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Relationships and Causation in Living Matter: Reframing Some Methods in Life Sciences?

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Abstract

In this paper I want to enrich, on the methodological and epistemological side, an earlier review of mine (in which there are more details on the physics of electrodynamic coherence), aiming to stimulate attention to some seemingly trivial or irrelevant aspects, but, in my opinion, very subtle and of crucial importance in the study of living dynamics in various disciplines (physics, biology, medicine, philosophy of science). The conceptual core is: to understand that a living system cannot be conceived, and therefore neither studied, as "an object", "a body." The (in essence) relational nature of the living being finds its foundations in dissipation, symmetry breakings and field theories capable to count for multiple levels of vacuum (such as Quantum Field Theory, QFT), and sees the living phase of condensed matter (on an aqueous basis) as a consequence of bosonic condensation of correlation quanta (the well-known Nambu-Goldstone bosons) over an extended and interrelated hierarchy of degrees of freedom to which a (super)coherent is associated state. In there the matter and energy components of the biological system are subjected to phase correlations to give rise to a holo-state, shared over the whole system, from which a self, endowed with continuity, emerges and thus also a biological identity rooted in a dissipative thermodynamic history. However, this "identity" is like the river of Heraclitus' anecdote: it is a flow and not an object existing in itself, nor static; dynamics, change, are all that lasts, while water, is always different. So holds for an organism that is, in fact, an organizationally closed system, but (and precisely because) thermodynamically open. This condition implies that the study of any biological system is de facto the study of a flow of relationships, and the living system (whether a cell, a complex organism, or an ecosystem) should be conceived as a process dissipatively coupled to its environment and as a producer of responses following an autopoietic order, inherent in the very condition of coherence (as long as it exists). Once this is recognized: • We obtain the possibility of reducing (without ontological discontinuities) sophisticated emergent properties (such as sensing, perception, semantics, teleology, adaptation, memory) irreducible to the deterministic laws of the elementary components of which, nonetheless, the living matter is composed (and to the laws of which it is therefore equally subjected); • Such properties result in the emergence of "biological laws" that, in addition to physical laws, dictating action-reaction relationships, describe stimulus-response relationships (with enormously greater logical openness) valid only for the living state; • The existence of these "laws" (analogical, but now physically grounded) forces us to revisit the definition of causality in biology, understanding that the method of inquiry must be revisited on both the theory and praxis fronts (details in the text); • It is understood that the complex view is to be applied ab initio, but also advanced to a further step (on a quantum
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Relationships and Causation in Living Matter: Reframing Some Methods in Life Sciences? Phys Sci & Biophys J
Relationships and Causation in Living Matter: Reframing Some
Methods in Life Sciences?
Renati P*
The World Water Community, Netherlands
*Corresponding author: Paolo Renati, The World Water Community, Marconistraat 16, 3029
AK Rotterdam, The Netherlands, Email: paolo.renati@gmail.com
Review Article
Volume 6 Issue 2
Received Date: August 15, 2022
Published Date: September 30, 2022
DOI: 10.23880/psbj-16000217
Abstract
In this paper I want to enrich, on the methodological and epistemological side, an earlier review of mine (in which there are
more details on the physics of electrodynamic coherence), aiming to stimulate attention to some seemingly trivial or irrelevant
aspects, but, in my opinion, very subtle and of crucial importance in the study of living dynamics in various disciplines (physics,
biology, medicine, philosophy of science). The conceptual core is: to understand that a living system cannot be conceived, and
therefore neither studied, as “an object”, “a body.
The (in essence) relational              
theories capable to count for multiple levels of vacuum (such as Quantum Field Theory, QFT), and sees the living phase of
       
Nambu-Goldstone bosons) over an extended and interrelated hierarchy of degrees of freedom to which a (super)coherent is
associated state. In there the matter and energy components of the biological system are subjected to phase correlations to
give rise to a holo-state, shared over the whole system, from which a self, endowed with continuity, emerges and thus also a
biological identity rooted in a dissipative thermodynamic history.
                  
dynamics, change, are all that lasts, while water, is always different. So holds for an organism that is, in fact, an organizationally
closed system, but (and precisely because) thermodynamically open.
        
system (whether a cell, a complex organism, or an ecosystem) should be conceived as a process dissipatively coupled to its
environment and as a producer of responses following an autopoietic order, inherent in the very condition of coherence (as
long as it exists). Once this is recognized:
We obtain the possibility of reducing (without ontological discontinuities) sophisticated emergent properties (such as
sensing, perception, semantics, teleology, adaptation, memory) irreducible to the deterministic laws of the elementary

Such properties result in the emergence of “biological laws” that, in addition to physical laws, dictating action-reaction
relationships, describe stimulus-response relationships (with enormously greater logical openness) valid only for the

  causality in
biology, understanding that the method of inquiry must be revisited on both the theory and praxis fronts (details in the

It is understood that the complex view is to be applied ab initio, but also advanced to a further step (on a quantum-
Physical Science & Biophysics Journal
2
Renati P. Relationships and Causation in Living Matter: Reframing Some Methods in Life Sciences?.
Phys Sci & Biophys J 2022, 6(2): 000217.
Copyright© Renati P.
electrodynamic basis) in which the occurrence of not-only-diachronic causality in the living matter would be uncontemplable
through “classical” observables only, considered within dynamical systems theory, chaos physics and complexity science.
             
      
sensitive gesture towards the web of Life.
Keywords:         

Premise: Presentation of the Problem
  
table at time t0, it is possible, under the ideal approximation
of perfectly elastic/conservative collisions, to predetermine
the state of the system at time t11-t0). Under
that ideal approximation, the predictive power of the laws
of motion would, in principle, be the same whether the
spheres were 10 or 1 million. For systems consisting of only
a few elements, such as a common 15-ball billiard table, the
         
fact, while also considering the friction term, the description
         
rather short times, of course, within which the damping of
         
million or more, the description of the state of motion at time
t1 in the real case becomes impractical (not only because of
computational limitations, but because of the multitude of
paths in phase space that can be travelled by the system,
given the same initial conditions, as a result of the unmovable

trajectories at each collision between the spheres and against
the walls).

been well dealt with by the dynamical systems, chaos and
complexity sciences, which have revealed to us the existence
of metastable states, attractors, Lyapunov exponents,


Totally different issue, however, concerns those systems
(i.e.: living ones) that, although also constituted, as in the
previous example, by immense multitudes of material
elements (also qualitatively heterogeneous), manifest
dynamics and emergent properties not at all traceable to
stochastic processes and/or describable tout court by laws
of motion of material micro-components alone. When it
concerns biological systems, in fact, categories come into
play in the temporal evolution of states (such as meaning,
teleology, adaptation, memory, etc.) that-even in the advanced
complexity paradigm-are not reducible to interactions
described by deterministic laws (those involving fundamental
components, such as atoms, molecules, electrical charges,
photons, phonons, etc.), hence they are not even computer-
modellable. Yet, to those deterministic laws the resulting
system must still be subordinate as well, precisely because it
is also made up of those elementary components.
Clearly, then there is a need for an additional conceptual
      
   
          
showing how it is possible to physically trace a causal
continuity between the level of material components and
the emerging level of physiology or organism behaviour,
without falling into ontological discontinuities. In this way, it
is possible to recompose a Cartesian split between function
and structure that is still hard to die (just see how it has
survived even in the constructivist theoretical scaffolding

of Quantum Mechanics (QM).
Another crucial aspect that radically distinguishes a
living system from a “merely complex” inanimate system
(such as an array of coupled pendulums, a heap of sand
grains on an oblique plane, a set of seismic discharges, the

is that the living, as we shall see, in its intrinsic essence:
• Consists of “relation to,” of constant “trespassing” of
and from itself in space and time (forward-purposes,
    
