The Machinistic Paradigm Collapse

Posted by Anirudh Sridhar at Apr 14, 2014 10:10 AM |
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Looking at the example of the scientific practices surrounding protein folding study, this blog explores the modern relevance of Thomas Kuhn’s conception of a paradigm. This blog posits that because of the heavy reliance on computational technology and simulation, the philosophical basis of Kuhnian scientific paradigm has ceased to exist and hence science, along with the Digital Humanities has moved into a post structuralist age.
The Machinistic Paradigm Collapse

Protein Folding

One of the great scientific challenges that have ridden along the furrowed brows of all three branches of natural science’s practitioners is of understanding protein folding. This, to the uninitiated as I am, is the process by which newly synthesized proteins or new born proteins, as random coils are given their biological destinies by their amino acid sequences through folding in three dimensional space into their secondary, tertiary or quaternary structures. [1] It helps me to think of a paper rocket that is a plain sheet of paper, a trapped 2 dimensional figure, limp and physically impotent as if in Abbot’s Flatland until it is introduced to a 3-dimensional space and itself becomes a 3 dimensional entity which can then travel particular distances, velocities and directions based all on the precise folding. Proteins, straying from their destined path of structure, even by the slightest can become toxic, cause allergies and many neurodegenerative diseases like Alzheimer’s, Huntington’s and prion. [2] This immediately places the uncovering of the precise folding pathways in the interest of the whole modern medical enterprise. Indeed, this old scientific problem dates back almost a century to the experiments of Anson and Mirsky in the 1930’s. [3]It is also quite possible that the story of protein folding, in which machine vision replaces theory and mathematics, unveils another story; the erosion of the scientific paradigm itself.

Thomas Kuhn, in his 1962 book called the “Structure of Scientific Revolutions”, gave the word paradigm its contemporary meaning. At a mere definitional level, Kuhn describes the paradigms as “universally recognized scientific achievements that, for a time, provide model problems and solutions for a community of practitioners.” [4] In terms of methodology, a paradigm governs what is to be observed, what questions are asked, how they are asked, how the data is interpreted and how the experiments are conducted. However, Kuhn had a greater vision for a paradigm when he characterized it as an emergent system from a revolution which means it is a change in the world order itself. Or to camber the previous sentence, paradigms order the world around them. Commenting on the scientists world view, Kuhn says “in so far as their (scientists) only recourse to that world is through what they see and do, we may want to say that after a revolution, scientists are responding to a different world…what were ducks in the scientist’s world before the revolution are rabbits afterwards”.

My previous blog on the collapse of the semiotic sphere of capture spoke about the substitution every epoch of the center of the sphere or transcendental signifier that lends meaning to the world upon which it reigned. It, however, (as a consequence of Derrida’s concentration on results more than process) did not lay down the steps that led to the replacement of the center of meaning with a different set of signifiers leading to a different vision of the world. Kuhn, on the other hand, adumbrates the exact process by which this paradigmatic transformation in scientific world order takes place. As a non scientist and a denizen of a post metaphysical age, I’m at a severe disadvantage when trying to comprehend what it must mean to have these seismic shifts in the way the mind is ordered and perceives the world so I tried to meditate De Revolutionibus Orbium Coelestium (on the revolutions of the heavenly sphere) through the Renaissance Astronomer Copernicus to try to understand the process. [5]


Paradigm Shift




The Ptolemaic earth centric model, his astronomical system, was first developed during the time of Christ. This system worked admirably in the prediction of changing positions of both stars and planets in the ancient world, far outstripping any other system. However, over the fifteen centuries leading upto Copernicus, many holes and problems, what Kuhn refers to as anomalies, started appearing in this system. It could not account for certain planetary positions, equinoxes and these problems kept compounding as astronomical observation became more sophisticated as the theoretical basis grew more antiquated. Almost the whole enterprise of astronomy was involved with the mitigation and reduction of minor discrepancies by adjustments and tweaks made to the Ptolemaic system of concentric circles. Kuhn explains this as a process of resilience where scientists play a game of Whac-a-mole and as the apparatus of discovery complicates the science much further than the accuracy allowed by the existing paradigm, the theoretical stereotypes within the paradigm are loosened to accommodate the discrepancies so much that they bring about their own collapse. As Karl Popper says in “Science as Falsification”, the strength of a scientific theory, or any theory, is its falsifiability or is directly proportional to its prohibition of certain observations. He warns that when a theory, or in this case, a paradigm, has been refuted, its adherents attempt ad hoc auxiliary modifications or reinterpretations of the theory to rescue it from refutation by what he calls a conventionalist twist.[7] This rescuing is possible, but it comes at the price of destroying its scientific status and moving it into the metaphysical or mythical realm. By the time Alfonso X came about in the thirteenth century, looking upon the Ptolemaic model as a scandal, he was claiming that if God has consulted him when creating the universe, he would have received better advice. [8] Finally, in the 16th century the painful process of denial ended with Copernicus’s rejection of the Ptolemaic paradigm in favor of his own heliocentric paradigm as in the diagram above.

