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Science

Biotech Makes the News 59

Posted by Hemos from the chips-and-money-oh-me dept.
hoppy wrote to us in regards to the recent EE Times article about a tuberculosis detecting biochip. The United States and Russia are teaming up to make the chip, as variant drug-resistant strains are infecting thousands in Russian jails, and making a big comeback in poorer areas in the US. The chip will be used to identify the strain of TB, so that appropriate treatment can be used, rather then the shotgun approach In other news, James Clark, co-founder of SGI and Netscape has given 150 million US to his former school, Stanford. The donation is to be used just for biotech.
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Biotech Makes the News

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  • just thought that i would be the first to bring up the subject of the "mark of the beast." What happens when they start requiring the chips in all people?
  • That's one thing that natural selection in bacteria (and virii) can't compensate against.

    Once we are able to design a micro-machine capable to recognising a disease carrying agent, and physically tearing it apart from the inside, resistance via natural selection ceases to be a factor.

    Of course, assuming the 20 minute generation of bacteria, these would have to be some very nimble little nanites - but still, we can dream.

    And the new possibilities of nanotech-based diseases... The mind boggles.
  • This assay depends upon PCR amplification of the MTB sample. You're completely correct, there would be no use waiting for the sample to grow up and then use this assay (it would then take as long as it does now!). But this assay is like all the other microarray ones used for DNA sequencing by hybdridization (we use them now too!), they have to PCR up the baby first. And that poses additional problem as you mentioned along with cross contamination (something we always find in other labs when we screen their stuff as part of our gov't duties).
  • Excellent information, and truly interesting. This post deserves a place in the spot-light. Moderators, please, don't let it get lost.

    A billion people infected with TB? ~17% of the world's population? Frightful.
  • ...and people pestering their doctors for antibiotics and then not taking the full course.

    Not only not taking the full course... but people pestering their doctors for antibiotics when they have a VIRUS. People have gotten far too accustomed to "taking something" to make them better when they are sick and this has lead to many doctors prescribing antibiotics when the problem is not bacterial at all.

    Antibiotics are useful in killing a bacterial infection and they serve no other purpose. People need to be educated about this fact and doctors need to act appropriately by explaining this to their patients.

    ~m
  • Well, congratulations. You made me laugh: when I talk about computers, computer geeks laugh at me - "lamer". Now it's my turn to call someone that name :-) You seem to know about biology as much as I do about TCP/IP (or less, in fact).


    1. You know that one: if architects make houses the way programists... etc. How about that one: if biologists worked the way programists...etc.?


    2. People have been doing biotech much longer than they have been doing programming. You could say abacus is a primitive computer. Well, it is nothing compared to what our ancestors did to the ancestor of an apple (and I don't mean the computer company :-) ).


    3. Remember that you work with DNA and not living organisms.


    4. Remember that you have to do with randomly evolving clones every time you take a breathe. You have no idea how much diversity is surrounding you.


    Regards,


    January

  • Once we are able to design a micro-machine capable to recognising a disease carrying agent, and physically tearing it apart from the inside, resistance via natural selection ceases to be a factor.

    The problem is you're basically describing, ah, the human immune system. This is what the immune system does, it recognizes a bug as foreign and zaps it, killing it dead (tm). It's got an elaborate and complex mechanism for recognizing existing bugs and learning new ones. The problem, usually, is bugs don't conveniently remain constant, i.e., if Mr. T-cell is killing off all the cells with o-antigen on their surface, some bacteria will evolve with an o-antigen that will avoid it. I doubt nanotech would be a good antibiotic.
    Now what it WOULD be good for is going into human cells, snipping retroviral inserts (like HIV) from the human genome, and thus curing people of HIV efficiently.

    SA
  • donors operate on a standard basis--whatever amount of control is standard, they'll probably want a little more

    Well, there are two limiting factors here:

    1. The "standard" donations that most people make (through alumni associations, wills, annual fund, etc) are of the "no strings attached" variety. That's not likely to change. Most people who donate are quite satisfied with the institution's goals, which is why they're donating in the first place.

    2. Multi-million dollar donations (like the biotech one) are regulated by the media. The purpose of big grants is to generate good PR for the donor. If Bill Gates set up a foundation solely for the purpose of destroying Linux and installing Win2000 on all campus computers, he'd be soundly reviled. Also, the IRS could disallow it as a deduction.
  • I was hospitalized for 17 days, and felt terrrible. I have to take antibiotics for 6 months. I come out and then I see this! Sheeesh!
  • Many forms of resistance carry a significant cost for the bacteria. E.g. the "multiple drug resistance" genes tend to encode fairly nonselective channels that pump out many things from the inside of the bacterium. Unsurprisingly, bacteria that aren't leaking their guts grow faster...unless they are placed in an antibiotic.

    This means that if we have alternate strategies that we can use--a drug or whatever--while we avoid certain antibiotics, resistance will probably be lost. However, it is extremely hard to have the discipline to avoid prescribing an antibiotic that might work now to save someone on the grounds that doing so will allow it to certainly save people in the future. We prefer to--and with some justification--wait for a newer tech fix.

