Biological Information Processing as Natural Computation

Full text

1
Biological Information Processing as Natural Computation
Gordana Dodig Crnkovic
Gordana
Dodig
Crnkovic
School of Innovation, Design and
Engineering
Mälardalen
University
Engineering
,
Mälardalen
University
,
Sweden
European conference on Computing and Philosophy, E-CAP 2009
The Universitat Autònoma de Barcelona http://ia-cap.org/e-cap09
/

2
Natural Computation
Natural
Computation
If t ti i t b bl t t h th b bl t l
If
compu
t
a
ti
on
i
s
t
o
b
e a
bl
e
t
o ma
t
c
h
th
e o
b
serva
bl
e na
t
ura
l
phenomena, relevant characteristics in natural computation should
be incorporated in new models of computation such as: adequacy,
generality and flexibility of real
-
time response adaptability and
generality
and
flexibility
of
real
-
time
response
,
adaptability
and
robustness. (MacLennan, 2004)

3
Info
Computationalism
Info
-
Computationalism
Information and com
p
utation are two interrelated and mutuall
y
definin
g
pyg
phenomena – there is no computation without information (computation
understood as information processing), and vice versa, there is no
information without computation (all information is a result of computational
processes).
Being interconnected information is studied as a structure while
Being
interconnected
,
information
is
studied
as
a
structure
,
while
computation presents a process on an informational structure.

4
Information
A special issue of the
Journal of Logic Language and Information
Information
Journal
of
Logic
,
Language
and
Information
(Volume 12 No 4 2003) dedicated to the different
facets of information.
A Handbook on the Philosophy of Information
(Van Benthem, Adriaans) is in preparation as one
volume Handbook of the philosophy of science.
htt // ill l/HPI/
htt
p:
//
www.
ill
c.uva.n
l/HPI/
The Internet
http://www.sdsc.edu/News%20Items/P
R022008_moma.html

5
Information
“IT IS TEMPTING TO SUPPOSE THAT SOME CONCEPT OF
Information
“IT
IS
TEMPTING
TO
SUPPOSE
THAT
SOME
CONCEPT
OF
INFORMATION COULD SERVE EVENTUALLY TO UNIFY MIND,
MATTER, AND MEANING IN A SINGLE THEORY.”
Daniel C. Dennett And John Haugeland. Intentionality.
in Richard L. Gregory, Editor. The Oxford Companion To The Mind. Oxford University
Press, Oxford, 1987.

6
Computation
The
Computing Universe: Pancomputationalism
The
Computing
Universe:
Pancomputationalism
C t ti i ll d fi d i f ti i
C
ompu
t
a
ti
on
i
s genera
ll
y
d
e
fi
ne
d
as
i
n
f
orma
ti
on process
i
ng.
(See Burgin, M., Super-Recursive Algorithms, Springer Monographs in
Com
p
uter Science, 2005
)
p)
For different views see e.g.
http://people.pwf.cam.ac.uk/mds26/cogsci/program.html Computation and
Cognitive Science 7–8 July 2008, King's College Cambridge
The definition of computation is widely debated, and an entire issue of the
journal Minds and Machines (1994, 4, 4) was devoted to the question
“Wh t i C t ti ?”
E
Th ti l C t S i 317 (2004)
“Wh
a
t
i
s
C
ompu
t
a
ti
on
?”
E
ven:
Th
eore
ti
ca
l
C
ompu
t
er
S
c
i
ence
317
(2004)

7
Computing Nature and
Computing
Nature
and
Nature Inspired Computation
In 1623, Galileo in his book Il Saggiatore - The Assayer - , claimed
that the language of nature's book is mathematics and that the way
to understand nature is through mathematics
Generalizing
to
understand
nature
is
through
mathematics
.
Generalizing
”mathematics” to ”computation” we may agree with Galileo – the
great book of nature is an (self-generating) e-book!
J
ournals: Natural Com
p
utin
g
,
I
EEE Transactions on Evolutionar
y
Com
p
utation
,
pg
,
yp
,
International Journal of Natural Computing Research