“instinct”),
• Is characterized by an irremovable transcendence
of itself, precisely in order to produce itself as a self,

• And therefore it does not exist as an observable system
          

and heat with the environment), although we all have the

it is a cube of niobium or a fox or a lymphocyte), place it

measurements, and obtain data that are meaningful. In
reality for living systems this is so only for a small subset
of aspects and cases.
Physical Science & Biophysics Journal
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Renati P. Relationships and Causation in Living Matter: Reframing Some Methods in Life Sciences?.
Phys Sci & Biophys J 2022, 6(2): 000217.
Copyright© Renati P.
All of this forces us to problematize (as much
philosophically as physically) the question of “what” we are


critiques of the methodologies by which we identify cause-
effect relationships in living matter.
      
more physical events, within contexts composed of inanimate
(i.e.: non-living) objects – disposing of laws that rigorously
describe the constraints under which changes in states of
motion, entropy variation, conservations of charge, energy,
angular momentum, invariance relations (gauge, Coulomb,
Lorentz, etc. ), those of symmetry and their possible violations
          
approximation, usually quite simple, straightforward. And
the effective methodology for determining or verifying such
a causal relationship has long been well established: it is the
     
       
       
portion of physical reality, allows us to determine whether

only one used to date on the experimental front and is the

This simplicity with which causal relationships can be
      
is basically due to the fact that in such “ordinary” material
systems only action-reaction laws that are either perfectly
deterministic (at meso and macroscopic scales) or that
are deterministic, but (at very small scales) also subjected
       
In any case, the transition of an electron from one state to
another, for example, although described by a quantum
probability function, is in essence a process governed by, and
describable through, precise action-reaction laws that, on
large numbers or long timescales, converge to the classical,
bluntly mechanistic ones.


relationship between a given input and a (predeterminable)
output, as there are in force not only action-reaction
relationships, but also stimulus-response 


of the process (since a cat, in addition to changing its state of
motion as a result of the transfer of energy and momentum,
          

activated in the cat as a response to the “experience” it has
undergone).
   
why 
material systems, such as living beings are anyway – inasmuch
as they are still made up of the same quanta of matter and
energy as inanimate matter – no longer describable by
deterministic laws (despite the fact that they must always
be subjected to such laws anyway)? To that question, one
could also associate this one: what is the difference between
          
semiconductor diode and “experiencing” light (by a cell, or
a seeing eye)?
These questions, as is easy to guess, all converge to a
fundamental question. If we have already understood that,
for example, the biochemistry found within biological matter
is the outcome      
non-ordinary physical states) that connote it (a fact well
evidenced by the near impossibility of reproducing such
biochemistry in vitro       
difference between the physical states underlying a living
system and those proper to an inanimate system: what is the
    
non-living (between a living cat and a just-dead cat1)?
Perhaps by deepening insight on this point, it becomes
possible to answer in a well-founded way the initial question
regarding why in living systems a description by action-
reaction laws only is not possible and why it is not so obvious
causal relationships between inputs and outputs in
general.
Complexion and false autonomy of the
“parts”
Living systems are highly ordered systems, whose
structural states and developments do not occur according
to random succession, but neither do they occur according

crystals” endowed, that is, with order without repetition
     
      
and the level of ordering is pushed to the limits of possibility,
simultaneously involving spatiotemporal scales ranging from
electron transfers, protein folding rates, cellular respiration
cycles, membrane pulsations, to endocrine and circadian
rhythms, and beyond to the life cycle of the considered living
being. Yet despite this very high degree of ordering, even
       
1 Keeping in mind that the absence of “functioning,” which made
the cat “alive”, cannot be traced, in the just dead cat, to a change in chemical
composition, since it is still absent. Clearly, there is the cessation of certain
conditions (states) underlying the “concertation” of material and energetic
components in the living state, which, as we shall see, are necessarily struc-
tural conditions as well (otherwise they would be just an abstract idea).
Physical Science & Biophysics Journal
4
Renati P. Relationships and Causation in Living Matter: Reframing Some Methods in Life Sciences?.
Phys Sci & Biophys J 2022, 6(2): 000217.
Copyright© Renati P.
describable a priori by any set of states: placing, for example,
     
we cannot tell what it will do at each instant.
Precisely because there is such a high degree of ordering,
the argument that would impute the impossibility of
adopting apodictic descriptions to the wide range of states
that can be occupied according to statistical and probabilistic
criteria (as in the case of the million spheres mentioned
above), would be immediately refuted by the fact that, if this
         
in biological matter would be impossible. Indeed, just the
multitude of events (chemical and physical) per unit of
time that are carried out by even a single cell, if they were


system such as a human being, such randomness would
imply that if certain molecules were encountered, someone
  
        
and if even others were doing so, a “cancerous” cell would
be created. And it is here that the problem arises of what
we can really and logically consider to be the “cause” of
biological phenomenology (such as physiology) and “where”

of what we usually call “disease” and for a more consistent
understanding of the related aetiology (we discuss this in
Section 6).
Of course, on the question of why in living systems a
deterministic description conducted through action-reaction
type laws no longer applies, many try to trace the answer
(not completely wrong) to the dynamics of complexity
and emergent properties     
successive levels of organization, typically consisting of a
        
living being), not only expresses an evolution of its phase
space that is impossible to predetermine even under the
same initial conditions (either because of computational
      
develops new descriptive categories, physical quantities
and observables that are absent at the level of individual
components (such as, for example, the index of refraction or
the density of a diamond are quantities that are meaningless
and not attributable to the level of individual carbon atoms).
Such a perspective is already a good step forward,
        
the logical openness of a process, that is, the amplitude of
        
  

      
randomness and surprising “appropriateness” (sense)
found in biological functioning (evident, for example, in all
phenomena of adaptation), and it still leaves unresolved
the physical (and, we might say, ontological) question
concerning the true reasons for a self-updating ordering
    
appear (such as memory, evolution, behaviour, perception,
sensing, semantics, etc.) which:
a) in that approach are totally irreducible to a purely
bottom-up description, that is, starting from the
microscopic level of components and then producing the
system as a whole.
b) and imply a type of synchronic causality, in which the

      
      
     
from the outside (an option I would avoid, as it would only
move the problem one step further, implying, moreover an
untenable ontological dualism in which reality is no longer
one 
qualitatively, a physical principle, a framing of the question,
which is capable of reducing the unfolding dynamics of the
living system to  without, however, collapsing
its intrinsically holistic, relational and semantic nature.
    
characterise the living phase of matter, and which motivate
e fundamento why a living being is never “per se, and before
exploring what these states imply from a methodological
point of view, it is useful to recall what it means to be capable
of a properly and factually complex vision.
    
physics essay Growth and Form, reminded us that «when we
analyse a thing in separate parts, we tend to give them undue
importance, exaggerating their apparent independence,
hiding (at least for the moment) the essential integrity of the

the arbitrary “parts” within the ontological relations they
have with each other and with the context is to describe
“things” without the relations and to omit the intrinsic
complexity given by the ontological primacy of the relations
         
       
momentary reduction unfortunately becomes permanent.
       
ubiquitous and the price we are paying is very high: besides
the reductionist and de-personalised approach to the
        
living (human) being to its clinical parameters, there is in
Physical Science & Biophysics Journal
5
Renati P. Relationships and Causation in Living Matter: Reframing Some Methods in Life Sciences?.
Phys Sci & Biophys J 2022, 6(2): 000217.
Copyright© Renati P.

of data from studying at the microscopic level (with very
expensive experimental setups) details such as replacement
of functional groups on proteins, methylation of genome
       
        
granted that they are the reason (the why) of what a living
system expresses, when in fact they are, at a different scale
of observation, only the way (the how) by which the living
being itself conducts its vital logos, its physiology and its
    
