“Life itself is a quotation” – Jorge Luis Borges

If you took a pen and and a piece of paper and wrote the word “water”; and suppose I asked you to determine how the chemical and physical properties of the paper and ink determine the meaning of that word – you would probably respond with a blank stare. If you took the ink and paper and gave it to a chemist for analysis- they could describe exhaustively the chemical properties of ink such as its density, molecular weight, chemical composition, polarity, intermolecular forces etc. However they could never explain to you how the meaning of the word is determined by the physical properties of ink. Simply because meaning, representation, information is not determined by and identical to the physical properties it is conveyed through. I could take a piece of chalk and write “water” on a black board. The meaning of the word would be identical even though the physical medium is completely different. Ink and chalk have different chemical properties and yet the meaning in each case is identical. Therefore the meaning of the word is not determined by the chemical properties. We could take the same ink and paper and write different words – it would be a categorical mistake to think the difference in meaning of the words is determined by differences in the physical and chemical properties of the ink precisely because in both words the chemical properties are identical.

Another illustration would be a red traffic light that tells you to stop if you are driving or walking. It would be categorical mistake to think that the meaning of the red light is determined by the physical properties of the light such as wavelength, frequency, luminosity, brightness. The meaning is imposed on the red light by human beings, we could have easily chosen a red light to mean or represent go or slow down. Meaning, information, representation are not physical properties at all and therefore not determined by physical properties; they are to put it in a technical sense physically indeterminate.

Life, by which I mean organisms such as bacteria, lions, humans and trees; I would argue displays intrinsic properties that are not reducible to material properties. This is not even referring to problematic features such as consciousness, rationality or any other feature debated within philosophy of mind. Even the most basic bacteria that lacks consciousness displays intrinsic properties irreducible to physics and chemistry.

There are two main competing theories about the origin of life from non-life : RNA first theory and the metabolism first theory. Both theories assume materialistic reductionism in that they assume that life can originate from chemical reactions and physical processes alone because life is reducible to chemistry. There are serious problems with both theories and most of them focus on what I call the “soft problem” of chemical evolution. The soft problem is basically solving problems such as the parts list; how were the necessary basic chemicals such as phosphate, sugar, amino acids, nitrogen bases made? Once you have basic organic molecules how did they polymerise to form longer chains? Once you had longer chains how do you find the correct sequence that will produce self-replicating molecules. The soft problems are a long way from being solved.

Then there is the hard problem which is basically how do you produce properties intrinsic to life that are not reducible, identical and intrinsic to chemical properties of molecules. A case in point being the genetic code which will be the focus of my article.

The genetic code

Each living organism contains deoxyribonucleic acid (DNA) which is a large macromolecule consisting of a 5 carbon sugar (deoxyribose) with a nitrogen containing base (such as adenine) attached to it with phosphoric acid as the backbone. The three molecules together make up a nucleotide. There are four different types of nitrogen bases used in DNA: Adenine (A), guanine (G), cytosine(C), thymine(T).

An illustration of a single nucleotide consisting of deoxyribose (sugar base); phosphoric acid and a nitrogen base/nucleic acid.
There are four different types of nitrogen bases uses in DNA and RNA. The difference between DNA and RNA is that RNA uses Uracil as one of its nitrogen bases rather than Thymine.

DNA contains information for building proteins. Proteins are long chain molecules made up of molecules called amino acids. Protein size can vary from consisting of 50 amino acids to thousands of amino acids. There are 20 different type of amino acids and by varying the combinations, order and size  one can produce a diverse number of proteins.

Dogma biology
Illustration of how DNA contains information for making proteins. DNA makes RNA which is then used by ribosomes to make proteins.

Where DNA comes in is that it contains information for the specific order and type of amino acids required to make up a certain protein. Recall that DNA is a linear chain of nucleotides – each set of three nucleotides called a codon represents a specific amino acid. The genetic code specifiies which amino acid is represented by the the different codons. For example the amino acide Lysine (Lys) is coded for by 4 different combinations of nitrogen bases: AAA, AAG. In other words a linear order of adenine three in a row or two adenines followed by guanine represent the amino acid lysine.

The genetic code showing which codons (a set of three nucleotides) codes for which amino acid. For example UCU codes for the amino acid Serine (abbreviated as Ser)

The genetic information conundrum

It is the capacity to represent an amino acid or to possess information that makes DNA so unique and perplexing because information, symbolic representation and meaning is neither identical nor determined by physical and chemical properties.

Suppose you gave a knowledgeable chemist a DNA strand and asked them to give you the full chemical properties of it they would tell you things such as its molecular weight, electronegativity, polarity, type of intermolecular and intra-molecular bonds present. However they could never deduce that a specific number of nucleotides represents some specific amino acid. They could never conclude that there is a genetic code present even if they had all the physical and chemical facts about the DNA strand. The fact that lysine is coded for by a specific order of adenines in a row is not determined by the chemical properties of adenine. What chemical properties are present in three nucleotides of adenine that is not present in 1, 4, or 7 adenines that gives it the capacity to represent the amino acid lysine. There is simply none – the chemical properties present in three nucleotides are precisely the same as those present in 1,2, or 4 nucleotides. There is no chemical property that could possibly explain how or why a certain type of molecule “represents” some other type of specific molecule. Representation, information and content is not a physiochemical property. As Michael Polanyi says, “chemical structures established by the stabilizing powers of chemical bonding have no appreciable information content”. The chemical facts do not determine the symbolic representation facts.

