41,885 research outputs found
No entailing laws, but enablement in the evolution of the biosphere
Biological evolution is a complex blend of ever changing structural
stability, variability and emergence of new phenotypes, niches, ecosystems. We
wish to argue that the evolution of life marks the end of a physics world view
of law entailed dynamics. Our considerations depend upon discussing the
variability of the very "contexts of life": the interactions between organisms,
biological niches and ecosystems. These are ever changing, intrinsically
indeterminate and even unprestatable: we do not know ahead of time the "niches"
which constitute the boundary conditions on selection. More generally, by the
mathematical unprestatability of the "phase space" (space of possibilities), no
laws of motion can be formulated for evolution. We call this radical emergence,
from life to life. The purpose of this paper is the integration of variation
and diversity in a sound conceptual frame and situate unpredictability at a
novel theoretical level, that of the very phase space. Our argument will be
carried on in close comparisons with physics and the mathematical constructions
of phase spaces in that discipline. The role of (theoretical) symmetries as
invariant preserving transformations will allow us to understand the nature of
physical phase spaces and to stress the differences required for a sound
biological theoretizing. In this frame, we discuss the novel notion of
"enablement". This will restrict causal analyses to differential cases (a
difference that causes a difference). Mutations or other causal differences
will allow us to stress that "non conservation principles" are at the core of
evolution, in contrast to physical dynamics, largely based on conservation
principles as symmetries. Critical transitions, the main locus of symmetry
changes in physics, will be discussed, and lead to "extended criticality" as a
conceptual frame for a better understanding of the living state of matter
Optimal phenotypic plasticity in a stochastic environment minimizes the cost/benefit ratio
This paper addresses the question of optimal phenotypic plasticity as a
response to environmental fluctuations while optimizing the cost/benefit ratio,
where the cost is energetic expense of plasticity, and benefit is fitness. The
dispersion matrix \Sigma of the genes' response (H = ln|\Sigma|) is used: (i)
in a numerical model as a metric of the phenotypic variance reduction in the
course of fitness optimization, then (ii) in an analytical model, in order to
optimize parameters under the constraint of limited energy availability.
Results lead to speculate that such optimized organisms should maximize their
exergy and thus the direct/indirect work they exert on the habitat. It is shown
that the optimal cost/benefit ratio belongs to an interval in which differences
between individuals should not substantially modify their fitness.
Consequently, even in the case of an ideal population, close to the optimal
plasticity, a certain level of genetic diversity should be long conserved, and
a part, still to be determined, of intra-populations genetic diversity probably
stem from environment fluctuations. Species confronted to monotonous factors
should be less plastic than vicariant species experiencing heterogeneous
environments. Analogies with the MaxEnt algorithm of E.T. Jaynes (1957) are
discussed, leading to the conjecture that this method may be applied even in
case of multivariate but non multinormal distributions of the responses
Oncogenesis- kaleidoscopic and multi-level reality
Oncogenesis is an extremely complex phenomenon. The mechanisms by which cancer is induced is only partially known. Consequently, therapeutic targets may be uncertain and results are often unsatisfactory. The purpose of this paper is to develop a trans-level and multiple transdisciplinary perspective describing the kaleidoscopic reality of oncogenesis. This manner of understanding oncogenesis as a complex process characterized by a non-linear dynamic, far from equilibrium and with unpredictable evolution, transcends the classical perspective and requires a paradigm shift. This approach is also facilitated by recent studies that focus on group phenomena, with emerging behaviors in a continuous phase transition. Biological systems, and obviously the human organism, express this type of behavior with critical self-organizing valences in the context of a genome - mesotope (environment) - phenotype interaction. For example, nature has transposed in the ecosystem, among other things, the performance pattern of its mineral history represented by the dynamic energy-matter-information unit (the principle of invariance). And multi-cell biological systems in the phylogenetic tree crown have multiple directed aerobic metabolisms in accordance with specific functions. Cancers, in turn, have a hybrid (anaerobic and aerobic) and unidirectional metabolism whose only and ultimate reason is the survival of the malignant cell. Understanding the transdisciplinary reality of oncogenesis offers novel development paths for new therapeutic strategies compared to current ones which have relatively limited efficiency
Numerical Complete Solution for Random Genetic Drift by Energetic Variational Approach
In this paper, we focus on numerical solutions for random genetic drift
problem, which is governed by a degenerated convection-dominated parabolic
equation. Due to the fixation phenomenon of genes, Dirac delta singularities
will develop at boundary points as time evolves. Based on an energetic
variational approach (EnVarA), a balance between the maximal dissipation
principle (MDP) and least action principle (LAP), we obtain the trajectory
equation. In turn, a numerical scheme is proposed using a convex splitting
technique, with the unique solvability (on a convex set) and the energy decay
property (in time) justified at a theoretical level. Numerical examples are
presented for cases of pure drift and drift with semi-selection. The remarkable
advantage of this method is its ability to catch the Dirac delta singularity
close to machine precision over any equidistant grid.Comment: 22 pages, 11 figures, 2 table
BV solutions constructed by epsilon-neighborhood method
We study a certain class of weak solutions to rate-independent systems, which
is constructed by using the local minimality in a small neighborhood of order
and then taking the limit . We show that the
resulting solution satisfies both the weak local stability and the new
energy-dissipation balance, similarly to the BV solutions constructed by
vanishing viscosity introduced recently by Mielke, Rossi and Savar\'e
Resolvent Positive Linear Operators Exhibit the Reduction Phenomenon
The spectral bound, s(a A + b V), of a combination of a resolvent positive
linear operator A and an operator of multiplication V, was shown by Kato to be
convex in b \in R. This is shown here, through an elementary lemma, to imply
that s(a A + b V) is also convex in a > 0, and notably, \partial s(a A + b V) /
\partial a <= s(A) when it exists. Diffusions typically have s(A) <= 0, so that
for diffusions with spatially heterogeneous growth or decay rates, greater
mixing reduces growth. Models of the evolution of dispersal in particular have
found this result when A is a Laplacian or second-order elliptic operator, or a
nonlocal diffusion operator, implying selection for reduced dispersal. These
cases are shown here to be part of a single, broadly general, `reduction'
phenomenon.Comment: 7 pages, 53 citations. v.3: added citations, corrections in
introductory definitions. v.2: Revised abstract, more text, and details in
new proof of Lindqvist's inequalit
Amino acid metabolism conflicts with protein diversity
The twenty protein coding amino acids are found in proteomes with different
relative abundances. The most abundant amino acid, leucine, is nearly an order
of magnitude more prevalent than the least abundant amino acid, cysteine. Amino
acid metabolic costs differ similarly, constraining their incorporation into
proteins. On the other hand, sequence diversity is necessary for protein
folding, function and evolution. Here we present a simple model for a
cost-diversity trade-off postulating that natural proteomes minimize amino acid
metabolic flux while maximizing sequence entropy. The model explains the
relative abundances of amino acids across a diverse set of proteomes. We found
that the data is remarkably well explained when the cost function accounts for
amino acid chemical decay. More than one hundred proteomes reach comparable
solutions to the trade-off by different combinations of cost and diversity.
Quantifying the interplay between proteome size and entropy shows that
proteomes can get optimally large and diverse
- …