CoLIS 7: Doctoral forum

June 25, 2010 at 10:40 am | Posted in lecture, thesis, work | Leave a comment
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Presented at the CoLIS 7 doctoral forum on Monday and got some very encouraging feedback from the session leaders and the other students.

It was really fascinating to get an insight into how everyone else’s research is coming along, the different approaches they are taking, and the unique problems each of us face in trying to get anywhere with our research.

Our doctoral group included students working on everything from tagging in archives and online communities based around the Twilight saga to the philosophical idea of ‘information refusal’ to retrieval challenges for Quranic resources. Oh, and I should mention a project looking at social media use in public libraries and bibliometrics in the literature studies domain. I think that was everyone – you know who you are!

My (unused) project presentation

Some notes I made to prepare

Many thanks to Jutta Haider for her hard work in organising the forum – it was great!

Information requirements for scientists using human biological samples

April 6, 2010 at 8:26 am | Posted in lecture, web | Leave a comment
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What information do biological reserachers need?

Kim’s study looks at biomedical researchers working with human tissues and tissue bio-banks, and uses a questionnaire to delve into what types of users and what types of information these users need to do their work.

Unsurprisingly, users can be divided into two broad types: clinicians and basic scientists. It is perhaps interesting given the drive towards translational research and efforts to bridge this divide that studies keep on identifying this important gap between these camps in the biomedical sciences.

Tissue bank users presented with a braod spectrum of requirements for information pertaining to the samples they used or wanted to use. In terms of managing the physical specimens, there are strong parallels between tissue samples and museum artifacts. In both cases, information about how the sample/artifact has been stored, moved, processed and used is important to the users, which is quite different to how library users might treat books or journals.

You might not care if a book has been re-bound in the last ten years, but it is important for a biomedical researcher to know how many times a sample has been thawed and re-frozen.

Kim highlights that what researchers do with tissue samples is also relevant to users. The data and results produced from a tissue sample should be fed back into the repository systems for the samples themselves, so users can integrate this data into their own research.

The implications for bio-bank systems designers are obvious. Managing storage information and metadata about bio-samples is on thing, but tntegrating the complexities of empirical biological data and leveraging this information for tissue bank users is a quite different and major challenge.

Kim, S. (2010). “A conceptual framework of information requirements for scientists using human biological samples.” Information Research, 15(1) paper 427. [Available at http://InformationR.net/ir/15-1/paper427.html]

Full text available

Information domain : the biological sciences, data and images

March 10, 2009 at 11:45 am | Posted in lecture | Leave a comment
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These images show the range of data and information associated with the BRCA1 gene.

The full FASTA format sequence for the BRCA1 gene.

Information domains : the biological sciences

March 10, 2009 at 11:44 am | Posted in lecture | Leave a comment
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The lecture will last about 60 minutes and revolve around three questions:

  1. What is the point of biology? (A theory bit)
  2. What is not information in biology? (A pictures + websites bit)
  3. Are science librarians useless? (A librarians-are-great bit)

This Daily Mail article about a cancer gene will be used to show that if we perform only a few simple searches in the biological sciences domain for the gene in the newspaper story, we can find lots of relevant biological information, and this information illustrates several information problems pertinent to the life sciences domain.

The images and resources in ’2′ above are available under the Delicious link bundle and post below:

Some links for this biological sciences information domain lecture

Some images of data and biological information relevant to this lecture

Further reading about information problems in bioinformatics :

Zweigenbaum, P., Demner-Fushman, D., Yu, H., and Cohen, K. B. (2007). Frontiers of biomedical text mining: current progress. Briefings in Bioinformatics, 8(5):358-375. FULL TEXT

Further reading about whether scientific knowledge is a privileged type of true knowledge :

Lipton, P. (2005). The Medawar Lecture 2004 : the truth about science. Philos Trans R Soc Lond B Biol Sci, 360(1458):1259-1269. FULL TEXT

And for plenty more reading about information in biology, see  :

My CiteUlike library

Two creative types and thirsting for Next Big Things

November 25, 2008 at 1:32 pm | Posted in lecture | Leave a comment
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Malcom Gladwell, Age Before Beauty.
New Yorker Nights Lecture, 21st February 2006

Lecture audio
Transcript by John Lennox

Gladwell talks in this lecture about Galenson’s theory of creativity. Galenson is an economist and author of ‘Old Masters and Young Geniuses‘, his book in which he argues that creative persons can be divided into two groups: the conceptualists and experimentalists.

