Links for 29th October 2004


The Filing Problem: Some Replies

Just a few responses i had to my post about the filing problem. I’m still interested to hear from any one else who has good advice on information management systems

MD said:

You know you’re having a frustrated day when you reply quickly to emails about filing. Nonetheless:

All my bibliography stuff is handled by something called BibTeX which is part of a typesetting system called LaTeX. Maybe you’ve come across it? (It’s all very open source and free etc..)

You essentially have a text-based database that stores all your referebces, with as much or as little meta-info as you want. Then you write all your writing in LaTeX which is a mark-up language useful for mathsy documents (but I reckon dead useful in general) which can include citations. The LaTeX document looks at your BibTeX file and pulls out and formats the appropriate references.

LaTeX is generally great, especially when you want to combine two documents and you don’t want to re-number everything (sections, figures, equations etc). So my thesis will be a cut-and-paste job of my articles/reports, and I’ll not have to re-format everything. Plus it looks good.

LaTeX might represent an over the top learngin curve for non-maths stuff, I don’t know. Have no idea how to keep track of paper stuff.

RS said:

Personally I would just build a small access database. Each discrete item gets several properties: format, keywords, location etc. for hard copies you can then just have a numerical index linked to a database entry. For soft copies each item could be hyperlinked or embedded in the database. You would then find it easy to generate search queries based on keywords. You could easily flag sources that are referenced in individual papers you are working on and if laid out correctly you could then auto-generate a list of bibliographic references. Whilst I don’t know how you could exactly do it I think it should also be possible to link references within a document to the database entry. Whilst it would take a while to build I think it would be quite a powerful tool.

You could store notes separately and cross reference papers within the database directly. It would mean entering a bunch of data each time you read a paper but it would probably repay the time invested.

WJ, displaying an uncharacteristic lack of rigour, said:

Disorganisation is the key to innovative academic research 😉

I’m not a good example…. hard copies are rare…. pdfs are by
subject mainly (and with replications for when i’m writing a
particular paper)…. format is always of the type “Jennings (2004)
The Politics of Celebration.pdf” [i.e. name (date) short title for own
personal reference].

have a few articles stored by author. but only a few.

KG said:

M$ Access all the way. I’d love to know if there is a GPU licenced alternative with similar functionality, but last time I asked a free software geek he suggested that if you want a graphic interface you’re stuffed.

Access cos flexible, hyperlinkable, searchable, expandable and webable (if your really keen). I store references to all my info in one integrated database, (split according to source type: authored book, edited book, journal, web, other) including a section for notes on each. I store a list of things to read there too, and can search titles and authors in the whole lot in one go, but filter unread if you just want something you’ve actually seen. My bibliography creation is pretty clunky (read: doesn’t work) but will be sortable by the time I’ve got a thesis to add a bibliography to.

There’s also the potential bonus that if you’ve got a bunch of friendly academics or research team all using access on the same network you could actually use the same db and choose to just see your references or the whole project’s, including notes they’ve made on readings – if you trust x and he says paper y is crap, then thats one less to read!

Anyways, come round for a test drive, and you can have the shell of mine to play with if you like.


100,000 dead

100,000 civilians dead in Iraq, mostly women and children [1]. Even Jack Straw seems to accept the more conservative figure of 15,000 which is offered by

Let’s just run over the other figures too:

  • Weapons of Mass Destruction found: 0
  • Peaceful Democracies established: 0
  • Al-Qaeda operations disrupted: 0
  • Support given to international law: 0
  • Promotion of human rights: 0
  • Understanding between US and Europe enhanced by: 0
  • Similarly, between ‘Western’ and Islamic cultures: 0

  • Ref:
    1: Lancet articles here. BBC news report here


    The Filing Problem

    I am back in academia, and now i must decide how i’m going to sort out my papers. I’ve been avoiding the problem, but the rate at which i’m accumulating paper, and PDFs, means I’ve now got to settle on some method for keeping track of everything. Whatever the system is, it needs to facilitate the these things for me:

  • 1. Keeping track of my paper copies of journal articles (which ones i have, where they are)
  • 2. Keeping track of my PDF copies of journal articles (which ones i have, where they are)
  • 3. Searching both paper and electronic copies of journal articles
  • 4. Easily inserting (auto-formatted) journal references into manuscripts
  • 5. Organising and searching of non-journal bits of paper (newspaper cuttings, unpublished manuscripts, miscellaneous text, etc).
    [Or, at least, those are what I think my needs are]

  • I’m interested in how everyone else does this. I presume that all academics (and most informational professionals, for that matter) have to deal with the overwhelming amount of information it is possible to accumulate. I feel/hope there’s a good solution out there, but I’m struggling to reconcile all the different types of information i want to keep and use, and the different purposes for which I want to use them.

