Book sequences

You may have seen some of my #nimrlibrarybyebye tweets. These were a sequence of tweets showcasing books that we have been transferring to other libraries. Each tweet included a photo of a book or a handful of books. I will write a proper post about them sometime soon. The ‘byebye’ in the hashtag is to signify that nearly the whole of the library stock is being disposed of.  Transferring books to other collections means that part of our library will live on.

I’ve also been selecting things to keep (as mentioned in my recent Library day in the life post). I’ve focused quite a bit on science history – but that includes recent history such as the early days of the human genome project and bioinformatics. Related to that topic, two things in particular caught my eye down in our store.

Protein sequences – Dayhoff

Atlas of protein sequence and structure

One of these I’d seen before – it is an book of sequences. My memory told me that we had a small hard-bound book of Genbank sequences, but I must have imagined that.  The book is a softbound book of protein sequences, from 1967-68. However, I did remember the author correctly: Margaret O. Dayhoff.

Margaret O. Dayhoff was originally a physical chemist and was one of the founders in the field of bioinformatics. She created this first public comprehensive, computerised and publicly available listing of protein sequences, The Atlas of Protein Sequence and Structure. I think it started out in 1965. Read this biographical article for more details about her.

Dedication page

Mainly I’m tickled by the idea of printing sequences in a book!  I love this book because today the very idea of a book full of gene or protein sequences seems bizarre. It shows how naturally we use books to share information. There were more volumes and supplements published in this series in the next few years.

I like the image on the dedication page too – though I’m not quite sure what the origin of the sculpture depicted is.

The book later turned into the protein identification resource (PIR).

 

 

There is an interesting account in Nucleic Acids Research in 1981 of another of Dayhoff’s projects – a nucleotide sequence database which became the model for other databanks, such as GenBank.

On September 15. 1980, the Nucleic Acid Sequence Database Demonstration Project of the National Biomedical Research Foundation was made available to interested users through telephone access to our computer. Over two hundred user groups requested access during the ten months of the demonstration. …

We had been using the computer system ourselves for some time and had found that a computerized management system was essential to minimize the overall cost of collecting, updating, and critically reviewing the data.

Margaret Dayhoff was held in some esteem by her peers, and I discovered we also have a festschrift dedicated to her, a special issue of the Bulletin of Mathematical Biology.

Genbank online service – manual

 

 

 

While sorting out some old files in my office (I’m doing a lot of sorting out and throwing away these days!) I found a manual for the Genbank online service (GOS), 1992. I thought I must have thrown this away ages ago so was pleased to see it again.

I remember that the GOS was my first direct contact with Genbank. Back then I occasionally had people asking me about gene sequences. I discovered that I could search on Medline for a gene name and then identify the sequence accession number. This allowed them to retrieve the sequence from other sources. With GOS, accessed using telnet,  I was able to search GenBank directly in its most current format, and I could even get the sequence too. The interface was plain but no worse that what I was used to in other online systems.

Not long after this Gopher came along, followed swiftly by the WWW (as we called it then). These made it dead easy for everyone to find sequence information and my newly acquired skills with GOS became redundant. Information skills had a high churn rate even in 1992.

Martin Bishop’s 1994 book.  Guide to human genome computing / edited by Martin J. Bishop. London: Academic Press.

Some brave souls wrote books about sequence databases and manipulation – knowing that by the time the book appeared in print another dozen databases and software tools would have been developed. Martin Bishop, a scientist at the MRC Human Genome Mapping Project Resource Centre (HGMP-RC), was better placed than most to keep up-to-date and his was one of the first books on the subject I remember buying for the library .

Other classics were Russell Doolittle’s
Computer Methods for Macromolecular Sequence Analysis, part of the Methods in Enzymology series – vol. 266 in 1996.  And Andreas Baxevanis and Francis Ouellette’s Bioinformatics : a practical guide to the analysis of genes and proteins – part of the Methods of Biochemical Analysis series in  1998.  These days we have both of these online as ebooks.

Immunological sequences – Kabat

The other book that summoned up memories of the days when sequences were printed in book form was Kabat.  I remember the 1987 edition was an enormous book that received quite a bit of use when I first started here in the Library. I was excited when I spotted that there was a new edition in 1991 and went to some lengths to purchase a copy for the Library. That was the last edition of the book as it then turned into a database.  See this account by Martin in 1996:

“The chief drawback of this database has been that it has only been available in the form of a printed book. These data have recently become available on the global computer Internet, but no method of searching the data has, as yet, been provided. Here, the development of a specialized database program for accessing the antibody data is described. This database software has been made accessible over the World Wide Web, together with a program which allows a novel antibody sequence to be tested against the Kabat sequence database, to identify unusual features of an antibody sequence which may represent cloning artifacts or sequencing errors.”

I was pleased to see that we have a copy of each edition of Kabat, from 1979 through to 1991, on the shelves in the Library store.

Kabat – 5 different editions, 1979-1991

A longer history of Kabat appeared in 2000 in Nucleic Acids Research. This described a 30-year history, going back to 1970 when the data compilation first appeared as an article in J Exp. Med.

Elvin Kabat died in 2000, and the US National Academy of Sciences published a biographical memoir of him saying he:

was a founding father of modern quantitative immunochemistry together with Michael Heidelberger, his doctoral mentor…

The printed and subsequent Web version [of Kabat] was a pioneering effort that preceded the current GenBank database. Indeed, Kabat was also instrumental in urging the National Institutes of Health to support a national DNA sequence database and the development of sequence manipulation software.

It is salutary to think that the early 1990s were such a different world – no web, hardly any internet, email was just starting to be used.  And people thought nothing of publishing gene and protein sequences in paper format.

A page from the Atlas of protein sequences and structure

Nowadays the only reason for printing out sequences is to create a museum exhibit:

When the human genome is printed out in a series of books, the DNA sequence fills more than 100 books. Image Courtesy: Russ London’s photograph of the Human Genome in the “Medicine Now” room at the Wellcome Collection in London.

 


A couple of reviews delve more deeply into the history of bioinformatics and computational biology:

 

Posted in Books, Collections, History, Research data | 1 Comment

Library Day in the Life – July 2016

The Library day in the life project was a great way to let people know what librarians do. It was an excuse for us to document a day or week in our working life in excruciating detail and, in my case, to inflict those details on the reader(s) of this blog. I joined in the project in 2011 and 2012 but it stopped in 2012 having run its course.  I persisted and in 2013 wrote about another week of my activities. You can read my past Day in the Life posts.

Recently I was musing on changes in what I do at work, and the interesting times that I’m going through, and thought it would be good to try Library Day in the Life again. I made notes in two consecutive weeks in July and here they are. I admit there was a delay between the activities and the writing-up, so they may not feel as fresh as my accounts from previous years.

These two weeks turned out to be busy times. Getting ready to move an institute is quite a challenge.

I had several meetings with labs, helping them prepare to put old lab notebooks etc into off-site storage. I gave a couple of internal talks to key groups (management and influencers);  happily these went well. I’ve been busy dealing with printed books (selecting and disposing) and with a collection of scientific equipment. And there’s been a number of forward-looking activities, starting to move new developments forward.

