Building Blogs of Science

[Open] Science Sunday – 18.04.10

Posted in Health and Medicine, Science, Science and Society by kubke on April 18, 2010

Opening content by traditional Toll Access journals

At about the time that I had made the personal commitment to only contribute to Open Access publishing (as service on editorial boards or peer review) I was contacted by Georg Striedter asking me to join the Editorial Board of Brain Behavior and Evolution. After hearing from him his views about the new direction he was planning to take the journal, I could not refuse. Georg Striedter took the Editorial position for the journal starting this year and a big change ensued. The journal now has a new section called Highlights and Perspectives in Neuroscience, and articles in this section have been made free to access. I have been quite impressed with this section, and the quality of the discussions there. As an example, you can go and look at Mark Changizi’s piece “Neuroscientis’s Embarassment: Artificial Intelligence’s Opportunity” and Anat Barnea’s piece “Wild Neurogenesis”. For the latter, I recommend reading first a great summary of the article around which the discussion centres which was posted by NeuroDojo when the article came out. Mark Changizi’s piece is self contained but you might also want to check this awesome discussion around brain size.

Many journals are opening up some of their content for free, and this is a good move. For example, on the 26th of March, Nature Publishing broke the news that the Nature News content free of charge. This is a great section and it is wonderful to have that content available to the general public.

Don’t mess with technology, what about BioTorrents?

On the 10th of April I participated in the Public Acta meeting in Wellington. One of the statements of the Wellington Declaration said that

“[Technological Protection Measures] should not infringe on or limit the rights of users to use or access copyright material in a manner that would be permitted without the TPM”

One of the arguments raised that day, is that technology is sometimes attacked when it is can be used to infringe copyrighted works, but that restricting such technologies may infringe on the ability of accessing material that is otherwise legally available.

This week saw the publication of a paper in PLoS One by Morgan GI Langille and Jonathan A Eisen. BioTorrents: A file sharing service for Scientific Data. As Tim O’Reilly said on his Tweet, this is a great use of the BitTorrent technology. Here is a technology that has valuable applications and should, too be protected as such.

One may ask what prompted me to attend the PublicACTA meeting. The answer is simple: Most scientific information is behind the copyright that as authors we often transfer to the journals where our work is published (for journals outside the Open Access model). Education, Health and Science rely heavily on having good access to this information. Any decision to regulate copyright will inevitably have an impact on Education, Health, Science and Technology. So ACTA cannot be framed around the protection of recording artists and the film industry and not consider its implications for these other areas of public good. The text of ACTA will be made public next week, at which time I hope scientists, educators and health professionals will collaborate in making sure the implications for their fields are taken into account.

Get your ACT(A) together

Posted in Science, Science and Society by kubke on April 12, 2010

The Anti Counterfeiting Trade Agreement (ACTA) is an international treaty that is being negotiated by a handful of nations, in a very secretive way. The text of the ACTA has not been officially released, but some of the issues under negotiation can be found through several leaked documents. However, public officials are unable to comment on such leaked documents.

Although its name may indicate that it is to deal with issues around counterfeiting, leaked documents have shown that the scope of the agreement may go well beyond that, to include other types of copyright and intellectual property infringements. And this raises two important questions:

  1. Why is an ‘antitrade agreement’ being negotiated by only a handful of countries to deal with issues that should fall under the umbrella of the World Intellectual Property Organization (WIPO) which has a greater representation of nations?
  2. Why the secrecy?

The next round of negotiations of ACTA is to be held in Wellington, New Zealand, this week. As a response, a conference known as PublicACTA was held on Saturday to draft a response to be presented to the ACTA negotiators in Wellington. The document now known as The Wellington Declaration can be found online and is linked to the petition signature page.

The document calls for transparency in the negotiation process and an opportunity for public participation, as well as a definition of the specific issues that are or should be associated with the ACTA itself.

Anyone that uses the internet will be either directly or indirectly affected by the ACTA resolutions. It is shocking to me that while on the one hand there is an increasing awareness of the need to open government and scientific data for public scrutiny, an agreement that will impact on the most ubiquitous medium for data sharing, open collaborations and discussions, is done behind closed doors and without significant public participation. If this is not a contradiction in terms, then I need to buy another dictionary.

  • Michael Geist’s blog is a great source of information.
  • The video of the Conference is now here.
  • The Wellington Declaration is here.
  • The petition signature page is here.

Thoughts on Hunter’s statement on Science, Climate Change and Integrity

Professor Keith A Hunter has published a statment on ‘Science, Climate Change and Integrity‘ in the Royal Society of New Zealand website. His position with respect to the controversies surrounding climate change issues are made clear, as is his call for a re-examination of attitudes on both sides of the argument.

The controversies surrounding the science of climate change underscore the need for a more open approach in the reporting of scientific data, and Professor Hunter’s statement makes a strong argument towards moving in that direction. A while back Cameron Neylon [1] wrote in his blog in reference to the CRU email leaks that

[…] scandal has exposed the shambolic way that we deal with collecting, archiving, and making available both data and analysis in science, as well as the endemic issues around the hoarding of data by those who have collected it.

There are many arguments in favour of making scientific data openly available. In a recent commentary on Science, Jean-Claude Bradley is quoted as saying:

“It’s sort of going away from a culture of trust to one of proof,” Bradley says. “Everybody makes mistakes. And if you don’t expose your raw data, nobody will find your mistakes.”