    One solution I’ve seen is to keep all the papers in topic-organised folders, and a list of what you’ve got in something like Endnote. Problem with this is that I’m never very comfortable with topic-based organisation. I’ve never managed to specialise (read: focus) on one field, so there isn’t really the coherence in my papers that makes organising my topic natural. Papers speak to several topics, or don’t fit neatly into any.

    My PhD supervisor uses biblioscape to keep a record of what he’s got on paper, and he organises the hard-copies by accession number – ie as he gets a paper he puts a number in the top corner and stores them all in numerical order. It’s a neat way of getting round issues with deciding how to store the papers. It means that recent papers are on top (so to speak), but it does mean you lose any other implicit organisation that might arise from, say, storing by first author or topic. Plus he’s dependent on his electronic index working (and by most reports biblioscape is a bit flakey. And the reference insertion add-on i never got to work perfectly too).

    One other guy in the research group writes short pieces of text which reference each paper he’s got. It’s a good way or giving more coherence to papers he has read before filing them away. I don’t know how he keeps track of the actual paper (and PDFs as well).

    Other people (including my co-author on the book) use a self-authored web-app to keep track of their notes, hyperlinks and documents. This has the advantage of being accessible anywhere, and – since it’s web based – there’s lots of cross-referencing and search functionality already ‘built in’. In fact, after the book, I was so taken with how useful wikis are, that i’ve started my own to keep my notes and hyperlinks – but it doesn’t seem ideal for organising my bits of paper. I’m happy storing my own short notes, memos and links on a combination of this blog and my personal wiki, but i’m still left with the paper problem (ie items 1 through 5 on my wish list).

    This is the system I adopted during my PhD: A filing cabinet with all journal papers organised by author; Using Endnote to keep track of what is in the filing cabinet, with a keyword to indicate if it was in electronic form rather than paper form. PDFs stored all in the same folder on the harddisk with the name in form for [First Author’s Surname] + [Year of publication] (ie Brown04.pdf). This meant that i had to put paper copies back in the right place (which could be fiddly) and also download their details from Web of Science or Pubmed when i acquired them.

    This all seemed to work okay, but it was quite high maintenance, and didn’t give me any good way of organising things that aren’t journal papers. So, at this point in time, i have ten years worth of random bits of paper i thought were interesting at the time, with no idea what is where or how they should be organised (they’re all in different piles by when i acquired them, and i acquired them usually on the impulse that the information felt important, but i didn’t know why – or i knew why but didn’t have anything to do with it). What do i do with all this paper information? And is there a way i can integrate the way I organise it with my academic paper collection?

    I’ve started a new academic project as part of my post-doc, and am facing the need to do something with all the new journal articles i’m acquiring, as well as the feeling that i really should organise all the papers I acquired while writing the book, and papers from four years of research in boxes somewhere – and all under the knowledge-shadow that everything will interconnect with everything else, so there’s no good way to keep paper separate by project (and who would want to lose out on the serendipity of accidental cross-links anyway?).

    Has anyone got any good advice?


    Burning Man pics

    Did i mention that i put our pictures from Burning Man 2004 on-line? There’s a shed load of them, and there will be more coming eventually. The ones I took are pretty dull (i tended to take them only when nothing was happening), but the other guys have some good ones. Enjoy


    Links for 27th of Oct 2004


    Quote #65

    To frame a philosophy capable of coping with men intoxicated with the prospect of almost unlimited power and also with the apathy of the powerless is the most pressing task of our time.

    Bertrand Russell, via Three-Toed Sloth


    Lazlo’s Chinese Relativity Axiom

    Remember Lazlo’s Chinese Relativity Axiom:

    No matter how great your triumphs, or tragic your defeats, approximately one billion Chinese couldn’t care less


    leunig image search

    Here’s something worth doing – a google image search for ‘leunig’. And bingo, a spread of wonders to enjoy!


