Slashdot Mirror
Profit vs. Science
graxrmelg writes: " The Washington Post reports that Science magazine has made a special agreement with Celera Genomics to allow publication of an article about its research without the requirement that the raw data be made publicly available (through an NIH database), as is done with all other articles. (Celera's patent-happiness has been discussed earlier on Slashdot.)
Science has put out a statement on the matter."
Well, since I'm the first, lets speak out the obvious:
I think that it is shame that a magazine of the scientific standing like Science and Nature take a stand in such debated terrain as patents on genomes.
As authorothies in science-land they should at least keep up the *appearance* of impartiality.
While I'm a big fan of free software and Open Source, in the grand scheme of things it probably isn't going to change the world.
It's in science that we really need the sort of freedom that RMS advocates. Imagine how much closer we would be to a cure for cancer or AIDS if researchers were forced to co-operate rather than hide discoveries from each other in order to protect the massive profits the drug company that comes up with such acure would no doubt make.
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enterfornone - logging in for a change
All natural sciences rely on the fair peer review process and the repeatability of the experiments. This is the credo, the consitution, of the scientific community. If data is allowed to be held back or the referees in future will have to comply with "you don't need to know that because it's a trade secret" kind of crap from companies, it's the science as whole that will suffer.
Peer review is an essential part of all science researches. Period.
If Celera is not providing the whole pictures how do the readers/other researchers know the values of their works? Their "publications" could be misleading either by accidents or intentional bias in their raw data. Without full peer reviews, there is no way to tell. This is completely against the spirit of science.
Science mag needs to be careful that Celera is not just publishing FUD to enhance their stock values. On the other hand, maybe, just maybe, some of the information they are going to publish could be usefull for some other real scientists.
This is what happens when science is being treated like the plague by many, especially the sport-crazied Americans (sorry guys). Be the sport guy/gal not the science nerd. More fundings are needed for science in schools and universities, where the open exchange of ideas is the main goal, not making money.
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Codeala - Just another mindless drone
According to the statement, the raw data is available and can be viewed in full by researchers. However there are restrictions on what you can do with the data. So you can view the data to verify their research, but you can't use it as a basis of your own research.
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enterfornone - logging in for a change
It states that the database WILL be made available to the general public. There will be the restriction that commercial access needs to sign a MTA, but the general public (not for profit) can search, download, etc, the database.
Wow, talk about a completely misleading article header slashdot!
Please read the article before posting. Comments on /. (and article descriptions) are quickly approaching the level of zdnet articles
The sequence (raw data) can be downloaded. Researchers are free to use the data, and publish papers based on the raw data. Commercial users must license the data for commercial use.
Yes, it would be good if the data were in the public domain. However, it is available to researchers, and nature has agreed to keep a copy of the data in escrow because of the particular situation
Before you decide to start typing up an uber-comment which is factless and basically a first post in disguise, please read the article.
pilot
If individuals can grab a megabase at a time, how long before the whole thing shows up on FreeNet? Dead Sea scrolls, anyone?
Okay the data is publicly available (with some restrictions) for peer review and further research. So Science (the mag) is not a (complete?) sold-out.
However I stand by my point that more money are needed for science in schools and universities. Where, hopefully, the free (beer and freedom) and open exchanges of idea are real and with no string attached in anyway.
BTW, I am sorry for the rush comment. (But hey this is slashdot ;-)
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Codeala - Just another mindless drone
Please don't try to post the whole sequence to Slashdot...
Correct but misleading. Public access and search are allowed for academic users, but downloads are limited to one megabase.
More precisely, researchers have unlimited search access but are only allowed to download one million base pairs of data.
An article that contains nothing but results with the disclaimer "if you want the data, you can buy it" is nothing more than an advertisement for the company selling the data
Firstly, as several other posters have pointed out, this isn't the case. If you want to make commercial use of the data Celera have invested vast sums of money in, you can pay them. For research, it's all available. You're even granted permission to make your own publications, to which Celera have no rights.
But then, this is a magazine article. If this was a legitimate scientific journal, how exactly could the peer review process occur when the data is kept secret?
I don't suppose you've ever heard of the term Impact Factor. It's a measure of how widely read and influential a journal is. Science is as legitmate as any other Journal, it conducts reviews of articles and has an impact factor, from my latest available numbers of just over 24. Nature has about 28. A typical specialist journal such as Applied Optics is lucky if it has a factor much over 1.
What this means is that you can't deride this as the work of some glossy magazine, nor as another result of a global conspiracy by megacorporations. This is decision by one of the most influential journals to develop new ways of dealing with intellectual property so that the results of research can be published and knowledge advanced.
This data just consists of a long string of quaternary digits (is this the right term for base four?). It doesn't actually mean anything by itself, except we know that the end result of this string being processed by an egg cell is a human.
