New Biological System Evolution Theory

Introduction

This document was written with two objectives:

The first objective is to propose a reflection exercise about how setting right or wrong
foundations in the theory of evolution impacts and may hinder the developments and direction
of the existing latest scientist findings in disciplines like Genetics, Molecular Biology, Cancer,
Medicine, and all levels of complex systems in biology.

Secondly, this document proposes an alternative theory of evolution and study method for
new directions and conclusions in the experiments and its results based on the study of the
theory of Systems and Complexity, applied to biological systems.

In this document the proposed description of a system for biological systems has considered
analogies with artificial systems created in technology, and especially in the
Telecommunications, Software and Computer science in the process to create abstraction
and organisms capable to predict, elements autorregulated by feedback, adaptation to
changes, learn, store in memory, control other systems, communicate, use “senses” or
“probes” (to feel environment), and tools to react, actions towards an objective of system
stability, phased cycles, amongst others which become some of the main characteristics in
live systems, which also differentiate from the artificial intelligent systems in the action
autonomy, quasi-intelligence level achieved by the most abstract elements in the systems
and communication processes closer to “languages” (more than protocols), which is used to
create more abstraction or new elements, even in the systems in a low grade in the hierarchy
of complexity.

There is no room for random or arbitrary changes to justify the evolution in this environment,
and the interrelation of all the systems make changes which can only be explained by the
study of the systems themselves and how they are interrelated in order to find the best
models that define each system, its properties, and predict its behaviour.

Please note that the term “Mutation” that sets the basis (according to the current genetic
accepted theory) for genetic variation in the DNA where all the protein manuals of the cell is
stored, is a concept based on the Neo-Darwinist theory of evolution founded on the
understanding of a mutation as an error or random event in the DNA.

If we change this by the hypothesis that the evolutionary changes are not random at all but a
direct consequence of the communication changes and sometimes quasi-intelligent systems
in the complex cycles created in the interaction and relationships established within these
systems.

Also please note that the concept of “Natural Selection” becomes too linear and simplistic to
explain the complex routes in the cycles and systems. We will assume that there is not
Natural Selection but a series of actions taken in a system to reach the most stable state for
all the elements in the system, or for those that have the control of the system. (which does
not mean a fix state that could favour some controlling elements versus others and become
instable, but a dynamic cycle of states).

In the following sections we will study the elements and characteristics of the biosystems
which has been briefly anticipated above and compare its meaning with some real cases.
 We will compare the explanation given by the currently official and adopted theory of
evolution and how this will change using our proposed hypothesys.

We will also apply this in some cases like Cancer, Brain structures, and some other cases
related to deseases and medical treatments in human beings.

Definition of a system

The systems and in particular the biological systems will be studied based on the following
elements and properties:

Element:

A system contains multiple elements in interaction and / or communication.

The elements will distribute the necessary functions to form an ecosystem in a status of
equilibrium.

The elements can be specialized in different functions and have a different size,
morphology and level of complexity.

The elements can be other systems that will be named as lower hierarchy systems, and
they will be characterized as elements for the purpose of the analysis of a specific
system.

When many particles, or bioparticles develop statistically a function for the system, they
will be deemed all in conjuction as an element in the system and characterized per their
properties as an element. (electrons, protons, proteins, anions, etc)

Generally all the elements are systems when they are analyzed in a lower hierarchy level
(whether at a Biology or Physic level of study, so this is not just a property in biological
systems).

Statistical characterization:

A system can be characterized under statistical parameters.

The behaviour of a system will need a different characterization subject to the size of the
study and the proximity to the size of the elements that form the system. (Similarly as the
light can be modeled as a particle in the typical Physic studies (above micrometers) or as
a wave in scales of size in the range of the light wavelength size (micrometers to
nanometers). As another example case, an electrical circuit can be characterized with a
different model of equations for equivalent impedances at different frequency ranges.

The variation of certain parameters is an intrinsic feature of the systems due to the
interrelations of the elements in the system in a stable status, but it can be simplified if
studied from a higher dimension than the size of the system and its elements.

We can see indicios of a system when we can see that certain parameters in samples
under study are maintained within a stable range and that would require energy and
autorregulation.
 As an example: The number of cells, proteins, and other factors in blood keep within
stable statistical parameters. In a different level of complexity the PH acidity and the
electrical voltage in a cell keeps within certain statistical parameters.

Please note the relationship of the statistical parametrical order with entropy and
information in many science disciplines as a method to measure the degree of order, and
system energy.

All the following concepts: statistic parametrical order, entropy, information, order,
energy; are terms related to the statistical characterization of a system.

Tolerance for stimulus:

A system, as mentioned above has a level of variance and statistical equilibrium.

The elements of a system and the nature as a system allow a certain degree within the
statistical limits to absorb internal or external sources of variance in the internal
interaction of their elements.

However if the tolerance is exceeded, the system may enter in a status that does not
allow that equilibrium status and may cause the collapse of the system since physically
the equilibrium in the new environment (internal and external) will tend to create other
more stable systems which can be non biological systems that get closer to the new
environment.

