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Open Source Drug Discovery Prompts a Fundamental Heart Failure Breakthrough

An anonymous reader writes "Case-Western researchers, led by Saptarsi Haldar MD., have made a fundamental discovery that could prevent heart failure after reviewing the "chemical recipe" for a cancer-treating molecule made open source by Jay Bradner MD. (whose TED Talk articulates the open source approach to drug discovery) This cross-discipline discovery, which was published in the August 2013 issue of CELL, is a fundamental breakthrough in heart failure research, and highlights the value of an open source approach outside of software development."

160 comments

  1. open source? by Anonymous Coward · · Score: 1

    What does it mean for a molecule to have source? How is the "source" of the molecule distinct from whatever passes for a "compiled binary"?

    1. Re:open source? by Anonymous Coward · · Score: 0

      It's not that open source is some kind of magical thing; It's just that the selfish baby boomer generation is finally dying out and everything is finally getting better.

  2. Awe Man! by Anonymous Coward · · Score: 5, Funny

    What's this?! Everyone jumping on the Socialist-Commie-Pinko Open movement?!?

    WTF!

    Before you know it, IP with be severely weakened and all of us will have increased standard of living - except for the poor poor billionaires!

    Won't someone think of the billionaires?!

    Without the billionaires lording over us, what will inspire us?

    We need IP to keep up the carriers to entry! We need to impede progress in order to preserve the billionaires! Our way of life will be destroyed!

    1. Re:Awe Man! by bill_mcgonigle · · Score: 4, Insightful

      Before you know it, IP with be severely weakened and all of us will have increased standard of living - except for the poor poor billionaires!

      Look, if we don't run our society according to everything that seemed like a good idea in 1781, nothing will ever get invented.

      --
      My God, it's Full of Source!
      OUTSIDE_IP=$(dig +short my.ip @outsideip.net)
    2. Re:Awe Man! by __aaltlg1547 · · Score: 1

      Most science has always been that way.

    3. Re:Awe Man! by bunratty · · Score: 1

      We need IP to protect the companies who are doing the research. But it can be difficult to know exactly where to draw the line between what can and cannot be patented. That's the real problem with our patent system -- too many obvious ideas being patented. As Jefferson himself said, "Considering the exclusive right to invention as given not of natural right, but for the benefit of society, I know well the difficulty of drawing a line between the things which are worth to the public the embarrassment of an exclusive patent, and those which are not."

      --
      What a fool believes, he sees, no wise man has the power to reason away.
    4. Re:Awe Man! by mspohr · · Score: 3, Insightful

      I'm not sure that it was a good idea even in 1781.
      Basically, the mercantile class wrote the constitution and early laws. The American Revolution was a mercantile uprising against the "tyranny" of England and it's taxes and regulations.
      Today, of course, the mercantile "class" are the corporations who have completely captured the government.
      Numerous studies have demonstrated that patents slow the process of invention and only provide benefits for the entrenched last generation of science and technology.

      --
      I don't read your sig. Why are you reading mine?
    5. Re:Awe Man! by bunratty · · Score: 1

      The companies that those billionaires own are what drive the economy and do things like grow and distribute our food. I don't know about you, but I would prefer to protect those companies so I can keep eating. And of course I like my gadgets, books, music, and so forth. Sure, I can read an open-source book or listen to open-source music, but typically I prefer the commercial products. Just because an idea works with software doesn't mean it will work with everything. In other words, if you give a man a hammer, all he will see are nails.

      --
      What a fool believes, he sees, no wise man has the power to reason away.
    6. Re:Awe Man! by ultranova · · Score: 5, Insightful

      The companies that those billionaires own are what drive the economy and do things like grow and distribute our food.

      No, the people working the fields grow the food and the people driving the trucks and manning the cash register distribute it. And even the organizational work is mostly done by middle managers. All the billionaires do is get a cut of other people's work and occasionally destroy their livelihoods.

      Sure, I can read an open-source book or listen to open-source music, but typically I prefer the commercial products.

      And you think it takes a billionaire to write a book or a song?

      In other words, if you give a man a hammer, all he will see are nails.

      And if you give him a billion dollars, all he will see are the serfs he's entitled to.

      --

      Forget magic. Any technology distinguishable from divine power is insufficiently advanced.

    7. Re:Awe Man! by Impy+the+Impiuos+Imp · · Score: 1

      Except we've run the experiment already where ideas can be stolen and used without paying the author for these virtual property rights. Measured results are far suboptimal compared to the current way.

      The OP is just an anecdote, and anybody with an ounce of scientific sense will realize it.

      It would be nice if these things could be presented as scientific advancements without trumpeting it through the lens of someone's political philosophy.

      --
      (-1: Post disagrees with my already-settled worldview) is not a valid mod option.
    8. Re:Awe Man! by Anonymous Coward · · Score: 0

      Do you remember when you became a corporate slave?

      Name one billionaire farmer. The corporations mainly buy from the farmers and mangle it into bland shit in a box. I just buy directly from the farmer. Much healthier.

      I bet you enjoy the latest $200 million mindless FX-athon instead of that really smart and funny indie movie. You should probably do a little introspection and find out why.

      Of course, if you were capable of introspection you wouldn't have written that corporations uber alles bullshit.

    9. Re:Awe Man! by OneAhead · · Score: 1

      Has been. Nowadays, most academic biomedical scientists will try to patent potentially promising new drugs, and most institutions strongly encourage this (it's called valorization). If you're a young researcher, not doing it may even harm your career. There do still exist granting agencies out there that require the results of their investment to become public domain, but in the biomedical field, they're becoming rare.

      What's really sad is that the approach that used to be the norm has become so exceptional that one can slap a new label on it (yes, "new" - let's not forget the term "open source" only exists since 1998) and get invited to talk at TED.

    10. Re:Awe Man! by Anonymous Coward · · Score: 0

      The advancement of mankind is predicated on open sharing and cooperation.

      Always has been, always will be.

      The current draconian IP laws is a major reason why the US is in decline.

    11. Re:Awe Man! by Anonymous Coward · · Score: 0

      This is similar to how the norm used to be focusing on attempting to treat the individual patient (with all the nuance involved), then for the last 20+ years an obsession with clinical trials arose. Now "individualized medicine" is a new thing.

    12. Re:Awe Man! by Pinky's+Brain · · Score: 2

      It's a bit trendy to hang the open source label on it, but that's TED for ya ... still there are differences between what was possible in the old days and what is possible now.

      Publishing reproducible research wasn't really possible in the past ... other researchers could beg for all the lab notes, good description of the lab set up etc etc etc to be send by snail mail, but it couldn't really be published. Only the tiny and most of the time insufficient bit of information from the paper was actually published. Now publishing reproducible research has become possible ... unfortunately only a handful of people are doing it.

    13. Re:Awe Man! by Anonymous Coward · · Score: 0

      And you think it takes a billionaire to write a book or a song?

      Sure, didn't you see that broadway musical written by Steve Jobs? No? Well, it sucked anyway.

      About the only semi-billionaire I'd trust to write a book or song that I'd watch is Mel Brooks. But hey, he made his 600 million writing and directing, and occasionally merely risking the lives of others while he certainly risked an academy award.

    14. Re:Awe Man! by pepty · · Score: 1

      The corporations are the farmers. Who do you think owns most of the acreage?

    15. Re:Awe Man! by chihowa · · Score: 1

      The corporations own the farms. The actual workers are the farmers. The corporations collect a cut of the productivity generated by the farmers, but the productivity doesn't actually come from them.

      --
      If you want a vision of the future, imagine a youtube comments section scrolling - forever.
    16. Re:Awe Man! by Anonymous Coward · · Score: 0

      I'm nut sure what way you meant. But, 'most' science? What is science? (I harken back to Sheldon Cooper teaching Penny "What is Physics?") Sometimes people mean science is equal to a technology. Sometimes people think it is a methodology, as I was taught in Jr. High. Then there is the modern Science with a capital "S," meaning the whole societal-legal-journals-grant making- and so on endeavour.

      Some sciences, astronomy and plate techtonics, are largely observational. Last time I checked, no one has patented a Quasar. Although I did have a microwave oven by that name. And my family did have a Ford Galaxy, and I thick a Comet....

    17. Re:Awe Man! by __aaltlg1547 · · Score: 1

      Clinical trials are required to get FDA (and other government) approvals for the use of new drugs. That's not just the last 20 years. What's changed in the last 20 years is the profile and profits of the biomedical industry.

    18. Re:Awe Man! by OneAhead · · Score: 1

      Depends on the field. It's not 100% clear from TFA what they mean with "JQ1's chemical recipe", but I took it to be a synthetic route. In organic chemistry, there exists a rigid standard format on how to report a synthetic method - has existed for many decades - and it's quite common to try to reproduce experiments from literature. True, it's a bit of a hit-and-miss thing, but if both the writer and the reproducer are competent, the success rate is substantially higher than the failure rate.

      Now in bioscience, things get fuzzier. Organisms are more complex than chemical reagents, so more unexpected things happen with living matter than with dead matter.

    19. Re:Awe Man! by Anonymous Coward · · Score: 0

      I don't think it's that simple. For industries where costs are low or where there is room for gradual improvement, patents are just like you said - adverse to humanity. On the other hand, for industries where costs are high and it's either make or break (1/0, nothing in between), then I don't know of anything economic model that is sound.

      Of course, if we're talking about how to make said costs lower/low, then that'd be something worth discussing.