  • I think rde is commenting on the overuse of antibiotics in everyday use. Over the years people have demanded antibiotics for things such as the common virus, many Doctors were pressured into prescribing them... even if they're not needed. Therefore, when they're actually needed to fight a bacterial infection like TB(when they of course would be used) your out of luck.

  • Hey, this is my field! (Score:4)

    by upstateguy ( 90019 ) on Wednesday October 27, 1999 @04:53AM (#1584092)
    I'm a TB molecular geneticist so I figured my two cents might be worth throwing in...

    There were actually two chips announced this last week. The drug diagnosis chip from Argonne [yahoo.com]and a research-based expression chip from Peter Small's lab at Stanford. [stanford.edu]

    The Argonne chip is a competitor to Affymetrix/BioMerioux's TB chip which is also still in development. What these gizmos are designed to do is DNA sequencing by hybridization. The TB genome is sequenced and we roughly understand how many of the antituberculosis drugs work and what genes mutate to confer drug resistance (mostly). The traditional (and only FDA approved) way is to grow the patient's TB specimen in the presence in each of these drugs and see if growth is inhibited. For strains that are multi-drug resistant (MDR), that can take many weeks or even months to correctly diagnose. In the early days of the MDR outbreak in NY city in the early 90's, many of the patients were dead before the results were available (aggrevated by HIV/AIDS in the pre-protease inhibitor days).

    Peter Small's chips are designed to understand which genes are turned on/off under different conditions. Their paper in the Oct 26th issue of PNAS is their results using these chips on TB treated with isoniazid (the first anti-TB drug).

    So molecular diagnostics is a goal of everyone's. Here in our lab we use both the traditional methods and then direct DNA sequencing as an experimental program. Direct DNA sequencing is a bit tedious and can get expensive for each hunk of the TB chromosome you need to sequence to cover all the potential sites for drug-resistance conferring mutations. Arrays let you "do it in one shot".

    And Argonne's reported ability to reuse these things 50x would be a huge thing. George Soros is probably footing some of this bill since he's been donating a ton of cash to try to check the expansions of TB in post-cold war Russia. Their prison system is a real nightmare and their "tough on crime attitude (much like the US!) doesn't mind if these prisoners give each other TB and they end up dying. But at least a few of these prisoners do get released and then the problem goes into the general population. The TB we're seeing from Russian immigrants now is really strange. It's not always resistant to the first line of drugs used (safer and more effective) but resistant to many of the second line drugs (full of nasty side effects, less effective, and much more expensive). Wealth individuals in Russia seem to be assuming they have drug resistant TB and just starting in the on the second line drugs.

    Our prison system was caught a bit off guard when TB resurfaced in the 80's. They've *vastly* improved now and while TB is still diagnosed in prisons, the transmissions seem to be checked. Here in NY about 20% of our prison population is HIV+ so keeping TB checked is really important.

    Problems with these chips arise when you have mixed populations of TB in a patient. Some cells have the mutation that causes resitance, and some don't. Since all these arrays start off with a PCR amplification reation, if the susceptable cell's DNA gets amplified over the mutant ones, you might get the wrong diagnosis. Or if a patient has two different strains of TB in them (can happen but mostly in immunocompromised individuals). But this is much less a concern than in the situation of HIV where these molecular diagnostics sometimes run into trouble.

    With 1 billion people in the world infected with TB (and here in NY, it's nearly 1 out of 15...though most will never come down with "active" disease even untreated), don't assume it's a Russia/third world/poor thing!

    Cheers!

  • The only way to stain the invading bacteria is to find some way of targeting the cell membrane of ONLY the pathogenic bacteria... what about your normal flora? If you kill them off, your dead anyway. And if you can find a way to distinguish them by some protein structure, you might as well use a vaccine, it's a much easier approach. Just a though...

    Also, don't forget: only retroviruses are RNA. Many viruses are composed of DNA :)

  • Were I that 13 yearish pale kid nowadays, I would not see the light of my future in computer science easing our lives, but rather in the chance to modify matter to be more serving and intelligent (doorsteps that would move out of the way before you hit your toes, anyclumsy?)

    Nanotech will not fulfill its promises in short term (eh, a hundred years?) without being able to copy most of the work already done in the nature. By modifuing already working solutions (DNA, cells, virii) we'll be able to code matter instead of just calculators. But now I am stating the obvious.

    If development turns out "well", our views of what is dead matter and what is life might have changed a lot after a chunk of time. On the other hand, some of the citizenry might be unrecognizable as humen in our current view: Internetworking lumps of neurons remotely controlling biologically grown fullereen limbs, to name a vision. Buy a hand? Viral warfare on the other might be scarier than the ole' A-bomb.

    In sense of the above, I view the donation as a good thing. Clark let it be understood that he had discussed targeting with the university, and actually changed the focus based on that discussion. What would be an appropriately dim focus for funding? Even the state tax part of funding universities is, at least here in Finland, based on a complex network of "results" such as the amount of doctorates (yuck). Same goes, methinks, for any free lunch.

    Kudos for Clark. And for the US-Russia co-effort as well. Best news for quite a while; I stand effectively surprised that there is a level of biotechnology such as DNA scanning that is already becoming mass-producable.

