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Biology Goes Open Source
cford writes "According to Forbes some of the drug company giants are finally realizing that their genetic research is worth more if they give it away. 'Novartis, the Basel, Switzerland, drug giant, has helped uncover which of the 20,000 genes identified by the Human Genome Project are likely to be associated with diabetes. But rather than hoard this information, as drug firms have traditionally done, it is making it available for free on the World Wide Web. "It will take the entire world to interpret these data," says Novartis research head Mark Fishman. "We figure we will benefit more by having a lot of companies look at these data than by holding it secret."'"
Maybe evil corporations are not that evil after all. Nah, can't be.
Great, let's all rush out and patent a vague application related to the gene(s) in question. We'll be rich.
I'll call it our open source money maker.
C'mon, we can do it!
It just seems unlikely that the darkside won't
come up with some 'problem' to squash this
wonderful idea.
You are being MICROattacked, from various angles, in a SOFT manner.
Cured in mice.
p osts
http://www.freerepublic.com/focus/f-news/1754006/
If people are wondering how much computing power we can possibly need..
The answer is we can never have enough. To cure many of our worst diseases we will need to simulate molecular interactions on the nanoscale and determine how to safely fix what goes wrong. That requires an unbelievable amount of computing power.
closed source is so much more secure... what we need is developers, developers, developers, yeah, whoo
Seriously, I think all findings on the human genome project should be open. It took a huge effort and even persons at home let spare cycles run on this project. Our bodies, and what's inside should be open since it's not something 'they' invented, manufactured or engineered. Whatever drugs they're developing could be closed, but generics should definitely be allowed too.
Custom electronics and digital signage for your business: www.evcircuits.com
Any of you 3 Womans on slashdot wanna give away some genetic research?
http://en.wikipedia.org/wiki/Woman
As a research scientist this move doesn't sound too strange.
However keep in mind that they are not providing the world with their raw data.
Rest assured that the milked it for anything that could give a profit, stripped that off and released the rest.
This is how it happens with large scale datasets all the time.
If an experiment works, something has gone wrong.
This is exactly how it should be for all the other nasty diseases we humans suffer from. Cancer, HIV, etc... maybe even the common cold could be brought down some levels with enough folks with access to all the data.
Patents on the medical and biological industry, while potentially good for the companies, are truly terrible for the rest of the world. The last thing we need is more expensive medicine, and having biological trade secrets released will help humanity as a whole.
I've done a little research on AIDS, for example, and to give you an example of what patents do for the cost of medicine, take a look at this quote from the New York Times article, "Look at Brazil."
"Until a year ago, the triple therapy that has made AIDS a manageable disease in wealthy nations was considered realistic only for those who could afford to pay $10,000 to $15,000 a year or lived in societies that could."
In developing countries, the cost of patented medication is the reason why many families cannot afford it and so many suffer from it. Now look at another quote from the same article:
"Brazil now produces some triple therapy for $3,000 a year and expects to do much better, and the price could potentially drop to $700 a year or even less."
Many countries cannot do this for fear of economic sanctions, which means the next logical step would be for companies to open up their medical and biological information, for the good of humanity. Not only will this help potential consumers of this medication, but also provide a base for other companies to build on to excel each other's knowledge.
Open Source Biology is the wave of the future. As Bruce Sterling says, the future is already here, but unequally dsitributed.
Example (kind of Ribopunk) of the great new Human Metabolome Database and how it can be mashed-up:
The Human Metabolome Database is an extremely important new comprehensive searchable online resource. It is a central encyclopedia about chemicals, embedded in us.
See the home page at:
http://www.hmdb.ca/
"The Human Metabolome Database (HMDB) is a freely available electronic
database containing detailed information about small molecule
metabolites found in the human body. It is intended to be used for
applications in metabolomics, clinical chemistry, biomarker discovery
and general education. The database is designed to contain or link
three kinds of data: 1) chemical data, 2) clinical data, and 3)
molecular biology/biochemistry data...."
or the browsable Metabolomics Toolbox at:
http://redpoll.pharmacy.ualberta.ca/hmdb/HMDB/scri pts/browse.cgi?hits=20&browsn=1&pag=1&acco=11
Dark Bands in the Human Spectrum
by
Jonathan Vos Post
1 Feb 2007
What is the human body made of? An odd way to answer this is with the inverse question: What is the human body NOT made of? I can give an answer in the following sense: for what natural numbers (i.e. positive integers) is there no ion or molecule found in significant quantities in a human being, which has that number as the average atomic or molecular weight, rounded down?
