Documente Academic
Documente Profesional
Documente Cultură
DOI 10.1007/s12304-008-9027-z
Abstract More than one researcher is currently proposing that the notion of
information become an important element for defining living systems as well as for
explaining conditions that make their origins possible. During the pre-biotic era, the
type of compounds encountered would mainly have been very simple in nature and
might have been immersed in the natural dynamic of the physical world and in
processes of self-organization. It is furthermore quite possible that they formed a
relationship between and among certain types of processes that here we are
specifically proposing as central for the emergence of cell organization. Consequently, an important initial step towards constructing a theory of biological information is
to ask ourselves the question: how do biological systems process information? In this
way, we will be contributing to the proposals of this paper where we seek to identify
general principles that govern biological computing and that deal with biosemiotic
approaches as they are defended in naturalistic normative terms.
Keywords Biological computing . Bio-meaning information . Evolvability .
Informational dynamic systems . Naturalistic normative emergence .
Small-world phenomenon
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The life science and the sign science thus mutually imply one another.
(Sebeok 1994, p. 114)
Introduction
How does one approach the causes that produced the initial stages of cellular
organization? For such a purpose, in this paper we will be following a line of
reasoning which has begun to receive recognition as a new means of shedding light
on this issue: the nature of signs and information in living systems. There is a
growing conviction concerning the emerging role of information as a fundamental
building block in physics and other sciences, and leading researches in these fields
claim that information it is not just a construct of the mind but a fundamental
element of the physical world (Lloyd 2000, 2006; Seife 2006; von Baeyer 2005).
It is our line of reasoning that the nature of biological information does not stop at
the mere idea of genetic information but is rooted in the foundations of biological
phenomena; thus, we need to look into the question of how living systems gather
information about their environment and respond adequately to it.
We shall organize the article as follows:
Preliminaries
In the past few decades, the debate regarding the origin of life has focused on the
controversy between which came first: RNA or metabolism. The most well-known
proposals, in terms of the origin of life, have to do with behaviours (and properties)
of nucleic acids, proteins, and lipids (Eigen and Schuster 1979; Gilbert 1986; Segr
et al. 2001; Szathmry and Demeter 1987).
Wchtershuser proposed an alternative to one of these scenarios. His surface
metabolism theory contains two main axioms: (1) the energy source for life is a
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pyrite formation of H2S and FeS and (2) an archaic reductive citric acid cycle is put
into the centre of a metabolic network (Wchtershauser 1988). Nevertheless, there
are shortcomings in this concept; for instance, it fails to explain how raw materials
are supplied to the reductive citric acid cycle.
We can visualize the dilemma between the RNA first or metabolism first
scenario from Eigens (1971) proposal, which identifies the relationship between
biological information and biological function as a sort of chickenegg quandary.
We now understand that this question moves beyond a mere historical problem. Yet,
before we inquire which came first, it is more important that we ask ourselves which
one of them could have given rise to pre-biotic evolutionary processes. At present,
we recognize that the solution for the aforementioned dilemma must necessarily pass
through the stage of understanding the notion of biological information (Wills 1994)
and of designing a definition of functions in naturalistic terms (Collier 2000).
There are still other interesting approaches to the dilemma of the origin of life,
like the chemoton concept, which searches for the minimum components that
encompass the most basic forms of life. This chemical supersystem comprises three
subsystems: a metabolic network, template replication, and a boundary system
(Szathmry et al. 2005). Gnti (2003) introduced the chemoton model in 1971 as a
fundamental unit model of living systems.
It is our contention, though, that the passage from the inanimate world to the
animate world needs a transition phase: the dynamics of the pre-biotic world. As a
consequence, we should ask ourselves what the essential properties are for
determining and characterizing the organizational dynamic of living systems.
We know that biological systems are self-organized and self-reproducing, and, in
this context, we also understand that the self-organizational dynamic of these
systems is composed of many levels and types of processes that are interconnected
and interdependent (Fontana and Buss 1994; Furusawa and Kaneko 2002). One of
the most characteristic global properties of biological systems is that which enables
the behaviour of an autonomous agent with respect to its environment (Kauffman
2000, pp. 4979).
