Synthetic ethics

Posted on August 18, 2009 by Frank Norman

Talking of new topics emerging , synthetic biology seems to be popping up all over the place these days. OK, it’s not exactly new any more but I keep seeing announcements from quasi-official bodies indicating an interest in looking at the ethics of, public interest in, or broader implications of synthetic biology. When the froth rises to the top it suggests there’s a lot brewing down below.
I went to a very interesting talk a few months back given by Thomas Murray president of the Hastings Center, which has an ongoing investigation into ethical issues in synthetic biology. He was invited over here to give the _”Nuffield Council on Bioethics Public Lecture 2009″:http://www.nuffieldbioethics.org/go/news/news_522.html_ and his talk was titled “New genetic recipes: are we cooking up trouble with synthetic biology?” A video of the lecture is available.
Dr Murray explained that ethics begin with facts, so he gave us a few definitions of synthetic biology. Essentially it entails the application of engineering principles to the fundamental components of biology. He also reminded us that as yet synthetic biology is mostly aspirational. Those in the field hope that they can use it for biological production, drug creation or bioremediation, but it’s still a hope.
Drawing on a recent review in Bioessays Dr Murray highlighted three major strains of synthetic biology, each of which may raise different ethical issues:

  • protocell creation
  • DNA-based device construction
  • genome-driven cell engineering

He also noted that with its mix of biology and engineering, synthetic biology brings together two fields with different attitudes to ethical issues. He suggested that biologists are more engaged in ethical debates about the consequences of their research than are engineers. This point was disputed by a representative of the Royal Academy of Engineering who was in the audience (oops!), who maintained that ethics are now part of engineers’ training, but I’m inclined to think that Dr Murray had a point.
He then looked at the very different approaches taken in the UK and the USA to the debates about a) GMOs and b) stem cells. In examining these differences he teased out the idea that some of our beliefs are based around “interests” (financial, personal, family) and some are based around “identities” (deepseated beliefs such as religion or politics). If a position is based on interest then there can be trade-offs and compromises and it is acceptable for there to be public and commercial interests. If a position is based on identity then there are no compromises and the two sides of an issue are probably mutually unintelligible. That certainly sounded like a familiar situation – just think of debates about the use of animals or hybrid embryos in research. Dr Murray thinks that this way of looking at bioethical debates could prove useful.
He talked a little of the potential benefits and risks of synthetic biology. I liked his term bio-errorism (sic). He dissected the precautionary principle (when in doubt, pause) and contrasted it with the pro-actionary principle (when in doubt, go ahead), asking “Who bears the burden of uncertainty?”.
Finally, Dr Murray commented that synthetic biology may be seen as a continuum with genetic engineering, and it may lead us to re-examine our ethical approach to genetic engineering. If we feel that synthetic biology has an impact on how we see ourselves we may treat it as an “identity” issue. He suggested that the debate needs compelling narratives of synthetic biology scenarios as well as philosophical arguments.
The lecture didn’t provide any answers, but it did provoke a good deal of interesting thoughts.
Here is my evidence of the synthetic biology froth:

  • Two Research Councils, BBSRC and EPSRC, have set up a steering group of independent members to “advise them on how to gauge and understand the public’s perceptions, aspirations and concerns around synthetic biology”.
  • The Royal Society have established a Synthetic Biology Policy Coordination Group which aims to “track and stimulate policy activities and processes to encourage the responsible and responsive development of synthetic biology”.
  • The National Endowment for Science, Technology and the Arts (NESTA) and the

Royal Society of Chemistry (RSC) are designing a series of workshops that will engage an interdisciplinary cross-departmental group of academics who are interested in developing new research ideas in synthetic biology.

  • Back in May Nature ran a story about the Centre for Synthetic Biology and Innovation at Imperial College, London, highlighting the fact that social scientists will be a key part of the Centre.
  • Also in May the Royal Academy of Engineering (RAE) report looked at practical, regulatory and ethical issues in synthetic biology
  • The RAE later issued another report that gauged public attitudes to the field.
  • Meanwhile, in Germany, a joint policy paper from the DFG and the Leopoldina academy looks at safety and ethical issues raised by synthetic biology.
  • I just noticed that there has been a special issue of EMBO Reports on this topic, in their Science & Society section.