8
Turing Machines Limitations –
Self
Generating Living Systems
Self
-
Generating
Living
Systems
Complex biological systems must be modeled as self
referential self
organizing
Complex
biological
systems
must
be
modeled
as
self
-
referential
,
self
-
organizing
"component-systems" (George Kampis) which are self-generating and whose
behavior, though computational in a general sense, goes far beyond Turing
machine model
machine
model
.
“a component system is a computer which, when executing its operations
( f ) b ild h d [W] h h
iilfi
(
so
f
tware
)
b
u
ild
s a new
h
ar
d
ware....
[W]
e
h
ave a computer t
h
at re
-
w
i
res
i
tse
lf
i
n a
hardware-software interplay: the hardware defines the software and the software
defines new hardware. Then the circle starts again.”
(Kampis, p. 223 Sel
f
-Modifying Systems in Biology and Cognitive Science)

9
Be
y
ond Turin
g
Machines
Ever since Turing proposed his machine model which identifies
computation
with the
execution of an
algorithm
there have been
yg
computation
with
the
execution
of
an
algorithm
,
there
have
been
questions about how widely the Turing Machine (TM) model is
applicable.
With the advent of computer networks, which are the main paradigm
of computing today, the model of a computer in isolation,
represented by a Universal Turing Machine, has become insufficient.
The basic difference between an isolated computing box and a
network of computational processes (nature itself understood as a
tti l h i )i th
it tiit
fttiTh
compu
t
a
ti
ona
l
mec
h
an
i
sm
)
i
s
th
e
i
n
t
erac
ti
v
ity
o
f
compu
t
a
ti
on.
Th
e
most general computational paradigm today is interactive computing
(Wegner, Goldin).

10
Be
y
ond Turin
g
Machines
The challenge to deal with
computability in the real world
(such as
yg
The
challenge
to
deal
with
computability
in
the
real
world
(such
as
computing on continuous data, biological computing/organic
computing, quantum computing, or generally natural computing) has
brought new understanding of computation.
Natural computing has different criteria for success of a computation,
halting problem is not a central issue, but instead the adequacy of the
comp tational response in a net ork of interacting comp tational
comp
u
tational
response
in
a
net
w
ork
of
interacting
comp
u
tational
processes/devices. In many areas, we have to computationally model
emergence not being clearly algorithmic. (Barry Cooper)

11
Correspondence
Principle
Correspondence
Principle
Natural Computation
TM
picture after Stuart A. Umpleby
http://www.gwu.edu/~umpleby/recent_papers/2004_what_i_learned_from_heinz_von_foerster_fig
ures_by_umpleby.htm

12
Computability Theory
Barry Cooper
http://www.amsta.leeds.ac.uk/~pmt6sbc/

13
Naturalist Understanding of Cognition
An idea that knowledge may be studied as a natural phenomenon
(
Naturalized e
p
istemolo
gy
- Feldman
,
Kornblith
,
Stich
)
im
p
lies that the sub
j
ect
(pgy
,
,
)p j
matter of epistemology is not our concept of knowledge, but the knowledge
itself.
“The stimulation of his sensory receptors is all the evidence anybody has had
to go on, ultimately, in arriving at his picture of the world. Why not just see
how this construction really proceeds?
Why not settle for psychology?
how
this
construction
really
proceeds?
Why
not
settle
for
psychology?
“("Epistemology Naturalized", Quine 1969; emphasis mine)
Iill
hth titb
Wh t ttl f ti ?
I
w
ill
re-p
h
rase
th
e ques
ti
on
t
o
b
e:
Wh
y no
t
se
ttl
e
f
or compu
ti
ng
?
(Computing of knowledge from information)

