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Scientists No Longer Sharing Information?
chill writes: "A little while back there was an item here on Slashdot about the debate over public funded research and whether or not it should be required to be "open". Well, here is some ammunition to one side of the debate. It seem there is an article in the Chicago Tribune about the increasing unwillingness of genetic researchers to share supporting information with colleagues. The study is from the Journal of the American Medical Association for those who want more than the second-hand summary of the Trib."
I know the humane genome project has been plagued by this since the start. The various companies working on it are very hesitant to release information to their competitors, as pharmeceutical companies could make literally billions of $$ with some of the discoveries that have been made.
This lack of sharing for sure has been detrimental to the progress of this research, but without the motivation of potential proft, I'm sure there would be even fewer people working on it. Let's face it, it would be great if everyone worked on things like this "to make the world a better place," but most of the financial backers are doing it "to make a crap load of money."
The future isn't what it used to be.
Not really. Independent validation is a wonderful thing, after all. It would only be wasteful if the duplication was for something widely accepted or clearly established. When it's cutting edge experimental work, the more the merrier. Not so useful for theoretical work, but genetics is a pretty applied field. If it's something important enough to keep secret, it's probably important enough to have duplication to ensure that the experimentation was correct.
One of the original goals of science was the pursuit for the truth, and to these ends scientists shared information freely, with the belief that no matter who made the breakthrough discovery, everyone could and would benefit... it was THE ultimate open source as so many people have pointed out.
Now with all the rampant patenting and profiteering going on, it's no longer about knowledge for the good of humanity but cold hard profits. Even scientists who normally share information may feel pressured to patent or keep secret their discoveries, if only to prevent someone else from depriving them of it.
Thankfully, most scientists in the fields of "pure science" haven't really been affected by this. But scientists working in fields in which profits can be made (biotech, computer science...etc) will likely find their research threatened.
-- Your local friendly mad scientist-in-training
What we have here is a a type of market failure. This does not mean that free markets have failed, but rather that the present market equillibrium is at a situation that is less than optimal for society, a situation that John Maynard Keynes addressed in his General Theory of Economics".
Keep in mind that classical economics assumes perfect information flow for its theories to hold. A situation like this, where academic career concerns and complexity of data interferes with the free flow of information is a clear situation for the government to step in and free up the market, as it is trying to do with the Microsoft monopoly.
Some sort of federally-funded central information clearing-house, where research information could be purchased by the government and put into a freely-accessible database, would be a good first step.
I'm running a database of histopathology images derived from experimental manipulation of the mouse genome at Cambridge University and it's funded by the EU.
We are publishing all our images and data freely and people seem to be happily using our data, but while we encourage them to share their images, we made the experience that it just doesn't happen. Hardly anyone seems to want to give anything back to the community!
It's quite sad, because the more people would share their information, the more useful the database would be for everyone...
We'll probably have to hire some people now to scan and upload some images.
MG
Einstein effect:
1) Gauss, Lobachevsky, Bolyai simultaneously discovered non-Euclidean geometry.
2) Abel, Jacobi simultaneously discovered elliptical integreal.
3) Vallee Poussin, Hadamard simultaneously proved prime number theorem.
4) Erdos, Selberg simultaneously find an elementary proof of prime number theorem.
And most famous of them all: Newton and Leibniz discovered calculus at the same time.
No, 80% SAID that it was either too much effort, they were protecting the ability of a junior member to publish, or their own right to further publishing.
Since when has the scientific community assumed that once you publish on a topic you have a further right to publish more? Since when is not sharing science helping anyone else publish? Furthermore, just publishing your methods does not prohibit future PhD students from using them. What it does allow is future PhD students that are unaffiliated with you to check and perhaps contradict your results.
And since scientists are apparently withholding information that relates to their research, why assume that they are perfectly honest with reguards to disclosing their reasons? Perhaps the summary really should say that 80% say it would take too much work--above and beyond the patent application.
... given the fact that molecular biology is becoming capital intensive (look at the multi-million dollar synchrotrons, protein-chips, sequencers, etc) the public system just cannot fund everyone. The acceptance of private funding means constraints as companies are not in the charity business. If you look at the impact of the medical system, you'd notice similar structural shifts as GPs are merged into medical centres clustered around MRI/X-ray/capital machines. A similar activity is happening in academia with greater infrastructure forcing consolidation into smaller clusters (e.g. take a look at the San Diego biotech cluster). The explanation is simple, better equipment equals higher throughput and thus productivity. Given that bioscience is basically a search through a multi-dimensional space of all combinations of proteins, you can see why the group that covers more area has a greater probably of discovering something interesting.
