making precise structures at the atomic level, but our mechanical processes rely on statistics and probabilities to get things right. The smaller the structures get, the more a small statistical variation can really mess things up. Carbon nanotubes are much-hyped, and guess what's really good at making carbon structures?

    - Another useful critter that was created for the last competition detected arsenic in water. The best manufactured/chemical solution costs is tens of dollars per test; using these kits, undergraduates from Edinburgh created something over a summer that is so cheap the bottles to put it in are the dominate cost.
    • by Mr.Ned ( 79679 )
      Few other things I forgot to mention:

      - They're working with BSL-1 critters, which he described as "don't eat them, but if you do, nothing bad will happen"

      - The critters they create are not as fit as the ones they created them from, so even if they did get out, they're not likely to survive. He's in the business of making them more simple so they're easier to understand and build, and by simplifying, they're losing functionality. Apparently a e. coli can act completely differently depending on its environm
    • by waveclaw ( 43274 )

      They've got ready-made kits of cell building blocks that you can piece together like Legos, and are adding thousands of new ones each year.

      So the race is on. Who will win?

      The backyarders [orionsarm.com] who try to grow their own Stage Trees [wikipedia.org] and escape into orbit?

      Or the href="http://en.wikipedia.org/wiki/Islamist_terrorism"Terrorists with super-Sarin [wikipedia.org] on their suddenly glowing, long-blonde [wikipedia.org] minds?

      Cells are enormously more efficient at storing information that we can in silicon

      Has Microsoft heard about this? It could be us

  • I read about this... what? A couple of months ago?
  • by davidwr ( 791652 ) on Thursday November 15, 2007 @03:54PM (#21369979) Homepage Journal
    Announcer: Hey kids! How would you like a chemistry set for Christmas?
    Kids: BOR-ING!
    Announcer: A ray gun?
    Kids: BOR-ING!
    Announcer: How about the new amazing Bio-Bricks!
    Kids: COOL!!!!!

    Announcer voice-over with kids in background hunched over a petri dish full of Bio-Bricks: With Bio-Bricks your kids will have hours upon hours of enjoyment creating new life forms. Bio-Bricks are available at fine genetic research supply stores everywhere.

    Announcer reading legal disclaimer:
    Neither the International Genetically Engineered Machines Competition, MIT, Bejing University, or the government of China is responsible for improper use of Bio-Bricks. Serious injury, mutations, illness, death, or the end of life on Earth may result from improper use of Bio-Bricks. Using Bio-Bricks to create dangerous life forms is not recommended. Adult supervision required.
  • Scares me (Score:2, Interesting)

    I don't think about it a whole lot, but back in my mind, I've thought that this is what will kill off all humans on the planet before the end of my natural life. Once you have cheap, easy engineering of microbial life, then all it takes is exactly ONE maniac to design a transmittable disease that will wipe out everyone.

    Don't think anyone would do that? Look at some of the more rabid environmentalists who think the worst thing that ever happened to Earth was humanity. Theodore Kaczinsky was a genius, and w

    • by account_deleted ( 4530225 ) on Thursday November 15, 2007 @04:15PM (#21370287)
      Comment removed based on user account deletion
    • I'm more worried about an accident... I mean, as many of us learned to program, who hasn't accidentally created a unending loop, etc?
    • Re: (Score:2, Interesting)

      Once you have cheap, easy engineering of microbial life, then all it takes is exactly ONE maniac to design a transmittable disease that will wipe out everyone.

      Once you have cheap, easy engineering of microbial life, you also have thousands of people competent to work on cures, genetic enhancements, immune system upgrades, rapid turn-around vaccines, and so forth. Computers and programming languages didn't just produce script kiddies, they produces all the other benefits of computers and programming languages, from security researches to flash games to robotic assembly lines to the pending promise of hand-held real-time universal translation widgets. Genetic en

      • Once you have cheap, easy engineering of microbial life, you also have thousands of people competent to work on cures, genetic enhancements, immune system upgrades, rapid turn-around vaccines, and so forth.

        That's assuming people know the doomsday virus even exists. By the time everyone starts dying, it's too late. Civilization would fall if that many people died at once -- including power plants. It's always easier to destroy than to create. Just because we have the atomic bomb doesn't mean we have "rap

  • What happens when someone uses the wrong block in the right spot by accident? Giving the tools to people that aren't able to understand the possible side effects could be dangerous. Not everyone has a containment level 3 facility in their basement.
    • If we continually lived in constant fear of the unknown, we'd still be living in caves (assuming we even survived at all...), completely ignorant of even the simplest things we now take for granted. (Fire, anyone?)

