Cameron Neylon

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I had been getting puzzled for a while as to why I was being
characterised as an 'Open Access' advocate. I mean, I do adovcate Open
Access publication and I have opinions on the Green versus Gold debate.
I am trying to get more of my publications into Open Access journals.
But I'm no expert, and I've certainly been around this community for a
much shorter time and know a lot less about the detail than many other
people. The giants of the Open Access movement have been fighting the
good fight for many years. Really I'm just a late comer cheering from
the sidelines.

This came to a head recently when I was being interviewed for a piece on
Open Access. We kept coming round to the question of what it was that
motivated me to be 'such a strong' advocate of open access publication.
I must have a very strong motivation to have such strong views surely?
And I found myself thinking that I didn't. I wasn't that motivated about
open access *per se*. It took some thinking and going back over where I
had come from to realise that this was because of where I was coming
from.

I guess most people come to the Open Science movement firstly through an
interest in Open Access. The frustration of not being able to access
papers, followed by the realisation that for many other scientists it
must be much worse. Often this is followed by the sense that even when
you've got the papers they don't have the information you want or need,
that it would be better if they were more complete, the data or software
tools available, the methodology online. There is a logical progression
from 'better access to the literature helps' to 'access to all the
information would be so much better'.

I came at the whole thing from a different angle. My Damascus moment
came when I realised the potential power of making *everything*
available; the lab book, the data, the tools, the materials, and the
ideas. Once you connect the idea of the read-write web to science
communication, it is clear that the underlying platform has to be open,
accessible, and re-useable to get the benefits. Science is perhaps the
ultimate open platform available to build on. From this perspective it
is immediately self evident that the current publishing paradigm and
subscription access publication in particular is broken. But it is just
one part of the puzzle, one of the barriers to communication that need
to be attacked, broken down, and re-built. It is difficult, for these
reasons, for me to separate out a bit of my motivation that relates just
to Open Access.

Indeed in some respects Open Access, at least in the form in which it is
funded by author charges can be a hindrance to effective science
communication. Many of the people I would like to see more involved in
the general scientific community, who would be empowered by more
effective communication, cannot afford author charges. Indeed many of my
colleagues in what appear to be well funded western institutions can't
afford them either. Sure you can ask for a fee waiver but no-one *likes*
to ask for charity.

But I think papers are important. Some people believe that the
scientific paper as it exists today is inevitably doomed. I disagree. I
think it has an important place as a static document, a marker of what a
particular group thought at a particular time, based on the evidence
they had assembled. If we accept that the paper has a place then we need
to ask how it is funded, particularly the costs of peer and editorial
review, and the costs maintaining that record into the future. If you
believe, as I do, that in an ideal world this communication would be
immediately available to all then there are relatively few viable
business models available. What has been exciting about the past few
months, and indeed the past week has been the evidence that these
business models are starting to work through and make sense. The
purchase of BioMedCentral by Springer may raise concerns for the future
but it also demonstrates that a publishing behemoth has faith in the
future of OA *as a publishing business model*.

For me, this means that in many ways the discussion has moved on. Open
Access, and Open Access publication in particular, has proved its
viability. The challenges now lie in widening the argument to include
data, to include materials, to include process. To develop the tools
that will allow us to capture all of this in a meaningful way and to
make sense of other people's record. None of which should in any way
belittle the achievement of those who have brought the Open Access
movement to its current point. Immense amounts of blood, sweat, and
tears, from thousands of people have brought what was once a fringe
movement to the centre of the debate on science communication. The
establishing of viable publishers and repositories for pre-prints, the
bringing of funders and governments to the table with mandates, and of
placing the option of OA publication at the fore of people's minds are
huge achievements, especially given the relatively short time it has
taken. The debate on value for money, on quality of communication, and
on business models and the best practical approaches will continue, but
the debate about the value of, indeed the need for, Open Access has
essentially been won.

And this is at the core of what Open Access means for me. The debate has
placed, or perhaps re-placed, right at the centre of the discussion of
how we should do science, the importance of the quality of
communication. It has re-stated the principle of placing the claims that
you make, and the evidence that supports them, in the open for criticism
by anyone with the expertise to judge, regardless of where they are
based or who is funding them. And it has made crystal clear where the
deficiencies in that communication process lie and exposed the creeping
tendency of publication over the past few decades to become more an
exercise in point scoring than communication. There remains much work to
be done across a wide range of areas but the fact that we can now look
at taking those challenges on is due in no small part to the work of
those who have advocated Open Access from its difficult beginnings to
today's success. Open Access Day is a great achievment in its own right
and it should be celebration of the the efforts of all those people who
have contributed to making it possible as well as an opportunity to
build for the future.