  3. Summary's not correctly worded by knotprawn · · Score: 2
    From the article

    Researchers from Case Western Reserve University School of Medicine and the Dana-Farber Cancer Institute have made a fundamental discovery relevant to the understanding and treatment of heart failure

    It does not say "prevent" heart-failure, anywhere in the article. It is implied in the article that treatment could be greatly improved by this therapy, however, I'm not sure where the line in the summary about prevention comes from.

    1. Re:Summary's not correctly worded by demonlapin · · Score: 1

      Since it's not linked to an actual scientific article, just a press blurb, who knows? It might not do anything.

  4. Re:More pointless 'research' by Anonymous Coward · · Score: 1

    Most heart disease is caused by living too long. Reproduce, then die, like nature intended.

  5. Re:More pointless 'research' by Anonymous Coward · · Score: 0

    caused by eating animal products (which humans aren't supposed to eat)

    Wrong!

  6. Re:More pointless 'research' by Anonymous Coward · · Score: 0

    As long as the cake isn't made from animal products why are you against eating it?

  7. Animal Studies & then years of human trials by BoRegardless · · Score: 1

    It sounds promising, but there is a lot of work ahead before it hits the market, if ever. Dosing, administration mode, side effects, when it can be used, what other drugs it will interact with and which it won't are all a part of what needs to be determined. The "drug" may have been discovered, but is really just a tiny part of what needs to be known before you can safely prescribe the use in people under all the varying conditions of use where it might be needed.

    Thus, just because the molecule is "open source" doesn't guarantee it will be viable or commercially developed. Now the real money has to be spent to justify it being approved by the FDA and released as a safe commercial product.

    1. Re:Animal Studies & then years of human trials by Anonymous Coward · · Score: 0

      Heed the words of an Anonymous Coward: bring on the Heart Disease clinical research and Kickstarter backed drug trials.

      Captcha: morbid

    2. Re:Animal Studies & then years of human trials by sjames · · Score: 1

      Even there, the open source nature is helpful. The same drug has stirred interest for multiple myeloma, heart failure, contraception, and HIV treatment (it is thought that it can activate latent HIV in the presence of anti-viral therapy to wipe out the reservoir). All 4 could share the phase I safety trial (and it's costs).

    3. Re:Animal Studies & then years of human trials by ColdWetDog · · Score: 3, Informative

      Is it going to help or hurt?

      Yes, it's created a lot of interest but that's pretty standard for a molecule that hits a relatively unique molecular pathway. What has happened in the past is that as soon as the basic science gets firmed up, the drug companies wander it and start trailing slightly different molecules (which are patentable). That's where the big money goes.

      By explicitly opening up access to the molecule early, you might find more applications faster and perhaps get more people working on the same receptor system, but the end result is that the drug that treats multiple myeloma will look slightly different from the one that treats heart failure or is used as a male contraceptive. The drug makers will work hard to make them as task specific as possible so they can charge more and control things better. The only possible 'good' outcome (for the open source concept here) would be that the 'generic' bromodomain receptor blocker (JQ1) works equally well for all, doesn't do anything bad in humans (an unlikely scenario - most promising drug candidates die here along with countless dogs, monkeys and other critters) and can be reasonably easily synthesized by the Indian and Chinese generic drug manufacturers and they make a shitload of it.

      Which will get blocked at the border so save us from commie chemicals.

      Grump again.

      --
      Faster! Faster! Faster would be better!
    4. Re:Animal Studies & then years of human trials by sjames · · Score: 2

      A back handed benefit is if the rest of the world considers those conditions a thing of the past while Americans are still dying of them. That would certainly bring demands for change that couldn't be fended off for long.

      I do find it interesting that the free trade cheerleaders in DC stop cheering when retired people want to freely buy inexpensive prescription drugs from Canada.

    5. Re:Animal Studies & then years of human trials by Anonymous Coward · · Score: 0

      it can do all of this and not have off-target effects, awesome!!!

    6. Re:Animal Studies & then years of human trials by sjames · · Score: 1

      I never said that. However, whichever of those it is used for, the other known effects could well be acceptable to the patient.

    7. Re:Animal Studies & then years of human trials by b4upoo · · Score: 1

      It seems to take a lot more than having a great new product to get it into public use to any great degree. For example the US Navy released Nitinol about 30 years back so that anyone can use it without patents. Despite being an amazing and wonderful product it sees very little use in the market place. We have some expensive eyeglass frames made of it and also some bras use memory metal to restore their shape every time they hit how water. But really we don't see it used much at all. How about car fenders that snap back to perfect shape when exposed to heat? A motorcycle gas tank could have a dent removed just from a hair dryer blowing hot air on it.
                        We are seeing this in battery designs as well. Several new battery designs are superior and more seem to pop up rather frequently. Industry fears investing in better batteries simply because the next big breakthrough could be just after they invest in a billion dollar factory.
                          One wonders if the medical industry is the same way. If a better cancer drug was created it could kill the sales of existing products owned by the same company. If the medication were cheap and easy to produce it would be hard to justify a high cost.
                            The music industry just saw a $150. plastic trombone introduced that plays as well as trombones that cost about $1000. . The product has certain great advantages but you can bet the band instrument industry hates the new product.

    8. Re:Animal Studies & then years of human trials by pepty · · Score: 1

      The cheapest clinical approval I've heard of in the past 15 years (Dificid from Optimer) was still $175M. That will be quite a kickstarter!

  8. Re:More pointless 'research' by demonlapin · · Score: 2

    What's the deal with all the crazy vegans around here lately? Go to your local hippie store and look at the vegans. Then go to your local CrossFit and look at the paleo eaters. Which group looks healthier to you?

  9. Re:More pointless 'research' by lxs · · Score: 2

    A cake made without eggs or butter? Who in their right mind would eat such an abomination?

  10. Re:More pointless 'research' by Anonymous Coward · · Score: 0

    If by "fitter" you mean suitable for a purpose, then the vegans look ideally suited to pontificating their opinions to anyone in the immediate area, whether the listener cares or not. Captcha was "vegetate"

  11. TED talk explains how the OSS philosophy applies by tepples · · Score: 5, Informative
    Anonymous Coward wrote:

    What does it mean for a molecule to have source?

    It can refer to what Eric S. Raymond referred to as the "bazaar" model, or it can refer to a license that grants rights to the public analogous to those listed in the DFSG or FSF definition of free software. I see hints of bazaar in the transcript of the TED talk:

    dissatisfied with the performance and quality of these medicines, I went back to school in chemistry with the idea that perhaps by learning the trade of discovery chemistry and approaching it in the context of this brave new world of the open-source, the crowd-source, the collaborative network that we have access to within academia, that we might more quickly bring powerful and targeted therapies to our patients.

    And here I see the spirit of publishing a discovery instead of locking it up behind secrecy and exclusive rights:

    We published a paper that described this finding at the earliest prototype stage. We gave the world the chemical identity of this molecule, typically a secret in our discipline. We told people exactly how to make it.

    This leads up to the benefits of bazaar and publication:

    the science that's coming back from all of these laboratories about the use of this molecule has provided us insights that we might not have had on our own. Leukemia cells treated with this compound turn into normal white blood cells.

    And finally, a direct answer to your question as to what is the source code of a molecule:

    This string of letters and numbers and symbols and parentheses that can be texted, I suppose, or [microblogged] worldwide, is the chemical identity of our pro compound.

  12. Cell by tepples · · Score: 1

    it's not linked to an actual scientific article

    The transcript of the TED talk mentions articles in Cell.

    1. Re:Cell by demonlapin · · Score: 2

      So does the summary, but the paper is behind Cell's paywall, so it really isn't all that open-source, is it?

  13. Re:More pointless 'research' by bill_mcgonigle · · Score: 3, Informative

    Most heart disease is caused by eating animal products (which humans aren't supposed to eat), lack of exercise, and smoking.

    That was considered very wise in 1982. Today we know that the main nutritional problem is excess fructose, which the liver turns straight into triglycerides, which stick to the arterial walls, and form nasty, sticky plaques. But go ahead and guzzle agave nectar - it's pure fructose, vegan, and trendy. :P

    Exercise, sleep, low stress, and of course not smoking are also key components to a healthy lifestyle (diet is just one part).

    --
    My God, it's Full of Source!
    OUTSIDE_IP=$(dig +short my.ip @outsideip.net)
  14. Re:More pointless 'research' by Anonymous Coward · · Score: 2, Funny

    Dilhole... Humans are omnivores - we can eat anything. Well not as much anything as say goats (who will eat tin cans), but pretty much anything.

  15. Re:More pointless 'research' by Anonymous Coward · · Score: 0

    At least the paleo eaters drop dead at thirty form malnutrition and bad teeth. Bloody vegans keep pontificating their opinions well into middle age.

  16. Well Duh: Open Source is better by cellocgw · · Score: 2

    The only thing drug patents do is make drug companies rich. If we as a nation (USAians here) truly wanted to maximize progress in medical treatment, we'd nationalize all drug research. Don't even bother arguing that profit motivates progress. The overwhelming majority of researchers and engineers are motivated by the joy of success, not crushing the opposition and getting filthy rich.
    As we've seen over and over again in nearly every technology area, the greatest progress occurs either in "open source" areas or when patents expire and everyone can innovate.
    (Yes, I'm a socialist. No, I don't think that in any way invalidates the fundamental claims I'm making here.)

