As has been noted in a few places, Neil Withers, one of the editors of soon to be newest Nature journal, Nature Chemistry put out a request last week for input on a range of issues to do with how people use journals, formats, and technical widgets. Egon Willighagen, Rich Apodaca, and Oscar the Journal Munching Robot (masquerading as Peter Murray-Rust, or is that the other way around?) have already posted responses. Here I want to add my own thoughts and possibly amplify some of the points others have made. Read more »

Posted: May 11th, 2008 under Nature Chemistry, data formats, publishing.
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Following on from the discussion a few weeks back kicked off by Shirley at One Big Lab and continued here I’ve been thinking about how to actually turn what was a throwaway comment into reality:

What is being generated here is new science, and science isn’t paid for per se. The resources that generate science are supported by governments, charities, and industry but the actual production of science is not supported. The truly radical approach to this would be to turn the system on its head. Don’t fund the universities to do science, fund the journals to buy science; then the system would reward increased efficiency.

There is a problem at the core of this. For someone to pay for access to the results, there has to be a monetary benefit to them. This may be through increased efficiency of their research funding but that’s a rather vague benefit. For a serious charitable or commercial funder there has to be the potential to either make money, or at least see that the enterprise could become self sufficient. But surely this means monetizing the data somehow? Which would require restrictive licences, which is not at the end what we’re about.

The other story of the week has been the, in the end very useful, kerfuffle caused by ChemSpider moving to a CC-BY-SA licence, and the confusion that has been revealed regarding data, licencing, and the public domain. John Wilbanks, whose comments on the ChemSpider licence, sparked the discussion has written two posts [1, 2] which I found illuminating and have made things much clearer for me. His point is that data naturally belongs in the public domain and that the public domain and the freedom of the data itself needs to be protected from erosion, both legal, and conceptual that could be caused by our obsession with licences. What does this mean for making an effective data commons, and the Science Exchange that could arise from it, financially viable? Read more »

Posted: May 11th, 2008 under Collaboration, academic credit, data commons, data formats, funding, linking papers to open data, open access, open data, open-science-charter, osci-protocol, science21.
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Once again a range of conversations in different places have collided in my feed reader. Over on Nature Networks, Martin Fenner posted on Researcher ID which lead to a discussion about attribution and in particular Martin’s comment that there was a need to be able to link to comments and the necessity of timestamps. Then DrugMonkey posted a thoughtful blog about the issue of funding body staff introducing ideas from unsuccessful grant proposals they have handled to projects which they have a responsibility in guiding. Read more »

Posted: May 5th, 2008 under academic credit, citation, ethics, linking papers to open data.
Comments: 5

Amongst the other things that I do I am a fairly serious amateur musician. I sing regularly and irregularly in choirs, have occassionally done some solo vocal work, conduct a bit, and in the past written fairly substantial pieces of music for orchestra and choir. When I started university I made a choice between doing music or doing science. Like a lot of other scientists I suspect I chose to go down the science route because it is much easier to be an amateur musician than and amateur scientists. I don’t regret the decisions I made then but like anyone I do think back to what might have been.

One of the criticisms of open practice in science and Open Notebook Science in particular is that we open up ourselves to harassment by ‘nutjobs’, ‘ignorant plebs’, and assorted other people who don’t appreciate a) how clever we are or b) how busy we are. There are two sides to this argument with merits on both. It is possible to get bogged down continually dealing with people who genuinely wish to explain to you how universal crystal harmonics explain the periodicity of the elements, or how their understanding of the interstitial spiritual lamina demonstrates the inadvisability of human cloning. There is no getting over the fact that there are nutters out there. On the other hand we do little to encourage the amateur scientist beyond allowing them occasional access to our hallowed existence through TV, NewScientist, and Wired. I wondered whether an exploration of the parallels between amateur music and amateur science might be interesting. I should note that I am using the term professional in rather a loose way here, not to mean whether someone that gets paid to do something, but someone who can devote the majority of their time to a specific pursuit, be that music, science, or anything else. Read more »

Posted: April 29th, 2008 under Uncategorized.
Comments: 9

One of the strong messages that came back from the workshop we held at the BioSysBio meeting was that protocols and standards of behaviour were something that people would appreciate having available. There are many potential issues that are raised by the idea of a ‘charter’ or ‘protocol’ for open science but these are definitely things that are worth talking about. I thought I would through a few ideas out and see where they go. There are some potentially serious contradictions to be worked through. Read more »

Posted: April 29th, 2008 under Uncategorized, open data, open notebook science, open science, osci-protocol.
Comments: 2

I am thinking about how to present the case for Open Science, Open Notebook Science, and Open Data at Science in the 21^st Century, the meeting being organised by Sabine Hossenfelder and Michael Nielsen at the Perimeter Institute for Theoretical Physics. I’ve put up a draft abstract and as you might guess from this I wanted to make an economic case that the waste of resources, both human and monetary is not something that is sustainable for the future. Here I want to rehearse that argument a bit further as well as explore the business case that could be presented to Google/Gates Foundation as a package that would include the development of the Science Exchange ideas that I blogged about last week. Read more »

Posted: April 27th, 2008 under economics, open data, open notebook science, open science, science21.
Comments: 3

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This has taken me longer than expected to write up. Julius Lucks, John Cumbers, and myself lead a workshop on Open Science on Monday 21^st at the BioSysBio meeting at Imperial College London.  I had hoped to record screencast, audio, and possibly video as well but in the end the laptop I am working off couldn’t cope with both running the projector and Camtasia at the same time with reasonable response rates (its a long story but in theory I get my ‘proper’ laptop back tomorrow so hopefully better luck next time). We had somewhere between 25 and 35 people throughout most of the workshop and the feedback was all pretty positive. What I found particularly exciting was that, although the usual issues of scooping, attribution, and the general dishonestly of the scientific community were raised, they were only in passing, with a lot more of the discussion focussing on practical issues. Read more »

Posted: April 23rd, 2008 under Open Science PSB09, biosysbio2008, ethics, identity, open notebook science, open science, open-science-charter, osci-protocol, psb2009, trust, workshop.
Comments: 1

I’m afraid I didn’t manage to record anything in the end. Video card on laptop wasn’t up to the job. Will try to write a report up over dinner tonight and post later.

Posted: April 21st, 2008 under Uncategorized.
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Tomorrow myself and a few of the usual suspects, who I have finally met in person are giving a workshop on ‘Open Science’ as part of BioSysBio 2008. If anyone else who I haven’t met yet is about at the meeting then feel free to introduce yourself, even if you can’t make it to the workshop. The workshop abstract is up on OpenWetWare if you want to have a look. I hope to be able to record screencast and video of the session to make it available to all of you who can’t make it. If you want to make comments in advance or raise any issues then drop a comment here or in the usual places.

Posted: April 20th, 2008 under biosysbio2008, ethics, workshop.
Comments: 1

Frank Gibson has posted again in our ongoing conversation about using FUGE as a data model for laboratory notebooks. We have also been discussing things by email and I think we are both agreed that we need to see what actually doing this would look like. Frank is looking at putting some of my experiments into a FUGE framework and we will see how that looks. I think that will be the point where we can really make some progress. However here I wanted to pick up on a couple of points he has made in his last post. Read more »

Posted: April 20th, 2008 under FuGE, biosysbio2008, data formats, data model, format.
Comments: 4