Building Blogs of Science

More on Open Access Week

Posted in Science and Society by kubke on October 25, 2012

It has been a busy Open Access Week for me. My last (well almost last!) duty is today at 4:00 pm at the Old Government House at the University of Auckland.

Stratus has organised a panel and invited me to participate, and I have just uploaded my upcoming presentation to Slideshare. If you have a chance, we would love to see you there!

Open access stratus 2012 from Fabiana Kubke
Oh, and thanks to Nat for 4-short-linking my previous post!

Kiwi foo’s eye view of Open Science

Posted in Health and Medicine, Science, Science and Society by kubke on February 13, 2012

I just came back from another amazing kiwi foo. I have talked about it before, so I will not bore you with the details of what kiwi foo is all about. This time, unlike other years, I went with a very focused view of what I wanted to achieve. And it was as stimulating as ever.

Over the past year, I have gone into a rather quiet reflexion of what ‘open science’ is and how to make it work. I have become increasingly frustrated with a model of science that increasingly rewards self-promotion rather than knowledge sharing. And the emerging theme of my reflexion was ‘context’.

If we want a ‘global’ open science, the formula for adoption needs to be able to adapt to local personal, institutional, social, political, economical and legislative contexts. I may be wrong, but I think many of us who support open science struggle at times with how to make it work in the particular contexts in which we need to operate.

As I was struggling with the frustration of the commodification of science over the past two years, I started thinking about the open source community.  I can’t blame universities for encouraging scientists  to produce revenue at a time when public funding for education are research appear to be in constant decline. So I went to Webstock a year ago to try to learn more about how open source projects generate revenue. After all, their business models are built around giving their ‘product’ away for free, something that is well aligned with the ethos of science. One of my highlights at kiwi foo was a conversation with Don Christie from CatalystIT, a company that produces high quality open source software. I am looking forward to continuing this conversation and exploring how these business models can be adapted to the different demands and constraints for science. I got a lot of insight from him, and am hoping he and people like him can help us move forward.

On the second day (or rather the first long day) there were a few sessions that centered around science. Great things came out of it, and it would be impossible to name everyone that provided insight. Nick Jones, Leonie Hayes, Alex Holcombe , Alison Stringer and I partnered in crime and ran a couple of sessions where we hashed a few issues around. I personally wanted to explore what Open Science meant in the New Zealand / Australia context (I can’t speak for the others’ motivations!).  I think that the local context in NZ/OZ is slightly different than in the Northern hemisphere and there are some things that differentiate this region. Perhaps we can/should capitalise on that.

For example, you will never see a ‘Research Works Act’ bill here, because we don’t seem to have Open Access mandates. Instead, we have NZGOAL and AUSGOAL which are frameworks for data licencing. The Australians have ANDS and NZ has eResearch, all focused on the data. Tim O’Reilly mentioned the PantonPrinciples  in this context – but the Panton Principles (which I have personally endoresed) cannot be exported ‘as is’ to Australia and New Zealand because neither Creative Commons AotearoaNew Zealand nor CCAustraliahave CC0, for example.  Software hopefully will not be covered by patents is covered by copyright (not patents) in NZ*, so maybe we can capitalise on that to develop tools for open science. New Zealand has a Treaty of Waitangi, and any local open science needs to respect and work constructively to meet our treaty obligations. Lets add to that, that different research groups are going to be subject to obligations related to the international treaties their countries have signed up to. We all have different copyright restrictions and freedoms, we have different systems that determine how to assign funding, and different mandates and guidelines, and are at different points of our careers with different job securities.

So, how do we make open science work within these diverse contexts? We can all agree on the philosophy, but perhaps we need to also agree that the implementation will take different shapes. I think wee need to continue the global conversation and continue to support each other, but we also need to start working locally in smaller groups to ‘make things happen’. And the battles we choose to fight perhaps should be aligned with local contexts so that we can each capitalise on our strengths. I loved having this dialogue at kiwi foo, getting great insights from a diverse group, and mainly feeling that this is something for which we have support.

The rest of the things that happened at kiwi foo will slowly seep into future posts.

