The genetic code - a study in reductionist denial

Note: A revised version of this article was subsequently published in the Winter 2020 edition of God and Nature, the online magazine for the American Scientific Affiliation.

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We have noted elsewhere that there is, at the core of all life, a genetic code. Over the course of the 1960s, the discovery of this code and the experimental determination of its details were heralded as triumphs of science, culminating in the awarding of the Nobel Prize in Physiology or Medicine to Holley, Khorana and Nirenberg in 1968. Per the Nobel Foundation, the prize was awarded for their interpretation of the genetic code and its function in protein synthesis.¹

Prior to the discovery of the genetic code, biologists had speculated about the mechanism of heredity. Many entities had been proposed, to at least include Plastidules, Gemmules, Pangenes, Plasomes, Idioblasts, Ids, Determinants, and Biophores.² The esteemed physicist Erwin Schrödinger had famously observed that the structure of a chromosome might suitably be called an aperiodic crystal, and prove to be the material carrier of life.³ With the elucidation of the structure of DNA by James Watson and Frances Crick in 1953, Schrödinger was proved right.⁴ The DNA molecule was, indeed, a bearer of aperiodic and irreducible information, by virtue of its long sequences of four nucleotides: adenosine, cytosine, guanine and thymine. As Wills has noted:

The obvious way in which information is stored in DNA, as sequences of letters drawn predominantly from the standard four-letter A, C, G, T nucleotide alphabet, has been understood since the discovery of the substance’s dual-linear-polymer, base-paired molecular structure and its mode of complementary chain copying.⁵

DNA, then, was found to be life’s repository of genetic information. But a separate question still remained: how did DNA sequences specify the sequences of proteins? Crick turned his attention there in the coming years. He would note:

It is widely believed (though not by every one) that the nucleic acids are in some way responsible for the control of protein synthesis, either directly or indirectly. The actual evidence for this is rather meagre.⁶

Crick aptly described this mystery as the coding problem. He would go on to observe:

If, as we have assumed, the sequence of bases along the nucleic acid determines the sequence of amino acids of the protein being synthesized, it is not unreasonable to suppose that this inter-relationship is a simple one, and to invent abstract descriptions of it. This problem of how, in outline, the sequence of four bases ‘codes’ the sequence of the twenty amino acids is known as the coding problem. It is regarded as being independent of the biochemical steps involved, and deals only with the transfer of information.

This aspect of protein synthesis appeals mainly to those with a background in the more sophisticated sciences. Most biochemists, in spite of being rather fascinated by the problem, dislike arguments of this kind. It seems to them unfair to construct theories without adequate experimental facts.⁷

Thankfully, a number of biochemists proved up to the task after all, as we have noted. Francis Crick continued to document our progressive understanding of heredity. Later, he would triumphantly write:

The inherited master plans controlling every living organism are written on the genetic material in each cell. These plans are coded instructions to the cell for making proteins. The recent breaking of the code opens a new era in biology.⁸

What is the genetic code?

We should be precise about what the genetic code is. It is not exactly right to say that a length of DNA — that is, a gene — is a code. Rather, the genetic code allows for the interpretation — or decoding — of the gene. Bedian has stated it plainly enough:

The genetic code, which establishes the relationship between polynucleotides and polypeptides, is the set of associations between components of the polynucleotide descriptors (nucleotide triplets or codons) and the building blocks (amino acids) of polypeptides, executed by protein derived from the same code.⁹

Bedian’s observation is hardly controversial. No one could reasonably dispute his description of the genetic code, and as we have seen, its discovery was loudly applauded in decades past. The genetic code is simply a collection of symbolic assignments — one for each of the 64 possible three-nucleotide RNA codons. Each codon is allotted either a sense assignment — meaning that codon is assigned to a specific amino acid — or else a nonsense assignment — meaning the codon serves as a signal to halt translation. But strangely, there are some who object to this plain understanding of the genetic code. They will make a variety of comments akin to these:

• It’s not really a code.
• "Code" is just a metaphor.
• That’s an analogy.
• Scientists use terms like "code" to help laypeople understand.