Finally, a couple of books:

– a comprehensive overview on relevant societal issues of synthetic biology
p.s. see also Pamela Ronald’s post on genetic engineering.

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Youth and experience

Posted on August 12, 2009 by Frank Norman

One of the good things about growing older is that you get to bully patronise mentor those who are younger and/or less experienced. One of my staff, who I mentored through the process of becoming a chartered member of CILIP, has recently had his application approved and is now a full member of CILIP – great rejoicing! I expect to take on another mentee soon.
I’ve also been putting some effort into providing work experience in the Library this summer for school students. In the past we have had mixed success with work experience students, but I think we now have it cracked. I aim to give them a broad experience of work, libraries and science. We have to be realistic, recognising that they can’t do anything very elaborate, but we shouldn’t expect them to be happy with 8-hours of drudgery. This is what we hope they (and we) gain from a placement:

  1. Get experience of what it’s like coming in to work every day
  2. Learn a bit about the Institute and the science here
  3. Learn a bit about libraries and information
  4. Learn a bit about some other sections in the Institute
  1. Do something useful for us

Last month we had two very different students, each here for two weeks one after the other. I gave each of them a talk about how research works, what MRC does and what the Institute does, and they also talked with each of the Library staff about their individual roles. The students worked on a range of tasks, from sorting out bibliographies in an Endnote database, and checking on online journal holdings, to producing listings of files in our archives.
One student was 15 years old, very much into IT. He spent some time with various people in our Computing department and with other non-laboratory sections (Health & Safety considerations meant he wasn’t allowed into any labs at his age). I also arranged for him to talk to computationally-intensive researchers in confocal image analysis, molecular modelling and crystallography. He was a willing worker but not very communicative so it was difficult to know what he made of it all. At the end of the fortnight though he said it had been “Great” and couldn’t have been any better.
The second student was 17 years old, very bright, and highly focused on medicine/medical research, with a particular interest in medicinal chemistry. I set up quite a few meetings for her to give her a broad flavour of modern medical research, and to let her talk both to some women scientists about women in science and to some clinician scientists about routes through medicine and science. She also had a talk with a real live medicinal chemist in MRC Technology which was useful. She ended up spending quite a bit of time helping out in one lab and getting some real experience.
It was quite a bit of effort preparing for their placements, setting up those visits, and making sure that they had something to keep them busy at most times. But we did get some good work out of both of them and I felt that we had given both some real windows into the practical world of scientific research.

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Old originals

Posted on August 10, 2009 by Frank Norman

I’ve commented before that librarians are great sharers and networkers. For those of working in small libraries the chance to get out and meet fellow practitioners is always valuable. I meet up with other MRC Librarians twice a year, most recently a few weeks back at the MRC Cognition and Brain Sciences Unit in Cambridge. Whilst in that lovely city we took the opportunity of visiting Corpus Christi College and its libraries, notably the Parker Library.
My first impression of the College was very favourable. It has a very striking old quadrangle with a classic gothic look.

I did wonder why it was called New Court, so I was not totally surprised to learn that the gothic features in this part of the college are in fact all 19th century neo-gothic, i.e. fake. We then walked through to the Old Court, which looked quite drab. The walls seemed to be rendered with concrete or pebble-dash, like an ugly 1930s council estate. Of course, this was the genuinely medieval part of the college.
With my historical and architectural senses duly confounded, we went on to the dining hall – another faux-gothic confection, and had an external look at the new undergraduate library, the Taylor Library. This opened last year and has won an RIBA award. It used to be a bank branch but was returned to the College and converted into a light and spacious library. It is adjacent to the Pelican Bar – and it seems that this juxtaposition is by design.
Then we moved on to the crowning glory of the College, the Parker Library. Named after Archbishop Matthew Parker (1504-1575), former master of the College, it is “a treasure house of Medieval and Renaissance manuscripts and early printed books“. It contains over 600 manuscripts – particularly medieval texts – including nearly a quarter of all extant Anglo-Saxon manuscripts in the world, And my own library doesn’t have even one Anglo-Saxon manuscript. One cannot help but marvel at the fact that the people in charge of this collection are librarians just the same as me and yet have such a completely different range of duties to perform and materials under their care. Many of the manuscripts are of course very beautiful, with their colourful illuminations.


