Maxine Clarke highlights a bit of recent controversy regarding Open Notebook Science that has been bouncing around the blogosphere and FriendFeedosphere.

There are some who interpret the ongoing publication of our laboratory notebook as an expectation for the world to read it like a magazine. For someone who is not a collaborator or working in a related area that would make about as much sense as reading the phone book.

Here is an example of how an Open Notebook should be used:

I'm back from the UCSD workshop on New Communication Channels for Biology held June 27-28, 2008. The talks were recorded and are now available here.

The first day mainly consisted of talks while the second was very heavy on breakout sessions (see agenda). Probably the most beneficial part for me was seeing old friends or meeting in person several people I had only interacted with online previously. For example was nice to finally meet Dan Gezelter from the OpenScience project and Hilary Spencer from Nature Precedings. I also had a blast over enchiladas on Friday night with Mike Nieslen and Jen Dodd. Mike gave a very engaging talk on the Future of Science on Thursday night.

The presentations were recorded and should be available within a week on the wiki link above - I'll post an update here when I am made aware of it.

I was asked by the Institute for the Future to highlight a dozen "Signals" that may point to new trends in science as part of the X2 Project:

A few weeks ago I received a very interesting email from Brent Friesen at Dominican University. He mused:

I am trying to put together a bridge between the type of opensource research you are instigating and the traditional Sophomore Organic Chemistry lab. There are over 4,000 college and universities in the United States - all of them teach Sophomore Organic Chemistry lab. How can we harness this resource? .....

SOC labs must fulfill 4 criteria:

1) inexpensive reagents and equipment
2) fit into the time constraints of 1 3-hour period per week.
3) Must be a robust reaction with fairly stable products. It doesn’t have to be “foolproof” but that helps.
4) Compatible with equipment, glassware, procedures that student know how to use and do.

Bottom Line: I am definitely interested in developing collaborative projects, especially if they can be performed as part of a Sophomore Organic Chemistry laboratory curriculum.

This is extremely encouraging news for open scientific collaborations and I am very impressed with Brent's initiative! It certainly is more work for him compared to maintaining the status quo.

Kevin Owens and I have discussed this possibility for some time now and he is willing to contribute by carrying out mass spectrometry if required.

The Journal "Open Medicine" has published a very thoughtful editorial on "Open science, open access and open source software at Open Medicine" by Sally Murray, Stephen Choi, John Hoey, Claire Kendall, James Maskalyk and Anita Palepu.

Not only are they writing about it but they want to get their hands dirty as well:

Open Medicine is an open access journal because we believe that free and timely access to research results allows scientific knowledge to be used by all those who need it, not just those who can afford expensive journal subscriptions or user fees for individual articles. But is access to the final polished version of research enough? Could we do more to en­courage the collaborative reuse and reanalysis of existing data, or the verification of analyses? Could we move from open access to open science?

The American Chemical Society will be offering a virtual poster session in Second Life from selected posters at the Sci-Mix session taking place April 6, 2008 at the next national meeting in New Orleans.

I'm helping out with that effort and I'm pleased to say that we have our first submission from Jodye Selco, Mary Bruno and Sue Chan: "Safe and economical chemistry inquiry for the K-12 classroom".

ACS island has the same shape as its logo of a phoenix, thanks to the skilled hand of Eloise Pasteur who carved out the Drexel island's dragon shape. The posters will be placed on the right wing, next to a "chemistry museum" area, also under development.

Collaboration is a requirement for the advancement of modern science. Researchers cannot be expert at everything and must specialize to make a unique contribution.

But if coordinating research within a group is challenging, effective collaboration between groups is even more so.

There is often a strong temptation for research units to treat each other like black boxes. There is some logic to this - the point of having a collaborator is to distribute the responsibility of tasks in a project. If I get involved with every detail of my collaborator's work I may as well do the work within my own group.

But problems can arise because of unstated assumptions between groups. A good example is a recent collaboration with groups testing for biological activity. We synthesized compounds and shipped them out for various tests (anti-tumor and malarial inhibition). The researchers performing the assays may have assumed that we had verified aqueous solubility and we didn't think of it since we were not familiar with their protocols.

Michael Barton has posted a brief essay on Open Notebook Science on his research web site:

From Bora Zivkovic's A Blog around the Clock:

Here is a video of SPARC-ACRL Forum '08 on 12 January, 2008 at the Pennyslvania Convention Center in Philadelphia:

The SPARC-ACRL Forum at ALA '08 entitled "Working with the Facebook generation: Engaging students views on access to scholarship." Panelists discuss the merits of student activism, patent reform, blogs as a communication medium for scientists, and students as active members of a discussion about the right to access information for scholarly work. Features Andre Brown, Nelson Pavlosky, Stephanie Wang, and Kimberly Douglas as panelists.

