**5. Integrating the triad: mechanization of speciation**

A combination of emerging technologies such as CRISPR, AI, and QC; new delivery models for products and services that form the core around which *Homo sapiens* organize themselves through collaborative division of labor; and talent migration, driven not by rote education but by innate creativity and global opportunities for employment open to them is disrupting and changing the character of the global talent pool that society needs today. Globalization has created opportunities for the talented to reach the skies, but in a resource-constrained world, it also means that many others must be or feel deprived. Sections 5.2 and 5.3 provide some glimpses of the dynamics of this situation captured in mathematics. Because mathematics is abstract, the depicted dynamics apply to entities and situations whether they are animate or inanimate. A resource-constrained world provides ample scope for adversarial dynamics in which some are predators and others are preys. Globalization has accentuated the problem at all levels of social structure, and since speciation is triggered by a changing environment, it affects the DNA. This has created survivability demands on the *Homo sapiens*. As this pressure mounts beyond endurance, *Homo sapiens* will face speciation by natural selection with uncertain outcomes. However, in the case of *Homo sapiens*, this process too may face a disruptive change because the highly intelligent among them may boldly initiate speciation using upcoming advances in synthetic biology, perhaps after perfecting their techniques by creating humanoids (a hybrid creation of life with embedded intelligent machinery). This will be a watershed event where a species takes on the task of speciation on itself. This remarkable possibility arises because *Homo sapiens* created and mastered mathematics, rational thought, computing machinery, and eventually deep data analytics so that life could be designed by them in the laboratory to create superior species.

Synthetic biology, using methods and rational knowledge of molecular biology, physical sciences, and engineering, aims to design and construct novel biological parts, artificial biological pathways, devices, organisms, and systems for useful purposes. This will also permit us, at all levels of the hierarchy of biological structures

**23**

introduce a few of these below in brief.

**5.1 The molecular logic of the living state**

*Synthetic Biology, Artificial Intelligence, and Quantum Computing*

of instructions for making all the proteins a cell will ever need.

(molecules, cells, tissues, and organisms), to redesign existing natural biological systems and may even help us recreate certain extinct species (if we can also recreate the environment, they had adapted to). It is not surprising that an extinct species has never revived itself since speciation and environment go together. Successes of synthetic biology will change the face of human civilization and almost certainly bring in new elements into play when *Homo sapiens* eventually speciate by playing

Since the discovery of the double-helix structure of cellular DNA by James Watson and Francis Crick in 1953 [43] and its significance that the "precise

sequence of the bases is the *code* which carries the genetical *information* …" (emphasis added) [44], the jargon and theory of information has invaded molecular biology (see Section 3). This enriched biotechnology and computational biology with nomenclature, definitions, concepts, and meanings. This also facilitates integration of synthetic biology with AI and QC. DNA is an information-carrying polymer. It is an organized chemical information database that *inter alia* carries the complete set

Just 20 years after Watson and Crick, in 1973 Cohen and Boyer published their pioneering work in recombinant DNA [45] and gave birth to genetic engineering and the biotechnology industry based on their patents [46] under liberal licensing terms. The next landmark was the creation of a bacterial cell controlled by a chemically synthesized genome by Craig Venter and his group in 2010 [47]. In 2014, Floyd Romesberg and colleagues [48] reported the creation of a semisynthetic organism with an expanded genetic alphabet by creating artificial nucleotides not found in Nature. Since its discovery in 2012 [49–51], CRISPR gene editing technology pioneered by Jennifer Doudna and Emmanuelle Charpentier, and Feng Zhang has come to occupy center stage in molecular biology as a new way of making precise, targeted changes to the genome of a cell or an organism. It has set the stage for major advances in synthetic biology (see Section 4.1). Another major advance was reported by Venter and his research group in March 2016 following their successful creation in 2010 of a bacterial cell controlled by a chemically synthesized genome noted above. In fact, they succeeded in creating a bacterium that contains the minimal genetic ingredients needed for free living. The genome of this bacterium consists of only 473 genes, including 149 whose precise biological function is unknown.

It is a minimalist version of the genome of Mycoplasma mycoides [52, 53].

Synthesis capabilities have developed at a pace where DNA synthesis is now automated. All one needs to do is to provide the desired DNA sequence to a vendor. Researchers in synthetic biology are now inching toward anticipating and preempting evolutionary events that if left to themselves would perhaps take a few million years to occur, and of even resurrecting extinct species. The time is ripe to integrate synthetic biology with AI and QC with a common language to enable seamless communication among them, connect with, and discover conceptual similarities for consistent integration of subsystems and validation of the whole system. That common language is mathematics; it comes with the added benefit that it can be used to also communicate between humans and machines. It is fortuitous that the DNA serves as the "Book of Life" that appears to have structure and grammar amenable to translation into mathematics. Once translated, biologists will discover some amazing patterns that have a direct bearing on life at the molecular level. We

All macromolecules are constructed from a few simple compounds comprising a few atoms. It appears paradoxical that the DNA that serves as the epitome of life is itself

*DOI: http://dx.doi.org/10.5772/intechopen.83434*

an active role in it.

