Opening up the Black Box of Scientific Research

I've written before about the idea of applying openness/open source ideas to science, but here's an interesting new project that attempts to go much further:

our fundamental goal is to render transparent the black-box of scientific research by affording all individuals an opportunity to both access and participate directly in the scientific research process. To achieve this goal, we are working toward developing an entirely research-based scientific curriculum, and three additional resources (the discussion forum, research microfinance platform, and research log platform) which shall function to dynamically feed information to this curriculum - thereby ensuring the accuracy of the information contained within it, and its ability to maintain par with the course of scientific research.

In addition, each of these resources will also serve to increase the accessibility of the scientific research process for non-researchers by allowing individuals to (1) directly invest in research projects (via the research microfinance platform), (2) pose questions directly to researchers working at the cutting edge of scientific research (via the discussion forum), and (3) observe the progress of ongoing publicly-funded research (via the research log platform).

Not quite sure how this will scale, but anything whose "fundamental goal" is "to render transparent the black-box of scientific research" sounds good to me.

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The Real Hope for Nanotechnology

Nanotechnology is one of those subjects that seem to veer between hope and hype. DNA-based solutions look among the most promising, because of the fact that the material has evolved to solve many of the same problems as nanotechnology; more subtly, it is inherently digital, which makes its manipulation much easier - and promises structures of almost infinite complexity under computer control.

To do that, or course, you need software, so it's great to see that there is already free software that lets you create DNA-based nanostructures:

caDNAno is open-source software based on the Adobe AIR platform for design of three-dimensional DNA origami nanostructures. It was written with the goal of providing a fast and intuitive means to create and modify DNA origami designs. You can learn how to use it, download a copy of the program and some example designs, or even modify the source code.

The software makes heavy use of several fantastic open-source libraries and resources, especially Papervision3D for 3D rendering, Michael Baczynski's AS3 data structures and tutorials, the Tango Desktop Project for icons, and the Blueprint CSS framework for this website. Additional people and resources are acknowledged on the links page.

As you can see from this, there's already quite a rich ecosystem of free code in this area, which augurs well for the future. The last thing we need is for nanotechnology to turn into the smallest black box ever made.

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When Will They Ever Learn?

On Open Enterprise blog.

Put Me Down for X

One of the interesting ideas for replacing the current patent mess is to use a bidding system. People - or, more likely, governments - would pledge a certain amount of money for any company that developed a drug to do "Y", with the result placed in the public domain. Clearly, these sums would be relatively large, but still much less than the current system, which involves pharmaceutical companies taking out patents on drugs that cost hundreds of millions to develop, and then charging thousands of pounds per individual course, and billions cumulatively.

That's not going to happen any day soon in the world of drugs, given the latter's rather inflated ideas of its own worth (just how many copycat drugs for rectifying rich people's excesses do we need?). But it might just work in the world of free software, and Cofundos are giving it a whirl:

1 Somebody misses an open-source software tool or library for a specific purpose, a feature in an open-source software or a plugin for an existing software. He describes the project to develop the software.
2 Requirements-Engineering: Other people help enhancing the description of the project by adding specific requirements and comments.
3 Bidding: Users who also like the project and need the resulting software, bid a certain amount of money, which they will donate to the project performer after its successful completion.
4 Offering: Specialists who are capable to perform the project and to develop the respective software offer to realise the project for a certain amount of money and within a certain timeframe.
5 Call for competitive offers: As soon as the sum of the bid amount exceeds the money requested by the first offer, a call for competitive offers is started and lasts for three week.
6 Accepting an offer: After the three weeks call period for alternative offers is elapsed, all bidders are requested to vote about which offer to choose. Bidders votes are weighted by the amount of their bid. The specialist with the majority of the votes is selected to carry out the project.

Neat. And, even better:

All ideas and contributions on Cofundos are licensed under a Creative Commons Attribution 2.0 License. All project outcomes must be licensed under an OSI approved open-source license.

Also worth noting is that this could never work for closed source, since you cannot, by definition, add arbitrary functionality to such black boxes.

The only thing I'd say is that the sums on offer for new bits of code are currently rather low. This may well be lack of publicity - which is why I've giving some to what sounds like a fascinating attempt to think and do differently.