This applies as much to an amoeba as to a mammal or an
olive tree plantation.
From the criticism just made, which we will
  causes
in the microscopic scale of what is observed in physiology,
for example, is an error of method and a conceptual
misunderstanding. Investigation in the microscopic, capable
of characterising the species and reactions involved, is
undoubtedly very useful for becoming aware of the detail of
the process and understanding its modalities (and in some

a potentially dangerous pathway), but it tells us very little
about the why, and why precisely that type of observed
physiology occurs. More importantly, such an approach a
priori prevents one from viewing that process with an open-
mindedness and a questioning necessary to leave a cognitive
space to understand the biological sense of that event (of that
response).
It is obvious that, in order to legitimise such stances,
          
being is a process of coupling to the environment in which
      
homeostasis of the living being itself, which acts as a hòlos.
As we shall see in a moment, the emergence of a biological
self 
of a perceptive process

        
resolving microscopic events, forgetting that living matter
is a semantic process       
 as studying bridges resting on lands or slopes
     
it is impossible to grasp their role and meaning. And so, for
example, the simple shape of the bones in an animal, their
mutual connection, the architecture and distribution of
apatite structures in the various zones of the bone, cannot be
understood as if those bones were pieces of a puzzle created
  
organism) were alive and those bones were stimulated.
       
aspects and “parts”: “we can study them separately, but that
          
         
sense that they are parts of a whole that when it loses its

The culture of complexity has always (since around the

begins as provisory and then - due to cognitive necessity and
    
object, losing a cognitive gesture, a complexion (in the words
      
upon before any reduction, not out of ideology, but out of

Symmetry Breakings
         
without which we can create the cognitive space necessary
for a critical attitude towards the methodological problem in


hand, the picture cannot be completed if on the physics side,
we are not provided with the basics, the laws at play, to reduce
the typical features of the living realm and to understand how
they emerge from the interactions between the fundamental
components of condensed matter (atoms, ions, molecules,
electrical charges, and various types of excitation).
Over the last 50 years, physics, in support of the
important branch of theoretical biology (nowadays,
compared to the greater ferment at the beginning of the
last century, too neglected in favour of an experimental
and molecular approach2) is allowing us to delve more and
more into the questions of how condensed matter is able
to produce itself in its living phase   
discussion will not be reported here, so we refer readers to
   
aspects concerning the physical basis of living matter, which
are useful in developing the theme we wish to focus on
(which in a nutshell is: understanding why we cannot apply
a general empirical method to the investigation of causes in
biological matter).
      
theoretical foundations laid by outstanding scholars in
      
      
2 That does not consider how much the experimentum, from the
-
pretation of its results, is a direct consequence of the Weltanschauung of the
one who is studying and what factors and observables it contemplates as

Physical Science & Biophysics Journal
6
Renati P. Relationships and Causation in Living Matter: Reframing Some Methods in Life Sciences?.
Phys Sci & Biophys J 2022, 6(2): 000217.
Copyright© Renati P.
fractal (scale free) systems and squeezed coherent quantum
 and the dissipativity and thermodynamics of
        
ordering of a biological system (obviously not stochastic, but
also not predeterminable starting from fundamental laws),
is a condition that dynamically emerges as a consequence of


      
  

      
of the elementary components. In quantum physics, the
        

the correlation and ordering between the quanta of matter
and the sharing of their quantum state between them.
The quanta associated with such dynamics (i.e.
     
       
and, in QFT, the dynamics that governs the behaviour of the
elementary components of a physical system in such a way as
to generate the formation of ordered structures has general
characteristics because, order is the absence of symmetry
        
also called the NG theorem, has been validated by robust
experimental evidence in both high-energy physics and

crystals, magnons in ferromagnets, polarons in ferroelectrics,
etc. ... are quanta of NG and are responsible for the space-time

correlations that produce the observed order, depending
on the case (geometric, magnetic, rotational, electric, etc.).

or where non-trivial forms of order emerge, as in biological
systems, the condensation of NG bosons relative to the

the emergence of order parameters.
The NG quanta are bosons (i.e. many of them can occupy
the same physical state), under ideal conditions (i.e. in the
       
low-momentum state they do not contribute to the energy
of the fundamental (vacuum) state: the emergence of order
is therefore the manifestation of the condensation of NG
bosons in the vacuum (ground) state.


occurs between the components of the system), let us start
with a simple example: the creation of a crystal lattice from
the cooling of a liquid or vapour.
In a liquid or a gas, the atoms (or molecules) experience
a condition such that their positions can be translated in
space without implying a change of the macro-state, i.e.

equivalent to others, which therefore has an identical free
energy (and entropic content): in practice, a gas or a liquid
are symmetrical systems on the degrees of freedom of
spatial translations. When the system is, for example, cooled
       
or, in general, the condensation temperature), this spatial
       
       
(i.e.: integer multiples of the lattice step). This condition,
 
range forces, as is often approximated in the generally

the establishment of long-range correlations in the form of
stationary elastic waves (in the case, the phonons) emerging
from the intrinsic oscillation that the components already
 
having passed a density threshold, they set in phase because
they are able to reach a level of minimum energy (vacuum)
lower than the one they had when isolated (in the vapour) or
less correlated (in the liquid).
For this reason, if the system is open and can dissipate
an amount of energy in the form of entropy (i.e. the latent
heat of condensation), a phase transition from a disordered,
disordered state to a more ordered one occurs spontaneously

In this new state, whose vacuum level is lower than the
previous one by a quantity called the energy gap (which, in
electron volts, expresses its thermodynamic stability, i.e. how
much energy has to be expended to send each component

as it is no longer possible to move along any direction of the
system while encountering the same potential landscapes:
moving along one crystalline direction, for example, is not
equivalent to moving along another arbitrarily chosen one

          
(ii) is the consequence of quantum dynamics in which the
       

  
           (the
order parameter
and gives rise to the macroscopic (classical) stability of large
quantum systems of matter (such as a piece of diamond)
      
thus appears as the dynamic effect of spatial translational
       
Physical Science & Biophysics Journal
7
Renati P. Relationships and Causation in Living Matter: Reframing Some Methods in Life Sciences?.
Phys Sci & Biophys J 2022, 6(2): 000217.
Copyright© Renati P.

The quanta of NG enter fully the list of elementary
components of the system, i.e. the mediators of correlation
are structural elements! They are an integral part of the
structure, true elementary components, which can be
measured by scattering techniques and of which a spectrum


can be done, for example, by extracting an atom or group of
atoms from their lattice sites in a crystal. For example, there
are no freely propagating phonons outside a crystal, since
they exist only as long as, if and only if, the crystal exists.

up the crystal prior to melting remain, but not the phonons.
The latter are the collective way of being of the atoms in the

with the function        
responsible, and thus they also express the functionality, the

       
properties (functionality and thus structure) (in which there

Since the NG bosons, as already noted, determine the
phase correlation over large distances of the elementary
components, a change in the degree of condensation is
equivalent to a change in the intensity of the correlation over
long distances. It is this correlation that is called coherence
and the condensed state is called a coherent state (over a
     
state referred to is thus the (thermodynamic) stability of the

As we can see, what the QFT approach dissolves is
precisely the Cartesian dualism (of previous Platonic and
then Aristotelian inheritance) between structure and
function        
declinations (e.g.: form-substance, information-matter,
software-hardware, psyche-soma, soul-body, mind-brain,

The formalism of QFT produces a  because
it describes a multiplicity of non-trivial phenomena through
the dynamic relationship between the microscopic and
macroscopic (mesoscopic) levels, without the need for
ad hoc added operations: it is precisely the coherence of
      
transition of scale (from the micro to the macro) possible.
The order parameter
  
behaviour is not “superimposed” but rooted in the quantum
description of the microscopic components. Systems in
which some sort of ordering is observed are therefore called
macroscopic quantum systems     
composed of elementary quantum components (atoms and

because their macroscopic properties are incomprehensible
except in terms of the underlying quantum dynamics of the
elementary components.
As can be understood from what has been discussed
   
disciplines often declined as the “matter-information”
duality) is only possible within a theoretical frame of
reference that admits the existence of a multiplicity of void
levels, such as QFT, so that phase transitions and symmetry

is not practicable in any classical or semi-classical theoretical
       
 
a set of molecules, or atoms, or electric charges, interacting
by means of forces, admits a unique ground state (a single
vacuum level and, hence, a phase) and phase transitions are

