Cameron Neylon

I've been fiddling with this post for a while and I'm not sure where its
going but I think other people's views might make the whole thing
clearer. This is after all why we believe in being open. So here it is
in its unfinished and certainly unclarified form. All comments
gratefully received.

One issue that got a lot of people talking at the [Scifoo lives
on](http://scifooliveson.wikispaces.com) session on Monday (transcript
[here](http://scifooliveson.wikispaces.com/transcriptONScases "transcript"))
was the question of where the boundaries between what should and should
not be open lie. At one level it seems obvious: the structure of a
molecule can't really have privacy issues whereas it is clear that a
patient's medical data should remain private. The issue came up a lot at
the recent All Hands UK E-science meeting where the issues were often
about census data or geographical data that could pinpoint specific
people. It seems obvious that people's personal data should be private
but where do we draw the line? I am uncomfortable with a position where
it is 'obvious' that my data should be open but 'obvious' that personal
medical or geographical data should not be. Ideally I would like to find
a clear logical distinction.

[Jean-Claude Bradley](http://usefulchem.blogspot.com) made the comment
in the session that molecules don't have privacy issues and I made a
flippant comment about patented genes. [Troy
McLuhan](http://www.troymcconaghy.com/) made the valid point that IP and
privacy are different issues but I want to use this example to try and
pick the problem apart. I will use a series of escalations and the
question is, where should I stop making the data, in this case the
structure of the molecule and associated information, open?

1.  I have synthesised an organic molecule.
2.  The molecule is a piece of DNA 20 bases long.
3.  The sequence of bases corresponds to a segment of a human genome
4.  It corresponds to a sequence obtained from a specific person
5.  The sequence is part of a gene where mutation is associated with an
    increased rate of heart disease
6.  The sequence contains a mutation known to be associated with an
    increased rate of heart disease
7.  The patient has no history of heart disease
8.  The patient has a very specific clinical history that in association
    with the DNA sequence provides a deep insight into the development
    of heart disease
9.  The specifics of the clinical history are enough to precisely
    identify this person
10. They are currently employed in a position where a risk of heart
    disease would preclude them from further empolyment

In nine points we have gone from an innocuous molecule to a serious
ethical dilemma. Incidentally I have used an example of a DNA sequence
because I think it makes the example clearer but the argument is not
limited to DNA structures. A similar example could be created using, say
a lipid derived hormone (that would probably be a more interesting
synthetic target).

So where do we draw the line? In practice medical scientists would
publish all the way through to point \#8. Anonymised clinical examples
are common in the medical literature. I do not know what the ethical
view would be on point \#9 but I suspect the view might vary depending
on jurisdiction and the local ethics committee, not to mention the
attitude of the patient in question. So one point of view is, if you
would publish the data then you should make it open.

If we return to our data and lab books we don't argue that there are no
risks associated with being open but that the benefits outweigh the
risks. It is possible that we may be scooped, that someone may take our
safety data, mis-use it and attempt to sue us, or that someone may have
a strong enough objection to what we are doing to attack us or our lab.
It is more likely that we may embarrass ourselves by making a silly
mistake or by publically heading down a blind alley. However the belief
is that by putting the data and procedures out there we enable both
ourselves and our community to do better. Making our data available lets
other people do more and better science and lets us make more effective
use of what we have done.

However this applies to our patient as well. By making their clinical
history available they are potentially benefiting a large number of
other patients. This 'deep insight' may save both their lives and
others. The arguements for open notebooks and open medical histories run
along similar lines. The potential benefits if the full medical history
of western world could be harnessed are huge. This is a massive store of
data on drug interactions, effectiveness, the effect of lifestyle,
location, environment...In a sense it is a massive clinical trial and we
insist that clinical trial data should be published so why not this
data?

So the radical answer is that everything should be open. This would have
benefits, unquestionably, but it is also clearly totally unacceptable.
Doing so would be to actively cause harm to specific people whose
privacy had been removed. So here is the first point of distinction.
Benefits versus risks with the usual philospophical issues of balancing
the good of 'the community' versus the good of the individual, which is
far too big an issue to go into here.

