Somewhere Between Light and Darkness

                               Proto-life and the First Pictures of the World

How did first life perceived the world? Whatever that “picture” was it must have been very simple: binary (light-dark) and discrete (proto-RNA bases).

We will most likely never be able to fully understand how we see things around us. I have asked myself many times: how does this process that begins with photons traveling a long way from the sun, hitting a tree in front of me, and  reflecting from it enter my eye, inciting numerous retina cells and converting into impulses, traveling through my eye nerves to the vision cortex in the back of my head, where this cluster of millions of connected cells somehow forms the picture of the tree I see in front of me but which is at the same time in my head as well? And this is just a very crude and schematic description of what is actually happening between this tree and its picture in my head. We might never be able to understand how all this is possible but perhaps we could try to go back in time, to the very beginnings of life itself, when things probably used to be a bit simpler and try to “reconstruct” or rather “imagine” where our capacity to see and feel the world around us could have come from.

This story is based on two notions, one is position and the other is value. Position is a defining property of an element expressed only through its place and neighborhoods within a structure, while value is based on the notion of content and is unrelated to the position. When values occupy elements in a structure of positions we get a 2D image called the state of space (Fig.1).


To define value, it is sufficient to have two distinct properties. They are both neighbors and oppositions at the same time. In this kind of binary structure, if one value is “warm” the other would be “not-warm”, or if one value is “light” the other would be “not-light”. (Fig.2)


We could assume that, in the process of formation of the earliest living molecule, a capacity to recognize these properties and thus distinguish itself from its surroundings emerged as one of its key components. However, the features that carry these properties have to be located in some places (positions) within the structure of this molecule. Thus the structure of values has to be in some way associated with a structure of positions, which in this case was probably a linear molecule, and one of its first distinctions was most likely “outside” and “not-outside”, which became “inside” (“me”). It became possible by distinguishing properties such as “warmer” (or “not-warmer”) than “me” that became properties of the “outside”. The ability to distinguish these binary properties had to first be “acquired” and then “remembered”. Acquisition of this capacity to distinguish “warm” had to be acquired at some point for the first time and then “remembered” (“encoded”) within the living molecule. Thus this molecule had to establish at least two different positions related to the capacity to distinguish “warm” from “not-warm”. One position would identify the current state around it, while the other would keep memories of previous (earlier) encounters with the property “warm” and “not-warm”. It is perhaps impossible to reconstruct how this mechanism was established for the first time, but it is almost certain that it was one of the key steps in turning one kind of molecule from non-living into living matter. Then at some point the property “not-warm” separated in two distinct and opposite values “hot” and “cold” while “warm” remained the property of the living molecule that could also be recognized as a third property of the environment. Thus, instead of binary, the system turned into trinary: “hot”, “cold” and “warm”. However, properties of “hot” and “cold” (or “not-warm”) at the same time were the same as “not-living” (“dead”) while the property “warm” became synonymous with “alive” indicating that the relationship of the living molecule with its environment remained in its essence binary: “alive” and “not-alive (“dead”). Another binary relationship remained between what was happening “now” and what happened “not-now” (or “before”) and the capacity for this distinction had to be located on two different positions within the molecule.  These binary and trinary structures of values could be visually represented as “light” and “dark” or as “white” and “black” while the value “warm” would be represented as “gray”(Fig.3). Interestingly, liquid water, where life most likely have first appeared, is in the middle between cold ice and hot steam.


Then, at some point a connection between the positions representing “now” and “before” had to be established, so that the state of the environment observed “now” could be compared to the state recorded (remembered) at the position “before”. Clearly this is quite a complex interaction within different parts the living molecule that was established at some point later in the development of living matter. However, in the earliest stages of formation this proto-living molecule was not able to distinguish itself from its environment. If the temperature was “good” it would continue to exist, but if, perhaps, the water current took it to a “not-good” place (let’s say “hot”) it would simply disintegrate. Thus, one of the key stages in development of living matter became its capacity to protect itself from the changes around it. In order to arrive to that point it was necessary to gradually develop very complex mechanisms consisting of several positions with distinct properties which could communicate with each other while located on certain fixed positions within the molecule.

