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Peter Murray Rust (author of this blog post) is a really great man. He's been a tireless advocate for dismantling privelege and setting knowledge free for sever

by Blahah 13y ago

Peter Murray Rust (author of this blog post) is a really great man. He's been a tireless advocate for dismantling privelege and setting knowledge free for several decades. I'm proud to say he's becoming a sort of mentor to me. Last week I spent a couple of days with his research group and saw this software in action - it's really impressive. They can take an ancient paper with very low quality diagrams of complex chemical structures, parse the image into an open markup language and reconstruct the chemical formula and the correct image. Chemical symbols are just one of many plugins for their core software which interprets unstructured, information rich data like raster diagrams. They also have plugins for phylogenetic trees, plots, species names, gene names and reagents. You can develop plugins easily for whatever you want, and they're recruiting open source contributors (see https://solvers.io/projects/QADhJNcCkcKXfiCQ6 https://solvers.io/projects/QADhJNcCkcKXfiCQ6, https://solvers.io/projects/4K3cvLEoHQqhhzBan https://solvers.io/projects/4K3cvLEoHQqhhzBan). As a side effect of how their software works, it can detect tiny suggestive imperfections in images that reveal scientific fraud. I was shown a demo where a trace from a mass spec (like this http://en.wikipedia.org/wiki/File:ObwiedniaPeptydu.gif http://en.wikipedia.org/wiki/File:ObwiedniaPeptydu.gif) was analysed. As well as reading the data from the plot, it revealed a peak that had been covered up with a square - the author had deliberately obscured a peak in their data that was inconvenient. Scientific fraud. It's terrifying that they find this in most chemistry papers they analyse. Peter's group can analyse thousands or hundreds of thousands of papers an hour, automatically detecting errors and fraud and simultaneously making the data, which are facts and therefore not copyrightable, free. This is one of the best things that has happened to science in many years, except that publishers deliberately prevent it. Their work also made me realise it would be possible to continue Aaron Swartz' work on a much bigger scale (http://blahah.net/2014/02/11/knowledge-sets-us-free/ http://blahah.net/2014/02/11/knowledge-sets-us-free/). Academic publishers who are suppressing this are literally the enemies of humanity.

yoha 13y ago
> Academic publishers are literally the enemies of humanity. I would not be so extreme: they used to be a necessary evil before the Internet became mainstream. They are more of a millstone from the past that research still drags with it because changing an institution is hard.
- Blahah 13y ago
  Edited to be more specific - it's only the publishers who are systematically restricting knowledge that are at fault. But no matter where they've come from, what they are doing now is holding humanity back on a massive scale.
- naterator 13y ago
  >They are more of a millstone from the past that research still drags with it because changing an institution is hard. It's not that changing is hard, since it would be easy if that's what everyone wanted. It's that you have many competing forces (perhaps that's what you mean by "hard"). The most important is scientists who made their careers in the current system--the people who publish yearly in Nature, for example. They have tremendous political sway and it is not in their interest to change. They will even admit that it is not an ideal system, but no one likes giving up being King. Edit: I should point out that it is more complicated. Science does need a way to judge which scientists are doing valuable work and which aren't, and currently Impact Factors are one of the main ways this is done now. We don't yet have a great alternative.
  - Blahah 13y ago
    Altmetrics is a growing field - I think in the next couple of years we will have an ecosystem of tools (like impactstory.org, altmetric.com) much better and more rounded than impact factors. I also think impact factors are poisonous in their own right.
  - ProblemFactory 13y ago
    I don't think anyone but the traditional publishers wants to keep traditional publishers. Every scientist I've ever met wants as many people as possible to read (and cite) their work. But the main issue is that the main metric for scientists' performance is number of publications in prestigious journals, and the oldest journals tend to be the most prestigious ones. If a scientist wants to get grant funding or promotions, they have to put up with the copyright terms of the traditional publishers. Any real change to the system has to start from the government agencies and councils handing out grant funding to research groups. As long as they prefer to fund people with Nature papers over SomeOpenAccessJournal papers, only a few scientists are willing to sacrifice their career for the principle of open access.
fidotron 13y ago
The fraud detection aspect is truly intriguing. The motivation for the fraud could well be seeing other people's fraudulent papers and comparing yourself to their impossible data, and making the change in a desperate move for acceptance. Academia as a whole has many diseases, but the emergence of the scientific academic world as a unified hive mind, which thanks to antics like this gets increasingly out of touch with reality, is seriously detrimental to progress.
pbhjpbhj 13y ago
>Peter's group can analyse thousands or hundreds of thousands of papers an hour, automatically detecting errors and fraud and simultaneously making the data, which are facts and therefore not copyrightable, free. // Facts aren't copyrightable but their presentation is. If they're copying the presentation of those facts in to a computer for commercial purposes (free release of the content of those papers is certainly commercial) then in the UK they'd be committing copyright infringement. There is also a possibility of infringing on EU database rights. The OP link says: >"Note that chemical structure diagrams are NOT creative works." Whilst a plot or diagram may appear at first to lack "art" the presentation is formatted and certainly a "sweat of the brow" analysis supports it being copyrighted. You can't scan someone else's molecular diagrams but you could look at them and enter the data yourself. Just like a chart, you can't duplicate the chart except by looking at it and copying the information - the presentation of which has been filtered away. Duplication in a computer produces an exact copy and AFAICT under UK legislation that would be infringing [silly as it is as the end result is the same it just takes more work]. Relying on only duplicating the image transitively in to non-persistent memory might satisfy the requirements not to make a copy. That would be an interesting test-case. How the law has been construed to allow the use of search engines would probably help here. >take an ancient paper // I'm curious what license you'd acquire the papers under that allows their duplication in this manner. Even ancient papers are often controlled by the library they're stored in or by those that performed their digitisation. [FWIW I strongly disprove of this sort of the strength and duration of currently granted copyright]
- Blahah 13y ago
  I agree with all your analysis. In this case the presentation is discarded and, as I see it, only the facts are retained. For example in parsing chemical structure diagrams what is recorded are things like the number of atoms in a section of a molecule, their angles and what kind of bonds exist to neighbouring molecules. These data are then analysed to generate the formula and re-construct a correct diagram. There are no licenses to my knowledge on older papers that allow publishing the analysis (but within the University we have agreements with JSTOR, for example). Looking at public domain stuff is OK. This is part of the issue - that knowledge should be a public good. If you're a lawyer I'm sure Peter would appreciate hearing your opinion.

