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Comment Re:Easy to explain (Score 4, Interesting) 418

why is key academic software not open source?

Because people do the minimum required to get publications (and/or money), and cleaning up source code (so it can be exposed to the world) is a lot of work. This is especially the case if the code depends on other libraries with various different software licenses.

One of the ways to help fix this problem is to place restrictions on publication, so that open source licences are required for software. F1000 Research has just changed their policy to do this:

We recently strengthened our stance on software availability to better align with our Open Science principles. Now, the source code underlying any newly presented software must be made publicly available and assigned an open license. We strongly encourage the use of an OSS approved licence, but will accept other open licenses including Creative Commons. Software papers describing non-open software, code and/or web tools will be rejected.

The current situation demonstrates that forcing these licenses is required in order to get people to use them. BMC Evolutionary Biology already had a recommendation for open source licenses in its policy:

BMC Evolutionary Biology recommends , but does not require, that the source code of the software should be made available under a suitable open-source license that will entitle other researchers to further develop and extend the software if they wish to do so. Typically, an archive of the source code of the current version of the software should be included with the submitted manuscript as a supplementary file. Since it is likely that the software will continue to be developed following publication, the manuscript should also include a link to the home page for the software project. For open source projects, we recommend that authors host their project with a recognized open-source repository such as or

Comment Re:The next question (Score 1) 120

That's about a kiloton of coal every four months to just replace the current carbon that's being lost. To actually make a dent in the planet's carbon supply, it would be necessary to add more than that. Good luck finding the fuel to transport that, and the people who would be happy to see so much carbon leave Earth.

Comment Re:Science Requires Effort (Score 1) 246

What, exactly, is useful about memorizing facts, in a world where any fact you want is at your fingertips on demand?

When you're talking to someone in a professional setting, saying "hang on, I'll just check up on that" multiple times is a very good way to encourage them to leave and not participate in an exchange of goods or services.

When I go to fast food restaurants, I would like cashiers to be able to instantly tell me the answer to allergy questions (e.g. are your chips fried in peanut oil).

If I'm presenting to biologists about a differential expression analysis on samples they've been working on, I need to be able to tell them what a particular statistic means so that they can better understand the results.

Comment Re:For a moment, I was excited (Score 1) 17

I've mentioned this before, but I might as well say it again. Our nervous system is designed to learn how to control random systems, so putting a "specialised processor" in between the nervous system and a control system is probably not going to improve things, and may make them worse. Just provide the most basic interface possible to the control system via the nervous system, and let the brain (or any other limb) do the training.

Comment Re:application of "whole proteome tiling microarra (Score 2) 111

They have a mixture of a very large (2 million) number of probes to match DNA/RNA sequences of all known viruses which infect vertebrates. They use these to amplify viral sequences and then use normal high throughput DNA sequencing (Illumina, in this case) to see what they've got.

Yep, that seems a fair explanation. I liken it to trying to hit an ant with a minigun. It's probably not higher profile because probe capture has been done before (e.g. for ribosomal enrichment / exclusion); this is just taking it to the extreme. I wouldn't be surprised if someone follows this up later on with a 1 billion probe capture design for bacterial sequencing -- there'll always be more probes that can be added into the mix.

Comment Re:Since processes can be patented... (Score 1) 215

Yes. People have this idea in their mind that all intellectual property is the same, which causes confusion when litigation happens correctly. In this particular case, the debate will be whether or not Lexmark's patents are infringed by the process that the second-hand suppliers use, rather than the sale of the end product.

Richard Stallman has a good talk about the differences between the three main types of intellectual property, and says that anyone who tries to lump them together to be dealt with as a whole is doing it wrong.

  • Patents protect the use of processes or functions by a business
  • Trademarks protect the mindshare of a product or business
  • Copyrights protect the creative/artistic presentation of a product

Disclaimer: not a lawyer; please consult a lawyer who is familiar with the specific area of interest to work out what is wrong with what I've typed here.

It is easier to change the specification to fit the program than vice versa.