Theoretical aspects of Systems Biology Review Article
Progress in Biophysics and Molecular Biology, Available online 3 April 2013, Subscription required Mariano Bizzarri, Alessandro Palombo, Alessandra Cucina
Abstract excerpt: In the past, biological research has focused on questions that could be answered by a reductionist program of genetics. The organism (and its development) was considered an epiphenomenona of its genes. However, a profound rethinking of the biological paradigm is now underway and it is likely that such a process will lead to a conceptual revolution emerging from the ashes of reductionism. This revolution implies the search for general principles on which a cogent theory of biology might rely.
Excerpt from Fig. 1. …each level is both characterized and governed by emergent laws that do not appear at the lower levels of organization. By this way, hierarchical organization in between different levels creates both bottom-up and downward causation.
Excerpt from Fig. 2. Cell differentiation is driven by the interplay between the morphogenetic field and the gene expression pattern. Biophysical forces are acting within and throughout the field in selecting phenotypes that arise according to a stochastic process.
My comment: The “…general principles on which a cogent theory of biology might rely” are nutrient-dependent and pheromone-controlled as indicated by Darwin’s “Conditions of Existence.” The insertion of statistical misrepresentations of Natural Selection subsequently bastardized Darwinian theory. Those who continue to propagate their nonsense about randomness and mutations theory are continuing to bastardize Darwinian theory. For comparison, see: Kohl (published to figshare.com): Nutrient-dependent / Pheromone-controlled Adaptive Evolution
This model of systems biology represents the conservation of bottom-up organization and top-down activation via:
Nutrient stress-induced and social stress-induced intracellular changes in the microRNA (miRNA) / messenger RNA (mRNA) balance;
Intermolecular changes in DNA (genes) and alternative splicing;
Non-random experience-dependent stochastic variations in de novo gene expression and biosynthesis of odor receptors;
The required gene-cell-tissue-organ-organ system pathway that links sensory input directly to gene activation in neurosecretory cells and to miRNA-facilitated learning and memory in the amygdala of the adaptively evolved mammalian brain;
The required reciprocity that links gene expression to behavior that alters gene expression (i.e., reciprocity from genes to behavior and back) in model organisms like the honeybee.
The model addresses some important aspects included in the review article on the Theoretical aspects of Systems Biology:
1) Emergent laws that do not appear at the lower levels of genetically predisposed invertebrate hormone-organized and hormone-activated behavior exemplified in the honeybee model organism by hierarchical organization across different levels, which creates bottom-up (i.e., nutrient-dependent) and top-down (i.e., pheromone-controlled) causation.
2) Interplay between biophysical forces that act on gene expression and morphology and result in phenotypical characteristics, which include behavior. Changes in behavior provide a feedback loop that also acts on gene expression associated with non-random nutrient-dependent pheromone-controlled stochastic processes for cell differentiation.
Simply put, natural selection of phenotype is nutrient-dependent and pheromone-controlled.