A MOLECULAR DYNAMIC NETWORK: MINIMAL PROPERTIES AND EVOLUTIONARY IMPLICATIONS

Abstract

Fundamental properties like robustness and evolvability are present in many dynamic systems. In biological systems, for instance, it seems that both properties are in continuous tension. However, this tension provokes throughout evolution the persistence of mutations and the existence of future evolutionary potential for changes. The special characteristics of biological systems, tell us that its distinctive properties could have been developed in pre-biotic era. In other words, the basic properties of life would have been better comprehended if we had realized that they arisen much earlier than previously thought. Hence, it is needed to be aware that it would come when we would hardly be able to find a molecule remotely resembling DNA, RNA, or even proteins. Nevertheless, it seems that a grand evolution must have happened between the phases of protocellular and bacterial evolutionary history. The design of this chapter is focus in proposing a working hypothesis, which addresses the problem of the emergence and self-maintenance of protocellular organization; and also the kind of evolutionary mechanism before life arose. Some results concluded from recent researches indicate that the development of interconnected molecular processes from scratch is possible, which would evolve from random initial conditions. At this point, it is shown that the most primary or basic properties of biological systems found in evolution are connected with new observations, and theoretical and practical implications. This happened due to how prebiotic protocells adapted and survived on that remote era. Moreover, the special self-organizing

Full text

1
To appear as a chapter in "Information and Computation"
book, published by World Scientific.
CHAPTER 12
A Molecular Dynamic Network: Minimal
Properties and Evolutionary implications
Walter Riofrio
Complex Thought Institute Edgar Morin, University Ricardo Palma, Lima-Peru
Complex Systems Institute (ISC-PIF), Paris-France
Email: walter.riofrio@iscpif.fr
Abstract:
Fundamental properties like robustness and evolvability are present in many
dynamic systems. In biological systems, for instance, it seems that both
properties are in continuous tension. However, this tension provokes throughout
evolution the persistence of mutations and the existence of future evolutionary
potential for changes.
The special characteristics of biological systems, tell us that its distinctive
properties could have been developed in pre-biotic era. In other words, the basic
properties of life would have been better comprehended if we had realized that
they arisen much earlier than previously thought. Hence, it is needed to be aware
that it would come when we would hardly be able to find a molecule remotely
resembling DNA, RNA, or even proteins. Nevertheless, it seems that a grand
evolution must have happened between the phases of protocellular and bacterial
evolutionary history.
The design of this chapter is focus in proposing a working hypothesis, which
addresses the problem of the emergence and self-maintenance of protocellular
organization; and also the kind of evolutionary mechanism before life arose.
Some results concluded from recent researches indicate that the development of
interconnected molecular processes from scratch is possible, which would
evolve from random initial conditions.
At this point, it is shown that the most primary or basic properties of biological
systems found in evolution are connected with new observations, and theoretical
and practical implications. This happened due to how prebiotic protocells
adapted and survived on that remote era. Moreover, the special self-organizing

Information and Computation
2
dynamics of biological systems suggests that its distinctive faculties could have
been developed in prebiotic era much earlier than hitherto thought.
Keywords: bio-meaning; cohesion; constraints; evolvability;
protocell; robustness.
1. Introduction
The application of informational concepts in biology was present for
many of the decades in the twentieth century (for instance, Schrödinger
1944).
Although we can see arguments defending its validity (Williams
1992, Godfrey-Smith 2000, Griffiths 2001), other studies point out the
importance that these concepts should be applied consistently (Sterelny
et al. 1996). Obviously, some researches state that these uses are
erroneous and they do not add knowledge to our understanding of the
more essential aspects in biology (Kitcher 2001).
Nevertheless, the use of the term ‘information’ exists and is
associated with the presence of contingencies and correlations between
certain variables inside the phenomena. The Shannon’s information
notion could be applied to almost everything that has some alternatives
stages in one specific moment (Shannon 1948).
It is clear that this specific use of information is not so problematic,
due to its usefulness of quantifying facts about contingency and
correlation. However, some new and special kinds of relation or property
into biological phenomena are not introduced.
In this sense, it is avowed that genes contain information of proteins
they make; but, in this case, it is concluded that no more than certain
gene- stage are closely related with the production (synthesis) of certain
proteins.
Despite, some researchers suspect there are some missing aspects in
biology with information notion application in the sense of Shannon’s
information.
Recently, Kauffman and co-workers has published a paper on this
topic. Initially, they proposed that while the Shannon theory is
compelling, its scope is limited. Particularly, they stated that Shannon’s
information cannot describe information contained in a living organism.
Subsequently, they introduced the notion of relativity of information and
explained that the concept of information depends on the context of
where and how it is being used. Finally, the authors examined the link

