information theory and programmable medicine
DESCRIPTION
Invited talk given at the IEEE International Conference on Bioinformatics and Biomedicine 2013 in Shanghai, China.TRANSCRIPT
Information Theory and ProgrammableMedicine
Hector Zenil
Unit of Computational Medicine, Stockholm, Sweden
Invited TalkIEEE International Conference on Bioinformatics and Biomedicine
(BIBM 2013) December 20, 2013, Shanghai, China
Hector Zenil Information and ProgrammableMedicine 1 / 27
Complexity and Computation in Nature Natural computing
Contents
What is computationSmall computing machines and emergent propertiesThe Turing test and what is (artificial) lifeInformation theory and spatial molecular computationKolmogorov complexity and programmable medicine
Hector Zenil Information and ProgrammableMedicine 2 / 27
Complexity and Computation in Nature Natural computing
The origins of modern computation
J. von Neuman’s self-replication interest (1950s).
von Neumann (with S. Ulam) started the field of Cellular Automata
Hector Zenil Information and ProgrammableMedicine 3 / 27
Complexity and Computation in Nature Natural computing
Cellular Automata
Hector Zenil Information and ProgrammableMedicine 4 / 27
Complexity and Computation in Nature Natural computing
Rule 30 continuation
Hector Zenil Information and ProgrammableMedicine 5 / 27
Complexity and Computation in Nature Natural computing
von Neumann’s universal constructor
Hector Zenil Information and ProgrammableMedicine 6 / 27
Complexity and Computation in Nature Natural computing
Life as self-replication?
Langton’s loop shows that self-replication does not require Turinguniversality.
But crystals self-replicate too, so it cannot be a sufficient condition for life.
Hector Zenil Information and ProgrammableMedicine 7 / 27
Complexity and Computation in Nature Natural computing
What is life?
An informational definition (Gerald F. Joyce, Bit by Bit: The Darwinian Basis ofLife, PloS, Bio. 2012) of life:
A genetic system that contains more bits than the number thatwere required to initiate its operation.
A computational view (John Hopfield, J. Theor. Biol. 171, 53-60, 1994):
All biological systems perform some kind of computation.Computation is inherent to adaptive systems and makes biologydifferent from physics.
A mechanistic view (Leroy Cronin, TED conference, 2011) proposes that:
Life is anything that can undergo evolution (survival of thefittest). Matter that can evolve is alive.
Borderline case: Virus evolve (not exactly by their own though) yet they areonly matter (encapsulated genetic material).
Hector Zenil Information and ProgrammableMedicine 8 / 27
Complexity and Computation in Nature A behavioural approach to computation
A behavioural approach to what is computation(and life)The Turing test is a reformulation of a question of non-factual character into ameasurable one: something is intelligent if it behaves like so. It is a clever strategyto tackle difficult questions!
Figure : A Turing-test like test strategy to the question of life (instead of machineintelligence)
[Zenil, Philosophy & Technology, Springer (2013)]Hector Zenil Information and ProgrammableMedicine 9 / 27
Complexity and Computation in Nature A behavioural approach to computation
A Turing test like approach to computation and life
[Zenil in Computing Nature, & SAPERE Series, Springer (2013)]
How to chemically recognize artificial life? (Cronin, Krasnogor, et al, NatureBiotechnology 2006). Talking to the cells with chells.
How closely simulators emulate the properties of real data (e.g. in silico reconstructionof genetic networks from synthetically generated gene expression data) (Maier et al., ATuring test for artificial expression data, Bioinformatics (2013) 29 (20): 2603-2609, 2013).
Hector Zenil Information and ProgrammableMedicine 10 / 27
Complexity and Computation in Nature A behavioural approach to computation
Algorithmic information theory to the rescue?
Which string looks more random?
(a) 1111111111111111111111111111111111111111(b) 0011010011010010110111010010100010111010(c) 0101010101010101010101010101010101010101
Definition
KU(s) = min{|p|,U(p) = s} (1)
Compressibility and algorithmic randomnessA string with low Kolmogorov complexity is c-compressible if |p| + c = |s|. Astring is random if K(s) ≈ |s|.
[Kolmogorov (1965); Chaitin (1966)]Hector Zenil Information and ProgrammableMedicine 11 / 27
Complexity and Computation in Nature A behavioural approach to computation
Behavioural classes of abstract computingmachines
Wolfram’s computational classes of behaviour:
Class I: system evolves into a homogeneous state.Class II: system evolves in a periodic state.Class III: system evolves into random-looking states.Class IV: system evolves into localised complex structures.