#### *Synthetic Biology, Artificial Intelligence, and Quantum Computing DOI: http://dx.doi.org/10.5772/intechopen.83434*

*Synthetic Biology - New Interdisciplinary Science*

mechanics that include such esoteric concepts as superposition of quantum states, entanglement ("spooky action at a distance"), and tunneling through insulating walls, which, though highly counterintuitive, play extremely useful roles in understanding Nature at subatomic levels. However, it is not clear if these concepts can be ignored in biology and living processes in the way they are ignored in the design of cars and airplanes. May be not because there are areas in biology where quantum effects have been found, for example, in protein-pigment (or ligand) complex systems [40]. Thus, while the role of quantum mechanics is clear in quantum computing and hence in advancing both AI and synthetic biology research, it is not yet known if in the design of DNA, knowledge of quantum mechanics is required or that natural selection favors quantum-optimized processes. Essentially, we do not know if any cellular DNA maintains or can maintain sustained entangled quantum states between different parts of the DNA (even if it involves only atoms in a nucleotide). But we cannot rule out the possibility that sporadic random entanglements do occur that result in biological mutations or that researchers will not be able to achieve it in the laboratory and find novel uses for it in synthetic biology [41]. For example, in principle, it is possible to design molecular quantum computers, insert them in cells that can observe cellular activity, and activate select chemical pathways in the cell in a programmed manner. There is increasing speculation that some brain activity, for example, cognition, may be quantum mechanical [42].

**5. Integrating the triad: mechanization of speciation**

A combination of emerging technologies such as CRISPR, AI, and QC; new delivery models for products and services that form the core around which *Homo sapiens* organize themselves through collaborative division of labor; and talent migration, driven not by rote education but by innate creativity and global opportunities for employment open to them is disrupting and changing the character of the global talent pool that society needs today. Globalization has created opportunities for the talented to reach the skies, but in a resource-constrained world, it also means that many others must be or feel deprived. Sections 5.2 and 5.3 provide some glimpses of the dynamics of this situation captured in mathematics. Because mathematics is abstract, the depicted dynamics apply to entities and situations whether they are animate or inanimate. A resource-constrained world provides ample scope for adversarial dynamics in which some are predators and others are preys. Globalization has accentuated the problem at all levels of social structure, and since speciation is triggered by a changing environment, it affects the DNA. This has created survivability demands on the *Homo sapiens*. As this pressure mounts beyond endurance, *Homo sapiens* will face speciation by natural selection with uncertain outcomes. However, in the case of *Homo sapiens*, this process too may face a disruptive change because the highly intelligent among them may boldly initiate speciation using upcoming advances in synthetic biology, perhaps after perfecting their techniques by creating humanoids (a hybrid creation of life with embedded intelligent machinery). This will be a watershed event where a species takes on the task of speciation on itself. This remarkable possibility arises because *Homo sapiens* created and mastered mathematics, rational thought, computing machinery, and eventually deep data analytics so that life could be designed by them in the labora-

Synthetic biology, using methods and rational knowledge of molecular biology, physical sciences, and engineering, aims to design and construct novel biological parts, artificial biological pathways, devices, organisms, and systems for useful purposes. This will also permit us, at all levels of the hierarchy of biological structures

**22**

tory to create superior species.

(molecules, cells, tissues, and organisms), to redesign existing natural biological systems and may even help us recreate certain extinct species (if we can also recreate the environment, they had adapted to). It is not surprising that an extinct species has never revived itself since speciation and environment go together. Successes of synthetic biology will change the face of human civilization and almost certainly bring in new elements into play when *Homo sapiens* eventually speciate by playing an active role in it.

Since the discovery of the double-helix structure of cellular DNA by James Watson and Francis Crick in 1953 [43] and its significance that the "precise sequence of the bases is the *code* which carries the genetical *information* …" (emphasis added) [44], the jargon and theory of information has invaded molecular biology (see Section 3). This enriched biotechnology and computational biology with nomenclature, definitions, concepts, and meanings. This also facilitates integration of synthetic biology with AI and QC. DNA is an information-carrying polymer. It is an organized chemical information database that *inter alia* carries the complete set of instructions for making all the proteins a cell will ever need.

Just 20 years after Watson and Crick, in 1973 Cohen and Boyer published their pioneering work in recombinant DNA [45] and gave birth to genetic engineering and the biotechnology industry based on their patents [46] under liberal licensing terms. The next landmark was the creation of a bacterial cell controlled by a chemically synthesized genome by Craig Venter and his group in 2010 [47]. In 2014, Floyd Romesberg and colleagues [48] reported the creation of a semisynthetic organism with an expanded genetic alphabet by creating artificial nucleotides not found in Nature. Since its discovery in 2012 [49–51], CRISPR gene editing technology pioneered by Jennifer Doudna and Emmanuelle Charpentier, and Feng Zhang has come to occupy center stage in molecular biology as a new way of making precise, targeted changes to the genome of a cell or an organism. It has set the stage for major advances in synthetic biology (see Section 4.1). Another major advance was reported by Venter and his research group in March 2016 following their successful creation in 2010 of a bacterial cell controlled by a chemically synthesized genome noted above. In fact, they succeeded in creating a bacterium that contains the minimal genetic ingredients needed for free living. The genome of this bacterium consists of only 473 genes, including 149 whose precise biological function is unknown. It is a minimalist version of the genome of Mycoplasma mycoides [52, 53].

Synthesis capabilities have developed at a pace where DNA synthesis is now automated. All one needs to do is to provide the desired DNA sequence to a vendor. Researchers in synthetic biology are now inching toward anticipating and preempting evolutionary events that if left to themselves would perhaps take a few million years to occur, and of even resurrecting extinct species. The time is ripe to integrate synthetic biology with AI and QC with a common language to enable seamless communication among them, connect with, and discover conceptual similarities for consistent integration of subsystems and validation of the whole system. That common language is mathematics; it comes with the added benefit that it can be used to also communicate between humans and machines. It is fortuitous that the DNA serves as the "Book of Life" that appears to have structure and grammar amenable to translation into mathematics. Once translated, biologists will discover some amazing patterns that have a direct bearing on life at the molecular level. We introduce a few of these below in brief.

