Chemoinformatics - some key points (by Ben Allen)

What is Chemoinformatics?

Definition

“The application of informatics methods to solve chemical problems”

Methods

·         Databases of chemical structures

o   Searching

§  Similarity methods

§  QSAR

§  Virtual screening

o   Creating

§  Computational library design

§  Molecular enumeration

§  Combinatorial  chemistry

·         Chemical structures

o   2D

§  Graph theory

o   3D

o   Plus other information

§  Calculated properties

§  Experimental values

·         High throughput screening

·         Databases

o   Can be very large (10³-10¹² compounds)

o   Often biologically active

Applications

·         Pharmaceutical

o   Biggest area of interest/development

·         Agrochemical

·         Food chemistry

Overlaps

·         Computer science

·         Information studies J

·         Bioinformatics

Notes for discussion on Academic Writing - by Simon Wakeling

In the early 1950s, world renowned (and future Nobel prize-winning) quantum physicist Richard Feynman was invited to attend a cross-disciplinary conference in New York to discuss the "ethics of equality." He writes:

"There was a sociologist who had written a paper for us all to read—something he had written ahead of time. I started to read the damned thing and my eyes were coming out—I couldn't make head nor tail of it […] I had this uneasy feeling of, "I'm not adequate," until finally I said to myself, "I'm going to stop, and read one sentence slowly so I can figure out what the hell it means."

So I stopped at random and read the next sentence very carefully. I can't remember it precisely, but it was very close to this: "The individual member of the social community often receives his information via visual, symbolic channels." I went back and forth over it and translated. You know what it means? "People read."

Then I went over the next sentence. And I realized that I could translate that one, also. Then it became a kind of empty business. "Sometimes people read. Sometimes people listen to the radio." And so on. But written in such a fancy way that I couldn't understand it at first. And when I finally deciphered it, there was nothing to it."

(Feynman, R. 1985. Surely you're joking Mr. Feynman! London: Vintage, pp. 281-282)

How often do we find ourselves repeating Feynman's experience? Is it a particular problem for the social sciences, or academia in general? How can we ensure we communicate our ideas clearly?

Facts and assumptions

Thanks to both Liz C and to Gibran for their contribution to last month's discussion group.


As is often the case, there was an unplanned synergy between the two sessions.  Gibran talked about his research into online communities.  He began by highlighting a number of oversimplifications that had pervaded the research literature on the subject.  These led to several significant factors being overlooked, with the result that assumptions made on the basis of the research were of dubious validity.


Liz summarized a talk she had attended on the invention of the fact.  The resulting discussion was both fascinating and challenging.  One of the challenges was to define a fact.  (I am now undergoing gender confirmation therapy since my attempt at stating a fact: "I am a man" was firmly challenged). 


Often, unquestioned assumptions can acquire the status of facts - until, of course, someone questions them.  In the course of my research interviews, subjects often refer to facts and I ask them what they mean.  One response is to suggest that, if something is corroborated by a number of sources, it can be treated as a fact.  Recently, when I asked a 6th form student to give an example of corroboration, she told me that she had found what she was looking for on WikiAnswers, Yahoo Answers and Answers.com.


Clearly, there is the risk that errors in one of these sites will be replicated in the others.  Experienced Web users will be aware of such risks and will be more thorough when seeking corroboration than was my student interviewee.  Such informed mistrust is, it now seems, routinely taught to school children.  Those I have spoken to however, profess to have total trust in books (though they rarely use them).


Even in books and journals however, errors can be replicated.  Generations of chemists, for example, were taught the wrong formula for mauveine, the synthetic purple dye produced by William Perkin in 1856.  A structure was published in a handbook of dyestuffs in 1924, and made its way into standard texts, from which  (according to an article in New Scientist in 1993), it carried on being disseminated throughout the literature for another 70 years.


Johnson, J. (1993) Science: The truth about the colour purple. New Scientist. 24 July, 1993. 

The Invention of the ‘Fact’ (by Liz Chapman)

On 5^th May I attended a fascinating talk given by Professor David Wootton on “The Invention of the ‘Fact’”, part of the series of Arts-Science Encounters directed by Dr Jessica Dubow and Dr Richard Steadman-Jones.  

Professor Wootton, whose research interests focus on the history of science as well as intellectual and cultural history, presented an argument which combined micro-history (i.e. local events and contingency) with a sense of long-term inevitability (i.e. we were bound to end up believing in facts).  Through this two-pronged approach, he analysed how the concept of the ‘fact’ entered early modern scientific thought.

The word ‘fact’ in its modern sense became established in English in the 17th century (via Italian and French).  The word itself was not new: it derives from Latin factum and has a legal meaning dating from the 13^th century.  However, in the legal context, the word fact implies a sense of agency, as in the phrase ‘an accessory after the fact’, where the fact is the crime.  Thus, the key linguistic shift that happened in the 17^th century was from the fact as act, to the fact as event – something known by actual observation.  Professor Wootton argued that this shift played an important role in the birth of modern science, enabling the discussion of ‘facts’ rather than ‘truth’ or ‘opinion’.

Professor Wootton’s study of contemporary scientific texts suggests that Hobbes has a strong claim to have introduced the word ‘fact’ in its modern sense to the English language.  It was used by many early members of the Royal Society, but it took a while to become respectable, as it was associated with dubious concepts such as the ‘weapon salve’ - this remedy was initially thought to be empirically proven to work, but it was later realised that this was because only successful healings were reported).  However, the word was a useful way of ending debates in turbulent times, and may also have gained respectability through Salisbury’s translation of Galileo.  

