To re-cap the preceding pages, passing matter flows in one temporal direction: the forward direction of matter time. The cell accumulates a record of this matter as information in the genetic language of the cell’s DNA library. When needed, the information is translated from the DNA language one codon word at a time into a string of amino acids that self-organize, folding into complex protein shapes that are a three-dimensional representation of the original DNA information. The resulting three-dimensional shapes are both directional and left-right chiral.
By directional, we mean that they’re assembled into a chain in a specific order with one end designated as forward and the other as rear. And, as we see in the orientation of the blue-shaded protein and yellow targeted object in the figure above, this directional reference also applies to a specific orientation of the folded protein relative to its targeted object. The in-and-out shape of the right side of the protein is forward facing as the surface that interacts with the corresponding surface of the targeted object. The term chiral refers to a quality of certain shapes that cause them to not be superimposable on their mirror image. Our left and right hands are familiar examples of chiral shapes. The directional and chiral features of proteins enable them to recognize and pass information to other three-dimensional shapes inside the cell and at the in-out boundary of the cell wall. In doing so, they sense a four-dimensional world.1
From the perspective of life, the flow of matter within and around the living cell is a changing, yet continual sequence. Fundamentally, it is a small-large blur from which the living being extracts parts out of the whole and stores them in a growing DNA library within the cell nucleus. Over time, the library acquires information that allows the cell to recognize and acquire additional similar parts that are added to the library, where they’re stored in the DNA patterns we refer to as genes. When translated into the protein language, these gene patterns become the physical shapes that form and maintain the functional structures of the cell body and that perform the tasks essential for survival.
At the most granular level we’ve examined so far, DNA is a string of information that serves as the memory of the cell. Patterns stored in DNA symbolize all the parts that have passed by and inside the cell wall, that have been retained and that subsequently have been used to build protein structures inside the cell. DNA retains parts, wholes and their correlative patterns in a way that’s organized to mirror all that has been recognized and retained.
In the protein-building process, genes are interpreted and translated one codon word at a time in the forward flow of living time. The figure shown here shows the stages of protein assembly just above the green arrow near the bottom. Described from the perspective of an observer, the process begins with a one-dimensional string of DNA codons in the past of living time (shown on the left) and results in a three-dimensional protein task in the present of living time (the blue and tan shape shown on the right). As the build proceeds in the forward direction of living time (represented by the small blue arrows shown between stages), information on each new state flows into memory, shifting information on all prior states further to the left – that is, further into the remembered past. Although all the molecules are structurally matter at each stage of the process, the transitions depicted reflect the status of the build at a given moment of living time. In fact, all the molecules shown at each stage are temporary functional tasks – not “permanent structures” of the cell.
Information is passed throughout the cell by way of tasks as they are needed by the organism. The completion of tasks relies on an interconnected looping flow of material task-structures built out of proteins that feed into one another. In this flow, the cyclic output of proteins performing various sub-tasks become the input of higher-level tasks performed by other proteins whose outputs feed into still higher-level tasks performed by more proteins. The result is an expanding nested hierarchy of looping task-structures that together comprise the living organism. Through protein-based recognition of shape, each task carries the information contained in its shape forward, beyond and above the energy required by a material world discovered by evolved humans.
1 We’ll talk more about protein direction and chirality in later chapters.
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