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Untangling Complex Systems
Untangling Complex Systems
A Grand Challenge for Science
CRC Press
Taylor & Francis Group
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Boca Raton, FL 33487-2742
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vii
viii Contents
Chapter 7 The Emergence of Temporal Order within a Living Being ..................................... 167
7.1 Introduction ................................................................................................. 167
7.2 Metabolic Events ......................................................................................... 167
7.2.1 Michaelis-Menten Kinetics ............................................................ 168
7.2.2 Hill Kinetics................................................................................... 169
7.2.3 The Nonlinearity of Allosteric Enzymes....................................... 170
7.2.4 Glycolysis ....................................................................................... 174
7.3 Cellular Signaling Processes ....................................................................... 176
7.3.1 The Simplest Signal Transduction System..................................... 176
7.3.2 Signal Transduction Systems with Positive Feedback ................... 177
7.4 Epigenetic Events ........................................................................................ 181
7.5 Biological Rhythms ..................................................................................... 185
7.6 Amplification and Adaptation in Regulatory and Sensory Systems ........... 187
7.6.1 Magnitude Amplification ............................................................... 187
7.6.2 Sensitivity Amplification ............................................................... 188
7.6.3 Adaptation ...................................................................................... 190
7.7 Key Questions ............................................................................................. 191
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x Contents
1. If the Second Law of Thermodynamics is true, how is it possible to observe the spontane-
ous emergence of order in time and space? Is it possible to violate the Second Law?
2. What are the common features of Complex Systems? When and how do the emergent
properties emerge?
To find answers to my questions, I have gone on a marvelous interdisciplinary journey. I dealt with
many disciplines; particularly, chemistry, biology, physics, economy, and philosophy. Chapter 1
presents an excursus on the evolution of the scientific knowledge and its mutual fruitful relationship
with technology. Chapter 2 is a thorough analysis of the Second Law of Thermodynamics and to
understand if its violation is feasible. Chapters 3 and 4 present the principles of Non-Equilibrium
Thermodynamics. Then, the theory of Non-Linear Dynamics is introduced by the description of
the emergence of the temporal order in ecosystems (Chapter 5), economy (Chapter 6), within a liv-
ing being (Chapter 7), and in a chemical laboratory (Chapter 8). Chapter 9 describes the emergence
of spatial order in chemistry, along with examples regarding biology, physics, and geology. Then,
Chapter 10 introduces the concept of Chaos in time, whereas Chapter 11 covers Chaos in space by
presenting fractals. Chapter 12 offers the typical features of Complex Systems and outlines the link
between Natural Complexity and Computational Complexity. Finally, Chapter 13 proposes strate-
gies to try to untangle Complex Systems and win the Complexity Challenges.
PURPOSES
This book has four principal objectives and one hope. First, it traces a new interdisciplinary didactic path
in Chemistry. This book is useful for graduate students in Chemistry, who want to learn the principles
and theories regarding Non-Equilibrium Thermodynamics, Non-Linear Dynamics, and Complexity.
xv
xvi Preface
Second, the contents I present should boost the spread of interdisciplinary courses in Complex
Systems to universities around the world. Teachers of Complexity can choose this textbook when
they want to highlight the relevant contribution of chemistry.
Third, this book contributes to the training of a new generation of PhD students and researchers
who want to comprehend Complex Systems and win the Complexity Challenges.
Fourth, I want to stimulate public and private funding agencies to sustain interdisciplinary
projects on Complex Systems.
This book terminates with a question: “Can we formulate a new scientific theory for under-
standing and predicting the behavior of Complex Systems?” I hope that someone, also inspired
by this text, will contribute to the formulation of that scientific theory that we have been waiting
for many years.
MATLAB® is a registered trademark of The MathWorks, Inc. For product information, please
contact:
xvii
About the Author
Pier Luigi Gentili is a PhD in Chemistry. His research and teaching activities are focused on
Complex Systems. He is trusting in Natural Computing as an effective strategy to understand
Complex Systems and face the Computational Complexity Challenges. In particular, he is developing
the innovative Chemical Artificial Intelligence. He has several collaborations and work experience
in many laboratories such as, the “Photochemistry and Photophysics Group” of the University of
Perugia (Italy); the “Nonlinear Dynamics Group” of the Brandeis University (USA); the “European
Laboratory of Nonlinear Spectroscopy” in Florence (Italy); the “Center for Photochemical Sciences”
of the Bowling Green State University (USA); the “Laboratory of Computational Chemistry and
Photochemistry” of the University of Siena (Italy).
