Saturday, June 26, 2010

The Digital Control of Life

In other blog articles such as Life is More Than Chemistry and Can Chemical Evolution Work? I point out how living things fundamentally differ from nonliving things. Both are controlled by the laws of chemistry, but in living things, the chemistry is guided by information from the DNA data source. That explains why organic molecules are generally much larger than inorganic molecules. To make such large molecules, the limitations of pure chemistry are overcome by 'helper' molecules such as chaperone molecules made according to the DNA design plan. If the DNA data source is cut off, the organic molecules decompose as the laws of pure chemistry take over.

In a recent blog article, The First Digitally Controlled Designs, I point out that each living organism is a digitally-controlled design, using the same design paradigm now commonly used in most household appliances, where an embedded controller uses symbolic digital codes (software) to control the functions of the appliance. Because the 'software' in these cases is stored in read-only memory (ROM), it is technically called 'firmware'.

The DNA is also firmware, because:

(1) It is digital: the digits are Adenine, Cytosine, Thymine, and Guanine, equivalent to a 2-bit code. The fact that genetic control uses 4-valued digits, and man-made controllers use 2-valued digits (bits) is a mere design detail.

(2) It is symbolic: Each codon, a sequence of three DNA digits, equivalent to a 6-bit code, is NOT an amino acid, but a symbol that represents an amino acid (or in one case, a stop signal). The fact that genetic control uses 6-bit codons, and man-made controllers use 8-bit bytes is a mere design detail.

(3) It is stored in read-only memory. There is no information flow from polypeptides to mRNA to DNA, or any writing process.

(4) In the reading process, selected information from the DNA is copied to mRNA (temporary copies) and then interpreted: that is, translated to polypeptides (the basic form of proteins). In man-made digital controllers, selected information from the read-only memory is copied to temporary memory and then interpreted: that is, translated to signals that produce desired actions.

In addition to the temporary (mRNA) copying, in cells there are two other copying processes. There is a copying process that occurs during cell mitosis for growth and repair, and a rearrangement/copying process that occurs during cell meiosis for sexual reproduction. Neither process creates new information. Man-made digital controllers are not designed to grow and reproduce by themselves, so similar copying is not provided. Instead, there is copying in the manufacturing process.

(5) There is a higher structure typical of digital control languages. These specialized languages have data units that operate somewhat like the verbs, nouns, and modifiers of 'natural' (human) languages. Some, like a noun, specify an object or subject; some, like a verb, specify an action; and others (modifiers) specify a condition or selection or limitation, etc. The DNA information is used not only to create the basic structures (nouns) of life, but also specialized molecules (modifiers) that control the operations (verbs) of these structures.

If you want to appreciate the complexity of life designs at the cellular level, consider the process of extracting energy from food molecules like glucose.  Simply put, the process is a "controlled burn" of the food-fuel, producing energy, carbon dioxide and water.  The released energy is transported by ATP molecules (like rechargeable batteries) to the sites of all the energy-consuming activities of the cell.

This process, called Cellular Respiration, involves 4 stages:

  • Glycolysis (10 steps), 
  • the Citric Acid Cycle (8 stages), 
  • the Kreb's Cycle (8 stages), and 
  • the Electron Transport Chain (4 steps).  

  •  If you click on each of the above links, you will see what organic chemists call a "simplified" or "summary" diagram of each part of the process.  Unless you are an organic chemist or a student of organic chemistry, you will not understand these diagrams, but one glance will give you a good idea of the level of complexity of so-called 'primitive' life.  These diagrams represent only some of the cell processes, and they are only summaries!  There are diagrams for other complex processes, such as Photosynthesis, which captures the energy of sunlight and stores it by making glucose (food-fuel).

    The process of reading and interpreting the DNA information creates all the chemical 'machinery' (such as enzymes) and chemical 'factories' (such as mitochondria) for these and many other complex processes of living things.