One could look to paradigm shifts in the humanities and social sciences and draw parallels to the scientific ones with the birth of deconstruction in the evolution of the text as explored in the previous blog but that would be across purposes as Kuhn himself prohibits this application. In the preface of his book, he explains that he concocted the concept of a paradigm precisely to distinguish the social from the natural sciences. Some like M.L Handa have attempted this concomitance but that sort of endeavor will be beyond the scope of this blog.[9] The windows of the laboratory will, for the most part, be shut out from the outside world in this blog. This argument was, perhaps easier to make under past paradigms as Bertrand Russell, when he sought to disprove the Natural Law argument in “Why I’m not a Christian” says “that (natural law) was a favorite argument all through the eighteenth century, especially under the influence of Sir Isaac Newton and his cosmogony. People observed the planets going around the sun according to the law of gravitation, and they thought that God had given a behest to these planets to move in that particular fashion, and that was why they did so. That was, of course, a convenient and simple explanation that saved them the trouble of looking any further for any explanation of the law of gravitation. Nowadays we explain the laws of gravitation in a somewhat complicated fashion that Einstein has introduced…you no longer have the sort of Natural Law that you had in the Newtonian system, where, for some reason that nobody could understand, nature behaved in a uniform fashion.”[10] Science may have inherited its ontology from philosophy which inherited its ontology from theology in the past but those dendrites in the past neurological connections seem to have been excised in the present.

Kuhn says that the striking feature of doing scientific research is the attempt to discover what is known in advance, hence identifying the scientific hypothesis as the locus of the human imagination in the scientific praxis. Popper, in “Science: Conjectures and Refutations”, says “At the same time I realized that such myths may be developed, and become testable; that historically speaking all--or very nearly all--scientific theories originate from myths, and that a myth may contain important anticipations of scientific theories. Examples are Empedocles' theory of evolution by trial and error, or Parmenides' myth of the unchanging block universe in which nothing ever happens and which, if we add another dimension, becomes Einstein's block universe (in which, too, nothing ever happens, since everything is, four-dimensionally speaking, determined and laid down from the beginning).”[11]

If we do run the hypothesis through a philosophical treatment, then as C.S Pierce observed, it is a form of abductive reasoning unlike the deductive and inductive reasoning that may play a more dominant role in other stages of the scientific praxis. Abductive reasoning takes the form of a guess where the scientist looks at a particular phenomenon in nature like a parched, dead tree and ventures a hypothesis that there was no rainfall.[12] While β (the result; i.e the dried up tree) could have been due to a host of causes a (eg forest fire), the scientist decides to propose a cause, α, based on the economy or likelihood of explaining power which is also called the Occam’s razor principle. Pierce said that abductive reasoning is "very little hampered" by rules of logic…Oftenest even a well-prepared mind guesses wrong. But the modicum of success of our guesses far exceeds that of random luck, and seems born of attunement to nature by instincts developed or inherent, especially insofar as best guesses are optimally plausible and simple in the sense of the ‘facile and natural’, as by Galileo’s natural light of reason.”[13]

It is precisely at this juncture that the scientific consciousness, ordered by the paradigm of an age escapes the laboratory and is subject to governance of the transcendental signifier potentates atop the Olympus of the outer world. The Occam’s razor principle of parsimony itself is premised on the theological notion of its time that the simplest explanation conceivable by man is likely the best one because man is made in the image of God. Popper further explicated on Pierce’s postulations in his hypothetico-deductive model in the twentieth century when he called the hypothesis just “a guess”.[14] The guess that the dead tree was brought about by a drought is then one that comes from the epoch of Being in which non-scientists live.