Humans have lots of water, and thus lots of hydrogen atoms and hydrogen ions, both of whose molecular weights (1.00783) round down to the integer 1. Heavy water (Deuterium oxide) has already been figured in by our using an average molecular weight, which this considers both protium (hydrogen with no neutron) and deuterium (hydrogen with a neutron, molecular weight averaged down to 2). There is not going to be a measurable amount of radioactive tritium (hydrogen with two neutrons) whose atomic weight rounds down to 3. The human body has essentially no helium (atomic
weight rounded down to 3 for the rare light isotope, rounded down to 4 for the rare light isotope). The human body, assuming this is not a person taking lithium as treatment for depression, has nothing of molecular weight 5, 6, or 7. Beryllium is rare, and a poison. So there is a gap in the average molecular weight mass spectrum of a human which is covered by the integers 2 through 10. There should be no atomic
carbon in a human body, not counting gunshot residue or charcoal from grilling or sketching, hence no 12 or 13. Carbon is in humans, but bound up in organic molecules.
In summary, the integers representing mass gaps in the
human spectrum include: 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 19, 20, 21, 24, 25, 36, 37, 40, 41, 42, 49, 52, 53, 56, 64, 66, 69, 70, 82, 91, 95, 98, 99.
We'll look higher, but these "dark bands" will become rare...
Source of data: the Human Metabolome Data Base
On 1/31/07, Jonathan Post wrote:
Sorted (by hand) by molecular weight
HMDB02106 1.00783 Hydrogen ion
HMDB01362 1.00783 Hydrogen
HMDB02386 11.00930 Boron
HMDB02714 16.03130 Methane
HMDB01039 17.00274 Hydroxide
HMDB00051 17.02655 Ammonia
HMDB02111 18.01060 Water
HMDB00662 18.99840 Fluorine
HMDB00588 22.98980 Sodium
HMDB00547 23.98504 Magnesium
HMDB02084 26.00307 Cyanide
HMDB02175 27.97690 Silicon
HMDB01361 27.99490 Carbon
HMDB01371 28.00610 Nitrogen
HMDB03378 29.99799 Nitric oxide
What this means is they can't figure out how to use the info before the patents expire. The idea that novartis or any other drug company would let loose proprietary info on a gene they thought would lead them to a drug for diabetes is ludicrous.
Wonder if it would be possible for someone to open source their DNA and thus protect themselves from paternity suits? It could certainly provide for an interesting court arguement. It would also be potentially frightening who might show up and demand a download.
But will anyone who uses this information for their own research follow suit? I strongly doubt this single act of gracious openness will inspire any other big pharmco to do the same with whatever findings they come across using this free information.
Q: Why won't they release a cure to the general public?
A: They make to much money off of suppressants.
Only use the cures on the rich "important" people that have a few million to blow.
I suspect that they have 20,000 patents already lined up, one on each of the interesting genes. With this they could enlist others to do the leg work to figure out how to use the gene information, secure in the knowledge that they can use their patents to get a piece of whatever anyone comes up with.
Pharma patents are the worst of an evil bunch.
This sounds like pretty good news. While I see nothing wrong with corporations wanting to make a profit, there are, I think, serious ethical problems with withholding information that could save many lives. And in particular, I think that the information in the human genome is something that belongs to all of humankind. Working together, not only will lives be saved and enhanced, but some serious money will be made as well, sooner rather than later.
To the making of books there is no end, so let's get started
While I applaud the company, the notion that the human genome or any part of it is anyone's to keep, license or give away is appalling.
They're not talking about licensing a portion; they're talking about giving away knowledge regarding which portion likely relates to diabetes.
