Visual Representation of DNA and RNA
An interpretation of DNA/RNA as visual structures with specific formal properties and relationships. Instead of the existing alphabet representation U, C, A, G and T, all the bases are expressed as five discrete values of the gray-scale: T=white, G= light gray, A= gray, C= dark gray and U= black. Arranged in 3 x 4 matrices DNA strands as linear structures consisting of alphabet letters are converted into 2-D images with distinct visual properties. In this representation, we could learn more about DNA/RNA, not only as biological (functional) structures but also as a specific language that can be expressed visually.
DNA – A Proto-observer
What is life*? It might be impossible for a living creature to give an adequate answer to this question. Perhaps to posit an “objective” answer we would require a state or position that is neither alive nor dead, some kind of “third state” that is neither of these two, or a combination of both, from where it would be possible to observe and distinguish both living and dead entities. For me, as a living observer, this third state seems to be impossible to comprehend or define, because an observer has to be alive to be a subject of change, and in order to be able to observe.
Any living observer has faculties that allow it to interact with its environment (sense), to process and store information, and to act accordingly. It seems that most living observers do not perceive themselves as separate from the world around them. However there are some living observers that are indeed aware of this separation. They also understand that there is a part of the environment (world) that will never be experienced by the observer, that will remain unknown, and that there is a part of the observer that is separated from the environment, that is not a part of the world, which we could call “I”. It is this kind of observer that is in fact able to observe itself, or to be self-reflective. Any living observer has its beginning (birth) and its end (death), but only the self-reflective observer is aware of this.
What is essential to note in all this, however, is that any form of observation includes a process of change, in both the observer and in what is being observed. The observer changes itself and the world while observing it. The emergence of life from the stage of the earliest living molecule is at the same time the emergence of its environment. However, the self-awareness of an observer implies as well an awareness of the environment (world) that is not possible without memory.****
Memory could be defined as a set of information and an algorithm in which this information is stored and retrieved. Since there is an order of storing information, there is a process of irreversibility that can be associated with acquiring memory, that is the opposite of entropy. It goes from a state of low organization (less information) to one of higher organization (more information). By remembering the initial state (low entropy), we may compare it with the end state (high entropy). And it is memory itself that allows us to make this distinction in the first place. The entire evolution of life could be interpreted as a process of acquiring memory. It has a direction of change, it is irreversible, and it moves from simpler toward more complex ways of organizing living organisms. It seems that the evolution of life could be interpreted as an anti-entropic but also irreversible process.
Since an observer itself can be understood to be a reflection, a picture of its environment, the more complex living organism (observer) is, the more complex image of the world it encodes. The interpretation of the environment that was “impressed” on the earliest living molecule was a very simple one, most likely binary in its nature. It is reasonable to assume that those first sets of information were about some properties of the environment vital for the living molecule to maintain its integrity, in other words, to survive, such as distinctions between hot and cold or dark and light. In order to recognize these properties around itself this first life had to know what is hot and cold, meaning that this knowledge had to be incorporated, stored within its own molecular structure. However, there must have been a moment when for the first time a new combination within a living molecule took place that enabled it to distinguish hot from cold and thus increased its chances to survive. Because there is life today, it is also reasonable to assume that this rudimentary knowledge about the environment, this early picture of the world, acquired by the first life form was vital and accurate enough to be passed through all subsequent stages of life until the present day. It could probably be found among the DNA strands of any living organism today.
Understandably, most of the research on DNA has been focused primarily on the biological properties of a certain sequence or strand, or on the functional role it plays in a living organism. In addition to finding out what a DNA sequence does, it might be also interesting to find out if it possesses any form of meaning, and what this meaning might be. What kind of knowledge might be encoded in a DNA sequence and how might we go about identifying and interpreting it? To answer these questions, first of all, it would be necessary to have an adequate means to interpret DNA and RNA as some kind of language.
The visual method introduced in this book is intended to provide such a language. It is based on a specific representation of DNA/RNA sequences that are expressed visually with well-established formal relationships derived primarily from the visual properties of its constitutive notions. This method is based on five discrete values of the gray-scale while the sequences are organized in 2D blocks of 3x4 matrices. With these two different kinds of structure, one structure of values and another of positions, it is possible to generate images connected with a set of formal rules that could be understood as syntactical in nature. Furthermore, it is also possible to attach certain meanings to this form of representation that would constitute some kind of DNA semantics. Thus the five values on the gray scale are interpreted as five DNA/RNA bases and their relationships are derived from the properties of the corresponding values. For example, all the base-pairs could be defined by a single rule: 50% value difference between the bases. It is also possible to attach some additional meanings to the values representing bases. Values black and white could be interpreted not only as U and T, but also as cold and hot, or dark and light, as well as large and small, or distant and close, while certain distributions of values within the 3x4 matrix could be recognized as highly organized states, and others as states of entropy.
Altogether, in addition to looking at DNA as a functional (biological) entity, it seems that it is possible to approach DNA as a specific living observer with a certain kind of knowledge impressed (stored) on it, as a set of information about its environment (world) that can be translated and interpreted through a language with its semantic expressed visually. This approach could enable a very different understanding of DNA, but also of ourselves as its more complex expression, and the strangely familiar world around us.
“What is Life” is the title of the famous book by Erwin Schrodinger published in 1944.
Perhaps one descriptive and incomplete definition could be:
Life is self-organized matter that maintains and improves its structural and functional properties through observation, growth and multiplication.