Modeling Life as Cognitive Info-Computation

Gordana Dodig-Crnkovic

School of Innovation, Design and Engineering, Mälardalen University, Västerås, Sweden

[email protected]
arXiv:1401.7191v1 [cs.OH] 28 Jan 2014

Abstract. This article presents a naturalist approach to cognition understood as

a network of info-computational, autopoietic processes in living systems. It pro-
vides a conceptual framework for the unified view of cognition as evolved from
the simplest to the most complex organisms, based on new empirical and theo-
retical results. It addresses three fundamental questions: what cognition is, how
cognition works and what cognition does at different levels of complexity of living
organisms. By explicating the info-computational character of cognition, its evo-
lution, agent-dependency and generative mechanisms we can better understand its
life-sustaining and life-propagating role. The info-computational approach con-
tributes to rethinking cognition as a process of natural computation in living be-
ings that can be applied for cognitive computation in artificial systems.

1 Introduction
It is a remarkable fact that even after half a century of research in cognitive science,
cognition still lacks a commonly accepted definition [1]. E.g. Neissers description of
cognition as “all the processes by which sensory input is transformed, reduced, elabo-
rated, stored, recovered and used” [2] is so broad that it includes present day robots. On
the other hand, the Oxford dictionary definition: “the mental action or process of ac-
quiring knowledge and understanding through thought, experience, and the senses” ap-
plies only to humans. Currently the field of cognitive robotics is being developed where
we can learn by construction what cognition might be and then, returning to cognitive
systems in nature find out what solutions nature has evolved. The process of two-way
learning [3] starts from nature by reverse engineering existing cognitive agents, while
simultaneously trying to design cognitive computational artifacts. We have a lot to learn
from natural systems about how to engineer cognitive computers. [4]
Until recently only humans were commonly accepted as cognitive agents (anthro-
pogenic approach in Lyon). Some were ready to ascribe certain cognitive capacities to
all apes, and some perhaps to all mammals. The lowest level cognition for those with
the broadest view of cognition included all organisms with nervous system. Only a few
were prepared to go below that level. Among those very few, the first who were ready to
acknowledge a cognitive agency of organisms without nervous system were Maturana
and Varela [5][6], who argued that cognition and life are identical processes. Lyons
classification, besides describing the anthropogenic approach, includes a biogenic ap-
proach based on self-organizing complex systems and autopoiesis. The adoption in the
present paper of the biogenic approach through the definition of Maturana and Varela is
motivated by the wish to provide a theory that includes all living organisms and artificial
cognitive agents within the same framework.
2 The Computing Nature, Computational Naturalism and
Minimal Cognition
Naturalism is the view that nature is the only reality. It describes nature through its
structures, processes and relationships using a scientific approach. Naturalism studies
the evolution of the entire natural world, including the life and development of humanity
as a part of nature. Computational naturalism (pancomputationalism, naturalist compu-
tationalism) is the view that the nature is a huge network of computational processes
which, according to physical laws, computes (dynamically develops) its own next state
from the current one. Representatives of this approach are Zuse, Fredkin, Wolfram,
Chaitin and Lloyd, who proposed different varieties of computational naturalism. Ac-
cording to the idea of computing nature, one can view the time development (dynamics)
of physical states in nature as information processing (natural computation). Such pro-
cesses include self-assembly, self-organization, developmental processes, gene regula-
tion networks, gene assembly, protein-protein interaction networks, biological transport
networks, social computing, evolution and similar processes of morphogenesis (cre-
ation of form). The idea of computing nature and the relationships between two basic
concepts of information and computation are explored in [7] and [8].
In computing nature, cognition should be studied as a natural process. If we adopt
the biogenetic approach to cognition, the important question is what is the minimal cog-
nition? Recently, a number of empirical studies have revealed an unexpected richness
of cognitive behaviors (perception, information processing, memory, decision making)
in organisms as simple as bacteria. Single bacteria are too small to be able to sense any-
thing but their immediate environment, and they live too briefly to be able to memorize
a significant amount of data. On the other hand bacterial colonies, swarms and films
exhibit an unanticipated complexity of behaviors that can undoubtedly be characterized
as biogenic cognition, [9][10][11][12][13][14].
Apart from bacteria and similar organisms without nervous system (such as e.g.
slime mold, multinucleate or multicellular Amoebozoa, which recently has been used
to compute shortest paths), even plants are typically thought of as living systems without
cognitive capacities. However, plants too have been found to possess memory (in their
bodily structures that change as a result of past events), the ability to learn (plasticity,
ability to adapt through morphodynamics), and the capacity to anticipate and direct their
behavior accordingly. Plants are argued to possess rudimentary forms of knowledge,
according to [15] p. 121, [16] p. 7 and [17] p. 61.
In this article we focus on primitive cognition as the totality of processes of self-
generation, self-regulation and self-maintenance that enables organisms to survive us-
ing information from the environment. The understanding of cognition as it appears in
degrees of complexity can help us better understand the step between inanimate and
animate matter from the first autocatalytic chemical reactions to the first autopoietic
proto-cells.

