In my general introduction to semiosis, I introduced several terms I’m using with a particular definition in mind, so I wanted to start by reiterating those definitions.
Adaptor: (this is a new one for me but it comes from Barbieri) an object which links a cause to an otherwise unrelated effect. Can have an unlimited number of intermediate steps or as few as one. The most basic unit of semiosis.
Semiosis: the emergence of causal links between two things otherwise unrelated by physical law, embodied by physical objects called adapters. “Causal duct-taping”
Code: a library of similar-but-distinct adapters that relate one kind of cause to one kind of effect. The archetypal example is the genetic code, which relates nucleotides to amino acids, but they can be far more elaborate or much simpler. Some have as few as two states (eg a light switch).
Nesting: the addition of a new single adapter to form a longer chain of causality. Adding another domino to the chain. May or may not alter the initial cause and effect.
Life: a self-perpetuating chain reaction of semiosis which maintains and replicates adapters that embody increasingly elaborate and nested codes. The single underlying process which enables evolution, metabolism, reproduction, response to stimuli, and all the other traits associated with life. Encompasses abiotic adapters constructed by living organisms.
Semiotic Degrees of Freedom
My introduction started at the smallest possible scale: the first biomolecular adapters. For many important philosophical questions, the very beginning of life’s semiotic chain reaction is the watershed moment we need to focus on. But for any scientific question, to understand the how and why of any aspect of biology, culture, or technology, we need to understand the second phase: the iterative nesting of new codes. Or, as I’ll coin the process here, the accumulation of semiotic degrees of freedom.
In the first post, I used the example of a piano key. A single key on its own is a straightforward example of nesting. The action uses a complex sequence of levers, pulleys, and springs to link the depression of a key to the vibration of a string. In the presence of the action, pressing the key always causes that vibration and only that vibration. No additional context is necessary to predict the effect of pressing that key.
As soon as we widen our scope to a chord, however, that’s no longer true. Now, in order to know what sound is produced—major or minor, diminished or augmented—we also need to know how our key relates to the state of several other keys. The meaning of the key is no longer fixed; it has the freedom to mean several different things depending on its context. Widening the scope to a sequence of chords confers even more degrees of freedom.
Seen another way, nesting additional codes over the original key-note code—first the chord, then the chord progression—increases the influence of that key over the rest of the world. That’s something you’re keenly aware of if you’ve ever performed. A single wrong note in the right place can ruin the whole piece.
It’s easy to overlook the significance of this insight. The accumulation of semiotic degrees of freedom is as central to the evolution of life on this planet as Darwin’s survival of the fittest. It is the process that underlies the origin of complex cell structures, sensory systems, multicellular bodies, societies, and industries, and explains the patterns of radiation and refinement that recur across all these domains. My plan for the next few posts in this series is to explore that pattern in biological and cultural evolution.
To start with, though, I want to directly address the fact that biologists have largely ignored semiotic degrees of freedom and make the case that the time has come for them to adopt the paradigm. I’m going to go into some detail on molecular biology here, so if that’s something you aren’t familiar with, feel free to skim through those parts. I’ll expand on the same concepts in a cultural context (where they are much more familiar and intuitive) in future posts. For now, I want to establish that the process is genuinely found in biology.
Unsung Heroes of the Genetic Code
Biologists have developed a strange habituation to codes. The discovery of the genetic code was a monumental event in scientific history, and nearly everyone now acknowledges that it is a genuine code; that is, that the relationship between amino acids and nucleotides is truly arbitrary and not somehow predetermined by universal physical law. Subsequent work in molecular biology has filled libraries with descriptions of nested codes which confer additional semiotic degrees of freedom on the genetic code. But outside of the nascent field of code biology, their significance as codes has gone almost completely overlooked. Because DNA is the near-exclusive vehicle of heredity in living organisms, biologists often act as if evolution can (or even must) be understood through chromosomes alone. This is plainly untenable for two reasons.
The first is that evolution acting on the genetic code is a very limited mode of change. Mutations can add, remove, or flip one nucleotide at a time. Beneficial mutations are highly unlikely, but in large populations and over many generations, unlikely events are inevitable. As the size of the genome grows, the number of mutations per nucleotide grows with it. But as the organism accumulates complexity, the odds that a combination of simultaneous mutations will be collectively beneficial or even viable decreases exponentially.