    (BTW, I just saw Fly 2 on TV last night :P)
  • so that appropriate treatment can be used, rather then the shotgun approach.

    Um, that isn't the same shotgun approach that horse doctors use, is it?

  • Hemos, don't get the kids fired up on biotech (Score:3)

    by heroine ( 1220 ) on Wednesday October 27, 1999 @05:17AM (#1584096) Homepage
    Now if Biotech was really that employable you would have gone into biotech instead of working at Andover and we all know you're a biotech freak. Don't get these kids fired up about something which is almost entirely post-docs who can't find jobs. After the first 6 years of grad school you realize how increadibly tightly pigeonholed it is. Then after selecting one small, discreet area of biotech and pigeonholing yourself you realize that despite all the hype, the one discrete area of the one gene that got your postdoc buddy that day job in North Dakota was one base pair away from yours so you didn't get it. None of the grad students I've encountered are happy and they all wish they were in CS. Now MD degrees, if you're famous enough to get one, have an easier time. The resources available to MDs makes postdoc work look like tinker toys.
  • Sorry. 's where I work, though not with anything as groovy as biochips. : (

    Anyway, there's a blurb about this on the Argonne home page, here [anl.gov]. Probably not a lot more informative than the above link, but it's got a hokey graphic (oooh! pictures!).

    --

  • Re:Sorry to be heavy and all... (Score:3)

    by Awel ( 28821 ) on Wednesday October 27, 1999 @08:19AM (#1584098)

    However, the reason we're in such shit from M.Tuberculosis and S.Aureus is the ridiculous overuse of antibiotics. Vancomycin -- the antibiotic that kills anything -- is proving less than effective against some strains of both. This is a problem that's entirely of our own making, and one that's being exacerbated by the overuse of animal feed, the growing of GM crops and people pestering their doctors for antibiotics and then not taking the full course.

    It`s got nothing to do with GM crops. But it`s certainly to do with antibiotics in animal feed. Farmers routinely stuff their animals with antibiotics even when they`re not ill, because it makes them grow faster. If you can be bothered ploughing your way through this [socgenmicrobiol.org.uk], there`s a lot of good stuff there. The most important thing I want to bring out of it is that many strains of antibiotic-resistant bacteria currently populating hospitals have been traced (by techniques related to DNA fingerprinting) to farm animal bacteria.

    Certainly in the UK, the problem of antibiotic resistance is severe. I never want to fall seriously ill here. The Glasgow Royal Infirmiary, just a few yards away from where I work, has the worst record in the country for antibiotic resistance, and you have a fairly high chance of going out of there with something far worse than you went in with. The hospital environment is overrun with `superbugs` (bacteria resistant to all hospital antibiotics), and iatrogenic diseases (iatrogenic=caused by doctors) are becoming more common because of this.

    The solution is, of course, to design new antibiotics. But these may in turn fail in the same way, even if they`re not given to the animals. Since 1950, animal antibiotics have been kept separate from human antibiotics (as in, they`re different chemicals), and yet they`re still sufficiently similar to enable the resistance mechanism to work against both. It`s a biological arms race. Our survival depends on developing new antibiotics. The bugs` survival depends on overcoming them. The trouble is that a resistance mechanism may (depending on the mechanism and the drug) confer resistance to a whole swathe of antibiotics in one go. And it spreads fast. Most of these resistance genes are on plasmids, which can be transferred from bacterium to bacterium as well as down the generations (which are fast as it is: a bacterial population will, under optimum conditions, double every 20 minutes).

    Overprescription of antibiotics is, of course, also a factor, and for this I tend to blame the patients rather than the doctors. But the reason that antibiotic resistance is so rife in hopitals is not overpresciption, at least not here (it tends to be patients coming to their GP with a cold and complaining if they don`t get a prescription for something - perhaps vitamin pills ought to be available on prescription..). It`s because there are so many ill people (who probably do need antibiotics) that there is a considerable selection pressure in favour of antibiotic-resistant bacteria. Once it gets in, it`ll spread like wildfire, and become stronger.

    I don`t think there`s such a thing as an antibiotic that no bacterium can become resistant to. If nothing else, the bug can change its cell membrane to prevent the antibiotic from getting in. But if we find new types on antibiotic, that work in a way that no current antibiotic does, then it`ll take a lot longer for the bugs to become resistant. And that gives us more breathing space.
  • Ok, sure you can always argue that the benefactors will take as much control as they can. But is this wrong? Where do you stop? Do you tell them they must donate to their alma matter? Or to charity XXXX?

    Might it have occured to you that the benefactors are trying to do more than just give to the school, and that they actually have a specific goal in mind?

    Sometimes this personal goal is "better" than the universities intended goals; sometimes it is not. Who is to judge? I've seen plenty of waste on both sides.

    The money is benefactors. The choice belongs to the school. Some schools do refuse to accept such donations as a matter of policy. But such policies can be detrimental to the school in the long run. In either case, I wouldn't advocate external regulation. It should be left to both parties to decide.
  • should donors be able to demand budget parameters? To what degree? Should donations be revokable?