3 Informational Structure of Reality for a Cognitive Agent

When we talk about computing nature, we can ask: what is the hardware for this
computation? We, as cognizing agents interacting with nature through information ex-
change, experience nature cognitively as information. Informational structural realism
[18][19][20] is a framework that takes information as the fabric of the universe (for an
agent). The physicists Zeilinger [21] and Vedral [22] suggest that information and real-
ity are one. For a cognizing agent in the informational universe, the dynamical changes
of its informational structures make it a huge computational network where compu-
tation is understood as information dynamics (information processing). Thus the sub-
strate, the “hardware”, is information that defines data-structures on which computation
proceeds.
Info-computationalism is a synthesis of informational structural realism and natural
computationalism (pancomputationalism) - the view that the universe computes its own
next state from the previous one [23]. It builds on two basic complementary concepts:
information (structure) and computation (the dynamics of informational structure) as
described in [24] [25] and [26].
The world for a cognizing agent exists as potential information, corresponding to
Kants das Ding an sich. Through interactions, this potential information becomes ac-
tual information, “a difference that makes a difference” [27]. Shannon describes the
process as the conversion of latent information into manifest information [28]. Even
though Batesons definition of information as a difference that makes a difference (for
an agent) is a widely cited one, there is a more general definition that includes the fact
that information is relational and subsumes Batesons definition:

“Information expresses the fact that a system is in a certain configuration

that is correlated to the configuration of another system. Any physical system
may contain information about another physical system.” [29] p. 293

Combining the Bateson and Hewitt insights, at the basic level, information is a
difference in one physical system that makes a difference in another physical system.
When discussing cognition as a bioinformatic process of special interest, there is
the notion of agent, i.e. a system able to act on its own behalf [26]. Agency has been
explored in biological systems by [30] [31] [32]. The world as it appears to an agent
depends on the type of interaction through which the agent acquires information, [33].
Agents communicate by exchanging messages (information) that help them coordinate
their actions based on the (partial) information they possess (a form of social cognition).