My working day usually starts by me scanning an assortment of science policy and science news sources, to create the daily Research Buzz news channel for Institute staff. Most days there’s between 2 and 8 items, and sometimes items on women in science or scholarly communications (these go into separate channels). A quick summary of topics covered over the two weeks in July:

Brexit – 10 items
Other EU – 6
Careers/Life in science – 5
Stories about People/Awards – 4
Animals in research – 4
Diversity – 4
UK politics – 3
Research ethics/hygiene – 3
20 other items

Week 1. 18-22 July 2016

Mon 18 July
I read and sent a few emails about an old FACscan machine that is no longer needed. We are hoping to transfer it to the Science Museum. Some paperwork will be needed before we can confirm the transfer. The Museum is also interested in taking an old bioreactor – it’s quite a size so will be challenging.

I went along to two lab records meetings (with a PI and our Records Manager). One was very brief – the lab was relatively new so there was no paperwork needing to be stored. The other one took a bit longer, but things are under control. I received a couple of spreadsheets from labs with details of the contents of boxes they wanted to put into store. That’s my cue to start processing boxes to go into storage.

I was spurred to join a librarians’s group on Slack, after spotting an interesting-sounding tweet. I signed up to Slack a while ago but never did anything with it.  I’ll see how this group goes.

Later in the day I travelled downtown to attend a meeting of the SPOTON advisory group, helping to plan the next SPOTON conference (see their website for more details). It should be good – discussing the future of peer review.

While I was in the SPOTON meeting I checked my email and saw one about a possible OA deal with a publisher. The sender was requesting a meeting with me. Funnily enough I was in the same building, just a few rooms away from him at the time!

After the meeting I made my way to our other lab site to pick up a 30-year old lab notebook and a couple of protein models. The models are bound for our scientific equipment collection, and the lab notebook (with details of a Nobel-winning series of experiments) will be going, along with some others from the same person, to the Royal Society archives. These notebooks were nearly discarded but I managed to intervene in time to rescue them.

Tuesday 19 July
I went early to our downtown offices and worked there for an hour or two. Since I got a new laptop a couple of months back I’ve been surprised at the difference it makes. I can now easily work from any location.  I have a bit more to do to free myself from a desk full of papers, but I’m nearly there.

I am due to talk today to our Executive committee, to update them about library services. They were running a bit late on the agenda so I had plenty of time to run through what I was going to say. They seemed attentive and I was comfortable addressing them. There were one or two searching questions. “What do you fear most?” Hmmm. I suggested that my biggest fear was becoming irrelevant (so we need to work hard to counter that). Another worry was about how open access is going to play out (there is so much uncertainty still). “What about searching and data access?”  I needed more notice for such a big question but sketched some of the parameters. Later I followed up with the questioner by email – I think we might have more to talk about. Then came a surprise – it was decided that space would after all be provided in the new building for a modest collection of printed books, focused on science history/heritage and broader issues (ELSI).

After the meeting I hung around a bit longer as the Chair (the big boss) wanted to have a quick one-to-one talk.

After lunch I had a couple more lab records meetings, then met with colleagues from our Comms team to show them the scientific equipment collection.  They were making preparations to move the objects that had been conserved in Phase 1 of the project, and to appraise and select objects to be conserved in Phase 2. Then I had another lab records meeting. My working day has far more meetings than used to be the case.  Some of this is a temporary thing, concerning tasks related to the impending move, but partly it’s due to a change in my style of working.

While I was out of the office my library colleagues had been somewhat overrun by institute staff wanting to select books to take away. Today was the first day we had invited them to come and select 1 or 2 books for their personal use, as mementos of the old institute. I’d thought only a few people would come but it was pretty hectic. In one or two cases there were multiple people wanting the same book, so some mediation was needed.

In other news, someone asked why he couldn’t access an article from a particular journal. The answer was simple – we don’t subscribe to it, never have and I don’t expect that we ever will. We got hold of a copy of the article through ILL for him.

I also took one of our senior group leaders down to the Library store to help him look through some of the old parasitology and malaria books. He chose four items, including some old books on quinine (Chininum). There is still a load of fascinating material in that thar store, but it seems t’s not fascinating enough that any other library wants any of it. Quite a few libraries have visited and selected books they want, but many books remain.

Late in the day I received an email invitation to talk to our internal Science Leaders’ Meeting next week about Open Access. I’d been expecting this. They just want 10 minutes from me.

I went to the institute bar for a quick drink and to wind down after a very full day.
I got talking with someone about old books, and then about Google as a way to search for articles. I was surprised when he said that he found Google was better than PubMed. When I probed he was talking specifically about searching for known items – articles he knew existed but needed to locate. I suspect this is because Google indexes the full text of articles (I think I’m right saying that).

Wednesday 20 July

An unusual start to the day: I attended a special breakfast viewing of the John Dee exhibition at the Royal College of Physicians. It featured books from the library of John Dee, put on by the RCP Library. The viewing was targeted at librarians and included coffee and pastries, plus a talk from the curator who had assembled the exhibition. It gave me much food for thought, about the benefits of putting on exhibitions, and the large amount of work involved. The story of John Dee’s library touched a nerve – the library of about 3,000 items was destroyed/sold while Dee was away travelling.  Only a few items remain.

Back at base I had a one-to-one meeting with one of my team members.  I try to do these one-to-ones weekly now and I’ve found it’s helpful.  All part of my new way of working.

I exchanged a few emails about the list of artefacts we hold (a mixture of sculptures, paintings, furniture). Decisions will soon be made about their fate.

I’m also catching up with some loose ends of subscriptions – one book series that we used to subscribe to in print only. Last time I asked the publisher, a few year ago, the volumes in the series weren’t available electronically except as part of a bigger package. Now they are available as a series, though the price is still not cheap. I was promised a ‘special price’ for the backfile but it didn’t look very special. After I pointed this out the publisher came back offering a 15% discount.

More good news – an abstract that I’d submitted to a conference on scientific archives has been accepted. That’ll be my first trip to Heidelberg; my first archives conference;  my first time to speak in public about archives; my first speaking engagement for a while.

Finally I went along to the Internal Mill Hill lecture – given by one of our neurophysiologists. I usually find that I can follow the first 10-25 minutes of these lectures but then comprehend less and less. This talk followed the usual pattern.

Thursday 21 July
I resolved a small dispute about which lab a particular book should be located in, and checked on the availability and cost of a couple of ebooks. It’s surprising how difficult it can be to arrange for access to some books in e-format.

I have another lab records meeting.  This lab is a dry lab so you’d think they’d have no paper to speak of. The complications came from the number of visiting workers they are hosting (mostly retired scientists from other parts of the institute) and records from past PIs in the lab.

Following Tuesday’s Exec decision about establishing a book collection, I am selecting books to go into the collection. I went down to our store to pick out interesting historical items.

Then I had a catch-up phone call with my boss. The job description for a new position is just about finalised, so the advert should be issued soon.

I’ve made some progress in planning an open access meeting in October.

Friday 22 July
I received some notification that some boxes of records are ready for collection.  There is going to be a regular flow of boxes over the next few months as labs move. It will be a challenge to keep up with them.

I received a spreadsheet from our other lab site with details of boxes to be collected.  I had to spend some time working through it to put it into the format required.

