Thoughts on bias are biased, so become a hardcore epistemological realist?
November 30, 2010 at 12:17 pm | Posted in article | Leave a commentTags: philosophy, popper, realism
I’m pretty sure there is a reality.
If there isn’t, then what is not reality is so damn convincing, I’m not bothered either way.
Yet one can choose to commit to realism, or the belief that there is one really real reality in which all our observations, perceptions, language, theories and beliefs, have their referents.
And somehow, we can know this reality free from all prejudice – we can know the universe as an unbiased, neutral observer.
Critics of scientific knowledge have claimed that subscribing to realism is bonkers, because bias exists in everything we see or think and believe. Since bias is ingrained into human nature – even that part of human nature which sees itself as scientific and objective – then epistemological realism is a pipedream. We must accept that every theory, even the the fundamental ones that seem to be entirely free of prejudice are, somewhere along the line, polluted by bias.
The author of the paper below,Ingvar Johansson, describes a view of biasism he terms Myrdal’s Biasism which claims the following:
“…we cannot know truths and that we should therefore speak of research results as being true-for-certain-valuations instead of being just true”
Johansson criticises all forms of biasism with several logical arguments, including the paradox that biasism itself would surely be biased, if we were to accept the version above.
Can we biased and align ourselves with epistemological realism? I don’t see why biased research programmes cannot lead to truth. The problem is when our biases blinker us from better truths than what we have now. We can be biased AND appreciate the kind of movement towards more ‘truthlikeness’ described by Karl Popper and explored by Johansson in this same paper.
I see this sort of productive research bias in Thomas Kuhn’s view of science. The interesting part is when the scientist realises these biases are untenable in the face of new evidence, though the process by which one truth is superseded by a better truth is a fascinating one to try and understand.
Revolution? Inspiration? Logical necessity?
Dictionary : do I even know the meaning of the word?
November 12, 2010 at 5:11 pm | Posted in thesis | Leave a commentTags: biology, controlled vocabularies
In a recent discussion about what my research is about, I found myself stating clearly and for the first time that I believed the Gene Ontology is essentially a glorified dictionary.
If one can put aside the pretensions garnered by that big word ‘ontology’, the GO project is a list of defined terms describing one part of the biological domain. The three separate ontologies, the relationships, the structure formed by the terms has occluded for me the simple fact that in a basic sense, the Gene Ontology is a dictionary of biological words.
Complexities of ontologies aside, if the GO project had originally been conceived as a universal dictionary for the biological domain, this in itself would have been a tremendously ambitious project which may, perhaps, have revealed just how difficult it is to obtain towards any sort of grand consensus between the competing perspectives and understandings of the numerous micro-domains in biology.
As it stands though, the Gene Ontology is a vastly more complicated endeavour which leap-frogged the difficult question of whether there did indeed exist any sort of universally dictionary of terms for the biological domain. Instead, GO muscled straight into the thorny world of classes, instances, parts and all manner of other complicated relations.
When I was explaining myself earlier, I was asked if biologists did not already have a universal dictionary, a simple, shared understanding of the words they use and what these words mean.
A quick search on Amazon revealed over a thousand hits for the search term ‘biology dictionary’.
I think the domain of biology would best be described as a confederation of states, each speaking in slightly different accents and idioms.
Description logic never got me a date
July 29, 2010 at 8:48 am | Posted in article | Leave a commentTags: description logic, ontology
I am no expert in description logic.
I just put that on the advert to get a girlfriend.
However it is interesting to hear about the limitations of representing biological knowledge in OWL-DL which, though powerful for implementing machine reasoning, can struggle with particular ways of thinking in biology such as:
- Similarity and ‘fuzziness’ : biology is grounded in the idea of similarity – similarity between molecules, between organisms, between functions. HOW similar two biological features may be is sometimes hard to describe (how similar are dogs and cats? how similar is DNA sequence A and DNA sequence B?) Indeterminacy like this is difficult to capture in description logic.
- Prototypes and exception : biologists often regard entities as prototypical, such that a human eye might be considered a prototype of all eyes even though something like an insectile compound, although totally different, is still in many senses related. Furthermore, exceptions to rules are quite normal in biology, so an enzyme class which catalyses transcription will always catalyse transcription, unless it is doing something else.
- Complex property restrictions : for example a transcription factor binds to a promoter and activates gene transcription – the biological process ‘gene transcription’ is a property of the factor + promoter complex
- Expressive datatypes : capturing in description logic the idea of a number ranging meaning ‘this is lots’ or dimensions translating to mean ‘this is a big cell’ – again, this type of thinking is rife in biology
The authors below give other examples and discuss just how some of these conceptual tools in biology might be captured in OWL-DL.
