Cameron Neylon

A whole series of things have converged in the last couple of days for
me. First was [Jean-Claude's](http://usefulchem.blogspot.com)
description of the work
\[[1](http://usefulchem.blogspot.com/2008/03/expanding-usefulchem-collaboration-to.html),
[2](http://usefulchem.blogspot.com/2008/04/were-gonna-ugi-all-night.html)\]
he and [Brent Friesen](http://ochemonline.wordpress.com/) of the
[Dominican
University](http://www.dom.edu "Dominican University"){rel="homepage"}
are doing putting the [combi-Ugi
project](http://usefulchem.wikispaces.com/combiugi) into an
undergraduate laboratory setting. The students will make new compounds
which will then be sent for testing as antimalarial agents by [Phil
Rosenthal](http://www.ucsf.edu/bms/faculty/rosenthal.html) at
[UCSF](http://www.ucsf.edu "University of California, San Francisco"){rel="homepage"}.
This is a great story and a testament in particular to Brent's work to
make the laboratory practical more relevant and exciting for his
students.

At the same time I get an email from [Anna
Croft](http://www.chemistry.bangor.ac.uk/akc/), University of [Bangor,
Wales](http://en.wikipedia.org/wiki/Bangor%2C_Gwynedd "Bangor, Gwynedd"){rel="wikipedia"},
after meeting up the previous day;

> \[...\] I discussed the idea of blog-labbooks with my student/PDRAs on
> the way back and we were all keen to trial your stuff. I have also
> taken the liberty of talking to a couple of my colleagues over morning
> tea, and they were also very interested in the project and the idea of
> open science -- I expect when a couple of my other colleagues are back
> next week they will also be keen.
>
> **We thought it might be particularly valuable as a teaching resource
> in the first instance -- ie making the undergrads use it as** \[CN --
> my emphasis\]  1. it is more like the technology they are used to and
> 2. transparancy might improve the quality of their record keeping. It
> may come in very handy for undergrad practicals even, because it will
> be obvious to anyone who has copied each other. So I'm sure we could
> provide you with more than enough trouble shooting and commentary on
> the practice of open science to support your thesis that it is better
> for all ;)

I think this is emerging as a theme. If we can get these systems into
the undergraduate laboratory we can do two things. We can help to engage
the students by providing tools that, to them, may seem more relevant to
their everyday lives. We can improve the educational experience by using
the social networking and commenting tools available to help the
students learn from each other. Perhaps most exciting, if as Jean-Claude
and Brent are doing this is embedded in a real science project,
particularly one with clear social significance, the students will be
*directly involved with the science.* We talk a lot about 'research led
teaching' in the UK but I've seen little evidence of people really doing
it. Here is a real chance to make that happen, and because it's [Open
Notebook
Science](http://drexel-coas-elearning.blogspot.com/2006/09/open-notebook-science.html)
they will be able to track the results from their own computers, at
home, perhaps even while uploading the results to their facebook page
(all right maybe not...).

But let's think bigger again. What if it were possible to spread this
out globally, using a coherent information tracking system. Chemistry
undergraduates all over the world could be making thousands of
characterised drug like molecules. Perhaps the screening could be done
in undergraduate biochemistry laboratories with well defined screening
assays for a wide range of targets: malaria, cancer cell lines, *S.
aureus*, HIV protease. You could expand this into physical
chemistry/biophysics with undergraduates looking at docking of the new
or proposed compounds against the available targets. A global programme
could link all of this together generating a massive library of
compounds screened against a wide range of targets.

And all of this would be open. [Deepak](http://mndoci.com) asked the
question the other day, '[What if the result of every docking result was
published online?](http://mndoci.com/blog/2008/03/28/what-if/)' and I
have previously imagined a '[Genbank of SAR
data](http://blog.openwetware.org/scienceintheopen/2008/01/27/picture-this/)'.
A programme like this could actually provide the impetus for such
repositories, while simultaneously adding value with characterisation
data for new compounds to existing initiatives like
[ChemSpider](http://www.chemspider.com/). Whether or not we actually
found hits the SAR data would be immensely valuable for future data
mining. Whether or not the SAR was useful to impetus towards building
these databases would be immensely valuable.

So -- what about the challenges. Converting research chemistry into
undergraduate labs is not straightforward. Jean-Claude's Ugi reactions
are a particularly good example for this because you can just mix three
compounds in methanol and in many cases the product precipitates. But
even here it's not trivial -- one component is usually smelly; the
compounds may not dissolve in methanol; the product may not precipitate.
Getting the fundamentals of a particular reaction right will take person
hours and quite a lot of them. In UK language this could be done with a
final year undergraduate project student to get one type of reaction
working in a three to six month project.

Screening can be just as hard. The reactions are not necessarily
straightforward, the reagents (and positive and negative controls) can
be expensive, and the equipment required to do it efficiently may not be
available. But again many reasonably straightforward assays are
available, and the rest just require time, expertise, and money. This
could be tracked down from a range of sources.

So, resources are required which really means money. Which is where the
third co-incidental strand comes in. [Via Pawel Szczesny on
FriendFeed](http://friendfeed.com/e/681654ce-7129-127e-03ff-27e15eec5eae)
I got a link to the following
[pos](http://phylogenomics.blogspot.com/2008/04/bill-and-melinda-gates-that-is-ask-for.html)[t](http://phylogenomics.blogspot.com/2008/04/bill-and-melinda-gates-that-is-ask-for.html)
about a [call from the Bill and Melinda Gates
foundation](http://www.gcgh.org/explorations/Pages/Introduction.aspx).
The problem with this call is that it really needs a drug resistance
angle to fly and while that is possible it complicates the whole idea
significantly. But between the B&MG foundation, Google, and others all
looking for projects that are both socially significant, make them look
good, and co-incidentally generate lots of data in the health arena that
they can process, this ought to be fundable. In particular this looks to
me like a great fit for Google. For us, it's great education, great
publicity, great science, and it demonstrates the benefits of openness.

A small scale project funding a development round for 12 months to try
and sort out appropriate reactions and assays, while trying to agree and
implement a data framework that will work for us would probably cost
around \$200-300k total costs. This would be followed by a larger scale
implementation phase, heading towards a few million probably, as it gets
rolled out. As it embeds in the education system the costs would
probably drop over time to eventually be absorbed in the programme
costs.

What do people think?

Further Reading: Jean-Claude's proposal on '[Crowdsourcing
Chemistry](http://usefulchem.blogspot.com/2008/01/chemistry-crowdsourcing-pre-proposal.html)'

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A whole series of things have converged in the last couple of days for me. First was Jean-Claude’s description of the work [1, 2] he and Brent Friesen of the Dominican University are doing putting the combi-Ugi project into an undergraduate laboratory setting. The students will make new compounds which will then be sent for testing as antimalarial agents by Phil Rosenthal at UCSF.

Messaggi di Rogue Scholar

Open Science in the Undergraduate Laboratory: Could this be the success story we’re looking for?