Then I spent another hour or two selecting books. I choose books with scientific relevance to our current programs, or with links to key figures from the past, or topics that seem worthy of current consideration. And some that pique one’s curiosity or seem too good to leave behind.

Week 2. 25-29 July 2016

Monday 25 July

I’ve been trying to set up an institutional account with one of our key publishers, to make it easier to process open access payments to them for papers we publish. After huge delays this is now almost done. I’m looking forward to some reduction in paperwork.

I had a brief email exchange with the questioner (about searching and data) from last week’s exec. It’s good to have someone interested in such issues, and aware of a broader vision of ‘library’. He even thinks that informationists are a good thing.

Much of my current focus is on paper records from labs, but going forward I will need to be actively involved with digital records from labs. One lab that is closing down (moving to California) hit me with a question about their digital lab records. A solution seems to be coming.

I responded to a question from a lab about how they can comply with open access requirements for a paper about to appear.

I was pleased to get a response from the UKSG about an idea I’d sent in for the 2017 conference. They agreed it was interesting, but want to defer it till 2018.

Tuesday 26 July
Interested to see the Royal Society’s #Scienceisglobal campaign on Twitter. I gave it a bit of a push through our internal communication channels, hoping that some of our labs might join in. A couple of them did.

A few emails exchanged with a medium-size publisher to arrange to meet up soon and discuss some kind of deal. I’m very much take-it-it-leave it with some of these publishers, so if they don’t offer something imaginative (i.e. low-cost, low-commitment) I will not be biting.

The big event for today was a meeting of the NIMR Archives Project Committee. This was set up by the MRC to examine NIMR archive collections and discuss their fate. A Project Archivist has been appraising and listing the collections, and it is her recommendations that the committee considers. We’ve had four meetings already and have already dealt with the main collections. Today we examined several smaller bits and pieces. IN most cases t was agreed to transfer them to other archive collections, but some things will be disposed of. For me it’s always painful to agree to dispose of things. There is always some value in these documents, but sometimes it would need too much effort to extract that value. We then went down to the store, to see other personal archives in situ. These were mostly things in filing cabinets. The Ita Askonas material was particularly impressive – very detailed and neat records of experiments undertaken.

Later in the day I uncovered another drawerful of archive files. I hadn’t realised they were there.  The archivist was not best pleased.

One of our staff (who used to be the institute web manager) had selected an old book about the internet (The Whole Internet Catalog) from about 1992. She found it fascinating. I remembered that somewhere I had a copy of Brendan Kehoe’s book Zen and the Art of the Internet also from 1992. This was a free book – I remember that I’d downloaded it as a postscript file and managed to print it. I was pleased with the result and had it bound. It was a great introduction for those days when few people were excited about the Internet. I thought I’d lost it but miraculously it turned up when I was sorting through my old drawers.  I gave it to our ex-web manager and she said “This is a fabulous book! I love the quotes”.

I’m starting to think about the practicalities of having a book collection in the new building. Of course we will need some shelving, but we’ll also need some kind of classification scheme, or categorisation scheme. I think we should also give the books from the store a good clean too. And I need to think about security for the books and a lending system.

I finished preparing my talk about OA for Friday. I will focus on what Group Leaders need to do.

Wednesday 27 July

I’ve now booked my induction for the new building. I’m not 100% sure when I will move yet, but it should be just weeks away. I have to attend a building induction session before I can move in.

I spent some time processing boxes of records from the labs – barcoding them and adding the barcodes to the spreadsheets. Once you get into a routine it’s OK, but it does get a bit tedious.

I received a notification about a forthcoming paper from one of the labs.  I get these primarily so that we can advise on the open access arrangements, but I also feed anything that looks interesting through to our press office.  This one did look interesting so I forwarded it. This part of my work has massively decreased in the past 18 months. I used to do much more of this, but another department now takes the lead in publicising new research.

A member of staff is retiring on Friday after many years and there will be a bit of a do. I was asked to dig out some information about exactly who he’d worked for and in which labs during his time at the institute.

I went along to another internal Mill Hill Lecture, by one of our developmental biologists. This subject usually involves a long cast-list of genes and proteins and this talk was no exception. I struggled valiantly to stay focused.

After the talk I went along to say farewell to our Project Archivist who has found a permanent job and so leaves us today. The Project is nearly complete so she can be satisfied she has done a great job with it.

Thursday 28 July
We have started integrating our work into that of the IT helpdesk.  So when we get requests for assistance we now respond to them via the helpdesk software. It had a little glitch today and our requests were coming through miscategorised. We got that sorted out.  I think it’s good in the long run to be integrated with the helpdesk, but I can’t help having slight doubts about it, and I fear my colleagues may also see it as a nuisance. hence I try to make sure it works as smoothly as it can.

I received an email from a publisher telling about their 2017 journal collection 2017, and announcing pricing for 2017. The summer is far from over and yet here we are starting to think about 2017 journal subscription renewals already.

Another lab record meeting, and another one-to-one session with a colleague.

Friday 29 July
The next phase of the scientific equipment project started today – all the conserved objects from Phase one (150 of them) were collected for transfer to the new building. That’s a great conclusion for these historical items. Many of them have been saved from destruction several times, and without the intervention of several people (including myself) they might have ended up in the bin. Another 100+ objects are now being considered for preservation or disposal.

I had another meeting with a group leader about lab records. This lab has been around for 25 years or more, so there could be a large amount of paper. The lab head has quite a robust approach though and will only be keeping a modest amount of paper.

I have finally agreed with our off-site storage company on the format I should use for the spreadsheets giving details of boxes we are sending them for storage. Soon I will be able to arrange for collection of the first batch of boxes.

After lunch I went downtown to attend part of the Science Leaders’ meeting, and give my short open access talk. That seemed to go OK, though there was one slightly crazy question at the end from someone with a beef against open access journals. Afterwards I talked to a few people (including an interesting discussion about Otto Warburg).

Then I headed back to the institute to attend the retirement party – this person has worked there for 45 years, so it was quite a party. It also served as an end-of-term party, an end-of-the-old-institute party, an it’ll-never-be-the-same-again party.

Posted in Libraries and librarians | Tagged | 3 Comments

ReCon 2016 – my favourite small conference

ReCon has become my favourite small conference about publishing and research. It’s held each June in Edinburgh. I attended it in 2015 and really enjoyed it. There were stimulating presentations on non-trivial topics, and plenty of interesting conversations over coffee and lunch. So I went again this year with high expectations that were not disappointed.

A few librarians attend, plus many researchers (mostly early career), some publishing people and information industry people. It is more research-focused than the UKSG or R2R conferences, and (to my mind) is more focused on cutting-edge topics.  There is also a Hackday on the day after the conference but sadly I wasn’t able to attend that this year. Last year I learnt a lot from the Hackday.

Here is some of what I found most interesting about the conference. You can watch videos of the talks on the ReCon website.

Citation

Geoff Bilder (from CrossRef) is one of those people who is physiologically unable to give a boring talk. He promised us a rant but his talk, while vivid, seemed too carefully argued and well-worded to be designated a rant. He called it “The citation fetish”.  He reminded the audience that citations can be inaccurate and distorted, leading to excessive concern with impact factors, h-indexes and the like. Then he complained that these metrics have gained too much influence on decisions about research careers. So far, so familiar.

