Thursday, 12 July 2012

What's the difference between biochemistry and chemistry, or is DNA just a molecule?

My note "On the operational zero and approximate computations" (available in Russian) was published by a popular Russian website here. A lively discussion followed. Some of the comments were, in my opinion, a result of a lack of understanding on the part of the readers of the semiotic nature of genetic information recording and processing in biosystems. One reader even asserted that DNA was just another molecule. Another molecule? Yes, but... Based on the responses from the readers I wrote this. 

So what is the difference between chemistry and biochemistry? Are DNA/RNA just molecules?

Biochemistry differs by its context and semantics, i.e. the contents of genetic instructions to synthesise biological structures of the next generation organisms. Roughly, the preprogrammed unfolding of an ensemble of biochemical processes has two layers:
  • lower layer А of physico-chemical interactions
  • upper layer B of control over the said interactions

This can be likened to the standard OSI model which is a stack/hierarchy of protocols that are used to organise communication over a computer network. Our layer A corresponds to the physical layer of the OSI stack (fig.1), while layer B is the OSI application layer, i.e. the top layer which is available to various end user applications.

Figure 1. Data flow in the standard OSI stack of protocols that are used to organise communication over a computer network

Information processing in the sender's personal computer or other device starts at the application layer and proceeds down to the physical layer where data is converted to bit streams and finally to voltage meanders in the cable medium. Information processing in the receiver's computer or device is inverse: voltage jumps are detected and transformed into bit streams and further all the way up to the application layer where data is presented in human readable form using an appropriate application. 

For example, you type the address of the web page you want to retrieve in a web browser. The browser processes it converting the address into the IP address of the server where this page resides, requests this page from the server and receives a response containing the contents of the page in the form of, say, HTML data (of course, assuming that the address is correct and that the network and the server are up and running). Finally, your browser processes the received information and presents it to you in readable form.

It is at the application layer that the semantics of the future information transfer is defined. The author of the page types in its contents using a text editor application and uploads it to the server. In order for the page to be read successfully, it must be stored at the known address in the format familiar to your application (in this case, a web browser). 

It is important to emphasise the following points which are essential to organising a successful information exchange between the sender and the receiver:
  • To correctly interpret information stored on a medium it is necessary to ensure compatibility/identity of the protocol of its recording, on the one hand, and of the protocol of its interpretation, on the other.
  • The presentation of information at the various OSI layers is formal. A protocol is a set of predefined rules loaded on top of physico-chemical interactions (on top of physicality, using David Abel's expression). The physico-chemical interactions only determine the constraints within which the system will operate, not rules. 
  • This is why the rules as such are irreducible to physicality. Likewise the rules of upper layers are irreducible to lower layers. More about this irreducibility can be found here.
  • The existence of rules reliably points to a priori intelligent agency of decision makers simply because physicality alone, being inert to rules of any kind, functions only in the confines determined by constraints and, ultimately, by the laws of nature. 

The process of information transfer in a living cell is similar to that in artificial systems, with differences in the way the recording/interpretation protocol is realised. The physical layer (layer A) is presented by biopolymers, i.e. by DNA/RNA molecules which carry nucleotides of four different types : A, C, T in DNA (or U in RNA), and G.
Figure 2. A series of codons in part of a messenger RNA (mRNA) molecule. Each codon consists of three nucleotides, usually representing a single amino acid. The nucleotides are abbreviated with the letters A, U, G and C. This is mRNA, which uses U (uracil). DNA uses T (thymine) instead. This mRNA molecule will instruct a ribosome to synthesize a protein according to this code. Source - Wikipedia, Transfer of information via genetic code.

Triplets of nucleotides called codons (fig.2) are interpreted by a reading polymerase. In protein-coding segments of DNA/RNA a codon usually corresponds to a particular amino acid residue which is synthesised as part of a future protein molecule. Recording/interpretation are initiated and stopped by special start/stop codons. The physical and chemical properties of synthesised proteins are determined by particular amino acid sequences. These sequences representing the application layer (layer B) define the biological meaning of the genetic instructions.

We can see that the reading/writing of genetic information is a formal process, an algorithm, a sequence of instructions given via a material symbol system and stored in biopolymers. Modern science knows no examples of a spontaneous and/or necessary mechanism of formal instruction generation or protocol specification/loading. On the contrary, based on massive evidence, these are properties of artificial information processing systems exclusively

The points we presented in the above discussion of the OSI protocol stack are also perfectly valid in the context of a living cell. The presence of an a priori defined protocol (set of rules) for coding/interpretation of genetic instructions in a biosystem is as necessary as the presence of similar protocols in human designed and implemented information processing systems. Consequently, it is incorrect to reduce life to chemistry, if, obviously, we want to have a good understanding of what life is from the point of view of contemporary science. 

Finally, I will point out that it would be wrong to interpret what I wrote here as an attempt to impart some mystique properties to biopolymer medium as such. Of course, DNA/RNA have chemical properties but that is not it. We would throw the baby out of the bath if we reduced the complex semiotic process of genetic information coding/interpretation exclusively to its chemical side. Borrowing an analogy from Stephen Meyer, one can, of course, say that a newspaper page has nothing but a sporadic collection of paint blobs on it. At the physical level, that is certainly the case. However, it is not all there is to the newspaper article. Similarly, the contents of a conversation cannot be reduced to sound waves spreading from mouth to ear in the air. For the same reason, the functioning of such complex systems as television or radio receivers cannot be explained only by the existence of the electromagnetic field.

As we said earlier, the semantic cargo of a message in all cases of the functioning of complex artificial information processing systems is a consequence of meaningful actions on the part of decision makers. That is why the detection of semantics itself reliably points to intelligent agency behind the functioning of cybernetic systems.

True, there is no mystery in the chemical properties of DNA/RNA. However, the simple fact that at the heart of life, in replication, lies a process which with scientific rigour, certainty and reliability points to intelligence behind it, and, what's more, to intelligence far greater than that of humans, will lead us to the greatest mystery of all. It will lead us to the One who created life in the beginning, of course, if we don't want to remain willfully blind.


  1. David Abel, The First Gene. 
  2. Blog and forum Uncommon Descent

No comments:

Post a Comment