    Umm...donors can make whatever demands they want. It's their money, and if the burden is too heavy then the recipient can turn it down. I presume it's basic contract law.

    Here's an extreme example. Harvard (I think it's Harvard, I'd have to check with my wife) has at least one ancient endowment that is contingent upon the university maintaining a particular building -- they can't even remove a single brick!

    Recently they wanted to put in a sky bridge to the building next door. The solution: The bridge is ramped up to go through a large window, with stairs to come back down.

  • This gives a whole new meaning to "source debugging."
  • Well, congratulations. You made me laugh: when I talk about computers, computer geeks laugh at me - "lamer". Now it's my turn to call someone that name :-) You seem to know about biology as much as I do about TCP/IP (or less, in fact).

    My ex is a combined science major leaning towards natural sciences, has a distinct leaning towards forensic criminology, and might pull off a FBI internship. I think I might have picked up a piece of Bio or two along the way.

    What does a guy hafta do to get your respect, describe the chemical structure of acytocholine(sp, doh) or put in a diagram of ATP reactions?

    No need for insults, Jan. Would have appreciated some constructive criticism--here's what followed:

    1. You know that one: if architects make houses the way programists... etc. How about that one: if biologists worked the way programists...etc.?

    ...then the pharmaceutical industry would be worshipping Dr. Mengel. You can't rollback to a previous age of a human to erase the detrimental effects of certain pills :-)

    2. People have been doing biotech much longer than they have been doing programming. You could say abacus is a primitive computer. Well, it is nothing compared to what our ancestors did to the ancestor of an apple (and I don't mean the computer company :-) ).

    Your point? I agree with you fully. Biotech is ancient. You could somewhat deign the above an ancient form of piping the output of one command through the filter of another, over and over again.

    3. Remember that you work with DNA and not living organisms.

    Remember that reverse engineers work on binary bits and undocumented protocol streams--DNA and RNA, if you wish :-)

    Unlike hardware, there's no evolutionary motive to obfuscate. Of course, the natural structure ain't exactly easy to decode.

    4. Remember that you have to do with randomly evolving clones every time you take a breathe. You have no idea how much diversity is surrounding you.

    I'm not sure all evolution is random. It is not ludicrous by any means to believe that lifeforms possess some degree of internal guidance of their progeny towards a more advanced version. Who knows--maybe an environmental condition of "always too cold" either causes gametes to be selected that suggest greater fur growth, or possibly even for internal systems to design innovative heating solutions to pass to the next generation. I'm very interested in any science you might know of to this regard--note, I'm not saying that any external force is guiding evolution; I'm saying I find it highly probable that advanced species might develop internal systems for the updating of their genetic code--that not all evolution is random.

    We don't particularly understand how the immune system profers pattern matching memories to T-Cells; perhaps the messaging components involved there are more influential than we might think.

    Yours Truly,

    Dan Kaminsky
    DoxPara Research
    http://www.doxpara.com



  • You can bitch about how little the biotech-oriented postdocs get paid and how there are limited jobs available but you miss the point. There is a scientific revolution ocurring in biology/biotech. Move over physics and chemistry, biology has the burning unknowns. If your motive in life is to make money...be a hore..pick your favorite profitable area. If you love science/information/knowlege and the creation of NEW ideas, then biotech can be an extremely rewarding career even if you don't get the patent/top job. You'll take part in the discovery and invention of ideas that may radically change the world we know..ultimately for the better (natural selection of ideas)
  • I think it is worth spending lots of research money on this disease and for many other diseases. Malaria kills 3 million/year world wide. With outbreaks of Ebola, Dengue, and other nasty things cropping up all of the time I applaud anyone who has the foresight to hand over some bigtime cash for biomed research. He definately gets an A+ in being a person who gives a damn about humanity.
  • If you had TB, you'd beg to trade it for a common cold. Anti-biotic resistant TB is a very scary thing, much more so than, say AIDS. AIDS you can sidestep through safe-sex, not re-using needles, etc. TB can be caught in public places with no contact from the person who sneezed up to 3 hours ago. My grandfather died from TB
  • Oh, I understand. If you cant afford to give away more money than the world's richest man then it is insignificant. What the hell?

    Some of the most outstanding acts of charity are performed by those who can least afford to give. Giving isnt about the number of commas on the check, its about helping others and your attitude towards them.

    The gift also has to match the needs. In this case, ten billion dollars would have been far too much to give to one institution. At some point, money isnt going to be the limiting factor in research progress. Giving more money will lead to inefficency and cause distractions.

    I wonder if any of your money is being used for biotech research? (I hope so...) Oh, wait, you dont have 10 billion dollars to give? Never mind, your contribution amounts to nothing.

    -BW

    • Remarks on misused antibiotics with TB are totally on topic.
    This kind of things gets every day nearer to debugging.
    In this sense we have had a buggy process in treating TB epidemics in the 40 and we are now facing some sort of "unintended use of our system"

    Sounds familiar? TB has hacked our response and has a new threat for us.
    This is an escalation and some sort of Security Model will be needed when the complexity of our response will be simply not manageble without specialistic analisys.
    Doctors aren't analists.