I would really like to thank Jenine, Nat Torkington and Russell Brown for putting kiwi foo together (and inviting me!), my partners in crime Alex, Nick, Alison, and Leonie for their hard work on the sessions, all the attendees for their contributions and especially Tim O’Reilly for providing us with valuable insights. You all have complicated my life, but I look forward to a 2012 of hard work and of ‘making things happen’.


*Edited on 16/2/2012 to reflect the correction made by @kayakr (thanks for that!). I was thinking of this bill: (which is probably the one that @kayakr refers to as pending legislation)

Drafting proposals in the open – sketching out project ideas

Posted in Health and Medicine, Science, Science and Society by kubke on May 4, 2011

[also posted in] This post is licenced under a CC0


“Professionally our methods of transmitting and reviewing the results of research are generations old and by now are totally inadequate for their purpose.” Vannevar Bush, 1945

As announced last week, we – Fabiana Kubke and Daniel Mietchen – are currently participating in the Getting your CC project funded course at Peer-to-Peer University, and have decided to draft our proposal collaboratively and in the open. Part of our motivation is our (and others’) perceived need for making scientific information more useful by positioning it where it can be easily found, used, linked to, repurposed, and updated.

The introductory meeting of the course took place on April 26 (UTC) via Skype. We have since incorporated some of the feedback we got so far, and in this post – which Claudia Koltzenburg helped us draft – we will outline the next steps in the hope to entice others to get involved as well.

The course is scheduled around a series of workshops, each focusing on a different aspect of the proposal-writing process:

  • May 3, Workshop 1: How do we move from having an idea to realizing those ideas in terms of having aims, and goals?
  • May 6, Workshop 2: Which funding bodies are there that can give financial support, and how do we find appropriate sponsors for our project?
  • May 10, Workshop 3: How can we structure our proposed work in terms of tasks and how do we make a realistic timeline?
  • May 17, Workshop 4: Knowing how long time we estimate, and the resources we need, how do we put together a reasonable budget?
  • May 24, Workshop 5: What happens after the funding period is over? How do we make the project sustainable?
  • May 31, Workshop 6: What would we look at when reviewing another proposal.

The grant proposals are to be drafted in parallel to these workshops until June, when the proposals produced will be peer-reviewed, and professional feedback will be provided to increase the chances of getting funded. In preparation for today’s workshop, we will use this post to explore the aims and goals of our project(s).

The candidate projects in a nutshell

The ideas submitted as part of the application for the course all center around what could be thought of as an Encyclopaedia of original research, which shall therefore be the default focus of the grant proposal (as idea 1). Two smaller projects (ideas 2 and 3) build on idea 1 but are more specific and could thus be integrated into a proposal about idea 1, or developed independently, whereas idea 4 is wider in scope than idea 1. We expect the final scope of our grant proposal to be defined more precisely before attending Workshop 3.

“In the academy [..] we need to recognise an ethical obligation […] which is at the core of our mission which is universal access to knowledge.” Larry Lessig, in the video embedded below, which is CC-BY-licensed.

The Architecture of Access to Scientific Knowledge from Lessig on Vimeo.

Idea 1: The primary aim of the Encyclopaedia of original research (henceforth EOR) is to arrange the existing scientific literature in a way that allows it to become dynamic in nature. The primary goal is to develop a platform that is able to capture and archive the open scientific literature such that the original work is being preserved (like at arXive or PubMed Central) but becomes dynamically and collaboratively editable (like at OpenWetWare). By way of such a platform, scientists and others could share their knowledge more effectively than through papers: Work on related matters could be more easily identified and conceptualized, and so could gaps in knowledge. Besides the possibility for direct editing, facilities for annotation, commenting and other ways of interaction with the community of researchers in the field would ensure the widest possible peer review.