ORCID: 0000-0003-1092-9190
xix
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1 Introduction
1 Feedback occurs when the output of an action becomes the input of another.
1
2 Untangling Complex Systems
Scientific
Technology
knowledge
FIGURE 1.2 Reciprocal positive feedback action between Science and Technology. Science is fed mainly by
epistemic curiosity, whereas technology by the dream of improving our welfare.
The journey to discovering the secrets of nature, made by humanity, has been punctuated by
two revolutionary intellectual events: (1) the birth of philosophy in the ancient Greek colonies, dur-
ing the sixth century BC, and (2) the use of the experimental method for inquiring about nature,
proposed by Galileo Galilei and finalized by Isaac Newton in the seventeenth century AD. These
two intellectual revolutions have been two “gateway events” (to use a term coined by Nobel prize
Murray Gell-Mann2). In fact, they have induced profound and fundamental changes in the human
methodology of gaining insights about nature. The two mentioned “gateway events” have been
cultural facts, and as such, they have not been abrupt, but gradual outcomes of slow evolution-
ary intellectual processes. Once across these gateways, scientific inquiry has never been the same
again. These two events split out the scientific journey into three main stages (see Figure 1.3). The
first stage is the period that preceded the birth of philosophy. It can be named as the “Practical
2 Murray Gell-Mann (1994) coined the term “gateway event” to indicate a change opening up a new kind of a phase space
with a huge increase in kinds and levels of complexity in system’s dynamics. Once through the gateway, life is never
the same again. For example, new technology is often an economic gateway event because it expands the production
possibilities frontier.
Introduction 3
Sixth century BC
Phylosophical The first philosophers
period in Greece and its colonies
Practical
period
1 × 103 BC
Stone Iron age
age ~3 × 106 BC
3 × 103 BC
Seventeenth century AD Bronze
G. Galilei age
and I. Newton
Twenty-first century AD
Experimental Computational
period period
FIGURE 1.3 The humankind journey to discovering the secrets of nature represented as a spiral
partitioned in four periods. First, the “Practical Period” started with the appearance of humankind on earth,
about 3 million years ago. Then, the birth of philosophy in sixth century BC initiated the “Philosophical
Period.” The formulation of the experimental method began the “Experimental Period” in the seventeenth
century AD. Finally, in the twenty-first century, we are waiting for the next gateway event to enter the
“Computational Period” and deeply understand Complexity.
Period” because humans, spurred by their necessities, were particularly ingenious in making arti-
facts for solving practical problems. Unconsciously, they obtained the first important achievements
in the technological development. The second stage is named as the “Philosophical Period,” because
authentic Philo-physicists started to investigate nature and human thoughts by using philosophical
reasoning. The rigorous and systematic use of experiments as a method of inquiry into nature began
only in the seventeenth century AD, opening a new stage that we can name as the “Experimental
Period.” We are still living it. Three hundred years of productive scientific investigation and aston-
ishing technological development have elapsed. Nevertheless, we still experience strong limita-
tions on our attempts to exhaustively describe systems, such as the climate and the geology of our
planet; the living beings; the human brain; the human immune system; the ecosystems on earth;
the human societies and the global economy. These are called Complex Systems. We are aware
that the traditional scientific methodologies, the available theories, and computational tools are not
enough to deeply understand and predict the behavior of Complex Systems. Therefore, we expect
that more efficient algorithms, brand-new computing machines, and probably new methodologies
and theories are needed. Do we need to study Complex Systems? Of course, yes. In fact, if we suc-
ceed to comprehend Complex Systems, we will surely possess new strategies and effective tools to
tackle the Natural Complexity Challenges. The Natural Complexity Challenges are: (1) predicting
catastrophic events on our planet (like earthquakes or volcanic eruptions) to save lives; (2) defeat-
ing diseases that are still incurable (such as glioblastoma, diabetes, HIV, etc.); (3) protecting our
environment and ecosystems from climate change and the risk of shrinking biodiversity; (4) guar-
anteeing worldwide sustainable economic growth, primarily by focusing on the energy issue; and
(5) ensuring stability in our societies.