    --
    https://app.box.com/WitthoftResume Code: https://github.com/cellocgw
    1. Re:Well Duh: Open Source is better by the+gnat · · Score: 5, Informative

      Don't even bother arguing that profit motivates progress. The overwhelming majority of researchers and engineers are motivated by the joy of success, not crushing the opposition and getting filthy rich.

      The problem with drug development is that the huge majority of efforts end in failure, and depending on how far along the pipeline the drugs are, these failures can be painfully expensive. Truth is, it's not really all that difficult or costly to come up with a nanomolar inhibitor for some key regulatory protein involved in heart disease or cancer. But that doesn't mean you've cured the disease. You might synthesize a molecule that completely shuts down your target protein, and start doing in-vivo studies. Here's where the bad shit starts: maybe your compound can't get past the cell membrane. Or maybe it gets shunted to the liver and immediately degraded - unless it fucks up the liver, of course (which one of the major reasons for negative drug interactions, and why many medications have labels saying "do not consume alcohol"). Or let's say it gets to exactly where it needs to be, but it also binds with high affinity to seven other proteins, three of which we know nothing about, and all of these are essential for other processes. So you come in the next morning, and half of your test mice are belly-up, another quarter are bleeding rectally, and the remainder will promptly croak if you feed them Tylenol.

      If you're really unlucky, your drug passes the animal models easily, and makes it into clinical trials with actual sick humans. If you're really, really unlucky, you make it all the way to Phase III trials, with thousands of patients, and only then do you discover that either a) your drug doesn't really work as well as it needs to, or b) a large fraction of patients manifest severe side effects over time, or c) both. At this point the cumulative expense of developing this candidate may be hundreds of millions of dollars. And companies fail at this stage all the time; it's always big news when this happens, and their market capitalization takes it in the ass.

      Now, I don't feel terribly sympathetic for drug companies as a whole; they do some pretty sleazy shit, and have paid some well-deserved fines for their malfeasance. But I would find it incredibly depressing to sink years of my life (and millions of dollars of investor money) into a promising clinical candidate, only to have it fail just shy of the endpoint. I'm an academic scientist, and this is one of the reasons why I've stayed in academia so long, for all of its faults. I get paid less, but I don't have to devote myself to narrowly-scoped projects which have a depressingly high risk of failure. If I had to start doing drug discovery as part of some newly nationalized research plan, I would leave without hesitation. Sorry, but if you want me to spend my life doing something that mind-numbing and soul-crushing, you'd fucking better pay decently me for it. The overwhelming majority of people who know anything about drug discovery will tell you the same thing.

      PS #1: Please, explain how the extraordinary improvement in computer hardware since WWII was encouraged by lack of patents. Another counter-example: genome sequencing technology has become orders of magnitude faster in the last dozen or so years. (No, I'm not arguing that we should patent everything; I'm still against patents on software and gene sequences.)

      PS #2: Don't assume that scientists aren't motivated by crushing the opposition. That's part of the joy of success, and while we may not be doing it for the money, our egos are at least as big as everyone else's.

    2. Re:Well Duh: Open Source is better by cellocgw · · Score: 1

      PS #1: Please, explain how the extraordinary improvement in computer hardware since WWII was encouraged by lack of patents. Another counter-example: genome sequencing technology has become orders of magnitude faster in the last dozen or so years. (No, I'm not arguing that we should patent everything; I'm still against patents on software and gene sequences.)

      PS #2: Don't assume that scientists aren't motivated by crushing the opposition. That's part of the joy of success, and while we may not be doing it for the money, our egos are at least as big as everyone else's.

      Re #1: go back and read about the (then legal) reverse-engineering of the IBM BIOS, without which most of our current software and hardware wouldn't exist.

      Re #2: Neither you nor I represent the median ego of "scientist" -- class humanoids. Sure, getting there first is more fun, but that sort of competition is rather different from locking down your knowledge so nobody can review your results, reproduce your results, or improve upon them.

      --
      https://app.box.com/WitthoftResume Code: https://github.com/cellocgw
    3. Re:Well Duh: Open Source is better by Rich0 · · Score: 1

      Yup - this is just discovery work. This kind of research often happens in university and other open settings.

      The problem is that 95% of the cost comes in during the boring and expensive process of testing the drug.

      That's a good FOSS analogy as well. Notice how few FOSS projects REALLY test their products? Now consider that testing a piece of software just consists of people or scripts spending a few hours rigorously exercising the software on commodity hardware. In the drug research world you have to get thousands of volunteers, give them all an experimental medication THAT COULD KILL THEM, and then do a variety of medical tests over a period of months or years to see how it works out. Oh, and the failure rate is over 90% (usually resulting in starting over from scratch, not patching a few lines of code).

      I think that this stuff could be done without patents, but until I actually see that happening I'm not going to jump on the kill patents bandwagon. There is no reason the NIH and similar bodies worldwide couldn't just do the end-to-end R&D on a few drugs as an experiment and see how it works out. They could file the patents (defensively) and license out the drugs free of charge. If it works out well, then you won't even have to abolish patents - there is no way that branded medications could compete against free ones anyway. Right now the NIH does the early research, but doesn't spend the boatload of money needed to actually test the stuff they come up with. They usually abandon research when it gets to the point where this article is at.

    4. Re:Well Duh: Open Source is better by Anonymous Coward · · Score: 0

      The core problem is that the process you describe is not really science. It is trial and error. That makes it boring and high risk. I don't say that trial and error does not have some place in science, but everything medical science seems too much based on trying stuff and doing statistics than on understanding things first. The scientific method is based on creating theories, making predicitions, and trying to falsify them. This is not what is happening here.

    5. Re:Well Duh: Open Source is better by Anonymous Coward · · Score: 0

      Who is going to do the research? Who is going to determine which diseases should be treated? Open Source is great for projects that don't need large capital investments.

      If our nation limited direct to consumer pharmaceutical advertising, then our nation would be richer... but not by letting some crony determining what diseases to treat.

    6. Re:Well Duh: Open Source is better by Anonymous Coward · · Score: 0

      I think Jay Bradner's response, and most of the TED-crowd's response would be, then how do we solve that problem? I really don't know anything about the topic of drug breakthroughs or testing, but if they are claiming they have come up with a good way to handle what Jay Bradner's linked TED-talk discusses, then how do we solve the next problem? If they are saying they've made "Step 1" much easier through open source or through crowdsourcing, and that you say "Well, 'Step 2' is the hard part!" The proper response is not to say "Oh well, we tried!" The proper response is to say "How can we revolutionize 'Step 2', the way we revolutionized 'Step 1'."

    7. Re:Well Duh: Open Source is better by the+gnat · · Score: 1

      I don't say that trial and error does not have some place in science, but everything medical science seems too much based on trying stuff and doing statistics than on understanding things first.

      That's because we still understand shockingly little about biological systems - I think around half of human genes remain uncharacterized. This means that even if we can say with certainty that "mutated protein X causes disease Y", and therefore inhibiting the mutant protein is a promising approach to curing the disease, we have no way of knowing what will happen when we introduce our candidate drug into the actual organism. We know some basic rules, e.g. certain chemical structures are more amenable to entering cells than others, and we can make educated guesses, for example protein kinase inhibitors tend to be non-specific, but there is still a huge amount of uncertainty. Eliminating the guesswork will take decades of painfully slow basic research. Should we simply not try to treat these diseases until we can comprehensively model the entire system and predict how drug candidates will work?

    8. Re:Well Duh: Open Source is better by the+gnat · · Score: 1

      Right now the NIH does the early research, but doesn't spend the boatload of money needed to actually test the stuff they come up with. They usually abandon research when it gets to the point where this article is at.

      Not really - what actually happens is typically that the universities patent the discovery and license it to a company which performs the development work. Which does have an element of "socialize the risk, privatize the profits", except that the expense of the product development is typically far more than the basic research done with public funding, and the failure rate is dismal. So at least if a drug candidate bombs in clinical trials, most of the money that just got flushed down the toilet belongs to pharma company shareholders or VCs, and not the taxpaying public. The NIH and the universities don't have much incentive to do this themselves, especially if they can be hauled before Congress and asked to account for the money.

    9. Re:Well Duh: Open Source is better by Rich0 · · Score: 1

      Right now the NIH does the early research, but doesn't spend the boatload of money needed to actually test the stuff they come up with. They usually abandon research when it gets to the point where this article is at.

      Not really - what actually happens is typically that the universities patent the discovery and license it to a company which performs the development work.

      Really two ways of saying the same thing. I realize that university labs often patent the stuff they come up with (something I don't have a problem with - the part I don't like is that the license fees that result don't predominantly go to the US Government). The bottom line is that they don't spend the huge sums of money that happen after an initial lead is developed.

    10. Re:Well Duh: Open Source is better by jfengel · · Score: 1

      Thanks a lot for this. Slashdot is full of very smart people who say, "I'm very smart, and I don't understand why it takes you so much time, effort, and money to do the thing that you do. Here, let me teach you your job." It's nice to have the occasional interjection from somebody who actually understands what's going on to explain at least a few of the complications glossed over in the process.

    11. Re:Well Duh: Open Source is better by Anonymous Coward · · Score: 0

      "The Scientific Method", the core of science.

      Observe something. Create hypothesis. Form experiment to test hypothesis. Observe results. If necessary, modify hypothesis to account for inconsistencies brought forth in test. Go back to form experiment to test. Repeat until hypothesis cannot be proven wrong.