A Molecular Dynamic Network 3
between information and organization, showing that these two are
intimately associated in biotic systems (Kauffman et al. 2008).
Furthermore, Maynard Smith & Szathmáry (1998) pointed out that
several major transitions in the organization and transmission of genetic
information from one generation to the next one occurred during
evolution.
Alternatively, Jablonka worked to widen the notion of biological
information developed by Maynard Smith. Not only she did not limit this
notion to just genetic information but she also addressed other types of
biological information, e.g. epigenetic information (Jablonka 2002).
On the other hand, there is a growing conviction concerning the
information emerging role as a fundamental building block in physics
and other sciences. Moreover leading researches in this field declare that
this conviction is not a construction of mind instead it is a fundamental
element of the physical world (Lloyd 2000, 2006, von Baeyer 2005,
Seife 2006).
Subsequently, it seems that information has become an important
issue in many sciences. On account of that, a study of what is involved in
biological information and its role in the dynamics of living systems has
turned into a timely and needed topic to address in biology.
Besides, research has been carried out for finding an answer to the
question of whether some self-sustaining, autocatalytic networks have
the capacity to emerge from random chemical systems once a determined
threshold has been passed or, if on the contrary, some fine tuning of the
underlying biochemistry is needed for these to be able to materialize
(Mossel & Steel 2005).
2. Genetic Information and its Relatives
As previously considered, genetic information consists in information
leading to proteins and is enclosed in sequence of DNA bases. Molecular
mechanisms involved in these processes imply several coordinated
molecular types and structures inside the cell, as well as, the existence of
external signals (Ichinose et al. 2008).
In past decades, subsequent to one of the most famous molecular
biology researches (Watson & Crick 1953), the immense quantity of
laboratory experiments lead to the current notion of the implicated
processes in the gene information transmission yielding proteins
production.

Information and Computation
4
The main steps in this issue are sketched in the well known “central
dogma of molecular biology”. Firstly, the information contained in DNA
is transmitted to RNA (Transcription). Secondly, the information in
RNA is used to construct proteins (Translation).
This schematic representation hides the intricate number of molecular
mechanisms involved in each of these steps. For instance, the existence
of pre and post processes of transcription and translation is found besides
the complex concerted action between macromolecules in transcription
and translation.
If deep problems in this study subject are sought, a question of how
much it is known in regulatory processes guiding gene transcription
would be asked. In particular, is the identification between a gene and its
corresponding transcription factor already reached?
In a recent study is pointed out the difficulties to unwind the
regulation of transcription for living-cell individual genes. It is proposed
a method of imaging the transcriptional dynamics in Drosophila. A
multiphoton microscopy imaging could provide an experimental ability
to visualize the assembly and dynamics of individual transcription
factors and regulators to target genes in living cells (Yao et al. 2008).
Going beyond, considering the importance of these results and this
study subject suggest another kind of inquiry. Do the specific
macromolecule action (e.g. DNA) and do the natural selection presence,
both in the intertwined relation evolution among macromolecules had the
role to fix like metaphorical architects in the process mentioned above?
In other words, how the process of transcription and the process of
translation are initially constructed many millions of years ago.
Furthermore, what causes such an impressive concerted macromolecular
interaction inside each of these important processes and the connection
precision of both parts?
Although it is crucial to identify the exact composition of the
macromolecules involved in each biological function, it is even more
important to provide an explanation for the natural dynamic assembly of
the components found in a particular metabolic route.
Thus, it is clear that as long as it has the knowledge of all components
in a particular metabolic route, and the understanding of molecular
actions of each of these components, the best plausible interpretations is
proposed. At the same time, this tentative explanation is expected in
concordance with the main body of biological theory.
As a result, few of other researches related to the genetic information
dynamics of transmission framework will be analyzed.

A Molecular Dynamic Network 5
The studying the dynamics of individual ribosomes which translate
single messenger RNA revealed that the translation occurs through
successive translocation-and-pause cycles. Each translocation step
contains at least three sub-steps. However, these researches do not
clearly explain what causes these sub-steps. Conversely, they detected
that the overall rate of translation would depend on the secondary
structure of the mRNA (Wen et al. 2008).
The main idea exposed in that study which includes the use of
techniques in vitro is impressive. Nonetheless, it is not confirmed if these
phenomena are also produced in vivo. Moreover, do the intricate
macromolecular interaction in cytoplasm and do the compounds forming
ribosomes play any role in the timing of translocation sub-steps?
On the other hand, it is interesting the pleiotropy considering the
analysis on the variety of effects perceived by the specific gene
expression. It is known that Phenobarbital is a barbiturate that reduces
brain and nervous system activity as well as triggering pleiotropic
responses.
In another study, the use of a novel human hepatoma cell line (WGA)
which expresses CYP2B6 gene is enlightened (Rencurel et l. 2005). That
gene encodes a cytochrome P450 enzymes superfamily member which
catalyzes many reactions involved in drug metabolism and synthesis of
cholesterol, steroids, and other lipids.
In this research, the authors obtain insights into the regulation of gene
expression by barbiturate drugs. They explained that AMP-activated
protein kinase (AMPK) could mimic the Phenobarbital induction of
CYP2B6. It was because the encounter AMPK activity which increases
in cells cultured with Phenobarbital (PB). These findings strongly
support a role for AMPK in the PB induction of CYP2B gene expression.
In view of more high levels, one connection among development and
epigenetic phenomena would be mentioned.
The origin of cellular identity corresponds to the final product which
results from multiple processes. These processes restrict transcription
and replication of totipotent-cells-producing programs (Hyrien et al.
1995; Dazy et al. 2006). Some studies focused in totipotent-state nature
hypothesize implicated epigenetic-modification deletions in the structure
of chromosomes in somatic cells. Those studies also pointed that it can
be induced to undergo dedifferentiation into pluripotent embryonic germ
cells (Lemaitre et al. 2007).
In the studies cited above, some common themes are able to discern.
Firstly, the phenomena addressed involve the presence of coordinated