14
Naturalist
Understanding
of
Cognition
Naturalist
Understanding
of
Cognition
Adit
Mt
d V l (1980) th i l t i
A
ccor
di
ng
t
o
M
a
t
urana an
d
V
are
l
a
(1980)
even
th
e s
i
mp
l
es
t
organ
i
sms
possess cognition and their meaning-production apparatus is contained in
their metabolism. Of course, there are also non-metabolic interactions with
the environment, such as locomotion, that also generates meaning for an
organism by changing its environment and providing new input data.
Maturana’s and Varelas’ understanding that all living organisms posess
some cognition, in some degree. is most suitable as the basis for a
computationalist account of the naturalized evolutionary epistemology
computationalist
account
of
the
naturalized
evolutionary
epistemology
.

15
Info-Computational Account of
Knowledge Generation
Natural computing as a new paradigm of computing goes
bdthTiMhi dldlitll
Knowledge
Generation
b
eyon
d
th
e
T
ur
i
ng
M
ac
hi
ne mo
d
e
l
an
d
app
li
es
t
o a
ll
physical processes including those going on in our brains.
The next great change in computer science and information
technology will come from mimicking the techniques by
which biolo
g
ical or
g
anisms
p
rocess information.
gg p
To do this computer scientists must draw on expertise in
subjects not usually associated with their field including
subjects
not
usually
associated
with
their
field
,
including
organic chemistry, molecular biology, bioengineering, and
smart materials.

16
Info-Computational Account of
Knowledge Generation
Knowledge
Generation
At the physical level, living beings are open complex computational systems in
a regime on the edge of chaos, characterized by maximal informational
content Complexity is found between orderly systems with high information
content
.
Complexity
is
found
between
orderly
systems
with
high
information
compressibility and low information content and random systems with low
compressibility and high information content. (Flake)
The essential feature of cognizing living organisms is their ability to manage
complexity, and to handle complicated environmental conditions with a variety
complexity,
and
to
handle
complicated
environmental
conditions
with
a
variety
of responses which are results of adaptation, variation, selection, learning,
and/or reasoning. (Gell-Mann)

17
Cognition as Restructuring of an Agent in Interaction with
the Environment
the
Environment
Altfltiiilllii iitht
A
s a resu
lt
o
f
evo
l
u
ti
on,
i
ncreas
i
ng
l
y comp
l
ex
li
v
i
ng organ
i
sms ar
i
se
th
a
t
are
able to survive and adapt to their environment. It means they are able to
register inputs (data) from the environment, to structure those into
information, and in more developed organisms into knowledge. The
evolutionary advantage of using structured, component-based approaches
is improvin
g
response-time and efficienc
y
of co
g
nitive processes of an
g
yg
organism.
The Dual network model, suggested by
Goertzel
for modeling cognition in a
The
Dual
network
model,
suggested
by
Goertzel
for
modeling
cognition
in
a
living organism describes mind in terms of two superposed networks: a self-
organizing associative memory network, and a perceptual-motor process
hierarchy with the multi
-
level logic of a flexible command structure
hierarchy
,
with
the
multi
-
level
logic
of
a
flexible
command
structure
.

18
Cognition as Restructuring of an Agent in Interaction with
the Environment
the
Environment
Nt li dk ld ti k ld th bd b i
N
a
t
ura
li
ze
d
k
now
l
e
d
ge genera
ti
on ac
k
now
l
e
d
ges
th
e
b
o
d
y as our
b
as
i
c
cognitive instrument. All cognition is embodied cognition, in both
microorganisms and humans (Gärdenfors, Stuart). In more complex
cognitive agents, knowledge is built upon not only reasoning about input
information, but also on intentional choices, dependent on value systems
stored and or
g
anized in a
g
ents memor
y
.
gg y
It is not surprising that present day interest in knowledge generation places
information and computation (communication) in focus, as information and its
information
and
computation
(communication)
in
focus,
as
information
and
its
processing are essential structural and dynamic elements which characterize
structuring of input data (data →information →knowledge) by an interactive
computational process going on in the agent during the adaptive interplay
computational
process
going
on
in
the
agent
during
the
adaptive
interplay
with the environment.