After reading this book, it will be evident that for the comprehension of Complex Systems we
probably need a new intellectual gateway event. This third gateway event will spark a new stage in
the scientific journey to discovering the secrets of nature. It seems plausible that a proper name for
the expected next and fourth stage is “Computational period” (see Figure 1.3). In fact, whenever we
4 Untangling Complex Systems
face the description of Complex Systems, or we tackle the Natural Complexity Challenges, we need
to collect and process a vast amount of data, the so-called Big Data (Marx 2013).
In the next three paragraphs of this chapter, I present just a few relevant historical events and
achievements in the first three stages of that exciting experience, which is the human journey to
discovering the secrets of nature. Then, I outline what we expect in the fourth stage.
3 The term serendipity come from the Persian fairy tale The Three Princes of Serendip, whose heroes “were always making
discoveries, by accidents and sagacity, of things they were not in quest of”. An inquisitive human mind can turn accidents
into discoveries.
4 The Stone Age is the first period of a Three-Age System proposed by the Danish archeologist Christian Jürgensen
Thomsen (1788–1865) for classifying ancient societies and prehistoric stages of progress. After the Stone Age, the Bronze
and Iron Ages followed.
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within us. We feel sure of rising from the perusal a wiser if not a
better man. In no instance are we deceived. From the brief Tale—
from the "Monos and Daimonos" of the author—to his most
ponderous and labored novels—all is richly, and glowingly
intellectual—all is energetic, or astute, or brilliant, or profound. There
may be men now living who possess the power of Bulwer—but it is
quite evident that very few have made that power so palpably
manifest. Indeed we know of none. Viewing him as a novelist—a
point of view exceedingly unfavorable (if we hold to the common
acceptation of "the novel") for a proper contemplation of his genius—
he is unsurpassed by any writer living or dead. Why should we
hesitate to say this, feeling, as we do, thoroughly persuaded of its
truth. Scott has excelled him in many points, and "The Bride of
Lammormuir" is a better book than any individual work by the author
of Pelham—"Ivanhoe" is, perhaps, equal to any. Descending to
particulars, D'Israeli has a more brilliant, a more lofty, and a more
delicate (we do not say a wilder) imagination. Lady Dacre has written
Ellen Wareham, a more forcible tale of Passion. In some species of
wit Theodore Hook rivals, and in broad humor our own Paulding
surpasses him. The writer of "Godolphin" equals him in energy.
Banim is a better sketcher of character. Hope is a richer colorist.
Captain Trelawney is as original—Moore is as fanciful, and Horace
Smith is as learned. But who is there uniting in one person the
imagination, the passion, the humor, the energy, the knowledge of
the heart, the artist-like eye, the originality, the fancy and the learning
of Edward Lytton Bulwer? In a vivid wit—in profundity and a Gothic
massiveness of thought—in style—in a calm certainty and
definitiveness of purpose—in industry—and above all in the power of
controlling and regulating by volition his illimitable faculties of mind,
he is unequalled—he is unapproached.
Rienzi, then, is History. But there are other aspects in which it may
be regarded with advantage. Let us survey it as a profound and lucid
exposition of the morale of Government—of the Philosophies of Rule
and Misrule—of the absolute incompatibility of Freedom and
Ignorance—Tyranny in the few and Virtue in the many. Let us
consider it as something akin to direct evidence that a people is not
a mob, nor a mob a people, nor a mob's idol the idol of a people—
that in a nation's self is the only security for a nation—and that it is
absolutely necessary to model upon the character of the governed,
the machinery, whether simple or complex, of the governmental
legislation.
THE ERROR.
For three days, the three fatal days, did Adrian remain bereft of
strength and sense. But he was not smitten by the scourge
which his devoted and generous nurse had anticipated. It was a
fierce and dangerous fever, brought on by the great fatigue,
restlessness, and terrible agitation he had undergone.