What's (Open) Source for the Goose...

A report suggesting that the Chinese military has hacked into German government computers could have a negative impact on the prospects in Western markets of Chinese equipment vendors Huawei Technologies Co. Ltd. and ZTE Corp. (Shenzhen: 000063 - message board; Hong Kong: 0763), believes an analyst at Dresdner Kleinwort .

...

"The ability of Huawei and ZTE to participate in, let alone win, telecom infrastructure tenders in the Western hemisphere may have lessened considerably following last week's shock report," writes Lindberg in a research note issued Monday. "It could trigger a return to national security clearance when it comes to procurement of telecom networks," he adds.

OK, so this may be pure paranoia, not least because it's not clear that the alleged Chinese spyware has anything to do with the Chinese telecom equipment.

But there's a more general principle: if it ain't open, you don't know what's going on, so all this kind of stuff could be going on, unbeknownst to you. Of course, it also applies to Chinese procurement as well, which is one reason why I think open source is bound to win out there, as elsewhere.

After all, if you are a (paranoid) government flunky, do you really want to risk national security (and your post) on that black box? No, I thought not. (Via GigaOm.)

Open Science Means Open Source

The need for open access and open data in science seems obvious enough - even enough some persist in denying it. But as science becomes increasingly digital, with ever-greater dependence on computers and software, there is another aspect, as Nature Methods has recognised (but some months back - I've only just caught this):

The minimum level of disclosure that Nature Methods requires depends on how central the software is to the paper. If a software program is the focus of the report, we expect the programming code to be made available. Without the code, the software—and thus the paper—would become a black box of little use to the scientific community. In many papers, however, the software is only an ancillary part of the method, and the focus is on the methodological approach or an insight gained from it.

In these cases, releasing the code may not be a requirement for publication, but such custom-developed software will often be as important for the replication of the procedure as plasmids or mutant cell lines. We therefore insist that software or algorithms be made available to readers in a usable form. The guiding principle is that enough information must be provided so that users can reproduce the procedure and use the method in their own research at reasonable cost—both monetary and in terms of labor.

However, the editorial rightly points out that releasing the code as open source has huge advantages:

Some authors who favor the highest degree of transparency and sharing for their software elect to develop their programs in an open-source environment. By doing so, the authors not only provide accessibility and transparency, they also allow the community to build upon their own developments and make continuous improvements to the tool. Open-source software has become extremely popular in various fields. In microscopy, for example, image analysis software tends to be modular, and users benefit from the flexibility of being able to replace some modules with others in an open-source framework. Despite the tremendous added value of open source, other authors prefer to release a compiled version of their program, so as to protect commercial interests tied to sophisticated custom-designed software. This option is not optimal because it turns the program into a black box, but it may be acceptable if the operations performed by the software are sufficiently clear.

Although it is probably appropriate that Nature Methods, given its focus, should be the first to articulate this issue, it is important to appreciate that its logic applies to all scientific publishing where computers are involved. Without open source, there can be no open science - the only kind that is worthy of the name. (Belatedly via Flags and Lollipops.)

Code is Law, Code is Politics

As Lawrence Lessig famously noted, Code is Law. Which means that Code is Politics, too, since laws are drawn up by politicians. But the intimate relationship between code and politics is becoming manifest in a rather different context (pity about the yellow on black text).

The issue here is about the software used in voting machines. Since, one day, all voting will be carried with such machines (unless we decide to go back to using ostraca), now is the time to consider why free access to the code that runs them is indispensable for political transparency.

It comes down to this: if you are dealing with a black box, you can have absolutely no faith in the results it produces. It might just make them up or - worse - change them subtly, or perhaps be pre-programmed to crash if a particular party gets too many votes, requiring a complete re-run, with knock-on effects on voting patterns.

If you have the source code you can run it and examine what it does with various voting inputs, and check that it has no nefarious sub-routines. However, even this is not enough for full confidence in the voting machine: paper audits are also indispensable for checking on the consistency of the outputs, and allowing for the ultimate fall-back - counting by hand.

Still, this is a clear instance of where, in a literal rather than metaphorical sense, closed source jeopardises the very basis of democracy. Looks like RMS was right.