Just as I was thinking that this library was all mired in the past, we were then led in to the digitization room (for some reason I wanted to say “chamber” there). I don’t know much about digitization, but when they said “76 Megapixel camera” I felt I ought to be impressed. Some pages have to be photographed in sections and then automagically stitched together by clever software. The project is drawing to a close now and the content is available on the web.
So, I felt outclassed not just by their history but also by their hi-tech.
They have a nice line in pelicans too. There are images of pelicans all over the college. Corpus Christi means ‘the body of Christ’, and the pelican was said to have offered its own blood to its children, just as Christ offers his body to his followers.

A recent addition to the college is the Chronophage, meaning “time eater”. It is a beautiful golden clock of unusual design, featuring a large metallic insect that seems to eat up the seconds as they pass. The wikipedia entry has more detail of this amazing public clock.

Just round the corner from the clock is one of Cambridge’s most famous pubs, The Eagle. I’m sure you all know why it’s famous.

All in all, it was a fascinating and thought-provoking visit and taught me not to judge a book by its covers, or even a college by its courtyards.

Posted in History, Libraries and librarians | 3 Comments

Policy and evidence – they’re all at it

Posted on August 6, 2009 by Frank Norman

I’m always intrigued by the way that new topics emerge, and suddenly everyone is talking about something that previously no-one was talking about. That’s the sign that we need a new library classmark or indexing term or a new journal (perish the thought!).
Anyway today I have observed that evidence and policy is suddenly “in”. My evidence:
1. Select Committee invites evidence on government policy-making
2. The Role for Science in US Regulatory Policy
3. Skeptics in the Pub, Westminster
Quick translation, if you’ve no time to follow the links:
The UK Select Committee on Universities, etc is commissioning work to assess the Government’s use of evidence in policy-making. This is in preparation for the creation of the new Science and Technology Committee on 1 October. They are looking policy on uncontentious issues like homeopathic products, dyslexia, swine flu vaccinations; the teaching of ‘pseudoscience’ at universities; measuring the benefits of publicly-funding research; the future of genetic modification, and synthetic biology.
Meanwhile, over in the States, the Science for Policy Project at the Bipartisan Policy Center in Washington, D.C., has suggested how U.S. regulatory agencies improve their use of input from outside scientists. They urge the government to be more transparent in selecting and vetting experts, clearer in defining what questions it wants answered, and more rigorous in reviewing the relevant literature.
Finally, the Twitterverse is buzzing with news of a new Sceptics in the Pub group, WestminsterSITP A possible new meeting of Skeptics in the Pub focusing on policy related matters such as regulation of complementary and alternative medicine, climate change policy, scrutiny of government policy and decision making. Their intention is to engage more with policy makers, decision makers, and regulators. There is a Facebook page and a Twitter presence.
Clearly policy and evidence is one of today’s hot topics.

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Science in the city (again)

Posted on July 23, 2009 by Frank Norman

I wrote previously about a visit to Newcastle-upon-Tyne. I recently visited again, this time to sing Tippett’s Child of Our Time and the (very fantastic) Berlioz Te Deum, in the rather attractive Sage concert hall. This is just next to the Baltic Art Gallery:

The Baltic is a converted flour mill that seems quite popular with the local birdlife:

I would have described the birds as seagulls, but I read an interesting sign underneath the Tyne Bridge telling me that the bridge is home to the farthest inland colony of breeding kittiwakes in the world. The bridge and ledges of nearby buildings, such as the Baltic, are a substitute for sea-cliffs. I rather suspect therefore that these are kittiwakes. My suspicions were confirmed by this story which suggests that not everyone is pleased to see the birds making themselves at home in the city.
Inside the Baltic Gallery there are several floors linked by elevators and a scary metal stairwell:

