petermr's blog

A Scientist and the Web

 

Archive for August, 2009

The Mind Wobbles at Science Online

Saturday, August 22nd, 2009

There’s hardly any need for me to blog the sessions at #solo09 because I’m sitting next to the author of The Mind Wobbles who’s typing at breakneck speed. There’s a full report at:

http://themindwobbles.wordpress.com/2009/08/22/blogging-for-impact-science-online-london-2009/

There’s also a lot of FriendFeed activity I find this more useful than Twitter as it’s threaded (and there’s transfer between the two).

Now we are contemplating What is a scientific paper? Four moderators; 2 spoken , 2 still to go. So far nothing world-shattering or even mind-wobbling or mid-teetering. .

Now Theo Bloom from PloS is saying it’s time for a radical overview. It”ll all be on The mind wobbles! So I’ll reserve comments for later. But I think I’ll be going to suggest that the panel isn’t going fair enough.

25% of authors can’t find one/any of the images (e.g. gels) that ther included in the paper. That’s a strong case for the sort of work we are doing in data capture with CLARION.

Galaxy Zoo at Mendeley

Saturday, August 22nd, 2009

Am returning the the blogosphere after some considerable hiatuses (due to debugging of Chem4Word which has taken many of the 162h w-1. That’s starting to ease up). So I’m at the Royal Institution in the company of 170 bloggers the meeting (#solo09) was oversubscribed and I’m grateful to being squeezed in. I may blog on some of the sessions, but the current one is off-limits for good reasons.

We had a great party last night hosted by Mendeley the new company which is gearing up to revolutionise how we use references. I hadn’t realised they were in London Farringdon we had a very pleasant rooftop gathering with about 50-70 others.

Twitpic of party

We had 4 sessions 2 planned 2 unconference where we shared aspirations, history, problems, etc. Had a great time talking about Galaxy Zoo the online community that annotates galaxies. There’s about a million galaxies that needed to be annotated do they look like spirals or green swirly things or processed peas? I knew GZ was large, but I was surprised to find out there were 230,000 registered members. About 70,000 are active.

So why do they do it? Apparently there are motivated by contributing to science. They’ve had 12 papers published on GZ work. So what a splendid idea to translate to other endeavours. We had a session at Scifoo on crowdsourcing science and this is certainly something that I’ll be taking on board.

More later…

Mon cher enfant, j

Wednesday, August 19th, 2009

Howard Flack is s crystallographer who has devoted many years to the crystallography of stereochemistry. Now he has published a fantastic review of one of the greatest feats of science Pasteur’s work on optical isomers: http://crystal.flack.ch/sh5092.pdf

Louis Pasteurs discovery of molecular chirality and spontaneous resolution in 1848, together with a complete review of his crystallographic and chemical work

I couldn’t even start to summarise this, but I would make it required reading for any young chemist. It’s almost impossible for us to recreate the mindset of chemistry 150 years ago and relating the geometry of crystals to life must have seemed fantastical. Weird ideas abounded and it would never have met the rigid and mechanical funding criteria of today. Not surprisingly Pasteur’s professor, Biot, was not convinced.

Howard quotes one of my favourite passages translated and written by Frankland over 100 years ago. It shows the scepticism necessary to science, the care required to plan an experiment with appropriate control and the readiness of a great scientist to change their world view in the face of new ideas and evidence.

He (J.-B. Biot) sent for me to repeat before his eyes the several experiments. He gave me racemic acid which he had himself previously examined and found to be quite inactive to polarized light. I prepared from it in his presence the sodium ammonium double-salt, for which he also desired himself to provide soda and ammonia. The liquid was set aside for slow evaporation in one of the rooms of his own laboratory, and when 3040 grams of crystals had separated he again summoned me to the Colle`ge de France, so that I might collect the dextro- and laevo-rotatory crystals before his eyes, and separate them according to their crystallographic character, asking me to repeat the statement that the crystals which I should place on his right hand would cause the deviation to the right, and the others to the left. This done, he said that he himself would do the rest. He prepared the carefully weighed solutions, and, at the moment when he was about to examine them in the polarimeter, he again called me into the laboratory. He first put the more interesting solution, which was to cause rotation to the left, into the apparatus. Without making a reading, but already at the first sight of the colour-tints presented by the two halves of the field in the Soleil saccharimeter, he recognized that there was a strong laevorotation. Then the illustrious old man, who was visibly moved, seized me by the hand, and said Mon cher enfant, jai tant aime´ les sciences dans ma vie que cela me fait battre le coeur!.

THE article: Do academic journals pose a threat to the advancement of science?

Thursday, August 13th, 2009

Times Higher Education has run an article by Zoë Corbyn on A threat to scientific communication – subtitled: Do academic journals pose a threat to the advancement of science? She interviewed a number of people (including me) on both sides of the fence and I think it’s a balanced article. If you work for a publisher (or own a publishing house) you may think differently.

I still believe in a role for publishers and I know many people in publishing who are trying to do exciting things but the current position must change.