Conceptual artists have strong ideas about what they want to achieve and peak at a young age – think TS Eliot, The Eagles or Orson Welles. Experimentalists struggle and test and refine their art over many years, often achieving recognition at an older age – think Twain, Cezanne or Fleetwood Mac (the examples are Gladwells and Glaenson’s).

Galenson backs up his arguments with investigations into art prices through they years, and extending these econometric analyses to other artistic domains.

I couldn’t see much in Gladwell’s lecture on exactly why the observation, interesting as it may be, should be the case. He touches on psychological and epistemological reasons for why certain people might work in a certain way, or why different types of explanations might be favoured under different circumstances.

Yet there could be all manner of reasons for why creativity is recognised adn rewarded by society. Does it take time for society to absorb new styles? Do some people get lucky early on, and live off the success? Is creative recognition absolute (“This album is a classic!”) or relative (“Compared to the other dross, this album will do as a classic!”)?

It would be interesting to investigate whether there is any pattern in the age at which biologists achieve recognition in the domain. A citation analysis coupled with author’s ages would be relatively straightforward.

My feeling is that in every generation, we have to choose some classics, some ground-breaking works, some fundamental innovations – otherwise society has no sense of progression. Academics, journalists, scientists, politicians and The People crave the Next Thing; it is a modern obssession. Progress distracts from the gnawing sensation of mortality. In retrospect we find patterns in that which become labelled as the Next Thing, the New Thing, the Big Find – and we can propose types to explain these patterns.

How much creativity is unheard in the annual ‘Huzzahing’ over a handful of Next Things? How many great artists are drowned out by Damien Hirst’s bellowing? How many exciting new novelists are shouldered aside by another Ian McEwan novel?

How many wonderful small ideas in biologists heads are set aside in accedence to the terms of normal science?

MIS requirements for a Palestinian healthcare system

October 27, 2008 at 3:53 pm | Posted in lecture | Leave a comment
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Yousef Al-Mimi, On the development of management information systems for the Palestinian Department of Health
Centre for Health Informatics PhD Transfer Seminar

The Palestinian healthcare system is divided geographically, between the West Bank and Gaza. Provision is funded in part by insurance contributions which cover simple procedures, whilst private system is necessary to pick up more complicated casework. A primary healthcare system does exist, and more often than not this is the first port of call for people needing medical attention.

Al-Mimi aims to investigate how a prospective management system might meet the strategy and objectives envisages by the Palestinian Department of Health. Since patient data is spread between different stakeholders, such as the Finance Ministry, private insurers, primary and secondary health care providers, international health aid agencies and NGOs, the challenge would be to imlpement a system that both met the needs of these different users, whilst at the same time remaining feasible.

Requirements analysis was discussed as a potential means to appraise different stakeholder needs. Feasability was the big question though. Users would want a quick, efficient, cheap system with complete coverage. Money, time and the reality on the ground might mean a very different management system would be the pragmatic solution for the Palestinian healthcare situation.

Hot, flat, crowded and no idea what to do next

October 14, 2008 at 9:34 pm | Posted in lecture | Leave a comment
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LSE Evening Lecture, Thomas L. Friedman. Hot, Flat and Crowded.
Lecture details and eventual page for the lecture Podcast.

Hot, Flat and Crowded at Amazon.co.uk

Friedman spoke this evening about his new book which sports the inordinately long and self-explanatory title, ‘Hot, Flat and Crowded: Why the World Needs a Green Revolution – and How We Can Renew Our Global Future’.

There’s no need to buy the book; it’s all there in the title.

I didn’t know much about Friedman before this lecture, and it turns out he’s a sort of hyper-nationalistic, all-American patriot with a job on the New York Times and the ear of the rich and powerful across the globe, judging from his liberal name-dropping.

The lecture was utterly lightweight, which perhaps was to be expected since it was tied to the launch of his new book. However, the audience at the LSE seemed highly receptive to his pro-capitalism, pro-Green, ‘Let’s save the planet and get rich whilst we do it!’ line of thinking.

