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Physics of Life

Emergence of life 



I n t r o d u c t i o n:

The goal of this chapter is to provide a complete cognitive model of the emergence of life on Earth, namely to answer the question

"What made certain objects, comprising of the same chemical elements as the Earth,
become thinking, feeling, arguing and passionate creatures?".

In a moment, though it may seem totally unbelievable, we will show you that our existence and rationality arose directly from the properties of chemical molecules, the conditions of gravity on our planet and the continual process that was triggered from these properties under these conditions, a process which started to inlfuence the properties of the particles...



D u a l i t y   o f   N a t u r e:

It all begins with the properties of matter named Duality of Nature, which manifests itself in the cyclic grouping of particles and the subsequent division of objects made by this grouping.

In space, particles tend to group into planets, stars, galaxies, etc. Each astronomical object is a single centre of concentration of matter. Larger objects absorb smaller objects. Black holes concentrate matter in the strongest way. When certain limits of concentration are overpassed, it explodes. An example of this could be the Big Bang.

This phenomenon also occurs on Earth. Our earthly gravitational conditions, particularly in areas of liquid matter, cause that certain types of grouping particles, after overpassing certain limits, divide into two.

This cycle of



R P D - t y p e   p a r t i c l e s:

Due to the dimensions of the Earth, some of the matter on its surface is in a liquid state. The original oceans were a mixture of water, methane, ammonia and hydrogen. Scientists named this mixture - primordial soup. In this fluid environment, under these gravitational and atmospheric conditions, particles such as amino acids and RPD-type particles naturally came into being. RPD-type particles bind its elements from the environment, leading to division. The divided particles don't change their behaviour, continuing to bind its elements until the next division, and so on.

Among the elements making up the RPD-type particles were the phospholipids that form liposomes (particles enclosed in a membrane like balloons) and ribose nucleotides which form RNA (chain particles). As one might guess, liposomes burst into smaller balloons, while in the case of RNA, things were more complicated. The chains formed from ribose nucleotides have different properties. Both the structure and properties of RNA depend on the sequence of nucleotides from which a given molecule is composed.



R e p l i c a t o r s:

Chains made from the ribose nucleotides have different properties, both the structure and properties of RNA are dependent on the sequence of nucleotides from which a molecule is build. Among the different types of RNA there exists one very special particle which replicates itself using copies, leaving the original particle in its original state. This particle forms complementary copies (also known as negative or mirror images) of itself, which means that each second division creates an identical copy of the original chain. This way, replicators - the particles able to copy itself - naturally came into existence. At this point, we need to explain the word "identical". Copies of the particles were identical, but after a large number of divisions, errors may have occurred. Therefore, the duplication was not a "100% identical copy", but "almost the same." A copy of the ribose nucleotide chain may, for example, differ from the original due to a lack or excess of one element.



P u l s a t i n g   h u n g e r   f o r   r e s o u r c e s:

It is easy to note that in an RPD-type particle's environment, the number of them increases in an exponential manner (1,2,4,6,16,32,64,128,256,1024, ...), while the number of free elements decreases. After a certain number of divisions, there starts to be a shortage of elements due to large numbers of RPD-type particles within the environment. But, the RPD-type particles continue to pursue resources to absorb. In this brand new condition, a new method of absorption emerged: if there are no free elements available, the "stronger" particles could steal them from their "weaker" twin brothers. Most replicators create identical copies of themselves but sometimes, by accident, it happens that a particle creates a slightly different copy of itself, with slightly (or even severely) different properties. These properties could be very different, but the one we are interested in is the ability to absorb elements. If such a particle absorbs them or retains them better than another particles, it may destroy all the other particles. So, in the primordial soup pulsating with replicating RPD-type particles, two phenomena emerged: "competitive struggle" for the elements (resources) and the "chain of succession". In fact, these particles, which were better in assimilation and/or duplication, thrived while the "weaker" stopped dividing and subsequently ceased to be.

Competitive struggle can be won in two ways, either by the perfection of tactics of absorption or by cooperation with other particles by combining their "strength".



S y n t h e s i z i n g   r e p l i c a t o r s:

Both the perfection of tactics and cooperation led to a new type of replicator - a synthesizing replicator. At present, it is difficult to say which kind of particles, a few billion years ago, created them. However, by observing the phenomenon occurring in every living cell, we can reasonably presume that the synthesizing replicators were brought into existence by three cooperating RNA chains (chains formed from ribose nucleotides):

  • mRNA particles (messenger RNA) - self-replicating particles which are strings (sequences) of information on which genetic code is stored;

  • tRNA particles (transfer RNA) - particles that transport, from the environment, the appropriate amino acids and attaches them in the right place according to the genetic code of the mRNA. By matching tRNA molecule linked to the corresponding amino acid in the ribosome joins the currently processed part of the matrix (mRNA), and this amino acid is attached to the synthesized protein, then the tRNA is released);

  • rRNA particles (ribosomal RNA) - particles catalyse (now included in the ribosomes, which are involved in the biosynthesis of polypeptides) - building protein structures from amino acids, attracted by the tRNA to the mRNA and arranged in the proper order based on the information stored in the information chain (mRNA).

It is this cooperation of these three types of RNA which were to be crucial in transforming the RPD phenomenon into synthetising replicators which can be considered as the first living objects.

Pic. Diagram showing how protein chains are built.

The diagram shows how tRNA builds protein chains from a design stored on the mRNA. The synthesis of protein chains is due to the close proximity of the rRNA. tRNA, rRNA and mRNA are all RPD-type particles.



P r o t e i n s:

Protein - one short word, only seven letters, and yet the protein is one of the most important elements of life! Without them there is no life. Polysaccharides and polynucleotides are needed as well, but proteins are crucial. There are three reasons why proteins are so important:

  • first: proteins are long chains made up of only twenty elements - (proteinogenic) amino acids,

  • second: the different properties of proteins are due to the order that the amino acids have been arranged in the peptide chain,

  • and third: the order of the amino acids in the protein chain can be created based on a design

From these 20 proteinogenic amino acids, the combinations can produce elements which can be large or small, soluble in various liquids or not, having (or not) an affinity with other chemicals, rigid or flexible, hydrophilic or not, alkaline or acidic, having an electric charge or not etc. In addition, many proteins respond completely differently to specific stimuli, for example, one can shrink due to a change in electric potential, and another produces an electric potential when exposed to light.

These properties resulted in proteins that have become important elements in the competitive game for resources: some of them contribute very significantly to strengthening the capacity of "absorption" and/or "stronger hold" of essential elements.



G e r p e d e l u t i o n:

At this point, let's stop thinking about absorbing particles for a moment and let's discuss the abstract process of gerpedelution. It is a cyclic process consisting of three, eternally repeating, consecutive stages:

  1. Production: A set of objects is produced based on a set of designs

  2. Selection: From the produced objects; those that fulfill certain criteria (the so-called selection criterion) are selected

  3. Copying (sometimes or always) with (slight or important) changes: The designs of the objects which have come through the previous stage are copied/replicated. The resulting set of designs is directed to the next production stage.

In this way, all kinds of products, including cars, televisions and shirts, are produced in factories around the world. A production consists of providing the necessary components into the factory and combining them in an appropriate manner on the basis of designs. It turned out that the same process was spontaneously initiated, by synthesizing replicators, in the primordial soup.

Synthesizing replicators reproduce themselves on the basis of their own design.

Do you remember the sentence A production consists of providing the necessary components into the factory and combining them in an appropriate manner on the basis of designs? Let's translate it into a microbiological environment: a production consists of providing (using the tRNA) the necessary components (amino acids) into the factory (rRNA) and combining them in an appropriate manner on the basis of the design (mRNA). The selection is due to a natural lack of elements for building the constantly absorbing and replicating particles. Therefore to the next stage of gerpedelution passes only those particles which have a better capacity of "absorption" and/or "stronger hold" of the essential elements.

Diag. Schematic of gerpedelution.

The improvement of designs in factories is a conscious process, which is implemented by constructors. Whereas, in the case of replicators, it is done in a natural way, as a result of random changes in the process of replication. Elements in some chains can be reorganised, removed or added, the rest remain unchanged.



A u t o d y n a m i c   s y s t e m:

The primordial soup was the environment in which, in a natural way (due to the laws of physics and chemistry), the RPD-type particles emerged, and these naturally generated the process of competitive struggle for the resources they needed to rebuild after dividing. This process, in turn, began to feed back to affect the original particles, causing changes in their structure in subsequent generations. Therefore, the primordial soup was an autodynamic system - which means a system that generates processes that alters the system itself or its components. And this reconstruction of elements continues to this day, and viruses, fungi and every person and een every one of their cells are part of this system.



C e l l:

A wall surrounding a town ensures that the inhabitants are more secure. By being covered, with a membrane, the cooperating elements of synthesizing replicators ensured a better cooperation and an improvement in their acquisition and/or maintenance of resources skills. As mentioned before, the phospholipid membranes are also RPD-type particles. Therefore, it is most likely that, through modification of mRNA which occurred during the duplication of the synthetizing replicators, a new type of peptide was created, a new special type which attracted the phospholipids and this created the cell membrane. And in this way, the primitive cells emerged, now considered to be alive.



B i o l o g i c a l   e v o l u t i o n:

With the emergence of cells, the gerpedelution process, as it is a component of the autodynamic system, also began to change. From a relatively simple process, with three well-defined and successive steps, it turned into a very complex one in which the stages began to overlap and internal genetic designs had been enhanced by external memetic designs. This includes knowledge orally transmitted, collected in books or stored on computer hard drives, all of which affect human behaviour.



T h e   p o w e r   o f   b i o l o g i c a l   e v o l u t i o n:

The opponents of the theory of evolution use the argument that the probability of the accidental creation of even quite simple protein molecules in the primordial soup is 1 out of 10113 attempts, and a simple enzyme 1 out of 1040 000 attempts, while the mathematicians say that even an event whose probability is expressed by the figure 1 out of 1050 will never happen. Often these numbers are replaced by comparing the likelihood of accidental origin of life on Earth with the likelihood of accidentally creating a working Boeing 747 after a hurricane has gone through a junkyard.

But it is enough to carry out some simple calculations to see the enormous creative potential inherent in the process of biological evolution. Calculate how many bacteria there would be after four and a half billion years, assuming that they reproduce once every single day? The first day there are two, the next - four, the third eight and so on... The general formula is known even to high school children: on the n-th day, their number should amount to 2n. So how many should there be exactly after, say, 1 642 500 000 000 days (4.5 billion years times 365 days)? The answer surprises most and gives food for thought: 10500 000 000 000! How insignificant do the previously quoted numbers of "extremely unlikely creation" look? This simple calculation shows that to build a specific chain of nucleotides (specific mRNA), nature may have had 10500 000 000 000 trials. This figure is based on the assumption that there is only one division per day, but bacteria under favorable conditions (where there are as many resources as needed) can multiply up to seventy times faster. Replication at a lower level than the cell had to run a lot faster, for example: DNA replication proceeds at a speed of one thousand nucleotides per second.

Therefore, assuming that the rate of division is, for example, one second, after only two days there would be 1052 016 objects created from one original object.

The problem with understanding how biological evolution proceeds is due to the fact that we humans perceive the world through the prism of linear processes, whereas biological evolution is an exponential process - in character similar to an avalanche or explosion.

An unimaginably large number of trials is the first of the powerful mechanisms of biological evolution, but not the only one, because there is another - the evolutionary ratchet.



C h a r a c t e r i s t i c s   o f   b i o l o g i c a l   e v o l u t i o n:

Competition for the necessary resources occurs very quickly. If we had a culture medium with the volume of Lake Baikal (Deepest lake in the world and largest freshwater lake in the world by volume), the situation where the bacteria would start to kill each other in the struggle for the necessary elements needed for reconstruction occurs after just 100 divisions. Therefore, if they replicated every twenty minutes, then the real struggle for existence between them would happen in less than two days!

The branch of science which deals with conflict and cooperation is mathematical game theory, and this theory was used to study the characteristics of biological evolution. The key in determining them are evolutionary games, such as: "Hawks & Doves", "Small evolution" and "Small group evolution". Analysis of these games shows that biological evolution has a ratcheting mechanism, which in subsequent cycles of biological evolution creates more and more perfect living objects, provided the selection function is strong enough. The natural tendency of this process favours, in successive generations of selected objects, two types of improvement in the absorption of resources: more perfect skills of the individuals and more perfect cooperation within groups of objects.

This leads to two characteristic paths of the creation of new biological species:
speciation - when the set of living objects (named by biologists species) splits into two new, different, sets and
symbiogenesis - the merging of separate organisms to form a single new organism. These paths are illustrated in the diagram called HeKroGram:

Diag. HeKroGram - paths of creation of new living objects schematic.



O r g a n i z a t i o n a l   l e v e l s   o f   l i v i n g   o b j e c t s:

This natural characteristic of the process of biological evolution has contributed to several levels of organization of living objects.