What will be more important is the decoding of this DNA, to work out exactly which bit does what and how all the digits interact. At the moment it's looking a bit like trying to learn to code from a binary dump of a kernel, or to speak egyptian from the heiroglyphics in the great pyramid. What wil be important and must not be patented/trade secreted is the results and methods of decoding DNA, which is going to require some serious mathematical and computer effort, hopefully leading to new insights into information theory. (can you imagine how compressed all the information involved in the formation of a human body is to fit into only 3 billion or so bases?)
The real problem involved in keeping this data secret is if the methods by which they got it are also secret, which means that other people can't reproduce the data.
It's not giving free access to academics, not in the open source meaning of "free" anyway.
If you want less than 1 Mb (that is, less than 0.03%) of the data, you agree to a clickwrap license on the Celera web site.
If you want all the data (about 3000 Mb), you and your institution cosign a formal license with Celera.
What does this license say, you may wonder? Well, so do we. Turns out, the details are still being worked out. But the gist is this: you can use the data for anything you want, so long as it is for noncommercial purposes. You can publish your results freely, with no reachthru rights being asserted by Celera. And you agree not to redistribute the data.
Oops. Look at that again. Ever see a scientific paper where you a) published your results and b) didn't "redistribute" (i.e show!) the primary data? Can someone define the bounds between publication and redistribution? I can't. Neither can Science, as of yesterday.
Science and Celera has not yet defined the bounds between trivial redistributions that Celera doesn't sue you for ("Figure 1 shows a BLAST alignment to my gene in the Celera database"), and real redistributions that they do ("Table 1 in the Web Supplement gives the positions of every DNA hexamer in the Celera database. Please don't use it to reconstruct the original data.") But I'll bet you that pretty much every large scale bioinformatics/computational biology analysis of the Celera data would be counted as a "redistribution"... potentially blocking the main use of the genome, which is for large-scale genomic analysis. And if the bounds aren't defined by the agreement, the bounds will be defined on a case-by-case basis by negotiation with Celera lawyers. Yes, I'm looking forward to that, I'll definitely get a lot of human genome research done.
It's a horrible precedent. Part of the reason for the success of bioinformatics has been the public availability of the international DNA databases. Science and Celera now threaten to set a precedent that could change that.
ob. disclaimer: I'm a coauthor on the competing Human Genome Project paper, and also a Celera stockholder. I'm conflicted both ways. I'm either going to be able to do human genome research freely, or I'll be rich. And I'd rather do research.
Here's why "open source AIDS research" won't work: it's not easy to learn how to to cure diseases, "debugging" requires that you already have AIDS and you're willing to sacrifice your last two or three years to help others find a cure, and biotech equipment is incredibly expensive. If you're going to do this kind of work, it's really a full time job. Even if you already have the schooling, each project is so different (curing AIDS vs. curing cancer) that it will still take you a while to get good at what you're working on. Finally, there's no way to make a profit off of open sourced medicine. You can't sell "support," your product isn't unique (because all your collaborators will be making exactly the same thing, they won't be customizing distros or any nonsense like that), and if your product ever loses commercial viability, it'll probably be after your 17 year patent expires.
Open Source is nice, but it can't be applied to anything. The fields in which Open Source will work will probably discover it on their own.
"The question of whether a computer can think is no more interesting than that of whether a submarine can swim" -EWD
As was clear from the Science statement,
Science clearly felt that it was more beneficial to the research community to have the information available to advance work in the field than to adhere to some artificial standard of economic "purity".
This Slashdot article is at best woefully inaccurate and at worst yellow journalism; it's hard to escape the suspicion that these kind of articles are purposefully intended to stimulate high volumes of indignant postings, thus boosting site ad revenue.
Wouldn't it be ironic if the motivation behind this article is the same old-fashioned capitalistic drive for which Celera is so roundly criticized?
Up to one what? And these people are scientists...
To publish a paper and not deposit your DNA data in Genbank, EMBL, or DDBJ is literally unethical; it is not consistent with accepted professional standards of behavior.
Apologists for this deal argue that little concerns like "ethics" should be subservient to bigger concerns like "expediency". Where have I heard that argument before throughout history?
Yes, this is all going to make a great example for that required course we teach in research ethics. We'll be able to shorten the course a lot now. The lesson, kids, is that if you're big enough, the rules don't apply to you. Science is no different than real life. Anyone surprised?
This tension between academic and commercial R&D is not new; any scientist doing work for a corporation is going to run into the issue that his work is owned be an organization with a profit motive, and that he does not have the right to freely publish his work.
Even the concept of free publication by academics is disapearing - universities now want to review all publications for potential patentability - some schools now garner very considerable income from licensing ideas developed as part of academic research.
