Category: Chemspy

I just listened to Cameron Neylon’s fascinating talk given at Drexel a short time ago, it’s available as a podcast/mp3 via the UsefulChem Blogspot. Neylon has turned to modified blog software to help his team capture their ongoing science and is now opening his laboratory notebooks to the world.

Several things struck me from his talk. First, he points out that grad students are generally reluctant to get involved if it means more work, especially if they are not so hot on keeping a neat paper labbook, but also because their work is suddenly on show to the world. In Neylon’s field there is also the problem of tagging the materials with which his group works – short DNA sequences and proteins. Chemists, of course, have Smiles strings and InChI keys, but there is no single, simple way of tagging a protein like this, that would make it readily searchable across the blogosphere, web or database. This is especially problematic given that many research groups will be working with their own unique sequences.

However, it is the potential power of open notebook science that came across most strongly in Neylon’s talk and it is exemplified by a little anecdote he told in response to a question from the audience at the end of the lecture.

Apparently, one of his students had been struggling with a DNA experiment, finding the heatshock process difficult and not getting the results she expected. Nothing was awry in her procedures until she ran out of sample tubes and Neylon pointed out that the shelves needed restocking. It was at this point that the he and the student realised she had been using a different brand in her experiments to that used in the previously successful runs carried out by other team members.

Of course, the tube brand was not mentioned in anyone’s lab book, it was assumed they were generic components and so brand was irrelevant. Not so. At the scale they are working at, and with highly temperature sensitive materials, a minute difference in tube thickness and precise composition makes all the difference in heat distribution. The students experiments with the other brand failed because this was not taken into account. Industrial chemical engineers would have recognised the problem immediately, I’d assume. Anyway, switching back to the original brand have her almost instantaneous success and results are now being written up.

The point being, that in an open electronic notebook, such problems could be flagged so that group members and supervisor would be alerted. A meta tag in the experiment’s blog post SUCCESS=0,1,NULL could easily be included. Moreover, fields could be added in the equipment section to specify brands so that a failed experiment in which the wrong brand was used might be spotted and a different brand of tube, for instance, used next time. Such information would be archived and available to future generations so that similar mistakes would be circumvented.

Meanwhile, you can listen to the complete talk from Neylon here.

My old friend Peter Gölitz this year celebrates a quarter century as Editor-in-Chief of the chemistry journal Angewandte Chemie. When he took over the editorship of the German Chemical Society’s premier chemistry journal in 1982, there were just four other chemists on the editorial staff and the journal published a mere 1000 pages a year. More than 9 out of 10 papers were from Germany. How things have changed.

Angewandte is now a weekly publication, is available online, and has an annual pagecount of 9000 pages. German authors are still the largest group of contributors, but four out of every five articles
published has an international team member. Oh, and Peter has a little more help these days than he did 25 years ago with 18 PhD chemists and 9 other colleagues helping run the show.

Peter is rather proud of the journal’s ISI impact factor, which ha srisen from a little over a “4” in 1982 to better than a 10 this year. It’s even surpassed several of its established competitors in this respect. During my New Scientist years, papers from Angewandte featured prominently in my reporting, partly this was because the journal seemed so much more accessible than the heavier grey tomes from other publishers. More than that though, much of the chemistry published seemed to have at least the potential of immediate applications and often flaunted this with an enticing graphic…perfect for pop science.

Congratulations, Peter, and here’s to the next quarter century ;-)

I suspect that a large proportion of the chemical blogosphere has either received the spam message from [email protected] some time this month or if they haven’t they will have seen it on one of the blogs. It’s on Chemical Forums, Peter Suber’s OA blog and from there it went to PeterMR’s blog, and the CHMINF-L discussion group, and several other blogs summarized in this Pg cluster.

The gist of the message is that a purported long-time ACS employee is frustrated by the size of the salary their boss receives and that this somehow relates to how the organisation operates and the profits it makes. Where’s the news in that? Bosses earn more than their subordinates! Shock! Salaries tied to success! Horror!

There is no way to validate the source of the original email from the headers alone, a free Yahoo account was used to send it and the YahooID is not in the membership directory of that site, so it may or may not be from a disgruntled ACS employee, we may never know, unless the person owns up.

My flippancy aside, the email does raise an important point, which Peter Suber and others wish to address and he suggests that the community should raise the following issue in open discussion: “If your professional society has opposed government OA policies, try to find out whether its executives get bonuses based on the revenues or profits of its publications. If they do, ask in a public meeting whether they believe this is a conflict of interest.”

I asked the ACS communications office to comment on the original email, and they got back to me with a statement. In it, the ACS categorically states: “The anonymous author makes erroneous and misleading claims about the compensation of these employees and alleges that the compensation is somehow related to the Society’s position on open access.”

It goes on to say that: “The ACS’s position on Open Access has been developed carefully over many years, in consultation with scientists and publishing experts from a wide range of scientific disciplines and interests. It is measured and seeks to balance the legitimate needs of all stakeholders in scientific publishing. That position has been fully reviewed and approved by the appropriate levels of ACS Governance, including Board Committees and the Board of Directors, and is not a ‘staff decision’ alone.”

So, on the one hand, we have a spurious claim from an anonymous emailer claiming to be an ACS employee, which has been taken up by the chemistry blogosphere and beyond and a statement from ACS denying all the claims in said email and consolidating their stance on Open Access.

Do ChemSpy readers have any thoughts on all of this?