I saw three exhibitions. One included some of Harland Miller’s work, large paintings based on dust jackets of old Penguin books, but with a twist. I particularly liked D.H. Lawrence. Dirty Northern bastard and Bridlington: Coastal erosion – not all bad news. Another floor showed Sarah Sze’s work, Tilting Planet. It was a large-scale installation, or series of installations, made out of small, everyday things. I liked the way she created patterns that looked like they had grown organically, like mould spreading. I also liked that contrast between the overall scale and the individual scale (such as thin threads that stretched the whole length of the room).
Finally there was A Duck for Mr Darwin , a collection of works by different artists “exploring evolutionary thinking and the Theory of Natural Selection“. I found it a bit of a curate’s egg. I loved Mark Fairnington’s close ups of the eyes of wild animals – circular paintings with a single eye in the centre. Dorothy Cross’ film Jellyfish Lake was mesmerising, pulsating jellyfish moving through the water. The film Pre-Retroscope by Conrad Shawcross was interesting and clever – showing a 360 degree view taken from a rowing boat. Marcus Coates’ film Intelligent Design was also interesting, showing an attempted mating between giant tortoises on the Galapagos islands. They are remarkable animals.
Personally, I failed to encompass all of the works into one vision of Darwin or evolution. I’m not sure if it was my failure or a failure of the exhibition. But I have my suspicions.
From the viewing gallery on the top floor of the Baltic there are rather fine views of the Millennium bridge. Also called the Newcastle Eye, it is a footbridge of unusual design that can be tilted to allow larger boats to pass under. Here it is at rest:

and here it is raised, with a tourist boat passing underneath:

Thanks to Wikipedia I learnt that

Six 45 cm diameter Hydraulic rams (three on each side, each powered by a 55 kW electric motor) rotate the bridge back on large bearings to allow small ships and boats (up to 25 m tall) to pass underneath. The bridge takes as little as 4.5 minutes to rotate through the full 40° from closed to open.

Finally, we went along to the Centre for Life – nice logo, shame about the sculpture. I can’t help wondering whether there shouldn’t be a moratorium on creating scupltures with a double helix theme.

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Research (information) for life (sciences)

Posted on July 8, 2009 by Frank Norman

The name Research4Life sounds to me like a funding agency programme, with a twist of textspeak thrown in to make it cool. In fact it is simply a rebranding exercise for HINARI, AGORA and OARE. On balance I think I prefer Research4Life to that unwieldy bunch of acronyms – OARE especially is hard to pronounce without making it sound like a piratical utterance!
These three schemes provide free access, for researchers at institutions in some of the world’s poorest countries, to over 7,000 journals provided by many of the world’s leading scholarly publishers.
The rebranding took place a few weeks back but I only caught up with it at the WCSJ and a news story that claimed a massive increase in research output by scientists in the developing world since 2002, when HINARI was launched. That’s a nice correlation.
It’s easy for those of a cynical bent (and I admit I am one of those) to imagine that these initiatives are really a fig-leaf for publishers to defend themselves against the charge that their journals are unaffordable to researchers in the developing world. I suspect that may indeed be the reason that publishers have signed up to these schemes, plus the realisation that providing free access to someone who couldn’t afford to subscribe anyway is not eroding your business model. But the original impetus came from NGOs working to provide health information to developing countries. I used to dabble in that area and went to a number of meetings in 2000/2001 where HINARI was discussed.
HINARI was the first of the three schemes, covering health and biomedical sciences. It grew out of the United Nations Millennium Action Plan as a way to provide a public health portal on the Internet for developing countries. This was called Health Internetwork. I recall discussions in 2000 about it, but I’m a bit hazy on the detail now. Somewhere along the way the WHO became involved and it became Health InterNetwork Access to Research Initiative (HINARI).
The popularity of HINARI led to the development of AGORA (for agricultural and food journals) and OARE (for environmental journals). I wonder whether the scheme under its new brand may expand further to cover other subject areas like engineering, economics and education.
I was interested to learn that some countries have “graduated” out of eligibility for HINARI etc. I was told that publishers work with local consortia in those cases to try and put suitable deals in place to provide continued access on a subscription basis.

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Music inspires

Posted on July 7, 2009 by Frank Norman

I took part in a concert yesterday, singing (with 140 other choir members) Faure’s Requiem and Vaughan Williams’ Sea Symphony in the Barbican Hall in London. I have mixed feelings about the Sea Symphony – it has some great moments but they don’t all hang together satisfactorily to my mind (or should that be ear?). I am also not a great lover of Walt Whitman’s poetry, or at least the portions of it that Vaughan Williams chose to set. I was struck by one section last night though, which at first made me think about Author identifiers but on closer inspection could be a description of the Interwebz:

A vast similitude interlocks all,
All distances of place however wide,
All distances of time,
All souls, all living bodies though they be ever so different,
All nations,
All identities that have existed or may exist
All lives and deaths, all of the past, present, future,
This vast similitude spans them, and always has spann’d,
And shall forever span them and compactly hold and enclose them.