Patents were developed to encourage publishing - they allow disclosure and at the same time protect the commercial rights of the publisher. However patents are not scientific literature.
What Science is doing is very interesting - they are recognizing that the value of publication of some works outweighs the issues of mere procedural restrictions on the location of a database. How this will work out is very interesting, not only because of its impact on this particular field, but also for the whole corporate-academic dynamic.
If you read the article, I'm finding that Science acted pretty well on that manner. The sequences are available. If you need to download more than 1 megabase at the same time, you're doing some uncommon research there.
The limits put there are a bit unfortunate, but still reasonable. You can still search, you can verify all the data that came from their papers, you can replicate the experiments. You might have problems designing new experiments from it if you need a very large sequence (which would be unusual in most cases), but then you can try to get an agreement with them.
And what Science did a good thing, because Celera didn't have it available before, and they can check the integrity of the database if there is any doubt about that. It's probably one of the best compromise available for everyone in that situation, IMHO.
Celera owes it's data to the world as they only finished a process that was started by public research funding.
These big companies would all be nowhere if the public sector protected it's research to the degree that the private companies do.
I don't know the specifics of who runs Celera but I'm suspicious that many of their top scientists did research in the public sector for years and then went private when they got close to a breakthrough.
There's too much of a mix of public research and private patents these days.
I've hit Karma 50 and gotten a Score:5, Troll... I win!
Nobody's bothered terribly about whether research is privately or publicly funded. (Hell, my research is funded by everything from your taxpayer money, to Howard Hughes' will, to Sun Microsystems.. and even, gasp, by Celera itself!)
The point is that publishing a scientific paper entails certain ethical responsibilities, among which is the free and open disclosure of your data to other scientists, so they can effectively build on your work. The community standard for *both* privately and publicly funded DNA sequence data is that *when it is published*, it goes to Genbank, EMBL, or DDBJ.
Companies that feel that disclosure will negatively impact their business model should not submit papers on their work, that's all. They should not seek the rewards of publication without meeting their responsibilities to the community of scientists that read their paper. Otherwise, their paper is an advertisement, not something that moves the field ahead. Other genomics companies seem to have no problem with this -- Incyte and HGSI, for example, don't try to muddy the waters by submitting papers on their proprietary genome databases.
Lots of the apologists for Celera say "shouldn't they be allowed to make money?" Sure they should. More power to them, my stock will go up, I'll be happy. But they can't have their cake and eat it too -- they shouldn't be able to get away with writing scientific papers about a proprietary database. It's not ethical.
The whole concept of Intellectual Property "rights" being held on a database of the Human Genome very much disturbs me. Last I checked, it was supposed to be impossible to obtain copyright or a patent on something that is *fact*, correct? Now, last I checked, the Human Genome was a *fact*. Celera didn't invent the Human Genome, *God* did. If there are any intellectual property rights to be upheld, they belong to God. At the very least claiming ownership of it is heretical.
I fully acknowledge that there was a significant amount of work required to actually sequence this fact, and there should be commercial reward. But it seems that there exists no system as of now to do this. What options are there that don't assert ownership of the facts of the Genome?
This country is simply property-happy, especially when something isn't ownable in the first place.
GStreamer - The only way to stream!
From the article:
And although much of the data will be freely available and researchers can even seek patents on what they find there, there will be limits on the amount of genetic data that can be downloaded by individual researchers and requirements that researchers under some circumstances sign agreements that limit their ability to redistribute or commercialize the data.
That sounds a lot more restrictive than you make it out to be, worse in fact, it sounds intentionally vague to leave room for tightening restrictions. There are "limits," "requirements," under "some circumstances," which does not sound like any non-commercial use is legal. Maybe you should read the article.
Why has a social darwinist post been moderated as 'interesting'? That viewpoint has been, and can be, debunked as irrational, and only serves as an attempt to legitimate inaction in making the distribution of resources more fair. I dare anyone to rationally explain here how something determined by the oh-so-rational and scientific, the 'Invisible Hand', can possibly be said to be a fair way of determining who is and who isn't 'fit enough' on this planet. That is, that because 1/10 of the world's population has around 9/10 of the world's resources, the 10 percent who control such a portion of the world's resources are the only ones who deserve to have access to modern medicine,. And the unnervingly high percentage of people born in the poor areas of the earth arn't 'fit' enough. You can't demonstrate that with logic, as the logical extension of that is that there is a connection between where someone is born and how 'fit' they are. Perhaps there are über-nano rays that eminate from the earth and de-fit people in certain areas. Or aliens have come down. Though there are a number of reasons you could give for this being true, there are no reasons you can state that would hold up to any critical observation. Besides, you're posting as an AC, so you don't feel you can justify what you're saying, anyway.