Then Geoff surprised us by pointing out that we use the wrong words in connection with citations.  When we talk about citations, we are talking about the inclusion of an article in a reference list. This is wrong we shouldn’t use ‘citation’ to denote the number of times an article is listed in a reference list. These are just references. Rather, when counting citations we should count each time an article is cited in the citing article. A cited article may be referred to several times in a citing article – but will only appear once in the reference list. This may seem a nit-picking point (I admit to thinking this) but Geoff suggested it is symptomatic of a problem with our citation habits – a concern with credit over reproducibility.

He also drew attention to ‘citation’ practice in the more informal world of blogposts. Typically a blogpost may include a link (just a hyperlink rather than a formal citation) to another web page (blogpost or something else). Sometimes a blog post may link to something which is in fact a DOI, i.e. a part of the world of formal literature. Sometimes blogposts may have more formal list of references at the end, with in-text citations. Some may include footnotes with links in.  In blogs all of these different styles of citing and linking are intertwingled (I’d not heard this word before, but apparently it was coined by Ted Nelson). As bloggers we’re not thinking that hard about how we cite/link.  We all do it, mixed up-wise.

Now Geoff got serious. He highlighted the Force11 data citation principles. The first three of these are: importance, credit/attribution, evidence. Geoff stated that the principles put too much emphasis on credit/attribution rather than on evidence (reproducibility), putting the cart before the horse.

I think this was the main point of his talk: citation practice should be at the service of reproducibility. Citing should be a way to help readers/researchers to follow through the arguments in a paper, and the execution of the research reported.

Focusing too much on credit/attribution harms this link. It occurs to me that there is a kind of diachronous Heisenberg uncertainty principle at work when we start to measure citations – the act of measuring affects future citation practice and thus deems all future measurements suspect.

Geoff enjoined us not to think magically about citations but to think critically and to doubt everything we think about citations.

After his talk I felt that we could quite profitably have sat around discussing what he said for the rest of the day. But sadly there were more talks to listen to. Luckily they were also thought-provoking.

Research data

Mike Jones (from Mendeley) had the difficult task of persuading us that we should be happy to trust his company (owned by Elsevier) with our research data.

I must confess I had missed the announcement that Mendeley now offered a data repository service.

It seems to have been around for about a year, though it was in beta for much of that time. Mendeley data is setting up as a competitor to broad repositories such as Figshare and Dryad, and will also work with Hivebench, recently acquired by Elsevier. Clearly Elsevier are putting together their own data ecosystem.

Mike rehearsed the well-known reasons underlying the current surge of interest in data sharing and data repositories. I liked his listing of the phases of data curation:

Storage (rescue) – Shared (needs incentives) – Discoverable (metadata) – Comprehensible (well-described/structured) – Valid (curation, review).

Finally, Mike mentioned that  they are developing a search engine called Data Search which will search across multiple data repositories. Jim Procter on Twitter pointed out  that its effectiveness will depend on the metadata.

I think it is useful to have another service in this general data repository space, but I think Elsevier will have an uphill battle to secure the trust of the research community. One of the questions from the audience highlighted this aspect.

Data viz

A major theme of the conference was data visualisation and there was a group of talks about this. Clearly it’s an on-trend topic as Nature also had a feature about it recently.   http://www.nature.com/news/the-visualizations-transforming-biology-1.20201

Jo Young gave an introduction to the topic, taking us rapidly through the history of data visualisation from 1786. William Playfair  invented several ways of visualising data. John Snow, with his famous map showing cholera hotspots grouped around a water-pump, was another pioneer, along with Florence Nightingale and Edward Tufte.

Jo gave us quite a broad definition of data visualisation, noting that IKEA self-assembly instructions can be categorised as such (personally I’d say they were fiction).  Others include: Barplots, Boxplots, Network diagrams, Choropleths,  Videos, Images / photos, Tables. I realised I am quite ignorant about this subject as I’d never heard of a ‘chloropleth’.

I’d never heard of Anscombe’s quartet either but Jo explained that it is a set of four small datasets having the same statistical features. However when visualised the datasets are revealed as being quite different. This provides a really persuasive example of the value of using dataviz.

Jo finished by giving some simple guidelines for designing data visualisations. She said that we are better at distinguishing different heights than different angles, so pie charts are not always the best choice for displaying data.  Other advice included:

  • consider your audience
  • focus on the substance of the data
  • pay attention to proportions and scales
  • avoid 3D, avoid colour if it’s unnecessary
  • don’t distort
  • don’t add irrelevant data
  • don’t prioritise design over data

Thus instructed in the basics, we then heard  Pawel Jancz from NumberTelling extolling the advantages of the Tableau system. It allows you to interact with your data, link to sources, publish it online. Tableau public is worth a look.

Pawel then gave some more guidelines on constructing visualisations. If interested, I would advise watching the video of this talk as it was quite visual and I can’t do it justice in words.

Next up, Ian Calvert from Digital Science told us to ignore all the guidelines we’d just heard about. We should just get on with generating visualisations. He explained that dataviz can be a tool for researchers to understand and improve their data. I’d not considered this use case before but it makes a good deal of sense.

Ian explained that visualisation can be a path to clean data i.e. to data with fewer errors, that is easy to process automatically, and easy to link with other datasets

He showed us a real example, using data about published journal articles from 1500 to present and highlighting how dataviz can make errors and anomalies obvious.

Innovations in scholarly communication

Next followed the highpoint of the conference – a detailed presentation about research software tools from a pair of Dutch info-wizards:

Jeroen Bosman and Bianca Kramer

They have been looking at tools used by researchers at different stages in the research cycle.  At first their project was called 101 innovations in scholarly communication – you may have seen the diagram they produced:

101 Innovations in Scholarly Communication

101 Innovations in Scholarly Communication: How researchers are getting to grip with the myriad of new tools. Image produced by Bianca Kramer and Jeroen Bosman.

Then the list of tools grew to 400, and now it is over 800. They have categorised each tool as either traditional, modern, innovative, or experimental and then examined whether you can characterise researchers by looking at the tools they use.

Another useful categorisation, aligned to the goals of scholarship, was their enumeration of tools as efficient, open or ‘good’ (or ‘ethical).

  • Efficient – connected tools, publish neg results, speed of publishing, standards, IDs, semantic discovery (text mining), etc
  • Open – peer review, lab notes, language (plain), open drafting, open access, CC-0/BY
  • Good – declaring competing interests, replication, reproducibility, quality checks, credit where due, no fraud

Each tool is associated with one or more stages of the research cycle, divided into 6 or 7 main stages and further divided into 30 sub-stages.

I’d seen this diagram and thought it interesting but not especially useful. Silly me. Their next step was to launch a worldwide survey of researchers (translated into 6 languages apart from English). The survey gained over 20,000 respondents, showing which tools people use.

Their data is in Zenodo and their is a data note in F1000research. Their scripts for analysing the data are also shared.

A rather cool dashboard allows you to interact with the data (though it can be a little slow).

