INTRODUCTION
After timelines (genesis), differentiations, and diversity, the next aspect of evolution is closely related to the development of memory structures. This aspect is the biological reproduction. Reproduction is like a sequential memory that can be replayed over and over. To describe it in detail, we need an overview of how life began and evolved as a context.
Evolution aspect 4): Self-Reproduction.
(picture) cycles of birth-growth-death
All living things can reproduce themselves while nonliving matters can't. The living arises out of the non-living by evolution. The phenomena of self-reproduction and living lifeforms probably emerged at about the same time. They seem inseparable. From non-living matters to living organisms, structural orders must evolve from less organized to more organized, and dynamic interactions related to those structures from less coordinated to more coordinated. This evolutionary direction towards more order and coordination can be described by stochastic processes.
Stochastic processes are usually defined mathematically: the Markov process, Bernoulli process, etc. Order emerges from a Stochastic process of random elements. The emerged order is a quality, calculated based on the probabilities of the random elements and biased restrictions that have selective effects on the elements. The selective biases can come from internal interactions of the elements themselves, or from pre-existing external forces or biases. And the emerged order is a probabilistic trait of the system.
Gregory Bateson (1904-80) pointed out that biological evolution were stochastic processes also. He noted that the emerged order of living things were dynamic patterns rather than static traits. They are dynamic in the physical structures of the entities, and in the interactions between the entities. This includes the interactions that become self-reproduction. In the biological world, things do change from less organized to more organized, from simple prokaryotes to creatures with complex nervous systems.
Biological evolution begins when the Earth was lifeless and chaotic. At first there were just molten matters, moved by forces of heat/coldness (radiation, friction, conduction), gravity (masses of Earth and Moon), motion (rotation of Earth, currents), and pressure differentials (material or thermal strata). Under the selective biases of these physical pressures and motions, new structural orders emerge. Matters will separate or intermingle into new distinctive structures, with certain densities and at certain locations. It's like changing from a homogeneous pureed soup to a stew with heterogeneous lumps here and there.
The Bible described this beginning as "...And the earth was without form, and void...", and then "...Let the waters under the heaven be gathered together unto one place, and let the dry land appear...".
Classical physics is a science that studies physically selective forces: pressure differentials (or forces) and motions. It also studies attributes or order associated with those forces: locations, distance, velocity, acceleration, mass, momentum, energy, and so on. Those physical attributes have an odd component - time. To a physicist, time is a dimension related to motion. But this dimension is expressed by numbers just like any other dimensions such as mass or distance. However, time is not a physical dimension like location. It is an idea about or a representation of change. If time were a physical dimension, it will allow paradoxes to happen, and one can go back in time to the past and change what would have happen in the present or future. In any case, time is not a selective force like motions that can displace matters physically. Rather, it is the physical displacement of things that give rise to the notion of time.
There are also cross currents from selective physical forces that will negatively impact and destroy structural orders established by them. A piece of dry land can be washed away by ocean waves. Densities and composition of matters in one place can get redistributed gradually by weather activities or suddenly by volcanic or meteoric disruptions. They may also change by compensatory reactions subsequent to those activities. So, selective forces can have both positive and negative influences on a system of random elements. This is similarly to the principle of yin-yang in Taoism, where polar opposites work jointly to create new orders that can change dynamically.
Electromagnetism is another selective force in physics. It brings about a new kind of structural order than those from pressures and movements. It is the order of compounds, combined from elements and other compounds. All chemical elements in the Periodic Table have electrons and protons that may push away or pull near other chemical elements. The electromagnetic bonding and breaking apart of the elements allow them to form myriads of chemical compounds, which can also change dynamically by the presence of other elements or compounds.
Inorganic chemistry is the study of chemical elements and compounds formed by electromagnetic bonding. Chemistry provides some of the rules about the formation and reaction of compounds like salts, acids, and alloy metals. The formation of compound comes not only from electric bonding, but can also from heating, cooling, and mixing. Chemistry classifies the properties of these matters, which are basically about how they react or bond with each other.
After inorganic chemistry, the next type of selective bias is the more flexible bonding capabilities of some elements/compounds. Flexible bonding possibilities of those elements give them special structures. They form organic compounds in which the bonded structures can be extended combinatorically. Each combination of organic elements produces a structure that may combine with other organic element(s) just like before. Inorganic elements can not combine so extendedly since their bonding possibilities are less flexible. And the varieties of organic compounds far exceed the inorganic ones.
-- picture of polymer, aromatics, and protein/enzyme, complex 3-d structure
Organic chemistry is a study of four elements that have flexible bonding capabilities: carbon, hydrogen, oxygen, and nitrogen. It also studies properties of organic compounds. Those four organic elements can form compounds with geometric bonding structures like chains (polymers), rings (aromatic compounds), and complex 3-d combinations of the two. The combinations produce various carbohydrates, fats, sugars, and organic acids. And those organic compounds can interact with each other under the influences of further selective forces.
The next stochastically selective bias is a trend toward complementarity among flexible bonding arrangements. Complementary arrangements enable quicker interactions between the reacting components with spatial and temporal compatibilities, in geometry and in response sequences. Spatially complementary structures are like mortise and tenon, or lock and key. Temporally complementary response sequences are like reciprocating movements between two tango dancers: one leads and the other follows, and vice versa, at each step.
The trend towards complementary geometries and response sequences is a selective bias that favors shortcuts among many pathways of interactions. Perhaps such a selective bias can be called geodesic pull or attraction of least resistant path? An example can be a piece of iron tool rubbing again a sharpening stone. Sooner or later the two surfaces where the rubbing taking place will become complementary. One will be concave and the other convex. Geodesic pull changes these two surfaces from being incongruent to complementary as convex-concave because that configuration is the least resistive one for the rubbing (interactions).
Having shortcuts allow interactions to take place more often. With more frequent interactions, the structures of reactants can change often as well. This will lead to a greater likelihood of changes going cyclic, both structurally and dynamically in the reacting compounds. That will turn into a coevolution of the structures and the interaction processes, the two mutually affect and change each other.
Cyclicity, or recycling of structures and dynamics, is a favored outcome because it is advantageous for survival. Structures that don't recycle back and forth will turn into something else and not survive as well as the recycling ones. However, shortcuts and cyclic dynamics are not pre-existing and definite. They become so after the surviving structures have emerged and changing towards becoming cyclic. It is like the idea of "survival of the fittest". The "fittest" in Nature is not predetermined because the selection process itself is indefinite at first. After the selective biases have emerged and stabilized, then the surviving units surface. But the selective biases themselves are partially arising from or affected by interactions involving the surviving units. So they were all tentative and indefinite at first.
To rephrase, shortcuts and cyclic dynamics are not a priori selective biases. Rather, recycling structures are a posteriori phenomena that co-emerge with shortcuts and cyclic dynamics. Mathematical probabilities cannot fully predict what will survive in Nature at various times. They can predict only those in controlled settings. This marks the difference between hard and soft sciences. Hard science like physics or chemistry have pre-existing selective forces that produce definite outcomes under controlled setting. Soft science like economics or evolution have emergent selective forces that can change along with temporarily observed outcomes.
What exactly will happen in Nature cannot be predicted specifically, but some general outline can be sketched. When complementary arrangements has emerged from flexible bonding possibilities, the structures of biomolecules will emerge from organic chemicals. The complementary situation makes biomolecules more responsive to certain other biomolecules, and to environmental disturbances that will break the complementary arrangement, such as the presence of water (hydrolysis, Brownian motion) or thermal pressure (cooking, freezing). And biomolecules react quicker than organic chemicals because complementary dynamics can catalyze reactions.
The study of biochemistry focuses on biomolecules that make or take shortcuts in their reactions, repeatedly and cyclically. These biomolecules can be amino acids, proteins, and enzymes. Enzymes in particular are known as bio-catalysts, or agents for shortcut reactions. They catalyze reactions of substrates, which are biomolecules that need enzymes to react properly. The configuration of enzymes and substrates make biomolecular reactions go faster or use less energy.
In vivo, all biomolecules continuously recycle their structures with the help of enzymes and energy-supply biomolecules. These frequent changes in their bonding arrangements can affect the surrounding environment and make it respond back in various ways. These two aspects, biochemical reactions within an aggregate and environmental responses to the aggregate, may come to reinforce each other, but also provide some measure of checks and balances.
Enzymes and energy-supply biomolecules are not living organisms yet. Additional selective forces are needed for the structures of lifeforms to emerge. Here we take a closer look at the enzymes and energy-supply biomolecules first, then continue on with the other emergent selective forces - feedback interactions and memory dynamics - and the corresponding emerged structures. With all those selective forces, structures that look and behave like lifeforms then emerge willy-nilly from biomolecules.
ENZYMES AND ENERGY BIOMOLECULES
-- pics of a,t,g,c,u
Energy and enzyme biomolecules in living organisms are composed of basic molecular building-blocks called nucleotides. Nucleotides are also the alphabets of RNA and DNA molecules, which are building blocks that compose cellular and organic structures of lifeforms.
There are 5 different nucleotides. Each nucleotide has 3 parts: 1) a nucleobase, which is an organic compound of either Adenine (A), Thymine (T), Uracil (U), Guanine (G), or Cytosine (C). 2) a 5-carbon sugar (pentose) that is either a ribose or a deoxy-ribose. Deoxyribose is ribose with a hydroxyl OH molecule replaced by a hydrogen at one of the carbons. 3) a phosphate group (SO4).
Some of the 5 nucleobases in part 1 have complementary geometries. Nucleobases A and T are complementary so they can pair together easily. Same for A and U, and G and C. But A cannot pair with G, nor C with T, because they lack compatible geometries. The RNA molecule is a sequenced chain of A-U and G-C base pairs, and DNA is a sequenced chain of A-T and G-C base pairs. The structural difference between the U and T nucleobases, and consequently between RNA and DNA, is that T has a methane (CH3) molecule while U has a hydrogen. All else are equal.
Both U and T nucleobases can bond complementarily with the A nucleobase. But the geometries of the two bonded pairs are slightly different. That difference requires a change in the part 2 pentose sugar to compensate, so that both the RNA and DNA are structurally stable. RNA has nucleobases bonded to ribose. DNA has nucleobases bonded to deoxy-ribose. These two differences, U and ribose in RNA and T and deoxyribose in DNA, make the geometries of the RNA and DNA different as well. RNA is a single helix, and DNA is double helices. Since structures generally evolve from simple to complex, the DNA molecules probably branched off from the evolutionary tree of RNA molecules.
The pentose sugar and the phosphate group of the nucleotides form a stably bonded structure of sugar-phosphate. They provide backbone-like stability for the nucleobases, A, T, U, G, and C, to attach to. In this combination, the nucleotide molecules are stable at one end (sugar-phosphate) and flexible at the other (nucleobase). This makes nucleotides capable of rebonding, and stable after bonding is formed.
The flexible bonding part lets the nucleotide building blocks to pair and chain together in different sequences. These sequences turn them into various product compounds. And if they survive various selective forces, they become different segments of the RNA/DNA molecules. The survival of any sequence of nucleotides is whether it can recycle back and forth through bonding and rebonding activities available and compatible to that sequence.
The sugar-phosphate backbone part allows the nucleotide chains to be structurally stable under environmental disturbances. A chain of nucleotides can further wind around specific proteins (histones or nucleosomes, also sequenced nucleotide chains) that act as bobbins. A very long strand of nucleotides can thus coil down into a very small volume and become highly stable. In order for that compactly coiled nucleotide chain to react and rebond again, some other proteins with the right kind of complementary structure and dynamics must be present. They will unwind the long nucleotide strand from the protein bobbins. Then the rebonding of the nucleotide chain can take place.
The nucleotide building blocks are moderately complex structures unlike simple methane or water molecules. Their complexity must have evolved from simpler prototypic structures during the early stage of biomolecular development. By chance and selective biases, the nucleotide structure emerged from prototypic organic compounds. And when they appeared, their bonding flexibility and structural stability were highly suitable for recycling dynamics. So they survived and proliferated and established a new structural order - biomolecules. They are like an economically viable product that appears in a market first and triggers a new industry. There will be other viable products to follow. And the followers will resemble the first one since that will be what is fit for survival.
In the various combinations of nucleotides there are two important types of biomolecules: the energy-supply biomolecules and enzymes. These two types of biomolecules probably co-emerged with the nucleotides around the same time. The ways they interact with other organic compounds or biomolecules is directly related to the dynamics of recycling/shortcuts.
ENERGY-SUPPLY BIOMOLECULES ATP
The main energy-supply biomolecule in all lifeforms is ATP, adenosine tri-phosphate. ATP is almost identical to nucleotide A, adenosine mono-phosphate (adenine + sugar = adenosine), in the RNA or DNA molecules. The only difference between ATP and nucleotide A is that ATP has 3 phosphates and the nucleotide A in the RNA or DNA has only one phosphate. If nucleotide A in the DNA/RNA polymer is broken loose and separated from the strand then it may not be in the mono-phosphate bonding configuration.
The other nucleotides in the RNA/DNA polymer are also mono-phosphates. If they have tri-phosphate bonding, then they can also be energy-supply molecules. They would be nucleotides T or U or G or C with triphosphates. GTP will be guanosine trisphosphate (guanine + sugar = guanosine), and CTP is cytodine triphosphate, etc. But when chained into the RNA/DNA structure, they all bond with one phosphate only, because only that way can the sugar-phosphate backbone be stably formed. These GTP and CTP energy molecules are not as common as the ATP, possibly because it is more efficient for any organism to deal mainly with a single type of fuel currency instead of with many. In any case, it is the addition/removal of phosphates in these molecules that enables the cycle of energy storage and release. Triphosphates with 3 phosphates have more energy. Diphosphates (2 phosphates) and monophosphates (1 phosphate) have less energy.
ATP can loose a phosphate and become ADP (adenosine diphosphate) by hydrolysis, a reaction where water molecules split apart the reactant ATP. This reaction releases energy, which can be used for reactions of other biomolecules at the right moment. So hydrolysis of ATP must be signaled by the demand of other biochemical reactions. For the reverse, ADP can attach a phosphate and reassemble back to ATP. This can happen when energy is supplied to them, by cellular respiration where glucose sugar broken down from food is oxidized.
In living organisms, the recycling of ATP to ADP and back to ATP must repeat continuously to support their energetic activities. Consequently all lifeforms must regularly acquire and digest foods as one of the primary activities in life. Along with that is the companion process of waste removal. Pathways of recycling can be seen in another perspective. The waste of one lifeform can become the resource for another, and vice versa. The food chain is actually cyclic rather than pyramidal. forming a give-and-take cycles between different aggregates.
The process of reassembling ADP back to ATP needs more than just energy from cellular respiration. It also requires the presence of a particular enzyme, the ATP syntase, in order for it to work. The ATP syntase enzyme is, like other enzymes, made of the nucleotides combined in some specific sequence.
ENZYMES
Enzymes come from segments of the RNA or DNA molecules. They range from short ribozymes from the RNA to long proteins from RNA or DNA. Reactions of substrate biomolecules will speed up greatly by enzymes because their interactions provide shortcuts for the substrates to react faster. One enzyme can catalyze only one type of substrate reaction and not others because of availability of compatible shortcuts or not. As there are many substrates, there are many different enzymes.
---- video of enzyme biomolecule movements
During catalysis, the enzyme and the substrates both go through changes. Each step of the interaction is accompanied by some movements and changes in the shapes of one or both reactants, which remain complementary but in different ways. One stage of complementary geometries leads to a new step of interaction, which results in a next stage of complementary geometries, with its subsequent step of interaction, and so on. Nonetheless, with all these movements and changes, the interaction between the enzyme and the substrates follows a stable course that produces a definite outcome. The enzyme will recycle back to its original shape while the substrate components will be changed to something else after the catalysis.
The web of metabolic interactions between various enzymes and substrates in vivo are not fully known because of the vast complexity involved. But the complex dynamics can be simplified with a few assumptions. 1) The complexity is an accumulation of individual factors, such as the geometry and movement / bonding dynamics of each biomolecule. 2) The accumulated complexity may be likened to that of chaining or fusion. A chained accumulation will play out the dynamics of individual link sequentially. A fused accumulation will play out a different dynamics than that of individual components, like a compound chemical acts differently than its constituent elements. 3) Contributing factors to the accumulation can emerge from the existing accumulation. This is like a company's valuation can come from the sum of its assets, plus emerged values such as stock, which reflects the economic influence (business or political clout) the company has from the volume of its business transactions or relation to other businesses.
In a chained accumulation scenario, the complexity increase exponentially with each segment added into the sequence. There is a correlation between the lengths of RNA/DNA molecules and complexity of the organism. The strands of RNA/DNA grow longer and more numerous as organisms evolve from the simple to the complex. Primitive lifeforms like bacteria and virus have shorter strands of RNA or DNA. Complex lifeforms from sponge to humans have longer strands of DNA that are separated into clusters (chromosomes).
Present-day biomolecules started out from prototypic organic compounds where recycling of structures were too slow or partial. With the emergence of geodesic pull among numerous interactions of the prototypic compounds, recycling dynamics and recyclable structures gradually became more definite. It is self-reinforcing that recycling dynamics will lead to recyclable structures, which then lead back to more recycling interactions. "Cyclicity" can perhaps be another name for "geodesic pull".
Eventually, the nucleotides emerged from the prototypes and dominated over other structures that may also recycle. The dominance of nucleotides over others is due to their combination into structures that act as catalysts (enzymes) or energy-supply (ATP), which accelerate both the assembly of nucleotides into other product compounds and the breakdown of those product compounds back to nucleotides. These bonding and breaking activities, from nucleotides to metabolic biomolecules and back to nucleotides again, involve interactions that can have many twists and turns, but overall a pattern of recycling.
Genesis 3:19 of the Bible: "...for dust thou art, and unto dust shalt thou return..."
While structures like enzymes and nucleotides can recycle back and forth, they still need to find ways to self-reproduce in order to proliferate and become the dominant building blocks inside of organisms. A possible way to self-reproduction will be suggested later, after a discussion of other selective forces that also contribute to the formation of living lifeforms. Here are some examples first.
RNA and DNA molecules are examples of biological self-reproducing structures. Some segments of the RNA or DNA strands can become a special enzyme called the polymerase. Polymerase interact with the whole RNA/DNA strand in such a way that they can make a copy of the main strand out of spare-part nucleotides that are floating around, which can come from digested food.
Another example is virus. A virus attached to a specific host can replicate itself with the help of that host under certain conditions. The host will interact with the virus like a replication machine (or enzyme?) and produce multiple copies of the virus. Such interactions may also have something to do with the mutation of virus. That is, a virus does not mutate by itself directly, but by incorporating some changes from the reproduction process it engaged with the host.
OTHER EMERGED SELECTIVE FORCES
The next emerged selective force is feedback interactions between active biomolecules made of nucleotides and enzymes and ATP. These biomolecules are active systems because they can use energy from the ATP molecules to respond to feedback signals with their own actions.
Biomolecules have specific ways of bonding that can be flexibly extended and combined. And feedback interactions can modify the structures of those interacting biomolecules, in ways that move them towards something that is more systemically efficient and interlocked. That is, interacting biomolecules will become more orderly (differentiated) in their ways of interactions, and also more integrated as an organized whole.
This process of differentiation of parts and integration of whole is similar to certain positive feedback interactions. An example of this is the biological cell structure. A cell has differentiated components like the membrane, cytoplasm, and organelles. One organelle can be the mitochondria that assembles the ATP energy molecules from the ADP molecules. These differentiated components are tightly integrated by the continuous and definite interactions among them, and between components inside and outside of the cell membrane. The interactions reinforce the components and the integrated cell structure to be the way they are. Without those interactions those components and the cell will fall apart and lose their distinctions.
How do differentiation and integration both happen by positive feedbacks? Positive feedback process amplifies the responses of the parts to the input signals they receive. The amplification of responses can change the parts, making them polarized and differentiated from each other (symmetrical or complementary differentiations, see schismogenesis by Gregory Bateson). The continuous responses of these parts also effectively lock (integrate) them into a whole that repeats those feedback interactions. The aggregated whole can respond and react to feedback signals from other aggregates or parts.
Biomolecular structures emerged from feedback interactions will be organized aggregates of pre-organism kind, something like primitive RNA/DNA molecules or virus.
One view of virus is that they are toxic semi-living structures from nowhere that aim to destroy healthy organisms. An alternative view is that viruses are everywhere since the early days of evolution. Organisms existing in modern history are actually descendants of aggregates like primitive virus and prototypic organelles. And viruses still reproduce themselves by interacting with living organisms under the right conditions. Viral reproduction process is a basis for the self-reproduction process of complex organisms emerged later. The reason why a virus can destroy a host cell is that the host cell's metabolic activities are disrupted by the matching but alternative metabolic activities of the virus.
The next emerged selective force is memory dynamics, which can be associative and sequential types. Previous articles have shown how memory dynamics can be induced by feedbacks and resonance. In a pre-organism biomolecular aggregate, sequential memory is a replay of some activities in the same sequence as before. To re-enact activities in the same sequence, the aggregate needs certain infrastructure to serve as signals and pathways for the triggering and playing out of the sequence of actions. Such infra-structures emerge perhaps at the same time as one component is differentiating from another by positive feedbacks. That is, while components are differentiating outwardly into symmetric or complementary inter-structures, infra-structures that expedite the response sequence to outside feedback signals are emerging within each component and between them.
The infrastructure expediting the aggregates' response sequence can be reinforced by similar feedback stimuli replayed repeatedly. The infrastructure can be so well reinforced that a partial input is sufficient to trigger a full response-actions sequence. When that happens, the aggregate has reached a new order of structure, a structure capable of sequential memory dynamics. Sequential memory capability turns an aggregate into a semi-automata, a proto-organism that can act out certain sequence of actions from memory with little or no external stimuli. They can be something like proto-organelles with specific capabilities. It is one step from a full living organism.
Living organisms, like prokaryote or eukaryote cells, are aggregates of organelles interlocked together by constant interactivities. The step that takes proto-organelles to cells is associative memory dynamics. They connect proto-organelles and combine them, letting them evolve into proper organelles with capacity for change in the sequence of actions, as a coordinated whole cell.
Associative memory dynamics are replay of sequences of actions in varying combinations. Each sequence of actions can be a sequential memory replay or sensory impression. The combination associates the stimulus sequence and the response sequence together. The stimulus signals are transmitted through feedback (signal) pathways and picked up by responsive circuits. Which circuit will respond most strongly will depend on other dominant actions at play at the moment. So the association of stimulus-to-response or associative memory replay can be variable. If the same kind of associative memory get replayed repeatedly, then the same signal feedback pathways get utilized and strengthened more. That repetition can constrict associative memory into sequential memory.
In biomolecular structures, associative signal pathways are affected by biochemical reactions surrounding the pathways. These biochemical reactions in turn are affected by actions of the components in the structures. Repeatedly similar biochemical reactions can be induced by repeatedly similar feedback signals to the components. That repetition reinforces the associative pathways. But the connections are likely biased towards desirable returns and avoiding undesirable responses, like increasing resources and pleasant feelings, and reducing the opposite. The reinforced pathways and surrounding biochemicals become conduits for motivation that stimulate the components to act and react associatively.
Criss-crossing signal pathways make associative memory dynamics possible. Signals travelling in the pathways can go in different directions and trigger various components to replay their responses in different orders. This is unlike sequential memory that has rigidly fixed replay sequence. With associative memory dynamics, involved components can integrate together into an aggregate that behaves like an intelligent automata. The associative linkages enable the components to trigger and respond to each other mutually in an orderly fashion, making a grand play of various action sequences that appear coordinated and intelligent.
An integrated automata with sequential and associative memory dynamics is still not an living organism, because it cannot motivate itself and act spontaneously. It needs outside trigger to get it started. To be capable of self-motivation, the automata needs imagination. Ideas or wishes or hopes or wants or needs can all be said as projections of imagination. Beside remembered automatic responses for acquiring food and removal of waste, it is imagination that motivates spontaneous actions.
Imagination is a derivative dynamics of associative memory. It is combination and transformation of associations. For example, memory of carpets and memory of clouds can combine and transform into imagination of a flying carpet, which can be found in a story in Arabian Nights. We will discuss more of that in the next article. It suffices to say that with imaginative associations and memory dynamics, intelligent aggregates become living organisms capable of motivating itself to learn and to explore.
Learning and exploring are similar activities. The first is related to some parameters (or goals) while the second may or may not be. Learning is, in response to some impetus signals, establishing new or rerouting existing signal pathways in an efficient manner out of an unlearned network of signal connections before the learning. The learned routes of signal pathways make the aggregate more tuned to efficient responses to the impetus parameters. The parameters can be anything within and without that can trigger the aggregate to respond. When the shortcut pathways made by learning are reinforced by repetition, it can also be called adaptation. The adapted structures and dynamics become physical or psychological traits of the aggregate. Those that are in the midst of adapting are still exploring and learning.
Donald Hebb discovers that there is proto-learning taking place in synchronous firings of neurons. When two nearby neurons are repeatedly firing at nearly the same time, the one firing later will reach out its dendrites to the earlier firing neuron's axon, making synaptic shortcuts between the two neurons so that they may fire together with greater efficiency. Gregory Bateson discovers that deutero-learning takes place when multiple sets of similar incident sequences are repeated, efficiency in the connections will be progressively greater in each addition of iteration (till it plateaus off). Hebbian proto-learning can be described as shortcut establishment within a cluster of neurons, while Bateson's deutero-learning is a shortcut development among neurons both within and between clusters.
Exploration, on the other hand, takes place when the constituents of an aggregated group make associative connections not necessarily in response to some environmental conditions, but to internal ones. If it is a response to internally imagined associations, then that exploration is self-motivated rather then environmentally triggered. And that makes it different from adaptation (learning) in terms of origination. But exploration and adaptation share similar outcomes, which are establishment of efficient associative connections.
It may be possible that, somehow, exploration have lead some (adaptable) components to some sequences of actions that become a process of self-reproduction. That is, by trial-and-error and by the pull of cyclicity, some members of an aggregate have associatively connected some sequences of interactions that turn out to be a process of making copy of the aggregate. This copying process reproduces some aspects of the aggregate - some of the structures and dynamics but not the whole. And such process will be preserved because it has survival advantage. The ones that can make copies will propagate the species and enable them to survive more, and the copying process will be repeated.
In summary, evolution of lifeforms starts from lifeless matters eons ago. They go through changes by existing and emerged selective forces, and become organized more and more till they have reached the state of present-day living organisms. At each stage of these evolutionary changes, the emerged structural order comes from both the selective forces that build order and the cross-currents of selective forces that destroy order. The construction and destruction of order, like yin-and-yang, together account for the changes in structures and dynamics.
Also, evolutionary changes are step-like in time if the forces driving them are from feedback interactions. When rapid changes by positive feedbacks lead to a new order of structure, that structure will dominate and proliferate and affect a large portion of existing population, forcing them to adapt to change or not survive. Changes that follow will either support or counter the dominant new order, till these changes reach a level of equilibrium or saturation that is a state of homeostasis maintained by negative feedbacks. Homeostatic state will last much longer than rapid transitional state. But eventually new abrupt changes will happen again due to accidents from explosive catastrophe or excessive builtup of confined pressures, and a new dominant order will rapidly emerge from that changes, and then back down to homeostasis, and the step-like cycles repeat.
SELF-REPLICATION
Now comes to the question of what may be a mechanism of self-replication in biomolecular structures. It is likely that selective biases promoting cyclicity of structural order have a hand in this. Some self-motivating bio-aggregates exploring randomly somehow hit upon the right sequence of actions and transition into a species that can self-reproduce. What may be a possibly right sequence of actions that lead to self-replication can be that of repeated complementary interactions.
Suppose two interactive components, A and B, are complementary in structure. Their complementary configuration may have originated from the process of complementary schismogenesis, which is separation of parts due to escalation of feedback responses in the manner of complementary reciprocation. One gives and the other takes. Then one gives more and the other takes more, and so on. When these two complementary components A and B interact not only with each other but also with other components, then the reproduction of component A can come from the interactions of component B with other components, and the reproduction of component B can come from that of component A with others.
Suppose the interaction between components B and A is a strong one. That strong interaction pattern can cross over to the interaction between component B and other components, biasing the other components to respond back to component B in a way similar to how component A responds to B. This will turn the other components behaviorally similar to component A. When the response of the other components also prompt them to change structurally, making them adapt their structures to that similar of component A, then that new structure becomes a copy of component A. This then is a reproduction of component A by component B's complementary action on other components.
In the same fashion, the reproduction of component B can come from the interactions of component A with some other components, turning those other components into a copy of component B. If the original complementary components A and B work together as a pair, they can each reproduce a complementary copy that is half of a pair. When the two half copies also are paired together, then a full copy is made, a copy of A-B pair emerged from an original complementary pair A-B. This then is a process of self-replication.
Why would complementary components A and B be paired together and work as a unit in reproducing complements that will also be paired together? One reason is the feedback interactions between the two components, and another is the component's memory of response-sequence. Constant interactions make the involving components paired together. And internal memory that responds to feedback interactions also strengthens mutual attachment.
Biological components are not static. Their internal parts change constantly - discarding expired cells and replenishing with new ones - while their outward appearance remains the same. This is seen at all levels, from cells to organs to organisms. For this coherence to happen, it is due to feedback interactions taking place at the inter-component and intra-component levels, as well as exchanges happening between the outside and inside of the components.
While the process of self-reproduction is possible by repeated complementary interactions, it has one fundamental problem, which is that the amount of information in the child copy must be less than that of the parent(s). This is pointed out by the Incompleteness Theorem by Kurt Godel. This theorem proves that no system can have all the information about itself. It needs something outside to create some of the information within. In mathematical systems like algebra and geometry, that something are the axioms that establish the rest of the system. The axioms can't be established by the axioms themselves or by the rest of the system. They come from human imagination.
The biological extension of this theorem is that living beings can't have all the information about itself to reproduce itself fully. While men are born out of men and fish of fish, the reproduced copies at birth are not exactly the same as the original. There are much resemblances but also many small differences. The body structures and functions can be partially similar, but pigmentation and sizes may be different.
Self-reproduction does happen in all living things. So how does that square with the Incompleteness Theorem? One answer is that biological self-reproduction is not a full reproduction, at least not at first. A system can reproduce only a part of itself but not the whole. The partial product of a biological lifeform will grow and transform into a full copy later. That growth comes from dynamic metabolic interactions of the components in the child copy. The metabolic activities are not completely scripted in the reproduction code because some of that activities will take place under conditions emerged later. The reproduction only makes components that can and will interact metabolically.
The emergent growth, dependent partly on interactions with the environment as well as the composition of the partial copy at conception, will likely make the offspring mature into something that is somewhat different from the parent unit. If a child at maturity is a spit image of its parent in every way, then its growth environment and initial copy composition must be the same as that of the parent.
In giving birth, an adult human does not reproduce another adult or baby directly. What is reproduced is a fertilized egg cell that the adult once was. This fertilized egg cell grows into an embryo by constantly dividing and interacting, both intercellularly and with the hormones and nutrients in the mother's womb. The embryo develops into a baby that will separate from the mother's body. Then it will interact with the environment in different ways than in the womb. For non-mammals like birds, the embryonic growth happens outside the mother's body.
A baby is still only a partial copy of the adult's body. Its organ structures and metabolic activities are a little different than the adult's. The immune and skeletal and reproductive and all other systems of the body are still immature. Only by growth will the baby mature into a settled form that functions like the adult.
The emergent growth partly depends on environmental factors that may or may not be accounted for in the DNA code. The DNA code is like a sequentially arranged memory of metabolism for growth/development on the organism side. It is information that directs the organism's components how to interact with each other. It also includes information about how to interact with some factors of the environment such as nutrients. If environmental conditions match the interaction directives of the DNA, then that will lead to a "remembered" normal development, like growing the right shape of fingers or locations of nervous system. And the offspring will develop and mature into a normal, full copy of the parent.
If the environmental conditions badly mismatch the organism's developmental codes of the DNA by things like contaminated food or lack of proper stimuli at certain stage of growth, or if the environmental conditions induce the organism to over or under produce some proteins which will turn on or off some genes differently than normal, then the organism's developmental growth will go askew. That can lead to misshapened or diseased organs or unusual physiology. Then the offspring will not be a normal, full copy of the parent.
If the environmental conditions deviate only mildly and fall within a range of normal development. That will result in normal variations of the child copy. Those variations can be slightly faster or slower metabolic rates or darker or lighter pigmentation. The matured offspring is still considered a normal, full copy of the parent.
In the case of single-cell organism or virus, the child right after birth is already a mature copy of the parent unit apparently. Does this negate the Incompleteness Theorem? Not quite. The reproduction of single-cell organism or virus is not done by the parent unit alone. It is aided by factors outside of the parent unit. In the case of viruses (computer or biological) the external factor is something supplied by a matching host. In the case of single-cell organisms, that will be special enzymes or hormones from the environment or the parent that are not present in the child copy.
In biological cases, the special enzymes and hormones work complementarily with the RNA of the parent cell or virus, resulting in replication of the RNA and construction of the rest of the body. The complementary interactions of the two parts, the cell's RNA and factors from external source, suggests that such coordination came about by repeated complementary interactions originated way back before. From simpler biomolecules to complex biological structures, complementary interactions have always been preserved. Those complementary interactions are extended, and replication of complex structures become materialized.
Around the time of birth, the enzymes/hormones needed to replicate a new cell are present in the parent cell but not in the child copy. Otherwise, those enzymes were copied to and present in the child's body, and the reproduction process would go on again, and the child will reproduce a grandchild right away. That is not the case for living organisms. Self-reproduction requires a period of emergent development in the child for it to reach the stage of sexual or asexual maturity. Only then will the replication enzymes/hormones become available to the child copy. But for viruses, reproduction can go viral because their host may keep supplying the needed hormones or enzymes.
In short, the self-reproduction process of living beings has two stages: A) the partial copying stage, and B) the emergent growth (epigenesis) stage. After both stages, the child becomes a full copy of its parent. The copying stages involves replication of the RNA / DNA, by interactions of the DNA/RNA molecules and special complementary enzymes and triggering hormones. The emergent growth involves interactions of the components within the copy and between the copy and its environment. The components are biomolecules and proteins produced from the RNA / DNA in the copy, and those existed in the environment. In particular, the interactions center around recycling of structures that can store and supply energy (like ATP), or speed up the rates of interactions (like enzymes).
EMERGENT GROWTH (EPIGENESIS)
(picture) Twins
If the DNA sequences of two living units are exactly the same, then it will lead to very similar outcomes of emergent growth even if environmental factors are different for the two. Examples can be found in identical twins. Studies show that identical twins will grow up to be very similar to each other even if they are separated at birth and placed in different environment. They grow into adults greatly resembling each other, not only in appearance but also in life experiences. This may be attributed to the identical genetic sequences unfolding in the same way, so that their interactions with the environment are very similarly replayed. It is as if the unfolding of same sequences will have a selective bias to future interactions with the environment, and filter out at least some similar outcomes despite different available choices in the environment.
Outside of identical twins, the genes of any population are not identical. Similarities and differences in genetic materials will lead to similarities and divergences in epigenetic growth and forms. The majority of genetic codes are the same across animal species. The percentage of identical codes is greater within a species than between species. So a human baby resembles more to another human baby than to an ape baby. The similarities are reflected not only in the shapes but also in metabolic activities. So they similarly eat and digest food. On the other hand, the small percentage of differences in the genes can lead to incredible varieties of differences in epigenetic development and structural forms. That divergences are reflected also in the shapes of structures like body coverings (skin, hair, scale, mucus), limbs, sensory systems, and other organs in terms of sizes and compositions. Furthermore, they lead to varieties of psychological choices, habits, and outlooks.
(picture) embryo
The unfolding of developments by genetic materials can be observed in embryos where the conditions of gestation are similar but the outcomes showing similarities and differences. All embryos look alike when they begin as a single (fertilized) cell. They become more and more different as the embryos grow. They also retain some similarities passed down from a common past. A human embryo goes through stages that reflects its ancestry shared with other species. It resembles an amoeba at first, then to something like a sponge, then an embryo of an invertebrate, a reptile, a mammal, till finally it becomes differentiated as a human fetus. These stages move from a single cellular structure to complex and organized multicellular structures. The chronology of embryonic stages in a single species is the same for all members of that species because they share the same DNA sequences. But their youths at birth are all different in some respect due to the minute differences in the genetic compositions of that species.
NEXT
Self-reproduction of biological structures are closely tied to memory dynamics that take place as organic matters interact and evolve. The structures that support memory dynamics, such as the central nervous system in animals, can produce further interactive dynamics as evolution continues. We will look at some dynamics derived from associative memory, which include imagination, dream, language, and spirituality.