An autonomous agent, as defined by Kauffman, is a system capable of
reproducing itself and carrying out one or more thermodynamic work cycles
(Kauffman 2000, p. 53). This relational definition connects the notion of work with
the concept of constraint (Kauffman 2000, p. 97). In another paper, Kauffman further
develops the notion of autonomous agent. In this definition, we see the autonomous
component as well as the agent component such that the capacity to reproduce itself is
connected with both aspects. According to Kauffman, in this hypothetical autonomous
agent, the DNA hexamer is able to behave as an enzyme that links the two trimers, thus
forming a copy of the initial hexamer. This reaction is coupled to the exergonic
breakdown of pyrophosphate (PP) to two monophosphates, P+P. The characteristic ratio
at equilibrium between hexamers and trimers is not achievable because of this kind of
chemical motor, the PP P + P reaction cycle; this exergonic breakdown is used to
drive endergonic excess synthesis of the hexamer (Kauffman 2003).
As Kauffman says, ...The system eats trimers and photons, and...Pumps that
energy into the excess synthesis of hexamer... The system only works if displaced
from chemical equilibrium...towards an excess of trimers and photons. Agency only
exists in systems displaced from equilibrium... (Kauffman 2003, p. 1093).
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We now accept that autonomy is one of the most important global properties in
living systems. Nevertheless, the question about how it emerges from the dynamics
of self-organization of simple molecular compounds still remains unanswered.
From the thermodynamic point of view, the dissipative structures are open
systems (they exchange energy and/or matter with their environment), and the selforganization phenomena are produced due to the continuous changes in the local
interactions of the components that form the dynamic system (Nicolis and Prigogine
1977). But if we take, for example, the BelouzovZhabotinskii (BZ) reaction,
which is an oscillating, autocatalytic chemical reaction (Strogatz 1994), we are
unable to see in it similarities to the kind of self-organizing dynamics that we
encounter in living systems. In other words, living systems are self-organizing
systems with properties that go far beyond the common phenomena of selforganization. We propose that these properties could have been formedcould have
emergedat the beginning of the transition from the inanimate to the animate.
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If an energy variation does not have the capacity to be incorporated in the form of
a variation (any kind of variation) in the system, then it is not a sign for the system,
and, as a consequence, the system cannot develop a response. This is the form in
which signs emerge from physical reality.
Biological Information and Meaning
At this point in the paper, it is important that we relate our ideas to certain recent
developments that are taking place within the discussion on biological information.
In order to establish the main features of our contribution to the debate, we will do a
brief comparisoncontrast with other works (Jablonka 2002; Kauffman et al. 2008;
Maynard 2000).
One important common aspect is expressed by Jablonka: ...There is nothing
necessary in a particular aspect of the environment acting as information...
(Jablonka 2002, p. 586). First, we agree that signs and biological information are
relational notions. Secondly, it is necessary to identify the connection involving
information, evolution, and living systems.
Other authors address this last point from an evolutionary perspective, with
arguments stating that information is strongly connected to natural selection.
Maynard Smith, for instance, contends that the most important characteristic of
biological information is that it is designed by natural selection and, in this sense,
is intentional (Maynard 2000, pp. 189190). It should be noted that this proposal is
a function-related notion of biological information, mainly focused on genetic
information. For Maynard Smith, the notion of biological information is intimately
linked to the idea that the signal carrying the information and the response to it are
both products of natural selection. Moreover, his claim for the notion of design
makes a connection between natural selection, information, and function that is very
similar to Millikans (1984) proper function.
Jablonka also uses the notions of design and intentionality (Jablonka 2002,
p. 588). Her goal was to widen the notion of biological information developed by
Maynard Smith, by not limiting it to just genetic information but also addressing
other types of biological information (e.g., epigenetic information). She maintains
that the system receiving the information must be an interpretive system (Jablonka
2002, p. 602). The notion of function in Jablonkas work is similar to Kitchers
(1993) general design-based notion.
Kauffman et al. (2008) have recently published a paper on this topic. First, they
have proposed that the Shannon theory is powerful but limited in scope; in particular,
Shannons information cannot describe the information contained in a living organism.
So they introduced the notion of the relativity of information and showed that the
concept of information depends on the context of where and how it is being used.
Finally, they examined the link between information and organization, showing that
these two are intimately associated in biotic systems (Kauffman et al. 2008).
Compared to the interesting proposals outlined above, our approach to biological
information through an evolutionary perspective need not be related to any specific
ontology which involves design or intentional notions, or to any kind of interpretive
sub-system inside the receiver system. We are interested in the basic properties of
life and the way they initially emerged, generating the conditions that allow a kind of
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between the endergonic processes linked with the exergonic ones and with the added
capacity of generating work, a necessary and sufficient condition to produce the
organizational dynamic phenomena (Kauffman 2000). It is important to highlight
that both types of constrictions are so interrelated that a very basic, direct
communication exists between them.