The Encyclopaedia of original research combines two of the principles for open science that have been put forward by Science Commons: it takes the “Open Access” literature and recognizes that it too – like data – is a lost opportunity “without structure and annotation”. The characteristics of the platform that would contain the encyclopaedia are complex: it needs to track individual contributions to enable proper attribution, the content needs to be granular enough to be able to be cite individual elements within an entire piece, individual pieces of works or elements within it need to be able to be dynamically linked, indexed and contextualized, and the metadata needs to be structured to enhance discoverability, an attribute that is essential for reuse. The user interface also needs to be suitable for the different technological levels of knowledge or levels of comfort appropriate for individual scientists, so that technology is not a barrier for adoption and/or contribution.

We expect that the encyclopaedia will benefit science by helping to avoid duplication of research efforts (and related funding), providing a faster means of updating information otherwise delayed by prevalent publication cycles or not deemed “worthy” of formal publication (practical example case) and promoting the open discussion of research findings in light of new evidence.

The approach, though initially focused on contemporary literature, could likewise be applied to legacy literature – a start in this direction has already been made, as discussed here.

Idea 2: The aim here is to take advantage of such a repository to facilitate the delivery of scientific and health-related information to remote areas where this information may not be readily available but where access to it is essential for the well-being of those communities. What we imagine is that the above EOR could incorporate (or lead to) lay summaries (similar to AcaWiki of the scientific literature or such as those that already exist in blogs) as part of its knowledge base and both the original research as the lay summaries can be translated to local languages. Specific content that is relevant to specific world regions (e.g., malaria in Africa, Chagas in South America) can be bundled in formats that are compatible with existing local technology. One way to at least partially achieve this goal is to bundle region-relevant information so that it can take advantage of ongoing deployments associated with the One Laptop Per Child (OLPC) project and where it can reach the communities that would benefit most from that research.

Idea 3: The aim here is to take advantage of the infrastructure of the EOR (and part of the information contained within it) to complement (or support) digital collections not typically considered part of the scientific “literature”, e.g. from museums or databases. Take, for example this artifact from the Matapihi digital collection. The interaction of the user with the digital object could be enhanced by linking it to different representations of the same specimen (say, an MRI scan), or to relevant scientific information pertaining to similar specimens. It could further be brought back to life by linking it to other cultural artifacts: for instance, ‘Have specific works of poetry or music been inspired by these types of specimens?’, or ‘Are there local traditions or myths that are associated with the artifact?’, or ‘Is there a personal notebook of the individual who brought this specimen to where it is? As an example, this other digital object from the New Zealand National Library presents not just the artifact but the cultural context of what the object represents and how it relates to the local cultural heritage.

The fate of these ideas will depend on how the grant writing develops; the project as a whole could be shrunk to either of these projects (or similar ones), or these projects could be spinned off or retired.

Idea 4: The project could in principle also be expanded in scope, e.g. to test the efficiency of open versus traditional science. However, in order to produce a competitive grant on this big issue, we would require considerable support from beyond our current team of three.

The next steps

By May 10, we will need to identify in a first instance the type (or types) of funding bodies that would be suitable (at least in principle) to fund and/or sponsor the project. We would like to invite feedback and suggestions for that part of the process as well. For that purpose, we have set up a page on Wikiversity were we will be aggregating the relevant feedback we receive, and draft the next blog post in this series.

We would also like to invite feedback on which platform would be most suitable for the drafting of the full proposal. Different wiki spaces seem to be appropriate, as are Google Docs, but the idea of drafting it on GitHub is also on the table.

Drafting proposals in the open

Posted in Health and Medicine, Science, Science and Society by kubke on April 27, 2011

[By Fabiana Kubke and Daniel Mietchen, Original post in]

This is the first of a series of initially 5 posts in which we – Fabiana Kubke[1], Daniel Mietchen, and anyone interested to join us –  are planning to reflect on a number of projects related to science in the digital age. We have applied for (and admitted to) the Getting your CC project funded course at P2P University that started today and is scheduled to help participants on their way to submission-ready grant proposals by mid-July.

Default to open

The underlying assumption is that open collaborative environments would have a positive impact on science and the relationship between science and society.