Information and Computation
6
molecular mechanisms displayed in specific pathways; although, a
metabolic pathway is only a network. It is important to consider scale-
free and small-world networks as essential features of biological systems.
For instance, it has been demonstrated that certain kinds of metabolic
pathways shows small-world behavior (Wagner & Fell 2001).
Secondly, molecular species behave in certain mechanical ways
depending on their dynamic spatial structures; their location and time in
where their action is recorded. In presence of other conditions the
behaviors or effects not always will be the same.
Thirdly, the intervention of external molecules, whose action is
mediated by some structures able to ‘recognize’ its presence and
concentration, exist.
Up to now, two issues could be inquired. Initially, how these
networks are formed; and afterward, what could explain in the biology
current knowledge the appearance of these kinds of networks emerging
spontaneously in nature.
The experiments with Phenobarbital and AMPK directed our inquiries
to more thoughtful questions. At first, how molecules match its specific
location or how they are ‘detected’. In biological systems, the needed
short time between some cause and its answer is crucial. Does genetic
information control all this dynamic organization? Was natural selection
the only driving force which caused the appearance of an extraordinary
coordination between biological networks and biological structures?
Moreover, terms such as signals, codes, information, computations,
translations, decodes are part of nowadays terminology used in biological
papers.
Why can it be concluded that only genetic information is what is called
biological information? Or is biological information more than genetic
information?
3. Minimal complexity in Prebiotic Systems
Several authors have put forward the notion that biological information is
not exclusively limited to genetic information (for example, epigenetic
information in Jablonka 2002).
Nevertheless, there are certain aspects to the notion of biological
information that would seem important to discuss if the purpose is to
construct it in naturalistic terms.
Once it has been developed in those terms, it would be our guarantee

A Molecular Dynamic Network 7
of not using this concept to refer to any sort of adscription or to any type
of epiphenomenon.
In other words, we are talking about an explanation that rests on an
ontological proposal that defends the existence of emerging phenomena,
understood in a strong sense (Holland 1998; Laughlin 2005; Chalmers
2006), an ontology that might explain the causal efficacy of a determined
emerging phenomenon:
"The ability to reduce everything to simple fundamental laws does
not imply the ability to start from those laws and reconstruct the
universe…The constructionist hypothesis breaks down when
confronted with the twin difficulties of scale and complexity…at each
level of complexity entirely new properties appear…Psychology is
not applied biology, nor is biology applied chemistry…" (Anderson
1972, p. 393)
Living systems began a new level of complexity in terms of universal
phenomena, and it is not possible to limit that complexity to just one
chapter of applied chemistry. Even though biological phenomena do not
run contrary to any law of physics, chemistry, or physical chemistry, it is,
however, impossible to reduce them to a lower level of reality.
And this circumstance is owed to the fact that each new level of
complexity materializing in the universe implies, by necessity, the
emergence of new properties containing causal efficacy that will, in the
end, produce new events in our universe.
This is the reason why we also have the certainty that normative
emergence is necessary for any naturalistic account of biology. And only
within a process metaphysics could the corresponding causally
efficacious ontological emergence be defended (Bickhard 2004).
The case of the emergence of living systems implies efficacy to cause
determined events, among them being the condition that makes it
possible for the materialization of new levels of complexity (interaction
with other living systems, the set of cognitive phenomena, human social
experiences, etc.) which could not be produced by any event exclusive to
physics, chemistry, or physical chemistry.
Therefore, it would seem important for us to study carefully that
which made it possible for this new level of complexity to be produced
in reality, known as the origin of living systems.
We will approach this issue starting with the time just before life
appeared. Put differently, we will dedicate ourselves to the thesis and

Information and Computation
8
analysis of one kind of system that could have been present in what we
will call the transition stage between inert phenomena (governed solely
by the laws of physics, chemistry, and physical chemistry) and the
appearance of the first forms of living systems.
This transition stage holds special interest for us since it is what we
know as the prebiotic world; hence, we will establish a line of
demarcation, separating the inert world from the prebiotic world. The
latter is a section of road leading to the world of living systems, and so it
might have fundamentally held determined types of systems that would
have featured certain degrees of self-organization.
Moreover, we contend this prebiotic world might have been
comprised by an almost continuous series of systems, and when we talk
about continuous, it is in the sense that the most fundamental properties
of these different types of systems – behaving as the details of a specific,
self-organizing kind – would have been shared by all of them.
The trigger for all this movement or dynamic from the world of the
inert to the world of living systems was the system that originated the
prebiotic world.
We are calling it the Informational Dynamic System (Riofrio 2007),
and it would have already contained within itself a certain degree of
complexity that could not be reduced into its parts or constituents.
Expressed in another way, we assert the Informational Dynamic
System is one that spurred the emergence of certain properties that will
turn out to be grounds for the appearance of definite events concerning
its surrounding environment as well as its dynamic internal milieu,
events that would not be possible to generate by any phenomenon
exclusive to physics, chemistry, or physical chemistry.
Therefore, we hold the Informational Dynamic System was already an
autonomous agent and, at the same time, a kind of adaptive complex
system.
In the words of Kauffman, an autonomous agent is:
“…the autonomous agent must be an open thermodynamic system
driven by outside sources of matter or energy –hence “food”- and the
continual driving of the system by such “food” holds the system away
from equilibrium… [Then]…An autonomous agent is a reproducing
system that carries out at least one thermodynamic work cycle…”
(Kauffman 2000, p. 64).