      What part of that isn't trial and error?

    12. Re:Well Duh: Open Source is better by Anonymous Coward · · Score: 0

      The proper thing to do in the current state of ignorance is to describe the results of experiments in as much detail as possible (no dynamite plots, no standard errors) so that we can all look for similar patterns to adduce general rules that may underly these systems. The entire significance testing or hypothesis testing concept is flawed. We need to describe results in detail, then *replicate the results* multiple times to ensure they are worth trusting, and finally look for patterns to develop mathematical models of what is going on. Then you can use stats on testing the predictions of these models, rather than the opposite of your research hypothesis (two means are exactly equal, and everything was controlled perfectly).

      Also check out Albert Laszlo Barabasi. I agree with him, this entire approach of swapping out one factor of a time is flawed. You have 20k + genes, how many different combinations of those do we need to test to understand how the system works?

    13. Re:Well Duh: Open Source is better by Anonymous Coward · · Score: 0

      The difference is in the "create hypothesis" step. If your hypothesis makes a specific point prediction the above can qualify as science in the way that has been so successful in the past. If you hypothesis only predicts "this drug does something", or "this drug causes more of a response", almost any random error will lead to a false positive. Paul Meehl has some good papers on this.

    14. Re:Well Duh: Open Source is better by Anonymous Coward · · Score: 0

      I am not saying that we leave these diseases untreated. I am not even saying that we should stop developing drugs. But I am arguing that we would advance faster if we would spent more resources on basic science than on trial and error. I also doubt that most drugs which are currently developed are really necessary. Spending more money on prevention, having insurance for everybody, and reducing the cost of education, would be a much better use of this money.

    15. Re:Well Duh: Open Source is better by Anonymous Coward · · Score: 0

      At this point the cumulative expense of developing this candidate may be hundreds of millions of dollars.

      Sounds insanely inefficient to me. Maybe there needs to be some competition to remove the inefficiencies. i.e. no, or at least highly restricted, patent monopolies.

      extraordinary improvement in computer hardware since WWII was encouraged by lack of patents.

      All the major, early, hard work was done without patents. Patenters usually arrive later to an industry when they see there's money to extract. They are an effect, not a cause.

    16. Re:Well Duh: Open Source is better by Anonymous Coward · · Score: 0

      As a former researcher, perhaps there's a bit of bias here...

      The only problem with drug development is that a huge majority of efforts end in failure, but that doesn't make the research effort painfully expensive for the drug companies. The pure research is mostly done off of NIH or DOE grants. The only drug-money research is the attempt to add an extra protein here, or swap an atom there to make it patentable, and then get the analogue through human trials, so you can milk the molecule for all it is worth, by claiming a 5% increase of something, or a 5% decrease of something else, over a similar best seller in that slice of the market.

    17. Re:Well Duh: Open Source is better by Anonymous Coward · · Score: 0

      so, lets see if I've got this right. You think science is wrong? You think it's more important to replicate results then creating tests of a hypothesis?

      mmmhmmm. I'm forced to ask, how did you do in high school physics class and exactly what do you do for a living? I'm an electrical engineer myself and got straight A's through physics myself, and I think what you just spouted is....what's the term, horse shit. Replicating results is unimportant, what is important is to fail to be able to disprove a hypothesis. I agree understand the results in detail is VERY important to disproving a hypothesis, but that's just part of the test formulation stage.

    18. Re:Well Duh: Open Source is better by the+gnat · · Score: 1

      The pure research is mostly done off of NIH or DOE grants. The only drug-money research is the attempt to add an extra protein here, or swap an atom there to make it patentable, and then get the analogue through human trials,

      Drugs discovered using NIH or DOE grants are usually already patentable if they don't fail one of the other tests. But these only account for about 25% of new drugs; the remainder are genuinely discovered by drug companies. That doesn't mean that the drug companies don't benefit in other ways from public research - most of what we know about the mechanisms of disease and the biochemistry of individual proteins comes from academics. But there's a huge leap from "we know this protein causes cancer" to "we have a drug to stop cancer".

      In any case, even when academics do find a promising drug, the human trials are usually still vastly more expensive than the basic research. And in many cases there is still a great deal of trial and error necessary to come up with a drug that has the desired functional and pharmacological properties.

    19. Re:Well Duh: Open Source is better by the+gnat · · Score: 1

      Sounds insanely inefficient to me. Maybe there needs to be some competition to remove the inefficiencies. i.e. no, or at least highly restricted, patent monopolies.

      I think you're missing the fundamental point of patents. If there is no temporary monopoly on a novel drug, what is to prevent a bunch of bottom-feeders from simply copying it and selling it at a tenth of the price? It's far easier to copy someone else than to come up with something genuinely new, especially with a product that's so ridiculously easy to reverse engineer. On the other hand, just because one company has a drug that treats heart disease, does not prevent another company from making an entirely different drug to treat heart disease. (Unless it's one of those sleazy cases like Ariad Pharmaceuticals and their NF-kappaB patent, which basically prevented anyone from developing drugs that altered that pathway. Fortunately, the courts eventually nixed this.)

    20. Re:Well Duh: Open Source is better by Anonymous Coward · · Score: 0

      The strategy of failing to disprove the opposite of your hypothesis is what I have a problem with.

    21. Re:Well Duh: Open Source is better by pepty · · Score: 2

      The problem is the general rules underlying the systems don't point you at drugs that work, they just point you away from some of the ones that don't. Once you are at the level of drug design you are dealing with lots of specific cases that resulted from billions of years of evolutionary ad-hoc.

      Reproducibility is currently a big movement in academic chemistry/biology labs, and on the Pharma end most discoveries like the one above die during target validation due to not being reproducible, not being reproducible in humans, or just not being relevant in humans.

      Also check out Albert Laszlo Barabasi. I agree with him, this entire approach of swapping out one factor of a time is flawed. You have 20k + genes, how many different combinations of those do we need to test to understand how the system works?

      That's not the right question.

      Right now we can't predict how the product of a single gene (a protein) will behave in the presence of a novel pharmaceutical compound. We can't predict where it will bind, how it will affect activity, whether it will have an intended effect. Thinking of 20 thousand genes as 20 thousand bits of data or 20 thousand simple predictable machines won't work.

    22. Re:Well Duh: Open Source is better by Anonymous Coward · · Score: 0

      So then lets stop confidently advising the medical professionals...

  17. don't prematurely ejaculate by iggymanz · · Score: 1

    the drug in the article has been proven to do exactly nothing.

    no trials yet.

    put it back in your pants.

    1. Re:don't prematurely ejaculate by cellocgw · · Score: 1

      You didn't read a word of what I wrote, did you.

      No comfy chair or chocolate for you.

      Molpy down.

      --
      https://app.box.com/WitthoftResume Code: https://github.com/cellocgw
    2. Re:don't prematurely ejaculate by Anonymous Coward · · Score: 0

      Please go to Cuba, they don't have patents there and please report how that works for them...

    3. Re:don't prematurely ejaculate by iggymanz · · Score: 1

      I did read it. please provide a single instance where "open source" has created a medicine to cure disease

    4. Re:don't prematurely ejaculate by iggymanz · · Score: 1

      average life expectancy in cuba is greater than the USA, infant mortality rate less than USA and only 1/6 the rate of AIDS.

  18. Re:TED talk explains how the OSS philosophy applie by __aaltlg1547 · · Score: 3, Insightful

    When it comes to science, there is no need to license a discovery to make it available to all. Simply publish and don't attempt to patent it. Scientific knowledge is public once published.

  19. Re:More pointless 'research' by Anonymous Coward · · Score: 0

    Most heart disease is caused by eating animal products (which humans aren't supposed to eat), lack of exercise, and smoking.

    Humans are designed for eating a diverse diet including animal products.
    Vitamin A - Basically only found in animal products. Vitamin A found in green vegetables are beta carotene and must be converted into a usable form of vitamin A. This requires bile salts that is produced by the liver when eating fat. But the problem is that you need to eat about 6 times much beta carotene to get the same level as pure vitamin A.
    B12 - Only available from animal products.
    Vitamin D - Well, you need at least 15 minutes of sun per day, full body exposure, and for people with darker skin it takes even longer.. How would people living very north or south on the globe where light is very limited during half the year survive?
    Protein - Yes, this is quite a bit thing... Animal protein is very easy for the human body to digest. 100g of beef gives you about 25g of protein while 100g of tofu gives you about 5 grams of protein.

    Actually living as a vegan is very tricky since it requires lots of knowledge about what nutrias the human body needs and it what amounts.

    People saying that the vegan diet would save the world since some of the nutrition-supplements required require quite a bit more of work.
    The way to a sustainable society is more likeley to consume in moderation..
    - We do not really need 100kg of meat per year (this is the avarege for the US).. 15kg should be more than enough as long as you are healthy.
    - We should eat more natural fish, skip the fish-farms. If not enough then reduce intake (higher prices), not production.
    - Egg's are perfect and contains almost every thing we need... If other animal products are too expensive this is a very good substitute. Easy to have all over the world. Small village - let them run around.. When getting too old then you get some meat. In a industrialized country then chicken-farms, but we don't really need 10 eggs per week per person.. Maybe 1-3 per week would be enough.
    - Moving to a more vegetarian-like diet, but with animal products from time to time can help in reduction of resources to produce food, but some things are still better that we get from animal products, both for us and for nature as a whole.