by Blahah 13y ago

yoha 13y ago

> Academic publishers are literally the enemies of humanity. I would not be so extreme: they used to be a necessary evil before the Internet became mainstream. They are more of a millstone from the past that research still drags with it because changing an institution is hard.

Blahah 13y ago
Edited to be more specific - it's only the publishers who are systematically restricting knowledge that are at fault. But no matter where they've come from, what they are doing now is holding humanity back on a massive scale.
naterator 13y ago
>They are more of a millstone from the past that research still drags with it because changing an institution is hard. It's not that changing is hard, since it would be easy if that's what everyone wanted. It's that you have many competing forces (perhaps that's what you mean by "hard"). The most important is scientists who made their careers in the current system--the people who publish yearly in Nature, for example. They have tremendous political sway and it is not in their interest to change. They will even admit that it is not an ideal system, but no one likes giving up being King. Edit: I should point out that it is more complicated. Science does need a way to judge which scientists are doing valuable work and which aren't, and currently Impact Factors are one of the main ways this is done now. We don't yet have a great alternative.
- Blahah 13y ago
  Altmetrics is a growing field - I think in the next couple of years we will have an ecosystem of tools (like impactstory.org, altmetric.com) much better and more rounded than impact factors. I also think impact factors are poisonous in their own right.
- ProblemFactory 13y ago
  I don't think anyone but the traditional publishers wants to keep traditional publishers. Every scientist I've ever met wants as many people as possible to read (and cite) their work. But the main issue is that the main metric for scientists' performance is number of publications in prestigious journals, and the oldest journals tend to be the most prestigious ones. If a scientist wants to get grant funding or promotions, they have to put up with the copyright terms of the traditional publishers. Any real change to the system has to start from the government agencies and councils handing out grant funding to research groups. As long as they prefer to fund people with Nature papers over SomeOpenAccessJournal papers, only a few scientists are willing to sacrifice their career for the principle of open access.

fidotron 13y ago

The fraud detection aspect is truly intriguing. The motivation for the fraud could well be seeing other people's fraudulent papers and comparing yourself to their impossible data, and making the change in a desperate move for acceptance. Academia as a whole has many diseases, but the emergence of the scientific academic world as a unified hive mind, which thanks to antics like this gets increasingly out of touch with reality, is seriously detrimental to progress.

pbhjpbhj 13y ago

>Peter's group can analyse thousands or hundreds of thousands of papers an hour, automatically detecting errors and fraud and simultaneously making the data, which are facts and therefore not copyrightable, free. // Facts aren't copyrightable but their presentation is. If they're copying the presentation of those facts in to a computer for commercial purposes (free release of the content of those papers is certainly commercial) then in the UK they'd be committing copyright infringement. There is also a possibility of infringing on EU database rights. The OP link says: >"Note that chemical structure diagrams are NOT creative works." Whilst a plot or diagram may appear at first to lack "art" the presentation is formatted and certainly a "sweat of the brow" analysis supports it being copyrighted. You can't scan someone else's molecular diagrams but you could look at them and enter the data yourself. Just like a chart, you can't duplicate the chart except by looking at it and copying the information - the presentation of which has been filtered away. Duplication in a computer produces an exact copy and AFAICT under UK legislation that would be infringing [silly as it is as the end result is the same it just takes more work]. Relying on only duplicating the image transitively in to non-persistent memory might satisfy the requirements not to make a copy. That would be an interesting test-case. How the law has been construed to allow the use of search engines would probably help here. >take an ancient paper // I'm curious what license you'd acquire the papers under that allows their duplication in this manner. Even ancient papers are often controlled by the library they're stored in or by those that performed their digitisation. [FWIW I strongly disprove of this sort of the strength and duration of currently granted copyright]

Blahah 13y ago
I agree with all your analysis. In this case the presentation is discarded and, as I see it, only the facts are retained. For example in parsing chemical structure diagrams what is recorded are things like the number of atoms in a section of a molecule, their angles and what kind of bonds exist to neighbouring molecules. These data are then analysed to generate the formula and re-construct a correct diagram. There are no licenses to my knowledge on older papers that allow publishing the analysis (but within the University we have agreements with JSTOR, for example). Looking at public domain stuff is OK. This is part of the issue - that knowledge should be a public good. If you're a lawyer I'm sure Peter would appreciate hearing your opinion.