Cameron Neylon

There is an interesting meta-discussion going on in a variety of places
at the moment which touch very strongly on my
[post](http://blog.openwetware.org/scienceintheopen/2009/01/27/the-integrated-lab-record-or-the-web-native-lab-notebook/)
and talk
([slides](http://www.slideshare.net/CameronNeylon/the-lab-that-was-born-on-the-web-presentation),
[screencast](http://www.viddler.com/explore/CameronNeylon/videos/4/))
from last week about "web native" lab notebooks. Over at [Depth
First](http://depth-first.com), Rich Apodaca has [a
post](http://depth-first.com/articles/2009/02/07/of-web-centric-science-telegraphs-and-telephones)
with the following little gem of a soundbite:

> Could it be that both [Open
> Access](http://depth-first.com/articles/2006/11/16/electric-cars-and-open-access)
> and [Electronic Laboratory
> Notebooks](http://depth-first.com/articles/2009/01/02/the-electronic-laboratory-notebook-trap)
> are examples of telephone-like capabilities being used to make a
> better telegraph?
>
> [Web-Centric
> Science](http://depth-first.com/articles/2009/02/04/web-centric-science)
> offers a set of features orthoginal to those of paper-centric science.
> Creating the new system in the image of the old one misses the point,
> and the opportunity, entirely.

Meanwhile a discussion on The Realm of Organic Synthesis blog was
sparked off by [a post about the need for a Wikipedia inspired chemistry
resource](http://therealmoforganicsynthesis.blogspot.com/) (thanks again
to Rich and Tony Williams for pointing the post and discussion out
respectively). The initial idea here was something along the lines of;

> I envision a hybrid of Doug Taberâ€™s [Organic Chemistry
> Portal](http://www.organic-chemistry.org/), Wikipedia and a condensed
> version of SciFinder.Â  Iâ€™ll gladly contribute!Â  How do we get the
> ball rolling?

This in turn has led into a discussion of whether
[Chemspider](http://www.chemspider.com) and ChemMantis partly fill this
role already. The key point being made here is the problem of actually
finding and aggregating the relevant information. Tony Williams makes
the point in the comments that Chemspider is not about being a central
repository in the way that J proposes in the original TROS blog post but
that if there are resources out there they can be aggregated into
Chemspider. There are two problems here, capturing the knowledge into
one "place" and then aggregating.

Finally there is an ongoing [discussion in the margins of a
post](http://www.realclimate.org/index.php/archives/2009/02/antarctic-warming-is-robust/langswitch_lang/aw)
at [RealClimate](http://www.realclimate.org). The argument here is over
the level of "working" that should be shown when doing analyses of data,
something very close to my heart. In this case both the data and the
MatLab routines used to process the data have been made available. What
I believe is missing is the detailed record, or log, of how those
routines were used to process the data. The argument rages over the
value of providing this, the amount of work involved, and whether it
could actually have a chilling effect on people doing independent
validation of the results. In this case there is also the political
issue of providing more material for antagonistic climate change
skeptics to pore over and look for minor mistakes that they will then
trumpet as holes. It will come as no suprise that I think the benefits
of making the log available outweigh the problems. But that we need the
tools to do it. This is beautifully summed up in one comment by Tobias
Martin at number 64:

> So there are really two main questions: if this \[making the full
> record available -- CN\] is hard work for the scientist, for
> heavenâ€™s sake, why is it hard work? (And the corrolary: how are you
> confident that your results are correct?)

And the answer -- it is hard work because we still think in terms of a
paper notebook paradigm, which isn't well matched to the data analysis
being done within MatLab. When people actually do data analysis using
computational systems they very rarely keep a systematic log of the
process. It is actually a rather difficult thing to do -- even though in
principle the system could (and in some cases does) keep that entire
record for you.

My point is that if we completely re-imagine the shape and functionality
of the laboratory record, in the way Rich and I, and others, have
suggested; if the tools are built to capture what happens and then
provide that to the outside world in a useful form (when the researcher
chooses), then not only will this record exist but it will provide the
detailed "clickstream" records that Richard Akerman refers to in answer
to [a Twitter proposal from Michael
Barton:](http://friendfeed.com/e/5f5fcf89-6cc6-240b-eef2-9d6f61b9083f/Website-idea-Rank-scientific-articles-by/)

> Michael Barton: Website idea: Rank scientific articles by relevance to
> your research; get uptakes on them via citations and pubmed "related
> articles"
>
> Richard Akerman: This is a problem of data, not of technology. Amazon
> has millions of people with a clear clickstream through a website.
> We've got people with PDFs on their desktops.

Exchange "data files" and "Matlab scripts" for PDFs and you have a
statement of the same problem that they guys at RealClimate face. Yes it
is there somewhere, but it is a pain in the backside to get it out and
give it to someone.

If that "clickstream" and "file use stream" and "relationship" stream
was automatically captured then we get closer to the thing that I think
many of us a yearning for (and have been for some time). The Amazon
recommendation tool for science.


There is an interesting meta-discussion going on in a variety of places at the moment which touch very strongly on my post and talk (slides, screencast) from last week about “web native” lab notebooks.

Messaggi di Rogue Scholar

What are the services we really want for recording science online?