    Links for 20th of October 2004

    technical notes

    finding hosting

    So how do you go about finding a good host for your website? A google search turns up a million people and i’ve no real way of choosing between them. I want lots of space (250 MB +), Unix hosting (with PHP, Phython, MySQL) and preferably the ability to run at least 2 domains…And decent technical support would be nice too. Can anyone recommend a company in the UK who could do this for me please?


    European Social Forum in London

    I’m at the ESF in London. The workshop i’ve come to has turned out to be an empty room. An empty room in LSE with an unattended networked computer. So here i am. Read this, on Indymedia, Dan on ‘The ESF: Hacking Networks of Power’.


    Quote #63

    Whatever you can do or dream you can do, begin it. Boldness has genius, power and magic in it. Begin it now.

    – Goethe


    Quote #62

    In mathematics you don’t understand things. You just get used to them.

    John Von Neumann


    Links for 13th October 2004


    priming for social control

    Catching up with my journal abstracts, I noticed this:

    Rotteveel, M.; Phaf, R.H. (2004). Loading working memory enhances affective priming. Psychonomic Bulletin & Review, 11. 11, 2, 326-331(6).
    Abstract: Stronger affective priming (Murphy & Zajonc, 1993) with suboptimal (i.e., reduced consciousness) than with optimal (i.e., full consciousness) prime presentation suggests that nonconscious processes form an important part of emotions. Merikle and Joordens (1997) have argued that both impoverished presentation and divided attention can produce suboptimal conditions and result in parallel effects. We manipulated attention by means of a concurrent working memory load while keeping presentation duration constant, as participants evaluated Japanese ideographs that were preceded by happy,neutral, or angry faces (affective priming) and male or female faces (nonaffective priming). In contrast to nonaffective priming, affective priming was larger with divided attention than with focused attention. It is concluded that manipulations of stimulus quality and of attention can both be used to probe the distinction between conscious and nonconscious processes and that the highest chances of obtaining the pattern of stronger priming with suboptimal presentation than with optimal presentation occur in the affective domain.

    Which I can’t help thinking implies: if you want to pull people’s emotional strings (without them knowing it) then you should keep them busy.

    Call me a social-control conspiracist, but i think this is another good reason for us all to spend more time sitting down with a cup of tea and less time working to keep the economy going



    1. What a frikkin’ good day to be alive! Hello World!

    2. It occurs to me that soundbite culture, like so many cultural phenomena, is the product of technological change. The television, and radio, technologies that carry the soundbites are those that create the need for the soundbites. We’ve always had slogans but the depthless soundbite is the product of the shift in political media from discursive to broadcast technologies.


    hacker ethics

    Thanks to dan for this

    Warnick B.R. (2004). Technological Metaphors and Moral Education: The Hacker Ethic and the Computational Experience. Studies in Philosophy and Education, 23, 4, 265-281.

    This essay is an attempt to understand how technological metaphors, particularly computer metaphors, are relevant to moral education. After discussing various types of technological metaphors, it is argued that technological metaphors enter moral thought through their “functional descriptions.” The computer metaphor is then explored by turning to the “hacker ethic.” Analysis of this ethic reveals parallels between the experience of computer programming and the moral standards of those who are enmeshed in computer technology. This parallel suggests that the hacker ethic is being pushed by a computer metaphor and its functional descriptions in a direction of individualism and systems thinking. After examining some possible implications of the computer metaphor, this essay offers suggestions concerning how technological metaphors may be critiqued.

    Ironically for a paper about the hacker ethic you can’t get the PDF on-line, but i did find Biella Coleman, from the University of Chicago and her blog, Sato Roams and her research proposal The Social Creation of Productive Freedom: Free Software Hacking and the Redefinition of Labor, Authorship, and Creativity. which contains, in the section headed ‘UNIX: A Living, Breathing Software Entity’, a quote from the wonderful In the Beginning was the Command Line by Neal Stephenson (1999):

    ..UNIX, by contrast, is not so much a product as it is a painstakingly compiled oral history of the hacker subculture. It is our Gilgamesh epic… Likewise, UNIX is known, loved, understood by so many hackers that it can be recreated from scratch whenever someone needs it.


    an hour of being 75 years old

    Quoting Slovic et al (1982), Facts versus fears: Understanding perceived risk:

    …Sowby (1965) provided extensive data on risks per hour of exposure, showing, for example, than an hour of riding a motorcycle is as risky as an hour of being 75 years old.