A Molecular Dynamic Network 9
Accordingly, an autonomous agent possesses a set of characteristics
which needs to be underscored. First, it is an open thermodynamic
system. Second, it is one far from thermodynamic equilibrium (since it is
capable of obtaining matter or energy from its surroundings). Lastly, it
can reproduce itself and carry out at least one thermodynamic work
cycle.
We consider, then, our hypothetical system could have contained the
minimum necessary capacities to lead us towards the first forms of life as
well as have all characteristics of an autonomous agent.
Informational Dynamic Systems (IDS) are comprised of at least three
classes of processes (Riofrio 2007, pp.235-240). The first of these
enables the system to maintain itself in the far from thermodynamic
equilibrium state, a micro-cycle that is capable of generating work
(chemical work).
The second one is the spontaneous self-organization of a protoplasmic
membrane – made of simple amphiphilic structures – which mimic, at
least qualitatively, some of the basic processes displayed by the current
plasma membranes (Segré et al. 2001).
The third group is a network of reactions that would perform the
regeneration of the organizational dynamic, maintenance, and
reproduction processes of the informational dynamic system.
The minimum complexity we have just pointed out is necessary for
conditions to be ripe for the emergence of the most fundamental
properties of life:
“…As the constriction maintaining them far from equilibrium
is an intrinsic part of their dynamic organization, there are
strategies they can develop that manage to keep this state in
conditions compatible with the laws imposed on them by the
material world… two new characteristics that emerge in the system –
in the local interactions – and are directed at maintaining the
far from equilibrium state… information and function…..
Therefore, our proposal of the notion of information-function – as a
characteristic emerging in the informational dynamic systems – is
a relational concept that is strongly governed (ruled) by the far
from thermodynamic equilibrium state…” (Riofrio 2007, pp. 240-
241)
“…Everything taken together brings us to the thesis that
starting the process from inanimate to animate could have been

Information and Computation
10
produced by the appearance of a type of dynamic system whose
organization is an informational and functional dynamic
organization…” (Ibid, p. 243)
On the other hand, the IDS is also a Complex Adaptive System
(CAS) since it is reasonable to think a type of evolution can be found
throughout the prebiotic era that (1) caused these systems to achieve a
certain amount of adaptation to their surrounding environments and (2)
brought about the existence of a sort of “inheritance” among different
types of systems that materialized during that remote time period.
4. The tree of Life
The three great domains on the tree of life are bacteria, eukarya, and
archaea.
According to Woese, discovering the existence of Archae in different
environments on planet Earth (Woese & Fox 1977; Woese et al. 1990;
Theron & Cloete 2000; Pace 2006), together with uncovering the
growing importance of Horizontal Gene Transfer (HGT) during early
evolution (Gogarten et al. 1989; Hilario & Gogarten 1993; Gogarten et
al. 2002; Huang & Gogarten 2009), impels us to review seriously and
profoundly a topic that has not, until today, been broached in its real
magnitude.
The upshot is, then, the evolution of the modern cell becoming one of
the most important issues in biology when taken as a whole (Woese
2002; Woese 2004).
The following statement is known as Darwin’s Doctrine of Common
Descent, evolution’s most primary assertion and the cornerstone of
modern biology:
“Probably all of the organic beings which have ever lived on this
earth have descended from some one primordial form . . . .” (Darwin
1859, p. 484).
Nonetheless, recent study results seem to have brought that claim into
question:
“…There is evidence, good evidence, to suggest that the basic
organization of the cell had not yet completed its evolution at the
stage represented by the root of the universal tree. The best of this

A Molecular Dynamic Network 11
evidence comes from the three main cellular information processing
systems. Translation was highly developed by that stage: rRNAs,
tRNAs, and the (large) elongation factors were by then all basically in
near modern form; hence, their universal distributions. Almost all of
the tRNA charging systems were in modern form as well… But,
whereas the majority of ribosomal proteins are universal in
distribution, a minority of them is not. A relatively small cadre is
specific to the bacteria, a somewhat larger set common and confined
to the archaea and eukaryotes, and a few others are uniquely
eukaryotic.” (Woese 2002, p. 8742)
On one hand, outcomes from completed comparative studies seem to
be suggesting the three great cellular designs we are currently managing
did not simultaneously achieve the state of modern cells (a situation that
would imply being in possession of the sufficient macromolecular
arsenal required for replication, transcription, and genetic translation
mechanisms):
“…A modern type of genome replication mechanism did not exist at
the root of the universal tree… Virtually no homology (orthology)
exists between the bacterial genome replication mechanism and that
basically common to the archaea and the eukaryotes (although a
number of bacterial and archaeal DNA polymerases, some of which
serve repair functions, do show sequence homology). Modern
genome replication mechanisms seem to have evolved twice… These
fundamental differences in the genetic machinery constitute a prima
facie case to the effect that the era of cellular evolution continued
well into the evolutionary period encompassed by the universal
phylogenetic tree. It would also seem that the order of maturation of
the information processing systems was first translation, then
transcription, and finally modern genome structure and replication…”
(Ibid, p. 8743)
So, cellular entities that lacked the capacity to establish evolutionary
lineages might have been the ones populating the epoch prior to the one
in which materializing was the new cellular organization so called
modern cells contain.
As a consequence, the most important evolutionary motor during that
remote, previous time period could have been Horizontal Gene Transfer
(HGT):