Stevens, R., Aranguren, E. M., Wolstencroft, K., Sattler, U., Drummond, N., Horridge, M., and Rector, A. (2007). Using owl to model biological knowledge. International Journal of Human-Computer Studies, 65(7):583-594.
Own harshest critic judges himself to be doing a good job
July 28, 2010 at 2:57 pm | Posted in article | Leave a comment“I am my own harshest critic.”
I doubt this statement.
Bada et al., authors and instigators of the Gene Ontology, write a (not) entirely disinterested analysis of how the implentation of the Gene Ontology has useful lessons for other ontologies.
The Gene Ontology is a marvelous creation. However I would not go to the Tory party headquarters for impartial political advice on whether I should join the Tory party.
The authors highlight community involvement and simplicity as two very important factors in the success of the Gene Ontology, factors other ontology designers might bear in mind.
How else might we explain the success of the Gene Ontology? The first product in a marketplace has a natural advantage over its competitors, and complex products may have a high startup cost that deters alternatives. The economics make it unlikely the ontology will fail.
Biologists may use the Gene Ontology because it is there and there are no alternatives. They may contribute to the ontology but feel beholden to the curators as to whether the changes they want will be made. A community is formed and involved as a consequence of the technology rather than any sense of ownership.
Established norms may also play a strong role in take-up of the Gene Ontology. Everyone else is using it as a standard, therefore I must use it too.
Bada, M., Stevens, R., Goble, C. A. et al. (2004). A short study on the success of the gene ontology. Web Semantics: Science, Services and Agents on the World Wide Web, 1(2):235-240.
Irrelevant truth in functional genomics
July 28, 2010 at 2:33 pm | Posted in article, web | Leave a commentAlways interested to see the issue of ‘relevance’ rearing its noble / ugly / annoying / informative head in the bioinformatics literature, much as relevance has long skulked about the information science domain.
The ontology and description logics literature spends a lot of time avoiding the question of uncertainty which, in my opinion, is fundamental to the practice of science. Scientists often gauge the importance of variation within their empirical framework using all manner of expertise, guesswork and voodoo.
In developing machine learning algorithms designed to take advantage of Gene Ontology annotations, Akand et al. note:
“… any gene is annotated with all of the categories with which it has been associated in the published scientific literature. In any particular experimental setting, however, only a subset of the known annotations of a gene will be relevant.”
All annotations are not created equal, and although the human p53 gene may be annotated with 90 different Gene Ontology terms, in the context of an experiment designed to investigate the process of double-stranded DNA repair, the existence of many of these other annotations may be ignored by the biologist for the sake of simplicity.
What then if all analysis in functional genomics is a matter of attention, in which the biologist is free to ignore accessory information which, although objectively true, is deemed superfluous to the task?
Akand, E., Bain, M., and Temple, M. (2007). Learning from ontological annotation : an application of formal concept analysis to feature construction in the gene ontology. volume 85, pages 15-23.
For abstract and full paper see here
Does 100% reliability between indexers or annotators exist?
July 19, 2010 at 3:52 pm | Posted in article | Leave a commentTags: annotation, classification
How do we measure the reliability of coding, annotating, indexing or classification by different coders, annotators, indexers or classifiers?
Lombard et al. reported just how poor authors in the mass communication research literature were at reporting in detail the consistency between different coders in analyzing content in their research.
Coders in this situation are individuals reading say, a newspaper, and deciding whether that newspaper contains information about a particular topic or subject, say Wayne Rooney’s wedding. Reliability is the measure of matching judgments between different coders. In the classification world, it might be two librarians choosing subject headings for the same book, or in the Gene Ontology world it might be two different annotators choosing index terms for the same biomedical article.
From failing to report how many coders had coded the sample, to omitting how or whether the coders had been trained or even stating exactly how reliability had been calculated, this paper is a striking investigation into the importance of transparency in reporting research methods.
It is of particular interest to myself since I am interested in the value biologist place on manually created annotations between Gene Ontology terms and biological entities, like genes and proteins. Since this type of coding / classification reliability work has long-shown the impossibility of 100% agreement between different coders, what are the implications of this for bioinformatic tools using ontology annotations?
How much trust can biologists possibly place in even good quality manual annotations if there is always a difference between annotators?