    When flesh and silicon (if moore's law lets silicon live) will merge the complexity of the response will boom.

    Do we need new tools such as debuggers, profilers and such to manage the new risks in tinkering with our internal ecosystem??

  • It`s got nothing to do with GM crops.

    The suggestion is that genes are transferred into the crops as plasmids which have previously been grown in bacteria. These plasmids also contain a gene for antibiotic resistance, because it makes it easy to kill off all but the successfully modified bacteria.

    I don't know whether this does make modified crops a significant risk; antibiotics in animal feed are definitely reason for concern.

  • Of course we could start re cycling 25 year old antibiotics. The bacteria have probably evovled out of being resistent to those.

    I have heard this hope before. But I think in practice results have been disappointing. It looks as if there just isn't enough selection pressure against the mutations in the wild; a large enough pool of resistant bacteria always survive.

  • No offence meant. Sorry, but you can only write some constructive critiques on a meaningful statement - and yours was, ehem, just a metaphore, with no constructive arguments, proliferating a stereotype view on biosciences. Nothing to discuss with, only something to be a little upset about, especially when you expect to find something interesting in the first article you read in the discussion.

    I admit that your comparison was funny, but - pardon my french - not what I call "insightful" (on the other hand, my english is, as you can read, miserable).

    As to the randomness of evolution - well, my point was not about evolution beeing random or not, I just wanted to point out that analysing the biological diversity is not the same thing as playing around with it.

    There were some experiments done trying to show that some bacteria can at least enhance the mutation rate, when not even exercise a selection process of randomly transcribed mRNAs, which then could be reverse transcribed onto the genome, but all of these experiments had also an easier explanation. If you want any literature, mail me. The matter was hot in the late 80s- early 90s.

    One last thing: you can moderate me down, ignore me, offend me - I don't mind. But please, do not abbreviate my first name. "Jan" is another name, it comes from another language. I know it is a good american tradition to have short names but - just don't do it.

    Regards,

    January

  • Re:PCR (Score:1)

    by jw3 ( 99683 )
    Thanks for the article - and for the other as well! Direct sequencing chip - OK, that makes a lot more sense now. Thanks again!


    Regards,


    January

  • That's pretty sizable donation from our buddy Jim. I know it said to be only used for biotech, but will it only be used for biotech like this? Don't get me wrong, any donation back to your school is nice, but I can see $150 million going down the drain fast on less-than-urgent biotech on things like fingernail-cell regeration techniques, or a bioengineered gopher that will run MAME :)

    -----------

    "You can't shake the Devil's hand and say you're only kidding."

  • When was the last time someone (who didn't already have a serious problem with their immune system) died from "the common cold"?? I think TB get's a higher priority than that, although I can certainly think of other, more debilitating diseases that I'd like someone to throw $150 million at.

    -----------

    "You can't shake the Devil's hand and say you're only kidding."

  • Tech Analogues and Earmarked Donations (Score:4)

    by Effugas ( 2378 ) on Wednesday October 27, 1999 @04:27AM (#1584115) Homepage
    Two comments, actually.

    1) PacketBioStorm. Every time I see an announcement about Biotech, I feel like I'm seeing a convergence between the both utterly dissimilar and disturbingly reminiscent fields of Network Security and Human Biology. Beyond the obvious "virus" appelation, much of the technology being applied to deal with both script kiddies and randomly evolved pathogens (you decide who you'll respect more) has to do with quick identification of massive streams of information through ingeneous code. Biotech adds another layer, since organic materials must be parsed, but it's still the same old schtick.

    Sorry to the speakers at Linuxworld, incidentally, but the Human Genome Project is easily the world's largest reverse engineering effort. And will you take a look...a battle between open and closed source. Who's surprised?

    2) So Jim Clark has specified the task his money is to be used for. There's actually alot of controversy about that--should donors be able to demand budget parameters? To what degree? Should donations be revokable if, say, a professor at the university violates some specific usage clause? Keeping in mind that most of our college educations either are, were, or will be endowed quite heavily by Alumni and Corporate Sponsorship.

    Also remember that Gates intends to donate his fortune in entirety, and that Microsoft is a tremendous benefactor of educational institutions across the country. Think about what Clark's specification means in that context.

    There are no easy answers, are there?

    Yours Truly,

    Dan Kaminsky
    DoxPara Research
    http://www.doxpara.com

  • And when the hell can we get a cure for the common cold?

    Well, if all of the various strains of cold virus somehow become similar enough that we wouldn't need new drugs for each one, I'll let you know.

    Marissa
  • Much of the research done in the research community doesn't directly produce anything consumer-useable. You'd be surprised, however, at how many of those supposedly useless research projects end up giving us the understanding necessary to go the next mile and get somewhere important.

    For instance, there are nanotech facilities that create little bugs -- this doesn't help us as a society a lot as most of us aren't too fond of bugs (sorry to all you entymology people). But since this experimentation and research slowly brings down the sizes of componentry, we get ever closer to being able to work at thos sizes effectively, at which point we start making useful consumer technologies.