Joana Mendonça and Rui Baptista of the Centre for Innovation, Technology and Policy Research at the Technical University of Lisbon, working with Paulo Conde of Solvay in Brussells, Belgium, have examined how innovation occurs within the chemical industry, by examining the processes and activities undertaken by the Portuguese branch of a multinational chemical company. They have looked at the company’s formal innovation process and from that they have gleaned a map of the knowledge bases used in the search for innovative, new products.

Europe is a major player in the global chemical industry, but recently supply has begun to shift towards the Asian and Middle East markets. Demand from these regions is increasingly rapidly but their own fast-developing industries may not face the same high production costs and strict environmental regulations that increasingly make Europe a less attractive investment.

Couple this socioeconomic and geographical shift in production with a fall off in R&D spending in Europe and the exodus of skilled labour and on the surface it appears that chemical industry innovation within Europe is on the wane. Faced with this prospect, Mendonça and colleagues suggest that it, “is of crucial importance to analyse its processes within the chemical industry.”

Their analysis of the chemical industry has allowed them to produce a map showing the spread of the industry’s widely distributed knowledge bases and to demonstrate how knowledge flows between them and how it is used. They have found that the ability to generate value-creating knowledge is concentrated in the early stages of the industry’s lifecycle regardless of region. In contrast, the Portuguese industry is mostly concentrated on activities that have already reached maturity and, in some cases, are in decline rather than looking to innovation. “Owing to this asymmetry, disembodied knowledge flows are difficult to create, and other types of relationship should be pursued,” they suggest.

They also point out that multinational companies tend to rely strongly on internal improvements and do not seek new knowledge from outside sources that might lead to profitable innovation or improvements in efficiency. Indeed, any innovative activities that take place are actually focused on preventing “unwelcome surprises and to minimise risk” as opposed to facilitating the kin of “freewheeling, imaginative, and risk-taking approach that characterises entrepreneurship”.

All is not lost, add the researchers, “large multinational companies can have a decisive role in the innovation process by providing their market expertise to entrepreneurs and the case study presented shows a path other companies may follow.”

The original research paper, “A map of the knowledge bases for the chemical industry” can be found in the current issue of the International Journal of Technology, Policy and Management (2007, 7, 245-262)

The American Chemical Society (ACS) website got a makeover. They haven’t gone totally two-point-oh (thankfully) but they have made a few improvements (ten to be precise, at least according to their announcement), two of which are comprehensiveand at least 2 or 3 of which amount to the same thing. Still, it is nice a nice layout, albeit, a bit toooo web one-point-ohhhh and a little more 2005 than 2007. If you’ve used the features leave a comment and tell us about your experiences.

Anyway, here’s the top ten according to the ACS itself:

• Consistent, global navigation
• Unified look and feel
• Ten comprehensive categories
• Member focused
• Home page highlights
• Comprehensive search
• Easier to read
• Faster access
• One stop for help
• User Tested and Approved

Molecular Networks Inc this week launched SYLVIA, software to rapidly evaluate the synthetic accessibility of any given organic structure and to prioritize thousands of structures according to their synthetic complexity. The company describes SYLVIA as the link between computer-aided de novo molecular design, chemoinformatics and synthetic chemistry.

SYLVIA scores compounds based on structural elements, similarity to commercially available chemicals and a reaction-based component extracted from reaction databases.

No doubt to the irritation of many potentially interested parties you have to purchase a license for SYLVIA, although a free evaluation download is available. Input file format is MDL, SDFile (incl. Molfile), SMILES, and CTX file. No mention of InChI unfortunately. Output is as MDL, SDFile (incl. Molfile), and CTX file. In fact, I couldn’t even find InChI mentioned on the Molecular Networks site, which is odd given this unique identifier’s potential in the field of organic chemistry.

The Chemical Blogspace Zeitgeist page is an interesting round up of chemical blogs. The ChemSpy blog resides at #9 in the top fifty chemistry blogs (trailed slightly by Sciencebase at #13). That in itself is quite gratifying, but it is the other statistics that make for more entertaining reading. Apparently, ChemSpy has a reading index (Gunning-Fog as it happens, based on the most recent three months posts) equivalent to a scientific journal (index of 14). Reading Sciencebase on the other hand is like picking up a Thomas Pynchon novel. But, at least, the site doesn’t rank alongside
In the Pipeline, The Bioenergy Blog, Cheminfostream, and it’s a puzzle…, which all have a Gunning index of between 17 and 20 and so are apparently equivalent to reading a “Manual for Taiwanese DVD player”. Not my words, Cb’s!

By the way, sites also seemed to be ranked on the basis of their use of InChIs, it’s worth checking out this page to see what molecules are being discussed and to see their structures.

Scrolling down, I learn that Sciencebase is fifth most active blog, while, not unexpectedly, Chemspy is not in the top 20 based on activity (frequency of posting). Once again, Sciencebase features in the top 20 based on wordiness (average posts being around 500 words), while Chemspy’s terse commentary (until today, that is) nestles much further down the tree. The final statistic of interest is the measure of friendliness, which might also be referred to as blog nepotism, or blogotism, to coin a word, just how many times a blog links out to other sites in the chemical blogspace. Again, not unexpectedly, neither Sciencebase nor Chemspy feature in the top 20, basically because my posts tend to be standalone write-ups referencing the primary literature and only occasionally have a need to backlink to other blogs. That said, I’d be interested to know if ChemSpy readers would prefer to see more outbound links to related content elsewhere in the chemical blogspace. Please leave your suggestions in the usual place.