Dissipation
The condensation of bosons to form the coherent state
clearly expresses that the biological system, being a (super)
coherent system, as we shall see in the next session, is
       
therefore an intrinsically open system. Isolating it implies
the elimination of its functionality, its destruction (its death).

accessible today (suitable for isolated or closed systems)
requires that in the study of an open system, let us say the
α
     
environment in which it is immersed, so as to constantly have
 
the
α
system and the environment. We can refer to the latter
as ‘system
β
      
leaving
α
,
()E
α
, must be equal to that entering
β
,
()E
β
, and vice versa. It must hold in each case that
() ()EE
αβ
 
( )
,
αβ
of systems
α
and
β
thus behaves as a
  
into or out of the system.
         
balance of any other quantity exchanged between
α
and
β
), the
β

α
system, in the

α
 
are concerned, provided that the direction is reversed: in
fact, what is an input for
α
, is an output for
β
, and vice

exchanging
α
for
β
, or vice versa.
Physical Science & Biophysics Journal
8
Renati P. Relationships and Causation in Living Matter: Reframing Some Methods in Life Sciences?.
Phys Sci & Biophys J 2022, 6(2): 000217.
Copyright© Renati P.

     
β
  
α
for which the direction of time
has been reversed (
β
is the reversed time copy - time mirror
image - of
α
). In summary,
β
is the system that describes
the environment in terms of the equilibrium of the energy

α
and is also the mirror image of
α

the time axis: Vitiello expressed this effectively by saying that
β
is the double of
α

Thus, in the case of open systems (such as living
organisms, for example), we must consider their doubles,

First of all, given that
α
denotes the living system
considered (organism, cell, brain, ecosystem, etc.) and
β
its thermodynamic double, the energy balance
() ()EE
αβ

() ()NN
αβ

()E
α
and
()E
β
denote the energies due to the number of quanta
involved in the exchange.
()N
α
and
()N
β
of
α
and
β
,
respectively, are condensates of quanta in the fundamental
state of (
α
,
β
), i.e.:
()E
α
Ω
()N
α
and
()E
β
Ω
()N
β
, with
Ω the energy of a single quantum. This relationship, which
describes the energy balance between
α
and
β
, is rich
with meanings. For example, it tells us that
()N
α
and
()N
β
can certainly vary, provided, however, that these variations
compensate each other. The fundamental state of the entire
system (
α
,
β
) must be the condensate of an equal number
of quanta referable to the system
α
and (oppositely) to the
system
β
, so that the correspondence
()N
α

()N
β
holds at
any time in the history of the system
α
.
Another consequence of the relation
()N
α
-
()N
β
  
that it does not establish either the value of
()N
α
or that of
()N
β
. It only requires that they be equal. There is therefore

()N
α
, and correspondingly for
()N
β
     
       vacua)
states of (
α
,
β
) indexed by those values of
()N
α
, which
are orthogonal to each other (technically they are said to be
unitarily unequal
of this fact is that, as already mentioned, we are forced to use
 

This is very important for understanding living
matter, since the amazing degrees of order by which it is
characterised implies that symmetry with respect to temporal
(before/after) and spatial (translations and rotations, etc.)
         
        
appear, corresponding symmetries and invariances in space-
         

collection of interacting (albeit sophisticated) components.
    
α
,
β
)

stimuli, whereby:
a) A multiplicity 


b) The coexistence      
space of states is given by the fact that these fundamental
states are orthogonal
c) Their succession in time is given by the dissipative
dynamics, i.e. the thermodynamic history, i.e. all possible
pairs of values of
()N
α
and
()N
β
, satisfying the relation
()N
α
-
()N
β

The succession of states of the living system is actually a
time-dependent (dissipative) thermodynamic history, along
which successive states depend on the previous ones in a
deterministic manner, but a priori unpredictable due to the
dialectic with its thermodynamic double (the environment,
including every possible quality and type of stimulus).
It can already be understood here that the semantic
    
of a stimulus, is in fact always a  (and
not something abstract or superimposed on the energetic/
quantitative term of the stimulus itself). Therefore, when
 
       meaning of events for
          
     
        

         
not an invariant, as well as being a particularly analogical,
qualitative observable, but not unworthy of inclusion in

In the next section, we also see why the thermodynamic
stability of the living coincides with the tension to maintain
homeostasis (i.e. coherence).
Coherence: The Living Phase of Matter
The thermodynamic openness, in addition to the
       
phase and for the inalienable continuous exchange of quanta
of matter and energy, is even better understood by delving
into what the coherence condition really implies.
Living systems, both individual cells and those of
multicellular organisms, are generally made, by molar
Physical Science & Biophysics Journal
9
Renati P. Relationships and Causation in Living Matter: Reframing Some Methods in Life Sciences?.
Phys Sci & Biophys J 2022, 6(2): 000217.
Copyright© Renati P.
fraction (not by weight!), of a percentage of water close to
      
      
     
      

understanding the role of water (far from being a mere

the vaguest idea of how and why living matter produces the

      

water is a biphasic system.
In particular, within the description of Quantum Electro-
dynamics (QED) conducted without the approximations
        
to demonstrate from   that many of the
anomalies typical of this element (such as trends in density,

       

         
of molecules in the system (whose abundance is inversely

coherent oscillations.
Such coherent oscillations exist within regions roughly as
large as the wavelength of the electromagnetic mode coupled
to the aforementioned oscillation between two electronic
levels and whose energy size is equal to the spectral distance
between the two levels on which the electron of each water
       
are called coherence domains (CD) and, for liquid water,
coherence being established between sp3 and 5d levels, their
size is nominally about 100 nm. In reality, at temperatures
other than zero Kelvin, this size is reduced due to thermal
noise, which sends a fraction of molecules out of tune (which
         

As mentioned above, the new fundamental (vacuum)
state of the coherent phase has a lower energy than that of
the incoherent molecules by an amount called the energy gap,
which expresses the thermodynamic stability of the coherent
state with respect to de-cohering agents from outside (such
       
forces). If the excitations are small enough (smaller than
the energy gap), the CD receives them acting as a whole,
if they are larger, one or more oscillators are put out of

       
established on the oscillation of the electron cloud per each
molecule (in practice 1 electron per molecule ) - this energy
gap is of the order of 0.2 eV, depending on temperature and
position within the CD (it is smaller in the periphery than in

The molecules belonging to the coherent fraction
          

(
ϕ
), which is the quantum observable complementary to the
 N): the uncertainty (
) relationships
expressed in natural units (where
/2 1
B
h ck
π
= = =
, where ‘h    c     
in vacuum, ‘kB       
½
N
ϕ
−∆

In a perfectly coherent state, the number of oscillators
becomes completely uncertain, while the phase, the wave-
      
         
the individuality (and countability) of the oscillators loses


     
as a quasiparticle   

This is equivalent to having a minimisation of the
uncertainty of the phase (
ϕ
) and thus a maximization
of the uncertainty of the number of quanta (
N
). For this
to happen, the system tends to have a large number (N) of
quanta because
NN∆≤
, and to have a continuous cross-
over, an exchange, of the same between the coherent phase
and the external environment. Since the coherent state is
thermodynamically more stable, as it has a lower vacuum
level than the disordered state, coherent systems have a
tendency to share their oscillations with other systems with
which they are able to resonate (so as to increase N) and are
open systems in which ΔN is further increased by continuous
exchange with the environment. This is a fundamental
characteristic for understanding how a living system, de

quanta of matter and energy, i.e.: it exists as an exchange, as
a coupled process, as a relationship, as a resonator that shares
its oscillation phase with everything that can.
Therefore, as phase correlations are non-local
correlations, which do not imply the exchange of any
     
       
the coherent essence of living systems has suggested a more
       
within which living systems share the oscillation phase on
      
cover very large spatial ranges (even of the order of
Physical Science & Biophysics Journal
10
Renati P. Relationships and Causation in Living Matter: Reframing Some Methods in Life Sciences?.
Phys Sci & Biophys J 2022, 6(2): 000217.
Copyright© Renati P.