Finally, there is one more set of processes that makes up the dynamic identity of
an IDS system. This third group is a network of reactions involved in regeneration,
maintenance, and reproduction processes and is, in one way or another, connected to
the constrictions. An IDS is therefore organized by the interdependence of the above
three sets of processes, and we know that a correlation among processes is to be
expected whenever a system is in a far from thermodynamic equilibrium state
(Kosztin and Schulten 2004; Levine 2005).
The basic constriction in our conceptual model is the most important step towards
the origins of the pre-biotic world. The correlation between endergonic and
exergonic processes could have significantly benefited from the existence of
compounds with high energy bonds, forming in this way a micro-cycle that is
capable of generating work (chemical work). Inorganic pyrophosphate and/or a
simple thioester could have been the ancestral energy currency molecules of these
types of chemical bonds. It was de Duve who proposed the thioester world, which
represents a ...hypothetical early stage in the development of life that could have
provided the energetic and catalytic framework of the protometabolic set of primitive
chemical reactions that led from the first building blocks of life to the RNA world
and subsequently sustained the RNA world until metabolism took over... (de Duve
1995, p. 436 and further developed in his last book, de Duve 2005, pp. 5465).
The interesting point here is that the thioester bond is what biochemists call a
high-energy bond, equivalent to the phosphate bonds in adenosine triphosphate
(ATP). In current cells, we find that thioesters are bound up with the esters
formation, including those that exist in complex lipids. We also find them actively
participating in the synthesis of peptides, fatty acids, sterols, terpenes, porphyrins,
and others. This underlines the feasibility of maintaining an adequate exchange of
energy between the exergonicendergonic cycle and the production of compounds
(doing chemical work) that have much to do with the formation (and regeneration)
of a proto-membrane.
We now see how signs turn into meaningful information (bio-meaning). If a
matterenergy variation becomes incorporated in the form of a variation somewhere
inside the system, then it will turn into a sign for the system. Once inside the system,
if this sign has an effect on its cohesion, in one way or another, then it will become
meaningful information for the system. Cohesion is the idea that gives the IDS its
identity in all its transformations through time (Collier 1986, 2004).
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It is because of the basic constriction that we postulate the emergence of information and function in the local interactions among the processes in the integrated
molecular network that makes up the IDS. As we said above, information and function
emerge at the same time in the IDS, and the physical emergence of both characteristics
takes place in such an interrelated way that it has two aspects: an informational
function aspect and a functional information aspect (Riofrio 2007, p. 241).
This is the reason why we said that, from the beginning of the emergence of the IDS,
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.
It is reasonable to postulate that the compounds encountered during the pre-biotic
era would have mostly been very simple in nature, and might have been immersed in
the natural dynamic of the physical world and in phenomena of self-organization.
Therefore, it is quite possible that they would have formed a relationship among the
three types of processes that we have proposed, and the IDS allows us to understand
the emergence of the global property known as autonomy.
First, the basic constriction is fundamental for providing the system with a certain
degree of independence with respect to its environment since it generates the
conditions for being in the far from thermodynamic equilibrium state, that is, the
endergonicexergonic cycle capable of producingin each cyclequantities of free
energy in the system that are appropriate to generate work (of a fundamentally
chemical type). In other words, being a system in the far from thermodynamic
equilibrium state is an intrinsic priority to the system, and, because of that, it is the
basic, most fundamental aspect of the IDS.
The second constriction gives another important contribution to the dynamic
organization of these systems, since it is involved in the making up of the
protoplasmic membrane. This structure creates a separation, a physical barrier,
between the system and its environment, thus producing a different distribution of
compounds, a different dynamic, and a different interaction among the processes.
The protoplasmic membrane is the place where we are objectively able to observe
the emergence of autonomy. It is the part of the system that regulates the interaction
with its environment in conditions compatible with its survival. And it is this kind of
protoplasmic membrane that made it possible for systems from their very beginning
in pre-biotic times to be evolvable.
We talk about evolvability when we can observe a phenotypic variation that is
susceptible to being a target of natural selection or, in other words, when an
organism has the capacity to generate an inheritable phenotypic variation (Altenberg
1994; Conrad 1990; Dawkins 1989; Kirschner and Gerhart 1998). Notwithstanding,
the term evolvability has been defined and used in different ways; it is a
sophisticated, new concept that is solidly grounded in empirical data (Colegrave
and Collins 2008).