I don't understand this obsession with the cost of the drugs. It is not like it is obvious how to treat AIDS for example, it definitely takes decades of research and development and it requires funds. If a company or even a person finds something that helps in this fields, I do not see any problems with them being able to charge and arm and a leg for the treatment, after all, if you do not pay the arm and the leg, you will lose both arms, both legs, the torso and the head to the disease. At the end it is irrelevant how the research gets done and how much the drugs cost, what is important is that the research gets done. And this kind of research will not get done without decades of investment effort, which will require probably thousands or tens of thousands or millions of percent of return. It's all good, in a hundred years noone will remember most of the people who died from AIDS but the treatement will be available (at that time at a very low cost, since the patents do expire after all.)
Don't worry, it's not a problem if millions die now, they will die anyway, to have this research done means more than to lose even a billion people to a disease.
Cheers.
You can't handle the truth.
What we really need is more people with AIDS... this would give other companies incentive to start producing the drug, the increased competition would drive prices down.. supply shouldn't be a problem if it can be guaranteed the # of people suffering from AIDS continues to rise in 1st world nations. My suggestion would be to ban condom use as a way to kick-start the market.
This is not really about 'open source', it's about 'Big Pharma' trying to address its problems by leveraging its (diminishing) assets, and trying to access multiple sources of innovation. See the informative article in 'The Economist' - Jan 25th - 'Billion dollar pills' (Economist.com). Since it's a subscription site, here are a few extracts, (fair use): "The industry's share prices have performed pitifully and a new report from Accenture, a consultancy, calculates that a whopping $1 trillion of "enterprise value", which measures future profitability, has been wiped out because investors have lost faith in drugmakers' growth prospects" "Three of the biggest drugs firms have brought in new bosses to help turn things around." "The risks have been compounded by vertical integration" "Mr Kindler [new boss of Pfizer] also wants his secretive researchers to open up and work more closely with outsiders. He has put the company's drugs pipeline on the internet for all to scrutinise and declared his intention to pursue outside collaborations and acquisitions keenly. There's much more, but the underlying truth is that large corporations seem to have to have problems 'institutionalising innovation', and thus end up like Cisco, Microsoft & others - spending fortunes on R&D, but then spending even more on buying ideas in from start-ups or Academe. You can bet that as soon as someone finds a use for this information, 'Big Pharma' will be there with it's chequebook wide open. Is that a bad thing? Well, as another poster noted, perhaps it would be better if so-called 'underdeveloped' countries had the rights to produce & distribute in their local markets. Of course, another wildcard could be the Bill & Melinda et al. foundation. That would be ironic, the 'king' of closed-source using his $ to finance a somewhat 'open-source' model.
The study of biology was already open source. There is a wealth of data at the NCBI and other sources. We are seeing a renaissance in molecular biology right now and I, for one, attribute it to the hard work of thousands of researchers freely sharing their work. It's not just the data either, it's journals and software, too. We have more information than we know how to handle, and it's being created much faster than it will ever be understood. It's gotten to a point where new fields of study are being created just to interpret the collected data and try to make some sense of it. Bioinformatics and computational biology are truly amazing fields, the only trouble is attempting to explain just what it is you do to friends and relatives. Trust me, it's not always easy.
Novartis announced this (funding and sharing) in October, 2004; I guess they now have some results.
This is not the first time this has happened.
A lot of private firms have identified disease susceptibility genes. There is a company in Iceland called 'deCode' - http://www.decode.com/ which has been doing this stuff for many years now, exploiting the fact the iceland has a relatively stable and homogenous genetic population. They have genetic data available for more than 25% of the population of Iceland and they have innumerable papers and free online resources.
Not to mention the federal govt. has been doing this forever now and 'Human Genome Project' and 'Hapmap project' are well known.
How do they know the gene is novel? Just because they can create it in a lab doesn't mean it doesn't already exist in the wild. Even worse, what happens to people who have their patented gene naturally occur? Can they be sued for patent infringement because they have a mutated gene that happens to have been patented by some huge multinational? It's like patenting subatomic particles with the logic that "well, I created it in a bloody particle accelerator, therefore I own the rights to it". That's absurd, it's a fucking subatomic particle! Patenting genes is absurd, it's a fucking gene!