Information and Computation
12
“…The degree of connectedness of the componentry of the cell
has profound evolutionary implications… were that organization
simple and modular enough, all of the componentry of a cell could
potentially be horizontally displaceable over time. The organismal
genealogical record would be ephemeral; no stable record could exist.
Suppose that the primitive ancestors of modern cells were of this
nature. That would mean that at its beginning, cellular evolution
would have been driven in the main by HGT…” (Ibid, p. 8744)
What is more, on account of the fact there was no sort of heredity
between parent and offspring cells, the time it took to pass through the
stage of the origin of modern cells is also the time in which we can see
the appearance of the capacity for possible species genesis.
Hence, that barrier becomes the Darwinian Threshold and turns out
to be, at the same time, the Origin of Species since it is the origin of
speciation:
“…In its subsequent evolution a primitive cell of this type would
become ever more complex… In other words, there would come a
stage in the evolution of cellular organization where the organismal
genealogical trace (recorded in common histories of the genes of an
organism) goes from being completely ephemeral to being
increasingly permanent… This point in evolution, this transition, is
appropriately call the ‘‘Darwinian Threshold.’’ On the far side of
that Threshold ‘‘species’’ as we know them cannot exist. Once it is
crossed, however, speciation becomes possible… The Darwinian
Threshold truly represents the Origin of Species, in that it represents
the origin of speciation as we know it…” (Ibid, p. 8744)
Out of this entire, huge collection of studies, Woese suggests, in his
most recent work, certain reasons that could allow him to make a case for
there being a time in which biological evolution was produced in a non-
Darwinian manner:
“…The root of the universal tree is an artifact resulting from
forcing the evolutionary course into tree representation when that
representation is inappropriate... In the pre-Darwinian era the
evolutionary course cannot be represented by an organismal tree
topology. It is only after a more advanced stage in cellular evolution

A Molecular Dynamic Network 13
has been reached that tree representation begins to become useful.
That stage is the Darwinian threshold, the critical point before which
HGT dominates the evolutionary dynamic and after which it does
not—thus allowing stable organismal genealogies to emerge... Only
then can living systems finally be conceptualized in discreet,
idiosyncratic species terms …” (Woese 2004, p. 184)
Moreover, Woese deems we must respond to three fundamental
questions in order to understand cellular evolution, and the most
important of these makes reference to the origin of the great many
novelties needed for constructing the incredibly coordinated,
macromolecular scaffolding that constitutes modern cellular
organization:
“Three questions are central to understanding cellular evolution:
(i) when (under what circumstances) did the evolution of
(proteinaceous) cells begin, (ii) how was the incredible novelty
needed to create these first proteinaceous cells generated, and (iii)
did all extant cellular life ultimately arise from one or from more
than one common ancestor? The second of these questions, how the
overwhelming amount of novelty needed to bring modern cells into
existence was generated, is the central and most challenging question
of the three…” (Ibid, p. 182)
5. Pre-Darwinian Evolution
Our intention here is not to analyze Woese’s proposals in detail. Instead,
it is to find a possible explanation to the second of the three questions
raised above: “…the incredible novelty needed to create these first
proteinaceous cells generated…” (Woese 2004, p. 182).
As stated above in the beginning, our proposal is set at the start up of
the prebiotic world.
Hence, we hold (with greater conviction than does Woese) the kind of
evolution in that ancient time, in this, the initial prebiotic era (from the
origin of the Informational Dynamic System onward), was of a non-
Darwinian nature (Riofrio 2008).
In that remote time, it is practically impossible to uphold the
hypothesis that suggests existence of genetic information; neither genes
nor any such other macromolecular component as RNA or proteins were

Information and Computation
14
part of reality then (Zimmer 2005; Bernstein 2006; Norris et al. 2007;
Gleiser & Walker 2008).
We assume, then, it could be possible to think there was a type of
cellular organization, separate from its environment, yet with the
capacity to interact with its surroundings and its internal milieu.
The latter is a capacity the Informational Dynamic System possesses
because the kinds of processes its “plasma membrane” exhibits.
In the same way, it is a system that maintains itself far from
thermodynamic equilibrium because the connection between one
exergonic process linked to an endergonic process and both linked to
ancestral “energy currency” molecules is a type of process the IDS uses
and that enables it to have sufficient amounts of needed free energy for
doing some type of chemical, molecular work (Kauffman 2000, pp. 63-
69).
It should be pointed out that both types of processes are also two
types of constraints the IDS possesses (Riedl 1978; Schwenk 1995).
Besides, the third type of process regulates the connection among all
three, thereby enabling this network of simple molecular compounds to
perform well, to grow, and to reproduce.
Maintaining the far from thermodynamic equilibrium state is a
fundamental characteristic enabling the IDS to be able to explore new
connections and new compounds in respective processes as these allow
and /or contribute to that state, i.e. the state of being far from
thermodynamic equilibrium.
This will be the principal characteristic of the IDS (for more
information, consult Riofrio 2007, particularly pg. 242 – 245).
So, all behaviors, happenings, mechanisms, components, etc.
influencing the IDS will lead to one of two possibilities: maintaining /
increasing its far from thermodynamic equilibrium state or, quite the
opposite, reducing and weakening that state.
As with evolution prior to the appearance of the domains of bacteria,
eukarya, and archaea, which was mainly governed by HGT, reproduction
of these initial groups of prebiotic systems was dominated by some type
of horizontal capacity and novelty exchange that enabled them to adapt
to ever changing and completely hostile surroundings.
In other words, appearance of a prebiotic, adaptive evolution would
have involved some type of component or process exchange (through
direct protocell-to-protocell contact) that would have produced a benefit
or maintained these systems in the far from thermodynamic equilibrium
state.