Devil's advocate? I'm pretty sure that viewpoint was presented to point out the stupidity of making scientific information available only to the highest bidder, and the threat it poses to the integrity of the scientific community. I'm also pretty sure that's what the moderator saw in the post.
Bugrit! Millenium hand and shrimp!
Just to nitpick:
Nature's impact factor is 29.491. Please don't confuse it with those, ahem, "lesser" journals like the New England Journal of Medicine.
Who are you replying to? I'm always astounded by the lack of rationale that goes into some ines of thinking. At no point did the argument even border on social selection. Merely stating that research is expensive and that people need to recoup costs is not racist or bigoted. The "expensive medicine" debate is fair, but hasn't been touchd on here. Coverall arguments are unintelligent and don't help anyone progress. Medical and biotech gear isn't going to get less expensive, because modst of it is based on open knowledge, like PCR. Can you find a cheap way to build a temperature-controlled centrifuge which is capable of balancing the current volume of genetic material used? Are you aware that that's in the picolitres? This isn't a text file, it's heavy, precise, industrial equipment. That's one of the most ubiquitous pieces of lab gear. There will in the future be a bunch of patent-based creations, like gene chips. Now, these will be based on patented genes, but don't have to be. It will mean you can take a dro pof blood and within minutes tell if you have any one of jundreds of genes. This is finally the kind of gear which will brig genetics to the world of mass production. Then, we will be talking about too-expensive solutions, but come back then. Right now, it's incredibly expensive and takes highly talented people. Not everyone wants to be a plumber, and Einstein was no biologist. I'd like to see him paying for most of that gear with a plumber's wage. Let's not forget, he mostly did math. That's a brain-and-paper deal - nowadays a computer one. Things have changed. While I could see the idea of corporations donating to individuals as an option, I'd like to see more than a few hundred people benefiting from this. So they'd form cooperatives to work on the stuff with government funding, and get jobs like say, teaching, ro make ends meet. Sounds alot like a university, doesn't it?
toeslikefingers.com - because
Academic researchers are required to publish and get grants to keep their jobs. Publication makes whatever work they're doing know to people doing similar work. Patents allow them to publish their work without fear of some big company reading the article and throwing 100 flunkies at the project to go the last yard to a product.
Commercial researchers (eg drug companies) are required to demonstrate safety and efficacy to the FDA before selling a medical product. Other researchers won't buy their research products unless those products have been proven effective and accurate. Either of these tests require publication in believable, peer-reviewed journals that insist on releasing methodology so that other people can reproduce the experiments.
The business of science comes down to a choice between trade secrets, which prevent anyone outside the company from knowing anything about a process, and patents, which allow everyone to know what's going on and build upon that progress. Either method is aimed at protecting the investment _someone_ has made: one is cooperative, one is not.
It is a longstanding tradition in science, and a requirement of major scientific journals, that researchers make their raw data available to other scientists when they publish...
Mr_Dyqik wrote:
If the data can't be checked by an independent researcher then it's not science. Noone can tell if they've actually done this research or not, unless the data is available and able to be checked.
Both these statements seem to be either oversimplifications or to betray a lack of knowledge about how scientific publishing works. The article's statement is not true. For instance, I've published various papers in the field of experimental nuclear physics. We never, ever made our raw data publicly available for downloading, and this was never an issue with the journals. First off, a typical experiment generated about twenty 8-mm tapes worth of raw data. I'd like to see the internet connection that would make that practical to download. Furthermore, someone who hadn't been involved in the actual experiment probably wouldn't have been able to interpret the data correctly without a lot of help.
Of course if someone wanted to work with the data, they could get in touch with us about forming a collaboration.
It's simply not true that you can't check results without access to the raw data. Do you have access to Galileo's notebooks? No, but you can check whether what he did was correct.
There is a fuzzy area in between completely raw data and well-cooked data. What you normally see in a published paper is the highly cooked stuff. Where to set the boundary between raw and cooked is a matter of opinion, and this would normally be handled by the peer-reviewing process.
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The newspaper article, however, makes it clear that what's really happening is Celera is going to require a EULA that prohibits any commercial use whatsoever. This is bad. Very very bad.
In the past, it was assumed that you could either keep your scientific data to yourself, or you could publish some or all of it, and there was no third option. If you wanted prestige (and tenure) and wanted to contribute to society, you published. If you didn't publish, you got none of the benefits. If Celera is publishing their cooked data but subjecting their raw data to a EULA, that blurs the line between what is science and what isn't. EULA'd information is arguably even less free than secret information. At least if I obtain secret information about my neighbor's marital problems, he can't sue me for a license violation! If this goes on, pretty soon scientists will need lawyers to tell them which parts of the scientific literature they can use without legal problems.
No no no no no !!!!
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Most that can afford it, inherited it from their parents.
Nothing Darwin about that.