Top down and Bottom up Signaling
The approach outlined in chapter 1.4 is principally a bottom up description of the system since it explains the behavior of a macroscopic observable as fluorescence light in dependency on the population of substates which could be single molecules or compartments. Assuming that single elements and their probability can be transferred into another state and/or that the interaction between those compounds is the only input that defines the systems properties is typically bottom up because the single constituents and their dynamics are the only elements that define the overall dynamics.
The system constraints are important factors that define the dynamical properties. Constraints can have impact on the microscopic level with or without time delay, however, constraints can also be macroscopic, for instance when the biochemical reactions are restricted to the size of the reaction volume. This could be a single molecule, cell organelle or, for other cases, such as the spread of ROS waves, the whole organism (for ROS waves see chapters 3.2 and 4.6). Importantly such constraints are not necessarily extrinsic system limitations, like the finite capacity or size of the reaction vessel or ecosystem, but can also be understood as the intrinsic interaction between system components that “emerge” due to pattern formation or self-organization in the system. Macroscopic processes that occur in form of self-organized patterns have the potential to “slave” the microscopic dynamics (Haken, 1981).
Such constraints might themselves be time dependent and underlie dynamical changes. One example is the birth of “predators” in an ecosystem due to evolutionary processes. In the moment such a new predator arises, it starts to limit the population of its prey. Therefore, from the point of view of the prey, the emergence of the new predator is a new constraint. In chapter 4.6 we will especially see how prey-predator models can be used to describe the appearance of different properties of ROS, especially ROS waves.
However such obvious interactions of macroscopic species on the microscopic level are not necessarily the only way in which top down messaging occurs. Intrinsic effects can also contribute to a change of dynamics on the macroscopic level due to the influence of a macroscopic phenomenon. This is well known in nonlinear dynamics of nonequilibrium systems, where it is stated that the macroscopic processes might “slave” the microscopic processes. This concept became known as the “slaving principle” or the generalized “order parameter concept”. Haken described such phenomena as the enslavement of microscopic effects by macroscopic dynamics.
The bottom up dynamics follows the constitution of the overall system by its individual compounds which are, for example, given by the formation of a radiation field from individual wave elements that are emitted by individual atoms:
“Below laser threshold, light consists of individual wave tracks which are emitted from the individual atoms independently of each other. [...] In order to make contact with other processes of self-organization let us interpret the processes in a lamp or in a laser by means of Bohr’s model of the atom. A lamp produces its light in such a way that the excited electrons of the atoms make their transitions from the outer orbit to the inner orbit entirely independently of each other” (Haken, 1981). However, above the laser threshold the system develops a new property:
“Above laser threshold the coherent field grows more and more and it can slave the degrees of freedom of the dipole moments and of the inversion. Within synergetics it has turned out that is a quite typical equation describing effects of self-organization. ...This is probably the simplest example of a principle which has turned out to be of fundamental importance in synergetics and which is called the slaving principle” (Haken, 1981).
Without a real scientific formulation of the underlying principles, everyone should agree that the development of consciousness might be an overwhelming “control parameter” for the slavery of microscopic dynamics. The question that remains is not whether there is any top down messaging but how these forms of top down messaging are conducted. Order parameters such as blood pressure or body temperature can be manipulated by free will and serve as prominent examples of when the activation of genes, and therefore the absolutely basic dynamics in the biological system, is activated top down by order parameters introduced by the free will. While that is not the case in general there might be a link how an organism can influence the activation of certain genes by influencing its state (for example if it consumes a large amount of alcohol which is also a consequence of the free will).
There are simple approaches to show how, for example, protein kinases are activated or deactivated at a certain critical temperature, which might even work as a switch for the activation of genes by phosphorylation on the basic molecular level. These can be activated due to external constraints (temperature), induced stress or by free will in the form of the organism “deciding” to raise its body temperature by conducting a sport program. For an example of a mitogen activated protein kinase (MAPK), see for example (Mertenskotter et al., 2013).