    - Michael T. Babcock <homepage [linuxsupportline.com]>

  • Sorry to be heavy and all... (Score:3)

    by rde ( 17364 ) on Wednesday October 27, 1999 @04:30AM (#1584118)
    Anything that'll combat TB is a good thing, and this biochip could well be a vital part of the anti-TB arsenal.
    However, the reason we're in such shit from M.Tuberculosis and S.Aureus is the ridiculous overuse of antibiotics. Vancomycin -- the antibiotic that kills anything -- is proving less than effective against some strains of both. This is a problem that's entirely of our own making, and one that's being exacerbated by the overuse of animal feed, the growing of GM crops and people pestering their doctors for antibiotics and then not taking the full course.
    I realise that this could be seen as somewhat offtopic, so I apologise if it pisses you off. But it needed to be said. Again.
  • It's nothing compared to Bill Gate's 10 billion dollars! I wonder if any of that is being used for biotech research? (I hope so...)

    --
  • Wouldn't it be just as bad if we let people suffer from tuberculosis without administering antibiotics? I see your point, but I don't see where you suggest an alternative.

    Sure, the use of drugs brings about mutations of a disease which are immune to the drug, but you don't let people die of a disease for the sake of preventing a mutation of the disease from coming about.. do you? I really don't know the answers to these questions and am hoping you can shed some light on this for me and possibly other readers.

  • I personally lived overseas, about twenty years ago, and witnessed the misery and suffering TB inflicted. As some here have pointed out, TB has changed strains often, through improper use of antibiotics and it's own insidious nature. A source of constant monitoring is vital for catching TB before it damages or kills the victim and before it spreads. I fully support the development of this chip and bioware tech that benefits humanity.

    However, it does not take a genius to realize the potential for abusing this technology. After all the Russians want to use this tech to monitor the health of it's prison population. But realize that this chip is most likely going to be surgically implanted. How does the inmate remove the chip once his or her prison term is completed. After all the chip can be configured to monitor other aspects of your physiology.

    Food for thought

  • When you have $150 million in cash to donate, you can dictate terms of its dispersal. Until then, quit your yapping. None of us are old enough to remember any out breaks of TB. Our parents probably barely remember the epidemics at all. This disease is cause by a bacterium and is therefore easier to identify than a virus. If the cofounder of Netscape wants to spend some money to try to eliminate the spread of a pandemic by helping to develope a technology that would obviously have cross applications in medecine, then so be it.
    TB used to be as bad a killer as influenza and smallpox. The former is mostly now just an annoyance and the latter has been eadicated from the population. Before you reply , yes, I know that the flu has strains that are tenacious and ccan kill but at least this is not the pandemic of 1919.

  • ...but will it only be used for biotech like this ?

    Do you mean useless research that will rapidly improve on diagnosis times, especially when those times can mean the difference between life and death ?

    When I was in school, you had to grow the bacteria before you could identify it, and that took anywhere from 1-7 days. Using single strand DNA such as this biochip does to detect which strain of of a virus or bacteria makes this into an hourly proposition. Tuberculosis is just one of many useful applications of this technology. Any rapid onset infection could be diagnosed and treated far more quickly, and that means saving lives.

  • Also remember that Gates intends to donate his fortune in entirety, and that Microsoft is a tremendous benefactor of educational institutions across the country. Think about what Clark's specification means in that context.

    I think I see where this is going. You are tring to get us coming and going. The differenct here that that Gates was trying to INFLUENCE the curriculm/research, not AUGMENT it. At my school, we literally had a company build us a new engineering building all on it's own. It's a nice building, but we do what we want in it. Research like TB is always going to go on because it's important - It's just easier to do when there is a roof over your head.
  • My mother is a medical technologist (aka. the person that does your blood work) and nowadays her lab is starting to get more computerized than my local ISP. Automation seems to be becoming a big deal in her field, as many of the tests they do are very manual intensive.

    Someday soon all you will have to do to find out what's wrong with you is to stick your finger in a machine. We already have home glucose meters anyway.

    It's going to be a lot harder to play hookie from school or work in the future when Dr. Computer is keeping a close eye on you.
  • Umm...donors can make whatever demands they want. It's their money, and if the burden is too heavy then the recipient can turn it down. I presume it's basic contract law.

    Ah, but what should universities accept? What policies may be purchased? What's not for sale?

    Remember, donors operate on a standard basis--whatever amount of control is standard, they'll probably want a little more but not the whole bag. As that "little more" becomes the standard, "little more" begins to mean more...and more...

    That's the nice thing about zero influence: The standard never shifts.