Another argument is that of who is taking the risk. If I make data open
then the risk I am taking is largely for me (and my group). There is a
potential risk of exposing my institution to liability or ridicule but
hopefully this is a small risk that is not significantly increased
beyond that already created by publication. In our example however it is
the patient who is taking the risk, not the person collecting the data
and making it open. The patient could choose to take that risk if they
were convinced by the benefits, although I imagine again the local
ethics committee would take a view on this. A similar argument can cover
collaborations -- I don't have the right to take risks, however small,
that could harm a collaborator unless they agree the benefits are worth
the risks to them.

There are however risks associated with not making the data open. Peter
Murray-Rust has
[argued](http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=608) that open
data [can save the
world](http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=601). Inaction poses
its own risks. Balancing the risk of inaction against the risks of
action raises again the balance of the many with the individual. So some
sort of pragmatism is required.


I’ve been fiddling with this post for a while and I’m not sure where its going but I think other people’s views might make the whole thing clearer. This is after all why we believe in being open. So here it is in its unfinished and certainly unclarified form. All comments gratefully received.

Limits to openness – where is the boundary?

Yesterday afternoon the Open Notebook Science case studies session was
held as part of the [Scifoo lives on](http://) sessions at Nature
Island, Second Life. [Jean-Claude
Bradley](http://usefulchem.blogspot.com/) organised, moderated and spoke
first followed by me and [Jeremiah
Faith](http://blog-di-j.blogspot.com/). We all spoke about experiences
and implementation of different approaches to open notebook science.

Jean-Claude has put the transcript up
[here](http://scifooliveson.wikispaces.com/transcriptONScases).

There was an active discussion about the need for more fun in science
and the way in which science has become secretive has taken a lot of the
fun out of it. CW Underwood talked about being sick of the 'Secret
Squirrel' nature of science. One thing that was very encouraging was
that Jeremiah said that in his search for his next post he had raised
the issue as to whether the possible PI objected to him keeping his
notebook open. So far he had had no objections.

Other issues that came up:

**Open notebook science takes work and discipline.**

It does involve some effort to get set up and to keep systems running as
well as to maintain the observation that makes sure that things are
running properly. CW pointed out that his PI would regard this as a
waste of time. I can see this perspective being quite a strong one and a
slow one to counter. Arguably the benefits of putting the effort in are
not yet tangible enough to be convincing to people who are happy with
the way their science works as it is.

**What is the best system for holding the notebook?**

Three different systems were presented. The [UsefulChem
Wiki](http://usefulchem.wikispaces.org/) by Jean-Claude using publically
available hosted services. Our [Blog based
notebook](http://chemtools.chem.soton.ac.uk/projects/blog/blogs.php/blog_id/10)
which is a custom built and somewhat closed system. And Jeremiah uses
Tex to generate a [PDF of the whole
thing](http://www.jeremiahfaith.com/open_notebook_science/). Jeremiah's
presentation included the comment that he had shown several people both
a Wiki and the Tex based system and they had all preferred the Tex based
one. This is the opposite of my experience where people seem to prefer
whatever is closest to Word. This may be different communities or maybe
just different people we have had contact with.

My feeling is that the three groups have evolved different systems
because of three main things. Firstly a different initial aim, my
initial aim for instance was not really an open notebook but an
effective means of capturing data and procedures. Secondly differences
in the procedures being carried out and the culture we work within. I am
still slowly working my way through putting up [Exp098 from
UsefulChem](http://usefulchem.wikispaces.com/Exp098) in [our
blog](http://chemtools.chem.soton.ac.uk/projects/blog/blogs.php/blog_id/15/meta/SANDPIT_GROUP/value/Usefulchem_exp098)
system and this is certainly showing up some differences but I'm not
sure I know what they mean yet.

Finally I think we have a different view of what the lab book is and
what the 'ideal' lab book would look like. Jeremiah's point was that he,
and others, wanted it to 'look like a lab book', which is fair enough. I
think my group is somewhere in the middle and Jean-Claude has pushed the
idea of what a lab book is one step further. The finished product is a
summary of the experiment -- not precisely a point by point record of
everything that happened along the way, that is all in the history tab
-- but the visual product is a clear description of the experiment that
is immediately accessible to an outsider as to how to repeat the
experiment and what the data and conclusions were. The point is,within
the wiki framework, there is no need to worry about editing the page
because the history is all still there. This means that it can be taken
from the record as it goes -- which is still kept -- right through to
'finished' in a form that can go straight into a thesis or paper. I'm
still not entirely comfortable with this, but I'm not entirely sure that
this is particularly logical.