No professional mediciner could be found to attend him but a
good friar, better perhaps skilled in the healing art than many
who claimed its monopoly, visited him daily. And in the long and
frequent absences to which his other and numerous duties
compelled the monk, there was one ever at hand to smooth the
pillow, to wipe the brow, to listen to the moan, to watch the
sleep. And even in that dismal office, when, in the frenzy of the
sufferer, her name, coupled with terms of passionate
endearment, broke from his lips, a thrill of strange pleasure
crossed the heart of the betrothed, which she chid as if it were a
crime. But even the most unearthly love is selfish in the rapture
of being loved! Words cannot tell, heart cannot divine, the
mingled emotions that broke over her when, in some of those
incoherent ravings, she dimly understood that for her the city
had been sought, the death dared, the danger incurred. And as
then bending passionately to kiss that burning brow, her tears
fell fast over the idol of her youth, the fountains from which they
gushed were those, fathomless and countless, which a life could
not weep away. Not an impulse of the human and the woman
heart that was not stirred; the adoring gratitude, the meek
wonder thus to be loved, while deeming it so simple a merit thus
to love;—as if all sacrifice in her were a thing of course,—to her,
a virtue nature could not paragon, worlds could not repay! And
there he lay, the victim to his own fearless faith, helpless—
dependent upon her—a thing between life and death, to thank,
to serve—to be proud of, yet to protect—to compassionate, yet
revere—the saver, to be saved! Never seemed one object to
demand at once from a single heart so many and so profound
emotions; the romantic enthusiasm of the girl!—the fond idolatry
of the bride—the watchful providence of the mother over her
child.
And strange to say, with all the excitement of that lonely watch,
scarcely stirring from his side, taking food only that her strength
might not fail her,—unable to close her eyes—though, from the
same cause, she would fain have taken rest, when slumber fell
upon her charge—with all such wear and tear of frame and
heart, she seemed wonderfully supported. And the holy man
marvelled, in each visit, to see the cheek of the nurse still fresh,
and her eye still bright. In her own superstition she thought and
felt that Heaven gifted her with a preternatural power to be true
to so sacred a charge: and in this fancy she did not wholly err;—
for Heaven did gift her with that diviner power, when it planted in
so soft a heart the enduring might and energy of Affection! The
friar had visited the sick man, late on the third night, and
administered to him a strong sedative—"This night," said he to
Irene, "will be the crisis—should he awaken, as I trust he may,
with a returning consciousness, and a calm pulse, he will live—if
not, young daughter, prepare for the worst. But should you note
any turn in the disease, that may excite alarm, or require my
attendance, this scroll will inform you where I am if God spare
me still, at each hour of the night and morning."
"You have not marked the door, nor set out the body," said one
gruffly, "but this is the third night! He is ready for us!"
And the grisly carrier sullenly withdrew. The cart moved on, the
bell renewed its summons, till slowly and faintly the dreadful
larum died in the distance.
Shading the lamp with her hand, Irene stole to the bed-side,
fearful that the sound and the intrusion had disturbed the
slumberer. But his face was still locked, as in a vice, with that
iron sleep. He stirred not—his breath scarcely passed his lips—
she felt his pulse, as the wand lay on the coverlid—there was a
slight heat—she was contented—removed the light, and, retiring
to a corner of the room, placed the little cross suspended round
her neck upon the table, and prayed—in her intense suffering—
to Him who had known death, and who—Son of Heaven though
he was, and Sovereign of the Seraphim—had also prayed, in his
earthly travail, that the cup might pass away.
It was not many minutes after Irene had left the room, ere, with
a long sigh, Adrian opened his eyes—an altered and another
man; the fever was gone, the reviving pulse beat low indeed, but
calm. His mind was once more master of his body, and, though
weak and feeble, the danger was past, and life and intellect
regained.
He soon found himself in the open street; the air revived him;
and that morning, the first known for weeks, had sprung up the
blessed breeze. He wandered on very slowly and feebly till he
came to a broad square, from which, in the vista, might be seen
one of the principal gates of Florence, and the fig-trees and
olive-groves beyond. It was then that a pilgrim of tall stature
approached towards him as from the gate; his hood was thrown
back, and gave to view a countenance of great but sad
command; a face, in whose high features, massive brow, and
proud, unshrinking gaze, shaded by an expression of
melancholy more stern than soft, Nature seemed to have written
majesty, and Fate disaster. As in that silent and dreary place,
these two, the only tenants of the street, now encountered,
Adrian stopped abruptly, and said in a startled and doubting
voice: "Do I dream still, or do I behold Rienzi?"
The pilgrim paused also, as he heard the name, and gazing long
on the attenuated features of the young lord, said: "I am he that
was Rienzi! and you, pale shadow, is it in this grave of Italy that I
meet with the gay and high Colonna? Alas, young friend," he
added in a more relaxed and kindly voice, "hath the Plague not
spared the flower of the Roman nobles? Come, I, the cruel and
the harsh tribune, I will be thy nurse: he who might have been
my brother, shall yet claim from me a brother's care."