4 Information Self-Structuring through

Morphological/Physical/Intrinsic Computation and
PAC Algorithms

Regarding computational models of biological phenomena, we must emphasize that

within the info-computational framework computation is defined as information pro-
cessing. This differs from the traditional Turing machine model of computation that is
an algorithm/effective procedure/recursive function/formal language. The Turing ma-
chine is a logical construct, not a physical device [34]. Modeling computing nature
adequately, including biological information processing with its self-generating and
learning real-time properties, requires new models of computation such as interactive
and networked concurrent computation models, as argued in [7] and [35] with reference
to [36] and [37].
Computation in nature can be described as a self-generating system consisting of
networks of programs [38], a model inspired by the self-modifying systems of [39].
In the course of the development of the general theory of networked physical infor-
mation processing, the idea of computation becomes generalized. Examples of new
computing paradigms include natural computing [40] [41] [42] [43]; superrecursive
algorithms [44]; interactive computing [45]; actor model [36] and similar “second gen-
eration” models of computing [37].
Among novel models of computation of special interest are Valiants ecorythms or
algorithms satisfying “Probably Approximately Correct” criteria (PAC) as they explic-
itly model natural systems “learning and prospering in a complex world”. [46] The
difference between PAC learning algorithms and the Turing machine model is that the
latter does not interact with the environment, and thus does not learn. It has unlimited
resources, both space (memory) and time, and even though it is sequential, it does not
operate in real time. In order to computationally model living nature, we need suitable
resource-aware learning algorithms, such as ecorithms, described by Valiant:

“The model of learning they follow, known as the probably approximately cor-
rect model, provides a quantitative framework in which designers can evaluate
the expertise achieved and the cost of achieving it. These ecorithms are not
merely a feature of computers. I argue in this book that such learning mech-
anisms impose and determine the character of life on Earth. The course of
evolution is shaped entirely by organisms interacting with and adapting to their
environments.” [46] p. 8

A different approach to evolution is taken by Chaitin, who argues for Darwins the-
ory from the perspective of gene-centric metabiology [47]. The interesting basic idea
that life is software (executable algorithms) run by physics is applied in the search for
biological creativity (in the form of increased fitness). Darwins idea of common descent
and the evolution of organisms on earth is strongly supported by computational models
of self-organization through information processing i.e. morphological computing.
The cognitive capacity of living systems depends on the specific morphology of
organisms that enables perception, memory, information processing and agency. As ar-
gued in [48], morphology is the central idea connecting computation and information.
The process of mutual evolutionary shaping between an organism and its environment
is a result of information self-organization. Here, both the physical environment and the
physical body of an agent can be described by their informational structure that con-
sists of data as atoms of information. Intrinsic computational processes, which drive
changes in informational structures, result from the operation of physical laws. The en-
vironment provides an organism with a variety of inputs in the form of both information
and matter-energy, where the difference between information and matter-energy is not
in the kind, but in the use the organism makes of it. As there is no information without
representation [49], all information is carried by some physical carrier (light, sound,
radio-waves, chemical molecules, etc.). The same physical object can be used by an
organism as a source of information and as a source of nourishment/matter/energy. In
general, the simpler the organism, the simpler the information structures of its body,
the simpler the information carriers it relies on, and the simpler its interactions with the
environment.

5 Cellular Computation

The environment is a resource, but at the same time it also imposes constraints that
limit an agents space of possibilities. In an agent that can be described as a complex
informational structure, constraints imposed by the environment drive the time develop-
ment (computation) of its structures to specific trajectories. This relationship between
an agent and its environment is called structural coupling by [5]. Experiments with
bacteria performed by Ben-Jacob and Bassler show that bacteria interact with the envi-
ronment, sense it, and extract its latent/potential information. This information triggers
cognitive processes (“according to internally stored information”) that result in changes
of their structure, function and behavior. Moreover, Ben-Jacob explains how informa-
tion can be seen as inducing “an internal condensed description (model of usable infor-
mation)” of the environment, which directs its behavior and function. This is a process
of intracellular computation, which proceeds via “gene computation circuits or gene
logical elements”, that is gene circuits or regulatory pathways. As bacteria multiply by
cell division, complex colony forms.
Every single bacterium is an autonomous system with internal information manage-
ment capabilities: interpretation, processing and storage of information. Ben-Jacob has
found that complex forms emerge as a result of the communication between bacteria
as interplay of the micro-level vs. macro-level (single organism vs. colony). Chemical
sign-processes used by bacteria for signaling present a rudimentary form of language.
Waters and Bassler [14] describe the process of “quorum-sensing and communication
between bacteria that use two kinds of languages – intra-species and inter-species chem-
ical signalling. That is how they are capable of building films consisting of a variety of
species.
Experiments show that the colony as a whole “behaves much like a multi-cellular or-
ganism” governed by the distributed information processing with message broadcasting
that stimulates changes in individual bacteria (plasticity). Communication, cooperation
and self-organization within a swarm/colony enable decision-making at the group level
as a form of social cognition.

