May 31, 2015

Kuhnian Practice as a Logical Reformulation

Are 01110000 01100001 01110010 01100001 [1] shifts a loss, a gain, a mismatch, or an opportunity for intellectual integration and the birth of a new field?

In the Kuhnian [2] approach to empiricism, a well-known outcome observed across the history of science is the "paradigm shift". This occurs when a landmark finding shifts our pre-existing models of a given natural phenomenon. One example of this: Darwin's finches and their evolutionary history in the Galapagos. In this case, a model system confirmed previous intuitions and overturned old facts in a short period of time (hence the idea of a scientific revolution). 

During a recent lecture by W. Ford Doolittle at the Insititute for Genomic Biology, I was introduced to a term called "Kuhn loss" [3]. Kuhn loss refers to the loss of accumulated knowledge due to a conceptual shift in a certain field. One might consider this to be a matter of housecleaning, or a matter of throwing out the baby with the bathwater. The context of this introduction was the debate between evolutionary genomicists [4] and the ENCODE consortium over the extent and nature of junk DNA. During the talk, Ford Doolittle presented the definitions of genome function proposed by the ENCODE consortium as a paradigm shift. The deeper intellectual history of biological function would suggest that indeed junk DNA not only exists, but requires a multidisciplinary and substantial set of results to overturn. Thus, rather than viewing the ENCODE results [5] as a paradigm shift, it can be viewed as a form of intellectual loss. The loss, paradigmatic or otherwise, provides us with a less satisfying and robust explanation than was previously the case.

A poster of the talk. COURTESY: IGB, University of Illinois, Urbana-Champaign

Whether or not you agree with Ford Doolittle's views of function, and I am of the opinion that you should, this introduces an interesting PoS issue. In the case of biological function, the caution is against a 'negative' Kuhn loss. But Kuhn loss (in a linear view of historical progress) usually refers to the loss of knowledge associated with folk theories or theories based on limited observational power. In some cases, these limited observations are augmented with deeper intuitive motivations. This type of intuition-guided theory usually becomes untenable given new observations and/or information about the world. Phlogiston theory [6] can be used to illustrate this type of 'positive' Kuhn loss. Quite popular in Ancient Greece and Medivel Europe, phlogiston theory predicts that the physical act of combustion released fire-like elements called phlogistons. Phlogistons operated in a manner opposite of the role we now know oxygen serves in combustion and other chemical reactions. Another less clear-cut example of 'positive' Kuhn loss involves a pre-relativity idea called aether theory predicts that the aether (an all-enveloping medium) is responsible for the propogation of light in space.

In each of these cases, what was lost? Surely the conclusions that arose from a faulty premise needed to be re-examined. A new framework also swept away inadequate concepts (such as "the aether" and "phlogistons"). But there was also a deeper set of logical structures that needed to be reformulated. In phlogiston theory, the direction of causality was essentially reversed. In aether theory, we essentially have a precursor to a more sophisticated concept (spacetime). Scientific revolutions are not all equal, and so neither is the loss that results. In some cases, Kuhn losses can be recovered and contribute to the advancement of a specific theoretical framework. Midwinter and Janssen [7] introduce us to the physicist/chemist Van Vleck, who improved upon the Kuhn loss introduced when quantum theory was introduced and replaced its antecedent theory. Van Vleck did this by borrowing mathematical formalisms from the theory of susceptibilities, and bringing them over to physics. While neither a restoration nor a paradigm shift, Van Vleck was able to improve upon the ability of quantum theory to make experimental predictions.

Tongue-in-cheek description of an empirically verified of phlogiston theory. COURTESY: [8]

Now let us revisit the Kuhnian content of the ENCODE kerfuffle vis a vis this framework of positive/negative Kuhn loss and Kuhn recovery. Is this conceptual clash ultimately a chance for a gain in theoretical richness and conceptual improvement? Does the tension between computational and traditional views of biological function neccessitate Kuhn loss (positive or negative)? According to the standard dialectical view [9], the answer to the former would be yes. In such case, we might expect a paradigm shift that results in an improved version of the old framework (e.g. 'positive' Kuhn loss). But perhaps there is also a cultural mismatch at play here [10] that could be informative for all studies of Kuhn loss. Since these differing perspectives come from very different intellectual and methodological traditions, we could say that any Kuhn loss would be negative due to a mismatch. This is a bit different from the phlogiston example in that while both approaches come from a scientific view of the world, they use different sets of assumptions to arrive at a coherent framework. However, what is more likely is that computational approaches (as new as they are to the biological domain) will influse themselves with older theoretical frameworks, resembling more of Kuhnian recovery (the quantum/antecedent theory example) than a loss or gain.

It is this intellectual (and logical) reformulation that will mark the way forward in computational biology, using an integrative approach (as one might currently take for granted in biology) rather than reasoning through the biology and computation as parallel entities. While part of the current state of affairs involves a technology-heavy computation being used to solve theoretically-challenging biological problems, better logical integration of the theory behind computational analysis and the theory behind biological investigation might greatly improve both enterprises. This might lead to new subfields such a the computation of biology, in which computation would be more than a technical appendage. Similarly, such a synthetic subfield would view of biological phenomena much more richly, albeit with the same cultural biases as previous views of life. Most importantly, this does not take a revolution. It merely takes a logical reformulation, one that could be put into motion with the right model system.

[1] the word "paradigmatic", translated into binary. COURTESY: Ashbox Binary Translator.

[2] Kuhn, T.S.   The Structure of Scientific Revolutions. University of Chicago Press (1962).

[3] Hoyningen-Huene, P.   Reconstructing Scientific Revolutions. University of Chicago Press (1983).

[4] Doolittle, W.F.   Is junk DNA bunk? A critique of ENCODE. PNAS, 110(14), 5294-5300 (2013).

[5] The ENCODE Project Consortium   An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74 (2012).

[6] Vihalemm, R.   The Kuhn-loss Thesis and the Case of Phlogiston Theory. Science Studies, 13(1), 68 (2000).

[7] Midwinter, C. and Janssen, M.   Kuhn Losses Regained: Van Vleck from Spectra to Susceptibilities. arXiv, 1205.0179 [physics.hist-ph] (2012).

[8] DrKuha   The Phlogiston: Not Quite Vindicated. Spin One Half blog, May 19 (2009).

[9] what we should expect according to dialectical materialism: adherents of two ideologies struggle for dominance, with an eventual winner that is improved upon the both original ideologies. Not to be confused with the "argument to moderation".

[10] for more context (the difference between a scientific revolution and a scientific integration) please see: Alicea, B.   Does the concept of paradigm shift need a rethink? Synthetic Daisies blog, December 25 (2014).

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