High quality communication, as I and others have said, and will continue
to say, is Just Good Science. The success of Open Access has shown how
one aspect of that communication process can be radically improved. The
message to me is a simple one. Without open communication you simply
can't do the best science. Open Access to the published literature is
simply one necessary condition of doing the best possible science.


I had been getting puzzled for a while as to why I was being characterised as an ‘Open Access’ advocate. I mean, I do adovcate Open Access publication and I have opinions on the Green versus Gold debate. I am trying to get more of my publications into Open Access journals. But I’m no expert, and I’ve certainly been around this community for a much shorter time and know a lot less about the detail than many other people.

Where does Open Access stop and &#8216;just doing good science&#8217; begin?

Something that [has been bothering
m](http://blog.openwetware.org/scienceintheopen/2007/08/23/blogs-vs-wikis-and-third-party-timestamps/)e
for quite some time fell into place for me in the last few weeks. I had
always been slightly confused by my reaction to the fact that on
[UsefulChem](http://usefulchem.wikispaces.com) Jean-Claude actively
works to improve and polish the description of the experiments on the
wiki. Indeed this is one of the reasons he uses a wiki as the process of
making modifications to posts on blogs is generally less convenient and
in most cases there isn't a robust record of the different versions. I
have always felt uncomfortable about this because to me a lab book is
about the record of what happened -- including any mistakes in recording
you make along the way. There is some more nebulous object (probably
called a report) which aggregates and polishes the description of the
experiments together.

Now this is fine, but point is that the full history of a UsefulChem
page is immediately available from the history. So the full record is
very clearly there -- it is just not what is displayed. In our system we
tend to capture a warts and all view of what was recorded at the time
and only correct typos or append comments or observations to a post.
This tends not be very human readable in most cases -- to understand the
*point* of what is going on you have to step above this to a higher
level -- one which we are arguably not very good at describing at the
moment.

I had thought for a long time that this was a difference between our
respective fields. The synthetic chemistry of UsefulChem lends itself to
a slightly higher level description where the process of a chemical
reaction is described in a fairly well defined, community accepted,
style. Our biochemistry is more a set of multistep processes where each
of those steps is quite stereotyped. In fact for us it is difficult to
define where the 'experiment' begins and end. This is at least partly
true, but actually if you delve a little deeper and also have a look at
Jean-Claude's recent efforts to [use a controlled
vocabulary](http://usefulchem.blogspot.com/2008/01/modularizing-results-and-analysis-in.html)
to describe the synthetic procedures a different view arises. Each line
of one these 'machine readable' descriptions actually maps very well
onto each of our posts in the LaBLog. Something that maps on even better
is the log that appears near the bottom of each UsefulChem page. What we
are actually recording is rather similar. It is simply that Jean-Claude
is presenting it at a different level of abstraction.

And that I think is the key. It is true that synthetic chemistry lends
itself to a slightly different level of abstraction than biochemistry
and molecular biology, but the key difference actually comes in
motivation. Jean-Claude's motivation from the beginning has been to make
the research record fully available to other scientists; to *present*
that information to potential users. My focus has always been on
*recording* the process that occurs in the lab and particular to capture
the connections between objects and data files. Hence we have adopted a
fine grained approach that provides a good record, but does not
necessarily make it easy for someone to follow the process through. On
UsefulChem the ideal final product contains a clear description of how
to repeat the experiment. On the LaBLog this will require tracking
through several posts to pick up the thread.

This also plays into the [discussion I had some months
ago](http://blog.openwetware.org/scienceintheopen/2008/04/20/more-on-fuge-and-data-models-for-lab-notebooks/)
with [Frank Gibson](http://peanutbutter.wordpress.com) about the use of
data models. There is a lot to be said for using a data model to
*present* the description of an experiment. It provides all sorts of
added value to have an agreed model of what these descriptions look
like. However it is less clear to me that it provides a useful way of
*recording* or *capturing* the research process as it happen, at least
in a general case. Stream of consciousness recording of what has
happened, rather than stopping halfway through to figure out how what
you are doing fits into the data model, is what is required at the
recording stage. One of the reasons people feel uncomfortable with
electronic lab notebooks is that they feel they will lose the ability to
scribble such 'free form' notes -- the lack of any presuppositions about
what the page should loook like is one of the strengths of pen and
paper.

However, once the record, or records, have been made then it is
appropriate to pull these together and make sense of them -- to
*present* the description of an experiment in a structured and sensible
fashion. This can of course be linked back to the primary records and
specific data files but it provides a comprehensible and fine grained
descriptionof the rationale for and conduct of the experiment as well as
placing the results in context. This 'presentation layer' is something
that is missing from our LaBLog but could relatively easily be pulled
together by writing up the methodology section for a report. This would
be good for us and good for people coming into the system looking for
specific information.

