DNA Information: Laws of Perception

98 Pages·2015·2.657 MB·English

by  Georgi Muskhelishvili (auth.)

SPRINGER BRIEFS IN BIOCHEMISTRY AND
MOLECULAR BIOLOGY
Georgi Muskhelishvili
DNA Information:
Laws of
Perception
123
SpringerBriefs in Biochemistry
and Molecular Biology
More information about this series at http://www.springer.com/series/10196
Georgi Muskhelishvili
DNA Information: Laws
of Perception
123
Georgi Muskhelishvili
School ofEngineering andScience
JacobsUniversity
Bremen
Germany
ISSN 2211-9353 ISSN 2211-9361 (electronic)
SpringerBriefs inBiochemistry and MolecularBiology
ISBN 978-3-319-17424-2 ISBN 978-3-319-17425-9 (eBook)
DOI 10.1007/978-3-319-17425-9
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Preface
The suggestion to write this booklet was provoked by our article published in one
of the Springer journals and describing the DNA double helix as a coding device
carrying two logically distinct types of information. The idea behind this is over a
decade old. In the experiments carried out in mid-1990s together with Andrew
Travers and Malcolm Buckle, we stumbled over a striking phenomenon indicating
that during the injection of DNA binding proteins into a flowcell with surface-
immobilized DNA fragments, the DNA molecules successively adopted different
dynamic configurations. These distinct configurations were directly pertinent to
regulationofgeneticfunctionandthus,embodiedinformation,butincontrasttothe
genetic code, this information was not discrete, but rather continuous, as it
depended by large on the distribution of torsional strain in the DNA molecule. To
distinguish this latter from the digital genetic code, the continuous DNA infor-
mation was subsequently dubbed analog code.
In principle, the relationship between the analog and digital DNA codes is akin
to the relationship between the syntax and semantics of natural language. It
occurred to me that a closer examination of this remarkable similarity between the
most ancient coding device and the most recently invented means of social com-
munication was worth trying. But how can one bridge so widely disparate phe-
nomena?It was clear from theoutsetthat thebooklet woulddealwith information
in a most broad sense, and that the definition of the term “information” would be
crucialfortheentireenterprise.ItookadvantageofGregoryBateson’sdefinitionof
information. In common sense, information is something that is transmitted, but
Bateson maintained that for example, for the tax office an unpaid tax bill is also
information, although in such a case, nothing is being transmitted.
In this booklet I argue that application of the double-coding principle of DNA
informationto variousfields of scientific inquiry enablesto relate widely disparate
phenomena within a common exegetic framework, with a notable caveat that dis-
tincttypesofinformationcannotbegraspedsimultaneously.Thispeculiaritycanbe
fathomedbytheHinduconceptofAdhyasa,describingoscillationoftheminddue
toambiguityinidentifying,whetheranobjectontheroadisasnake,orarope.This
phenomenon of oscillation of our perception obtains a deeper meaning with
v
vi Preface
examples from natural science and especially, the indeterminacy principle of
quantumphysics.Inallsuchcasesoneinferenceexcludestheother,andthishasin
turnagenuinesimilaritytotheproblemscausedbylogicalparadoxes.AndasItry
to show in this booklet, all this has something to do with our perception of time.
Inanutshell,thisbookletisanattempttoshowthatthebasicdeviceofcreating
information in the living world, including our perception and social communica-
tion, is already provided in structural organisation of the DNA molecule, which
alike the human mind, has a property of both, distinctness and wholeness to it.
I surmise that it is this highly elaborate double coding mechanism with two
structurallycoupledcodesmutuallydeterminingeachother,whichprovidesforthe
wholeness that no artificial device can ever attain.
I am grateful to Beatrice Menz for motivating me to write this booklet and to
Jutta Lindenborn for her care and professional assistance. I am greatly indebted to
mycolleagues,especiallyAndrewTraverstowhomIowealot,andthemembersof
mylaboratoryforthecountlessdiscussionsofmanyofthetopicsaddressedinthis
booklet. I am grateful to Marc-Thorsten Hütt for his comments on regulatory
networks, to Levan Muskhelishvili for helpful comments on the contents of the
manuscript, and to Joel Wellbourne-Wood for editing the text. I owe a debt of
gratitude tothelate VasilMakhaldiani for coining theterm“optimalcooperation”.
To his memory I dedicate this book.
Bremen Georgi Muskhelishvili
Contents
1 Introduction: Some Facts About Our Universe . . . . . . . . . . . . . . . 1
Information as a “Difference that Makes a Difference”. . . . . . . . . . . . 2
Abstract Knowledge Versus Direct Perception. . . . . . . . . . . . . . . . . . 3
Distinction and the Directionality of Choice . . . . . . . . . . . . . . . . . . . 4
The Difference Between Animate and Inanimate Matter . . . . . . . . . . . 7
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2 Problems of Logical Typing: The “One” and the “Unity”. . . . . . . . 11
Confusion of Logical Types Beget Paradoxes . . . . . . . . . . . . . . . . . . 12
Russell’s Paradox. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Bohr’s Complementarity Principle . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Application of the Axiomatic Method to the Real World. . . . . . . . . . . 16