“I definitely believe that science in general is more effective the more open people are,” says evolutionary biologist Jonathan Eisen of the University of California (UC), Davis, who keeps much of his research open. “There are unquestionably risks for people that come with [openness], but the benefits to society are enormous. Given that taxpayers are paying for our work, I think that the default should be to be open unless you can prove that it’s a bad idea.” [2]

The ultimate goal of defaulting to ‘open’, as Eisen suggests, requires suitable (and sustainable) collaborative environments with low adoption barriers. The initial focus must therefore be on how to ‘build’ those environments (or on how to re-purpose existing technology to serve this goal).

Reusing and repurposing existing knowledge

“Knowledge emerges only through invention and re-invention, through the restless, impatient, continuing, hopeful inquiry human beings pursue in the world, with the world and with each other.” Paulo Freire[3]

What we want to address is how to encourage the re-use and re-purposing (Freire’s re-invention) of scientific knowledge through collaboration between the scientific community and the wider society. This ‘invention and re-invention’ is currently hindered by the traditional systems through which science operates: closed notebooks, manuscripts behind pay-walls, no access to the primary data, etc., and especially copyright and licensing limitations. This inevitably leads to duplication of efforts that could otherwise be avoided if the processes were to be made more open.  (See also [4].)

One place to start is by making existing scientific literature licenced under Creative Commons (or other open licenses) available in ways such that it can be edited, updated, commented upon and re-purposed. The goal is to shift the scientific literature from its current static format to a more dynamic one that is more aligned with both how science is done and how information is used[5].

The bigger picture

“Increasing the number of things you have can be useful, but increasing the amount of knowledge you have can be transformative.” Clay Shirky [6]

The general scheme of how we think of the bigger picture is here [7]:

We see science as providing information; but that information can only be transformed into knowledge when the different spheres of society can interact with it in a usable manner. One crucial initial step is to make the information available in a way that allows diversifying the ways in which information/knowledge is being put to use so that it can have the desired transformative effect.

How are we planning to achieve (some of) this?

One proposal on how to achieve openness in scientific information was led by Daniel Mietchen and took the shape of the COASPedia project that aimed  to “demonstrate to the scientific community that scientific articles published online under CC-BY-licenses can be arranged in a different and — importantly — more efficient manner than those published in classical journals.” The COASPedia project – initially presented at COASP 2010 – was a finalist in the Wissenswert initiative of Wikimedia Deutschland, but did not get funded.

We have now signed up (and were accepted into) a course on “Getting your cc-project funded”, run by P2PU. The course starts on April 26th, and we will be working on expanding on the original project during the course and after and drafting a proposal to get the project funded. To be admitted into the course we had to offer 3 ideas; each will specifically be described (and opened for discussion) in each of the following posts. They all sit around the concept of a basic repository (whatever shape this may take).

“Hence, in the name of the ‘preservation of culture and knowledge’ we have a system which achieves neither true knowledge nor true culture.” Paulo Freire [3]

This basic framework of our ideas for the course is not too different from what was proposed in the original COASPedia proposal:  What we would like is for information to become useable, findable, and linkable while still capturing not only the original work but also the different contributions and their authors (i.e., preserving the cultural heritage of science). The 2 other ideas sit more specifically around how the usability, findability and linkability can help transform the way we relate with the information at hand.

The ultimate goal is not simply a modernisation of the way that information is made available, we also hope to capture the possibilities that this modernisation affords to improve the outcomes of science as a whole – with respect to how it interacts with society, how it becomes transformed into knowledge, and how it becomes part of our cultural heritage. Or in Shirky;’s words:

“what matters now is not the new capabilities we have but how we turn those capabilities, both technical and social, into opportunities[6] (emphasis added)

The proposal

In the spirit of openness, we will keep the entire drafting process as open as possible, so as to invite feedback and other contributions from early on.

In order to help us identify the platforms that are best suited to a collaborative writing process of this kind, we will use this series of blog posts to experiment a bit with several potential drafting environments.

An aggregated view of the project will be maintained at

Footnotes and references:

We will link directly where possible, and use the endnotes mainly to store the metadata of some key references.