The article, which you should read, covers:

  • the impact factor

  • the monopolistic position of certain publishers

  • some barriers to innovation

  • a feeling that change has been far too slow and that change will happen anyway

My quoted remarks are probably no surprise to readers of this blog, but THE is widely read at least in the UK and my opinions were intended to reach the heads of Universities and spur them to action. Simply put, Universities get the publication process they deserve. They have the financial power to change it to suit the twenty-first century they haven’t done so. They must.

Zoe puts the value of scholarly publishing at 3 B GBP == 5 B USD. It’s obviously a difficult figure to compute ans many publishers publish things other than journals (e.g. databases, handbooks, series, etc.). I guess the global academic research budget at ca 500 B USD. Cambridge Harvard, Stanford have research incomes of ca 500 M USD. Allow a power law and you get somewhere near that. As a rough check Wellcome will pay 1-2 percent of a grant for the cost of publishing a paper, which gives roughly the same ballpark. I’d be grateful for other figures. What’s the NIH spend? 30 B USD (http://www.nih.gov/about/budget.htm). Again use a power law and you get somewhere in that region.

The people who should jointly control this half-a-trillion USD are the funders and the researchers. So why does a metric system outside their control have such massive influence?

Universities have lost their Presses as major forces, their Libraries have no influence, so it has to be those who run the Universities to reclaim their standing.

The least they can do is read THE and start to address the problem.

The Pauling Blog

Friday, August 7th, 2009

I was delighted to get a request today to link to a blog about a very special person indeed, Linus Pauling:

The Pauling Blog is run by the Oregon State University Special Collections staff.  It is devoted to informing the public of our various holdings, most notably the Linus and Ava Helen Pauling Papers.  We post a minimum of twice weekly on Paulings life and work, often focusing on his contributions to the field of chemistry.  We also post on his work in physics, biology, and medicine.

[...]

Please feel free to visit the Pauling Blog (http://paulingblog.wordpress.com) or contact us with any questions you may have.  [] you may be especially interested in Linus Pauling: The Nature of the Chemical Bond, a documentary history website hosted on the OSU Special Collections homepage (http://osulibrary.oregonstate.edu/specialcollections/).

There can be no doubt that Pauling was the chemist of the twentieth century – he covered so many fields and was influential in all he touched. I had the privilege to meet him in 1984 (I think) and listen to him talk in this case not about DNA or strontium or proteins but about minerals the area where he started. In fact his thesis at Caltech was simply 5 papers in JACS on mineral crystal structures which at that time were great intellectual feats. I was also presenting my own ideas on the automated analysis of crystal structures and he gave me interested attention.

I’ve blogged about him on a few occasions, but mention here

Impact Factors! Hirsch, Erdős and Pauling

where I suggest I suggest that after the success of the Erdős number in mathematics we could generate a Pauling number in chemistry.

And finally a personal connection Catherine Murray-Rust was in the library at the time that the Pauling collection was being compiled.

This is an inspiration to us all.

Chem4Word: Semantics is a hard challenge

Thursday, August 6th, 2009

This is a brief update… Although I have lots to communicate we have been spending most of our time working on Chem4Word and I don’t have time for blogging. We’ve (== Joe and bits of me, with Tim) frozen the API, and now we are fixing bugs. Although programming is over 50 years old (and I wrote my first program 45 years ago), bugs are universal. There are better bugkillers now, but there are bigger and more bugs. The greats of compSci have all recognised this, see: http://www.comp.nus.edu.sg/~damithch/pages/SE-quotes.htm

which should be required reading for anyone before they touch a keyboard. I’ll take just one:

Even the best planning is not so omniscient as to get it right the first time.
– Fred Brooks

Every experienced software developer knows this, and almost every software developer represses it. We are driven by optimism in principle we should improve as we do projects and therefore we should do better and faster work. But, of course, we also increase our expectations. And the world expects more of us.

We didn’t get it right first time. We couldn’t. Because we are embarking on something new this is not YACE yet another chemical editor. This is a semantic chemical environment. And semantics are hard. Not impossible, but hard. And there is no way round.

Here’s a brief example. Many chemical editors have a button with a + sign (and another with a -). It’s meaning is add a positive charge to the atom. Sounds simple enough CMLAtom has a integer formalCharge attribute all we have to do is increement or decrement it. But what does it mean? This is where semantics (and CML attempts to be a semantic language) bites us. A semantically valid molecule in CML must know exactly what atoms and how many electrons it contains. What does + do to the electron count? Presumably it decreases it by one? Well sometimes it does, and sometimes it doesn’t. Because many editors are oriented towards organic chemistry where + can mean add a proton to an atom (a proton is H+) rather than remove electron (whihch might be signified by . (add radical). The + convention is so implicit that it’s universally understood, but never stated.

We’ve identified several different meanings of the + semiotics which depend on element identity and chemical environment. It’s so polymorphic and woolly that it proved impossible to write semantically consistent code. So we’ve had to redesign. We now have a button called add H+. This is not a common approach I don’t know whether other tools use it. But for us it’s a logical and semantically clean approach. Is this a bug? It certainly fits Fred Brooks’ maxim. And have we got it right the second time? Until we get human chemistry feedback we won’t know.

So back to the unit tests. We can’t do it without them. Boring boring boring. But at least I can watch the TV as well interesting program on Spanish ‘flu. And do about 6 tests an hour…

More blogging at some time.