Gödel’s Formal System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Gödel’s Mapping. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Analogy Between the Formal System and the Genetic System. . . . . . . 20
Differences of Logical Typing in the Formal and Genetic Systems. . . . 21
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
3 Logical Typing and the Notion of Time in Biology. . . . . . . . . . . . . 25
Saint Augustine’s Conjecture. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Time as an Interval Between Successive Distinctions . . . . . . . . . . . . . 28
A Little Bit of Evolution Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
The Essential Biological Unit of Evolution . . . . . . . . . . . . . . . . . . . . 31
The Replicator Hypothesis and Errors of Logical Typing . . . . . . . . . . 33
A Little of Methodology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Autopoiesis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
vii
viii Contents
4 Organization of the Genetic System: Proteins as Vehicles
of Distinction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Transcriptional Regulatory Network. . . . . . . . . . . . . . . . . . . . . . . . . 45
The Couplon Matrix. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Digital and Analog Control of Gene Expression. . . . . . . . . . . . . . . . . 49
Two Types of Information in the DNA. . . . . . . . . . . . . . . . . . . . . . . 50
DNA Supercoiling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
The Role of Supercoiling in Shaping the DNA . . . . . . . . . . . . . . . . . 53
Changes of Supercoiling and Digitalization of DNA Transactions . . . . 55
Structural Coupling and Reciprocal Determination. . . . . . . . . . . . . . . 58
The Spatiotemporal Model of Genetic Regulation . . . . . . . . . . . . . . . 59
Chromosomal Perception . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
5 Harnessing Energy and Information: Time-Irreversibility
of Thermodynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
The Nature of the Second Law . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Optimal Cooperation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Organizational Invariance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Thermodynamics of Living Systems. . . . . . . . . . . . . . . . . . . . . . . . . 73
Conversion of Energy into Information in a Sociopolitical System. . . . 74
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
6 Social Communications and Logical Typing
in the Social System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Language as a Means of Structural Coupling. . . . . . . . . . . . . . . . . . . 82
Similarities Between the Social and Genetic Systems . . . . . . . . . . . . . 83
Shannon Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Chapter 1
Introduction: Some Facts About
Our Universe
Einstein:Thisisapurelyhumanconceptionoftheuniverse.
Tagore:Therecanbenootherconception.Thisworldisa
humanworld—thescientificviewofitisalsothatofthe
scientificman.
—WhenEinsteinmetTagore
Abstract The scientific “truths” appearing as coherent constructions connecting
the scientifically verified observations by the rules of logic are always relative and
neverabsolute.Furthermore,thereisagenericlimitationofthetheoriesandabstract
models of reality as such, which become overly conspicuous in the attempts to
epitomizetheprocessoflife.Thisissimplybecauselifeissomethingmostrealand
tangible to us. Strictly speaking it is our direct experience, such that life and
perception are inseparable and therefore, the device of our perception yields the
onlymodel-freeapproachtotheprocessoflife.Onlyifwechooseourperceptionas
a guide and observe ourselves unobstructed by any preconceived ideas, we do not
violate our own nature. Therefore, we shall get to grips with operation of a most
ancienttypeofinformation-generatingdevicematerializedonthisplanetandrelate
its organizational logic to the operation of our perception.
(cid:1) (cid:1) (cid:1) (cid:1)
Keywords Epistemology Abstract knowledge Perception Information
(cid:1) (cid:1)
Paradigm shifts Distinction and directional choice Animate and inanimate
(cid:1)
matter Dissipative systems
TheageofourUniverseisestimatedtobeabout13.8billionyears.Thetimeelapsed
after the emergence of life on our planet approximately corresponds to the last
quarterofthiscosmicperiod.Humanbeingshavebeenonstageforonlyabout0.1%
of the entire time since the origin of life, whereas the period of human civilization
(ca. 6000 years) comprises about 2 % of the time elapsed after the emergence of
“primitive” men. While our scientific data concerning the physical world grew
exponentiallyduringthelast100yearsorso,thetotalmattermadeaccountableby
elementary particle physics comprises just a few percent of the entire known
Universe. The rest, called“dark matter and energy,”remains unknown.
The human body is a universe on its own right. Whereas we all originate in a
unique fertilized egg, our body contains about a hundred trillion of cells in total,
andourintestineaccumulatesatenfoldexcessofsymbiotic(friendly)bacterialcells
—the microbiota. Our brain—the assumed “hardware” of consciousness, engaged
©TheAuthor(s)2015 1
G.Muskhelishvili,DNAInformation:LawsofPerception,
SpringerBriefsinBiochemistryandMolecularBiology,
DOI10.1007/978-3-319-17425-9_1