Parameters Estimation in Phase-Space Landscape Reconstruction of Cell Fate: A Systems Biology Approach

Abstract

The thermodynamical formalism of irreversible processes offers a theoretical framework appropriate to explain the complexity observed at the macroscopic level of dynamic systems. In this context, together with the theory of complex systems and systems biology, the thermodynamical formalism establishes an appropriate conceptual framework to address the study of biological systems, in particular cancer.The Chapter is organized as follows: In Subheading 1, an integrative view of these disciplines is offered, for the characterization of the emergence and evolution of cancer, seen as a self-organized dynamic system far from the thermodynamic equilibrium. Development of a thermodynamic framework, based on the entropy production rate, is presented in Subheading 2. Subheading 3 is dedicated to all tumor growth, as seen through a "phase transitions" far from equilibrium. Subheading 4 is devoted to complexity of cancer glycolysis. Finally, some concluding remarks are presented in Subheading 5.

Complexity in Biological Organization: Deconstruction (and Subsequent Restating) of Key Concepts

“…Overall, the development of a primary tumor from a microscopic level (avascular growth) to a macroscopic level (vascular phase), and the subsequent appearance of metastases, is not simply the accumulation of malignant cells, but results from a nonlinear process involving true “biological phase transition” downstream critical bifurcations [ 86 , 87 ]. This dynamical behavior leads to self-organization away from thermodynamic equilibrium, providing the system with a high degree of robustness, complexity, and hierarchy [ 88 ], which, in turn, enacts the creation of new information and learning ability.…”

Phase transition in tumor growth VIII: The spatiotemporal of avascular evolution

“…As we have shown in previous works [16], cancer can be seen as a complex network made up of cells that have lost their specialization and growth control, and that emerges through what we can call "biological phase transition" [17][18][19].…”

“…We mean that cancer is seen as a self-organizing nonlinear dynamic system, far from thermodynamic equilibrium [4,5,6], exhibits a fractal structure that allows it to evade the action of the immune system and host cells [7][8][9][10][11][12]. Shows growth dynamics in the metastatic stage, deterministic chaos type, which confers high robustness, poor long-term prognosis, adaptability, and learning capacity [13][14][15][16].…”

The entropy production rate a bridge between thermodynamics and chemical kinetics

“…Finally, we have successfully extended the method to the study of the glycolysis mechanism of cancer [22][23][24][25]. In the last year, glycolysis of cancer has been a target in oncology [26] Most tumor cells show a higher glycolytic rate than normal cells; this phenomenon is known in the literature as the Warburg's effect.…”