Now they can say how many tools a typical researcher uses: the median is 22, but the distribution follows a typical bell curve, slightly skewed to a higher number.

The number of survey responses to each sub-area also shows which are the busiest in terms of tool development and use – search and write win out, peer review is least busy.

They are now starting to work on a heatmap analysis to find out which tools co-occur.

This talk started all kinds of hares racing in my mind and I advise you to read some of their material, or look at the video of the talk. They will also be presenting at Internet Librarian International in October in London.  I’m hoping to see them again at that time.

I recommend any librarian involved in publishing or research support to check out ReCon 2017 (no details yet but follow ReCon on twitter). See you there next year.

Posted in Information skills, Journal publishing, Research data, Research tools, Uncategorized | Tagged , , , | 1 Comment

Important conversations and confusing journals

A few weeks back I was a roomful of senior librarians, having Important Conversations about Publishers (ICP). More recently I sat and listened to a number of ICPs at the UKSG Conference – bookended by talks from Ann Rossiter and Cameron Neylon, each with important things to say to publishers.  So far so momentous: the tectonic plates of scholarly communication are shifting and no-one is quite sure what the end result will be.

It is surprising to reflect that ICPs are a relatively recent phenomenon. Until about twenty years ago libraries’ key relationship was with their serials agent rather than with any publisher. I remember in about 1987 I had a visit from the rep for a major publisher and I didn’t really have much to say to him, certainly nothing in the ICP mold. Librarians back then did talk amongst themselves about publishers – mostly complaining about the daft things that publishers did to make librarians’ lives difficult. Generally the daft things relate to changes made to journals.

Journals can be confusing things. They differ from each other in myriad ways. They may be published monthly, weekly, semi-monthly, biweekly, quarterly, bimonthly, or at some irregular frequency (my favourite is sesqui-monthly). There may be split issues, combined issues; there may be volume numbers or not; there may be cover dates or not; the cover date may or may not correspond with the actual date of issue. We get used to all these things. And of course every journal needs its own title.

Changes can cause particular headaches for librarians, and for readers. Some changes are not too disruptive: a change in the frequency is only mildly confusing. Minor changes in title (adding a word or two) are not too troublesome, but major changes can mean that  readers fail to find the journal unless clear signposts are in place to redirect from the old title to the new title (and vice versa). In the days of print libraries could put signposts in their catalogues and lists, and even on the shelves themselves. Now we rely more on publishers to put the signposts in their websites. It gets worse when journals merge or split.

Some journals create confusion by having multiple sections, almost amounting to separate titles. One prominent example is Biochimica et Biophysica Acta (BBA). Currently it has ten separate sections, but over the years other sections came and went. On ScienceDirect about 20 different sections (past and present) are listed in total.

The confusing thing about BBA is that there is a single sequence of volume numbers through all the sections. So volume 1804 might be in one section, volume 1805 in a different section and volume 1806 in a different section again. Elsevier, the publisher of BBA, had a number of journals with this kind of structure; Mutation Research springs to mind as another prominent one.

This complex structure created challenges back in the days when we handled print issues of journals. We needed to know which issues to expect and in which sections they would fall; we had to decide how to shelve the issues (by title or by volume number); we had to decide how to bind them (different colours for each section?). All this is pretty much a non-problem now, in the days of online journals. But, as noted already, we rely on publishers websites to provide easy navigation.

This week a confused reader came seeking assistance in tracking down an article in a Wiley journal, Biopolymers. The article was in Biopolymers volume 94. Someone sent him the reference in an email, so he went to the Biopolymers website to find the article, but could not see volume 94 listed there, thus he sought my help.
bioplymer-issues

I wondered if it was perhaps a supplement volume, with conference abstracts, as these are sometimes published separately from regular journal issues. It wasn’t. As I inspected the listing of volume numbers on the website it struck me that only odd volume numbers were listed there, which seemed rather odd.

I was intrigued by this mystery. I searched PubMed and found the article listed there, then followed the link to the full-text and easily found the article on Wileys’ website.

So, I had the article but was still perplexed as to why I couldn’t see it (or any even-numbered volumes) on the Biopolymers web page.

Looking more carefully at the page for the article, I saw it had a large blue Biopolymers’ banner image at the top. But there was also a prominent red banner below it, showing the words Peptide Science prominently, and the word ‘Biopolymers’ in a smaller font running vertically up the red banner.
biopol-pepsci-banner
I looked up Peptide Science in Wileys’ alphabetical list of journals, followed the link and found all those even-numbered volumes listed, that were missing from the Biopolymers page.

peptide-sci-issues

In PubMed (and Scopus and Web of Science) all articles published in Peptide Science are listed as articles published in the journal Biopolymers. But on the publisher’s website, they are listed only under Peptide Science and the image of the cover clearly shows only the Peptide Science brand.
pept-sci-clue
That seems a bit unhelpful to me.

I see that Peptide Science is the official journal of the American Peptide Society, so perhaps that is the reason it holds fast to a separate identity. It might be better to separate from Biopolymers more completely but I guess there is some brand advantage in associating with it.

In the world where we only ever click on a link, or follow a DOI, maybe it doesn’t matter so much. But if someone emails you a reference, or you scribble down a journal reference, and then go about trying to find it you will fail.

Publishers love to claim that everything they do is for the good of the academic community.  But making it difficult to find articles, charging high prices for subscription journals, and putting barriers in the way of open access are all signs that this is an empty claim.

Posted in Journal publishing, Scientific literature | Comments Off on Important conversations and confusing journals

Metavation

I first came to work at NIMR Mill Hill back in the blessed innocent times of 1989. After a few months my boss sent me on a course about ‘Motivation’. The course was organised by Aslib, and was held at their grand HQ in London’s Belgrave Square. It was good to be out of the office dor a day, having some thinking time with a group of other librarians, but I wasn’t entirely sure what the course would do for me.

One of the first exercises we had to do was to explain our motivation for coming on the course. In my typically spiky way I told the unadorned truth, explaining that I had only come along as my boss had pushed me into it. The trainer couldn’t fault my logic, though I suspect he marked my card as an awkward sod.

Back in those days my motivation for work was pretty high. I was in a new job and was settling into the organisation and role. I found plenty to get on with and was given a good degree of freedom to do it in whatever way I saw fit. I absorbed as much as I could about the activities of the institute, and got to know people. I also closely observed what was happening elsewhere, to see what other institutions were doing. Then it was copy, paste, edit. The results were generally good. As time went on I went off-piste quite a bit, straying from straightforward library tasks into web management, research data, public engagement, and publishing.

This motivational honeymoon lasted a good 20 years. Over the last few years my motivation at work has gradually declined. Slowly at first, but then more rapidly, until by 2015 it had shrunk to something very small. Uncertainty about the future of the Institute (it was closing and becoming part of a new Institute), and my role in its future, were at the heart of this shrinkage.

To some extent it was a failure of nerve, a loss of confidence. Before, during the 20 good years, I was unafraid to strike out in new directions at work. I was confident of the core of my responsibilities, my room for manoeuvre and my ability to take on new things. There was no-one else in the space – I took on tasks that no one else was interested in.