Living systems clearly fall in class IV systems.
[Wolfram, (1994)]
Hector Zenil Information and ProgrammableMedicine 12 / 27
Complexity and Computation in Nature A behavioural approach to computation
Asymptotic behaviour of compressed evolutions
[Zenil, Complex Systems (2010)]Hector Zenil Information and ProgrammableMedicine 13 / 27
Complexity and Computation in Nature A behavioural approach to computation
A behavioural approach to computation (and liferecognition)A Turing-test like test strategy to the question of life (instead of Turing’soriginal question of artificial intelligence):
[Zenil, Philosophy & Technology and SAPERE, (2013)]Hector Zenil Information and ProgrammableMedicine 14 / 27
Complexity and Computation in Nature A behavioural approach to computation
Answering Chalmer’s rock question
Figure : ECA R4 has a low Ctn value for any n and t (it doesn’t react much to external
stimuli).
[Zenil, Philosophy & Technology, (2013)]Hector Zenil Information and ProgrammableMedicine 15 / 27
Complexity and Computation in Nature A behavioural approach to computation
Turing universality
Figure : ECA R110 has large asymptotic coefficient Ctn value for large enough choices
of t and n, which is compatible with the fact that it is Turing universal (for particularsemi-periodic initial configurations).
Hector Zenil Information and ProgrammableMedicine 16 / 27
Complexity and Computation in Nature A behavioural approach to computation
A hierarchical view of computing systems (and life?)The measure can be applied to other than computers.Programmability of physical and biological entities sorted by variabilityversus controllability:
The diagonal determines the degree of programmability.
[Zenil, Ball, Tegner, ECAL MIT Press Proceedings, (2013)]Hector Zenil Information and ProgrammableMedicine 17 / 27
Complexity and Computation in Nature A behavioural approach to computation
Proof of concept: The EMBL-EBI BioModel’sDatabase
The EMBL-EBI BioModel DB is a curated database of mathematical published(about 400) models related to living organisms.
Hector Zenil Information and ProgrammableMedicine 18 / 27
Complexity and Computation in Nature A behavioural approach to computation
Cell cycle versus metabolic pathways
Variability analysis: Models cluster by their role in living processes.
[Zenil, Ball, Tegner, ECAL MIT Press Proceedings, (2013)]Hector Zenil Information and ProgrammableMedicine 19 / 27
Complexity and Computation in Nature A behavioural approach to computation
Variability and controllability of biologicalmodels
Information content trajectories(from EMBL-EBI model simulations):
Programmability is a combination of variability and controllability
[Zenil, Ball, Tegner, ECAL MIT Press Proceedings, (2013)]Hector Zenil Information and ProgrammableMedicine 20 / 27
Complexity and Computation in Nature A behavioural approach to computation
The main challenges in biology
Parameter to conformational space mapping in biological systems from thefact that shape is function in biology!
DNA sequence→ protein structure mapping / Signalling→ cellsself-organization
Environmental conds. → virus mutations / drugs→ diseases reaction
I call it the conformational space problem in biology.Hector Zenil Information and ProgrammableMedicine 21 / 27
Complexity and Computation in Nature A behavioural approach to computation
Case study: Phorphyrin molecules simulation withWang tilesPorphyrin interaction dynamics are extensively well known and accuratemathematical models exist. We ran a kinetic Monte Carlo simulation on 2different porphyrin molecules deposited on a solid substrate. Porphyrinsself-assemble in structures depending on the binding energy between:
molecules of the same functional typemolecules of different (2) functional typemolecules and the substrate
(They give red color to blood. They envelop hemes in hemoglobin that delivernutrients (in particular oxygen!).)
[Terrazas, Zenil and Krasnogor, Exploring programmable self-assembly in non-DNAbased molecular computing, Natural Computing, vol 12(4), pp 499–515, 2013.]Hector Zenil Information and ProgrammableMedicine 22 / 27
Complexity and Computation in Nature A behavioural approach to computation
Self-assembly of porphyrin molecules
How to map stimuli (energy binding) to conformational space?
With information theory and Kolmogorov complexity.
[Terrazas, Zenil and Krasnogor, Exploring programmable self-assembly in non-DNAbased molecular computing, Natural Computing, vol 12(4), pp 499–515, 2013.]