A Molecular Dynamic Network 15
It is also possible there might have been some form of asexual
reproduction (similar a binary fission found in both bacteria and
archaea).
Since it is not possible to talk about different “species” of prebiotic
systems, we furthermore cannot bring up the idea of biological heredity
as understood in Darwinian terms.
Indeed, during those distant times, evolution was a community based
experience with no stable genealogical records:
“…the primitive cell is a loose confederation of a relatively small
number of rather simple modules. For cells of this type, most if not all
cellular componentry would be open to HGT, making the
combinatorics of gene transfer far and away the major factor in early
cellular evolution…” (Woese 2004, p. 181)
6. Prebiotic Information
During a time period when it is not even possible to imagine a possible
horizontal gene exchange between prebiotic cellular systems, we have to
wonder what, reasonably, can be asserted.
Let us start, then, from the design of our Informational Dynamic
System and focus on the self-assembly and self-organization logic of our
proposal.
In essence, the protocell we are advocating is a dynamic structure
containing three kinds of processes, each one relating to the other two.
And it is through a constraint which maintains the protocell in the far
from thermodynamic equilibrium state that we find a condition which
fundamentally defines our IDS at its most basic of definitions.
What our IDS will seek out at all times is to maintain or to increase its
far from thermodynamic equilibrium state; therefore, each of its
processes (or those it will gain) contribute (or will contribute) to the
protocell expressing its fundamental nature.
This network of interconnected processes constituting the IDS is an
informational and functional dynamic network.
This means information is transmitted and functions are performed at
the same time in each particular IDS process.
Yet, before analyzing the notion of information in our protocell, it is
important to discover if it would be possible to produce naturally some

Information and Computation
16
similar collection of processes, in accordance with the laws of chemistry
and physics.
Specifically, what similar, prebiotic, dynamic structure (to our IDS)
might have appeared in that distant past without necessitating prior
existence and guidance from any type of genetic information.
A model of protocell self-assembly and replication was recently put
forward that might demonstrate emergence of cellular structures where
simple metabolism is linked to a protoplasmic membrane, something that
is much easier than was before believed.
And what is even more revealing is this protocell is capable of
reproduction, an expected outcome that likewise may be recreated at
some point in lab experiments:
“…This result strongly suggests that the basic set of rules and the
logic of the process (more than the exact parameters) is the key for
finding a self-replicating protocell. Such positive result indicates that
very simple mechanisms of micelle-metabolism coupling in a
primitive Earth scenario might have been to trigger the proliferation
of simple protocells…it fairly well illustrates how robust is the
coupling between self-assembled amphiphiles coupled to an external
source of precursors and displaying a simple catalytic reaction. The
robustness of the observed results supports the view of cellular life as
a likely event to happen provided that the basic molecular logic is in
place.
Self-assembly is an essential component in the path towards
cellular systems. The spontaneous generation of spatial order,
allowing to easily define a container, is still at work at different scales
of biological organization…the dynamics of many subcellular
compartments take advantage of the physics of self-assembly…”
(Solé 2009, pp. 282-283)
Our thesis does not just comprehend a protoplasmic membrane
connected to simple metabolism, but also a very important process
connected to these two, one that enables the Informational Dynamic
System to maintain a thermodynamic state which makes possible and
simplifies process correlation (Kosztin & Schulten 2004; Levine 2005).
So then, it seems that our dynamic protocellular structure might
include an additional factor that would positively contribute to the
possibility of it being simulated and even perhaps reproduced in future
lab experiments.

A Molecular Dynamic Network 17
On another point, the fact that the previously introduced model is
“…within the context of information-free systems…” (Solé 2009, p. 279)
has obliged this researcher to arrive at the conclusion that evolution of
his protocells is not possible “…since no information is included in this
system, no further evolution is expected to occur…” (Ibid, p. 282).
What type of information is this author referring to? It is evident he is
thinking in terms of a blueprint or instructions containing information,
whose expression in current cells is the DNA molecule.
To us, biological information is one of the most essential properties of
living beings. In fact, we deem it to be of the utmost importance, so
much so that we state without pause it can be found within the most basic
aspects of the definition of a living entity.
For that reason, we believe this property emerged at the exact same
point in time the door to the prebiotic world was flung open, and thus it
produced not only biological information, but also biological function,
these appearing at the absolute critical moment of the first protocell
genesis on primitive earth:
“…information emerges in the biological world as ‘information
with meaning’ or ‘meaningful information’. To be exact, it emerges
as information with biological meaning or what we like to call ‘bio-
meaning’…” (Riofrio 2008, p. 365)
But when we bring up the matter of information in protocells, we are
not making exclusive reference to genetic information. As a result, we
believe this is a type of information distributed within the interior of all
Informational Dynamic Systems:
“…the information flow could be detected by the occurrences of
mechanisms that are related to the execution of some function inside
the dynamic organization of these systems…” (Riofrio 2008, p. 371)
Besides, what holds great importance to us is preparing a proposal on
biological information that is developed in naturalistic terms; hence, the
notion of information must be connected logically to something in the
real world.
That is why our thesis includes relating the ideas of “information with
meaning”, a “sign”, and “matter-energy variations”:
“…It seems appropriate, in a naturalistic approach, to connect the