This claim—that complex structures are “irreducibly complex” and couldn’t have emerged through the undirected recombination of nucleotides—is a familiar one in creation-evolution debates and one that evolutionary biologists rightly feel they have a good answer to. The problem is that the answer they give isn’t the one that actually addresses the point. The conventional answer is that natural selection trims the improbability by retaining any steps toward the outcome and eliminating steps away from it. Intermediate parts may be favored because they serve a distinct function on their own, or because the irreducible structure is in fact useful even in part.
The problem with that explanation is that it takes for granted the existence of the genetic code itself. This is the second reason the gene-centered view is untenable. The genetic code is obviously unable to perpetuate itself in isolation. To enact even the most basic expression of the code requires nucleotides to serve, by my count, at least eight distinct semiotic roles:
Sequences of nucleotides called promoters cause a protein called RNA polymerase to bind and begin transcribing the following nucleotides. The structure of RNA polymerase embodies a code that relates the promoter to the frequency of transcription and thus the abundance of each protein.
Another sequence called the terminator causes the polymerase to stop transcribing. The relative location of the promoter and terminator together control the length of the RNA strand, which varies from seventy-five to thousands of nucleotides.
The presence of a sequence of nucleotides at the start an mRNA strand causes a ribosome to bind to it and begin translation. The absence of that sequence ensures tRNA and rRNA are not translated. This code is embodied by the ribosome.
The sequence of nucleotides in each tRNA strand causes a particular structure which embodies a single codon in the genetic code.
The sequence of nucleotides in each rRNA strand causes a particular ribosomal structure that catalyzes the interaction between tRNA and mRNA.
The sequence of nucleotides in each mRNA strand enters the ribosome, where it is interpreted by the tRNA in triplet codons to cause a given sequence of amino acids to be assembled.
The start of the amino acid strand is caused by a special codon that is recognized by a special tRNA distinct from the one that adds the same amino acid elsewhere in the sequence.
The end of the amino acid strand is caused by another special codon that is recognized by the ribosome.
Even in the most stripped-down model of the genetic code, therefore, each nucleotide already has a substantial number of semiotic degrees of freedom. The “genetic code” is in fact an interlocking ring of seven distinct codes. To predict what a mutation to any given nucleotide means, a biologist needs to recognize which of these codes it is part of and know how the molecules in the cell would interpret a change at that particular point in that code.
Semiotic freedom amplifies the influence each nucleotide can have on the phenotype of the organism. On one hand, that dramatically increases the damage a single mutation can cause. For instance, a frameshift mutation, which inserts or deletes a nucleotide and thus shifts the entire genome off by one, alters the meaning of a significant number of downstream nucleotides in a way that almost certainly makes them incoherent. Conversely, because each nucleotide can have such a large impact, the number of mutations needed to create a novel functional structure is much smaller.
This is the solution to the paradox of irreducible complexity. New adaptive structures always remain within reach of random mutations because at every step, increasing size and intricacy are accompanied by new codes that increase the semiotic freedom of each nucleotide. Evolution cannot be understood by studying DNA alone because DNA base pairs only acquire meaning from the codes nested on top of them. As we’ll see, biologists have managed to get along without acknowledging this by studying codes as if they were simply names for what genes do. Recognition that the accumulation of semiotic degrees of freedom is a universal generative process in evolution is a paradigm shift still waiting to happen.
A Visual Aid
I want to end with a brief example from a much higher level, which will hopefully provide a more vivid intuition for “semiotic degrees of freedom.” The tweet below shows two images, one of a feminine face and another of the same face masculinized by FaceApp.
The accompanying text implies that sensitivity to a change of only “a few pixels” would be considered a weakness in a visual processing system. But this is of course the only way such a system can ever work at all. Each pixel gains meaning only relative to the context of nearby pixels, again and again and again through countless nested visual processing codes. FaceApp takes advantage of the semiotic freedom those codes confer to transform our overall interpretation from feminine to masculine by changing so few pixels it feels like magic.