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Biotech Science

The Pace and Proliferation of Biological Technologies 65

Posted by michael from the it'll-be-on-you-before-you-know-it dept.
bio-droid writes "Several years ago Slashdot covered an essay in Spectrum about Open Source Biology. Here is a follow on academic paper entitled The Pace and Proliferation of Biological Technologies in the new journal Biosecurity and Bioterrorism ."
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The Pace and Proliferation of Biological Technologies More

The Pace and Proliferation of Biological Technologies

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  • Application forms please? (Score:5, Funny)

    by DarkHand ( 608301 ) on Tuesday October 07, 2003 @06:16PM (#7157623)
    I KNEW I should have patented my gene sequence.
  • Doesn't Heidi Fleiss have a doctorate in the field?

  • I don't wanna be open source! (Score:4, Funny)

    by OwlofCreamCheese ( 645015 ) on Tuesday October 07, 2003 @06:19PM (#7157654)
    I don't wanna be open source! I don't think anyone would patch me if a security hole was found... I don't need script kids gaining root on me and makeing me a zombie...

  • Can't put a genie back... (Score:3, Insightful)

    by citabjockey ( 624849 ) on Tuesday October 07, 2003 @06:22PM (#7157677) Homepage
    Synthesize polio with mail order components? egads! One would expect that this genie can't be put back into a bottle.

    This being the case we better figure out how to minimize incentives to build weapons. Thus far we in the good'ol USofA have a rotten track record in this regard.
    • Which technology will be the first to threaten, or save, or improve, or inconvenience, our lives: biotechnology (gene sequencing/synthesis, retroviral agents, protein analysis/design) or nanotechnology (borg nanoprobes in our blood)?
      • "Which technology will be the first to threaten, or save, or improve, or inconvenience, our lives: biotechnology (gene sequencing/synthesis, retroviral agents, protein analysis/design) or nanotechnology (borg nanoprobes in our blood)? "
        Actually, midi-chlorians have already ruined a good 3 hours of my life.
      • Protein analysis is already allowing my mother to expect a relatively normal lifespan. Her multiple schlerosis medication (Avonex, interferon-B) had to come from somewhere.
      • There's a natural synergy there, IMO. Nanotechnology offers us ways to study (and in some cases, alter) living systems in a way that's impossible with macroscopic methods; at the same time, living systems offer elegant models of molecular machinery that works, and does something useful, rather than being an interesting toy in the lab. In short, the answer to the question "nanotechnology or biotechnology?" is "both."

  • Tricorder (Score:5, Funny)

    by OECD ( 639690 ) on Tuesday October 07, 2003 @06:29PM (#7157735) Journal
    I love it when the first paragraph of a serious article contains the sentence, While there is no Star Trek "Tricorder" in sight, the physical infrastructure of molecular biology is becoming more sophisticated and less expensive every day.

    It reminds me of some friends of mine who were constantly challenging each other to slip odd words or phrases into their serious work.

    "Hey Carlson, I bet you can't work "Tricorder" into your next paper!"

    • really. If I recall, Science mentioned that a new technology would make a tricorder-like device to exist. I don't have my subscription anymore. (boo hoo) Perhaps somebody with one would do a search? It was a few months ago.

      Was it a robust/durable squid or something?
  • "One indication of this trend is that the parts for a DNA synthesizer --mostly plumbing and off-the-shelf electronics --can now be purchased for approximately $10,000."

    Now that's a do-it-yourself project I'd like to see. Come on, one of you guys who spends way too much time on inane case mods can make time for this...

    Also, what do you think about the comparison between Moore's law and the rate of genes sequenced. The only negative I see is that you'll eventually run out of genes to sequence on Earth (unt

  • Sequence != Understand (Score:5, Insightful)

    by enkidu ( 13673 ) on Tuesday October 07, 2003 @06:35PM (#7157777) Homepage Journal
    The basic idea behind this article seems to assume that as sequencing and synthesis technology and skills become widely available, there will be a parallel increase in the danger from the misuse of this technology. I beg to differ. Sequencing DNA does not give you that much insight into how things really work. Nor does tweaking out protein structure. That's the easy step. But the dynamic equilibrium of a cell is maintained by the DNA, the RNA and the proteins, all simultaneous interacting in an essentially stabilized chaotic system. Sure we can "knock-out" a gene here and there, replace one protein with another, but doing so is no more a display of knowledge then is pruning a tree. We're still a long (long long long) way from designing trees from scratch or people developing the new "super-bug" in the garage or even university lab.