Along those same lines Hunter argues that

“Science is a rational endeavour that is based on logical and critical analysis of scientific theories in the light of actual evidence. It follows that scientific information, including a transparent description of how the data has been processed and tested against hypotheses, must be publically available, especially when it has been publicly funded […]”

Without this open approach, the validity of scientific information has to be entrusted to the peer review system, but even Professor Hunter echoes what are concerns of the scientific community at large, that

“while we place great faith in the peer review process to weed out ideas that are wrong, peer review is not perfect and can be abused by both sides.”

And further argues that:

“If the intensity of the personal attacks on climate scientists over recent months are to have any positive effect, it will be the adoption of a more transparent approach to the dissemination of information.”

Two sides of the coin: Public/Open access vs Open Data:

Although the issues surrounding open data and open access can be seen to sit under the same umbrella, they really deal with two slightly different issues regarding the dissemination of information. While public or open access to published data is now a requirement by many public funding agencies, and is important for the public dissemination of information,  it does not in itself solve issues such as those raised around climategate.

I am a strong supporter of Open Access publishing — whereby the public has access to the published information — but unfortunatley it shares some of the same shortcomings with toll access publishing when it comes to the review process: the process is not fail-proof. The Public Library of Science has to be commended for opening the post-publication discussion of the work they publish and making it possible to highlight both shortcomings and strengths in the published material, and in this way allowing to correct any errors associated with the peer-review process. Yet even within this open model the criticisms are raised about the published material itself, and this solution falls short of solving the kinds of issues raised by the opponents of climate change: The raw data is not published by default (although it can be requested and it is PLoS policy that it should be made available by the authors).

Open Data on the other hand makes the raw data available: the analysis can be checked, rechecked, rehashed and reanalysed by other people. And as Jonathan Eisen is quoted as saying in the Science article, people do find mistakes.

Opening the data allows those mistakes to be found and to be corrected, and that can only be good since the ultimate goal of science is not to defend one’s pet theory but to keep one’s mind open to find the answer that is most consistent with the data. As Lawrence Krauss said in his lecture:

“I would argue that the definition of open-mindedness is forcing our beliefs to conform to reality, and not the other way around.”

Opening the data will inevitably lead to agreed upon interpretations that conform with reality: It allows the conversation to centre around scientific facts rather than around personal attacks to the scientific community or to the groups of vocal skeptics. And, ultimately, finding the best answer is the one common ground that is shared by both groups.

So what next?

Hunter states that:

[…] it is only fair to expect the critics of the mainstream scientific views […] to adopt an equally transparent approach with their own information, and with their own use and re-analysis of data entrusted to the public domain. They should also subject their findings to rigorous peer review. Opinion, however forthrightly expressed, will not change the laws of basic science.

As far as I know, there is still an Open Access Mandate to be had in New Zealand’s public research funding agencies. Let alone one on Open Data. So it was not without surprise that I read Hunter’s statment that

“In this regard, the Royal Society of New Zealand intends to play its part by developing a Code of Practice for Public Dissemination of Information that it hopes will assist the various New Zealand science organisations in improving their practices.”

This approach is needed if common ground is to be found between scientists and between scientist, society and policy makers. Disagreement is perhaps the strongest force that moves the interpretation of scientific data within the bounds of the most likely explanation. But disagreement can only move in a positive direction when all parties involved have equal access to information. In science that is called the data.

[1] Cameron Neylon’s blog has now moved here.

[2] Disclaimer: I receive and have received research funding from the Royal Society of New Zealand and am an Academic Editor of PLoS One.

On the perils of becoming a dinosaur

Posted in Science, Science and Society by kubke on April 5, 2010
[Crossposted from Talking Teaching]

As a student I always complained about the ‘dinosaur teachers’: those that had lost touch with the students and with the teaching material. Those whose attitude seemed to scream: ‘I cannot be bothered any more’.

Patricia Cranton says, in the context of why someone teaches:

“Another person may have defined himself as a teacher through having a vision of the role of teaching in society but may now, after many disillusioning years of practice, maintain his perspective of himself as a teacher because it is a social expectation or obligation from which he feels he cannot escape. “

And that seems to sum up what a dinosaur teacher is. Teaching is neither foreign nor new to me, I have been teaching one way or another since 1982, and most of the women in my family were teachers of one sort or another.Yet I am not a teacher. I never received any formal training in teaching, and whatever I learned to do or to avoid, I did through trial and error. I am a scientist. I know how to do science. I received formal training, and though I (somehow) know how to navigate that world, it does not instantly qualify me as a good science teacher.

So after all these years, it was time for me to ask: have I become a dinosaur teacher? And if I have, can I do soemething about it?

I am now facing the challenge of replacing Colin Quilter in his teaching at the Medical School. These are not small shoes to fill, and it is a huge challenge. First, I am going back to teaching first and second year, which I have not done in a long time and which I consider much more difficult to do than higher level courses. It is not only the language but the size of the class. How do you engage with over a thousand students, especially when some are in an overflow room, which I cannot see? Colin was, to say the least, beloved by his students. If you do not believe me you can become a fan of a page called ‘Shrine to Colin Quilter’ on Facebook, or read his feature profile in Ako Aotearoa Academy of Tertiary Teaching Excellence. And facing a class knowing that the students expect a ‘Colin’ experience can be nothing less than terrifying.

But since I face fear as a scientist, I have decided to take a degree in education. For the next two years, I will become a student in tertiary education: I will sit in class, I will do homework and assignments, I will be assessed while I try to learn how to become a better teacher. I am not sure what to expect from the programme, but one thing is for certain: I will be in my student’s shoes again, shoes I vacated many years ago. And the programme, one way or another will make me sit down and think about issues around teaching in a more formal way. And that cannot be a bad thing.

Patricia Cranton (2001) Becoming an Authentic Teacher in Higher Education. Krieger Publishing Company, Malabar, Florida.