If we accept the concept of The Physics of Life that a living object is a set of interacting, replicating elements that actively absorb the external resources, then we can distinguish several organizational levels of living objects, depending on the elements of which they are composed.

  1. Level 1 – synthesizing replicators, which are groups of particles which not only rebuild themselves after division, but also create side products – on the basis of a natural design, which they themselves are;

  2. Level 2 – prokaryotic cells, bacteria and mitochondria; these are forms of life of the second organisational level because they are systems comprising of cooperating elements of the first organizational level of life.

  3. Level 3 – eukaryotic cells; The form of third organisational level of life are systems of cooperating elements of the pre-existing levels.

  4. Level 4 – multicellular WSS-type objects (object subjected to selection as a whole), such as human beings or ants;

  5. Level 5 – social WSS-type objects, such as ant colonies.

In turn, the specific RPD-type particles that initiated the gerpedelution process and whose successors are synthesizing replicators, may be considered as a form of zero organizational level of life. At this moment in time, neither zero level nor level one are thought of as being living objects in the majority of today's scientific community.



P e r f e c t i o n   b y   s e l e c t i o n:

So, what are living objects? The result of a process in which the vast majority of objects does not survive or kills each other before producing offspring, but those that remain are the perfect minority. I think it best captures the rephrased quote from "Faust" by Johann Wolfgang von Goethe: "So in the end, who are you? I am part of that process which creates excellence by eternally doing evil".



T h e   k e y s   t o   u n d e r s t a n d i n g:

To quickly gain a basic understanding of all this material, it is recommended to study and understand the following topics:

  1. Emergence - the way the complex systems acquire brand new properties out of a multiplicity of interactions between relatively simple elements.

  2. The natural absorption of the external resources by certain types of particles to build themselves.

  3. The RPD phenomenon - a cyclical process of reconstruction and division of chemical molecules.

  4. Two properties of nucleobases: first - they are part of the nucleotides second - they form a combination of two unique pairings.

  5. Properties of nucleotides - which naturally form such chains as RNA and DNA

  6. Properties of proteins: chains composed of amino acids, characterized by various (even very extreme) properties

  7. tRNA properties: depending on the sequence of three nucleotides in the so-called anticodon, it connects only to one type of amino acid

  8. The workings of ribosomal (rRNA): construction of a chain of amino acids based on the information (the sequence of codons), stored in the mRNA

  9. The natural distortion of replication - mutations

  10. Special features of biological evolution (based on the gerepedelution process) with its perfecting evolutionary ratchet mechanism.

Detailed understanding of these issues is the key to understanding the emergence and further development of life.



O b s t a c l e s   i n   u n d e r s t a n d i n g:

  1. A lack of adequate and unambiguous concepts, there is no precise and unique definition of evolution, there are no such concepts as "chain of succession" or "prevoluant" - instead of this we use ancestor ("evoluant" extends descendent)

  2. Inadequate language used in literature: "animals must adapt", "must alter their genes", "fish underwent a genetic mutation to adapt"

  3. Non-intuitive mechanisms that govern the process of biological evolution, such as: changes are not dependent on time but on the number of cycles

  4. A lack of knowledge of the mathematical game theory - educational systems and media are trained in reductionism not in systemics, theory of game and set (population) thinkings

  5. In biological evolution, the genes are principally modified in the subsequent generations of individuals but not in individuals during their life cycle

  6. Emotionlessness of biological evolution - selection is a deprivation of the right to multiply, mainly by killing

  7. Anthropomorphic personification - the human trait of attributing consciousness to natural processes which we do not understand (in other words, confusing determinism with natural tendencies of the systems)

  8. Phenomenon of nesting and intermingling of gerpedeluiton stages in biological evolution; multiple storage of genetic designs in one individual living object (for instance: DNA and mitochondrial DNA); emergence of memetic designs

  9. Non-intuitive concept of autodynamic system

  10. Non-intuitive understanding of exponentially growing processes

  11. Non-intuitive understanding of non-linear processes

  12. The scale of the speed of biological evolution, most of us have seen only a fragment (grandparents, parents, children, grandchildren). For the average observer, evolutionary processes are so slow that they are practically invisible. The activity of an average man is reduced to about 45 years, and evolution has been going on 4 500 000 000 years. These two figures are to each other as 0.3 of a second to a year.