You are quite right when you say that patent may be good for the pharmaceutical companies, but are terrible for the rest of the world.
In India, Novartis is using all its legal muscle to challenge a provision in the Indian patent law that has made it possible for India to develop a strong generic drugs industry. This has made affordable medicines available not only in India, but to other developing countries as well. If Novartis wins the case, this could mean that access to affordable drugs in the third world will be drastically reduced.
There was an article at OneWorld South Asia about the case recently:
So if anyone thinks of Novartis and the other big pharma companies as a bunch of good guys, he should think again.
Christian Engström, Former Member of the European Parliament 2009-2014 for The Pirate Party, Sweden
A little bit of sanity in this world.
Where do I commit my code?
Summation 2
large corporations seem to have to have problems 'institutionalising innovation', and thus end up like Cisco, Microsoft & others - spending fortunes on R&D, but then spending even more on buying ideas in from start-ups or Academe.
As a physician I am often shocked to think about how much pharmaceutical companies charge for medications. Especially considering that my practice is in the "third world", price is the absolute foremost concern for all my patients when it comes to prescribing a medication. They will often insist on an inferior generic product instead of paying three or four times as much for a newer, better drug. I understand that research is expensive.
I also know that a lot of money is spent "visiting" doctors trying to convince us that their product is the "best", organizing "conferences" for us (which are nothing more than sales pitches) with free dinner included, etc. Not to mention all the free pens, calculators, calendars and other promotional materials. Some of my colleagues virtually thrive on this stuff. I for one would rather see cheaper medication. Less price, higher volume is what I think they should be looking at. And if they can't make profit on volume, then they should stop trying to push that product as if it was the new Holy Grail - only the very rich will buy it - period.
A case in point - the vaccine for HPV (cervical cancer's principle cause). It costs over $300 PER DOSE and you need 3 doses. Whoa, that's $1000. With the average monthly salary at around $350 a month here, how many of those do they expect to sell? Even in the US a lot of people would stop and think about this. And how many do they expect me to keep on hand in my fridge at that price, taking into account expiration dates, breakages, etc? Great concept. Completely useless at that price.
Anyway, my $.02 worth. They shouldn't complain about being unprofitable - they've priced themselves out of the market. People will always get sick. They just can't afford to pay for the medication anymore.
Seven puppies were harmed during the making of this post.
Because the people I work with wouldn't have participated in the data generation and analysis if the data wasn't free and open. I believe that the data had to be 'open sourced' within something like 6 weeks of when we agreed that the generation of said data was finished.
If they had the money, the deals we do with companies like Affy, and the expertise to do this on their own, why would they open source it? This is really a story of how powerful some parts of academia are becoming, that we can FORCE research to be open, or not support it (and correspondingly, how dependent biotechs are on our abilities.)
Yes, I was on this project (at the Broad), and participated in the analysis.
Very true. Closed source as you put it, led to the problems of Vioxx (Rofecoxib) and Celebrex (Celecoxib) cover ups with regards to heart attack risk, in the sense that the drug companies were not forthcoming on research which showed negative outcomes and only sold the good news to the FDA (although this is now a prohibited practice). This is not going to happen very often any more, since the payouts from lost lawsuits far outweigh the profits.
Placing the genetic information into the open arena may result in more research on diabetes, but I am fairly sure the move is designed to play into the drug company's hands, since they undoubtedly have withheld other information which may prove to be valuable, or is already the basis of research which the company believes will score them a marketable drug. In a sense, other researchers can do the expensive research while the drug company sits back and incorporates the results of other people's work into its own findings.
Now to speculate a bit more, it may well be that the drug company can't really do any broader research without having this information leaked (ie: they need to provide this data to labs around the world, which means too many people will know and it's too easy to let the cat out of the bag). Therefore it is easier to publish the information and look good at the same time. The only way to avoid leaked information is to run the company's operations from one or two very large research facilities, which probably limits their potential employee base and leads to intellectual incest (a bit like Redmond!).
Maybe drug companies are coming to realize that centralized, monolithic R&D is not the cheapest way to get the work done, and that much of their research can be done more cheaply in smaller, possibly independent outfits whose incentive is to obtain a small royalty for the research they can then sell to the drug companies.