I do like the Faure Requiem. The In Paradisum especially has a luminous and, well, heavenly feel to it that is very special. This Requiem was also a learning experience for me many years ago. Let me explain …
When I left school I worked for a year in a public library service as a library assistant. We lowly assistants rotated through different departments, normally on a monthly basis. Luckily for me I ended up stuck in the Music and Drama section for six months. As I showed an interest in the music side I was allowed a bit of responsibility which included preparing orders for sets of orchestral parts. This meant checking how many oboe or trumpet parts etc there were in the score and then ordering the required number. For the strings we usually ordered 6+6+4+4+2 for the 1st & 2nd violins, violas, cellos and double basses. I remember that Bach’s St Matthew Passion was a tricky one as it has in effect two orchestras, partnering the two choirs.
Then one day I had to order the parts for the Faure Requiem. I was pleased to be doing this as the parts were required for a concert that I was singing in with the local choral society. I checked the required instruments and sent off the order. Back came the parts and were packaged up and sent off to my choir. All seemed well until on the day of the concert I happened to speak to the conductor.
He told me that the orchestral set had been a bit problematic. Faure had chosen a rather unusual instrumentation for his Requiem – a single violin part, 1st and 2nd violas, 1st and 2nd cellos, and double basses. So my order (6,6,4,4,2) meant that there were 12 copies of the violin parts, and 2 copies of each other string part. They’d had to to a certain amount of photocopying to provide enough parts for the players. I was mortified, but I don’t think he realised it was all my fault.
So, that experience taught me that it is always wise to check, even things that you think you know very well. Never make assumptions as they are likely to come back and bite you later.

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I’m a conference twit

Posted on July 5, 2009 by Frank Norman

I’ve been intertwittently tweeting for a little while. I haven’t yet got into a regular habit but it has increased since I got a phone with a good internet connection two months ago. I know there is some hatred of scepticism about interest in Twitter amongst fellow NN-ites so thought I’d post a recent experience.
I saw how useful conference tweets can be at a conference earlier this year. On that occasion I enjoyed reading the tweets but didn’t contribute any of my own. Last week I went to the World Conference of Science Jounalists and something moved me this time to jump into the conference tweetstream. I tweeted from several sessions on the first two days. On balance I enjoyed the experience and found it valuable, though I still have things to learn.
Here then is an account of my experience. First, some suggestions for successful conference tweeting.
Do one thing or the other – don’t try to twitter and write handwritten notes too. I tried it for one session but very quickly discovered that with only two hands I could not both write and tweet.
Check the hashtag. I tagged my first couple of tweets with #wcsj2009, which was the name of the conference. But then I searched Twitter to see if anyone else was posting and realised that everyone else was using #wcsj so I switched. On the last day I saw a tweet from someone bemoaning the fact that they’d been using #wcsj2009 for the past two days so hardly anyone had seen their 140-word pearls of wisdom. The conference website will probably have something about the recommended hashtag.
Start early in the conference. At first only a small number of people at the conference were tweeting so it was easier to gain visibility. Later the stream went into spate so it was harder to stand out.
Follow the stream. OK, it’s hard to listen and type at the same time but it’s possible. Unfortunately you also really need to see who else is tweeting and what they are saying, so you have to read as well as listen and write. I found it useful too to see how others styled their tweets.
Report or comment. If several others are already reporting a session then there’s not a whole lot of point in tweeting the same content. You might prefer to step back and fill in any gaps you see, or to add your reflections, reactions or humorous interjections.
Hardware. I used my phone for much of the time as I had some troubles with the conference wifi. It did make it rather slow. For the sessions I was using my netbook it was much easier. I think netbook/laptop is better if you want speed.
Software. Something that lets you easily flip between reading other people’s conference tweets and typing your own is best. I noted that Tweetdeck is popular. I used Twitterfall on my netbook and Twidroid on my phone. Neither was ideal. I will do more research before the next time I need to tweet.
I found a few benefits:
Parallel sessions. When there are parallel sessions it can be nice to see what’s happening in the other sessions (yes, you have to listen, type, and read multiple tweetstreams!). Once or twice I noted tweets from people I knew were in a different session to me, but they were tweeting very much the same points that were being made in the session I was at. A nice bit of intextuality.
Followers. I was surprised to see how the number of my followers increased rapidly during the conference. Tweeting begets followers it seems. I was flattered to see some estimable names among my new followers.
Conversations. More than conversation started up when someone saw my name badge and said “Oh, I’ve been reading your tweets”.
Notes. At the end of the conference the twitterstream (either your own, or the whole lot) makes a pretty good set of notes to draw on if you want to write a report.
I still have a few reservations, or questions:
Tweeting for the hashtag or for your followers? Producing all these snippets from the conference so that others can read them when they search for the conference hashtag is all very well, but I wonder what my regular followers made of it all?
Retweet or not? Retweeting is useful if you see a good tweet from another conference attendee that you want to share. But then that tweet gets duplicated in the conference twitterstream. Maybe that’s OK, but it does get a bit boring when you see the same thing for the sixth time. OTOH, it was exciting the first time I saw one of mine retweeted.
Is it scalable? Rather like blogging, it’s only useful while only a relatively small number of people do it. If all 900 conference delegates had been tweeting all the time, there would be no way to absorb that much information.
Why me? Following on from that, why should I presume to be one of the Twitterers? It was dispiriting inspiring to see someone else tweeting brilliantly and in great volume. @edyong209 was so quick and accurate that I wondered what was the point of continuing with my slow tweeting. I felt a bit better when he was given an ABSW award at the conference grand reception – he is a genius science writer so of course he is a great twitterer too. I need to work better on finding my angle.
As Martin Fenner has written there are good reasons not to go to conferences, and I expect that following conferences remotely will become more popular over the next few years. Twittering at conferences is one way to share your experience with people not at the conference.