    That said, there is a real danger from people using the techniques described above to create hybrid strains (SARS+influenza etc.) to create new virulent strains based on existing virii and bacteria. Of course, even that is much harder than said, primarily because the only way to test which strains work, is to infect people. Any failure and your subject will develop resistance and be useless for future testing. So, you'd need a large number of subjects, or you'd need to develop on a disease which infects both humans and rats (or something) and then hope that the virulence will be analogous for humans. Fortunately, this is rarely the case, what kills rats like, well rats, often doesn't even faze humans and vice versa.

    Hmm, I wonder if I should worry about men in dark suits showing up at my door now...

    • Re:Sequence != Understand (Score:1, Interesting)

      by Anonymous Coward
      Yes indeed. I worked in the analogous field of digital signal processing for music technology and we developed great tools to analyse, sequence and synthesise sound. This did lead to some great breakthroughs, like MP3, but on the whole the ability to subject a time domain signal to say a wavelet transform, FFT, frequency diffraction and then resynthesise it using an arsenal of techniques like additive, FM, walsh and granular synthesis doen't actually add up to much despite all the big words and equations in
    • Don't you think it's more like pruning a tree's genes? I don't buy this idea that there's some inherent depth that is lost as soon as the technology becomes available at lower costs. That sounds like an outlook that subcribes to the mythology of unknown; anything that is known is somehow degraded. I believe such thinking is based in the religion metaphor of Heaven. It has to be unknown and unknowable to be powerful.
      And I'm also quite curious why people are so quick to look at the down side when ther
      • Naw, I'm not that kind of a person when it comes to science. I'm just trying to point out that alot of the assumptions are based on a fundamental misunderstanding about the complexity of life. The "Genetic Code" has underlying implications which are quite misleading.

        Just because you can hack the code of Doom to make a 'bot, doesn't mean that you now have the ability to write Doom. And the simple fact is that a cell doesn't work because of its genes, it works because of its DNA and its enzymatic content

        • Alright, I grant I just woke up and hadn't had any coffee, so I was being a bit snipish.

          But it's not just sequencing that is becoming accessible to bio-newbies, proteomics is the next step and the current head of the NIH is surprisngly proactive about open government funded databases. In fact, he's taking flack from industry people about his ambitious proposal for a large molecule mapping project.

          And then speaking of drop at a time instead of useless but impressive sounding mega cluster number c

          • Sure, send me the links or post them. I've exposed my SPAM protected email address.

            Protenomics ain't all that yet. Like I said, just because you get the playbook, it doesn't mean you can predict how the game gets played. Still, the amount of information is very impressive. I'm just not convinced that all that information will necessarily lead to knowledge, especially information at such a lower level than the control processes that work inside and outside a cell.

            If you're interested in this stuff, c

  • interesting text from the article (Score:4, Interesting)

    by civilengineer ( 669209 ) on Tuesday October 07, 2003 @06:42PM (#7157835) Homepage Journal
    The best way to keep apprised of the activities of both amateurs and professionals is to establish open networks of researchers, perhaps modeled on the Open Source Software (OSS) movement, and potentially sponsored by the government during their embryonic phases. The Open Source development community thrives on constant communication and plentiful free advice. This behavior is common practice for professional biology hackers, and it is already evident on the Web amongst amateur biology hackers.14 This represents an opportunity to keep apprised of current research in a distributed fashion. Anyone trying something new will require advice from peers and may advertise at least some portion of the results of their work. As is evident from the ready criticism leveled at miscreants in online forums frequented by software developers (Slashdot, Kuro5hin, etc.), people are not afraid to speak out when they feel the work of a particular person or group is substandard or threatens the public good. Thus our best potential defense against biological threats is to create and maintain open networks of researchers at every level, thereby magnifying the number of eyes and ears keeping track of what is going on in the world.

    Two questions:
    1.Where would OSS be with government support in embryonic phases?
    2. Slashdot is so powerful??
    • OSS would be without BSD, (developed at a university) without Mozilla, (spawned from a really old web browser I can't quite recall the name of), and without GNU (quite a bit of which came from BSD).
    • Two questions:
      1.Where would OSS be with government support in embryonic phases?