After 1663 there were frequent references to facts in the English language, and the term had become institutionally entrenched through the Royal Society’s official aim of establishing new facts.  Professor Wootton then went on to discuss the practice of the fact.  Bruno Latour has argued that the printing press made facts harder; Professor Wootton suggested it might be possible to go a step further and argue that the printing press made facts.  The public space of the printed book, along with the public space of the dissecting theatre, turned private information into public knowledge.  Professor Wootton argued that “fact is an epistemological shadow cast by a material reality” – the printed book.  He concluded by suggesting that technological change may have implications for the way we think in the future.

(Apologies to Professor Wootton if I have misrepresented his argument in any way.  Thanks to Liz Brewster and Angharad Roberts for comments on my summary.)

Understanding the failure of an organisational online community: A practice-based interpretation (by Gibran Rivera Gonzalez)

Previous research into online communities has, on many occasions deliberately simplified the factors affecting (non-)participation. 

1.         Some studies have looked at online communities from a static point of view and thus neglected

a)  the existence of previous relationships, which certainly affect the way in which current interactions occur,

b)  previous usage of certain media which causes people to continue using certain media, thus making it more difficult for them to adopt new technologies,

the fact that participation occurs as an evolving  process rather than as a one-time-event. Many studies tend to assume that participation is a static event and so cannot explain how participation changes over time,

c)  previous experiences of users in regard to their use of other similar communities.

2.         Other studies have regarded online communities as information infrastructures located in a vacuum, with internal characteristics (such as technological features) and internal dynamics (such as the content of contributions) treated as the only factors defining how participation takes place.  Such studies therefore ignore other important forces that exist outside the boundaries of these communities and thus:

a)  ignore the existence of alternative competing media which can potentially hinder participation in these online spaces,

b)  minimize the effects of the organizational local practices in which online communities reside, and

c) neglect the importance of current ways of interaction (and their rationale) already taking place at specific organizational contexts.

3.                  Other simplifications have regarded online communities as ones in which only active participants are relevant, and have therefore disregarded different levels of participation, and have overlooked the place of more passive participants.

My research aims to improve understanding of participation in online communities, and focuses on the failure of an organisational online community created to support Knowledge Sharing amongst HR Directors of a Multi-Campus University System in Mexico.  During the implementation of an organisational Human Resources (HR) project across the whole organisation, a decision was made by the HR President to introduce an online community that could support the project implementation. After 6 months there was virtually no participation in the online community; however the project continued to be implemented.  

This research uses a battery of different methods for data collection (mainly semi-structured interviews) and is based on an inductive thematic analysis informed by a Practice-based approach which acknowledges the fact that online communities are located within a specific field of practices which has its own spirit, priorities, history, ways of interaction, and practitioners. Therefore, the research aims to study not only the online community, but also the overall context in which this community is located, and the practices it supports. The study is expected to provide a more holistic picture of the forces shaping online community (non-) participation.

Censored libraries and non-existent blackmailers

HIV and information behaviour
Robinah's talk last month provided yet another reminder of how important information behaviour can be in helping people come to terms with terrible circumstances. 

In the discussion, as well as discussing positive aspects of information behaviour, she talked about more negative ones, which are rarely considered in models of information behaviour.  In particular, she referred to the concealment and destruction of information by HIV victims who have either still to come to terms with their circumstances, or who feel stigmatised by their condition .  These parallel other situations.  The denial experienced by many bereaved people may lead them to refuse or destroy information relating to a situation which they refuse to recognize.  Similarly, unemployed people, wishing to conceal their status, may hide documents relating to their welfare claims.

Some interesting points were raised in the course of the discussion.  One of those attending talked about her response to books dealing with alternative medicine.  Suppose, for example, she worked in a library containing books that claimed to control HIV by crystal healing.  She would not feel able to point them out to anyone who came in and asked for information about treatments of HIV.  Arguably therefore, she was hiding information.  Similarly, old books on HIV treatment could well be out of date and so should be destroyed.

Rival detectives
After Robinah's presentation, we enjoyed a lively discussion based on the G.K Chesterton story "The Absence of Mr Glass".  Two detectives who featured in the story: Dr Hood and Father Brown.  Both were confronted with a situation that appeared suspicious.  Dr Hood made several deductions based on theories he held, while, by contrast, Father Brown induced a theory specific to the circumstances.  The relative merits of the two approaches were explored.  Clearly the author's sympathies lay with Father Brown, but Liz C noted that he was guilty of not explaining the working that led to his conclusion.  However, it was noted that research is a creative act and sometimes it can be hard to make explicit the thinking that leads to a creation.

iSchool skill set
It is always a pleasure to gain new insights into the skills of colleagues within the department.  Mark Hall's explanation of the offside rule was impressive, but did not answer the question that gave rise to his explanation, which was - "Does the offside rule exist in subbuteo?"  The answer, it seems, is yes.

Future discussions
Two suggestions for future discussions include Second Life, and the nature of academic writing (does it have to be so dry?)

Hope to see you on 14 July.

Understanding the complexities of HIV/AIDS related information behaviour (by Robinah K. Namuleme)

My doctoral study seeks to generate in-depth knowledge of the real world “lived information experiences” of people affected by HIV/AIDS. I am using ethnographic approaches to understand the complexities of HIV/AIDS related information behaviour within the context of people’s lives.

This research is very important because it is a clear demonstration of ways in which Social Science can come help to solve problems in Society. This study generated rich data illuminating the complex nature of HIV and AIDS-related information behaviour. 

The initial impact of this study is a successful 3-month community outreach project proposal “Fighting HIV on an information front”, funded from the Roberts PGR placement fund. I am convinced that the findings of my research have the potential to support innovations in society including health information design, health information management practice, policy and strategy.