#### **5.1 The molecular logic of the living state**

All macromolecules are constructed from a few simple compounds comprising a few atoms. It appears paradoxical that the DNA that serves as the epitome of life is itself lifeless. The molecule conforms to all the physical and chemical laws that describe the behavior of inanimate matter. All living organisms extract, transform, and use energy by interacting with the environment. Unlike inanimate matter, a living cell has the unique capacity, using the genetic information contained completely within itself, to grow and maintain itself and do mechanical, chemical, osmotic, and other types of work. But its most unique attribute is its programmed capacity to self-replicate and selfassemble. The great mystery that engulfs molecular biology is: "How does life emerge from an interacting collection of inanimate molecules that constitute living organisms to maintain and perpetuate life?" Once this is understood, chemical engineers will create a new life industry and commoditize it! Imagine buying customized pets as starters.

As noted in Section 3, the mystery of life is almost certainly encoded in mathematics. The chemical basis of life is one indication because chemistry now has a strong mathematical foundation via quantum chemistry. Even more striking is the fact that all living organisms—bacterium, fish, plant, bird, animal—share common basic chemical features, for example, the same basic structural unit (the cell), the same kind of macromolecules (DNA, RNA (ribonucleic acids), and proteins) built from the same kind of monomeric subunits (nucleotides and amino acids), the same pathways for synthesis of cellular components, the same genetic code, and evolutionary ancestors. The monomeric subunits can be covalently linked in a virtually limitless variety of sequences just as the 26 letters of the English alphabet or the two binary numbers (0, 1) in binary arithmetic can be arranged into a limitless number of strings that stand for words, sentences, books, computer programs, etc.

Organic compounds of molecular weight less than about 500, such as amino acids, nucleotides, and monosaccharides, serve as monomeric subunits of proteins, nucleic acids, and polysaccharides, respectively. A protein molecule may have a thousand or more amino acids linked in a chain, and DNA typically has millions of nucleotides arranged in sequence. Only a small number of chemical elements from the periodic table of chemistry appear in biomolecules. The carbon atom dominates and, by virtue of its special covalent bonding properties, permits the formation of a wide variety of molecules by bonding with itself, and atoms of hydrogen, oxygen, nitrogen, etc. Nature has placed further constraints. DNA is constructed from only four different kinds of subunits, the deoxyribonucleotides; the RNA is composed from just four types of ribonucleotides; and proteins are put together using 20 different kinds of amino acids. The 8 kinds of nucleotides (4 for DNA and 4 for RNA) from which all nucleic acids are built and the 20 amino acids from which all proteins are built are identical in all living organisms. So, at this level, living organisms are remarkably alike in their chemical makeup. This by itself provides a tantalizing hope that the DNA may indeed be completely decipherable as to its grammar and information content.

The above observations strongly suggest the likelihood of an underlying, as yet undiscovered set of "axioms" of life that enforce emergent, organizing principles around which diverse life forms evolve and adapt to the environment at various levels, without transgressing any physical or chemical law. The organizing principles appear to include (1) Nature is red in tooth and claw (species are connected to each other in a predator-prey, food-chain relationship in a sparse resource matrix), (2) rules of genetic inheritance, (3) rules of environmental adaptation, and (4) rules of speciation. At each level, the rules are likely to appear stochastic given that there are innumerable interacting factors ranging from nature to nurture.

#### **5.2 Law of network phase transition**

In 1960, Erdős and Rényi [54, 55] proved a remarkable result in graph theory, which implies that when a large number of entities (e.g., men, machines, ideas,

**25**

among the millennials.

the reorganization.

*Synthetic Biology, Artificial Intelligence, and Quantum Computing*

or arbitrary combinations of them represented by dots) begin to connect (link) randomly, a critical condition arises, following which a phase transition occurs in the way the entities form or reform into clusters of connected entities. The critical condition is reached when in a set of *n* dots, *n*/2 random links are made. The phase transition abruptly creates a giant connected component, while the next largest component is quite small. Such giant components then grow or shrink rather slowly with the number of dots as they continue to link or delink. Such behavior is observed in protein interaction networks, telephone call graphs, scientific collaboration graphs, and many others [56]. This immediately suggests an *involuntary* mechanism by which a society at various levels of evolution, by connections alone, spontaneously reorganizes itself as nodes (people, machines, resources, etc.) link or delink in apparent randomness. It is highly pronounced in an Internet of Things (IoT) connected world where the millennials spontaneously polarize on issue-based

Synthetic biologists must never forget that between the molecular and environmental levels, there are multiple intermediate levels through which regulated command and control communications pass. At all levels, level-related phase transitions and predatory fights for resources can occur and spread to other levels. In fact, the intimately coupled relationship between *Homo sapiens* and the environment is often

*[I]n making sense of the world, acting intelligently, and solving problems creatively, we do not rely solely on our mind's internal resources. Instead, we constantly have recourse to a vast array of culturally and socially embodied idea-spaces that populate the extended mind. These spaces … are rich with embedded intelligence that we have progressively offloaded into our physical, social, and cultural environment for the sake of simplifying the burden on our own minds of rendering the world* 