    I would prefer a 200g nice juicy stake from a free-ranging animal once per week over 500g steaks 2 times per week from a farmed animal ...
    I prefer buying 'natural' fish over any fish-farms.. It just tastes better, and is much healthier. (fish from fish-farms contains less of the omega-3 and more of the bad fat's. Also they have a tendency to have higher mercury levels)

  20. Is another myth about to bite the dust? by erroneus · · Score: 1

    For a long time, commercial activities have claimed that only through commercial enterprise could quality and value be achieved. This has been claimed of software for a long time as well as with other industries. Among these is the drug/pharmaceutical industry because only they can afford the R&D needed to make important things happen. (Conveniently we forget that many of the most important drugs predate the big pharma industry.)

    With 3D printing edging into device manufacturing space, just about everything is going to face free/public competition, not the least of which will be energy production. Big business with its dependency on having the public dependent on them has its days numbered. I look forward to those days... I wonder if I will live that long?

    1. Re:Is another myth about to bite the dust? by ColdWetDog · · Score: 2

      With 3D printing edging into device manufacturing space, just about everything is going to face free/public competition, not the least of which will be energy production. Big business with its dependency on having the public dependent on them has its days numbered. I look forward to those days... I wonder if I will live that long?

      No you won't.

      Because 3D printing isn't going to replace anything much beyond the utensil selection in Walmart for the foreseeable future. Hell, you'll be lucky if you can shoot yourself in head with a 3D printed object in your lifetime. You'd be most likely to blow up your hand and have to go the the hospital and get treated with stuff that's been woven, extruded, grown, spun or glued.

      --
      Faster! Faster! Faster would be better!
    2. Re:Is another myth about to bite the dust? by the+gnat · · Score: 1

      Among these is the drug/pharmaceutical industry because only they can afford the R&D needed to make important things happen.

      It's less the "R" than the "D". The government spends large amounts on basic research, including some expenses which drug companies, at least individually, can't afford. For instance, the US Department of Energy builds massive X-ray generators called synchrotrons, which are used by biologists to determine the structures of proteins, and drug companies make heavy use of these to investigate drug candidates. A new state-of-the-art synchrotron is around $1 billion. Naturally, drug companies pay the DOE to use these facilities without revealing their data (which is a requirement of use for everyone else). It's a situation that just about everyone is happy with. (Also, more generally, the government funds studies which increase our knowledge and understanding of biological systems, which can inform drug development even though they usually don't magically lead to new therapies.)

      What the government can't or doesn't want to spend money on is the laborious process of taking a drug candidate from the lab bench to the consumer. I made a longer post about this above, but the short version is that it typically costs hundreds of millions of dollars. and most drug candidates don't even make it that far. The government would naturally prefer not to spend huge amounts of taxpayer money on projects that have an exceptionally high risk of failure, and academic scientists are reluctant to work on such projects both in general, and without being well-compensated. So the "development" phase is farmed out to companies.

      It is an imperfect process, and I think much could be done to improve the system (I am on the record as supporting the repeal of the Bayh-Dole Act), but right now I do not see any magical alternatives. Maybe with another 20 years' improvement in biotechnology and automation we'll do things differently; I certainly hope so.

    3. Re:Is another myth about to bite the dust? by King_TJ · · Score: 2

      Well, first of all? Who are these commercial activities you speak of who supposedly claimed quality and value were ONLY achievable via commercial enterprise?

      I can't think of a single business making that claim today? Clearly, technological progress means that ideas starting out as massive, costly endeavors become mundane with time. I remember when recordable CDR technology was brand new, for example. The only people possessing CD writer drives were generally government contractors and educational institutions because the drives themselves were thousands of dollars, with blank media as expensive as $25-30 per disc. They only recorded at 1x speeds, and were all external drives, because any vibration during the recording process ruined the disc. So you had to carefully place the recorder in a spot where it wouldn't get bumped or shake. That's just a small example of a technology everyone takes for granted today. (Can you even buy a CD-ROM reader that doesn't include writing functionality today, if you wanted to??)

      It's this same principle that caused space travel (once thought so complicated and expensive, only Federal government could do anything with it) to become privatized today. It's the reason individuals are now doing DNA splicing in their own homes as hobbies and why 3D printing is becoming something you can do on your own with equipment you build yourself.

      There will always be a use for the resources and capabilities of big business (and arguably even government, at a tier above that -- as a way to get a VERY large project completed by the will of the taxpayer in a certain time-frame). But whatever these entities come up with with eventually trickle down to a more manageable size and scope, suitable for interested individuals to undertake.

    4. Re:Is another myth about to bite the dust? by Rich0 · · Score: 1

      Among these is the drug/pharmaceutical industry because only they can afford the R&D needed to make important things happen.

      They're not the only ones who can afford it, but right now they're about the only ones willing to spend it.

      The research in this article did NOT develop a new drug. It only discovered a compound that has biological activity. That is the very first step in drug research, and usually it takes about 5 years and $100M to prove conclusively that it won't work in the real world. Maybe 5% of the time it will take 5 years and $100M to prove that it actually does work.

      I'm all for expanding the publish research model instead of relying on patented drugs. The problem is that this will require a HUGE increase in public funding. Duplicating what the pharmaceutical industry is already doing would probably require tripling the funding of the NIH (perhaps with a few first world nations pitching in). The resulting drugs would be cheap, but taxpayers would pay for them. Oh, and in the industry model the public only pays for drugs that work (granted at a substantial premium). In the publicly funded model the public pays for every drug with no real accountability for failures.

      I think it is an experiment worth trying, perhaps on a small scale at first. However, this kind of early research (which happens all the time) shouldn't be confused the cost of coming up with new drugs.

  21. Re:More pointless 'research' by __aaltlg1547 · · Score: 1

    Most heart disease is caused by eating animal products (which humans aren't supposed to eat),

    Depends on who's doing the supposing. Most humans suppose they will. And most scientists (all of those who aren't working from a religious or diet industry agenda) suppose humans are adapted to do so -- in some quantity or other.

    ...lack of exercise, and smoking.

    Does this magic pill cure all of those too?

    Most people want to have their cake and eat it too.

    There's no meat, tobacco or lack of exercise in cake. But you forgot to mention gluten. As many a 1% of people might have trouble with cake.

  22. Re:TED talk explains how the OSS philosophy applie by Anonymous Coward · · Score: 0

    Either your thinking is confused, or you are doing this deliberately...

    In the software world, there is a very big difference between source code and executable binaries.
    In chemistry, there is no such distinction.

  23. Re:TED talk explains how the OSS philosophy applie by bunratty · · Score: 3, Insightful

    Absolutely. And guess what would happen to any drug company that did not patent their drugs? How would they be able to compete with companies that did not have to pay the hundreds of millions in research to get the drug approved? The only reasonable alternative to patent systems that I can see are (a) trade secrets, which means that the discovery is not made available to all, or (b) go back to a patron system where a generous benefactor foots the bill for research, in which case the research that the scientists do is only what the benefactor wants, which may be the ultimate cure for baldness or a little dick. I think patents are better than the alternatives. That is, unless you can come up with a better idea. Just be sure to think it through...

    --
    What a fool believes, he sees, no wise man has the power to reason away.
  24. Re:TED talk explains how the OSS philosophy applie by maxwell+demon · · Score: 1

    So there's no difference between the instruction on how to create a substance and the substance itself?

    --
    The Tao of math: The numbers you can count are not the real numbers.
  25. Re:More pointless 'research' by Anonymous Coward · · Score: 0

    How do you know if someone is a vegan?

    Don't worry, they'll tell you.

  26. Re:TED talk explains how the OSS philosophy applie by the+gnat · · Score: 2

    trade secrets, which means that the discovery is not made available to all

    Which is extraordinarily difficult for drugs, because everyone will simply buy a bunch of their competitors' pills, and figure out exactly what they're made of down to atomic detail. A typical university chemistry lab could do this in a few days. There are some aspects that are more tricky - the exact packaging is sometimes key to getting the drug absorbed by the body at the desired rate, and the chemical synthesis can be messy - but figuring these out is still way cheaper than coming up with your own drug.

  27. Re:More pointless 'research' by Anonymous Coward · · Score: 0

    eating animal products (which humans aren't supposed to eat)

    Says who? Your childish ethical sense? Because human have K9 teeth for a reason and it's not for eating plants.

  28. Re:TED talk explains how the OSS philosophy applie by Anonymous Coward · · Score: 0

    Yeah, just as there is no difference between an algorithm/source code and machine code that implements it. Both are equally readable, right?

  29. Re:More pointless 'research' by fermion · · Score: 1
    Aside from the validity of the statements, which are overreaching, the Pharmaceutical industry does survive on the idea that one can live however one wishes and there will be a pill or procedure that will correct the damage. If you are unhappy take a pill. If you eat food that gives you indigestion, take a pill. It seldom occurs to people to think about why they are unhappy or stop eating food that makes them sick.

    Heart disease is a natural degradation of the body, but is accelerated by diet and lack of appropriate motion.

    --
    "She's a scientist and a lesbian. She's not going to let it slide." Orphan Black
  30. OMG how do people not understand this? by Anonymous Coward · · Score: 0

    you can charge for open source software... it's just if you get the program, you get the source.

  31. Re: TED talk explains how the OSS philosophy appli by Anonymous Coward · · Score: 2, Informative

    The "patron system" is already in place - the gov't foots the bill for nearly all the research, and private corporations add the last 1% of the bill before patenting and reaping 100% of the profits.