      Huge. Bigger than many of us realize and even from a Republican standpoint, OSS models can make companies, individuals and governments large amounts of cash. Think where we would be with an OSS model for healthcare software instead of the nightmare that is currently present in electronic health care records.

      2. Slashdot is so powerful??

      Slashdot is getting quite a bit of press and it helps that many of the folks who lurk a

  • UGH! Sick of the references to Moore's Law! (Score:5, Informative)

    by Not_Wiggins ( 686627 ) on Tuesday October 07, 2003 @06:43PM (#7157841) Journal
    First, the article uses references to Moore's Law as though that's an accurate guage of how quickly we should expect bio technology to advance based on the comparison to advances in computer technology.

    That premise is inherently flawed. Moore's Law was applicable as an *observation* of the rate at which computing technology advanced... not a rule governing it. I don't think its application is valid for other technologies.

    For example, for Artificial Intelligence, one would have expected us to have solved a lot of the problems simply because the base of the technology (computer technology, no less!) can double in power every few years. This isn't the case for AI, however... we've been stuck with virtually the same models and limitations for well over 50 years, despite the availability of better computer power; the fundamental mathematics and algorithms are what stump that growth... how does one apply Moore's Law to that?

    In this same respect, suggesting that biotech is also going to advance at the same pace as computer technology is loaded with the same folly. Perhaps the power available to analyze will increase as per Moore's "law" (because of more powerful computers being available), but that doesn't mean the answers to questions will necessarily be made readily available.

    We're going to need plain-old experimentation and scientific method to progress through this technology.
    • IMO there's a good reason Moore's law won't apply.

      Semiconductor technology had the benefit of starting from a blank slate. Moore's law started out measuring chips with only a few thousand very simple components. As the technology matures, it will eventually hit fundamental limits and the exponential growth in component count will slow.

      With biotechnology, nature has already provided a very mature technology refined over billions of years. We already have organisms that contain trillions of very complex c

      • The progress we are making is not in producing a better DNA. It would be really difficult to beat nature here and design a better genetics system from scratch (although possible in the long term). But we are making progress is our ability to understand the nature (genetics and molecular biology) and do various exciting thing with existing "technology" (viruses, cells, DNA, etc.).

        The sequencing speed is growing exponentially and will continue to do so until we can do it approximately as fast as the cell doe
    • I can imagine al_Qaeda right now, reading this paper written by Mr Carlson, saying to themselves: "Shit! We can buy stuff like that on eBay? Why didn't we think of that?"

      After months of observing the news and media, I have discovered a new Law (modeled after Moore's Law).

      This new Law states that the number of new and frighteningly creative ways in which terrorists can attack us grows exponentially which each instance of someone breathlessly pointing out a previously unimagined hole in our security infrast
    • > First, the article uses references to Moore's
      > Law as though that's an accurate guage of how
      > quickly we should expect bio technology to
      > advance based on the comparison to advances in
      > computer technology.

      > That premise is inherently flawed. Moore's Law
      > was applicable as an *observation* of the rate
      > at which computing technology advanced... not a
      > rule governing it. I don't think its
      > application is valid for other technologies.

      and your point is...? If you had read the a

  • I don't get it... (Score:5, Insightful)

    by Ieshan ( 409693 ) <ieshan@g[ ]l.com ['mai' in gap]> on Tuesday October 07, 2003 @06:46PM (#7157871) Homepage Journal
    All published science is "Open Source". You publish your methods, your statistical tests - you're even required by most Journals to submit your data to anyone who asks.

    Everything you use is referenced. The only thing that's closed is your thought process - and that's supposed to be described thoroughly in your Introduction and Discussion.

    So as long as we're talking about Published Science, I have no idea what you're all talking about.

    • Re:I don't get it... (Score:3, Insightful)

      by BWJones ( 18351 )
      All published science is "Open Source".

      That is technically true, but the key work is published. You would be stunned to know how much science is funded and done by corporations and governments whose results are never, ever, published. However, that said, secrecy in published science also is present and many times it has its place, for instance in a coy response to a targeted question that the author is either 1) unsure of scientifically, or 2) wants to protect until they can actually publish or patent t

    • Re:I don't get it... (Score:1, Insightful)

      by Anonymous Coward
      Sure it is, in principle. But your living in the dream world of Hume and Popper. Modern science, and particularly bioscience, is carried out behind closed doors often guarded by armed staff.