[1] Disclosure: Fabiana Kubke is a member of the advisory panel of Creative Commons Aoteaoroa New Zealand

[2] Wald, C. (2010). Scientists Embrace Openness. Science. doi:10.1126/science.caredit.a1000036

[3] Quote was taken from Freire, P. (1985). Pedagogy of the oppressed. Harmondsworth  Middlesex: Penguin. A website devoted to this work ( has useful information on both the author and the text.

[4] Radder, H. (2010). The commodification of academic research : science and the modern university. Pittsburgh  Pa.: University of Pittsburgh Press.

[5] An article along these lines of thought sits in SpeciesID and in Nature Preceedings.

[6] In Shirky, C. (2010). Cognitive surplus : creativity and generosity in a connected age. London: Allen Lane. (ISBN 978-1-846-14218-5) (see book review here)

[7] This mindmap began as a discussion with Tabitha Roder over a NZ olpc testing session in Auckland. These ideas were thrown into a prezi and the derived mindmap now includes modifications suggested by Claudia Koltzenburg

Science lessons from 8 year old children

Posted in Science, Science and Society by kubke on December 22, 2010

[Cross posted from Talking Teaching]

Ed Yong in Not Exactly Rocket science alerted me to an article published in Biological Letters Biology Letters from the Royal Society. I will not discuss the content of the article, Ed Yong has (as usual) done a wonderful job. I would like instead to share the ‘concept’ of the article.

The article reports on some research that shows that bumble-bees use both colour and spatial relationship in their foraging behaviour. But enough about that. What is unique about this article is that the research was conducted by a group of school children. It is also unique in that it is written by a group of school children (in their language). And the icing on the cake are the figures: pencil coloured; no fancy graphic software.

This is, in my opinion, authentic teaching at its best. And authentic learning. And while we are at it, authentic publishing.

So what have I learned from this group of children? That, as they say, science is fun. And that teaching science, whatever the student age group, can be made fun and authentic and can get children motivated.

The background reads:

Although the historical context of any study is of course important, including references in this instance would be disingenuous for two reasons. First, given the way scientific data are naturally reported, the relevant information is simply inaccessible to the literate ability of 8- to 10-year-old children, and second, the true motivation for any scientific study (at least one of integrity) is one’s own curiosity, which for the children was not inspired by the scientific literature, but their own observations of the world.

I could not agree more. I love biology because I ‘played’ with biology as a child. I was fortunate enough to have a father who never answered my question with ‘I don’t know’ without following that up with ‘but lets try to find out’. As a child my father valued my questions and my curiosity, more so about things he didn’t have an answer for. And I will always be grateful to him for that. For my teachers, well, that was a different issue: rather annoying having a pupil in the class that just refused to overcome the ‘why?’ stage.

And these children have been given a great gift by being it let known that their thoughts and ideas have value. And that, once that barriers that have to do with the specific language of the scientific literature are withdrawn, their ideas and thoughts can bring about new knowledge.

These children will also grow up having learned a few fundamental things about science: How an idea is brought into shape, how scientific questions are narrowed, and the hard work and discipline that is needed to see an experiment through. Oh yes, and that no matter how good an idea may be, reviewers may still reject your grant.

None of this they could have learned from a science textbook.

The editors of the Royal Society should also be commended for not requiring that the manuscript adjust to the traditional publishing formats and allowing the authentic voice of the children to come through. This paper should become obligatory reading in science classes. If nothing else, children will recognise their own voices and curiosity in the reading, and, who knows, other groups of children with innovative teachers may teach us (adult scientists) another thing or two.

P. S. Blackawton, S. Airzee, A. Allen, S. Baker, A. Berrow, C. Blair, M. Churchill, J. Coles, R. F.-J. Cumming, L. Fraquelli, C. Hackford, A. Hinton Mellor1, M. Hutchcroft, B. Ireland, D. Jewsbury, A. Littlejohns, G. M. Littlejohns, M. Lotto, J. McKeown, A. O’Toole, H. Richards, L. Robbins-Davey, S. Roblyn, H. Rodwell-Lynn, D. Schenck, J. Springer, A. Wishy, T. Rodwell-Lynn, D. Strudwick and R. B. Lotto (2010) Blackawton bees. Biology Letters DOI:10.1098/rsbl.2010.1056