Information and Computation
18
matter–energy variations with the possible emergence of
signs…whatever kind of energy variation may occur in a biological
system, it will only turn into a sign…when the system has the
capability to react accordingly. And this happens when the energy
variation impacts something in the system and is incorporated into the
system—as a variation—with the capacity of becoming part of the
system’s processes…” (Ibid., p. 365)
When a matter-energy variation is produced in the surrounding
environment, it may have an effect on an Informational Dynamic
System. First, the variation, whatever it might be, could be transmitted to
certain protoplasmic membrane components. As the transmission process
of this variation continues, the IDS will face one of these possibilities at
some point in time: (1) variation will either help maintain or increase the
far from thermodynamic equilibrium state or (2) variation could weaken,
negatively influence, or destroy the far from thermodynamic equilibrium
state.
The first possibility would be positive for the IDS. For the second, it
will depend upon variation’s degree of negative influence and the
robustness of the group of IDS’s experiencing the situation:
“…Once these systems are confronted by a specific,
environmentally-generated problem, the different possible solutions
(strategies), produced in the system’s protoplasmic membrane as a
product of the reproduction of these systems, are nothing more than
the maintenance of the integrity of their dynamic organization, i.e.,
the maintenance of the close interrelation between the three kinds of
processes that would result in the physical expression of information,
function, and autonomy at every moment and in each type of pre-
biotic system. In other words, the system evolved by overcoming
environmentally-generated problems through different ways of
preserving the basic properties which characterized it…” (Ibid., p.
372)
Strictly speaking, since the IDS possesses both biological function
and biological information and a strong connection exists between them,
it therefore has the capacity to be an autonomous agent.
When it is time to start a reproductive cycle, a specific IDS will use
components it finds to ‘duplicate’ its process network. This duplication
does not refer to a specific series of components forming a determined

A Molecular Dynamic Network 19
type of process. Rather, it is a reference to the capacity of being a
protocell, the dynamic organization of which is informational and
functional, and this was the class of “heredity” produced during those
beginning stages of the prebiotic world:
“…The control property is distributed in the interdependence
between the networks of processes so that the system’s cohesion
towards the far from the thermodynamic equilibrium is maintained by
the intertwined correlation between biological functions and bio-
meaning…preserving not so much the chemical structure of the
molecules as the interrelation between the three kinds of processes
that make up the dynamic self-organization of the IDS. It is the
environment that created conditions that were influencing—but not
determining—the specific self-organization of the protocells. Faced
with an environment filled with materials that could be used to build
systems from scratch, the IDS would have developed ways to
construct a network of processes that were maintaining the
characteristic self-organization of Informational Dynamic Systems
and their offspring...” (Ibid., p. 373)
This means each mechanism at work inside every process
“contributes” to the entire system being in a state far from
thermodynamic equilibrium.
Every process will accomplish its “biological function” as it carries
out a specific action in these protocells’ molecular dynamic and
simultaneously participates in keeping or increasing the far from
thermodynamic equilibrium state.
Likewise, every energy variation that accompanies a specific
mechanism inside a molecular reaction that is part of a process type
which increases, maintains, or weakens the far from thermodynamic
equilibrium state of our protocell will be the biological information
eliciting a response within the IDS, in accordance with variation itself.

Information and Computation
20
References
Anderson, P. W. (1972). More is Different. Science, 177, pp. 393 – 396.
Bernstein, M. (2006). Prebiotic materials from on and off the early Earth. Phil.Trans. R.
Soc. B, 361, pp. 1689–1702.
Bickhard, M. H. (2004). Part II: Applications of Process-Based Theories: Process and
Emergence: Normative Function and Representation. Axiomathes — An
International Journal in Ontology and Cognitive Systems, 14 (1), pp. 121-155.
Chalmers, D. J. (2006). Strong and Weak Emergence. In P. Clayton and P. Davies (eds.)
The Re-emergence of Emergence. Oxford University Press.
Darwin, C. (1859). On the Origin of Species. Harvard Univ. Press Cambridge, MA, and
London.
Dazy, S., Gandrillon, O., Hyrien, O. and Prioleau M. N. (2006). Broadening of DNA
replication origin usage during metazoan cell differentiation. EMBO Rep, 7, pp.
806-811.
Gleiser, M. and Walker, S. I. (2008). An Extended Model for the Evolution of Prebiotic
Homochirality: A Bottom-Up Approach to the Origin of Life. Orig. Life Evol.
Biosph., 38, pp. 293-315.
Godfrey-Smith, P. (2000). On the Theoretical Role of 'Genetic Coding'. Philosophy of
Science, 67, pp. 26-44.
Gogarten, J. P., Doolittle, W. F. and Lawrence, J. G. (2002). Prokaryotic evolution in
light of gene transfer. Mol Biol Evol, 19(12), pp. 2226-2238.
Gogarten, J. P., et al., (1989) Evolution of the vacuolar H+-ATPase: implications for the
origin of eukaryotes. Proc. Natl. Acad. Sci. U.S.A., 86(17), pp. 6661-6665.
Griffiths, P. E (2001). Genetic Information: A Metaphor in Search of a Theory.
Philosophy of Science, 68, pp. 394-412.
Hilario, E. and Gogarten, J. P. (1993). Horizontal transfer of ATPase genes--the tree of
life becomes a net of life. Biosystems, 31(2-3), pp. 111-119.
Holland, J. H. (1998). Emergence: From Chaos to Order. Basic Books.
Huang, J. and Gogarten, J. P. (2009). Ancient gene transfer as a tool in phylogenetic
reconstruction. Methods Mol Biol., 532, pp. 127-139.
Hyrien, O., Maric, C. and Mechali, M. (1995). Transition in specification of embryonic
metazoan DNA replication origins. Science, 270, pp. 994-997.
Ichinose, N., Yada, T., Gotoh, O. and Aihara, K. (2008). Reconstruction of transcription-
translation dynamics with a model of gene networks. J Theor. Biol., 255(4), pp.
378-386.
Jablonka, E. (2002). Information: Its Interpretation, Its Inheritance and Its Sharing.
Philosophy of Science, 69, pp. 578-605.
Kauffman, S., Logan, R. K., Este, R., Goebel, R., Hobill, D. and Shmulevich, I. (2008).
Propagating organization: an enquiry. Biology and Philosophy, 23(1), pp. 27–45.
Kauffman, S. (2000). Investigations. Oxford University Press.
Kitcher, P. S. (2001). Battling the Undead: How (and How Not) to Resist Genetic
Determinism. In R. Singh, C. Krimbas, D. Paul and J. Beatty (eds.), Thinking
about Evolution: Historical, Philosophical and Political Perspectives. Cambridge
University Press.