      'We the people' have lost our science to corporations. In some areas there is still a popular front, all you need to start to code is a $20 second hand computer. True (popular) science works because people are naturally curious and wish to share.

      Look at all the ugly things that happen with plain old bits and bytes. Hum

      • Re:I don't get it... (Score:2, Insightful)

        by Anonymous Coward
        I disagree that we have completely lost science to corporations. While corporate funding does account for a large percentage of research (depending on who your source is you'll hear different numbers - the NSF estimates it to have been ~$2.2 billion in 2001), government-funded research is still huge (the NSF stated that $19 billion when to American universities for funded research and development in 2001).

        I think there are two main reasons for this - the government wants 'basic' research to be open (eve

  • Speaking of biotech proliferation (Score:2, Interesting)

    by Anonymous Coward
    I had an exterminator come to my house yesterday to deal with some termites.

    He injected some food laced with A VIRUS to infect and kill the colony.

    How messed up is that? There's a WMD in my wall.

    Now I don't know if this some engineered virus, or just something they dug up out of the brazillian rain forest, but it's a bioweapon none the less.

    Kinda freaky.

  • Bioterrorism: a scam, just like SDI (Score:4, Interesting)

    by Jonathan ( 5011 ) on Tuesday October 07, 2003 @08:41PM (#7158714) Homepage
    My field is microbial genomics and am rather tired of the whole "bioterrorism" angle. The simple fact is that biological agents just aren't very effective weapons, despite what fiction and movies would lead you to believe. That's why just about every country except the Soviet Union abandoned biowarfare programs by the 1960's.

    And while good old Ken Alibek tells good horror stories about the supposed successes of Biopreparat, consider for a moment the vast number of unemployed former Soviet scientists -- Ken has good economic reasons to be a prophet of doom.

    Similarly, people studying harmless Bacillus strains and who had trouble getting grants suddenly realized that anthrax is caused by a related strain, and shifted focus to anthrax, where grants are easy.

    It's just like the physicists in the Reagan admin who got money by tying their reasearch to SDI.
  • Slightly Offtopic, yet when the article referenced Opensource Biology I got the urge to post about Internet Archive.org's [archive.org] collection of opensourced education material. It has some excellent subjective matter for anyone looking for information to read between your own class books. It's Biology [archive.org] section only has one title "Uses of Waste Water", so anyone with material willing to contribute would indeed strengthen the freedom of information movement.

  • The real bottleneck in biological systems: (Score:3, Interesting)

    by $now Crash ( 629892 ) on Wednesday October 08, 2003 @01:15AM (#7160449)
    While Carlson makes the analogy to Moore's law in exponential growth of biological sequence information, the real bottleneck is not the sequence but actually understanding the biology of each gene. Currently all human genes have been sequenced and most are even classified to families. Paradoxically, pharmaceutical companies are finding it harder and harder to find targets. The problem is validating what each gene is useful in the context of thousands of others which form networks. A simple example is how little we know about HIV which has only 9600 nucleotide genome and despite the fact that 110,000 papers have been published on HIV (about 12 paper/nucleotide of the virus!). I don't even want to extropolate that to human genome which is magnitutes and magnitutes more complex. The issue of home grown Biohackers is also very complex. Unlike computer hackers, biohackers need highly sophisticated labs and many many years of advanced training. Biological systems are very fragile and require expensive equipment and reagents to manipulate (incubators, freezers, pcr machines). Unlike computer technology biological experiments are getting more expensive to perform every day. It is true that the cost of sequencing a gene has followed the Moore's law but the actual cost of experiments have not decreased becuase sequence of a gene nowadays is a trival aspect of the biological experiments. An average serious biology labs have yearly budgets in hundreds of thousands of dollars. It is therefore not realistic to imagine a similar open source movement in biology can be established simply by hobbiest. However there is a serious open source movement at the level of biology scientist for publication of results as an online journal PLOS (plos.org). So the real bottleneck in biology is not the lack of information (in fact there is too much of it) but lack technological means and high level concepts to rapidly decode the meaning of biological programs.
    • Plos is great, but it's a bit of a chicken and egg problem. When you're reading journal articles, the references are as important as the article and since most of them are only available in research libraries or by way overpriced subscription the disenfranchised researchers are still left having to find other means.
      I think there's an answer along the lines of MP3 that will be upsetting to some, but in many ways it's simply inevitable. If you have a 3Megapixel digital camera and some OCR software, try t

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