It is believed that evolvability depends on biological phenomena, such as the
degree of modularity of developmental systems (Callebaut and Rasskin-Gutman
2005), as well as on their robustness vis--vis perturbation (Lenski et al. 2006;
Wagner 2005). Perhaps the most profound usage of evolvability is related with the
ability to generate novel variation or to acquire novel functions (Wagner 2005).
In order to be able to grasp the most important connections between evolvability
and evolutionary innovations that occurred at the beginnings of the pre-biotic era, we
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has two main features: (1) a control property and (2) a preservation property
(Kaneko and Yomo 2002).
The control property is distributed in the interdependence between the networks
of processes so that the systems cohesion towards the far from the thermodynamic
equilibrium is maintained by the intertwined correlation between biological
functions and bio-meaning. The preservation property, on the other hand, is about
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 influencingbut not
determiningthe 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.
This ancient epigenetic form of heredity was the origin of heredity as we know it
and has more in common with Lamarckian evolution than any other type (Jablonka
and Lamb 1995). In a more recent work on Lamarckian evolution, the researchers
argue that there is more to heredity than genes; for instance, some hereditary
variations are nonrandom in origin, while some acquired information is inherited
(Jablonka and Lamb 2005). Moreover, Jablonka and her co-author have pointed out
ideas that extend heritable, adaptive changes beyond natural selection to include the
action of evolved internal systems that generate nonrandom alternatives in
response to environmental challenges (Jablonka and Lamb 2005, p. 361).
All in all, this sets the stage for our next working hypothesis, which is a new
interpretation of Lamarckian evolution that could shed light on the transition from
random to nonrandom processes in biology.
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system (Lloyd 2000, p. 1049). In the same spirit, we ask the following questions: 1)
exactly how much meaningful information, or bio-meaning, can a living system
store? 2) to what extent it is possible to know this? 3) what kind of states could be
related with the amount of meaningful information or bio-meaning? These are
difficult questions to answer, and further research is needed to determine if there is a
causal relationship or correlation between the possible variables/states and the
amount of bio-meaning.
Moving to another theme, we often find that biological systems function through
decentralized control mechanisms in which the systems numerous subunitsthe
molecules of a cell, the cells of an organism, or the organisms of a groupadjust
their activities by themselves on the basis of limited, local information. It happens
without guidance from an external controller or even from an internal control centre.
The way in which biological systems behave, grasping a hold of any information
close at hand, compels us to hypothesize that a situation like meaningful biological
computation could exist.
Put in a different way, suppose that biological systems possess computational
abilities (Badre and Wagner 2006; Hopfield 1982). Then we would be required to
ask the following question: are there general principles governing natural-biological
computing? As we know, small-world structures have emerged spontaneously in the
biological realm. An important associated research topic, then, is how this could
have happened (Gong and van Leeuwen 2003, 2004). Small-world networks have
interesting potential as models for interacting structures in complex systems (Amaral
et al. 2000; Strogatz 2001; Watts and Strogatz 1998).
Our conceptual modeltranslated into a formal onemay be used to help us
understand the formation of the structured networks in some real systems with
dynamic units. One of our future research objectives is to find certain criteria that
will help us clarify the possible ways in which meaningful biological computation
may emerge in the physical universe. In this way, we will be contributing to the
discussion that seeks to reveal general principles governing biological computing.
Another objective is to uncover a possible way of explaining the emergence of
small world phenomena (Duchon et al. 2006; Kleinberg 2000)containing, among
other elements, scale-free characteristics and evolutionary capacitieswithin the
dynamic of simple physical phenomena (simple molecular compounds
interconnected to the three types of processes of our IDS conceptual model). It
would also be interesting to find out how could have emerged a sort of relative
reference point that enabled the development of something to be greedy about on
the routing paths of the biological small-world (Fraigniaud 2005). It seems to us that
our input to this discussion might point us in a new direction, aside from DNA
computation, for understanding emergence, robustness, resilience, scalability, and
evolution of living systems from the perspective of the theory of computation.
Conclusion
How can meaning be related to information? Are they two separate things? What
kind of things are they? Are they, after all, even remotely like things? In this
paper, we proposein a context of process metaphysicsthat information arises in
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