Within biological matter, due to interplay with other
molecular and ionic species, as well as the ubiquitous presence
of interfaces and niches that further stabilise coherent water
      
at room temperature and pressure, this fraction would be
         
and all interrelated with one another so that the system is

biological matter, although consisting of 90% or more water,

The size of the various types of coherent domains that
can be established (on different degrees of freedom, such as
oscillations of the electron cloud on different possible excited
      

s never smaller than the maximum distance between any

Thus, the entire water matrix in living matter experiences
multimodal coherence, termed supercoherence, which allows
      
system (be it a single cell or a multi-cellular organism, but to

        
molecular biology - capable of identifying the ‘building
   
   
      

biochemical activity also allows living matter to express
one of its most sophisticated characteristics, impossible to
simulate in vitro, which is the capacity to perform cycles
of chemical reactions      
reagents perfectly selected out of a variety of others, co-
present in the cellular landscape and capable of reaching a

of the Krebs or Calvin cycles, for example). How can this be
explained...?
Trying to summarise this very articulate aspect (for more
       
     
species, i.e. an oscillator characterised by its own precise
frequencies (modes). Given that the coherence established
on a given mode is a dynamics in which only oscillators
capable of resonating on that mode (i.e., oscillating at that
frequency) can participate, it is clear that the chemical
species participating in the construction of biological matter
are those that possess proper modes of oscillation (we could
say spectral lines, over the entire electromagnetic range)
shared with those of the super-coherent aqueous matrix and
with at least some of the other molecular species present
different from H2O.
Where there is a coherent phase, there are regions within

as a director and coordinator of the molecular encounters.
More precisely, where there is a gradient
( )
( )
2
A
of the
  A, such as that self-trapped within a
CD of water molecules and decaying exponentially outwards,
having frequency at a given instant ωCD, the following
dynamical laws apply for the molecular or ionic species

( )
2
2
rep
Q
M
=−∇FA
(1)
( )
( ) ( )
22
2
2
22 2
CD i
i CD
CD i
C
ωω
ωω
=
FA
(2)
( )
( ) ( ) ( )
22
12 2
12 22
22 22 2
12
int
CD CD
C
ωω
ωω ωω
=



FA
(3)
        
describes the ponderomotive force term, always repulsive,
with intensity proportional to the quantity q2/m (where
q is the electric charge and m 
second equation expresses the selective attraction/repulsion
force in relation to the difference in the “eigenfrequencies”
          
i-th species, ωi      
the same selective interaction on a resonant basis in the
presence of two chemical species (1 and 2, and respective
eigenfrequencies ω1 and ω2 C is a constant and
Γ
a

These algebraic relationships describe the reason why


charges arriving on the periphery of a CD is strongly polarised
by decentralising the lighter charges (typically electrons)
much more outwardly than the heavy charges (nuclei): this
polarisation leads the molecules to a strong instability that
  
        
other two equations express how only certain species arrive
at the CD surface not randomly: at a given instant, only
molecules with the appropriate proper (resonant) frequency
can be brought to encounter one another (typically at the CD

Once the reactant species have been convened and
activated, it is the water CD that catalyses the biochemical
reaction (typically an oxidation-reduction reaction) by
Physical Science & Biophysics Journal
11
Renati P. Relationships and Causation in Living Matter: Reframing Some Methods in Life Sciences?.
Phys Sci & Biophys J 2022, 6(2): 000217.
Copyright© Renati P.
releasing electrons (which in the coherent phase occupy
states very close to the ionisation threshold and are therefore
 
     
implies, however, a change in the state of the CD, with a

capable of attracting other reagent species and thus enabling
a second reaction step. And so on.
       
paths (decided by the succession of modes of oscillation of
the coherent fraction) are deterministic and not random at
all, but not predeterminable, since they are governed (i) by
the entire thermodynamic history that preceded a certain
       
          
conditions regarding various factors (reagents and their
    
     

given input will be transduced into output.
The supercoherence of living matter consists in the
establishment of further levels of coherence due to the
dialectics of coherent water with other molecular species,
which act as recipients of quanta of free energy released by
CDs (in the form of electrons or photons or rotary excitations
       
are not allowed to relax thermally (otherwise it would
mean that they would lose coherence and that would cost
      
other biomolecules then act as multimodal lasing devices,
extending coherence to the next step, from which others and
further ones stem, in a retroactive and dialectical genesis

Supercoherence is a crucial condition regarding the
     
stimulus, if small enough not to destroy coherence in its
entirety, is received by the unicum of the coherent whole, not
by individual, numerable portions of it. This aspect expresses
what is physically meant by the emergence of a self within
which a single molecular event affects the entire organism
as it is concerted by the entire supercoherence (since each
species of oscillator shares, on at least one degree of freedom,
the eigenstate of the phase with others that, in turn, share
it on still other degrees, etc., so that it ultimately results in
      

A nutrient detected (sensed) by an amoeba, for example,
implies that the possible interaction between receptor and
          
because that receptor is part of a choir of oscillators that
      
is the state change of the whole). This is why the single
event of the interaction between nutrient and membrane
          

       
        
     
     

The Emergence of Perception, Memory,
Adaptation, Meanings and Biological Laws
          
elementarily coherent system, such as a CD of liquid water,
could be said to be already a system capable of producing
“responses to stimuli” and not just “reactions to actions.
This could apply because, acting as a unicum that depends
on the antecedent thermodynamic history and that has at
      
coherent) at essentially the same energy, it can produce – as

state) – a variety of states in output.

of “responses” and “perception” (features typical of the living
state only). The distinction - now we explain it better - lies in
the term of supercoherence, which implies total correlation
over all living matter in the organism. It should be made clear
that such a high degree of ordering, by no means implies
rigidity and stereotyping of responses, since the hierarchy
         
phase-locking of all oscillators, but rather implies a complete
interrelation of each level of organization, though permitting
its organizational closure.
This is possible because of the tunability of the

proper to the various hierarchical levels of biological matter
      
        
allows the management of free energy transfers from one
coherent scale to another on demand (i.e., by modulating the
eigenfrequencies so that they enter a condition of resonance,
    
when their ratios equate irrational values, e.g., the golden
mean      
extended over the whole system, even to the point of allowing
the emergence of the self in which the whole is the new
“character,” compressive to the possibility of having various
       
metaphor of the jazz band in which the common phase (i.e.:
   a tempo) does not imply their having
Physical Science & Biophysics Journal
12
Renati P. Relationships and Causation in Living Matter: Reframing Some Methods in Life Sciences?.
Phys Sci & Biophys J 2022, 6(2): 000217.
Copyright© Renati P.
to play the same notes and at the same moments, but also
allows (and indeed encourages) improvisation (generated
moment by moment by what happens as they go along in the

matter as a jazz quantum in which there is no “conductor,”
but an autopoiesis of the music from the music itself played

A simple CD cannot already be said to be a living thing,
therefore, because where coherence is in force over a small
number of degrees of freedom (such as, for example, within
an ordinary volume of water, over the oscillation of the
electronic cloud of the molecule, over dipole spins, over the

    
number of thermodynamically equipollent microstates, so
the system is allowed to still be “itself” (macrostate) although
     