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Science in the city

Posted on June 21, 2009 by Frank Norman

Following on from my Parks theme yesterday, I had a lovely stroll in the park today. I think it just about qualifies as a park, but it’s a long thin one, based around a small stream.

Jesmond Dene is just to the edge of the city. Which city? Well, this is its cathedral:

The city has a nice line in public scupture:

and

It has a famous old Literary and Scientific Institution (forgot to take a photo) and a good few scientific and technical figures such as these two:


You might see a clue to its sister city across the water in this photo of the famous art gallery:

shown here again with some more icons of the city:

That bridge in the background should be the clincher. See it again here:

Hmm, I was going to ask you to guess where I was but after checking the post in preview I realise I have given the game away completely in one of the photos and I don’t have time to re-edit. I’ll have to be more devious next time.

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The beauty of parks

Posted on June 20, 2009 by Frank Norman

There is a lovely essay on Parks in the Guardian today. I say Parks rather than parks as the author takes a very strict line on what is or isn’t a Park, proposing five criteria that must e met in order to qualify (large trees, random planting, undulations, scale, and a gate or portal). William Boyd, the essay’s author, was one of eight writers commissioned by London’s Royal Parks to write a story set in a London Royal Park; one writer for each of the 8 parks.
In his Guardian piece Boyd ranges widely, discussing fiction set in parks, Orson Welles, plane tree, Rio de Janeiro, Queen Victoria, pyschogeography, cemeteries, zoos, Wittgenstein, and sex, though not all at once. Is what he says about plane trees correct? He says that the London plane tree is

a hybrid derived from the Platanus orientalis and the Platanus occidentalis. This hybrid sheds its bark, a fact that is believed to make it more resistant to the city’s polluting toxins,

A good friend of mine is a great lover of parks – a complete nut about parks in fact. He made me realise that I love them too – a walk (or run) in a beautiful oark can have a wonderfully calming effect. I also like the dissonance you find in city parks between the urban setting and the rural appearance. Walking through St James Park in London, Central Park in New York, or Lumpini Park in Bangkok you can see the city around you but it is not touching you.
If you love parks read Boyd’s essay. I think I may need to look the 8 stories too in due course.
P.S.
Forgot to say. Boyd also discusses the distinction between town and country writers. This made me wonder if there is a similar split between toｗn and country scientists?
Is the science done at Colｄ　Spring Harbor, Hinxton or Keyworth any different from that done in South Kensington, Toronto or Manchester?

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