We must remember that a paradigm is a universal belief of scientists that permits the very selection process of the pursuit. The guess that eventually becomes the hypothesis is one that is made robust as many abductions are rejected and modified by better abductions. Although the eventual hypothesis could be one rising solely from the hermetically sealed paradigm, one cannot ignore this process happening behind the scientific consciousness. Methodologically distinct though the paradigm remains from cultural pursuits, its ontologies remain the same. Derrida, while analyzing Levi Strauss’s Elementary Structures: The Savage Minds says “On the one hand, he will continue in effect to contest the value of the nature/culture opposition. More than thirteen years after the Elementary Structures, The Savage Minds faithfully echoes the text I have just quoted: “The opposition between nature and culture which I have previously insisted on seems today to offer value which is above all methodological.” And this methodological value is not affected by its “ontological” non-value…: “It would not be enough to have absorbed particular humanities into a genera humanity; this first enterprise prepares the way for others ... which belong to the natural and exact sciences: to reintegrate culture into nature, and finally, to reintegrate life into the totality of its physiochemical conditions””[15]

If then there is this neurological connection that exists as a fast multiplying parasite that is a different species by the time it enters the laboratory then it must be true that the paradigm is vulnerable to extinction when that mutated parasite, the postmodern idea, comes from an alien world of no ontological or transcendental fixity. In other words, along with the collapse of Gebser’s integral sphere of semiotic capture, the structure of the scientific paradigm as Kuhn saw it should have also collapsed. Kuhn preempts this thought, unintentionally perhaps when he says “Once a first paradigm through which to view nature has been found, there is no such thing as research in the absence of any paradigm. To reject one paradigm without simultaneously substituting another is to reject science itself.” This is evocative of Heidegger when he laments that with the end of the metaphysical age where there are no more universal structures of consciousness, comes the death of real art. To test the validity of Kuhn’s challenge, we come back to our initial foray into the world of protein folding discovery.

Recently, there was a multi-player online game called Foldit where players have to collaborate and compete to create accurate protein structure models. Foldit player solutions started to create waves in the scientific community when player solutions began to outperform the most state-of-the-art methods including the other computational methods. Two particular “recipes” became particularly famous and a paper on this discovery called “Algorithm Discovery by Protein Folding Game Players” says “benchmark calculations show that the new algorithm independently discovered by scientists and by Foldit players outperforms previously published methods. Thus, online scientific game frameworks have the potential not only to solve hard scientific problems, but also to discover and formalize effective new strategies and algorithms.”[16]

This is not a typical example of a state of affairs but an extreme example illustrative of a larger technological shift in the business of science. As Pierce said about the “attunement to nature by instincts” the computer game is a case of this instinctual visual acuity being harnessed by machine intelligence. This mode of scientific production, I would posit at a fundamental level, is completely incompatible with the Kuhnian conception of a paradigm.

The paradigm is not merely a set of rules and shared assumptions but a rigid system of inherited dogma that draws the horizon of exploration universally but is limited in scope and precision at its inception. Therefore normal science (science conducted at non-revolutionary times within paradigms) is a mop-up operation or “an attempt to force nature into the pre-formed and relatively inflexible box that the paradigm supplies”. Normal, non-revolutionary science is a relatively linear, cumulative process whose horizon is defined by the inherited beliefs, theories, methods and the mental labor of the mop-up crew. The moment when computer modeling began to provide the fineness of observation that it currently does, it replaced the physical, dynamical modus vivendi of mathematical science and started to determine the horizon of the scientific endeavor.

Dr. Bengt Nӧlting’s book, Protein Folding Kinetics: Biophysical Methods, begins with a quote from Faust, which in my opinion is innocent, if not naïve.

Then shall I see, with vision clear,

How secret elements cohere,

And what the universe engirds,

And give up huckstering with words.

Johann Wolfgang von Goethe

He says, with the advent of computational modeling and experimental advances in technology, “the pathways and structures of early folding events and the transition state structures of fast folding proteins can now be studied in far more detail…which… allows fast processes that would normally be hidden in kinetic studies to be revealed.”[17] He is then able to see, with vision clear, how elements cohere on screen, he thinks. However, if we are to recall Kuhn, seeing in science is a sense given by the paradigm that allows the scientist to observe nature but truly see it in coherence with the paradigmatic ordering of her world view. Therefore, Nӧlting is not really seeing at all (unless he programmed the computer simulation which brings him a little closer). He merely has “the notion that the quantitation of kinetic rate constants and the visualization of protein structures along the folding pathway will lead to an understanding of function and mechanism and will aid the understanding of important biological processes and disease states through detailed mechanistic knowledge” (italics mine). “Beyond this, protein structures along the folding pathway can now be visualized at the level of individual amino acid residues in nearly any biologically relevant time scale. This detailed mechanistic knowledge will further aid the understanding of biological processes and disease states, and will eventually help us to find rational ways for re-designing biological processes, and to find cures for diseases.”