Another way to illustrate this point: Imagine giving a DNA strand such as (CGCAGC) to a biochemist who knows all about the genetic code and asking them to tell you which amino acids are represented by the DNA strand. The problem is they could give you all of the physiochemical properties about the DNA strand such as its molecular weight, bond angles and bond lengths, type of bonds, activation energy to break the bonds however when it came to telling you which amino acids are represented by the DNA strand there are a number of possible interpretations all equally possible but mutually exclusive.

First interpretation could be [CGC] is Arginine and [AGC] is Serine. Second interpretation could be the strand is broken in between a codon and that C[GCA]GC only represents one amino acid. Therefore in this case GCA is Alanine. Third interpretation could be the strand contains one codon starting from the third nucleotide CG[CAG]C and in this case (CAG) is Glutamine.

There are other interpretations possible  such as the codon should be read backwards instead. Perhaps the strand does not represent any amino acids because it was created from scratch in a lab rather than being taken from an organism. One could argue that of course the context is required to understand the meaning of it – but then that is precisely the point that things such as context, representation and interpretation do not apply to chemical properties and laws. The main point is that the physical facts are indeterminate with regards to the information content. There are a number of different possible interpretations of what the nucleotides represent even though in all possible interpretations the chemical and physical properties, as well as the molecules involved are exactly the same. This demonstrates that the symbolic representation of amino acids by nucleotides is not identical and is not determined by the chemical and physical properties of the chemicals. In the same way that a red traffic could equally and easily symbolically represent stop or go because the physical properties do not determine what it represents. To drive the point home again, it is similar to how the meaning of a word written in ink is not determined by the chemical properties of the ink.

Variations in the genetic code also serve to highlight this fact. The codon UGA in the bacterial species Mycoplasma represents and codes for the amino acid tryptophan whereas normally in other species it codes for “stop”. You have the same set of nucleotides (UGA) coding for stop or tryptophan demonstrating that the chemical and physical properties of nucleotides does not determine and fix the symbolic representation of the nucleotides.

Michael Polanyi in his article, Life’s irreducible structure, makes a similar point in that in order for a genetic code to be effective as a code regardless of what one thinks about its origins it has to be physically indeterminate.

“It [The DNA code] must be as physically indeterminate as the sequence of words is on a printed page. As the arrangement of a printed page is extraneous to the chemistry of the printed page, so is the base sequence in a DNA molecule extraneous to the chemical forces at work in the DNA molecule.”

What this demonstrates is the chemical reactions alone are insufficient for producing the genetic code. Molecule A reacting with Molecule B will always produce molecule C – no chemical reaction could ever possibly produce symbolic representation. This is one of the hard problems of abiogenesis (the idea that life could be produced from non-life through chemical means). Many origin of life researchers are trying to solve the soft problem – getting the parts and yields and separations and conditions and thermodynamics right and assuming that solving the soft problem automatically solves the hard problem. The genetic code cannot be produced by chemical and physical processes alone because it is not determined and reducible to chemical and physical laws. This means then abiogenesis, underpinned by its materialistic presuppositions, is simply not possible because it is like trying to explain the meaning of a book on the basis of the chemical and physical properties of the paper and ink – a simple categorical error. Materialism then is incapable  of accounting for the origin of life, as philosopher Thomas Nagel rightly points out:

“Whatever one may think about the possibility of a designer, the prevailing doctrine—that the appearance of life from dead matter and its evolution through accidental mutation and natural selection to its present forms has involved nothing but the operation of physical law—cannot be regarded as unassailable. It is an assumption governing the scientific project rather than a well-confirmed scientific hypothesis.”

For further reading

  1. Life’s irreducible stucture -Michael Polanyi. An excellent and timeless article (it was published in 1968) on how life transcends physics and chemistry. He looks at the implications of the genetic code and its physical indeterminacy.
  2. Synthetic Life and the bruteness of immanent causation – David Oderberg. A great philosophical analysis of life. Oderberg argues life displays immanent causation as opposed to transient causation. He goes on to argue that transient causation cannot produce immanent causation.
  3. Top five problems with current origin of life theories – Casey Luskin
  4. Animadversions of a Synthetic Chemist -world renowned synthetic chemist James Tour writes an excellent technical review on the “soft problem” of how life originated. He details his work on nanomachines like nanocars explaining the level of specific procedures required to build highly specific molecules. An excellent article magnifying the richness and beauty of chemistry, as well as the great obstacles facing a naturalistic explanation of the origins of life.
  5. Mind & Cosmos: Why the Materialist Neo-Darwinian Conception of Nature is Almost Certainly False – Thomas Nagel