  • Slovic, P., Fischhoff, B. & Lichtenstein, S. (1982). Facts versus fears: Understanding perceived risk. In D. Kahneman, P. Slovic & A. Tversky (eds.). Judgement under uncertainty: Heuristics and biases. Cambridge: Cambridge University Press
  • Sowby, F.D. (1965). Radiation and other risks. Health Physics, 11, 879-887.
  • Categories

    Folding the Hakama

    At last – I have learnt how to correctly fold my hakama. This site was most useful, although this site was prettier. The meaning (supposedly) symbolised by each fold in the hakama is discussed here. Now all I have to do is learn the correct way to put the thing on and I’m sorted...


    Two more quotes

    Real revolution means people choking to death on their own shit

    Graffiti seen by Andy, London 2001

    The universe is full of magical things patiently waiting for our wits to grow sharper

    Eden Phillpotts


    Quote #59

    My feeling about technique in art is that it has the same value as technique in lovemaking. That is to say, heartfelt ineptitude has its charm and so has heartless skill, but what you really want is passionate virtuosity.

    John Barth


    Shambala photo gallery

    I’ve just put up a gallery for Shambala photos. Here.


    With clear and open desire

    Murray is able to produce a look that is sneaky and frank at the same time. It is a look that gives equal credence to disaster and lecherous success. He says that in the old days of his urban entanglements he believed there was only one way to seduce a women, with clear and open desire. He took pains to avoid self-depreciation, self-mockery, ambiguity, irony, subtlety, vulnerability, a civilised world-weariness and a tragic sense of history – the very things, he says, that are most natural to him. Of these he has allowed only one element, vulnerability, to insert itself gradually into his program of straighforward lust. He is trying to develop a vulnerability that women will find attractive. He works at is consciously, like a man in a gym with weights and a mirrow. But his efforts so far have produced only this half sneaky look, sheepish and wheedling.

    Don DeLillo, White Noise (1984)


    A logic necker cube

    Andy found a spiritual-epistemological necker cube! We both agree with the majority of the statements below, but reach exactly the opposite of conclusion from that intended by the original author.



    I got a job at the University of Sheffield. Part time doing some social psychology (!) on a sustainability project, part time doing some social network work, and part time free for me to indulge my other interests (some cognitive psychology experiments have come up, during writing the book, which I would like to run, and I’m sure there’s some cog neuro / neuroimaging pies I can stick my fingers into).

    So, back into academia, back to Sheffield…Is it like i’ve ever been away?



    US to make legal the torture, without trial, of British citizens. Our government won’t be able to protect us from the US government’s breathtaking disrespect for human rights. Read about it here

    (via helmintholog)

    Update 9 Oct: here


    Map fun

    Usually I use to get a quick O/S map of an area by postcode or street name, but today I’ve found more useful (the interface is more graphical, the zoom in and out is better – it’s easier to use if you’re not sure where what you are looking for is in relation to everything else).

    I found a map of all the counties of Great Britain and a postcode map of the same

    This guide tells you what the different parts of the postcode mean. And a map and list of all the london postcodes (strictly areas and districts, but not sectors or street information) is here


    The Other Tom Stafford

    A friend writes:

    if you click on ‘tom stafford’ on the amazon page for pre-ordering Mind Hacks,
    you get a link to your other book. You know, the one you wrote when you were
    minus three, about the space race.

    And it’s true. The other Tom Stafford is an astronaut who flew on Apollo 10, amongst others. For a while he was top of google for a search on ‘Tom Stafford’, but i tipped him off the top spot.

    Incidentally, he’s also quoted by my favourite band, the New Model Army (who are playing in manchester on the 16th of December, by the way). On their song Space from the album Impurity, Joolz reads this quotation by the astronaut:

    The white twisted clouds and the endless shades of blue in the ocean make the hum of the spacecraft systems, the radio chatter, even your own breathing disappear. There is no cold or wind or smell to tell you that you are connected to Earth. You have an almost dispassionate platform – remote, Olympian and yet so moving that you can hardly believe how emotionally attached you are to those rough patterns shifting steadily below.

    So there you go


    Mind Hacks pre-order

    Mind Hacks is now available for pre-order, e.g. from Amazon ( and .com)