Lombard, M., Snyder-Duch, J., and Bracken, C. C. (2002). Content analysis in mass communication: Assessment and reporting of intercoder reliability. Human Communication Research, 28(4):587-604.
dx doi 10.1111/j.1468-2958.2002.tb00826.x and Full text available
CoLIS 7: Doctoral forum
June 25, 2010 at 10:40 am | Posted in lecture, thesis, work | Leave a commentTags: colis7
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
Many thanks to Jutta Haider for her hard work in organising the forum – it was great!
Ontology as concept representation: reality as conjecture
May 18, 2010 at 7:01 pm | Posted in article | Leave a commentTags: ontology, philosophy of science
Is an ontology a representation of subjective, social knowledge as it stands in a plurality of competing concepts in the wild?
Or is an ontology a representation of reality, thus avoiding the woolly vagaries of ‘concepts’?
“Good ontology and good modeling in support of the natural sciences can, we conclude, be advanced by the cultivation of a discipline that is devoted precisely to the representation of entities as they exist in reality. In the framework of such a discipline [...] we would talk not of concepts as linguistic or computer artefacts but rather of universals, conceived as that in reality to which the general terms used in making scientific assertions correspond.”
The quote above is taken from the article below and I find this attitude to be surprisingly optimistic with regard to how scientists observe reality and distinguish between scientific things and non- or pseudo-scientific things (which I presume Smith would exclude from ontologies in the natural sciences).
The view above presumes we can observe reality from a neutral perspective when in fact (and this is old news), all observations are coloured by the spectacles of theory. If there are no theory-neutral observations, there can be no single representation of reality, but this is not necessarily a problem ( I may justify this another time).
Smith also avoids the question of how we decide what ought to be represented in an ontology ‘based on reality’. A scientific conjecture may create a new thing in reality, os how do we decide when a new thing gets added to an ontology?
Scientific knowledge is fallible, and if an ontology is reality representation, then we need criteria for deciding what gets added to an ontology. Does ESP make it? Reality is not straightforward point-and-see exercise, and if we can use the word ‘concept’ to describe competing conjectures about reality, which can be tested and refuted, then I have no problem with ontology as concept representation.
Smith, B. Beyond concepts: ontology as reality representation, in Proceedings of the third international conference on formal ontology in information systems, pp. 73-84 (IOS Press, 2004).
Full text available here
Do I believe in collective knowledge?
April 15, 2010 at 8:38 am | Posted in personal, phd, thesis | Leave a commentTags: epistemology, personal, popper
Popper’s 3 Worlds alludes, by a metaphysical lunge which leaves most philosophers shaking their heads in disdain, to a third world to complement the oft-accepted worlds of physical knowledge and mental knowledge.
A book is read, and thus the physical is transmuted, briefly, into the mental. The flickering neurones in our brains ignite thoughts in the thing or are the thing we call consciousness.
Knowledge splurges from mind to page and back again, yet Popper argued that we are ignoring a third sense to knowledge, beyond the material we can read, hear and touch, and beyond the cognitive where in word and thought we create and criticise in abstractions.
Popper’s World 3 is akin to collective knowledge, the sum of all our learning and creativity which persists beyond our thoughts and our deaths. World 3 is the pooled expertise of millions of minds, engaging with a reality, estabishing problems and proposing solutions to why the rains fall or how Labour could ever serve a fourth term.
Do I believe in a collective knowledge? I think there exists a very strong sense in which knowledge is considered to be a shared experience. The library is a place to store all our knowledge. We work together to create and share new ideas. The Internet is a place where we can access and exchange all sorts of thoughts and theories about the world.
We are feel reassured because there is coherency in the world, a confidence that knowledge, that a collective making-sense-of-things, extends beyond what we might understand on a personal level. I trust aeroplanes will not fall out of the sky, even though I don’t know anything about why they stay in the air.
I like Popper’s World 3 because it has this collective, shared element to knowledge. It is a place for the bringing together of ideas. It establishes communalism for ideas, a means for the bringing together of human thought.
Complex vocabularies indicative of the development of scientific disciplines
April 13, 2010 at 1:26 pm | Posted in article | Leave a commentTags: epistemology, kuhn
“If we represent our disciplinary scientific knowledge as a taxonomy of concepts, higher success in problem-solving can be only achieved when the taxonomy gets more complex, populated by new concepts and in new relations with each other, until the complexity of some portions of it makes the taxonomy unmanageable by a single group (better: by individuals belonging to a single group) and new disciplines arise. bringing further complexification. It is almost commonplace that powerful scientific practices are associated with high-level specialization and complexity.”
Renzi, B. G. (2009). Kuhn’s evolutionary epistemology and its being undermined by inadequate biological concepts. Philosophy of Science, 76(2):143-159.
Full text on Google books
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