Person Frank Gibson

Right click for SmartMenu shortcuts


Something that has been bothering me for quite some time fell into place for me in the last few weeks. I had always been slightly confused by my reaction to the fact that on UsefulChem Jean-Claude actively works to improve and polish the description of the experiments on the wiki.

The distinction between recording and presenting &#8211; and what it means for an online lab notebook

I'm a little shell shocked really. I've spent the last couple of weeks
running around like a lunatic, being at meetings, organising meetings,
flying out to other meetings. And then flying back to try and catch up
with all the things that need doing before the next flurry of activity
strikes (which involves less travel and more experiments you will be
pleased to know). There are two things I desperately need to write up.

The [Open Science workshop at
Southampton](http://sotonopensciworkshop.wikispaces.com/) on September 1
seemed to be well received and was certainly interesting for me.Â 
Despite having a very diverse group of people we did seem to manage to
have a sensible discussion that actually came to some conclusions. This
was followed up by discussions with the web publishing group at Nature
where some of these ideas were refined -- more on this will follow!

Following on from this (and with a quick afternoon jaunt to Bristol for
the [Bristol Knowlege
Unconference](http://knowledgeunconference.eventwax.com/bristol-knowledge-unconference)
on the evening of September 5 I flew to Toronto en route to Waterloo for
[Science in the 21st Century](http://www.science21stcentury.org/),
allowing for a brief stop for a Nature Network Toronto [pub night panel
session](http://network.nature.com/forums/toronto/2368) with [Jen
Dodd](http://jendodd.com/), [Michael
Nielsen](http://michaelnielsen.org/blog/), and [Timo
Hannay](http://network.nature.com/profile/timo). The organisers of
Science21, but in particular [Sabine
Hossenfelder](http://backreaction.blogspot.com/), deserve huge
congratulations for putting together one of the most diverse and
exciting conferences I have ever been to. With speakers from historians
to sociologists, hedge fund managers to writers, and even the odd
academic scientist the sheer breadth of material covered was quite
breathtaking.

You can see most of the talks and associated material on the [Perimeter
Institute Seminar Archive](http://pirsa.org/) page
[here](http://pirsa.org/C08021). The friendfeed commentary is also
available in the [science21
room](http://friendfeed.com/rooms/science21). Once again it was a great
pleasure to meet people I kind of knew but hadn't ever actually met such
as [Greg Wilson](http://pyre.third-bit.com/blog/) and [John
Dupuis](http://jdupuis.blogspot.com/) as well as to meet new people
including (but by no means limited to) [Harry
Collins](http://www.cardiff.ac.uk/socsi/contactsandpeople/academicstaff/C-D/professor-harry-collins-overview.html),
[Paul Guinnessy](http://www.ostina.org/content/view/2024/), and [David
Kaiser](http://web.mit.edu/dikaiser/www/). We have yet to establish
whether I knew [Jen Dodd](http://jendodd.com/) in a previous life...

Very many ideas will come out of this meeting I think -- and I have no
doubt you will see some interesting blog posts from others with the
science21 tag coming out over the next few weeks and months. A couple of
particular things I will try to follow up on;

- Harry Collins [spoke about](http://pirsa.org/08090033/)
  categorisations of tacit (i.e. non-communicated) knowledge and how
  these relate to different categories of expertise. This has obvious
  implications for our mission to describe our experiments to a level
  where there is 'no insider information'. The idea that we may be able
  to rationally describe what we can and cannot expect to be able to
  communicate and that we can therefore concentrate on the things that
  we can is compelling.
- Greg Wilson [made a strong case](http://pirsa.org/08090037/) for the
  fully supported experiment that echoed my own thoughts about the
  recording of data analysis procedures. He was focussed on
  computational science but I think his point goes much wider than that.
  This requires some thought and processing but for me it is clear that
  the big challenge in communicating the details of our experiments now
  clearly lies in communicating *process* rather than data.

Each of these deserves its own post and will hopefully get it. And I am
also aware that I owe many of you comments, replies, or other things --
some more urgent than others. I'll be getting to them as soon as I can
dig myself out from under this pile of......


I’m a little shell shocked really. I’ve spent the last couple of weeks running around like a lunatic, being at meetings, organising meetings, flying out to other meetings.

Rogue Scholar Beiträge

Where does Open Access stop and ‘just doing good science’ begin?

The distinction between recording and presenting – and what it means for an online lab notebook

The long slow catchup…