      That much aside, it's often an unavoidable necessity to tread into unknown territory because our survival might eventually depend on one of us to take the first step before someone else does. Surely you learned about Mutually Assured Destruction in school, right? It doesn't quite work if only one
  • by greg_barton ( 5551 ) * <greg_barton @ y a h o o.com> on Thursday November 15, 2007 @04:09PM (#21370173) Homepage Journal
    My daughter was born three months ago. My wife jokes, "She won't be allowed to date until she's 25!" I always add, "Yeah, and not until after she gets a PhD in Programmable Genetics..."

    I was only half kidding. Now I'm not kidding at all. :)
  • ...this will stay legal for what? Five minutes? As soon as they're successful, this is going to be locked up tighter than a drum (as an old employer used to say). There won't be any namby pamby warm and fuzzy open community feelings for long. I see the end result being collusion by big pharma and their de-balled government lackies to outlaw this. Especially if it would mean "illegitimate" alternatives to big pharma. The companies that make medicine today aren't here to cure you. They're here to make
  • by syrinje ( 781614 ) on Thursday November 15, 2007 @04:40PM (#21370627)
    ...I, for one, welocme our synthetic Bio-Lego-lical overlords!
  • by Pugio ( 816116 ) on Thursday November 15, 2007 @05:10PM (#21371037) Journal

    I don't often post, but most of the comments here are completely wrong. I'm a bioengineer and have been following this project since its inception. Some points:

    - This technology is NOT any more effective or dangerous than "traditional" genetic engineering. You will not be able to make a unicorn, dragon, or some unholy dog/cat combination.

    - Building an Über Death Virus from this takes just as much skill, equipment, and knowledge as it would using standard tools. First, the BioBricks are made for use inside of a living bacterial organism. They will not work without a cell to operate in. A virus, by contrast, is just a specialized collection of proteins that is not in any way alive - something very very different from BioBricks.

    "But what about a killer bacteria?" I hear you ask. Well, while technically possible, it's not easy to make something that can live comfortably in our bodies. To a foreign bacteria, our bodies are a fortress crawling with guards and death traps. It has taken nature millions of years to develop microbes capable of harming us (as our immune systems have also grown to combat each new threat.) The key point here is that, to create a NEW bacterial threat, one would have to be very well versed in biology and genetic engineering. What's more, for someone of this skill level, it would be much easier to create such a bacteria using standard biological techniques, not BioBricks.

    These BioBricks are incredibly cool and powerful, within their problem domain. Making bacteria do things is very different from giving them the ability to successfully harm our bodies and spread to other hosts.

    • "You will not be able to make a unicorn, dragon, or some unholy dog/cat combination."

      aww.

      Will we at least be able to create a superplague using the chinese knock-off?
    • Yeah, I wasn't quite sure what this was when I first read it, and there isn't a lot of technical information on their website (at least within easy reach). Basically, from what I can gather, it looks like they have simplified methods for making custom bacterial strains. So whereas before, if you wanted E. coli to overproduce "your favorite protein" you had to make a knockout, and then construct a plasmid, and then transform, and then cross your fingers and hoped it worked the first time otherwise you had to
  • Hey, i guess we all gotta go sometime. Might as well make it child's play to wipeout 1/2 the planet from one 'oops' .
  • Wait.. back up. "Synthetic biologists"? Who cares about some kit, they're already making synthetic biologists? I assume these biologists can then make more of themselves, so...

    I, for one, welcome our new self-replicating biologist overlords.
  • (a parody of his famous 197x letter to people copying MS Basic)...

    Hey you people!

    Stop ripping off my cells! It's our intellectual property, copyright law applies, and we will sue the hell out of you!

  • I was a participant in the iGEM competition this year (Davidson/Missouri Western, check out our wiki [mit.edu]). Some people are talking about the potential dangers these BioBricks have if they are publically available and easy to use. First, it might be important to clarify what they are. Four restriction enzyme sites on plasmids allow the stitching together of DNA sequences into any desired configuration. The registry contains hundreds (soon to be thousands) of parts that can be put together and dropped into ce

  • Call me a corporate drone full of lobby money if you wish but... Isn't making a easy to use open source devkit for biology akin to giving away a SDK to make computer virus in a world where all users are locked with an unpatched Windows ME on an unfiltered internet connection ?

One person's error is another person's data.

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