This residual multiplicity of energetically equivalent
microstates, obviously, corresponds to a residual entropy
quota and is incompatible with the need to produce the
        
       
a homogeneous system, certainly cannot accommodate a
manifold of “equipollent” microstates (as would be the case
in a volume of ordinary matter, albeit in a condensed phase)
without its integrity and functioning being compromised,
since any slightest change conducted on an entropic basis
      
(electronic, molecular, and supramolecular) in which, a
substitution of a functional group or a change of chirality
        

Moreover, an entropic residual would not even be
compatible with the proven emergence of a self, according

other, as sharing more or less directly phase correlations,
within the hierarchy of nested coherences.

is present on one degree of freedom only, the components
are still entropic on other degrees and thus the system still
has a multiplicity of equivalent states, i.e., it still possesses
      
responses or with a criterion that aims at maintaining/
maximizing the coherence already present (homeostasis/
homeoresis), as is typical for a living system.
This last property, which – because of the existence of
      
– corresponds to the spontaneous tendence to minimize
the energy of the vacuum level (since thermodynamically
pursued by the biological system, as it is an open system),
is possible only when the internal entropy is close to zero,
a condition in which (ideally) a single microstate yields
a unitary corresponding macrostate. Approximation to
the entropic “zero” is possible due to the existence of the
      
cycles, within which any entropic fraction possibly produced
is expendable as free energy in subsequent levels, with
longer characteristic times
To state it again, such a tendency to zero entropy is the
condition that allows, in the dissipative relationship with
the environment, the spontaneous tendency to minimize
the vacuum energy while being able to comply with the
constraint of assuming successive macrostates that are also

and unique microstates are subtended, updated at each step
of the thermodynamic history.
This idea would explain the physical basis of the
ubiquitous and fruitful dynamics of adaptation, in which the
physiological response is exactly what is needed to perform
the coping with stimuli of whatever nature. Namely, one
could thus explain why at every stimulus/situation (either
cohering or decohering) the “turned on” state in the living
 
ones) that already produces processes and arrangements
suitable to implement or maintain its own coherence (i.e.,
thermodynamic stability, i.e., homeostasis) by restoring
it right on the very front where it was compromised. Thus
        
a stimulus involving a structural injury, a physiology is
activated that involves biochemical and electrodynamic

to a hindered biological function (felt) necessary to be
performed, such as the digestion of a “nutritive morsel,” a
physiology corresponding to the enhancement of that faculty

In practice, every input in the living implies the
   
pertains, precisely for thermodynamic and quantum-
electrodynamic reasons, in the sense that this response
is aimed at maintaining or restoring homeostasis
(supercoherence). This is the step that, from physical laws,
  
within which the stimulus is endowed with a “meaning,” not
invariant, which depends on the unique and unrepeatable
  

see in the next section).
Physical Science & Biophysics Journal
13
Renati P. Relationships and Causation in Living Matter: Reframing Some Methods in Life Sciences?.
Phys Sci & Biophys J 2022, 6(2): 000217.
Copyright© Renati P.
Teleology (the fact that there are for the living being
       
        
     
favourable states (and coincident with the minimization of
entropy and energy of the fundamental level). Obviously,
however, unless this idea is relegated to the level of an
      
to be physically substantiated and supported. In reference
to this, it is important to remember that, in a quantum
fashion, a coherent system is able to collectively explore (via

space of potential coherent states (phase eigenstates) and
      

Reinforcing this, in a series of fundamental articles,
theoretical physicist Ke-Hsueh Li has shown that the concept
of coherence is actually rooted in the Heisenberg uncertainty
principle and that the space-time within which coherence
holds is actually equivalent to the space-time within which
   
insight, regarding the fact that the uncertainty relation is
just an alternative approach to describing the coherence
         
       
length, of the order of the spatial size (the wavelength) and
the period of oscillation of the coherent mode in force, are
respectively that duration and spatial range within which
      
          
     

As we have already pointed out, within the coherent sate,
properties cannot be attributed to any countable “particle,
         
measurement) phase information is completely lost. Within
the coherence volume, since phase correlations are in force,
it is as if all phenomena occur “at the same time” and are in
       


If coherence is organized on increasing levels of spatial
and temporal extension, as it is the case with living matter,
this synchronic “suspension” and temporal verticality within
which (within a certain interval) past, present and future
coincide can be extended. This aspect would be a crucial
factor in the emergence of biological self, a condition from
which the experience of identity and continuity of experience
emerges, on the threshold between memory of the before
and tension toward the after.
      
the spectroscopy front: the modelling of the imaginary part
of the dielectric function of liquid water in the THz range,
in order to match the experimental data, in addition to the
partitioning over two fractions of the liquid system (the
normal and the coherent one, in proportions dictated by
temperature), also required the insertion of a linear term
that implied the violation of the Kramers-Kronig relations
within a time span of the order of magnitude precisely of the
duration of the oscillation period of the coherent domains of

         
probe beam and the dipole reaction of the water molecules
of the coherent fraction needs a term expressing a non-local
relationship of instantaneousness and “time suspension.
This, in addition to being consistent with the fact that
coherence leans precisely on phase (non-local) correlations,
further substantiates that, within the space-time scales
typical of a given coherence domain, there is a suspension of
diachronic causality and the system is found to experience as
“present” and “contemporaneous” states of the recent past
and recent future.
Clearly for a water CD, whose spatial range is of the
order of 100 nm maximum and whose period of oscillation
       
       

in each other up to oscillations that have wavelengths as large
as fractions of a meter and having periods on the order of the

exploration of states on the time axis becomes considerable.
        
exploration of a plethora of thermodynamically favourable
    
perhaps, this could also be the explanation for the well-
measured “anticipatory response” phenomena conducted by
neuroscience researchers who reported how human subjects
exposed to images with content that was emotionally

       
        
viewing the target pictures.
Finally, it is important to emphasize how entropy
minimization is also performed through another
crucial attribute of biological matter: heterogeneity
        
components, niches, interfaces, folds, vesicles, and (just
        
impossibility of treating living matter as a homogeneous
        
Physical Science & Biophysics Journal
14
Renati P. Relationships and Causation in Living Matter: Reframing Some Methods in Life Sciences?.
Phys Sci & Biophys J 2022, 6(2): 000217.
Copyright© Renati P.
ordinary condensed matter), in addition to seeing necessary
       
       
two central aspects that we stress again:
• the minimization of entropy possibly produced at an (n)-

at the (n+1)-th dimensionally larger one (see here for

• the tension toward a principle of ideal “univocal
correspondence” between each microstate and
       
characterized by the super-differentiated and precise
     
molecules, structures (1D, 2D, 3D), and their dynamics.
Replacing an atom in a diamond crystal with its neighbour
changes nothing, but in a living system, replacing a molecule
         
place now rather than later disrupts the entire biochemical
syntax.
All this gives us a way to physically root the variable of
meaning in relation to a history  

of providing the emergence of a biological self, the etiological
and reasonable basis for understanding every living being as
a   , memory and purposes, as a perceptive
process       
their maximisation up to the point that no molecular event in

Major Implications
I am well aware that what has been examined so far,
perhaps in a forced synthesis (but purposely so as to allow as
much cross-sectional framing as possible of various aspects,
all of which are salient), has very profound implications and
       
and practices currently in vogue in the life sciences (from
philosophy to physics, biology, medicine, and neurosciences).
If the physical condition underpinning the living state
is necessarily (super)coherence, a fact that cannot be
denied (since, if it were not so, the prerequisites for the
most characteristic and evident phenomenologies of living
       
perspective concern the following topics:
a) the idea of “cause” attributed to factors that are external/
         

b) the method of investigation conducted at the level of
genetics, biochemistry, cytology, and histology
c) the role of the genome
d) the epigenetic dynamics
e) the concept of “disease” and its aetiology
f) the germ theory
g) abiogenesis and pleomorphism
h) the theory of evolution of the species
i) the psyche-soma dualism and the stress-physiology
relationship
j) therapy
 relationships in the “nature-human-technology” triad
    
because each of them constitutes a very extensive topic
that would require dedicated development space (partly