At that earliest binary stage, “me”(“warm”) – “not-me” (“not-warm”), there was no distinction between “warm” and “light” and between “not-warm” and “not-light” (“dark”). If the environment was “warm” it was “good”, and this proto-living molecule could not distinguish itself from the environment. When the environment changes into “not-warm” (which later became “hot” or “cold”), it was “not-good” and at that point proto-life could distinguish itself from its environment. The question is how this proto-living molecule managed to maintain its structural integrity while the temperature around was changing and becoming “not-good” (“not-warm”)? It is most likely that, for a certain period of “time” (very long in human terms), this kind of molecule could not do anything regarding its environment, it would simply disintegrate when the temperature around it became too hot or too cold. But it is clear that at some point it managed having a more interactive relationship with its environment. Parallel with that it also begin distinguishing “warm” as “light” and “not-warm” as “not-light”, that would in the next stage separate into two opposite values: “very light” or “white” (equivalent of “hot”) and “very dark” or “black” (equivalent of “cold”) while “warm” became a value between – “gray”. This might be considered as the beginning of development of the “vision” system characteristic for many life forms today, consisting not only of the “perception” of the properties of the environment but also their interpretation and memory. It was this kind of structure, after being successful and surviving, that was later passed to proto-RNA and then to RNA and finally to the DNA double helix. What is important to underline here is that these structures were not only carrying information of vital interest for maintaining the metabolism of living matter, but at the same time these are also “pictures” of the environment impressed and stored onto them. When many years ago I came up with a different representation of the RNA and DNA that was visually based, it was just another way of representing the bases. Instead of the widely accepted representation of bases as five, in essence, arbitrary letters of the alphabet (U, C, A, G and T) organized in a linear structure, here were proposed five values of the gray scale (black, dark, gray, light and white) organized in 3×4 matrices forming 2D images.(Fig.4)


The structure of five values is itself linear and there are 120 different ways to place these five values into a linear structure of five positions. Of all possible combinations the only one proposed here (and its negative) corresponds to certain formal relationships between the RNA/DNA in the best possible way.  The bases are represented as discrete values of the gray scale in this way U = Black, C = Dark, A = Gray, G = Light, and T = White. The value of “black” is defined as “absence of light”, thus U = 100% black, C = 75% black, A = 50% black, G = 25% black, T = 0% black. This is a linear structure with two elements U and T having one neighbor, while three elements, C, A, and G are with two neighbors. The difference between neighboring values is 25%. If we identify all the pairs that differ 50% we will get:  U-A, C-G, A-T. With this single rule we have established all the base pairs for both DNA and RNA and the exchange value which defines these relationships is the value of Gray that represents Adenine (A). However, it took me a while to realize that these images are not just a much better way to represent RNA/DNA but that this is an algorithm to decode the information impressed on life and that these 2D images are in fact as close as we can get to what might be the “earliest pictures of the world” stored within living matter since its origins. Thus, the way we see the world today originates from these earliest life forms. The basic principles of seeing the world remained the same, only the “picture resolutions” have changed, becoming higher. Also, this is not only about images but also about the notion of “change” from which “space” and “time” seems to be originating as well as all related complexities of perception and memory. Memory was encoded in the structure of the molecule, and by copying one molecule on another even the earliest memory must have been preserved and distributed. Since this proto-life was at the same time a proto-observer, these first memories were the earliest pictures of the world and its earliest interpretation.

Perhaps it would be interesting to try to re-construct in some rather formal way how this capacity to “see” might have emerged and what might have been those earliest pictures of the world recorded by the earliest life form and in this way perhaps follow the transition from proto-life to the earliest viable life form. It is based on two kinds of structures, one structure of values (five discrete shades of the gray scale) and another structure of positions, in our case a 3×4 matrix already implemented in the visual representation of RNA/DNA mentioned above.

Conceptually, the simplest structure of values consists of one value v and a structure of positions of one position p), and the only possible state is when the value v occupies the position p – ( p,v) (Fig.5).


There is no other state possible and thus no change can happen in this world. The next initial conditions could be a structure of one position p and two different values v1 and v2 (Fig.6).  Here there are two possible states p,v1 and p,v2 but this change cannot be recognized from within. For this we would need an outside observer.


Similarly, in the case of  one-value v and a two-position structure (p1, p2), the only state possible is when this single value occupies both positions(p1,v and p2,v)(Fig.7).


