Abstract: The classical view of information flow within a cell, encoded by the famous central dogma of molecular biology, states that the instructions for producing amino acid chains are read from specific segments of DNA, just as computer instructions are read from a tape, transcribed to informationally equivalent RNA molecules, and finally executed by the cellular machinery responsible for synthesizing proteins. While this has always been an oversimplified model that did not account for a multitude of other processes occurring inside the cell, its limitations are today more dramatically apparent than ever. Ironically, in the same years in which researchers accomplished the unprecedented feat of decoding the complete genomes of higher-level organisms, it has become clear that the information stored in DNA is only a small portion of the total, and that the overall picture is much more complex than the one outlined by the dogma.DNA has the following:The cell is, at its core, an information processing machine based on molecular technology, but the variety of types of information it handles, the ways in which they are represented, and the mechanisms that operate on them go far beyond the simple model provided by the dogma. In this chapter we provide an overview of the most important aspects of information processing that can be found in a cell, describing their specific characteristics, their role, and their interconnections. Our goal is to outline, in an intuitive and nontechnical way, several different views of the cell using the language of information theory.
Information Processing at the Cellular Level: Beyond the Dogma by Alberto Riva
1. Functional InformationHow could such a system form randomly without any intelligence, and totally unguided?
2. Encoder
3. Error Correction
4. Decoder
What would come first - the encoder, error correction, or the decoder? How and where did the functional information originate?
…it is increasingly clear that the long-reigning neo-Darwinian paradigm is collapsing – and despite many efforts to deny what is obvious – clearly “the emperor has no clothes.” The extremely sophisticated hardware and software systems that enable life simply cannot be built by any trial and error system. In particular – it is very clear that software can never be developed one binary bit at a time. Apart from a fully functional pre-existing hardware/software system, a single bit has absolutely no meaning. I feel that if we are to preserve our scientific integrity, we must acknowledge that we have a major explanatory problem, and we need to go back to the drawing board in terms of understanding the origin of biological information.
- John Sanford
I'd say any putative "system" formed out of blind, random causes is unrealizable from the get-go — either in the mind, in the world, or in the laboratory. To say a "system" can be the product of dumb, blind luck strikes me as kind of silly — even under the conditions of the "eternal universe model," which postulates infinite time.
The machine model (or machine metaphor) has found its way from physics into theoretical biology in recent times. Indeed, Alberto Riva's intriguing Abstract is based on language of the machine — e.g., "cellular machinery" that "process information."
The machine metaphor sheds great light on certain biological/physical problems, but only up to a point. After that, it begins to obscure some very important facts about machines that some methodological naturalists deem irrelevant to their interests.
In particular, there are two vital, indispensable universal facts about machines that the scientific "machine metaphor," as applied to theoretical biology, totally omits/ignores, despite the fact that cells are biological existents — they are living systems.
(1) As a user of dozens of machines every day, I must report that not once have I detected any sign of Life in any one of them. They're all pretty inert till used.
(2) I use them because they're awfully good at extending my actions; they also happen to be purpose-built in support of my particular purpose: If I need transportation, I use a car. If I need to dry my hair, I use a blow dryer. If I want to plink targets at the range, I use a pistol. Etc. They were all designed to facilitate the purpose for which they were built. But not only did they not build themselves, neither can they autonomously execute their specified purpose themselves.
It seems to me for the machine model of cellular activity to be really apt, it would reflect the subjectivity of cells to the considerations outlined in (1) and (2).
If we do that, we might recognize that machines are subordinate to their users. If that is the case, in what relation of subordination does a living cell subsist?
Possible clue — to higher-order intelligence?
It seems theoretical biology in its present state finds such speculations totally irrelevant to the conduct of the biological sciences.
Anyhoot, thanks so much, Heatlander, for your splendid essay/post! (Sorry it took me so long to get back to you....)