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May 11, 2011

Science 2.0: Time to throw open the laboratory doors?

by Michelle Ly

Almost three years ago, Scientific American asked if we were entering an age of Science 2.0.  Would science now be conducted in the open access realm –- freely publishing data, drafts and even whole papers? The economic cost of academic publishing has long been considered unsustainable. As well, the lack of freely accessible papers and results is a frequently heard criticism of academic research. Animal rights groups, for example, often use the perceived absence of transparency in science to cast doubt upon ethical practices involving animal testing. 

Open access has the support of many prominent scientists. This support has certainly increased over the years with diverse voices such as stem cell pioneer and cancer researcher James Till and microbiologist Jonathan Eisen joining the fray. But have we ended up in the Science 2.0 that Scientific American speculated?  While some blogs and open access journals have flourished, the majority of published data still ends up in subscription-based journals. 

One area of biology which has consistently embraced open access models is the field of bioinformatics.  Open access tools for genome analysis, molecular modeling and data visualization are common and frequently used. Recently, researchers from the RWTH Aachen University and Kiel University in Germany, together with The Scripps Research Institute in San Diego, California, published results detailing a new method for testing stem cells.  he procedure, called PluriTest, is freely available online and may satisfy the needs of both grant-starved researchers and animal rights activists alike. 

The current standard for proving pluripotency in a new cell line is through the generation of human cell derived teratomas in immunodeficient mice. Teratomas are solid tumors which contain a mixture of histologically distinct tissue types. Pluripotency is confirmed through tissue collection and subsequent histological analysis of the teratoma to determine if the cell line was able to form tissues of all three embryonic germ layers -– ectoderm, mesoderm and endoderm.   

Despite its widespread use, teratoma assays are not standardized, raising questions and concerns about the assay’s effectiveness as a stem cell quality control and regulatory tool. As well, the procedure spans 6-8 weeks between cell implantation and histological analysis, which may be unrealistic for use in large scale production.

In contrast, PluritTest uses a pattern recognition algorithm which is able to distinguish between pluripotent and non-pluripotent cell lines without the need for animal models. The algorithm relies on a large database of gene expression patterns from known human stem cell lines and returns results in about ten minutes. One of the authors, Dr. Franz-Josef Muller, describes the standardized verification process of PluriTest as a way for researchers to “forgo data from animal testing laboratories and simultaneously achieve more precise results”. As the use of stem cells in cell therapy and regenerative medicine increases, any method which reduces the cost of cell line production and testing ultimately benefits patients.     

Will it help further the open access cause? The original paper was, ironically, published behind a Nature paywall and lack of access may limit the number of PluriTest early adopters. However, it is encouraging to see the development of free tools in stem cell research and I am hopeful that more will follow.



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Good points - Science 2.0 is not only about open access any more than Web 2.0 was just about blogs. I guess open access is the topic I am most drawn to, being interested in the computer science aspect of biological research!

Science 2.0 was never limited to just open access, new publication models was one of the tenets. I endorsed a model of open publication instead, because I don't see any superiority in charging scientists to publish over charging readers to read, but also laid out changes in participation, communication and collaboration, along with publication.

Are we any closer? Not really. My belief after spearheading Science 2.0 for much of the last decade is that a collaboration tool would have to be unreal to get anyone to pay for it and that can't be done for free (because it is complex) and most don't want to pay. Participation is done well by groups like Foldit, Galaxy Zoo, etc. and BioMed Central, PLoS and a lot of others are doing open access. I like to think we have the communication aspect covered. :)

Hank Campbell
Science 2.0

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