In any case in the end I think it will depend on what you want and why
you want to go down the ONS route. There's still a lot of work to be
done.

**Limits to openness**

There was a discussion on where the boundaries should lie as to what can
be open or not. I will handle this in another post because I think this
is something I want to think about quite hard.

**Postscript**

On my way into work on Thursday last week I bumped into one of my RAL
colleagues who, among other things, works on our communications and
public relations. He thought that the 'talk' in SL made a nice little
story and went to our central STFC comms people to see whether he might
place it somewhere (website, newsletter, etc). Apparently the answer
came back that they wouldn't issue a press release (which would have
been rather over the top in any case) because we didn't have an
institutional policy on Open Access.

**Postscript 2**

Jean-Claude has also reviewed the session at the
[UsefulChem](http://usefulchem.blogspot.com/2007/09/ons-case-studies.html)
Blog.


Yesterday afternoon the Open Notebook Science case studies session was held as part of the Scifoo lives on sessions at Nature Island, Second Life. Jean-Claude Bradley organised, moderated and spoke first followed by me and Jeremiah Faith. We all spoke about experiences and implementation of different approaches to open notebook science. Jean-Claude has put the transcript up here.

Scifoo Lives On session: Open notebook science case studies

I attended the session held on Nature Island as part of the Scifoo Lives
On series being organised by Jean-Claude Bradley and Bertalan Mesko and
wanted to record some of my impressions. The mechanics of the meeting
itself were interesting. My initial reaction to the idea of meetings in
Second Life was pretty sceptical. My natural inclination would have been
to setup some sort of video cast or conference call. However there are
advantages to the sense of actually having people milling around (and I
apologise to all the people I bumped into or whose slides I
inadvertantly changed). It was good to 'meet' Jean-Claude if not in the
flesh then in the fur and the sense of actually seeing a person or at
least a representation makes this somethow seem more natural.

The disadvantage was that as the dialogue is typed and at least on my
connection was coming through quite slow it is difficult to have a real
conversation. Several times I would start typing a question or comment
and by the time I'd got through to the end the conversation seemed to
have moved on. Audio would be better and this can be enabled but it
would probably have its own problems with people talking over each
other. Maybe we would need to learn to put our hands up? The advantage
of SL is that it is a single package which once you've got working,
gives you the slides, the talk, and the questions all in one package. I
use video conferencing quite regularly for meetings but there are real
issues with ensuring that participants are compatible with the package
you are using -- in practise it is almost entirely used either for
internal (multi-site) meetings or one-to-one meetings via Skype or
something similar.

The Scifoo Lives on session itself has been covered by Jean-Claude who
also provides a
[transcript](http://usefulchem.blogspot.com/2007/08/scifoo-lives-on-medicine-20-session.html).
An issue that came up with several of the posters is how big the
community that supports them is or needs to be and how you go about
growing that community. Sites that provide a 'Wikipedia for Medical
Information' or a 'digg for the bioscience literature' are laudable
efforts. Their succes, like that of other sites featured depends on a
large enough community actively contributing to the site and providing
added value. Wikipedia 'works' (not wishing to get into the argument
about accuracy here) because an enormous number of people provide their
time freely to add value. Arguably a number of other Wiki sites aimed at
smaller communities have not achieved as much as hoped because the
community support isn't enough to provide critical mass. Its a tough
world out there and competing sites will rise and fall but there is some
critical mass required before they attract a big enough audience that
the site builds itself.

This is also true of open research more generally. We are a long way
from the critical mass that makes it worthwhile for people to put in a
little bit of effort on a regular basis because they get a lot back.
They key question to my view is what are the best steps to take that
will put us on the right path as fast as is sensible. And where can we
find some sociologists to help us on this? An argument for using the
term 'Open Research' may be that we need the help of the social sciences
community to figure out how best to proceed.


I attended the session held on Nature Island as part of the Scifoo Lives On series being organised by Jean-Claude Bradley and Bertalan Mesko and wanted to record some of my impressions. The mechanics of the meeting itself were interesting. My initial reaction to the idea of meetings in Second Life was pretty sceptical. My natural inclination would have been to setup some sort of video cast or conference call.

Messaggi di Rogue Scholar

Limits to openness – where is the boundary?

Scifoo Lives On session: Open notebook science case studies

How to get critical mass? Scifoo Lives on Session on Medicine and Web 2.0