Encyclopedia of Life 2

In February I wrote in this weblog that I had signed up to the Encyclopedia of Life. This is an ambitious project that aims to provide access for scientists to multiple sources of information on the Internet. I was very excited by the idea, The aims of the project inspired some of the comments I placed here.

However on receiving the second newsletter I have to admit that I was disappointed to find that the EOL had decided to promote the use of closed source photographic software. eol_newsletter_issue2 . Even though this software is free, it usage is restricted to those running the well known proprietary operating system. Furthermore, although I am an advocate of the use of photographic tools and 3d graphics in research, I simply couldn’t see the practical purpose of this particular software tool for research. It appears glossy, but it hardly revolutionizes research practice and knowledge of the world in the way something like Google Earth has done. I also thought that the EOL could complement an Open access information source such as Wikipedia. I am now concerned that the underlying philosophies differ.

I find the the  use of 3d graphics and animation thrilling and inspiring. However I  believe that initiatives such as the EOL should concentrate their attention on the science first and the presentation later. They should always aim to use cross platform open source solutions for the latter. The showcased plant I was presented with on visiting the site (Calanthea roseus) may perhaps have played an important role in my own family’s destiny (my wife was successfully treated for Hodgkins 10 years ago). However it was detailed knowledge of its chemical composition that allowed this to happen, not a pretty presentation in pseudo 3d. Maybe  accepting sponsorship money from Microsoft can further research in some situations. But there is a danger that it comes at the expense of restricting  developing elements of academic bioinformatics. Gift horses should sometimes be looked at in the mouth.

3 thoughts on “Encyclopedia of Life 2

  1. For clarification in respect of Phoptosynth, no $$ passed between microsoft and EOL.

    In respect of ‘science’ the discipline of taxonomy is anchored in the specimens that are held in museums and herbaria around the world. When a taxonomist is seeking to establish the identity of a taxon, they often have to call upon these unique specimens, and this involves very expensive travel and/or the materials, often in a fragile condition, have to be shipped. Photosynth as a technology has the capacity to give us access to these specimens in a way that reduces the demand on the actual specimens, and therefore reduces the risk to them.

    Finally, technologies such as this, like Google Earth, not only reinvigorate interest in the natural world, they can become foundations upon which much grander knowledge structures can be built.

  2. Hi Duncan,
    Being a mac user, I was also concerned with the idea of being stuck with Windows if I wanted to use Photosynth. At the moment, I need to use the beta version of VMware Fusion 2 in order to access Photosynth which is less than ideal – I do know however that a cross platform is in the works and I’m looking forward to using it natively in Safari. With Photosynth it’s actually the client side plugin that processes most of the “synthing” and therefore it’s likely a more involved process to port this functionality to mac than it would be for, say, a firefox extension.

    EOL, like MS / Photosynth, is keen to get tools into people’s hands and hence the enthusiasm for the Photosynth tool at such an early stage. I don’t think this represents an issue with the underlying philosophy, EOL is still strongly committed to the open source community. The tools that are used to build and host the site are all open source. Last week EOL ran a drupal code sprint with members of the Drupal community, with all of the code being open and available through google code.

    I’m not a biologist myself, however I understand that outside the thrilling and inspiring aspect of the 3D browsing there is in fact great benefit when it comes to the very real issues posed by of shipping precious specimens around the world. Photosynth enables an efficient method of viewing these (sometimes fragile) specimens in great detail without having to necessarily move them out of their environment.

    As for sponsorship from Microsoft, this is nothing more than a great project utilizing a great tool, there is no sponsorship or financial arrangement from either party.

  3. I appreciate the helpful clarifications made in the two comments I have received. The point I was making regarding Microsoft’s involvement is not that money has changed hands. Rather it is that the business model that Microsoft has adopted involves distributing some free software to ensure that the Windows platform remains essential for as many people as possible. I think that is worth questioning. If windows were a good platform this wouldn’t matter too much. Unfortunately its vulnerability to viruses causes many problems, especially in developing countries.
    Serious taxonomic work usually involves detailed study of small sections of an organism rather than a view of overall morphology. I am sure being able to rotate specimens as if they were in hand can be very useful, but is it really essential? Here in Mexico we unfortunately haven’t even reached the stage of scanning herbarium specimens in 2d.

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