  32. Scripting languages by tepples · · Score: 1

    In the software world, there is a very big difference between source code and executable binaries.

    Authors of computer programs stored in files whose names end in .js, .py, or .pl might disagree with you. Glance up at the location bar to see "comments.pl", then look at this page's markup to see "engage.js".

    1. Re:Scripting languages by Dog-Cow · · Score: 1

      And neither of those are executable by hardware. Virtual machines are just more software and do not count for this discussion.

  33. you're doing it wrong by Goldsmith · · Score: 1

    Collaboration and sharing results is standard in science and has been for the last few hundred years. Practically speaking, patents on their own are meaningless for new scientific advancements and do nothing to prevent or encourage scientific advancement. They're a non-issue. What does matter is how much it costs to read the published results.

    The equivalent to open source in science is open access. CELL is not open access. As a result, I (as a scientist without access to CELL) don't have access to their results in the final form. Nor do I have access to their raw data or any discussion of the analysis. How is this open?

  34. Re:TED talk explains how the OSS philosophy applie by icebike · · Score: 1

    Can you get away with not telling the FDA what is in a drug?

    Seems counter-intuitive.

    --
    Sig Battery depleted. Reverting to safe mode.
  35. Drug Patent by agrisea · · Score: 1

    I was wondering how long a drug patent lasts right now and if it is tied at all to how long it took to research whatever the drug patent is for? A solution could be simply to put a time limit on drug patents, after which it becomes a part of the public domain.

    --
    Agrisea Tsunami - Epyc Servers... https://agrisea.net/products
    1. Re:Drug Patent by Anonymous Coward · · Score: 0
    2. Re:Drug Patent by Anonymous Coward · · Score: 0

      WTF? There is this new fangled thing called 'Google' that will give you links to everything. Try it. Or just read the constitution to find out if patents are time limited and then look up the appropriate law to see what that limit might be. I hope you are not an American, we already have enough stupid people.

    3. Re:Drug Patent by Trax3001BBS · · Score: 1

      I was wondering how long a drug patent lasts right now and if it is tied at all to how long it took to research whatever the drug patent is for?

      Drug patent's don't expire anymore, and if a generic is available they are able to restrict it's purchase in the US.

      Modafinal is the generic name and can't be purchase in the US, Provigil is the brand name and was due
      to lose it's patent in 2012. Nuvigil was released at that time and I can't find a reason but the patent has
      been extended to Provigil to some time in the far future

      Modafinal http://en.wikipedia.org/wiki/Modafinil > Provigil >
      Nuvigil http://en.wikipedia.org/wiki/Armodafinil generic is Armodafinil

      Both are the same chemical structure. Not sure if you can purchase Provigil anymore, Nuvigil is cost prohibitive - say $20 a pill in the US.

  36. Re: TED talk explains how the OSS philosophy appli by Gavagai80 · · Score: 2

    Perhaps government patents would be a solution. Let the government license its patents freely to education and research but take a percentage of profits for corporate use.

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    This space intentionally left blank
  37. Re:TED talk explains how the OSS philosophy applie by fibonacci8 · · Score: 1

    The traditional way is append the word "herbal" onto anything to avoid having to disclose the contents.

    --
    Inheritance is the sincerest form of nepotism.
  38. Re:TED talk explains how the OSS philosophy applie by icebike · · Score: 1

    Yeah, just as there is no difference between an algorithm/source code and machine code that implements it. Both are equally readable, right?

    Readable for who?

    To a person well versed int the arts? Absolutely.
    To a decompiler, you bet. The code you get out of a decompile may not look like the original, but it is still the code.

    --
    Sig Battery depleted. Reverting to safe mode.
  39. Re:TED talk explains how the OSS philosophy applie by gl4ss · · Score: 1

    they would compete in the way they used to compete.. by being the best in making the compound.

    --
    world was created 5 seconds before this post as it is.
  40. Link to parts of the paper: by Hartree · · Score: 1

    What's claimed is pretty impressive. They say they've gotten 60% improvement in heart function from a month long treatment course in mice and even quicker protective effect against declines in function. The caveat, as always, is that many things work well in mice, but don't translate into human therapies.

    This is still paywalled, but it has many of the figures from the article as well as the abstract.

    http://www.sciencedirect.com/science/article/pii/S0092867413008842

    This is of direct interest to me as I have some right side heart enlargement (precursor to failure) and take medicine for it.

    1. Re:Link to parts of the paper: by Anonymous Coward · · Score: 0

      http://biostat.mc.vanderbilt.edu/wiki/pub/Main/TatsukiRcode/Poster3.pdf

  41. Re:TED talk explains how the OSS philosophy applie by paiute · · Score: 1

    So there's no difference between the instruction on how to create a substance and the substance itself?

    Yes, there is a big difference.The instructions are much more valuable. The instructions never go bad. The substance itself will eventually go bad.

    --
    If Slashdot were chemistry it would look like this:Cadaverine
  42. Re: TED talk explains how the OSS philosophy appli by Anonymous Coward · · Score: 0

    The vast majority of government funded biomed research is a waste of time. It may be useful for other social reasons (get more people to know "a scientist") but most of that research money goes down the drain and creates confusion rather than advancing knowledge.

  43. Re:More pointless 'research' by Antique+Geekmeister · · Score: 1

    > Today we know that the main nutritional problem is excess fructose

    As opposed to malnutrition from poverty? Think again.

    As for nutrition causing heart disease, wait a few years. I'm afraid the cause will be "discovered" to be something else. The last few decades have seen the blame cast on smoking, excess preservatives, excess sucrose (not fructose!), excess protein, excess fat, excess trans-fatty acids, excess salt, excess liquor, excess body fat, excess work, excess processed food, excess caffeine, lack of vitamin C, lack of exercise, or poor sleep habits.

    The claim that humans are "not supposed to eat animal products" is even less well founded. Humans have incisors and canine teeth, like other omnivors, for rending flesh. We also have rather short intestinal tracts and livers that handle animal proteins and fats reasonably well, neither of which are so common to herbivores.

  44. Re:Awe Man! (Get your year right!) by Artagel · · Score: 2

    The first patent act was in 1790. The Constitution only permitted Congress to have patents. Congress had to decide to do it.

  45. Long Odds by Artagel · · Score: 1

    Let's see. This is a molecule in pre-clinical testing. I would give this specific molecule about a 1 in 1,000 chance of actually being marketed. Those are damn good odds for a molecule at this stage. This is why you always have to take the word "potential" with a boulder of salt.

  46. Will evil triumph? by Anonymous Coward · · Score: 0

    I am neither a doctor or a chemist (IANADOAC) but it's actions like these that bring me some measure of hope about the human spirit. Sure the odds are stacked against them with the evil Pharmaceutical conglomerates circling round like evil Pharmaceutical compagnies, but still.

    I wish for more.

  47. Re:TED talk explains how the OSS philosophy applie by ewibble · · Score: 1

    The inventor of the drug, could be the only one that was able to state that they developed the drug. Most people have a sense of fairness and will pay extra to reward the discover of the drug. Not to the point where they go bankrupt or die because they can't afford the drug, but in that case they person making the drug would not get there money anyway.

    If you don't believe me that reputation can make money for the drug industry simply go down to the chemist and look and the difference in price between Panadol and generic paracetamol (same thing, 3 times the price).

    I find it amazing that people believe that the only way to develop drugs for large drug companies to develop them? No matter how big the company is, to say that the rest of the people in world are unlikely contribute more than them seems the height of arrogance.

    Also a public company structure seems like the worst possible way of developing drugs. Public companies by their very nature must optimize for profit, (otherwise they are not doing their job) therefore it is never in their interest to cheaply an effectively cure a disease, it is much better the bottom line to keep the person alive while charging them an ongoing fee for living, until they run out of money and die.

  48. Re:More pointless 'research' by 50000BTU_barbecue · · Score: 1
    heart disease is caused by eating animal products (which humans aren't supposed to eat)

    Inuit aren't human?

    --
    Mostly random stuff.
  49. Re:TED talk explains how the OSS philosophy applie by Anonymous Coward · · Score: 0

    Yes, there will be a mexican standoff between drug companies. They will simply 'agree" not to pilfer, and then ALL drus will be administered via careful monitored 'health centres' where as machine will be used to do the injection so the nurse can't game it for a small start up company.

    what people for get to ask is how much the 95% of drugs that never make to market actual cost to develop and go through trials.

  50. Re: TED talk explains how the OSS philosophy appli by Anonymous Coward · · Score: 0

    Wrong.
    Private corporations are the ones who supply the $ to do research. Without that money either student fees would more than double or the government would have to pay more than double.

    By careful planning you can show government funding does NOT go into research, on teaching and infrastructure.

  51. Re:More pointless 'research' by jedidiah · · Score: 1

    > Most heart disease is caused by eating animal products (which humans aren't supposed to eat),

    You are not a cow. No matter how much you would like this to be the, case it simply is not true. If you try and pretend that you are a cow then you will DIE.

    We are omnivores.

    Being able to (mostly) eat what happens to be available is one of our key adaptive advantages and a key reason you even exist at all.

    Opportunitistic carnivores are the only reason you're here to spout your political nonsense.

    --
    A Pirate and a Puritan look the same on a balance sheet.
  52. Thank you by Anonymous Coward · · Score: 0

    As someone who lost his mother to heart failure when she was 59, I applaud these researchers who put patients before their own financial gain.