His motivation was justified, yet the solution to climate change, the massive increase in the global population, energy poverty and our thirst for oil were to be, he said, energy technologies. All we need is a new ‘Green Race’ comparable to the great arms race between American and Russia, with the Red Threat replaced, seemingly, by the rising Chinese Economy and our problems will be solved.

Friedman expects industry and individuals to seize upon a great, innovative drive to develop green technologies since, he argues, they will get rich and secure their home nation if they do. Tweak the markets rules and the lure of huge profits based on petrochemicals (as supply falters, prices balloon) can be neutered. This achieved, we can all concentrate on making super-efficient toasters and live happily ever after. Frankly, his whole thesis was flimsy to say the least, and premised on nothing other than his own opinion and a few anecdotes about energy and the environment posted by his friends.

Personally, I would invest heavily and immediately in nuclear power in the UK, dissolve the army, deploy the ex-troops to build high-speed railways, close all but one airport somewhere central like Manchester and spend the next century weening our high-energy consuming society from a voltaic drug we have become utterly dependent on.

We should not leave free markets to solve the problems they created. Foxes will never be chicken farmers.

Declining variation in the human gene pool : is human evolution over?

October 7, 2008 at 2:06 pm | Posted in lecture | Leave a comment
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UCL Lunchtime lecture, Prof Steve Jones. Is human evolution over?
Steve Jones’ website at UCL

Steven Jones is head of the Department of Genetics, Evolution and Environment and gave the first UCL Lunch Hour Lecture for the new term, entitled ‘Is human evolution over?’

[Note : If you're thinking of attending one of these Lunch Hour Lectures, it might be worth turning up before 1pm - I arrived at five past and the place was nearly full.]

Jones introduced his lecture with a brief meditation on Moore’s Utopia before plunging into a whistle-stop tour of evolution, natural selection, variation and whether Homo sapiens is steering itself into an evolutionary cul-de-sac through relatively recently changes in our migration and sexual habits.

Though certainly an entertaining speaker, I think I missed any over-arching opinion the Professor held on whether the patterns he was arguing are becoming a common feature in the development of our species (reduced variation in the gene pool due to patterns in male fertility, when we decide to have children, the movement of genes with migrating persons across the globe, racial mixing) are a good thing or a bad thing.

His term ‘one genetic continent’ neatly captures his view on the current state of global human evolution, but whether this a temporary state of affairs, the beginning of the end or a happy terminus for our species was not clear.

A true Darwinist, I was struck by Jones’ commitment to certain elementary facts. Firstly, that variation exists and is worth paying attention to. Genetics is premised on small changes being passed on from generation to generation and the geneticist ‘decides’ what a significant difference is. Height, skin colour, blood pressure or wing span are observed through successive generations – that these facets are interesting is a given.

Secondly, natural selection is a process by which positive attributes are in a sense ‘picked out’ from a population. That an attribute is positive is post-selection or in other words, selection is natural and useful because we can look backwards through time and say, “Yes, it was handy we humans developed webbed feet because the Thames barrier broke and the south east submerged by floodwaters, a la ‘Waterworld’.”

Thirdly, there was no doubt in Jones’ use of scientific language. ‘Evolution’, ‘natural selection’, ‘fertility’, ‘mutations’, ‘variation’ – these words were used liberally and casually. They were possessed by a mythic quality and having read Kuhn over the last week, when one listens to a scientist one understands why Kuhn used words like ‘tradition’, ‘convention’, ‘community’ and the nebulous term ‘paradigm’ to try and capture how normal science is sustained through commitments to scientific beliefs.

From an information perspective, there is likely to be mileage in delving into how scientists decide what to observe, the descriptive languages, terminologies and standards they develop to describe these observations and also how a community decides on acceptable degrees of difference.

Variation from norms is not restricted to evolutionary biology and genetics, but extends to all scientific observations. Measurements outside the norms are regarded as mistakes.

It is perhaps ironic that modern biology is both committed to paradigmatic norms and at the same time is built around the notion of ‘mistakes’ (or mutations) in genetic codes. Normality and abnormality in messages might be something I could investigate from an information science perspective.

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