19
Natural Computing in Cognizing Agents
- Agent-centered (information and
computation is in the agent)
- Agent is a cognizing biological organism
or an intelligent machine or both
-Interaction with the physical world and
other agents is essential
- Kind of physicalism with information as a
s
t
u
ff
o
f th
e
u
niv
e
r
se
su o e
uese
- Agents are parts of different cognitive
communities
-
Self
-
organization
-
Self
-
organization
- Circularity (recursiveness) is central for
biological organisms
http://www.conscious-robots.com

20
Self-Reflection
http://brain.oxfordjournals.org/cgi/content/full/125/8/1808

21
What is computation? How does nature compute?
Learning
from Nature
*
Learning
from
Nature
“
It always bothers me that according to the laws as we understand them
It
always
bothers
me
that
,
according
to
the
laws
as
we
understand
them
today, it takes a computing machine an infinite number of logical
operations to figure out what goes on in no matter how tiny a region of
space, and no matter how tiny a region of time …
space,
and
no
matter
how
tiny
a
region
of
time
…
So I have often made the hypothesis that ultimately physics will not require a
mathematical statement
,
that in the end the machiner
y
will be revealed
,
,y,
and the laws will turn out to be simple, like the chequer board with all its
apparent complexities.”
Richard Feynman “The Character of Physical Law”
* 2008 Midwest NKS Conference, Fri Oct 31 - Sun Nov 2, 2008
Indiana University — Bloomington, IN

22
Summary: An Ongoing Paradigm Shift
•Information/Computation as basic building blocks of understanding
•Discrete/Continuum as two complementary levels of description
•Natural interactive computing beyond Turing limit – not only computing as is
but also computing as it may be
•Complex dynamic systems (grounds for future communication across
cultural
g
a
p
s of research
)
gp )

23
Summary: An Ongoing Paradigm Shift
•Emergency (emergent property - a quality possessed by the whole but not by its parts)
•Logical pluralism
•Philosophy (“Everything must go” approach synthetic besides analytic
approaches)
•Human-centric (agent-centric) models
•Circularity and self-reflection (computing, cybernetics)
Ethics returns to researchers agenda (Science as a constructivist project
•
Ethics
returns
to
researchers
agenda
(Science
as
a
constructivist
project
–
what is it we construct and why?)

24
INFORMATION AND COMPUTATION
Forthcoming Book by World Scientific Publishing Co.
Dr Gordana Dodig
Crnko ic (Mälardalen Uni ersit S eden) and
Dr
.
Gordana
Dodig
-
Crnko
v
ic
(Mälardalen
Uni
v
ersit
y,
S
w
eden)
and
Dr. Mark Burgin (UCLA, USA), Editors
GChiti
Mth ti bil i l
G
reg
Ch
a
iti
n -
M
a
th
ema
ti
cs as
bi
o
l
og
i
ca
l
process
Jean-Paul Delahaye & Hector Zenil - On the algorithmic nature of the world
Barry Cooper - From Descartes to Turing: The computational Content of
Supervenience
Søren Brier - Cybersemiotics and the question of knowledge
Christophe Menant
-
Computation on Information, Meaning and Representations.
Christophe
Menant
Computation
on
Information,
Meaning
and
Representations.
An Evolutionary Approach
Oron Shagrir - A Sketch of a Modeling View of Computing
John Collier
Information computation measurement and irreversibility
John
Collier
-
Information
,
computation
,
measurement
and
irreversibility
Walter Riofrio - Insights into the biological computing
Aaron Sloman - What's information, for an organism or intelligent machine? How
?
can a machine or organism mean
?