  53. Re:More pointless 'research' by jedidiah · · Score: 1

    The main risk from heart disease is genetic.

    Although even that typically manifests only once a person has outlived their natural lifespan and are no longer able to breed and help perpetuate their family line.

    Trying to maintain a lifestyle based on a cuisine that's not your own is a serious effort that can be easily f*cked up. Engaging in something that doesn't even have some cultural origin is just living of of some fad diet.

    People in general are too stupid and aren't educated enough or aware enough of themselves. This includes vegans.

    --
    A Pirate and a Puritan look the same on a balance sheet.
  54. Re:TED talk explains how the OSS philosophy applie by fido_dogstoyevsky · · Score: 1

    ... go back to a patron system where a generous benefactor foots the bill for research, in which case the research that the scientists do is only what the benefactor wants, which may be the ultimate cure for baldness or a little dick. I think patents are better than the alternatives. That is, unless you can come up with a better idea. Just be sure to think it through...

    One of the things governments were invented for WAS to be the benefactor which foots the bill for research (usually, in the civilised parts of the world, they don't insist on micromanaging where the research goes).

    --
    It's NOT a conspiracy... it's a plot.
  55. Re:TED talk explains how the OSS philosophy applie by shaitand · · Score: 1

    Drug companies don't have any "their" drugs. Scientists who works for drug companies do. The drug companies are the "generous benefactor" in the current scenario. Ditch the patents, change the FDA oversight to something closer to what you have for food... check production is as it should be, confirm what they are selling is what they claim and not something known to be dangerous. Then take away all legal immunity that is granted by going through the current process. Toss out grants and funding to encourage the efforts.

    If scientists were working for themselves, pooling resources to get and share equipment and distribution lines. The money they make just being the first one to market with a drug would likely be much more than they are paid by drug companies.

  56. Re:TED talk explains how the OSS philosophy applie by pepty · · Score: 1

    In this case it probably means a similar (but patented) molecule will probably be the first to market. It could also mean that their JQ1 inhibitor, while successful in model trials as a lead or tool compound, has already failed a preclinical test. Either way: 50:1 odds against a new drug candidate succeeding in preclinical trials, 10:1 odds against a new drug compound succeeding in clinical trials. 500:1 odds against success, on average. The big discovery here isn't the inhibitor they waived the rights to; it's the pathway and the target (which aren't patentable anyway).

  57. Re:TED talk explains how the OSS philosophy applie by pepty · · Score: 1

    Nope. API (active pharmaceutical ingredient) and excipients (stuff in the formulation that has some function: stabilizer, solubility, crystallization aid) have to be disclosed.

  58. Re:TED talk explains how the OSS philosophy applie by pepty · · Score: 1

    But then you can't call it a drug and have to dance around saying it treats anything.

  59. Re:TED talk explains how the OSS philosophy applie by Anonymous Coward · · Score: 0

    Bayer still makes aspirin. Sure, it might not be their biggest profit margin drug, but they still sell a lot of it.

  60. Re: TED talk explains how the OSS philosophy appli by pepty · · Score: 2

    Bullshit. The vast majority of spending necessary to turn this discovery into a drug hasn't even been started yet. Even in cases where the drug is invented and patented in academia (~15-20% of drugs, and we won't know if that has happened here with JQ1 for at least another 5-10 years), universities license the molecule to a biotech or pharma to move it through clinical trials. The NIH is starting to spend more on translational research (the preclinical/clinical stuff Pharmas typically do), but it will be at least another decade before we can tell if the NIH is doing a better job at it than Pharmas.

  61. Re: TED talk explains how the OSS philosophy appli by pepty · · Score: 1

    Government (university) patents and "taking a percentage for corporate use" has been happening for over 30 years. the "freely to education and research" part is a bit more tricky.

  62. Re: TED talk explains how the OSS philosophy appli by pepty · · Score: 1

    It's useful for discovering pathways and targets that are later determined to be useful for developing drugs. Also about 15-20% of drugs are invented in academic labs. Those drugs are more likely to be first in class drugs and more likely to focus on unmet medical needs than drugs that are invented in Pharma companies.

  63. Re:TED talk explains how the OSS philosophy applie by pepty · · Score: 1

    Three times the price, is nice and all, but you'll need more like 100x the price of a generic small molecule pill to recoup the R&D investment cost and turn a profit. The multiples aren't nearly as high for biologics (antibodies, peptides, etc), but would you willingly pay 3x as much for a drug that costs $14K just to manufacture per patient-year?

  64. Re: TED talk explains how the OSS philosophy appli by Anonymous Coward · · Score: 0

    I was talking about the large percentage of non-reproducible studies in the literature

  65. Re:More pointless 'research' by mjwx · · Score: 1

    What's the deal with all the crazy vegans around here lately? Go to your local hippie store and look at the vegans. Then go to your local CrossFit and look at the paleo eaters. Which group looks healthier to you?

    Then go look at someone who eats a balanced diet including meat, dairy, grains, fruits and vegetables.

    Extreme diets like Vegan and Paleo are unhealthy, even if they dont look it.

    BTW, most gym junkies are steroid users. Your average healthy person does not look like that.

    --
    Calling someone a "hater" only means you can not rationally rebut their argument.
  66. Re:More pointless 'research' by demonlapin · · Score: 1

    While this was about eating vs not eating meat, not paleo per se (which I think you must be unfamiliar with - it's not extreme unless you want it to be)...

    Meatheads don't last long with CrossFit. It's a different animal, and I'd never describe some roided-up dude as healthy. And most people I know who eat grains are fat. I was when I did.

    Go read Why We Get Fat by Gary Taubes, or Doug McGuff's Body by Science. Be sure to check out Robert Lustig's "Sugar: The Bitter Truth" on YouTube (or the UC site, if that's blocked at work). There's really no reason in general to eat carbohydrates as such - the small amount you get from eating a good mix of non-starchy vegetables is more than adequate to supply most people's needs. If you're an actual elite athlete, of course, things may be different, but at a minimum that means competitive at the Division I collegiate level.

  67. Re:Awe Man! (Get your year right!) by Anonymous Coward · · Score: 0

    And you don't think someone came up with the idea before implementing it in the patent act?

  68. Re:TED talk explains how the OSS philosophy applie by __aaltlg1547 · · Score: 1

    I think government funded medical research is a completely viable alternative.

  69. Re:More pointless 'research' by Anonymous Coward · · Score: 0

    Then go look at someone who eats a balanced diet including meat, dairy, grains, fruits and vegetables.

    Uh... you seem to be confusing "paleo" with "eats nothing but meat."

    Paleo is mostly about eating unprocessed "natural" foods, where 'processed' is defined as anything that changes the shape/nature of the food between gathering and eating it."

    Strict paleo eaters tend to skip grains and dairy because they really weren't a significant part of the average diet until agricultural practices were developed - which is usually considered the dividing line between "paleo" and "non paleo" eating - agriculture was a shift from hunter-gatherer to agrarian based society. I assure you there are plenty of fruits, nuts, and vegetables in any reasonable interpretation of paleo. And many paleo eaters are pretty flexible about the grains and starches they'll eat - rice, and starchy tubers seem to get a pass from many of them.

    As for "gym junkies" - again, many (most) paleo followers are not roid-raging "gym junkies" - they focus on lots of low-intensity activity, with occasional "all out" bursts. They tend to be lean and flexible, with good muscle tone and definition - but certainly not giant freaks of nature like a bodybuilder. Go learn about CrossFit, and you'll see that the focus of whole-body exercises and short, intense workouts fits nicely with many of these principles, thus the overlap. I've YET to see a giant musclebound freak sweating through a WOD.

    If you're going to criticize something, you should probably have some idea of what it is you're criticizing.

  70. Re:TED talk explains how the OSS philosophy applie by __aaltlg1547 · · Score: 1

    Which in most cases is 100% OK because it's completely ineffective.

  71. Re:More pointless 'research' by Anonymous Coward · · Score: 0

    I would think that this has already been established.

    Hell, they're not even properly Canadian, and Canadians are scarcely human.

  72. Re:TED talk explains how the OSS philosophy applie by losfromla · · Score: 1

    Really it costs $14K to manufacture? Without counting NRE? I have strong doubts that any drug costs that much to manufacture given how much automation is in place for drug manufacturing.

    NRE = Non-Recurrent Engineering (just so I'm not accused of being obscure)

    --
    Only I can judge you.
  73. Re:TED talk explains how the OSS philosophy applie by Anonymous Coward · · Score: 0

    Imagine what a GPL like approach would cause here. The major secretive pharma conglomerates would be disadvantaged because they wouldn't want publish their contributions, therefore they wouldn't be allowed to start research on the already published stuff. While numerous smaller national firms would receive the benefits simultaneously. Way to go.

  74. Re:TED talk explains how the OSS philosophy applie by Anonymous Coward · · Score: 0

    > The only reasonable alternative to patent systems that I can see are (a) trade secrets,

    Public funding, crowd funding, public reward from success, etc. There are many alternatives that are better if your only motive is to get better health with least resources. Current system is good for making money. Cure for all would be a disaster to money system.

  75. Seriously? by Anonymous Coward · · Score: 0

    And this is new? Academic scientist gives a terrible compound with no bioavailabilty to his friends to test in irrelevant assays? Call it 'open-source' and it's somehow a TED talk?