Thus there is no change here either. However, here we could notice that in this state the same value occupies two spatially different but neighboring positions. This kind of relationship, when the same value occupies two neighboring positions, we will name the connection. With structures of two values two positions (p1, p2) and two values(v1,v2) we could generate four different states: 1. ( p1,v1 and p2,v1), 2. ( p1,v1 and  p2,v2), 3. (p1,v2 and p2,v1), 4. (p1,v2 and p2,v2) (Fig.8).


In addition to two sates (1 and 4) each with one connection (c = 1), here are two sates      (2 and 3) in which different values occupy different (neighboring) positions. These kinds of neighborhoods where different values occupy neighboring positions we will name junctions. Here we have the first case for possible distinction of some earliest living molecule from its environment. If in this molecule one value (v1) represents warm-light than the other value (v2) would be an impression of the environment on it: not-warm, not-light. In other words, states 2 and 3 are the simplest possible pictures of the environment as perceived from within, while the entire binary state is representing both observer and observed as seen from the outside. The next stage would be the introduction of one position and three-value and structures. (Fig.9)


In case of the structure of values we could identify warm-light as being value gray on the gray-scale, while not-warm, not-light, could be separated into two opposite values: cold-dark and hot-bright, represented with black and white values on the gray-scale. This would be a linear value structure with white and black neighboring gray, while they themselves are not neighbors. Here, these opposite values relate to each other as positive-negative, while the value gray remains neutral to this operation. Now the question is if these three values could be identified as existing RNA/DNA bases and in what way. It is most likely that the value gray would represent Adenine, however, what might be the bases represented by two opposite values?


One option could be Cytosine and Guanine. They form one of the base pairs that appear in both RNA and DNA, but they have no relationship with Adenine. Another option would be that these two values stand for Thymine and Uracil. Both of them form a base pair with Adenine and this is how they are connected, since they do not have a direct relationship and they play exclusive roles in DNA (Thymine) and RNA (Uracil). At this stage of development perhaps it was still too early to consider the bases the way we know them today. Perhaps some proto-Thymine, proto-Adenine and proto-Uracil appeared in what we call proto-RNA. But, let’s go back to the formal properties. Another case would be a two positions and three values structures(Fig.10). There are three different one-value states possible (white-white, gray-gray, black-black) with each having one connection while in the case of all three values and two positions we have different values occupying neighboring positions: white-gray, white-black, gray-black, black-gray, black-white and gray-white. Here in addition to three states with connections only, there are six states defined by junctions. In the case of three positions (codon) and two values we could have gray-gray-gray, black-black-black, gray-gray-black, gray-black-gray, black-gray-gray, black-black-gray, black-gray-black, gray-black-black (Fig.11).


Here there are stats with only connections (gray-gray-gray), with both connections and junctions (gray-black–black), and with junctions only (gray-black-gray). Similar sets of states could be defined with other two pairs of values (white-gray and white-black). It is interesting to notice that in the states with two different values, the states with both junctions and connections seem to have a higher organization (clear separation between values) while in those states having only junctions this distinction is not so clear. It is reasonable to assume that these two are the simplest cases where the distinction between states of higher and lower organization (entropy) could be recognized, here potentially within the earliest living matter thus enabling the distinctions between “me” and the “world” or between being “alive” or “dead.” Within the genetic code we could even identify proteins that might be carrying this kind of information: low entropy – UUA (leucine) and AUU (isoleucine) or high entropy-UAU (tyrosine) and AUA (isoleucine). With three positions and three values, the border cases are states with single value(only connections) and states with each of three positions having different value(only junctions)(Fig.12). We could notice here that junctions could have different value differences: white-gray and gray-black are 50% while white-black is 100%.


The next level would be to organize two codon-like linear structures of three positions into a 2×3 matrix (Fig13).

13. 2x3matrix1

In case of a three value structure we could generate numerous states including those with low and high entropy. Since there is a possibility that the earliest living forms were binary and similar to some kind of prot-RNA here are presented states with only two values representing bases that form a base pair: black-Uracil and gray-Adenine.(Fig.13a,b,c)



13.c 2x3matrix

Within these six positions and two value states organized as 2×3 matrices (two codons) there are 64 different states possible. Among those with an equal number of bot values        (3A + 3U)  we could identify six highly organized states (low entropy) each with  4 connections (c=4) and 3 junctions (j=3) and only two high entropy cases with no connections (c=0) and 7 junctions (j=7).  Fig.13d