What is the explanation for such objections? They are based in a flawed philosophy called physicalism.

The error of physicalism

The physicalist wrongly imagines that biology can be reduced to principles of physics and chemistry — that is, to purely physical phenomena. Barbieri effectively characterizes this misguided view:

According to physicalism, biological information and the genetic code are mere metaphors. They are like those computer programs that allow us to write our instructions in English, thus saving us the trouble of writing them in the binary digits of the machine language. Ultimately, however, there are only binary digits in the machine language of the computer, and in the same way, it is argued, there are only physical quantities at the most fundamental level of Nature.¹⁰

The physicalist’s misconstrual of biology is flatly wrong. In the actual context of living things, the biopolymers of life — genes and proteins — do not form spontaneously. Rather, they are assembled to specification by emergent macromolecular nanomachines. As Barbieri continues:

The physicalist thesis would be correct if genes and proteins were spontaneous molecules, because there is no doubt that all spontaneous reactions are completely accounted for by physical quantities. This, however, is precisely the point that molecular biology has proved wrong. Genes and proteins are not produced by spontaneous processes in living systems. They are produced by molecular machines that physically stick their subunits together and are therefore manufactured molecules, i.e. molecular artefacts. This in turn means that all biological structures are manufactured, and therefore that the whole of life is artefact-making.¹¹

The genetic code is a real code

Is the genetic code a “real code?” May we rightly call a codon a “symbol?” In each case, the answer is a decided yes. As Gonzalez fairly notes:

The genetic code is truly a code in the sense of communication theory: it is a set of arbitrary symbols used for the scope of communication, i.e. for information transmission.¹²

Barbieri draws a similar conclusion, while also rejecting a reductionist interpretation:

Today, in other words, we have the experimental evidence that the genetic code is a real code, a code that is compatible with the laws of physics and chemistry but is not dictated by them. Our problem, therefore, is to take stock of this reality and to account for it.¹³

Does a code imply meaning?

We have argued that all life is built around the assignment of symbolic meaning. It is no exaggeration to say so, and the view is supported by the pertinent literature. As Roederer has noted, information-driven interactions represent the defining property of life.¹⁴ But is it fair, even given the symbolic nature of the genetic code and the information-bearing nature of DNA, to ascribe meaning to a biological process? Certainly, it is. That is the only sensible understanding of a code to begin with:

A code is a set of rules that establish a correspondence between the objects of two independent worlds. The Morse code, for example, is a correspondence between groups of dots and dashes with the letters of the alphabet, and the genetic code is a correspondence between groups of nucleotides and amino acids.

To say that a code establishes a correspondence between two entities is equivalent to saying that one entity is the meaning of the other, so we cannot have codes without meaning or meaning without codes.¹⁵

Physicalism is merely reductionism

The error of physicalism, as it applies to the genetic code, falls under the broader category of reductionism. As Barbieri has noted:

The idea that life is an extremely complex form of chemistry is still very popular today, and is based on the physicalist thesis that all biological processes can be reduced, in principle, to physical quantities. According to this view, genetic information and the genetic code are metaphorical and teleological terms that we use only because they are intuitively appealing. We have seen however that the physicalist thesis is valid only in spontaneous systems, whereas genes and proteins are invariably manufactured by molecular machines, and all manufacturing processes require not only physical quantities but also additional entities like sequences and coding rules.¹⁶

Methodological reductionism can be useful when studying an emergent system, but any mature understanding of such a system must ultimately acknowledge the emergent dynamic as well. This is especially important where meaning-bearing constructs are concerned, for as Roederer has observed, A pattern all by itself has no meaning or function.¹⁷ Rather, downward causation from a strongly emergent, contextualizing tier is required. As Ball has noted:

Biological information and meaning do not simply arise from the bottom up. In complex systems, higher levels of organization may play an important or even dominant role in causation.¹⁸

Wills usefully elaborates further regarding the causative connection between DNA sequence information, which is an arbitrary abstraction of a material property, and the reality of events in the physical world of molecules embodying the sequence, noting that DNA-based molecular biological computation can be said to control, perhaps even ‘direct’, the entire panoply of biochemical events occurring in cells.¹⁹

Such direction, of course, is not volitional. As Walker has noted, causal intervention by an external agent does not occur ‘in the wild’, proposing instead that information…performs an analogous function to an external causal intervention.²⁰ But if biological systems are directed by — and indeed described by — an internal analog to external causation, this cries out for explanation. We have noted that symbolic meaning may be enshrined via instantiation in a strongly emergent construct. But as Wills has asked, how can we accept an arbitrarily defined class of abstract sequences as causes of biological events and preserve our analytical view of organisms as causally closed physical systems? We too have asked as much, to conclude that a transcendent tier of assignation is ultimately required.

This, to be sure, is why the physicalist adopts her awkward view. As Ball laments:

Purpose and design are of course fraught and dangerous words in biology, but there seems to be no avoiding them. Perhaps the truth is that we lack a language that enables us to speak of ‘design’ in an evolutionary context, free from implications of predetermined goals or intelligent formative agencies (let alone from the potential for calculated creationist abuse).²¹

But what Ball regards as an uncomfortable implication — or even an abuse — we will instead label a dispassionate acknowledgment of the truth. Where design is apparent, a designer should be presumed.

As Erwin Chargaff has wisely noted, Life is never "nothing but.” Is DNA a molecule? Certainly. But it is not just a molecule.²²

The biological significance of DNA lies in the role it plays as a carrier of information, especially across generations of reproducing organisms, and within cells as a coded repository of system specification and stability.²³

Is protein synthesis effected via molecular binding relationships? Certainly. But they are not just binding relationships.

These roles of DNA do not find any chemical explanation in terms of the average material properties of DNA as an irregular heteropolymer…. Information is ontologically different from chemistry because linear and digital sequences cannot be generated by the analogue reactions of chemistry.²⁴

Is gene expression biochemistry? Certainly. But it is not just biochemistry.

In the 1950s and 1960s…molecular biology uncovered two fundamental components of life — biological information and the genetic code — that are totally absent in the inorganic world, which means that information is present only in living systems, that chemistry alone is not enough and that a deep divide does exist between life and matter.²⁵

That deep divide is uniquely bridged by a particular, strongly emergent construct: the genetic code. And in light of our considerations here, we may safely conclude that it is a real one.

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1. https://www.nobelprize.org/prizes/medicine/1968/summary/ ↩︎
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4. Watson, J. D., & Crick, F. H. C. (1953). Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid. Nature, 171(4356), 737-738. doi:10.1038/171737a0 ↩︎
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11. Barbieri, M. (2016). What is information. Philos Trans A Math Phys Eng Sci, 374(2063). doi:10.1098/rsta.2015.0060 ↩︎
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15. Barbieri, M. (2016). What is information. Philos Trans A Math Phys Eng Sci, 374(2063). doi:10.1098/rsta.2015.0060 ↩︎
16. Barbieri, M. (2016). What is information. Philos Trans A Math Phys Eng Sci, 374(2063). doi:10.1098/rsta.2015.0060 ↩︎
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23. Wills, P. R. (2016). DNA as information. Philos Trans A Math Phys Eng Sci, 374(2063). doi:10.1098/rsta.2015.0417 ↩︎
24. Wills, P. R. (2016). DNA as information. Philos Trans A Math Phys Eng Sci, 374(2063). doi:10.1098/rsta.2015.0417 ↩︎
25. Barbieri, M. (2016). What is information. Philos Trans A Math Phys Eng Sci, 374(2063). doi:10.1098/rsta.2015.0060 ↩︎