“The cells thus co-generate new information that is used to collectively

assume newly engineered cell traits and abilities that are not explicitly stored
in the genetic information of the individuals. Thus, the bacteria need only have
genetically stored the guidelines for producing these capabilities.” [12] p. 88

A bacteria colony changes its morphology and organization through natural dis-
tributed information processing and thus learns from experience (such as encounters
with antibiotics). Ben-Jacob concludes that they “ possibly alter the genome organi-
zation or even create new genes to better cope with novel challenges.” All those pro-
cesses can be modelled as distributed concurrent computation in networks of networks
of programs, where individual bacteria form networks and bacteria themselves can be
modelled as networks of programs (processes or executing algorithms).
Empirical studies of the cognitive abilities of bacteria swarms, colonies and films
confirm the result of [50], proving a theorem that natural selection will always lead a
population to accumulate information, and so to ’learn’ about its environment. Okasha
points out that

“any evolving population ’learns’ about its environment, in Harms’ sense,

even if the population is composed of organisms that lack minds entirely, hence
lack the ability to have representations of the external world at all.” [51]

Experimental results by [10][11][12][13][14] have shown that bacteria indeed learn

from the environment even though the mechanisms of bacterial cognition are limited
to relatively simple chemical information processes.

6 Self-Organization, Cognitive Info-Computation and Evolution

of Life
In computational (information processing) models of bacterial cognition, the biological
structure (hardware) is at the same time a program (software) that controls the behavior
of that hardware both internally and in the interactions with the environment. Already
in 1991 Kampis proposed a unified model of computation as the mechanism underlying
biological processes through self-generation of information by non-trivial change (self-
modification) of systems [39]. This process of self-organization and self-generation of
information is what is elsewhere described as morphological computation on different
levels of organization of natural systems. Current research in adaptive networks goes in
the same direction,[7].
However, understanding of the basic evolutionary mechanisms of information ac-
cumulation, with resulting increase in information-processing capacities of organisms
(memory, anticipation, computational efficiency), is only the first step towards a fully-
fledged evolutionary understanding of cognition, though it is probably the most difficult
one, as it requires a radical redefinition of fundamental concepts of information, com-
putation and cognition in naturalist terms. According to Maturana:

“A cognitive system is a system whose organization defines a domain of

interactions in which it can act with relevance to the maintenance of itself,
and the process of cognition is the actual (inductive) acting or behaving in
this domain. Living systems are cognitive systems, and living as a process is a
process of cognition. This statement is valid for all organisms, with and without
a nervous system.” [6] p. 13

The role of cognition for a living agent, from bacteria to humans is to efficiently deal
with the complexity of the world, helping an agent to survive and thrive. The world is
inexhaustible and largely complex and exceeds by all accounts what a cognizing agent
can take in. Cognition is then the mechanism that enables cognizing agents to control
their own behavior in order to deal with the complexity of the environment, make sense
of the world and use it as a resource for survival, [52] p. 234. In this view, “ cognition ‘
shades off’ into basic biological processes such as metabolism.”
Through autopoietic processes with structural coupling (interactions with the envi-
ronment) a biological system changes its structures and thereby the information pro-
cessing patterns in a self-reflective, recursive manner [5]. But self-organisation with
natural selection of organisms, responsible for nearly all information that living sys-
tems have built up in their genotypes and phenotypes, is a simple but costly method to
develop. Higher organisms (which are more expensive to evolve in terms of resources)
have developed language and reasoning as a more efficient way of learning. The step
from genetic learning (typical of more primitive forms of life) to the acquisition of cog-
nitive skills on higher levels of organisation of the nervous system (such as found in
vertebrata) will be the next step to explore in the project of cognitive info-computation,
following [53] who distinguish genetic, epigenetic, behavioral, and symbolic evolution.
The studies of bacterial cognition suggest that there are some important processes that
operate during evolution such as self-organization and auto-poiesis, which guarantee
growth of order, and the propagation of structures in spite of the randomness of envi-
ronmental influences. Also, colonies, swarms and films seem to play a prominent role
in bacterial evolution (as swarm intelligence).
Interesting question arises in connection to AI and AL which are not based on
chemical processes: is molecular computation necessary for cognition? For example
[9] proposed that minimal cognition can be identified with sensorimotor coordination.
However, even though fundamental, sensorimotor coordination is not enough to explain
cognition in biological systems. Chemical processes of autopoiesis based on molecu-
lar computation (information processing) are essential, not only for simple organisms
like bacteria, but also for the functioning of the human nervous system. In the words of
Shapiro:

“molecular biology has identified specific components of cell sensing, in-

formation transfer, and decision-making processes. We have numerous precise
molecular descriptions of cell cognition, which range all the way from bacterial
nutrition to mammalian cell biology and development.” [54] p. 24

Info-computational approach provides an appropriate framework for studying the

above question of minimal cognition. The advantages of info-computational approaches
to the modeling of cognition are that they bridge the Cartesian gap between matter and
mind, providing a unified naturalist framework for a vast range of phenomena, and they
are testable. Dennett declared in a talk at the International Computers and Philosophy
Conference, Laval, France in 2006: “AI makes philosophy honest.” Paraphrasing Den-
nett we can say that info-computational models make cognition honest - - transparent
and open for critical investigation and experimentation. In that sense parallel research
in biology and cognitive robotics present a “reality check” where our understanding of
cognition, information processing and morphological computation can be tested in a
rigorous manner.
7 Conclusions

Studied as a natural phenomenon, cognition can be seen as info-computational pro-

cesses in living systems. The aim of this article is to present methodological and prac-
tical grounds for a naturalist computational approach to cognition supported by new
experimental results on cognition of simplest living organisms such as bacteria. The
hope is to contribute to the elucidation of the following fundamental questions accord-
ing to [55] [1] and [9]:
What cognition is. The nature of cognition, the question about how the concept of
cognition should be defined. In the info-computational framework it becomes trans-
formed into the question: what in the computing nature is cognition? Cognition for an
adaptive, developing and evolving living agent is the process of learning that operates
according to the PAC (Probably Approximately Correct) strategy [46]. Results from the
studies of natural cognitive systems will help resolve the question concerning artifactual
computational cognition.
How cognition works. Cognition as information processing happening in an infor-
mational network of cognizing agents with distributed computational dynamics con-
nects the agents inside structures with the outside world understood as potential infor-
mation, through interactions. Those interactions include all four levels on which evo-
lution operates: genetic, epigenetic, behavioral, and symbolic [53]. We have shown in
the example of bacterial cognition how all four levels contribute.
What cognition does. By elucidating the info-computational and evolutionary char-
acter of cognition we can understand its agent-dependency, its generative mechanisms
and its life-sustaining and life-propagating role. Cognition is the mechanism that en-
ables cognizing agents to deal with the complexity of the environment, through control
of their own behavior, [52] p. 234.
The info-computational approach can contribute to rethinking cognition as infor-
mation self-organising processes of morphological/chemical/molecular/natural compu-
tation in all living beings. Thus, we can start to learn how to adequately computationally
model living systems, which has up to now been impossible, [33]. “Second generation
computational models” [37] under current development promise to enble us to frame
theoretically, simulate and study living organisms in their full complexity. Based on
current work in the related fields such as information science, computability and theory
of computing, logic, molecular biology, and evolution, a new more coherent picture of
cognition can be expected to emerge. As a complement to Woframs idea of mapping
and mining the computational universe [56] this article suggests mapping and mining
the biological universe with the help of computational tools with the goal to reverse
engineer cognition and find smart cognitive computational strategies.

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