Now I am less confident of my core. The concept of a library is apparently no longer valued while ‘information’ has become something that everyone knows about and does for themselves. Information skills are nothing special, it seems. Other players have entered the broader information space and some have their own specialist expertise (communications, research data, training). My room for manoeuvre is more limited.

In 2015 my motivation to blog also evaporated. I jotted down notes, and mapped out some ideas for blogposts, but finished nothing. This post is an attempt to break out of my unmotivated straitjacket. I thought if I wrote about my lack of motivation then that might help to release more writing. A meta-post about why I wasn’t posting could turn the tap on.

It didn’t quite work like that. This post has been waiting to be finished off for nine months, so it suffered the same fate as all the others. But I think today is the day. Motivation is bubbling up. Fingers crossed, there will be more coming.

Posted in Uncategorized | Comments Off on Metavation

In an instant, in the twinkling of an eye

It’s the last trumpet.

It’s been an intense few months up on the Ridgeway; preparations for our big change have gathered pace. At first things went slowly – infuriatingly slowly –  but as the years crept on so we felt the pressure develop. It’s like the feeling of being in a crowd of people surging forward, slowly accelerating. You’re forced to break into a trot, and have to move faster and faster towards your target, trying not to trip, until you’re racing along breathlessly. At first the target is out of sight over the horizon and seems a little mysterious.  But when you look back at where you came from, it too seems strange to you now. As you get closer to the target you see it more clearly, and the details become visible. What does it mean?

Now we are there, we’ve entered into the singularity and we are about to emerge from the other side into … the Francis Crick Institute.

We’re no longer owned by the MRC, though we’re  still supported by them. We feel free: no more crazy civil service mentality, “bureaucracy rules OK”. But we also feel afraid: no more public sector protection and positive staff spirit. What will this new, third sector,  world mean for our lives, our careers, our science?

On the stroke of midnight a thousand huge removal vans will arrive on site and an army of removal technicians will load them up with every piece of equipment, large and small, on site. Acres of bubble wrap will enfold the hundreds of thousands of pieces of lab kit. Furniture will be manhandled along the corridors and down the stairs or down the goods lift and into the waiting vehicles. Freezers will be packed with padding to protect their valuable contents and carefully carried away.Computers will be unplugged and encased in protective boxes ready for the move. Paperwork will be filed; desks locked shut; books crated up. Everything will be labelled with a lab number and crammed into one of the vans.

The long convoy of removals vans will snake its way carefully down the hill, onto the North Circular Road then down the A1 through Archway, Holloway and onto the Caledonian Road towards St Pancras. Similar convoys will make their way from the Clare Hall and Lincolns Inn Fields sites of our sister institute.

Once they all arrive in Brill Place the removal fairies swing into action again, carrying multiple loads to their new destinations – “3rd floor, northwest quadrant! 1st floor! 2nd floor, southeast quadrant! basement level 1! 4th floor, southwest quadrant!”. Faster and faster they work so that every piece will reach its appointed location, be it general lab space, shared secondary space, the BRF, the admin floor, or a technology platform.

The unloading should be completed by 6 in the morning, everything checked over and powered up. Every lab and office in the new institute will be ready for occupation by the early birds coming in to start work at 7.30am. The research gets underway, ready to fire off hot new discoveries.

So, one hundred and three-quarters years of our institute history have drawn to a close, and another era of institutional history begins. Goodbye Mill Hill, hello Brill Place.

 

 

 


UPDATE 12:10pm

Some of the details above were not  entirely accurate (note the date).

True: NIMR has ceased to be. It has transferred to become part of the Francis Crick Institute, as the ‘Mill Hill Laboratory’. Other Crick sites include the Lincoln’s Inn Fields Laboratory, the Clare Hall Laboratory, and the project team offices on Euston Road.

False: there was no convoy of vans at midnight. The Crick will take possession of its new building in November 2015 and the physical transfer from the laboratory sites will start soon after that, taking about 6 months to complete. The thought of doing it all in one night would probably give the migration manager apoplexy. It is a huge and complex task.

True: I was onsite today just after 7am and there certainly were early birds coming in to work. Research keeps going forward.

See the welcome video on YouTube, with some great shots of the interior of the new building.

Posted in Froth | 4 Comments

Creativity – mixing it up

Over the past couple of weeks I’ve had cause to celebrate dramatic creativity in various forms, mixed and mingled. I’ve seen one film and two musicals; two with a biographical bent and one with a (fictional) scientific bent.

Two weeks back I went to my wonderful local cinema, The Phoenix in East Finchley, to see Hockney as part of an event badged as Hockney Live from LA. The cinema (1910) is a gorgeous artwork in itself, London’s oldest running  cinema,  and it is always a treat to go there.  The programme included a screening of Randall Wright’s new film about David Hockney, followed by an interview with Hockney broadcast live from LA. I’ve mostly enjoyed what I’ve seen of Hockney’s work – The Royal Academy show in 2012 was great  – so I expected the film to be a visual feast. I was not disappointed. His life story makes a great tale (boy from Bradford makes good and ends up in LA) and he is an engaging character on screen so the 112 minutes raced past. The Director had access to Hockney’s large personal collection of photos and video material dating back many years, so this film captured a vivid flavour over several decades of the artist’s life. What a gift to the director to have such a rich visual archive at his disposal! Hockney’s paintings often feature his friends; it was interesting to be shown a painting of someone, then an old photo or video of them, followed up with a modern interview of the same person (somewhat older) talking about Hockney.

The live interview with Hockney was slightly disappointing in comparison with the film (it made me appreciate the editing skill of the filmmaker all the more), but it was good to see nevertheless. The film had shown some of Hockney’s photo collages and in the interview Hockney explained how he had taken this further, using digital photography to create ‘reverse perspective’. It was interesting but puzzling. Jonathan Jones gave the film an appreciative review in the Guardian. If you like Hockney’s work I would recommend seeing the film.

This week I saw Here Lies Love, a musical about Imelda Marcos. This was in the National Theatre’s Dorfman Theatre (previously the Cottesloe), an intimate and flexible space. Some of the audience (including me) were sat in conventional theatre seats along two sides of the space, another large group of audience were stood around downstairs – very much part of the action. There was a stage at each end of the space and mobile stages in the centre of the space. The whole setup had a disco-dancing nightclub vibe (apparently Imelda loved disco). The action took place all around the space, and was slickly done. The show told the story of Imelda’s life – another tale of poor girl makes good – she married the man who was to become President of the Philippines (Ferdinand Marcos). It uses dance and song, but also mixed in a good deal of historical video and audio material, including one shocking scene towards the end. Again the video added an extra dimension to this biographical story.

It is a very fast-paced show, with lively music (by Fatboy Slim) and very strong dramatic and vocal performances. It portrayed the glamorous side of Imelda and Marcos (“Asia’s Jackie and John”) – this is crucial to understanding the love (yes, love, or even adoration) that Marcos followers had for them both, and that some still have for Imelda. One review suggested that the show was too soft in its portrayal of Imelda, but I disagree. Her flaws (ambition, ruthlessness, vanity) were shown clearly. The actions of the Marcos regime were laid bare. The programme note recorded that during the show’s New York run some Marcos sympathisers had walked out in protest. As a spectacle, an entertainment, and a little bit of history, I thought it worked very well; as a political statement it was not quite all there. Michael Billington suggested the subject needs a more complex treatment, which I wouldn’t dispute. If you want to learn a little bit of Filipino history, and like a bit of upbeat music, give it a go.