The deep significance of this intimate bonding between the *Homo sapiens* and the environment is that while they are adapting to the environment, they are also helping the environment to adapt to them. When entities connect, they also acquire emergent properties by virtue of the relationships they are bound by. Certain static group properties emerge based on the network's topology, while dynamic properties emerge depending on the rate at which entities make, break, or modify connections. The fluctuating dynamics witnessed in the social media, for example, is common

Rapidly increasing connectivity among men and machines has imposed upon the global socio-politico-economic structure, a series of issue-dependent phase transitions. More will occur in areas where massive connectivity is in the offing. Immediately before a transition, existing man-made laws begin to crack, and in the transition, they break down. Posttransition, new laws must be framed and enforced to establish order. Since such a phase transition is a statistical phenomenon, the only viable way of managing it is to manage groups by abbreviating individual rights. The emergence of strongman style of leadership and its contagious spreading across the world is thus to be expected because job-seeking millennials will expect them to destroy the past and create a new future over the rubble. It appears inevitable that many humans will perish during the transition for lack of jobs or their inability to adapt to new circumstances. Robots and humanoids will gain domination over main job clusters, while society undergoes radical structural changes. Ironically, robots neither need jobs, nor job satisfaction, nor a livelihood. There will be ruthlessness in

*DOI: http://dx.doi.org/10.5772/intechopen.83434*

networks that concern them on social media.

overlooked. We rarely note what Richard Ogle has that

*intelligible. Sometimes the space of ideas thinks for us. [57]*

*Synthetic Biology, Artificial Intelligence, and Quantum Computing DOI: http://dx.doi.org/10.5772/intechopen.83434*

*Synthetic Biology - New Interdisciplinary Science*

lifeless. The molecule conforms to all the physical and chemical laws that describe the behavior of inanimate matter. All living organisms extract, transform, and use energy by interacting with the environment. Unlike inanimate matter, a living cell has the unique capacity, using the genetic information contained completely within itself, to grow and maintain itself and do mechanical, chemical, osmotic, and other types of work. But its most unique attribute is its programmed capacity to self-replicate and selfassemble. The great mystery that engulfs molecular biology is: "How does life emerge from an interacting collection of inanimate molecules that constitute living organisms to maintain and perpetuate life?" Once this is understood, chemical engineers will create a new life industry and commoditize it! Imagine buying customized pets as starters. As noted in Section 3, the mystery of life is almost certainly encoded in mathematics. The chemical basis of life is one indication because chemistry now has a strong mathematical foundation via quantum chemistry. Even more striking is the fact that all living organisms—bacterium, fish, plant, bird, animal—share common basic chemical features, for example, the same basic structural unit (the cell), the same kind of macromolecules (DNA, RNA (ribonucleic acids), and proteins) built from the same kind of monomeric subunits (nucleotides and amino acids), the same pathways for synthesis of cellular components, the same genetic code, and evolutionary ancestors. The monomeric subunits can be covalently linked in a virtually limitless variety of sequences just as the 26 letters of the English alphabet or the two binary numbers (0, 1) in binary arithmetic can be arranged into a limitless number of strings that stand for words, sentences, books, computer programs, etc. Organic compounds of molecular weight less than about 500, such as amino acids, nucleotides, and monosaccharides, serve as monomeric subunits of proteins, nucleic acids, and polysaccharides, respectively. A protein molecule may have a thousand or more amino acids linked in a chain, and DNA typically has millions of nucleotides arranged in sequence. Only a small number of chemical elements from the periodic table of chemistry appear in biomolecules. The carbon atom dominates and, by virtue of its special covalent bonding properties, permits the formation of a wide variety of molecules by bonding with itself, and atoms of hydrogen, oxygen, nitrogen, etc. Nature has placed further constraints. DNA is constructed from only four different kinds of subunits, the deoxyribonucleotides; the RNA is composed from just four types of ribonucleotides; and proteins are put together using 20 different kinds of amino acids. The 8 kinds of nucleotides (4 for DNA and 4 for RNA) from which all nucleic acids are built and the 20 amino acids from which all proteins are built are identical in all living organisms. So, at this level, living organisms are remarkably alike in their chemical makeup. This by itself provides a tantalizing hope that the DNA may

indeed be completely decipherable as to its grammar and information content.

innumerable interacting factors ranging from nature to nurture.

**5.2 Law of network phase transition**

The above observations strongly suggest the likelihood of an underlying, as yet undiscovered set of "axioms" of life that enforce emergent, organizing principles around which diverse life forms evolve and adapt to the environment at various levels, without transgressing any physical or chemical law. The organizing principles appear to include (1) Nature is red in tooth and claw (species are connected to each other in a predator-prey, food-chain relationship in a sparse resource matrix), (2) rules of genetic inheritance, (3) rules of environmental adaptation, and (4) rules of speciation. At each level, the rules are likely to appear stochastic given that there are

In 1960, Erdős and Rényi [54, 55] proved a remarkable result in graph theory, which implies that when a large number of entities (e.g., men, machines, ideas,

**24**

or arbitrary combinations of them represented by dots) begin to connect (link) randomly, a critical condition arises, following which a phase transition occurs in the way the entities form or reform into clusters of connected entities. The critical condition is reached when in a set of *n* dots, *n*/2 random links are made. The phase transition abruptly creates a giant connected component, while the next largest component is quite small. Such giant components then grow or shrink rather slowly with the number of dots as they continue to link or delink. Such behavior is observed in protein interaction networks, telephone call graphs, scientific collaboration graphs, and many others [56]. This immediately suggests an *involuntary* mechanism by which a society at various levels of evolution, by connections alone, spontaneously reorganizes itself as nodes (people, machines, resources, etc.) link or delink in apparent randomness. It is highly pronounced in an Internet of Things (IoT) connected world where the millennials spontaneously polarize on issue-based networks that concern them on social media.

Synthetic biologists must never forget that between the molecular and environmental levels, there are multiple intermediate levels through which regulated command and control communications pass. At all levels, level-related phase transitions and predatory fights for resources can occur and spread to other levels. In fact, the intimately coupled relationship between *Homo sapiens* and the environment is often overlooked. We rarely note what Richard Ogle has that

*[I]n making sense of the world, acting intelligently, and solving problems creatively, we do not rely solely on our mind's internal resources. Instead, we constantly have recourse to a vast array of culturally and socially embodied idea-spaces that populate the extended mind. These spaces … are rich with embedded intelligence that we have progressively offloaded into our physical, social, and cultural environment for the sake of simplifying the burden on our own minds of rendering the world intelligible. Sometimes the space of ideas thinks for us. [57]*

The deep significance of this intimate bonding between the *Homo sapiens* and the environment is that while they are adapting to the environment, they are also helping the environment to adapt to them. When entities connect, they also acquire emergent properties by virtue of the relationships they are bound by. Certain static group properties emerge based on the network's topology, while dynamic properties emerge depending on the rate at which entities make, break, or modify connections. The fluctuating dynamics witnessed in the social media, for example, is common among the millennials.

Rapidly increasing connectivity among men and machines has imposed upon the global socio-politico-economic structure, a series of issue-dependent phase transitions. More will occur in areas where massive connectivity is in the offing. Immediately before a transition, existing man-made laws begin to crack, and in the transition, they break down. Posttransition, new laws must be framed and enforced to establish order. Since such a phase transition is a statistical phenomenon, the only viable way of managing it is to manage groups by abbreviating individual rights. The emergence of strongman style of leadership and its contagious spreading across the world is thus to be expected because job-seeking millennials will expect them to destroy the past and create a new future over the rubble. It appears inevitable that many humans will perish during the transition for lack of jobs or their inability to adapt to new circumstances. Robots and humanoids will gain domination over main job clusters, while society undergoes radical structural changes. Ironically, robots neither need jobs, nor job satisfaction, nor a livelihood. There will be ruthlessness in the reorganization.

#### **5.3 The logistic map and the Mandelbrot set**

Consider the iteration *xn* + 1 = *r xn* (1 – *xn*), called the logistic map, and a numberpair (*r*, *x*0) where *r* > 0 and 0 < *x*0 < 1, and plot the points (*r*, *xn* <sup>→</sup> <sup>∞</sup>). Note our interest is only in the long-term trajectory of *x*0 and not in its transitory phase. Note *xn* + (1 – *xn*) = 1. The plot (**Figure 3**) has numerous 2-pronged pitchforks and hence is called the bifurcation diagram. Depending on *r*, *xn* may be settled as for 0 < *r* ≤ 3, and beyond *r* = 3 migrating from one prong to another of available pitchforks for a given *r* in the bifurcation diagram. At *r* = 4 and beyond, migration is chaotic. In between *r* = 3.5 and 4, there is an intuitively unexpected white band where migration options are few. Such and other unexpected (not discussed here) display of rich complexity tethered to *r* independent of *x*0 (i.e., the starting state) caught researchers by great surprise.

There are countless situations for which the logistic map captures the essence of a situation. For example, in genetics it describes the change in gene frequency in time, or in epidemiology the fraction of the population infected at time *t*, or in economics it depicts the relationship between commodity quantity and price, or in theories of learning the number of bits of information one can remember after an interval, or in the propagation of rumors the number of people who have heard the rumor after time *t*, etc. The logistic map allows us to assess the volatility of an adversarial environment by assessing *r*, that is, the ferocity with which the predators and preys are battling for resources.

Now consider the following complex iteration. Given the complex variable *z* = *x* + *iy*, where *i* = √ \_\_\_ −1 and the complex constant *c* = *a* + *ib*, pick a value for *c*, and iterate with the seed *z*0 = 0. If the iterations diverge, then *c* is not in the Mandelbrot set (it is in the escape set), otherwise (even when it is trapped in some repeating loop or is wandering chaotically), it is in the Mandelbrot set (black points in **Figure 4**) *M*. (Setting *z*0 equal to any point in the set that is not a periodic point gives the same result.) This is perhaps the most famous mathematical object yet known. It is a fractal object, an object that is irregular or fragmented at all scales. It is a major discovery of the late 20th century. It cannot be replicated in Euclidean geometry.

In 1981–1982, Adrien Douady and John H. Hubbard [58] proved that the Mandelbrot set is connected. Quite astoundingly, the Mandelbrot set, when magnified enough, is seen to contain rough copies of itself, tiny bug-like objects (molecules) floating off from the main body, but no matter how great the magnification, none of these molecules exactly match any other (see **Figure 5** and follow the whitebordered square from left to right). The boundary of *M* is where a Mandelbrot set computer program spends most of its time deciding if a point belongs there or not.

**27**

*Synthetic Biology, Artificial Intelligence, and Quantum Computing*

The simplicity of the iterative formula and the complexity of the Mandelbrot set leave one wondering how such a simple formula can produce a shape of great

*Infinite variations of the Mandelbrot set are embedded in the set itself. Source: Ishaan Gulrajani, A zoom sequence of the Mandelbrot set showing quasi-self-similarity, 01 October 2011, https://commons.wikimedia.org/*

Since the logistic map and the Mandelbrot set map quadratic functions, and both represent behavior under iteration, it is not surprising that a one-to-one correspondence exists between the constants *r* and *c* and that the bifurcations created by *r* correspond to features that come with changes in *c* along the real axis where the Mandelbrot set compresses the information in the bifurcation diagram, that is, the map shows the points where the map converges to periodic oscillations and its periodicity, while the Mandelbrot set marks all the points, which end up oscillating, but the periodicity information is encoded in the bulbs of the set (see **Figure 6**). It appears that the Mandelbrot set, *inter alia*, mimics the working of the mind. Its infinitely many variations embedded within itself seem to say that once the mind latches on to an idea and begins to deeply explore it, it does so by investigating its many variations, often in a random fashion (i.e., choosing *c* randomly), but does not abandon the core idea (the iterated function, equivalent of a law of Nature). On the other hand, if a mind randomly discovers a few of the dispersed similar looking sets, it begins a search for the mother set, *M*, itself. Is it then surprising that researchers often tackle new problems through random exploration based on a hunch (the iterated function), and if they are persistent enough, a solution finally emerges if the hunch is right? We see a game of conjectures and refutations at play here. On the other hand, the logistic map appears to work on a species scale where random interactions among minds lead to forming of societies (say, along the lines of the Erdős & Rényi theorem) functioning under constrained resources and an adversarial predator-prey law where the bifurcation points stand for points of

organic beauty and infinite subtle variation.

*wiki/File:Blue\_Mandelbrot\_Zoom.jpg (Placed in public domain).*

speciation (measured in geological time scales).

*DOI: http://dx.doi.org/10.5772/intechopen.83434*

**Figure 4.** *Mandelbrot set.*

**Figure 5.**

**Figure 3.** *The logistic map.*

*Synthetic Biology, Artificial Intelligence, and Quantum Computing DOI: http://dx.doi.org/10.5772/intechopen.83434*

**Figure 4.** *Mandelbrot set.*

*Synthetic Biology - New Interdisciplinary Science*

tors and preys are battling for resources.

\_\_\_

ers by great surprise.

*z* = *x* + *iy*, where *i* = √

**5.3 The logistic map and the Mandelbrot set**

Consider the iteration *xn* + 1 = *r xn* (1 – *xn*), called the logistic map, and a number-

There are countless situations for which the logistic map captures the essence of a situation. For example, in genetics it describes the change in gene frequency in time, or in epidemiology the fraction of the population infected at time *t*, or in economics it depicts the relationship between commodity quantity and price, or in theories of learning the number of bits of information one can remember after an interval, or in the propagation of rumors the number of people who have heard the rumor after time *t*, etc. The logistic map allows us to assess the volatility of an adversarial environment by assessing *r*, that is, the ferocity with which the preda-

Now consider the following complex iteration. Given the complex variable

iterate with the seed *z*0 = 0. If the iterations diverge, then *c* is not in the Mandelbrot set (it is in the escape set), otherwise (even when it is trapped in some repeating loop or is wandering chaotically), it is in the Mandelbrot set (black points in **Figure 4**) *M*. (Setting *z*0 equal to any point in the set that is not a periodic point gives the same result.) This is perhaps the most famous mathematical object yet known. It is a fractal object, an object that is irregular or fragmented at all scales. It is a major discovery

In 1981–1982, Adrien Douady and John H. Hubbard [58] proved that the Mandelbrot set is connected. Quite astoundingly, the Mandelbrot set, when magnified enough, is seen to contain rough copies of itself, tiny bug-like objects (molecules) floating off from the main body, but no matter how great the magnification, none of these molecules exactly match any other (see **Figure 5** and follow the whitebordered square from left to right). The boundary of *M* is where a Mandelbrot set computer program spends most of its time deciding if a point belongs there or not.

of the late 20th century. It cannot be replicated in Euclidean geometry.

−1 and the complex constant *c* = *a* + *ib*, pick a value for *c*, and

pair (*r*, *x*0) where *r* > 0 and 0 < *x*0 < 1, and plot the points (*r*, *xn* <sup>→</sup> <sup>∞</sup>). Note our interest is only in the long-term trajectory of *x*0 and not in its transitory phase. Note *xn* + (1 – *xn*) = 1. The plot (**Figure 3**) has numerous 2-pronged pitchforks and hence is called the bifurcation diagram. Depending on *r*, *xn* may be settled as for 0 < *r* ≤ 3, and beyond *r* = 3 migrating from one prong to another of available pitchforks for a given *r* in the bifurcation diagram. At *r* = 4 and beyond, migration is chaotic. In between *r* = 3.5 and 4, there is an intuitively unexpected white band where migration options are few. Such and other unexpected (not discussed here) display of rich complexity tethered to *r* independent of *x*0 (i.e., the starting state) caught research-

**26**

**Figure 3.** *The logistic map.*

**Figure 5.**

*Infinite variations of the Mandelbrot set are embedded in the set itself. Source: Ishaan Gulrajani, A zoom sequence of the Mandelbrot set showing quasi-self-similarity, 01 October 2011, https://commons.wikimedia.org/ wiki/File:Blue\_Mandelbrot\_Zoom.jpg (Placed in public domain).*

The simplicity of the iterative formula and the complexity of the Mandelbrot set leave one wondering how such a simple formula can produce a shape of great organic beauty and infinite subtle variation.

Since the logistic map and the Mandelbrot set map quadratic functions, and both represent behavior under iteration, it is not surprising that a one-to-one correspondence exists between the constants *r* and *c* and that the bifurcations created by *r* correspond to features that come with changes in *c* along the real axis where the Mandelbrot set compresses the information in the bifurcation diagram, that is, the map shows the points where the map converges to periodic oscillations and its periodicity, while the Mandelbrot set marks all the points, which end up oscillating, but the periodicity information is encoded in the bulbs of the set (see **Figure 6**).

It appears that the Mandelbrot set, *inter alia*, mimics the working of the mind. Its infinitely many variations embedded within itself seem to say that once the mind latches on to an idea and begins to deeply explore it, it does so by investigating its many variations, often in a random fashion (i.e., choosing *c* randomly), but does not abandon the core idea (the iterated function, equivalent of a law of Nature). On the other hand, if a mind randomly discovers a few of the dispersed similar looking sets, it begins a search for the mother set, *M*, itself. Is it then surprising that researchers often tackle new problems through random exploration based on a hunch (the iterated function), and if they are persistent enough, a solution finally emerges if the hunch is right? We see a game of conjectures and refutations at play here. On the other hand, the logistic map appears to work on a species scale where random interactions among minds lead to forming of societies (say, along the lines of the Erdős & Rényi theorem) functioning under constrained resources and an adversarial predator-prey law where the bifurcation points stand for points of speciation (measured in geological time scales).

#### **Figure 6.**

*(Left) Connection between the logistic map and the Mandelbrot set. (Public domain) Source: Georg-Johann Lay, 07 April 2008, at https://commons.wikimedia.org/wiki/File:Verhulst-Mandelbrot-Bifurcation.jpg. (Right) Frank Klemm, Mandelbrot set with periodicity of limiting sequences. 12 August 2017. https://commons. wikimedia.org/wiki/File:Mandelbrot\_Set\_%E2%80%93\_Periodicities\_coloured.png licensed under the Creative Commons Attribution-Share Alike 3.0 Unported.*

The pace at which a system is driven through cyclic (iterative, also called selfreferential) processes, that is, cycles of construction and destruction constrained by recyclable finite resources, has a profound effect on how the system evolves. A remarkably simple model as the logistic map shows an amazing variety of nonintuitive dynamics that a nonlinear system can display. It too provides a basic involuntary mechanism by which a society spontaneously reorganizes itself. In his seminal paper on the logistic map, Robert May, a theoretical ecologist and former President of the Royal Society (2000–2005) was so struck by the deep relationship between complexity and stability in natural communities that he exhorted:

*Not only in research, but also in the everyday world of politics and economics, we would all be better off if more people realised that simple nonlinear systems do not necessarily possess simple dynamical properties. [59]*

What lessons can we draw from such simple mathematical models? For one, the logistic map indicates that the Earth's supply chain (the environment) has been grossly disrupted. In this predator-prey game where some *Homo sapiens* turn into predators and the rest into preys, a massive capture of supplies by predators results in a massive population of preys, and the preys must mutate or speciate to survive or die. The logistic map decides how the selfish genes play the game while the *Homo sapiens* mainly decide the value of *r*. The Mandelbrot set tells us that while the laws of Nature need not change for the environment to change, it does contain enough complexities in the form of fractal structures whereby the environment may change enough to force speciation to take place in niches. In the present innovation-driven environment, speciation will push to enhance the brain-mind system of the *Homo sapiens*. In the process, synthetic biology may discover life as we *do not* know it. The survival of the fittest is a statistical law and hence it rests on an ensemble being available. The world's current population certainly fulfills that.

In the present global environment, saturated by connectivity between humans, machines, and ideas, the largest component emerging in any socioeconomic context is populated by the deprived who cannot fend for themselves. *Inter alia*, this is highly visible at multiple scales of population size (global, national, provincial, urban, etc.) and context (employment, access to health care, education,

**29**

[60, 61].

*Synthetic Biology, Artificial Intelligence, and Quantum Computing*

QC, will strive to improve their gene pool by artificial speciation6

skill development, etc.). A wide spectrum of power, opportunities, and assets are grabbed by a minority by simply ignoring the plight of the desperate. This alone enforces a massive decimation of the *Homo sapiens*' gene pool. Among the predators, many with inherited wealth (and hence generally lacking survival skills but not the means) too will become preys. In this planetary-scale debacle, a unique minority endowed with an exceptional brain-mind system, perhaps aided by AI and

biology and insulate themselves in an artificially created environment to improve their cognitive abilities, life span, and fecundity. A look at the logistic map shows that as the new species advance even more rapidly, increasingly wild fluctuations in their fortunes will take place within their insulated, resource-constrained environ-

In the absence of irreversible ecological damage, it is possible that, in the early stages, replenishment may happen by itself since Nature would have decimated a large component of the population from the less developed countries, thus presenting the survivors with a sudden increase in per capita resources. We may infer by analogy from the Mandelbrot set that once a new species survives long enough to avoid extinction (because it begins with a small population, which needs time to grow into adulthood), even if it is in some remote fringes of the set, it will likely someday reach the main (central) part of the set since the set is connected. Once this happens, the new species will likely continue for a very long time until it is decimated by the Sun entering its dying phase by turning into a giant red star. That

The way we acquire knowledge is iterative and nonlinear—we conjecture and put our conjectures on trial, that is, put them to severe critical tests (refutations). As the trial progresses, we edit, discard, refine, and add to our conjectures in a pseudorandom manner controlled by criticism, driven by instinct, hunches, inspiration, etc. Conjectures and refutations in scientific research are deemed selfand community-driven adversarial processes. We connect the dots. At every step of linking the dots, we consult the axioms (conjectures) and the rules for deriving conclusions (theorems) to ensure that we are within the axiomatic system we have put on trial. This means that the process leads us to understand the Universe solely