In some cases the systems can operate in different states, and determined stimulus can
bring the system to another state, which will change the characterization of the system to
another equilibrium state.

Life time:

A system in a specific environment has a typical life time.

The systems have a longer typical time that the typical life time of their elements.
This means that there will be new required elements (which can also be systems) as
some of the elements reach their end of life.

Biological systems are open systems that require the interaction with an environment
from which energy to manufacture or from which the new required elements can be
obtained.

Size:

The size of a system is one of the parameters that admit a tolerance variance but the size
will keep a relationship with the size of their elements and interaction, there will be a limit
for the largest and smallest sizes that can be statistically defined, as when the equilibrium
defined by the interaction of the elements is broken. (Maybe this could be applicable for
the cosmos too), so it can not be infinite.

There is typically a size for the most optimum usage of energy. In biological systems self-
regulated the size tends to adjust to the most optimal levels.

Number of elements:

The number of elements is another parameter in a system that allows tolerance variance
but a number too high or too low of elements compared to the equilibrium and
 energetically more optimal level, may cause the destabilization of the system and as a
consequence: the change of phase (in a multiphased system), the replication, or
destruction of the system as more stable status for the elements in conjunction with the
situation internal and external under those conditions derived by the excess or lack of
elements.

This is a parameter that can be typically characterized with statistical limits, and there will
be a range of optimal number of elements.

Feedback and loops:

The systems can reach an equilibrium status when there are one or multiple loops which
create a feedbacked system.

The loops in conjunction with memory (or information order and storage that is mentioned
later) are the basis for adaptation and “system intelligence” that allows to create
conceptual abstraction.

Memory:

The effect of internal and external interactions creates element reordering.

Reordering requires energy, and this is again related to entropy and allows
conceptualizing and storing information.

A system will contain many sources of information storage as memory tools.

The memory tools can be of different complexity levels and of different duration.

The memory stores changes due to interaction and as mentioned reorders and
reorganization, but depending of the degree of complexity and hierarchical level of the
system there can be an abstract meaning in the reorders of the information storage
system.

The information storage will normally require sophisticated bidirectional interrelations and
can be characterized as a subsystem or system in itself.

The longest memory systems in a system normally will reside in the nucleus or core, and
the most volatile will reside near to the border to the external stimulus. This does not
mean proximity as a physical proximity but in the interaction communication chain,
although in many cases it will be found in the more centric areas of the system for an
easy logical distribution and equilibrium in the development of this function in the system.

Communication:

Systems interact with other external systems and other elements of the environment.
For systems of high complexity (high in hierarchy thus formed with other systems of lower
hierarchy) with a sophisticated mechanism of feedback loops, and memory capability the
communication can be established with abstract concepts, near to the complexity of a
language.

The communication is externalized through the set of action tools to the external area
(see below Action Tools), and perceived through the Sensors which in many biological
species can be identified with their “Senses”.

External and Internal Environment:

 A system has tangible or intangible borders when it is conceptualized as a system.
The internal area is the one that is kept within the equilibrium status of the system that
can be statistically characterized within certain values and established relationships
between their elements, and rest of properties mentioned here.

The external area has another equilibrium or characterization, and is subject to variations
based on external individuals, or conditions.

The system will react to adjust to the variations produced in the external environment, if
they are within the tolerance range.

Systems can learn to adjust to different external conditions above the tolerance range, if
they happen in a period of time in which a learning or adaptation can be developed.

The interactions to the external area can be perceived by certain senses or sensors and
interpreted as abstract concepts, and as a reaction the system can react with adaptation
actions that can drive internal reordering of some of their elements, which can be
modeled as information stored that will be reused if the same stimulus is repeated with a
faster adaptation and response.

The change from the internal and external environment may not have a physical border,
but will have different equilibrium and statistic conditions, similarly as the difference of
impedance when changing from one media to another media in electrical or
electromagnetic signals for example causing effects like diffraction in the case of light
when the light travels through physical media with a different dielectric value, which is in
the end a statistic parameter.

Sensors:

The perception of the external environment is grasped through a number of sensors.

The sensors provide information about the environmental changes, stimulus or external
aggressions.

Action tools

The actions that a system can develop as a response to external or internal changes or
for the normal activities in their ecosystem use a set of tools, or parts of their system (for
example human extremities, flagellums in cells) that can produce chemical, electrical, or
physical actions.

In the systems that comply with the conditions mentioned below for intelligent
biosystems, the tools can be perfected and become very precise in the action towards an
objective, and will use the system feedback and ability for self-construction features to
achieve it. The accuracy and perfection in the usage of the tools requires an iterative
method of trial, memory, feedback and action.

Although in a system the tools can be both internal and external, normally in the
characterization of a system the internal tools will belong to internal lower hierarchical
systems and we will refer with action tools to the external tools that will be the ones under
the control of the governing or controlling elements for the system under study.

Replication or Reproductive mechanisms:

The biological systems have the capability to replicate their individuals.

 The replication requires developing a storage system with the information of the phases,
learnt process and solutions for stimulus, environmental changes, external and internal
variations of the equilibrium. The processes and solutions will vary during the evolution
and interaction of the systems with the environment and ecosystems.