  76. Re:TED talk explains how the OSS philosophy applie by Anonymous Coward · · Score: 0

    I dunno, patronage system sounds like the surefire fastest way to develop biological immortality....

    And in all seriousness, what else should the ultra-wealthy be spending their coin on? Cars, shiny rocks, too-big houses and boats?

  77. Re:TED talk explains how the OSS philosophy applie by Rakishi · · Score: 1

    It costs $1 billion I believe to bring a drug to market, that's not engineering costs but rather FDA costs and costs of failed drugs. Drug trials are not cheap and you don't really know which ones will work beforehand.

    Someone needs to pay that or the drug can never be manufactured and sold. Do you have a billion lying around and are you willing to hope people pay you back?

  78. Re:TED talk explains how the OSS philosophy applie by StripedCow · · Score: 1

    This generous benefactor could be the government, you know.

    --
    If Pandora's box is destined to be opened, *I* want to be the one to open it.
  79. Since i686 by tepples · · Score: 1

    Please precisely define "executable by hardware". Modern x86 chips don't run x86 bytecode; it gets recompiled to micro-ops inside the CPU, and it's been that way since the Pentium Pro.

  80. Re:TED talk explains how the OSS philosophy applie by Anonymous Coward · · Score: 0

    None.
    Drug companies as they exist today don't deserve to. Putting them all out of business would be a benefit to the world. Capitalism has no place in health care. It's a violation of the Hippocratic oath.

    Restricting access to medication in the name of profit is immoral. Period. I don't give a wet fart if they spent money to develop the cure once it's known it's free game.

    The solution is publicly funded research. The free market will reward whoever can manufacture the drugs the cheapest.

  81. Re:More pointless 'research' by Hartree · · Score: 1

    "Reproduce, then die, like nature intended."

    Ok. You first.

    But feel free to give up the reproduce part.

  82. Re:More pointless 'research' by Hartree · · Score: 1

    "Most heart disease is caused by eating animal products (which humans aren't supposed to eat), lack of exercise, and smoking."

    Some of it. I'd also change that to eating too much in general.

    Of course, I've yet to hear of a nonsmoking vegan runner that's survived to tell us of, say, the Civil War. So, there's a pretty strong limit on the amount of benefit.

  83. We USAians? by Anonymous Coward · · Score: 0

    We USAians ?! wtf are you smoking? probably the first thing one would learn living here is how we refer to ourselves, you're not even past that step buddy.

  84. Re:More pointless 'research' by Anonymous Coward · · Score: 0

    I disagree with the parent pushing the 'vegan' thing with their '... eating animal products (which humans aren't supposed to eat) ...' thing. But I also disagree with your assumption that you can see vegans are not as fit or healthy as paleo eaters just by looking at them.

    Rather than assuming your stereotype is correct, let's have a look at some real life vegans.

    Woody Harrelson, Joaquim Phoenix, Clint Eastwood, Jason Mraz, Tobey Maguire, Dax Shepherd, Mickey Madden, Thomas Dekker, Russell Brand, Brad Pitt, Chris Martin, Mac Danzig (UFC fighter), Steve-O (from Jackass), Anthony Keidis, Casey Affleck. (Plus there are more). All have plenty of muscle and are very fit.

    If you go to CrossFit you wouldn't not know if you're looking at a vegan or a paleo eater. I know plenty of personal trainers and fitness instructors who are vegan or at least vegetarian. They all look 100% fit and healthy. The 'pale anaemic vegan' stereotype that Hollywood and the general population likes to throw around just isn't true.

  85. Re:TED talk explains how the OSS philosophy applie by losfromla · · Score: 1

    Rakishi, you are proceeding down a line which is irrelevant to the question I asked. My question was specifically aimed at pepty's absurd assertion that a drug costs $14K to manufacture per patient per year. I understand the absurd costs to get past the FDA hurdles, those are a different question though.
      Again:
    a drug that costs $14K to manufacture per patient per year? ...Anyone? ...Anyone?

    --
    Only I can judge you.
  86. The problem IS "new" drugs ! by ToddInSF · · Score: 1

    Look, we already have so many drugs that have been used for so long, and RESPONSIBLE researcher will tell you that MOST "new" drugs are unnecessary and dangerous, and developed primarily for the purpose of making corporate wealth.

    The system is broken to the core, and open sourcing it like this is probably the only thing that will mitigate that third leading cause of death in the US. (Doctors treating you with new drugs they get a kickback on).

    There are drugs that have fallen into disuse that are effective, well established, and so inexpensive that Big Pharma has no desire to make them anymore, because they do not yield the OBSCENE PROFITS for the shareholders.

    The entire system is based on fraud and lies and deception. Taking a known drug that's come off patent and fucking around with it a little so that you can claim it's novel enough to repatent and charge the public up the ass for is great strategy for the stockholders, but it KILLS people at worse, and rips them off when they could take something generic and established at best.

    Hell, BY FAR most drugs people take in the US are prescribed because people didn't take care of themselves to begin with.

    I don't believe corporatism/capitalism/wahtever you're calling it today is inherently evil; just that our version of it clearly IS.

  87. a common cause of plaque by Anonymous Coward · · Score: 0

    Homogenized milk. We know an inflammatory molecule is absorbed from homogenized milk. This molecule inflames arterial walls and plaque is laid down as protection..

  88. Re:More pointless 'research' by bhiestand · · Score: 1

    > Today we know that the main nutritional problem is excess fructose

    ...

    As for nutrition causing heart disease, wait a few years. I'm afraid the cause will be "discovered" to be something else.

    To my knowledge, this is the only experiment that has shown direct observation: Differentiation of multipotent vascular stem cells contributes to vascular diseases. I haven't followed the research lately, so this may have been debunked in the last year.

    That said, every other article I have read on the subject seems like purely correlational bullshit.

    --
    SWM seeks new sig for a brief fling
  89. Hypocrisy by Anonymous Coward · · Score: 0

    What is so ironic about this article is that Bradner didn't "invent" anything. JQ1 is a minor change to compounds first discovered by Mitsubishi Pharma, who told the world about them in patent WO/2009/084693. Bradner's group made one compound based on this and gave it to academics - fine, but he's also set up a company to exploit it, www.tenshatherapeutics.com. Doesn't sound so impressive now, does it.

  90. Re:TED talk explains how the OSS philosophy applie by pepty · · Score: 1

    There is automation in chemical synthesis and biological production of actual production batches of drugs, but it's not the kind that leads to unattended operation. Most of that type of automation is way downstream at the packaging stage.

    Drug manufacturing costs:

    small molecules (example: ibuprofen): $1 per gram

    peptides (synthetic insulin): $50-1000 per gram

    antibodies (Herceptin, Avastin): $500 - 5000 per gram

    The $14K figure was the cost of materials for 1 patient year of a peptide AIDS drug. The starting materials and reagents for peptide drugs are expensive compared to those used to make small molecule drugs, yields are low, purification and QC costs are higher too.

    Biological drugs (mostly antibodies) tend to be very expensive to manufacture. The processes are extremely difficult to carry out and have low yields, the products tend to degrade quickly. These costs are dropping fast though: they are much better at scaling up production of antibodies than they were a few years ago. Also, while it might count as NRE, the physical infrastructure needed to produce large quantities of many of these drugs means sinking several hundred million and several years into the manufacturing plant.

  91. Re:TED talk explains how the OSS philosophy applie by pepty · · Score: 1

    See above.

  92. Re:TED talk explains how the OSS philosophy applie by losfromla · · Score: 1

    huh? You stated "costs $14K just to manufacture per patient-year" (italics mine). I take issue with the statement as I don't believe any drug costs that much just to manufacture per year. Care to elaborate on your "See above"? Citations supporting such stupendous manufacturing costs are what I am looking for.

    --
    Only I can judge you.
  93. Re:TED talk explains how the OSS philosophy applie by pepty · · Score: 1

    Here's an article on the AIDS drug I was talking about. My number was from a personal communication.

    http://www.aidshealth.org/archives/news/birth-of-aids-drug-is-10-year-tale

    All along, producing Fuzeon on a commercial scale had been a concern. The cost of producing the drug for Phase I clinical trials was thousands of dollars per gram, said Michael Recny, Trimeris vice president of corporate development. With a prescribed dosage of roughly 80 grams a year, that translated into hundreds of thousands of dollars per patient.To streamline the process, the company recruited three manufacturing experts from what today is GlaxoSmithKline, a giant London-based pharmaceutical company with a U.S. headquarters in Research Triangle Park. Those experts came up with a shortcut. T-20 is a chain of 36 amino acids, and the company had been constructing it by adding a single amino acid at a time. The new team found a way to produce large quantities of three shorter chains, which could then be combined to create a fully-formed T-20. Even so, making the drug requires 106 steps, more than 10 times the norm. About 45 pounds of raw material are needed to produce 1 pound of Fuzeon. The production cost is cited as a driving force behind Fuzeon’s high price. Bolognesi, who remained at Duke in the company’s early years but was recruited to be CEO four years ago, said that because the cost of making Fuzeon is at least 10 times that of existing AIDS drugs, the profit margins on Fuzeon will be “significantly less” than with other AIDS drugs.

  94. Re:TED talk explains how the OSS philosophy applie by pepty · · Score: 1

    http://slashdot.org/comments.pl?sid=4050587&cid=44499733

    http://slashdot.org/comments.pl?sid=4050587&cid=44499185