Do it yourself, because no one else will do it yourself. [beta blockade 10-17 Feb]
If I invent something, but keep the details of my invention a secret, then that is certainly not free and not Open Source. But if I patent my invention, the use of the idea is still not free, but the knowledge practically is. Are patents Open Source?
The reason I'm asking this is I wasn't sure from the article if the company was actually giving anything away. It is not clear to me if I invent a new drug based off the information they provided, do I now owe them a royalty?
Open Source by patent (or copyright) is a great idea if you think you can make more money off licenses to others than by your own efforts. Secrecy is better if you think that your information is based on special insight and others will not be able to duplicate it independently for several decades. What they gave away (assuming they gave anything away) may not have much intrinsic value if it is easily duplicated by others.
For a change!
... I would immediately order the full and complete release of any and all "IP" pertaining to human genome into the public domain. On the threat of capital punishment for failure to comply.
Haha, that supposes it hasn't already happened. I suspect they are picking some random genes, saying 'these are the ones you guys should focus on,' while in secret they have already analyzed them and deteremined they are useless. That way, the competition spins it's wheels while they investigate other, more promising, genes.
--
WHO ATE MY BREAKFAST PANTS?
The major drug companies have indeed hit something of a wall - the low-hanging fruit has been picked, and new advances are much more hard-won at this point. If I may use economic language: the drug industry was enjoying a much less steep marginal investment-risk curve - each million invested was much more likely to produce some profit above the million invested. Now development of each promising novel drug entity is like a new space program - and the risks are just about as high (up to including people's lives). So, to ask that a new drug, fresh from the labs and monsterous investment in testing should be sold for 50 cents a pill, is simply illogical - that is almost like asking that the space shuttle program be cancelled because the flights are too expensive and you personally cannot afford a ticket.
So, after benefitting from this huge global effort called the Human Genome Project, they decide to give away a fraction of their spoils. Are we supposed to give them a standing ovation? Jump for joy?
That's like all of us contributing articles and money to Wikipedia, and then Wikipedia says, "Hey, here are some articles that you can read for free --we won't charge you any money."
<sarcasm>Thanks a lot, Novartis, for your huge contribution! I will express my gratitude by blinking my eyes. Once. (Just the left eye; the right eye blink is in honour of SCO not coming with a new press conference today.) </sarcasm>
404555974007725459910684486621289147856453481154 in hex is "You sank my Battleship?"
[GPG key in journal]
I applaud this and other companies who are releasing more and more of their data. However, lets not get too carried away with glorifying the biotech community for what appears to have been done here. The data release by Novartis and Broad is unusual in that there are few if any restrictions on the use of the data. But most of the other data I have seen from companies is released with so many restrictions on its use that it becomes almost worse to have seen it than not.
If the human body was meant to be open we would have evolved zips.
And on the other spectrum, Celera is using publicly available data from HGP while not allowing HGP to use their data freely.
In my daily paper it says this research was done by an international team that was co-led by Dr. Constantin Polychronakos of Montreal's McGill university. Maybe it is "open biology" because it was done by university scientists whose mission is doing public research, and not because Novartis suddenly got all philanthropic?
The tyrant will always find a pretext for his tyranny - Aesop
Nothing in TFA or from the Novartis or broad.mit.edu sites indicates that there is any licencing of the content they are making available. AFAICS they are giving it away free of charge and without restriction. This is public domain not open source isn't it?
Also they are giving away the results of the research (e.g. data) - open source is not normally a term used in such circumstances. The Creative Commons licences (among others) were created because typical open source/free (as in speech) licencing models do not suit data.
Now whilst I applaud them for not keeping this research under wraps I think it's wrong to call it "open source." Having said that I feel that perhaps some kind of condition _should_ have been attached to the research data. If only to stop someone analysing it and then keeping their analysis secret.
"Open source" is kind of "open technology". It has to do with some new _invention_
Giving up raw data is not "open technology". It is "open data". Does not involve new _invention_, just digging the facts.
I do not believe in karma. "Funny"=-6. Do good and forbid evil. Yours, Oft-Offtopic Flamebaiting Troll.