(As an example the tools, materials and process to build a highway or a house nowadays
are different than the tools and process used 1000 years ago, but the need is the same,
and they are produced for similar requirements in the societies. The solution that will be
developed by an individual element or a system will be a function of the stored processes
that have been learnt and stored, in conjunction with the society or ecosystem, please
see later the property based on Ecosystem development of the Element individuals).

The reproduction requires systems that contain the necessary information and very
importantly elements that have lived in the previous system to guide the reproduction
towards the same system in which they have lived before (so the parent systems of the
new born system), not all is stored information.

System topology (Nucleus or Core, and Edge layers):

The organization of one system is typically developed by creating a topology in

organizational layers based on the type of interactions. For those elements that need to
be interacting with the external environment, they will be near the edge.

This can give rise to specialization of all the elements in the interior areas becoming a
core system, and the elements in the external areas in edge systems; and defining the
interaction of the core and edge systems based on a series of communication /
interaction signals which could be similar to a protocol. (as it happens in the systems that
have a very close and frequent interaction).

The internal systems will keep less awareness of the physical environment, but will get
more conceptual or abstract information, since it will arrive modulated and transcribed
through the edge systems (cold, hot, acid, aggression, message from co-system, etc).

The external systems will take a more direct interaction with the physical environment as
it is and in low hierarchy levels of the edge systems it will be ended up translated in
general physics and chemical actions and reactions.

The elements develop task specialization (higher as systems gain complexity):

The elements in a system gain specialization.

This specialization tends to be higher in systems with a longer life time since it started, in
which the number of elements has grown and has created subsystems that develop
specific functions for the system.

Specialization normally requires time, growth and higher energy (since the system
becomes bigger in size and subsystems).

Complexity Hierarchy (Levels of complexity and abstraction):

The biological Systems in equilibrium have a series of inputs and outputs that coexist in a
ecosystem. When in the interaction and during the evolution in time of the ecosystem, the
system tends to specialization and growth if the elements can gain energy in their
environment.

In these conditions those systems in the ecosystem that comply the conditions of
intelligent biological systems may learn to use the outputs of other systems and the
 actions that need to develop to maximize the outputs and result of determined actions in
favour of their equilibrium, and energy acquisition for its growth and estability during its
own evolution.

When one system has learnt and stored the effect of determined actions can give an
abstract meaning internally that will be used to achieve the same result and control the
other systems.

The other systems may react or admit the control if it ends up causing their full instability.
There are many times symbiotic autoregulations established by some systems over other
systems, and sometimes some can control to some others in the same ecosystem.

As an example, the Krebbs cycle for the synthesis of ATP energy is regulated by many
enzymes positively or negatively that are used by other systems based on the ATP
energy required in the cell.

Elements that become controllers creating new abstraction / complexity levels

Biological system intelligence:

System organization and evolution in quantums (discontinuity)

Objective in a system:

Learning process (for biological intelligent systems):

Cascading and Translation along hierarchical levels

Trend to reach Resonance state (maximum energetic efficiency)

New Evolution Theory

This is under construction now, and some subsections are drafted preliminarily below:

- Chemical and Physical system stability in the earth

- Organic molecules in dynamic environment (fluids)
- Conditions for maximized solar energy absorption in chain reaction.
o Electron transfer and reorder cycles.
- Initial cycled systems in organic molecules, on fluids and with solar energy input.
- Higher hierarchical systems formed with initial systems, and self-regulators with loops are
used for actions towards an objective of maximization of energy efficiency.
- Initial systems around small RNA/DNA base chains in ecosystem (far still from virus and
bacteria) get established around the solar system cycles.
- RNA/DNA molecules interaction with polymers (precedent of amino acids). RNA/DNA
base triplets acquire meaning in interaction with polymers. More specialized elements
and ecosystem around the RNA/DNA..
- Pseudo-alive system ecosystems (capability to fast reaction (relative speed change-
action) and auto-regulation, communication). Membrane does not exist.
- Biosystems capable to build and combine polymers with a function in the ecosystem.
DNA becomes a polymerized more stable strand. Communication and interaction with
DNA with more specialized elements. External and Internal ecosystems are formed
based on proximity to DNA.
- Biosystems capable to build polymers of amino acids (initial proteins)
 - Biosystems with layers of complexities, protein systems (pro-virus)
- Biosystems with sophisticated protein and pro-virical systems of interaction and
construction of higher levels with DNA.
- Pro-Bacteria with specialized proteins and DNA.
- Virus used by Bacteria in internal and external communication with DNA information.
- Virus as an autonomous element (similar to a seed)
- Bacteria-Virus ecosystems
- Bacteria form Eukaryotes (by creating an external membrane and isolated ecosystem
conditions and the bacteria get specialized in a higher system)

Note the level of intelligence, abstraction, and self-construction of elements increases in each
step. (Not always will produce a physical reorganization, but some systems will increase the
abstraction in the definition of elements with a more abstract capability, similar to an abstract
language. The steps require stability in the previous step, energy is stored in new reorders,
energy drives growth, specialization of elements and division and replication as the biological
systems evolve during their life time).

Bilbliography: