Semantic Universe Website with Chemical/Polymer Informatics Contributions now Live

Over on Twitter, Semantic Universe has just announced the relaunch of their website. The purpose of the site is “to educate the world about semantic technologies and applications.”

To quote from the website:

“Semantic Universe and Cerebra today announced the launch of the “Semantic Universe Network”, a vibrant educational and networking hub for the global semantic technology marketplace. Semantic Universe Network will be the educational and information resource for the people and companies within the high-growth semantics sector, covering the latest news, opinions, events, announcements, products, solutions, promotions and research in the industry.”

As part of the re-launch, both Lezan Hawizy and I have written two short contributions reviewing the state of Semantic Chemistry and showcasing our work on how semantification of chemistry can happen. The contributions were intended to be short “how to..s” and as such are written in a somewhat chatty style. Here are the links:

Semantic Chemistry

The Semantification of Chemistry

Feedback is welcome.

Reblog this post [with Zemanta]

Something exciting, catalytic and quite delightful…

…has happened today.

I recently blogged about attending the first ESF summer school in Nanomedicine in Wales and speaking about our efforts in polymer informatics there.

After my talk, I was approached by an undergraduate, Hosea Handoyo, who wanted to know more about our work and who, amongst many other things, is currently a Neuroscience student in the Netherlands. When I asked him why he was interested, he said that he was attending the summer school in the capacity of a “student journalist”. Apparently, Hosea is part of a group of Indonesian students, which attend research conferences and try to find out what is going on in various areas of science at the moment. They then write this up in the form of “popular science” articles, which get published on the web.

Now if I remember our conversation correctly, there are several points to this. Firstly, it is intended to inform the Indonesian public in simple terms about what is going on at the cutting edge of research science at the moment. Secondly though, it also serves a landmark for students in Indonesia as to what research is going on where and which institutions/research groups they might consider joining in the future.

Now this morning, when I looked over my blog, I saw an incoming link from a website netsains.com (as annoying as the WordPress software may sometimes be when wanting to publish code in angle brackets, it is phantastic for all the housekeeping bits it offers). It looked a bit odd, but I could make out the terms “polimer informatika” in the link and so investigated further. And indeed, it turns out that the link led to an article that Hosea had written about our work here in Cambridge. Now his article is all written in Indonesian and I had no idea what it said, though I could make out some words “polimer informatika”, “kanker” (cancer – a lot of work in polymer pharmaceuticals is done in the area of anti-cancer drugs), the Unilever Centre was mentioned as was polymer markup language (PML), some of the databases I had discussed and Peter Corbett’s OSCAR (which always wows people every time it is demonstrated). I have since found out that his article has also appeared on the pages of the Indonesian Chemistry Forum.

Furthermore, there were links to all of the Unilever Centre blogs, my blog, a link to OSCAR 3 on sourceforge and even to the video on with a lecture on polymer informatics which is up on Google Video. I then got in touch with Hosea via email to make sure that I had remembered the details of our conversation correctly and I also asked him about the the purpose of the netsains.com website. Well, he told me that the site is supported by the Indonesian Minister for Research and Technology and is modeled on the Dutch Kennislink site. Kennislink was set up by the Dutch Ministry for Education, contains over 5000 popular science articles across all disciplines and is the most prominent Dutch language popular science site.

Now in his email (quoted with permission), Hosea said:

“All of these websites are aiming to bridge the gap between Indonesian scientists (and students) abroad and the ones in Indonesia. ICT especially internet is very limited in Indonesia (though the gadgets are quite sophisticated) so it is troublesome for people just simply browsing for information. By providing them the hottest issues from Europe, Japan, US, China, and many other countries, we share the information of research and development of scientific world with them. We could provide them the information of technology and in return, Indonesian communities abroad get updates of what happens in Indonesia and the link to translate their research/latest technology to what public in Indonesia needs. Simply like an open source idea but this is more to information sharing and empowering public awareness in scientific field.”

I found this really heartwarming and delightful for a number of reasons:

  • A genuine interest in science. It is phantastic to see that undergraduates go out to conferences with an interest in science and a desire to find out what is going on. In the past, I have worked in institutions where even the attendance of PhD students and post-docs was considered to be a “waste of time and money”. Personally, I think that it is never too early to expose someone who is genuinely interested in science to the cutting edge of what is going on in the world.
  • The idea of sharing and openness. It is an often quoted mantra, but one that is hardly ever practiced. We tend to lock up science and access to data in closed access journals, books or other resources. Often enough that already breaks our backs at well-resourced and well-funded institutions like Cambridge and makes scientific progress difficult. In other parts of the world, this is an absolutely insurmountable barrier. However, the more people like Hosea and others write about science on websites like kennislink.com or esains.com, the more people blog about their and other people’s science (the chemical blogosphere is exemplary in this) and the more students write their theses in the open, the more we can start to break these barriers down. And the internet, blogs, wikis etc. are the disruptive technology that will make it possible. Furthermore there is a social dimension here: those with access to resources (IT, conferences, literature etc….) enable access for those with fewer resources in the most efficient way through filtering and feedback.
  • The ability to set an agenda. Undergraduates turn into research students, post-docs, academics and decision makers. As research students, they have (always assuming the presence of an enlightened supervisor) the ability to determine what they work on (through choice of the research group they join) and maybe therefore also a choice over the culture in which science is done and in which they want to do science. As post-docs and academics they have the opportunity (together with their colleagues) to fundamentally change the way science is done and communicated. And as decision makers, they might just hold the purse strings, which enables them to tell academics how and where to publish (some funding bodies, for example, mandate that research funded through that body is published in open access journals or reposited).

I think that Hosea and people like him are the catalysts for positive change, which we need to move forward.

Pierre-Gilles de Gennes

Image

Pierre-Gilles de Gennes

In a now not so recent post I talked about the polymer reptation model and Pierre-Gilles de Gennes.

Well, last Friday, de Gennes died at the age of 74 and science lost a great man and a polymath. The New York Times has just published an obituary of the man. Please go and read it when you have a chance.

Polymer Snakes…

…is what I came across during tonight’s post-midnightly journey through the wild wild web. When searching for the keyword polymer in YouTube, I found a short animation about polymer reptation. I had to chuckle, because I had seen this movie before when someone taught me about the reptation model in a very elegant and wonderfully entertaining way.

The reptation model was developed by de Gennes and explains some of the behaviour of high molecular weight polymers in the melt. Consider a polymer chain, surrounded by other chains. Now the movements of such a polymer chain are constrained by the presence of other chains surrounding it and therefore the chain is only free to move within what is essentially a topological tube. Within that tube, it can carry out snake like motions (hence reptation) and only advance by diffusing it’s stored lengths.

de Gennes, by the way, is a polymath. A physicist by training, he made substantive contributions to such diverse areas as magnetism, liquid crystals, superconductivity and polymer physics. Though he formally retired in 2002, at the moment he is working on the comprehension of living systems and cellular mechanisms. Go and look him up, he is a fascinating character.

Hermann Staudinger

Hermann Staudinger (1881 – 1965) is the father of modern polymer chemistry and the man who gave us the concept of the macromolecule. Therefore I think it is only appropriate that he should lend his name to this blog and that I should quickly discuss who he was, before this blog starts in earnest.

Staudinger was born in Worms, an old Roman foundation and studied chemistry at the universities of Halle, Darmstadt and Munich. After receiving his doctorate from Halle (only four years after he matriculated at the university), he habilitated at the University of Strassbourg and at the age of 26 was appointed to a professorship in organic chemistry at the Technische Hochschule Karlsruhe and later on at the ETH Zurich as a successor to the famous Richard Willstaetter (who had received the Nobel Prize in Chemistry in 1915). At the time, Staudinger was only 31 years old. It was at Zurich, where his work on azide chemistry and the synthesis of synthetic diamonds first created a “bang” in the scientific world in more than one way. First there was the reaction named after him, the Staudinger reaction. This allowed the gentle reduction of an azide to an amine:

Image
Mechanistically, the triphenyl phosphine reacts with the azide to form a phosphazide, which subsequently looses nitrogen to give an iminophosphorane. Aqueous workup then leads to the amine.

The other “bang” resulted from Staudinger’s attempts to create synthetic diamonds: in a quarry close to Zurich he conducted experiments, in which he reacted carbon tetrachloride (InChI=1/CCl4/c2-1-1) with sodium metal (InChI=1/Na) in a closed container. The idea, of course, was that the reaction would form sodium chloride (InChI=1/ClH.Na/h1H;/q;+1/p-1) and elemental carbon (InChI=1/C), which would arrange into a diamond lattice given the high pressures generated by the explosion.
During his time in Karlsruhe, Staudinger started to pursure research into rubber chemistry and in a paper in 1920 floated the idea that rubbers and and polymers in general were composed of small repeating molecular units, which were all covalently linked.1 The idea put him at odds with a number of leading chemists of his time, most notably Emil Fischer, who, like many others at the time believed Grahams’s colloid theory, which stated that micellar self-assembly of small molecules, which were non-covalently linked, was essentially responsible for polymer properties. Another doubtor was Wieland, who wrote in a letter to Staudinger2:

“Dear Colleague, abandon your idea of large molecules, organic molecules with molecular weights exceeding 5000 do not exist. Purify your products such as rubber, they will crystallize and turn out to be low molecular weight compounds”

In his memoirs, Staudinger later added:2

“Those colleagues who were aware of my early publications in the field of low molecular weight chemistry asked me why I had decided to quit these beautiful fields of research and why I devoted myself to such disgisting and ill-defined compounds such as rubber and synthetic polymers which at that time in view of their properties were referred to as grease chemistry (“Schmierenchemie”).”

In 1922, he published a paper concerning the hydrogenation of natural rubber3 and it was in this paper that he first coined the term “macromolecule.” Upon moving to the University of Freiburg in 1926, Staudinger started to pursue grease chemistry full time, continuing to amass experimental evidence indicating the existence of macromolecules. His studies on crystalline poly(oxy methylene) (POM) using X-ray crystallography clearly proved the existence of macromolecules.4 Overall, his research in macromolecular chemistry resulted in the publication of 644 papers and the award of the Nobel Prize for Chemistry in 1953.
Rolf Muelhaupt, Staudinger’s successor in the chair for Macromolecular Chemistry at Freiburg, has recently published an eminently readable biography2 about the man and his chemistry, which I would urge you all to read.

[1] Staudinger, H. Ber. Deut. Chem. Ges., 53, 1073 (1920)
[2] Muelhaupt, R., Angew. Chem. Int. Edn., 43(9), 1054 (2004) DOI: 10.1002/anie.200330070).

[3] Staudinger, H., Fritschi, J., Helv. Chim. Acta, 5, 785 (1922)

[4] Staudinger, H., Johner, H., Signer, H., Mie, G., Hengstenberg, J., Z. Phys. Chem., 126, 425 (1927)