    Yours Truly,

    Dan Kaminsky
    DoxPara Research
    http://www.doxpara.com

  • Re:Sorry to be heavy and all... (Score:4)

    by rde ( 17364 ) on Wednesday October 27, 1999 @04:40AM (#1584129)
    Wouldn't it be just as bad if we let people suffer from tuberculosis without administering antibiotics
    You're missing the point. Or I wasn't clear. The problem isn't the administration of antibiotics, it's the improper administration thereof. Doctors have been known to prescribe antibiotics just to shut up whining patients, and this is a bad thing. Almost as bad is the hapless patient who feels better half way through the course, and decides not to bother finishing them. This allows any remaining nasties in the body to survive and multiply.
    I wasn't suggesting antibiotics never be used; just that they be used more judiciously.
  • These chips CANNOT be embdedded into a human. They aren't like computer chips at all. That's just an analogy that makes them sound cool. The chips just have synthetic pieces of DNA bound to them which you hybridize the sample from the patient's strain of TB. You could swallow one of these babies and it would do nothing.
  • The problem is that doctors will give you an antibiotic at the drop of a hat. And many people will be given 10 days worth of pills but stop taking them after 5-6 six days because they feel better. Not realizing that it is very improtant to take them.

    The antibiotic only kills some percent of the bacteria in your system. And ofcourse the most resistent ones survive.

    Ofcourse we could start re cycling 25 year old antibiotics. The bacteria have probably evovled out of being resistent to those.
  • These chips CANNOT be "implanted" into humans. They are just part of the evolution of "point of care" (POC) devices that make what would be sophisticated and expensive tests, cheaper and more easily peformed. Think more of glucose monitors available for diabetics to track their conditions at home more effictively.

    These glucose monitors I guess *do* control a person's actions but only to the extent of if they need a shot of insulin or eat a cookie. :)

  • I think I see where this is going. You are tring to get us coming and going. The differenct here that that Gates was trying to INFLUENCE the curriculm/research, not AUGMENT it. At my school, we literally had a company build us a new engineering building all on it's own. It's a nice building, but we do what we want in it. Research like TB is always going to go on because it's important - It's just easier to do when there is a roof over your head.

    That deal that was going to happen betweeen the California schools and Microsoft was something along the lines of standardizing/mandating MS at every college site, or so I was told.

    The deal got trashed, of course.

    My main point is that things don't always fall nicely into easy to discern categories--I'm sure not too many people came into the discussion thinking that Clark shouldn't have had any right to influence where his money went. I mentioned what MS both could and, in ways we'll never fully know, has coerced its way into certain markets via methods similar to what Clark did.

    I'm trying to spawn discussion, since honestly I'm not all too sure about this myself.

    Yours Truly,

    Dan Kaminsky
    DoxPara Research
    http://www.doxpara.com

  • January--

    No offence meant. Sorry, but you can only write some constructive critiques on a meaningful statement - and yours was, ehem, just a metaphore, with no constructive arguments, proliferating a stereotype view on biosciences.

    What stereotype? That biotech is essentially the equivalent of hacking a dynamically self evolving codebase composed of organics? This isn't a stereotype, it's a common observation.

    Using a virus to insert genetic codes to rebuild organs and inserting a trojan horse to send passwords to a remote site are not entirely different from one another.

    That biotech has been around for far longer than computer security doesn't make it any less interesting to watch the striking similarities. Packet generators vs. Gene sequencers, for example. Create the arbitrary, mix and match, pipe and filter.

    No, it doesn't work exactly like that. But the dreams are in both places.

    Yours Truly,

    Dan Kaminsky
    DoxPara Research
    http://www.doxpara.com
  • I don't know if biotech of the sort that's usually described is the way to go with cures like this. The approaches tend to be so untargetted, and thereby very destructive to the human body.

    What's needed is a very targetted, very direct system.

    I've mentioned before a thought I had on how to do that - unique molecules absorb unique frequencies and DNA is a unique molecule. In practice, there are lots of problems with that specific approach, but there are other ways to directly target pathogens.

    I know that cancer research specialists are planning to do something very similar to the idea I proposed, to treat cancers in a way that is less destructive on the rest of the body, by marking cancer cells with unique, simple chemical tags, then using the same trick I suggested to zap the cells with simply radio waves, only baking the cells that are marked and therefore only killing the cancer and nothing else.

    (Traditional radiotherapy and kaemotherapy destroys most of your white blood cells and red blood cells, and impairs your ability to produce either. It also mucks up your hairstyle something chronic.)

    Targetted cures against bacteria would seem viable, using a similar trick, then. Stain the bacteria with a known molecule that occurs nowhere else in the body, then fry it with radio waves.

    Viruses are trickier, but they're just RNA strands. The body must have built-in mechanisms for handling RNA, or your cells would get clogged in next to no time with the RNA it, itself, generates. Viruses must shut this mechanism down, swamp it, or have some kind of coating which inhibits it. If you know which method is used, you have the answer on how to cure viruses. If (1) or (2), you -do- want biotech, of a kind, to produce the same effect as the natural mechanism. This would, effectively, enhance the body's ability to fight the virus, with a very targetted approach. If (3), you simply need to find a way to remove such a coating, and the problem would go away, all on it's own.

  • Sorry to bust your bubble, but this is frankly bullshit. There's no such thing as proper administration of antibiotics - it's impossible to administer them in a manner that will prevent a resistant form from eventually evolving. Sure, if you use it judiciously you can maybe prolong your use of it. But it's always inevitable that it'll evolve resistance - this is how life is.