... even industry recognise that they cannot delay publications more than a certain amount (6-9 months??). Hence the excuse that they are preserving the publication track record of their apprentices is a bit of a cop-out. Basically they are saying yes but wait x months for some underling to publish. The problem comes in the rush to produce results, people ignore the fact that they have to be *reproduceable* results (otherwise by definition is it not science). There have been stories of groups losing original material so the only claim to fame is by squinting at a graph and hoping that the parameters they choose for their analytical process (trust me ... any mathematical analysis has zillions of twiddle factors) are not a fluke.
On the other hand, public science has the implicit assumption of peer-review
So either we go back to the slow but certain government funded research or accept that private incentives will create only temporary information asymmetry. The private market for knowledge is rather unformed at the moment as there are no clear guidelines as to what are acceptable practicese.
LL
Why is reproducibility important? Let's say group A reports some really neat genetics in mice. Group B doesn't have much interest in reproducing it in mice (little potential for scientific rewards) but tries the same thing in primates and it doesn't work. Without being able to reproduce the work of group A, group B doesn't know whether there is a genuine difference in primates, whether there is something wrong with their procedure, or whether group A just published an incorrect or fraudulent result.
Peer reviewers for reputable journals should insist on reproducibility, which should include a binding offer by the authors to make available all necessary materials to other scientists to reproduce the results and build on them. If anything else were to get published, it should at least be marked in big, red letters as "irreproducible" and should not count much towards someone's scientific publication record--after all, it might all be invented.
This is a place where research scientists could really use some good old fashioned technological and social help from programmers. Consider a typical computer-administered psychological experiment's process:
- Write code to run the experiment and log the data. If you didn't document the code or write self-documenting code, you'll have trouble when someone wants the data later.
- Run the experiment and collect those log files. If the log file format isn't self-documenting, you'll have trouble when someone wants the data later.
- Get all the log files transformed into a format that can be usefully imported into statistical software. If you didn't document all the variables and values in the resulting stat file, you'll have trouble when someone wants the data later. And most statistical packages allow you 8 characters for variable names and make detail labelling of variables and values highly tedious.
- Analyze the data and produce some output. If you didn't save the analysis details (as is all too easy to forget if you're doing stats with a dialog-box-based program), you'll
... (well you know the rest).
- Write a paper describing what you did and submit it to a journal. Have it accepted (hopefully) in 4-6 months. Have it appear about 6 months later. It is now probably 18-24 months since you started the study. If you're lucky, you've probably changed computers at least once by now, and possibly offices/buildings/universities, too. If you can find the data yourself and understand what it means, you're ahead of the game.
This is not too far from the problem of managing a source code project over time and across maintainers. It's not enough for professional scientists to have standards for retention and sharing of data -- we need a tutorial in documentation (and statistical and other software packages that better support it.)I think you'll find that very little has changed lately. Scientists have always been very careful about what information they share with others, for fear of giving an advantage to competitors.
If a project is in the early stages, you don't talk about it at all.
If a project has produced some great results, and it is well in progress, you'll talk about it, but might be a bit hazy on the details. For example, take a geneticist who is hunting for genes contributing to a certain disease. He/she has it partially narrowed down, and is showing a map of the BACs and YACs in the candidate region. Try asking them what chromosome they are looking at. They won't tell you.
If a project is near complete, and is being written up or has already been submitted to a journal, you'll be very open. The odds of being "scooped" at this point are minimal.
These rules vary somewhat depending on whether we're talking about a resource-rich lab that works on projects almost no one else can do, or a small lab doing projects that can be rapidly repeated somewhere else. But in general I think they hold true, and have for many years.
There seems to be a fair number of people actually employed in these fields responding to this article, so this seems like a good place to ask this question.
It appears to me that we're pretty far along when it comes to the biology of sickness-by-infection, where an illness is caused by being attacked by other organisms. There's a long way to go, but it seems to an outsider that most of the fundimental processes are understood, and the lion's share of what remains is of the nature of "find germ, study germ, develop treatment that kills germ without killing host"
But it also seems that we're not very far along when it comes to understanding sickness-though-internal-breakdown, where actual body processes either fail to function or function abnormally.
It strikes me that understanding how human genetics really work is the key to all survival. If we knew how every gene and every internal process functioned, then we cound re-engineer our own genome to fix problems. Eliminate cancer, eliminate AGING, and so forth.
It would thus suggest to me that working on deciphering the human genome is the most important problem in human biology in history, and perhaps even the most important problem EVER.
We should have huge amounts of public money poured into this problem, with all results made public, and all information shared.
Would you agree? Have I made any erronious assumptions?
DG
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