Pay particular attention to Andre Brown and minutes 42-55 as he talks about science blogs and Science 2.0 including
mentions of all the usual suspects (Jean-Claude Bradley, Rosie Redfield, Reed Cartwright, Bill Hooker, Peter Suber and me):

The results are in.

Jiri Gut from the Rosenthal group has run 2 of our Ugi products and they both show inhibition of falcipain-2 (EXP165) and Plasmodium falciparum (EXP166) in the micromolar range.

To put this in context the activities are roughly 2 orders of magnitude lower than the positive control used for the enzyme inhibition and chloroquine for the parasite.

But it is a start. And we have officially closed the Open Science Loop for the malaria project, meaning that we have openly documented the docking results from Rajarshi Guha (D-EXP014), our syntheses (EXP148 EXP150) and testing (EXP165 EXP166) in the Rosenthal group.

We can't tell much about the validity of Rajarshi's docking model from the results of two compounds but as more data come in the situation should become clearer.

However, Jiri did make this interesting observation:

The food vacuole abnormality, which is indicative of cysteine protease inhibition was not observed in the parasites, suggesting other mode of action.

Like last year, the North Carolina Science Blogging conference was a hit.

I moderated a session on public scientific data with Xan Gregg. Both of our talks were recorded and available here. (I used SciVee this time to store the screencast and was even able to use their supplementary document option to store the mp3 that Feedburner properly processed in the podcast feed.)

We spent about half the session with presenting then there was an active discussion. (Hopefully someone got some decent audio on that part and I'll post a link here if possible.) The usual issues of scalability, findability, fundability, scooping, academic validation and government policy came up. No resolution on any of these of course but that's not the point of the gathering. Some new contacts were made and maybe that will lead to some progress on the Open Science front.

Yesterday I had the privilege of attending a workshop at the NIH on the National Cancer Institute Clinical Development of Small Molecules:

This one-day workshop will provide specialized training and information to NCI-supported investigators who plan to undertake clinical development of novel concepts and who are directly involved with implementing translational clinical research. Individuals will benefit from the opportunity for direct interaction with FDA’s Center for Drug Evaluation and Research and NCI’s Developmental Therapeutics Program senior staff.

I am grateful to Dan Zaharevitz for the invitation to the workshop yesterday and to a visit of his screening labs later today.

Dan has a vision that the drug discovery and development process could benefit tremendously through openness at all stages by facilitating communication between all parties involved from discovery through clinical testing.

Mitch Waldrop has written an informative piece on the Science 2.0 movement in Scientific American:

Science 2.0: Great New Tool, or Great Risk?

Consistent with the content of the article, Mitch invites feedback:

Welcome to a Scientific American experiment in "networked journalism," in which readers—you—get to collaborate with the author to give a story its final form.

The article, below, is a particularly apt candidate for such an experiment: it's my feature story on "Science 2.0," which describes how researchers are beginning to harness wikis, blogs and other Web 2.0 technologies as a potentially transformative way of doing science. The draft article appears here, several months in advance of its print publication, and we are inviting you to comment on it. Your inputs will influence the article’s content, reporting, perhaps even its point of view.

So consider yourself invited. Please share your thoughts about the promise and peril of Science 2.0.—just post your inputs in the Comment section below. To help get you started, here are some questions to mull over:

* What do you think of the article itself? Are there errors? Oversimplifications? Gaps?
* What do you think of the notion of "Science 2.0?" Will Web 2.0 tools really make science much more productive? Will wikis, blogs and the like be transformative, or will they be just a minor convenience?

Chemical research has traditionally been organized in either experiment-centric or molecule-centric models.

This makes sense from the chemist's standpoint.

When we think about doing chemistry, we conceptualize experiments as the fundamental unit of progress. This is reflected in the laboratory notebook, where each page is an experiment, with an objective, a procedure, the results, their analysis and a final conclusion optimally directly answering the stated objective.

When we think about searching for chemistry, we generally imagine molecules and transformations. This is reflected in the search engines that are available to chemists, with most allowing at least the drawing or representation of a single molecule or class of molecules (via substructure searching).

But these are not the only perspectives possible.

What would chemistry look like from a results-centric view?

Lets see with a specific example. Take EXP150, where we are trying to synthesize a Ugi product as a potential anti-malarial agent and identify Ugi products that crystallize from their reaction mixture.