    Also the argument that vanc resistance is a result of farmers feeding antibiotics to cattle is bullshit, because vanc resistant strains develop and thrive in hospitals far earlier than they do agriculturally simply because 'magic bullet' drugs are reserved for clinical use. Vancomycin hasn't been used in agriculture, actually, as far as I know. It's ONLY used for human therapy. There's a ton of antibiotic drugs out there, and resistance to each one is different.

    And, as someone else pointed out, there's no way around it - even if you use antibiotics judiciously, they only have a limited lifespan. It's impossible to make them last forever, because selective pressure forces bacteria to develop around them (especially in hospitals, where they're used most and transmission is easy). If you want to stay ahead of the curve you have to find a new 'magic bullet' before your old one goes bad. There are some current favorites - I forget the name, Strathosomething or Sicosomething. This is not a mistake on anyone's part - it's a simple fact of nature.

    SA
  • In the case of tuberculosis, it does not appear to be a problem so much of "overprescribing" antibiotics that results in drug resistance (and TB does not seem to pick up other pieces of DNA that confer drug resistance such as the case for vancomycin resistant S. aureus). The problem has been that the antibiotic treatment requires pills every day for anywhere from 3 to 12 months. And many of these drugs have some nasty side effects.

    Even a survey of physicians who had to undergo TB prophylaxis showed that almost half of them couldn't even complete the full treatement!

    Another recent, not slashdot-kind-of-news article a few months back reported the trials on an anti-TB treatment that could be done in 2 WEEKS.

    Last problem has been coaxing pharmaceutical companies to invest in antiTB drug research. 3rd world countries aren't able to pay $200/pill for something. So keeping drug resistance from spreading and treating it completely to cure is the goal of both the CDC and WHO right now.

  • This is right up my alley also, and since several of the other posts have explained some of the technology, I won't dwell on it. I have worked with both a Russian doctor and an American doctor (both in Doctors Without Borders, the recent Nobel laureate organization) on this very problem of drug resistance. Right now the problem is not lack of diagnostic materials- they can do that fairly effectively already- the *real* problem is *money*. The old system (USSR) used an effective, though expensive, method of detection: X-rays. They would just blanket an area every few years with massive x-ray exams. People with TB, as well as people with other diseases that affect the lungs, would be found. Not very specific (ie only finds the TB cases) but fairly sensitive (finds real cases). Now the problem is that they can no longer fund this type of program and the Russian doctors don't know any other methods (or employ dated, ineffective methods), so the TB patients go undiagnosed, causing a "hidden" epidemic. Back to cost: It costs $250,000+ per patient to stop the drug resistant TB epidemic in New York recently (second-line drugs cost a unholy load of money). There are 100 times that many people infected with DR TB in Russia. I am sad to say that we won't be able to stop this epidemic. Complacency and inefficiency (and some would say, downright stupidity) has increased the disease burden to the point that it is economically impossible for Russia to fight it. Adding another potentially expensive test will not help things. -Just my pessimistic $.02 BTW - I really hope that we can stop this juggernaut of infection, but it won't be through this test.
  • It happens that my working group at the Center for Molecular Biology, Heidelberg [uni-heidelberg.de] is exactly into this thing - microarrays, biochips & co. So I might tell you some words on how does it work and why I think this is not the best solution for MT diagnostics in Russia. First, the preliminaries (if you slept at your biology class, try looking at Everything [blockstackers.com] :-). If you have a single stranded DNA sequence, then you can use it to fish out the so called complementary DNA sequence from a mixture of different molecules - the both single strands hybridize and make a double strang. It is easy to synthetise virtually any DNA sequence you need. Now, imagine that you want to detect whether in your mix there is a certain DNA species. What you do in the biochip technology is to bind your synthetized DNA on a glass plate (biochip) or nylon membrane (microarray) and label your unknown mixture of DNAs - say, a fluorescent molecule is attached to every DNA molecule in the mixture. Now, you wash the glass chip with the mixture: only the complementary DNA is specifically bound to the probe immobilized on the chip (or array). Now you wash with another solution - and what remains and can be detected by a fluorescence-detector will be the probe you are looking for.

    The clue about this system is that you can bind to your glassware an immense number of different probes, and so probe for different genes or regions of the genome (in fact, we are using this system to detect mRNAs - to see how an organisms expresses its genes).

    But this system has one major disadvantage: it is not nearly as sensitive as other methods - the PCR / RT-PCR, for example. That means, to identify the MT strain you have first to raise it on a culture medium, because direct patient isolates will not provide enough genetic material to acomplish the task. And rasing MT is not easy.

    It seems to me, someone wants desperatly to make the news: biochips have made the news a couple of years ago; right now commercial systems for many different tasks are available since many years. Check an issue of "Nature" for advertisments :) you can have the whole yeast genome on a small piece of glass for a couple of $$.

    What's more, the system described is very, very expensive, and I doubt that it is therefore suitable for diagnostics in Russia. PCR-based systems are much cheaper - though not allowing to check a couple of thousands genes with a single reaction - but much better suitable for cheap and quick MT diagnosis.

    It is, of course, quite possible that the EETimes got everything wrong and it does make sense after all. Journalists ;-)

    Regards,

    January

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