Stepping beyond the Newtonian Paradigm in Biology

Simeonov, Plamen L.; Brezina, E; Cottam, Ron; Ehresmann, Andrée; Gare, Arran; Goranson, H. T.; Gómez-Ramírez, Jaime; Josephson, Brian D.; Marchal, Bruno; Matsuno, Kōichirō; Root‐Bernstein, Robert; Rössler, Otto E.; Salthe, Stanley N.; Schroeder, Marcin J.; Seaman, Bill; Siregar, Pridi; Smith, Leslie S.

doi:10.1007/978-3-642-28111-2_31

Cited by 5 publications

(5 citation statements)

References 120 publications

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“…I hope that the Integral Biomathics approach (Simeonov, 2010;Simeonov et al, 2012;Simeonov et al, 2013) will help us advancing fast in the desired direction.…”

Section: Epiloguementioning

confidence: 99%

Yet another time about time … Part I: An essay on the phenomenology of physical time

Simeonov¹

2015

Progress in Biophysics and Molecular Biology

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This paper presents yet another personal reflection on one the most important concepts in both science and the humanities: time. This elusive notion has been not only bothering philosophers since Plato and Aristotle. It goes throughout human history embracing all analytical and creative (anthropocentric) disciplines. Time has been a central theme in physical and life sciences, philosophy, psychology, music, art and many more. This theme is known with a vast body of knowledge across different theories and categories. What has been explored concerns its nature (rational, irrational, arational), appearances/qualia, degrees, dimensions and scales of conceptualization (internal, external, fractal, discrete, continuous, mechanical, quantum, local, global, etc.). Of particular interest have been parameters of time such as duration ranges, resolutions, modes (present, now, past, future), varieties of tenses (e.g. present perfect, present progressive, etc.) and some intuitive, but also fancy phenomenological characteristics such as "arrow", "stream", "texture", "width", "depth", "density", even "scent". Perhaps the most distinct characteristic of this fundamental concept is the absolute time constituting the flow of consciousness according to Husserl, the reflection of pure (human) nature without having the distinction between exo and endo. This essay is a personal reflection upon time in modern physics and phenomenological philosophy.Keywords: space, time, consciousness, physics, mathematics, philosophy, phenomenology. ___________________________________________________________________ PrologueSpace and time are particularly modalities of human consciousness. Whereas space can be realized through our eyes and limbs, time remains elusive to our minds and still bothers philosophers since antiquity (Dyke & Bardon, 2013). In the beginning of the 20 th century science made a crucial switchover. Time was spatialized 1 . Until then the world was threedimensional. With the Special Relativity Theory (Einstein, 1905;Minkowski, 1909) the concept of time became the fourth dimension 2 and an integral element of the new physical worldview. It caused confusion among many of Einstein's contemporaries, and not only with its relativistic dilation in the well-known equation with the speed of light ť = t (1-(v/c) 2 ) ½ .1 It could be argued that time was spatialized earlier. Though time and space were separate for Newton (something that Einstein challenged), the clock time he assumed was laid out like space and was devoid of the dynamism of Bergsonian durée, (Bergson, 1912;Čapek, 1961). 2 It was Laplace who treated time as just another dimension equivalent to space, and thereby paved the way for the development of relativity theory as it came to be understood (but not as Čapek, following Bergson, understood it).This notion of relativistic time appeared wrong and unnatural, not without good reason, since:• Time is ineffable, eluding science and mathematics: it can only be grasped through intuition and shown indirectly and partia...

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“…I hope that the Integral Biomathics approach (Simeonov, 2010;Simeonov et al, 2012;Simeonov et al, 2013) will help us advancing fast in the desired direction.…”

Section: Epiloguementioning

confidence: 99%

Yet another time about time … Part I: An essay on the phenomenology of physical time

Simeonov¹

2015

Progress in Biophysics and Molecular Biology

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“…The following new Key Themes (KT) have been identified and added to our Integral Biomathics research programme (Simeonov et al, 2012;Gare, 2013;Kauffman and Gare, 2015) in the course of the JPBMB publication activities in 2013 and 2015 (Simeonov et al, 2013;Simeonov et al, 2015).…”

Section: New Key Themes For Future Researchmentioning

confidence: 99%

Integral Biomathics reloaded: 2015

Simeonov¹,

Cottam

2015

Progress in Biophysics and Molecular Biology

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Recap and antrorseMany biological phenomena do not have adequate mathematical representations. This is because living systems use structures that are not yet grasped by our present conceptions of mathematics and computation. In particular they are circularly organized and they use recursions. Mathematics and computation at the present time deal only superficially with circular organization or the consequences of recursion. We just have not yet found a way to adequately deal with such matters 1 ! Current approaches to complex problems rely on modelling, but one aspect of the problem is that they rely on a single form of mathematics, switching from it to another to address the next aspect, and so on. All this switching is an indication of how inadequate our mathematical tools are to date (ODE/PDE systems, stochastic models, discrete state-transition systems, topological algebra, etc.). Biological systems function at all these levels simultaneously. Yet, the real problem is that even the simplest recursions are beyond our capacity to analyse at the present time. It is not biology that is too messy to be modelled; it is our use of current mathematical paradigms that are not able to adequately address these biological problems (Root-Bernstein, R. S., 2012). These paradigms are keeping biology within the fixed boundaries of physics, the domain of nonliving matter. Despite being the most advanced mathematics-based natural sciences discipline, physics is currently experiencing its own crisis when trying to overcome the dichotomy between its major theories (Smolin, 2006) and remains not sufficiently developed to explain living systems. Is this a chance in disguise?We believe that further advances in the sciences -physical, biological, social -require new levels of integration across the domains. It is a commonplace to seek a "paradigm shift" (Kuhn, 1962) to advance the frontiers of a scientific domain. Such shift can also uplift the network of interdisciplinary connections among existing research areas. However, we are seeking more than a shift that advances the network of the complex dynamical system of knowledge. We seek to advance the nature of the links of this network by encouraging the development of mathematical and computational methods that will at once change the shapes of the nodes and the links, thus performing a simultaneous "quantum jump" in multiple disciplines, to enable a new integration and rationalization of knowledge: Integral Biomathics. The major implications of this new paradigm for reinventing and re-engineering mathematics and computation address the life sciences and medicine. They encompass meanwhile also the foundations of creativity and cognitive processes in the sciences and the arts, as well as the phenomenology of consciousness in general.

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“…In addition, richer Bayesian, contextual models, but also quantum models (Gomez-Ramirez & Sanz, 2013;Kitto & Kortschak, 2013;Gabora et al;, and post-Turing computation (Siegelmann, 2013) and elaborate forms of logic (Goranson & Cardier, 2013;Marchal, 2013) have changed the understanding about the role of mathematics in biology. The following two sections recapitulate two complementary approaches which both touch on the implementation of the Integral Biomathics strategy of (Simeonov et al, 2012b).…”

Section: Are There Any Solutions In Sight?mentioning

confidence: 99%

“…But whatever it is (the tools of RB, MES and WLI included), there will always lie something outside its expression powers. There will always be some kind of entity to place in the system description as a placeholder for the unexpected (Simeonov et al, 2012b). This entity (a 'homunculus', a 'Maxwell daemon' or a 'Turing oracle') could probably be captured to some extent when given a specific focus when using the complementary 1 st , 2 nd and 3 rd person system description perspectives (Matsuno, 2003) as borders of knowing.…”

Section: Perspectivesmentioning

confidence: 99%