If we extract the information contained here based on individual results, something very interesting happens. By using some standard representation for actions we can come up with something that looks like it should be machine readable without much difficulty:

I recently reported on a new collaborator who agreed to work with us in the open on modelling subcellular drug transport.

I am very pleased to report that Gus Rosania has now created an entire wiki (1CellPK) for his lab to use as an open notebook. From the home page of the wiki:

Open Notebook Science is ideally suited for community-wide collaborative research projects involving mathematical modeling and computer simulation work, as it allows researchers to document model development in a step-by-step fashion, then link model prediction to experiments that test the model, and in turn, use feedback from experiments to evolve the model. By making our laboratory notebooks public, the evolutionary process of a model can be followed in its totality by the interested reader. Researchers from laboratories around the world can now follow the progress of our research day-to-day, borrow models at various stages of development, comment or advice on model developments, discuss experiments, ask questions, provide feedback, or otherwise contribute to the progress of science in any manner possible.

How's that for a Christmas present to the Open Science community?

Rajarshi Guha has yet again made a key contribution to our UsefulChem project by connecting us with Gus Rosania at the University of Michigan. Gus is interested in a fully open collaboration to help us further prioritize our drug targets based on predicted subcellular drug transport:

It is the first time I hear about Open Notebook Science, but it sounds like a fantastic idea!

My research group studies the subcellular transport of small molecules. We are interested in combining cellular distribution of small molecules together with systems biology, to analyze the pharmacological activity of small molecules in a cellular (and organismic) context. For more information about our subcellular transport lab, you can visit us at http://www-personal.umich.edu/~grosania/

This term, the students in my organic chemistry class were presented with an opportunity to do an extra credit assignment using Second Life to represent concepts they learned in the course.

When I was an undergraduate, finding molecules in articles was mainly done using the Chemical Abstracts books. A convenient way to find a specific molecule would be to look up the molecular formula and find the corresponding IUPAC name. Theoretically, one could figure out the IUPAC name from scratch but this can be very tricky for complex molecules and prone to error. With the correct name, I could look for analogues of a molecule of interest in alphabetical catalogues by understanding how the chemical name works.

But when computer databases started to be used in chemistry, using the name of a compound became far less important. Searching for molecules now comes down to drawing them on computer screens and using computer generated text representations like SMILES and InChI. Knowing how to use these tools on free software and services is key to being fluent and flexible on the chemical web. And I think that is the most important benefit that students get from doing these assignments.

I recently submitted a Letter of Intent for the NSF Cyber-Enabled Discovery and Innovation competition. Kevin Owens is a co-PI and will assist with the laboratory automation component. ChemSpider will contribute the database support. The pre-proposal is due in early January 2008 and we'll be writing it openly here. Comments are welcome.

We would ultimately like to enable the chemistry community to directly control the actions of a robot to help us understand some chemistry problems. As we make our way towards this goal, it would be very useful to start with suggestions for protocols to be executed by students we currently have in the group.

We've reached an important milestone on our CombiUgi project involving the synthesis of falcipain-2 inhibitors. In my last update I described how our focus was more on doing many reactions in parallel and only looking for Ugi products that precipitate in pure form within a few days.

It took little longer than I hoped. In order to do more reactions, we reduced our efforts towards monitoring. One of the assumptions that we made was to trust a bottle's label to accurately describe its contents. That turned out to be incorrect for one of our key aldehydes, as we eventually found out by systematically taking NMRs of the starting materials. Soon after ordering a new bottle of phenanthrene-9-carboxaldehyde we were treated to the growth of beautiful crystals (see EXP150 by Khalid and Emily):

Most of us are familiar with the mantra of how science progresses:

A hypothesis can never be completely proved by any finite set of experiments but it can be falsified by a single result.

In mathematical proofs, clear cut algorithms can usually be applied to prove unequivocally the falsehood of a theorem (notwithstanding Godel's incompleteness theorems :)

But in real research in the physical sciences, that is not exactly how scientists process reports of experimental results. And an important reason is the way results are reported.

Lets pick an example from the Open Access Beilstein Journal of Organic Chemistry.

Here is the full description of the experiment from the supplementary materials page:

To a solution of 5a (196 mg, 0.433 mmol) in CH2Cl2 (1.8 mL) was added p-toluenesulfonic acid (19 mg, 0.11 mmol). After stirring for 0.5 hours at 0 oC, the mixture was concentrated under reduced pressure and purified by flash chromatography on silica gel (eluent: ethyl acetate: P. E. = 1: 3) to provide 7 (152 mg, 100%) as a colorless oil.