We have seen that the living organism is a responsive
system since it is endowed with order in space and time,
therefore the outputs produced as a consequence of stimuli
can be of three types: i) a response (when the stimulus has
        
(when the stimulus involves partial decoherence of the
system, such as mechanical, electromagnetic, thermal,
        
due to the stimulus, ceases to be in a living phase (total
         
important to understand, for the reasons we have examined,
that the response is always a process acted out by the living
being         
that it has an adaptive sense (of maintenance, restoration of
homeostasis) whose causes cannot be traced in microscopic
investigation, because this method will only deliver us how
this process is performed and not its why. A beating on the
head is not really the cause of the bump: it is the cause of
         
 
level). Or, similarly, the scar following a burn is not really
         
          
responding to that damage with biological intelligence. The
      

acted upon solely and exclusively by the supercoherence in
the living (and which is totally absent in a dead body).
       
         
         
my motor cortex and the action potentials that reach the
motor neurons of the muscles in my arms and hands (with
membrane depolarisation, release of Ca ions, etc.) and
       
The why, the cause, is a whole other story.
Physical Science & Biophysics Journal
15
Renati P. Relationships and Causation in Living Matter: Reframing Some Methods in Life Sciences?.
Phys Sci & Biophys J 2022, 6(2): 000217.
Copyright© Renati P.

because, just as coughing is welcomed and understood as
       
         
understood to be equally intelligent to cope with an extra-
       
underlying tissues over time (and we could give hundreds of
examples), it must be admitted that there is no threshold, no
line drawn, beyond which the processes, the responses, acted
by the soma cease to be intelligent and become senseless.
This is logically incompatible with the intrinsically coherent,
hence organised, connotation of the living state.
It is one thing to say that there is a threshold beyond
which (adaptive) responses may involve violent, or even
 
be managed, it is quite another to imply that the symptomatic
          
correct something that is an expression of disorder.

“cause” of a process in biological matter, especially when it is



       
not give us why I am writing, but only how 
for the causes of non-ordinary physiology (as, for example,
in a neoplastic process) in the genes will only give us (albeit
useful) information on how that process occurs, and how to
describe it on a microscopic scale. In order to understand
         

outlined here (the result of the descriptive tools provided
       
coherence): that is, a system of semantic relationships
coupled to its environment.
This means that what dictates the type of process in living
biological
meaning that such a process has as an adaptive response
       
implies a precise type of decoherence, of impairment to that

substance, damages a tissue or suspends its physiology, the
organism responds with a series of processes that necessarily
have an order, therefore a biological meaning, as in the case

      
completely with respect to the physiology developed as
a result: as long as there is a response, it means that there
      
rather we should understand that manifestation as a tissue

   
from a material point of view, but is real from a semantic point
of view, i.e. about how the living being perceives its biological
condition in a given context (for the human being also abstract
and symbolic). Through the overview we have presented so
far, much of what has been documented by the important
       
       
      
     
relationship between stress and physiology has a precise
    
“stress” in a general sense, but one must always consider the

of the living being is called upon to adapt, according to the
       
   
        
       
because their profound usefulness for medical practice is not
understood. It is a matter of realising that the perspective we
tout court of


Concomitant to the one just illustrated, the other
aetiological front concerns the fact that - coherent states
being the fruit of the succession of those that have previously
occurred - the coherence of a living being holds within itself
all the adaptive memory developed along the course of the

the physiologically expressed response (including neoplasia)
is caused by the existence of a meaning for the living being of
its experienced biological condition (with semantic quality,
as well as a merely chemical and physical one), and by the
existence of a strategy, developed in the course of the global
biological historia and usable at present moment because
      

Coming to the role of genes, a different reading is possible
         
semantic perspective of the living being, genetic mutations

as they are contextual to an ordered system) are understood
          
level, but as the consequence of the need to perform a

non-ordinary activities, such that it must express different


       
Physical Science & Biophysics Journal
16
Renati P. Relationships and Causation in Living Matter: Reframing Some Methods in Life Sciences?.
Phys Sci & Biophys J 2022, 6(2): 000217.
Copyright© Renati P.
     biochemical pathways performed

          
ribonucleic acids (DNA and RNA) within a broader vision,

       
        
the DNA and RNA of my cells were merely a substrate to be

nothing about where to put these proteins, or how to arrange
cells in a tissue, let alone what size and shape organisms
should be. In practice, the dynamics of morphogenesis


water in which they are housed) as physical actors capable of
  
          
their morphogenetic role and understand why alteration or

in the organism.

to what has been expressed above about the role of genes (as

processes), would be to point out the rich possibilities to
engineer the genome, or modify its expressions, to change
the somatic outcome of various species (from bacteria to
ornamental plants and vegetables, up to farm animals and

possibility of modifying the characteristics and connotations
of an organism (such as the molecules that can be synthesized
by a bacterium or the cholera of a rose) would seem to
disprove what I argued earlier.
       
in my opinion, further evidence in support of the fact that
nucleic acids act as coherent electromagnetic (and phononic)
          
not for nothing that researches has been published showing
how, in addition to the process of transcription and protein
       
and other biochemical species occurs by mediating phase
correlations and dipole waves within the coherent aqueous


described in Section 4, are able to manage the arrangement
and molecular encounters in the super coherent water-based


in epigenetics research, if we do not understand that the
expressed or non-expressed genome tracts are chosen on

       
        
the causal role in the onset of tumours or other so-called


in the perception of the environment and the responses felt to
be appropriate in reference to that perception (all biological,

      
contradictions: the example of the “health-generating” role
attributed to foods rich in micronutrients such as folic acid
          
   

        
         
since these substances are said to be methylating agents. In

on a diet rich in fruit and vegetables (folates and vitamins),

provided by such a diet are imputed to prevent the hyper-
methylation of eight genes whose expression is associated

Now - apart from the fact that it is unclear whether
       
pathological expression because they are methylating or
because they prevent methylation - the central question
        
sites in a genome segment rather than others, and what
       
         
cases above, the difference between methylating one trait
of a genome or another would cause an immense difference
(between health and disease) and would imply that eating
       

These discrepancies, perhaps veiled by statistics and
e fundamento

rather than the continuation of methods of investigation that

      
of the living being subscribed to by this line of approaches
would be totally unrealistic and implausible. It is, however,
an encouraging fact, in my view, that even in the epigenetic
  
      
       
from a biological point of view (i.e. the meaning implied by
      
to understand why a certain type of response (genetic/
Physical Science & Biophysics Journal
17
Renati P. Relationships and Causation in Living Matter: Reframing Some Methods in Life Sciences?.
Phys Sci & Biophys J 2022, 6(2): 000217.
Copyright© Renati P.


living lies in the relationship (always also semantic) of the
living with its context and its perceptual and phylogenetic
           
        
oscillating in coupling with its environment) and what has

 

fact applies as much to an amoeba (which, without neurons,
    
from a toxin) as to a cat or a human being. The causes of what
is expressed physiologically lie in the biological (and thus
thermodynamic and electrodynamic) meaning that a «living



entire holo-state (described by the electromagnetic phase
operator) of the living being coupled to its thermodynamic
double (the environment). “Feeling something” means
      
living being when it is in some physical (even non-local
     
       
corresponding physiological/biochemical expression.
Tasting a candy is not an event concerning the mouth only,
      
   
self
precisely because there is a holonomic state function that is
shared in an articulate manner by all the components of the