A Molecular Dynamic Network 21
Kosztin, I. and Schulten, K. (2004). Fluctuation-driven molecular transport through an
asymmetric membrane channel. Physical Review Letters, 93, p. 238102.
Laughlin, R. (2005). A Different Universe: Reinventing Physics from the Bottom Down.
Basic Books.
Lemaitre, J. M., Gregoire, D. and Mechali, M. (2007). Replication, development and
totipotency. Med Sci (Paris), 23(3), pp. 245-247.
Levine, R. D. (2005). Molecular Reaction Dynamics. Cambridge University Press.
Lloyd, S. (2000). Ultimate physical limits to computation. Nature, 406, pp. 1047–1054.
Lloyd, S. (2006). Programming the Universe. Knopf.
Mossel, E. and Steel, M. (2005). Random biochemical networks: the probability of self-
sustaining autocatalysis. Journal of Theoretical Biology, 233(3), pp. 327–336.
Norris, V., Hunding, A., Kepes, F., Lancet, D., Minsky, A., Raine, D., Root-Bernstein, R.
and Sriram, K. (2007). Question 7: The First Units of Life Were Not Simple Cells.
Orig. Life Evol. Biosph., 37, pp. 429–432.
Pace, N. R. (2006). Time for a change. Nature, 441 (7091), p. 289.
Rencurel, F., Stenhouse, A., Hawley, S. A., Friedberg, T., Hardie, D. G., Sutherland, C.
and Wolf, C. R. (2005). AMP-activated protein kinase mediates phenobarbital
induction of CYP2B gene expression in hepatocytes and a newly derived human
hepatoma cell line. J Biol Chem., 280 (6), pp. 4367-4373.
Riedl, R. (1978). Order in Living organisms: a systems analysis of evolution. John Wiley
& Sons.
Riofrio, W. (2007). Informational Dynamic Systems: Autonomy, Information, Function.
In C. Gershenson, D. Aerts & B. Edmonds (eds), Worldviews, Science, and Us:
Philosophy and Complexity. World Scientific, Singapore, pp. 232-249.
Riofrio, W. (2008). Understanding the Emergence of Cellular Organization. Biosemiotics,
1 (3), pp. 361-377.
Schrödinger, E. (1944). What is Life? Cambridge University Press.
Schwenk, K. (1995). A utilitarian approach to evolutionary constraint. Zoology, 98, pp.
251-262.
Segré, D., Ben-Eli, D., Deamer, D. W., and Lancet, D. (2001). The lipid world. Origins
Life Evol. Biosph., 31, pp. 119–145.
Seife, C. (2006). Decoding the Universe. Penguin Books.
Shannon, C. (1948). A Mathematical Theory of Communication. Bell Systems Technical
Journal, 27, pp. 279-423, pp. 623-656.
Solé, R.V. (2009). Evolution and self-assembly of protocells. Int J Biochem Cell Biol.,
41 (2), pp. 274-284.
Sterelny, K., Smith, K. and Dickison, M. (1996). The Extended Replicator. Biology and
Philosophy, 11, pp. 377-403.
Theron, J. and Cloete, T. E. (2000). Molecular techniques for determining microbial
diversity and community structure in natural environments. Crit. Rev. Microbiol.,
26 (1), pp. 37–57.
von Baeyer, H. C. (2005). Information: The New Language of Science. Harvard
University Press.
Wagner, A. and Fell, D. A. (2001). The small world inside large metabolic networks.
Proceedings of the Royal Society of London B, 268, pp. 1803-1810.

Information and Computation
22
Watson, J. D. and Crick, F. H. C. (1953). A Structure for Deoxyribose Nucleic Acid.
Nature, 171, pp. 737-738.
Wen, J-D, Lancaster, L., Hodges, C., Zeri, A. C., Yoshimura, S. H., Noller, H. F.,
Bustamante, C. and Tinoco, I. (2008). Following translation by single ribosomes
one codon at a time. Nature, 452, pp. 598-603.
Williams, G. C. (1992). Natural Selection: Levels, Domains, and Challenges. Oxford
University Press.
Woese, C. (2002). On the evolution of cells. Proc. Natl. Acad. Sci. U.S.A., 99(13), pp.
8742-8747.
Woese, C. (2004). A New Biology for a New Century. Microbiol Mol Biol Rev.,
68(2), pp. 173-186.
Woese, C. R., Kandler, O. and Wheelis, M. L. (1990). Towards a natural system of
organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl.
Acad. Sci. U.S.A., 87 (12), pp. 4576–4579.
Woese, C. and Fox, G. (1977). Phylogenetic structure of the prokaryotic domain: the
primary kingdoms. Proc. Natl. Acad. Sci. U.S.A., 74(11), pp. 5088–5090.
Yao, J., Zobeck, K. L., Lis, J. T. and Webb, W. W. (2008). Imaging transcription
dynamics at endogenous genes in living Drosophila tissues. Methods, 45(3), pp.
233-241.
Zimmer, C. (2005). How and Where Did Life on Earth Arise? Science, 309, p. 89.