*As we learn from our mistakes our knowledge grows, even though we may never know—that is, know for certain. Since our knowledge can grow, there can be no reason here for despair of reason. And since we can never know for certain, there can be no authority here for any claim to authority, for conceit over our knowledge,* 

As far as we can tell, creating an axiomatic system is a nonmathematical and a highly intelligent act. Developing a sequence of theorems with a specific nontrivial goal in mind (developing algorithms) is also a highly intelligent act. However, executing an algorithm, once developed, can be mechanized and does not require intelligence, in fact, none at all. If the most useful aspect of intelligence

<sup>6</sup> A controversial experiment to this effect seems to have been successfully conducted by He Jiankui who recently presented his work at the Second International Summit on Human Genome Editing in Hong Kong, November 27–29, 2018, http://www.nationalacademies.org/gene-editing/2nd\_summit/index.htm

ment unless they reduce *r* by allowing the environment to replenish itself.

using synthetic

*DOI: http://dx.doi.org/10.5772/intechopen.83434*

will be a few billion years hence.

**5.4 Creating novel DNA algorithmically**

based on our chosen beliefs (axiomatic system).

*or for smugness. [1, Preface]*

#### *Synthetic Biology, Artificial Intelligence, and Quantum Computing DOI: http://dx.doi.org/10.5772/intechopen.83434*

*Synthetic Biology - New Interdisciplinary Science*

*Commons Attribution-Share Alike 3.0 Unported.*

The pace at which a system is driven through cyclic (iterative, also called selfreferential) processes, that is, cycles of construction and destruction constrained by recyclable finite resources, has a profound effect on how the system evolves. A remarkably simple model as the logistic map shows an amazing variety of nonintuitive dynamics that a nonlinear system can display. It too provides a basic involuntary mechanism by which a society spontaneously reorganizes itself. In his seminal paper on the logistic map, Robert May, a theoretical ecologist and former President of the Royal Society (2000–2005) was so struck by the deep relationship between

*(Left) Connection between the logistic map and the Mandelbrot set. (Public domain) Source: Georg-Johann Lay, 07 April 2008, at https://commons.wikimedia.org/wiki/File:Verhulst-Mandelbrot-Bifurcation.jpg. (Right) Frank Klemm, Mandelbrot set with periodicity of limiting sequences. 12 August 2017. https://commons. wikimedia.org/wiki/File:Mandelbrot\_Set\_%E2%80%93\_Periodicities\_coloured.png licensed under the Creative* 

*Not only in research, but also in the everyday world of politics and economics, we would all be better off if more people realised that simple nonlinear systems do not* 

What lessons can we draw from such simple mathematical models? For one, the logistic map indicates that the Earth's supply chain (the environment) has been grossly disrupted. In this predator-prey game where some *Homo sapiens* turn into predators and the rest into preys, a massive capture of supplies by predators results in a massive population of preys, and the preys must mutate or speciate to survive or die. The logistic map decides how the selfish genes play the game while the *Homo sapiens* mainly decide the value of *r*. The Mandelbrot set tells us that while the laws of Nature need not change for the environment to change, it does contain enough complexities in the form of fractal structures whereby the environment may change enough to force speciation to take place in niches. In the present innovation-driven environment, speciation will push to enhance the brain-mind system of the *Homo sapiens*. In the process, synthetic biology may discover life as we *do not* know it. The survival of the fittest is a statistical law and hence it rests on an ensemble being

In the present global environment, saturated by connectivity between humans,

machines, and ideas, the largest component emerging in any socioeconomic context is populated by the deprived who cannot fend for themselves. *Inter alia*, this is highly visible at multiple scales of population size (global, national, provincial, urban, etc.) and context (employment, access to health care, education,

complexity and stability in natural communities that he exhorted:

*necessarily possess simple dynamical properties. [59]*

available. The world's current population certainly fulfills that.

**28**

**Figure 6.**

skill development, etc.). A wide spectrum of power, opportunities, and assets are grabbed by a minority by simply ignoring the plight of the desperate. This alone enforces a massive decimation of the *Homo sapiens*' gene pool. Among the predators, many with inherited wealth (and hence generally lacking survival skills but not the means) too will become preys. In this planetary-scale debacle, a unique minority endowed with an exceptional brain-mind system, perhaps aided by AI and QC, will strive to improve their gene pool by artificial speciation6 using synthetic biology and insulate themselves in an artificially created environment to improve their cognitive abilities, life span, and fecundity. A look at the logistic map shows that as the new species advance even more rapidly, increasingly wild fluctuations in their fortunes will take place within their insulated, resource-constrained environment unless they reduce *r* by allowing the environment to replenish itself.

In the absence of irreversible ecological damage, it is possible that, in the early stages, replenishment may happen by itself since Nature would have decimated a large component of the population from the less developed countries, thus presenting the survivors with a sudden increase in per capita resources. We may infer by analogy from the Mandelbrot set that once a new species survives long enough to avoid extinction (because it begins with a small population, which needs time to grow into adulthood), even if it is in some remote fringes of the set, it will likely someday reach the main (central) part of the set since the set is connected. Once this happens, the new species will likely continue for a very long time until it is decimated by the Sun entering its dying phase by turning into a giant red star. That will be a few billion years hence.