25
INFORMATION AND COMPUTATION
Forthcoming Book by World Scientific Publishing Co.
Dr Gordana Dodig
Crnko ic (Mälardalen Uni ersit S eden) and
Vladik
Kreinovich & Roberto
Araiza
Analysis of Information and Computation in
Dr
.
Gordana
Dodig
-
Crnko
v
ic
(Mälardalen
Uni
v
ersit
y,
S
w
eden)
and
Dr. Mark Burgin (UCLA, USA), Editors
Vladik
Kreinovich
&
Roberto
Araiza
-
Analysis
of
Information
and
Computation
in
Physics Explains Cognitive Paradigms
Darko Roglic - Super-recursive features of natural evolvability processes and the
dl
f
tti l
lti
mo
d
e
l
s
f
or compu
t
a
ti
ona
l
evo
l
u
ti
on
C.N.J. de Vey Mestdagh & J.H. Hoepman - Inconsistent information as a natural
phenomenon
Gordana Dodig Crnkovic and Vincent Mueller - A Dialogue Concerning Two
Possible World Systems
Wolf
g
an
g
Hofkirchner - Does Com
p
utin
g
Embrace Self-Or
g
anisation?
gg
pg
g
Bruce J. MacLennan - Bodies — Both Informed and Transformed
Mark Burgin - Information Dynamics in a Categorical Setting
Marvin Minsky
Interior
Grounding
Reflection
and
Self
Consciousness
Marvin
Minsky
-
Interior
Grounding
,
Reflection
,
and
Self
-
Consciousness

26
References
Gordana Dodig-Crnkovic
Semantics of Information as Interactive Computation
in Manuel
Moeller
Wolfgang
Neuser
and Thomas Roth
-
Berghofer (eds )
in
Manuel
Moeller
,
Wolfgang
Neuser
,
and
Thomas
Roth
Berghofer
(eds
.
)
,
Fifth International Workshop on Philosophy and Informatics, Kaiserslautern
2008 (DFKI Technical Reports; Berlin: Springer)
Gordana Dodig
-
Crnkovic
Gordana
Dodig
-
Crnkovic
Where do New Ideas Come From? How do They Emerge?
Epistemology as Computation (Information Processing)
Chapter
for a
book
celebrating
the work of Gregory
Chaitin
,
Chapter
for
a
book
celebrating
the
work
of
Gregory
Chaitin
,
Randomness & Complexity, from Leibniz to Chaitin,
C. Calude ed., World Scientific, Singapore, 2007 Book Cover
Gordana Dodig
-
Crnkovic
Gordana
Dodig
Crnkovic
Epistemology Naturalized: The Info-Computationalist Approach
APA Newsletter on Philosophy and Computers, Spring 2007 Volume 06,
Number
2
Number
2

27
Gordana Dodig
Crnkovic
References
Gordana
Dodig
-
Crnkovic
Knowledge Generation as Natural Computation,
Proceedings of International Conference on Knowledge Generation,
Communication and Management (KGCM 2007), Orlando, Florida, USA, July
8
11 2007
8
-
11
,
2007
Gordana Dodig-Crnkovic
Investigations
into
Information
Semantics
and Ethics of
Computing
Investigations
into
Information
Semantics
and
Ethics
of
Computing
PhD Thesis, Mälardalen University Press, September 2006
Dodig-Crnkovic G. and Stuart S., eds.
C t ti I f ti C iti
Th N d Th
Li i l
C
ompu
t
a
ti
on,
I
n
f
orma
ti
on,
C
ogn
iti
on
–
Th
e
N
exus an
d
Th
e
Li
m
i
na
l
Cambridge Scholars Publishing, Cambridge 2007
Gordana Dodig
-
Crnkovic
Gordana
Dodig
Crnkovic
Shifting the Paradigm of the Philosophy of Science: the Philosophy of
Information and a New Renaissance
Minds and Machines: Special Issue on the Philosophy of Information,
November
2003 Volume 13 Issue 4
November
2003
,
Volume
13
,
Issue
4
http://www.springerlink.com/content/g14t483510156726/