In “Protein Folding, Misfolding and Aggregation Classical Themes and Novel Approaches”, Victor Muῆoz furthers the notion of science’s boundaries being drawn by technology when he says “prevailing views about the mechanisms of protein folding have closely followed the idiosyncrasies in the catalog of available proteins and experimental approaches.” Although computational simulation is distinct from experimental techniques, one can interpret this statement, based on the rest of book, that the approaches include predictive simulation. The history of the development of protein folding study has been a technologically determined one of serendipity. When new experimental data on folding and unfolding rates emerged, Muῆoz says that “theoreticians immediately saw this avalanche of new experimental results as an opportunity to test results from theory and computer simulations, leading to the first de facto connection between the worlds of experiment and theory in protein folding.”[18] Therefore, the world of experiment and theory, a process that was previously mediated by the paradigm is now mediated by computer simulations. The structure of scientific pursuits is now determined by the randomness of programming and computer engineering.


This phenomenon of computational capabilities exceeding the mathematical conception is not contained to the world of biophysics but extends to material sciences like nanotechnology, ecology and many others. As was postulated in my previous blog, this is probably another symptom of the techno-capitalistic regime that demands to be spoken to through images rather than the esoteric language of mathematics. When Fred Whipple’s wanted to test his “dirty snowball” theory, he proved it by pointing towards Haley’s Comet, when Einstein wanted to prove his theory he pointed again to a light dance in the heavens. When the cosmic magic shows can no longer enthrall the science funding entity, computer simulations are all that are left in the midden heap. Remember that the success of a paradigm rests in its propagation and its appeal to future generations of scientists. Therefore, even if the atypical scientist is still carrying out research under a dogmatic rubric, it cannot gain the fervor and universal sense of order when big pharmaceuticals fund only the technological science and the Intellectual Property regime spurs the individual scientists to work at breakneck speeds allowed only by computers.


According to David Berry in “Understanding Digital Humanities”, one of its main objectives is to use computational methods to answer existing questions or challenge theoretical paradigms to generate new questions.”[19] The emergence of the non-human computational methods in the business of natural sciences has certainly generated new questions around an observation; meaning in the sciences has eerily followed on the destructive path of the Digital Humanities, slaying the Kuhnian paradigm in a twin collapse with the integral sphere of semiotic capture.


[1] Nolting, Bengt. Protein Folding Kinetics Biophysical Methods. Berlin: Springer, 1999. eBook.


[3] Munoz, Victor. Protein Folding, Misfolding and Aggregation Classical Themes and Novel Approaches. The Royal Society of Chemistry, 2008. eBook.

[4] Kuhn, Thomas. The Structure of Scientific Revolutions. University of Chicago Press, 1962. Print.

[5] ibid

[6]Picture taken from

[7] Popper, Karl. "Science as Falsification." Conjectures and Refutations. (1963): n. page. Web. 13 Apr. 2014.

[8] See citation 4

[9] Handa, M. L. (1986) "Peace Paradigm: Transcending Liberal and Marxian Paradigms". Paper presented in "International Symposium on Science, Technology and Development, New Delhi, India, March 20–25, 1987, Mimeographed at O.I.S.E., University of Toronto, Canada (1986)

[10] Russel, Bertrand. "Why I am Not a Christian an Examination of the God‐Idea and Christianity." England. 06 03 1927. Address.

[11] See citation 7

[12] Peirce, C. S. "On the Logic of drawing History from Ancient Documents especially from Testimonies" (1901), Collected Papers v. 7

[13] ibid

[14] Popper, Karl (2002), Conjectures and Refutations: The Growth of Scientific Knowledge, London, UK: Routledge

[15] Structure Sign and Play in the Discourse of the Human Sciences, J Derrida, 1966.

[16] Khatiba, Firas, and Seth Cooper. "Algorithm discovery by protein folding game players." PNAS. (2011): n. page. Web. 13 Apr. 2014. .

[17] See citation 1

[18] See citation 3

[19]Berry, David. Understanding Digital Humanities. Palgrave Macmillan, 2012. Web.

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