With these words, he wound his arm tenderly round Adrian; and
the young noble, touched by his compassion, and agitated by
the surprize, leant upon Rienzi's breast in silence.
"Is it so, really? Art thou a Colonna, and yet prize the fallen?
The same duty has brought me also to the City of Death. From
the farthest south—over the mountains of the robber—through
the fastnesses of my foes—through towns in which the herald
proclaimed in my ear the price of my head—I have passed
hither, on foot and alone, safe under the wings of the Almighty
One. Young man, thou shouldst have left this task to one who
bears a wizard's life, and whom Heaven and Earth yet reserve
for an appointed end!"
The Tribune said this in a deep and inward voice; and in his
raised eye and solemn brow might be seen how much his
reverses had deepened his fanaticism, and added even to the
sanguineness of his hopes.
"Talk not now of dreams," said the lover, "but if you have no
other guide, let us part at once in quest of her; I will take yonder
street, you take the opposite, and at sunset let us meet in the
same spot."
"Rash man," said the Tribune, with great solemnity, "scoff not at
the visions which Heaven makes a parable to its Chosen. Thou
seekest counsel of thy human wisdom; I, less presumptuous,
follow the hand of the mysterious Providence, moving even now
before my gaze as a pillar of light, through the wilderness of
dread. Ay, meet we here at sunset, and prove whose guide is
the most unerring. If my dream tell me true, I shall see my sister
living, ere the sun reach yonder hill, and by a church dedicated
to St. Mark."
"I feared you were sped, and that another had cheated me of
my office," said the grave-digger, "seeing that you returned not
to the old prince's palace. You don't know me from the rest of
us, I see, but I am the one you told to seek——"
"Irene!"
"Yes, Irene di Gabrini, you promised ample reward."
"Follow me."
"Irene di Gabrini, a Roman lady. But I told thee this was the
fourth day they left the house, terrified by the deaths within it."
"Yes, I have told thee, a blue mantle, such as I have rarely seen,
wrought with silver."
"It was!"
"Nothing."
"Signor Astuccio," said the Becchino, "pardon me; but I told thee
I might trouble thee again. This is the gentleman who wants to
know, what is often best unknown—but that's not my affair. Did a
lady—young and beautiful—with dark hair, and of a slender
form, enter this house, stricken with the first symptom of the
plague, three days since?"
"No, save that she raved much about the nunnery of Santa
Maria dei Pazza, and bravos, and sacrilege."
His guide now turned round to Adrian, whose face was set and
resolute in despair.
"Raven of bode and woe," answered Adrian, "seest thou not that
all I shrink from is thy voice and aspect? Show me her I seek,
living or dead."
"I will show her to you, then," said the Becchino, sullenly, "such
as two nights since she was committed to my charge. Line and
lineament may already be swept away, for the Plague hath a
rapid besom; but I have left that upon her by which you will
know the Becchino is no liar. Bring hither the torches, comrades,
and lift the door. Never stare; it's the gentleman's whim, and he'll
pay it well."
* * * * *
* * * * *
But who shall detail the ineffable and unimaginable horrors that
reigned over the Palace where the Great King received the
prisoners whom the sword of the Pestilence had subdued.
"So you have revived; ah! I thought it was only the effluvia; few
stand it as we do. And so, as your search is over, deeming you
would not be quitting Florence if you have any sense left to you,
I went for your good horse. I have fed him since your departure
from the palace. Indeed I fancied he would be my perquisite, but
there are plenty as good. Come, young Sir, mount. I feel a pity
for you, I know not why, except that you are the only one I have
met for weeks who seem to care for another more than for
yourself. I hope you are satisfied now that I showed some
brains, eh! in your service, and as I have kept my promise, you'll
keep yours."
"Take yon—yon clay from that fearful place. Inter it in some quiet
and remote spot—apart—alone! You promise me—you swear it
—it is well. And now help me on my horse."
"Farewell Italy, and if I die not with this stroke, may I die as befits
at once honor and despair—with trumpet and banner round me
—in a well-fought field against a worthy foe!—save a knightly
death nothing is left to live for!"
ROGET'S PHYSIOLOGY.