Hector Zenil Information and ProgrammableMedicine 23 / 27
Complexity and Computation in Nature A behavioural approach to computation
Phorphyrins: mapping behaviour to stimuli
Binding energies induced by chemical reactions with highest behaviouralimpact can be tested and programmed in silico and verified in the wet lab.
(Hemes in hemoglobin. They give the red color to blood)
[Terrazas, Zenil and Krasnogor, Exploring programmable self-assembly in non-DNAbased molecular computing, Natural Computing, vol 12(4), pp 499–515, 2013.]
Hector Zenil Information and ProgrammableMedicine 24 / 27
Complexity and Computation in Nature A behavioural approach to computation
Phorphyrins: mapping behaviour to stimuli
Binding energies induced by chemical reactions with highest behaviouralimpact can be tested and programmed in silico and verified in the wet lab.
(Hemes in hemoglobin. They give the red color to blood)
[Terrazas, Zenil and Krasnogor, Exploring programmable self-assembly in non-DNAbased molecular computing, Natural Computing, vol 12(4), pp 499–515, 2013.]
Hector Zenil Information and ProgrammableMedicine 25 / 27
Complexity and Computation in Nature A behavioural approach to computation
Capturing and clustering behaviour
The compressibility test retrieved phase transitions corresponding to changesin qualitative behaviour. Qualitative behaviour is captured by a quantitativemeasure.
Corresponding to different stimuli
[Terrazas, Zenil and Krasnogor, Exploring programmable self-assembly in non-DNAbased molecular computing, Natural Computing, vol 12(4), pp 499–515, 2013.]Hector Zenil Information and ProgrammableMedicine 26 / 27
Complexity and Computation in Nature A behavioural approach to computation
Towards programmable medicine
Building on molecular such as porphyrin computation imagine, for example,the introduction of an array of these molecules with a simple logic totreatments releasing a payload if expressing certain conditions (e.g. cancermarkers) are met.
Hector Zenil Information and ProgrammableMedicine 27 / 27
Complexity and Computation in Nature A behavioural approach to computation
H. Zenil, Compression-based Investigation of the Dynamical Properties ofCellular Automata and Other Systems, Complex Systems, Vol. 19, No. 1, pages1-28, 2010.
H. Zenil, What is Nature-like Computation? A Behavioural Approach and aNotion of Programmability, Philosophy & Technology (special issue on Historyand Philosophy of Computing), 2013.
H. Zenil, On the Dynamic Qualitative Behavior of Universal ComputationComplex Systems, vol. 20, No. 3, pp. 265-278, 2012.
G. Terrazas, H. Zenil and N. Krasnogor, Exploring Programmable Self-Assemblyin Non DNA-based Computing, Natural Computing, vol 12(4): 499–515, 2013.DOI: 10.1007/s11047-013-9397-2.
H. Zenil and E. Villarreal-Zapata, Asymptotic Behaviour and Ratios of Complexityin Cellular Automata Rule Spaces, Journal of Bifurcation and Chaos (in press).
H. Zenil, G. Ball and J. Tegner, Testing Biological Models for Non-linearSensitivity with a Programmability Test. In P. Lio, O. Miglino, G. Nicosia, S. Nolfiand M. Pavone (eds), Advances in Artificial Intelligence, ECAL 2013, pp.1222-1223, MIT Press, 2013.
H. Zenil, A Turing Test-Inspired Approach to Natural Computation. In G.Primiero and L. De Mol (eds.), Turing in Context II (Brussels, 10-12 October 2012),
Hector Zenil Information and ProgrammableMedicine 27 / 27
Complexity and Computation in Nature A behavioural approach to computation
Historical and Contemporary Research in Logic, Computing Machinery andArtificial Intelligence, Proceedings published by the Royal Flemish Academy ofBelgium for Science and Arts, 2013.
A Behavioural Foundation for Natural Computing and a Programmability Test. InG. Dodig-Crnkovic and R. Giovagnoli (eds), Computing Nature: Turing CentenaryPerspective, SAPERE Series vol. 7, Springer, 2013.
H. Zenil, Turing Patterns with Turing Machines: Emergence and Low-levelStructure Formation, Natural Computing, 12(2): 291-303 (2013), 2013.
J.-P. Delahaye and H. Zenil, Numerical Evaluation of the Complexity of ShortStrings: A Glance Into the Innermost Structure of Algorithmic Randomness,Applied Mathematics and Computation 219, pp. 63-77, 2012.
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