All these  visual representations of possible earliest molecules  are in essence partial and could be understood as precursors of perhaps the most accurate conversion based on a 4×3 matrix. Here 4 is the number of values (bases) in RNA/DNA, while 3 is the number of positions that defines codon. Initially I thought this is only a better and more meaningful algorithm to represent RNA/DNA strands and convert them into 2D images.(Fig.14)


I only began to realize much later that these are in fact  “pictures of the world” that are encoded in the RNA/DNA of all life since the earliest life forms emerged on Earth and this algorithm is a way to make them visible. It was not an invention but a discovery. These would be the most elementary “images of the world” perceived and recorded by any matter that can be called living, whether it is based on RNA / DNA or some other molecular structure, whether on Earth or some extraterrestrial object. Only binary cases are selected here with an equal number of bases (6A+6U) which represent the lowest and the highest states of entropy.  I encountered all of them among the many strands I have been working with (Fig.14a,b.c.d).






While the binary distinctions hot-cold, day-night, were and are vital for the entire biosphere, the stories about light and darkness, good and evil are in foundations of various versions of the “myth of origin” of almost all known cultures, past and present. Not only our existential/biological needs but also our cultural values and narratives are determined by the properties of earliest living molecules. We structure our life around day and night. Day is light, warmer and clear; night is dark, colder and uncertain. Simply, light is “good”, dark is “bad”. We structure each year according to seasons that all relate to warm-cold, light-dark and have numerous rituals marking the transitions from one season to another with the help of various sun-gods. (Fig.15 and Fig.15a,b)


15a Light



Ra or Re is the ancient Egyptian deity of the sun. By the Fifth Dynasty in the 25th and 24th centuries BC, he had become one of the most important gods in ancient Egyptian religion, identified primarily with the noon sun. Ra was believed to rule in all parts of the created world: the sky, the Earth, and the underworld. All forms of life were believed that have been created by Ra.(Fig.16)

16. RA


Helios also Helius in ancient Greek is the god and personification of the Sun in ancient Greek religion and myth,  often depicted in art with a radiant crown and driving a horse-drawn chariot through the sky.  Though Helios was a relatively minor deity in Classical Greece, his worship grew more prominent in late antiquity thanks to his identification with several major solar divinities of the Roman period, particularly Apollo and Sol. The Roman Emperor Julian made Helios the central divinity of his short-lived revival of traditional Roman religious practices in the 4th century AD.(Fig.17)

17. sun-god

Genesis 1. The Beginning

1 In the beginning God created the heavens and the earth. 2 Now the earth was formless and empty, darkness was over the surface of the deep, and the Spirit of God was hovering over the waters. 3 And God said, “Let there be light,” and there was light. 4 God saw that the light was good, and he separated the light from the darkness. 5 God called the light “day,” and the darkness he called “night.” And there was evening, and there was morning—the first day. (Fig.18)



Mithra commonly known as Mehr is the Zoroastrian Angelic Divinity (yazata) of Covenant, Light, and Oath. In addition to being the divinity of contracts, Mithra is also a judicial figure, an all-seeing protector of Truth, and the guardian of cattle, the harvest, and of the Waters. The Romans attributed their Mithraic mysteries (the mystery religion known as Mithraism) to “Persian” (i.e., Zoroastrian) sources relating to Mithra. Since the early 1970s, the dominant scholarship has noted dissimilarities between the Persian and Roman traditions, making it, at most, the result of Roman perceptions of (Pseudo-) Zoroastrian ideas. (Fig.19)

19. Mitras


In the pre-Columbian civilizations of Mexico and Peru, sun worship was a prominent feature. In Aztec religion extensive human sacrifice was demanded by the sun gods Huitzilopochtli and Tezcatlipoca. In both Mexican and Peruvian ancient religion, the Sun occupied an important place in myth and ritual. The ruler in Peru was an incarnation of the sun god, Inti.(Fig.20)

20. maya


In Ancient Chinese philosophy, yin and yang (/ j ɪ n / and / j ɑː ŋ, j æ ŋ /; Chinese: 陰 陽 yīnyáng, lit. “dark-bright”, “negative-positive”) is a concept of dualism, describing how seemingly opposite or contrary forces may actually be complementary, interconnected, and interdependent in the natural world, and how they may give rise to each other as they interrelate to one another. (Fig.21)

21 Yin Yang

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