        
(in its Descartes’ Error 
i.e. a necessarily material process, a very precise somatic

         
method of investigation, the way of doing research, needs to


the process happens, the way it materialises, but not why it
is the way it is. In terms of medical practice, we must revise
the meaning of therapy as a consequence of understanding
the intelligence of the physiological response and its
relationship to the meanings of what the organism perceives.
        
symptomatic one, which addresses to mange the emergency,
         
causal
responses whose biological meaning is now understood
       
interpretative models towards those same circumstances)

This paradigmatically different panorama, undoubtedly
indigestible or even inadmissible for many colleagues,
also suggests the reframing of other nodal themes for the
construction of a Weltanschauung (view of the world) as
close to reality as possible. Among these there is fore sure the
germ theory, of Pasteurian mould, which considers germs as
the “cause” of disease tout court
the terrain theory
up to a primarily cooperative role of the so called “germs”
       

in the case of Helicobacter pylori in the context of gastro-

The interesting aspect within the view that I have
summarised here is that germs - such as fungi, mycobacteria,
bacteria, yeasts, up to viruses (in fact only fragments of
biological material and not at all ascribable to living beings
and indistinguishable from those particles, such as exosomes
and extracellular vesicles, through which cells exchange


      
physical and biological sense for them to be modulated in
their expression and functioning by the choral organisation
of the living, which in some cases sees their involvement in
      
and biologically useful.
    
coherence provided the basis for understanding, without
ontological discontinuities, the transition - through
successive and further levels of coherence articulated on the
aqueous matrix and other molecular and structural partners
(such as interfaces) - from inanimate to living phase of matter,
reopening the plausibility of the a-biogenetic perspective on

The demiurgic role of coherent water, as an agent capable
of supporting and organising biological molecules (from
sugars to amino acids, lipids to proteins and so on) has been
suggested (i) both by the ability to reassemble a nucleotide
sequence from the electromagnetic signals sampled by
      
and (ii) by the detection of organic substances created by the
2 was dissolved
         
structures generated by iterated contact with hydrophilic
surfaces, which led, after freeze-drying, to the isolation of
a solid-phase residue, at room temperature and pressure,
composed almost entirely of hydrogen and oxygen, stable
Physical Science & Biophysics Journal
18
Renati P. Relationships and Causation in Living Matter: Reframing Some Methods in Life Sciences?.
Phys Sci & Biophys J 2022, 6(2): 000217.
Copyright© Renati P.
     
circular dichroism corresponding to that of the
β
-sheets of
      
  
functioning of biological molecules on the coherent phase of

With regard to a different conception of evolutionary
dynamics, I limit myself here to pointing out that, given
the phase correlations possible between coherent systems
     
can neither be considered random (except for the aspect
concerning adaptation to conditions relevant to the biotope -
climatic and geological events - and anthropogenic activities
 
sharing and transfer that occurs from the beginning of
         
existing species has a genome built on 4 bases.
Furthermore, if evolution of the species (as it is
 
the others) were true, we would have that almost all plant
species, to give an example, would have developed strategies
       
give an example) would have implemented and increased


allow itself to be grazed by an immensity of herbivores? Or:




the sense in which those species can produce themselves
within that eco-dynamic context. In fact, there is a tendency
       
         
explained by the phase correlations described so far between
coherent systems and that implies a different conception of
ecodynamics 
Summary and Conclusions
        
problem of the physical reduction of the sophisticated
properties exhibited by living systems (such as semantics,
    

from a condensed matter   (including the
living phase) it is possible to stitch up the structure-function
dualism (also conceivable as matter-information, or soma-

has a fundamentally dynamic origin, and not a static one, by

of freedom to which is associated the bosonic condensation
of correlation quanta that are as much structural as
determinant for the functionality of the system. Such bosonic
     
with the formation of a new state of the system, coherence,
characterized by the existence of phase correlations that set
in order the motion (and in certain cases also the position) of
the material components that, in this new state, have a lower
vacuum level than in the incoherent state.
Within living matter, the coherent dynamic is further
extended by the dialectics played out between the aqueous
matrix and the molecules participating in its coherence,
resulting in the establishment of a hierarchy of interrelated
levels embedded within one another, to which are associated
        
(from electronic motions up to circadian rhythms and

As long as coherence exists, for thermodynamic reasons,
every state assumed by the living (ordinary or otherwise)
should be understood as a response endowed with intrinsic
order with the purpose of maintaining/restoring coherence,
and therefore endowed with biological meaning. Thus,
the “cause” that dictates through which physiological or
biochemical state the living being is manifesting itself is not
     
concerns the fact that there is always a meaning that such
stimulus/event/situation has for that living being and implies
that the response is a process of adaptation developed along
a thermodynamic and phylogenetic history. The real causal

implied by meanings and on their dependence on the context,
rather than microscopic investigation which, at most, can
return how the response occurs and not why.
In essence, to be even clearer, the subtle point I wanted
to underpin in this analysis is the shift from a stance which
considers a reaction carried out at the molecular level
(biochemistry) to be the cause, for example, of a given state
of the physiology, to a stance that understands that such
a reaction is still the same physiology just observed at a
microscopic scale, and that this process (biochemistry/
physiology) is indeed the medium (the how) by which a
     
quality (now physically rooted, and no longer a category
possible within a cognitive/ “psychic” horizon only) that
each event has for a given living system.
To give an example, let us consider a mouse that is
sprayed with formaldehyde on its nose and develops a
melanoma in that area of the snout: this physiological
process does not happen because the formaldehyde directly
         
Physical Science & Biophysics Journal
19
Renati P. Relationships and Causation in Living Matter: Reframing Some Methods in Life Sciences?.
Phys Sci & Biophys J 2022, 6(2): 000217.
Copyright© Renati P.
producing “errors”), but because that “special” physiology
(the melanoma) is the desired and necessary response of
        
the formaldehyde and the way in which that encounter
       
formaldehyde, can no longer be understood merely as a
chemical/physical event describable by mechanistic laws
of action-reaction at the level of the fundamental material
components (atoms, electrical charges, molecules, ions, etc.),
but must also be understood as an experience, describable
analogically by biological laws, in which it necessarily
acquires a meaning (entirely ontological and having nothing
to do with cognitive/psychological aspects) that can only be
referred to the entire organism, and which is the result of the
unrepeatable semantic-dissipative-thermodynamic history
of that organism.
All of this, of course, also brings with it a radical
reinterpretation of what we call “disease” (in the case of the
mouse, melanoma), which from being a condition of disorder
simplistically “caused from the outside” or “from the
microscopic” of biochemistry, turns out to be an ordered and
sensible response (as it is adaptive) desired “from the inside”
to preserve/restore a biological order, an electrodynamic
coherence (compromised by meaning, i.e. by the physical,
chemical, thermodynamic and... biological implication that
any given event or circumstance has for the living).
This perspective grounds the impossibility of considering

therefore, as isolable) and highlights the need for a change in
the method to investigate its connotations and functioning.
There emerges the need to adapt the   to
a more analogical mode, capable of understanding cause-
effect relationships between stimuli and biological states

of health and disease and its aetiologies).
In addition to show that the causal factor lies in
the biological meaning, i.e. in the thermodynamic
and electrodynamic implication that the stimulus, or

        
       
relationship with a context without which – as complex
  

From here I reviewed a series of relevant implications
      
thermodynamic foundations for the existence of the living
phase of matter. First and foremost the critical review of
certain models of interpretation and the necessity to include,
within hard sciences (such as physics, biology, biochemistry,

neuroscience and philosophy), the analogical and semantic
features of the studied living systems (and their contexts).
         
physics, biochemistry, genomics, biology, medicine, etc. could
soon become the protagonists of a change of mentality, such
         

already assuming that the observed event, as non-ordinary, is

«what could be the biological sense according to which
this cell, or tissue, behaves differently?». A small change in



Acknowledgments
        

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
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