In between these two biographical productions, I attended Mouse TRAPP.  This was an amateur production put on in the Institute’s lecture hall by our in-house dramatic society. Whilst the production values were not quite those of the National Theatre, as a dramatic construction it was superb. This musical with a scientific theme was created by one of our postdocs. It was a fictional story about a PhD student – I suppose it could be classified as some kind of Lablit. The ironic posters advertising the show made it plain to see that the writer had a fine sense of humour, so I decided to give it a shot.  I was rewarded with a display of drama, humour, pathos and joie de vivre. There were a few in-jokes, and plenty of wry observations on the nature of science and careers in science.

The stars of the show

The story is about a PhD student, Michael, and his journey through his PhD. His lab colleagues and supervisor help get him started, telling him he has to choose a gene to work on. This is the cue for a hilarious song, “Any gene will do” (sung to a familiar tune from Joseph). Michael decides to work on the TRAPP gene, which was supposed to affect intelligence. He generates a strain of mice with TRAPP constitutively expressed – this gives them ‘near-human’ intelligence. Much of the play is about his interactions with these mice, and his affection for them. Naturally the mice can talk, and they are great comic creations. The show was funny, acutely observed, and had vivid characterisation. It was a commentary on lab life and scientific careers, the life of a PhD student, the issue of animals in research, inter-generational tensions, women in science, etc etc. It was relevant, but above all, it was funny!

These three shows of different kinds each left me with a buzz, an admiration for the huge talents of their creators and the creativity displayed. Each of them also had a curious mixture of different elements which is something I love. Truly we are in the age of the mash-up, the magical commingling of different elements to produce a surprising result. Narrative alchemy.

Posted in Film, Film and music, Music | Comments Off on Creativity – mixing it up

The rules

Rules can help us get by in life – everyone agreeing to drive on the left probably reduces the accident rate on roads quite a bit. But rules have a tendency to take over, a bit like Lord Acton’s dictum on power. Sometimes it seems as though The Rules have become an end in themselves, rather than a means of managing activities more efficiently or propitiously.

rules-activity

Two versions of reality. I prefer Version 2.

In libraries it was once common to see long lists of rules – some of these were necessary to help preserve library materials (“No food or drink”) or to preserve a studious atmosphere for other library users (“No talking”) or just to ensure fair access (“No desk-hogging”). Some rules were a bit random but probably well-meaning (“Loans of unbound journals are limited to four days”) and some sound like scare tactics (“In the event of a book being lost or damaged, the borrower will be required to replace or restore it in good condition at his own charge”). Over the years the list of rules tended to grow longer, as rules were added in response to particular situations.

We more or less tore up our Library rules a few years back and the world has not collapsed.  I think the world might be a better place if a few more rulebooks were torn up, and paperwork reduced. A recent study in the US found:

The average U.S. doctor spends 16.6 percent of his or her working hours on non-patient-related paperwork, time that might otherwise be spent caring for patients.

One of the frustrations of of working where I do is the necessity to observe some rules that are due to our being a remote part of government. We have to abide by a very strict IT security regime that is appropriate for protecting private information in the Department of Work and Pensions, but which is not at all suitable when dealing with scientific data about protein structures.  Some of the procurement rules and recruitment rules also seem designed to be cruel and frustrating. And as for records management policies, words fail me.

I am looking forward to the day when we are no longer bound by these Whitehall-inspired rules.

But I don’t think that all rules and paperwork are bad. Some are there to encourage good behaviour or to promote cultural change.

I think that open access rules (mandates) fall into this category. They can seem to be a pain in the neck, the product of petty bureaucracy, but they are there to help improve science. One day in the not-too-distant future it will be second nature for all researchers to make their work open access. I look forward to the day when open access becomes the default mode and we start to write about non-open access research as “privately published” or some such phrase. OA mandates will help that change come about.  Supportive services, such as those provided by many University and Institute libraries, can help to hasten that day too – making it easier for researchers to comply with the rules.

Perhaps this is just self-interest, but I firmly believe that (as a rule) researchers need a helping hand when it comes to complying with open access and open data mandates.

Posted in Open Access, Research Councils | Tagged | 2 Comments

Advanced photo technology

I do love the Today programme on BBC Radio 4, but when it comes to stories about science and technology or popular culture the presenters can be exasperating. This morning John Humphrey kept calling Philae the “Mars explorer” and seemingly no-one noticed or dared to correct him.

Then he introduced an item allegedly about some new photographic technology, a “great technological breakthrough” he called it, related to taking selfies. (Listen to the clip). This was the cue for his retreat into bumbling confusion – his stock response to any technology introduced since about 1990. I was a bit surprised therefore when he announced that they were talking about selfie sticks.

I first saw them in use while on holiday in the Philippines in May this year. On our trip to the island of Corregidor (a must-see for anyone interested in the history of the second world war) another person in the tour group had a selfie stick and took countless photos of herself and her boyfriend in various poses with the historical ruins and gun emplacements.  Intrigued, we purchased one when we got back to Manila and found that it was really useful for taking photos with your camera phone – not just selfies but all kinds of things. The stick (or monopod) helps you to take photos from different angles, and to reach things in difficult positions. In short, they are great for helping to take holiday snaps.

IMAG1077_1 IMAG1076_1
The stick – unextended (left); partially extended (right).

I thought that selfie sticks were probably well-known and it was only me that hadn’t heard of them, but our friends were as intrigued as we had been when they saw the stick. It is basically a telescopic pole, with an adjustable grip at one end into which you can slot a mobile phone and then adjust the angle. Provided your phone’s camera has a timer on it then you can use the stick to take photos of yourself from a distance that doesn’t make you look scary, unlike typical selfie photos.

14179967609_c1a451f38a_o

On the beach in Boracay, Philippines. OK, so I do look a bit scary here but that’s only because I am squinting due to the sun.

If pressed I would have guessed that the selfie stick started in the Philippines, which has a real love affair with mobile phones and communications tools. The Today programme suggested that it may have started in Indonesia and that it was somehow associated with extreme sports. A piece from March this year in the Huffington Post confirms that the sticks are very popular in Indonesia, Malaysia and the Philippines.

I’ve not looked to see if they are on sale in the UK, but you can find them on Amazon. It’s this year’s must-have Xmas stocking filler.

 

Posted in Froth | Comments Off on Advanced photo technology

Terrors transcended

On balance, I prefer laughing to crying but I am not afraid to let my tears flow. Powerful drama can do it, so can stirring music. I may cry when I recall events or times in my life when I have been sad. I can cry when I read about or watch representations of human cruelty. These things are all likely to give my tear ducts a workout. I cried when I read Schindler’s List. I cried at the end of the film Life is beautiful. I cried the first time I saw the ballet Romeo and Juliet, at the tragic denouement of the story intensified by the emotion of the music.

As a performer I struggle to contain the emotional impact I feel when I am singing music. I need to experience the emotion to help me put across the feeling in the music, but too much emotional reaction can interfere with my ability to control my voice. My choir’s next concert is a case in point. It’s a double bill featuring Michael Tippett’s A Child of our Time and a new piece of music written by James McCarthy about an extraordinary young woman whose story has just taken another extraordinary twist. Both pieces use music to tell true stories about awful events, and to point up strong messages for the world.

A few weeks ago my niece left home to start her university career in Bristol, the city where I started my own student life 38 years ago. This stirred up recollections of my time there – the feelings of terrific excitement (the freedom of life away from home!) and terror (the intellectual challenges of education). There were so many new things all happening at once. I tackled them with enthusiasm if not always success. Maths assignments were tough going, but on the home front I did carry out several successful proofs that throwing together lentils, herbs and spices into a saucepan was not a guarantee of creating something edible.

A Child of Our Time

Another challenge back then was my first encounter with Child of our Time. The Bristol University Choral Society, under the baton of Raymond Warren, rehearsed it for many weeks and performed it in concert in the spring of 1977. Prof Warren introduced us to Tippett’s dissonant and luxuriant harmonies, the expressionist pain of his storytelling and the warmth of his arrangements of the traditional spirituals that are interspersed throughout the work.

It tells the story of Herschel Grynszpan, a 17 year old Polish Jewish refugee who in November 1938 shot and killed an official in the German Embassy in Paris. It is a story of anti-semitic prejudice, oppression and exile. The story is tragic in itself but the events that followed the shooting defy description. The assassination “provided the Nazis with the pretext for the Kristallnacht, the antisemitic pogrom of 9-10 November 1938”. I visited Berlin last year, 75 years after Kristallnacht, and saw exhibitions and memorials all over the city. At first I didn’t realise what the memorial panels were – they had a name, a photo, birth and death dates and a brief life story. So many people, such a variety of interesting stories. As I read the stories the link between them became clear. All those people were murdered, executed, or disappeared.

This is the pain portrayed in Tippett’s piece – it is not just about one Polish boy. Composed between 1939 and 1941, it transcends his individual story to deliver a powerful message about all of us, and the evil that can happen if prejudice gains a hold.

Herschel Grynszpan nov 7 1938

Tippett wrote his own libretto. At the heart of the piece is a drama. He tells the bare facts of the story: how the 17 year old boy, worried about his mother back home in Poland and frustrated by official bureaucracy and prejudice, shoots and kills the official. The text is by turns narrative and poetic. We see into the mind of the boy and his family; we hear the antisemitic hatred of the people and the fears of those who are oppressed. Tippett  also gives space for wider reflections, and this is where the spirituals come in.

The first words we sing give a clue to what is coming:

The world turns on its dark side. It is winter.

A little later the chorus asks:

Is evil then good? Is reason untrue?

One of the longest choruses us aptly titled “The Terror”. It is terrifying for the choir to sing, with ugly jagged phrases and harsh violent words:

Burn down their houses. Beat in their heads. Break them in pieces on the wheel.

At the end of singing that chorus you feel disgusted with yourself. The storytelling ends, focusing on the boy:

He too is outcast, his manhood broken in the clash of powers.

But Tippett was an optimist. These words are followed by an instrumental evocation of spring, which leads into the powerful extended final chorus:

Here is no final grieving, but an abiding hope … It is spring.

In rehearsal this week our conductor, David Temple, pointed out how extraordinary it was for someone in 1941 to write such positive words and music. The soloists introduce the themes one by one, then the chorus pick them up and elaborate a little. The soloists return to sing an extended rhapsody leading to a musical singularity – a moment of infinite emotion that seems to last forever. The mood relaxes and the music eases into ‘Deep River’, the final spiritual which closes the whole piece in calm.

Back in 1976/77 when I was learning this music for the first time Raymond Warren did a great job of motivating his singers. While the spirituals are a joy to sing, and there are rapturous choruses, some of the other choruses might be described as squeaky gate music. (Richard Witts summarised Tippett’s style as ‘wild, thorny, splashy and opulent’). It was hard work and at first unrewarding. Prof Warren had started a correspondence with Tippett about our forthcoming performance and every few weeks he would read out the latest postcard he had received from the great man, including an assurance that Tippett would attend the concert. This was quite exciting.

Even better, my parents came down for the weekend to hear the concert. I couldn’t imagine what they would make of it. Their musical tastes were fairly conservative, as far as I knew, but they surprised me by expressing great enthusiasm for the work. They had lived through the war as young adults- my father in the North African campaign and my mother back in London. The horrors of the time were real for them and Tippett’s depiction of war and inhumanity bore into them in a way I could only guess at.

Malala

The other piece of music in our concert will be the first performance of Malala, by James McCarthy. It tells the story of Malala Yousafzai, the girl from the Swat valley in Pakistan who was shot in the head for insisting that all girls should have the right to go to school. This is another shocking story, with a message for humankind. The text was specially written by Bina Shah. James McCarthy wrote on his blog:

An educated mind tends to be inquisitive, doubtful, questioning, innovative, logical, playful and creative. … An educated mind, because it is questioning and doubtful, is less susceptible to brainwashing by extremists and it cannot easily be radicalised with promises of an eternal bliss in an afterlife.  As George Washington put it (in a line that Bina Shah quotes in the libretto), ‘education is the key to open the golden doors of freedom.’

James McCarthy talks about the piece in this video, which also features interviews with Bina Shah and David Temple.

If you haven’t read about Malala or seen her speak then take a look at this video of her addressing the United Nations. She is admirable: articulate and determined; calm and non-vengeful.

The text we sing in Malala describes Pakistan as

a land of ice-capped mountains and moonlit glaciers .. [with] forests of fruit trees, mulberry, pear, apricot

Malala is from Swat in Pakistan, and these words put me in mind of a trip to Pakistan I made in 2000. I visited cities, including Lahore which I loved (beautiful mosque), and the mountainous northern region of the Hunza valley. In Lahore I visited someone I had previously worked with. He was a pious Muslim, with a family of six daughters of whom he was inordinately proud. They all worked hard at school and the eldest was at University already.

15343067477_ed844ef90d_o

Hunza was famous for its apricots and I remember the disgusting-sounding bread and apricot soup which turned out to be delicious, and the delicious-sounding mulberry spirit, which turned out to be highly intoxicating and undrinkable. The most memorable point of my trip was watching sunrise in the mountains, as the sun’s rays kissed each peak in turn, waking it up for a new day.

15342893499_25b4df1e09_o14908704993_f90fa5cc70_o

The story and music of Malala are very different to Child of our Time. Less drama, perhaps, and less poetry, but there is an equal passion. There are moments when I feel emotion welling up in me as the choir tells the story:

Then came the day when they told her that girls could not go to school… Malala dreamed of freedom

Her enemies said: Malala has shamed us. We’ll put a bullet in her head. How dare a girl think that she can defeat us.

At the end of the piece we join forces with a choir of 100 girls voices, to sing:

Malala set the world ablaze. And the world sang back ‘We are all Malala’

If you are free tonight (Tuesday 28 October) then come to the concert at the Barbican. You will be moved by the music and the storytelling. You may see one of the tenors in the second row with glistening eyes, wiping away a tear.  That’s me.

Posted in Music | Comments Off on Terrors transcended