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Physics into physics won’t go

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I’ve read Chapter 4 of Stuart A Kauffman’s Reinventing the Sacred several times in the hope that I’ll finally get the point. But I still don’t. The chapter is called The Nonreducibility of Biology to Physics. But each time I read it I end up thinking that if he’s right that biology isn’t reducible to physics then physics isn’t reducible to physics either.

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Another Flew over the cuckoo’s nest #10

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What have typewriters, amino acids, kites and mountain streams got to do with the industrial production of ammonia…?

Tenth in a series responding to Antony Flew’s There is a god: How the world’s most notorious atheist changed his mind.1

See also:

Another Flew over the cuckoo’s nest #1

Another Flew over the cuckoo’s nest #2

Another Flew over the cuckoo’s nest #3

Another Flew over the cuckoo’s nest #4

Another Flew over the cuckoo’s nest #5

Another Flew over the cuckoo’s nest #6

Another Flew over the cuckoo’s nest #7

Another Flew over the cuckoo’s nest #8

Another Flew over the cuckoo’s nest #9

Coded chemistry

Flew now introduces a ‘third philosophical dimension’ to the origin of life.

RNA

RNA

He quotes mathematician David Berlinski, who is impressed by the transmission of coded information in the living cell from DNA to RNA and then to strings of amino acids:

By itself a code is familiar enough, an arbitrary mapping or a system of linkages between two discrete combinatorial objects. The Morse code, to take a familiar example, coordinates dashes and dots with letters of the alphabet. To note that codes are arbitrary is to note the distinction between a code and a purely physical connection between two objects. To note that codes embody mappings is to embed the concept of a code in mathematical language. To note that codes reflect a linkage of some sort is to return the concept of a code to its human uses.

…Can the origins of a system of coded chemistry be explained in a way that makes no appeal whatever to the kinds of facts that we otherwise invoke to explain codes and languages, systems of communication, the impress of ordinary words on the world of matter?2

I have duplicated the quote exactly as Flew presents it. Other quotations from other writers follow. But it is worth stopping a moment to consider just what is being said about the concept of a ‘code’.

To help the conversation along I would like to add another short quote into the mix – this time from Matt Ridley – about Alan Turing‘s

extraordinary mathematical proof that reasoning could take a mechanical form – that it was a form of computation…3

I am trying to fathom to what extent describing the DNA/RNA/amino acid mechanism as a genetic ‘code’ is metaphorical, and to what extent it is a real description. To what extent must we describe the mechanism as a code, because if not we miss something essential? (This is effectively repeating the question in David Berlinski’s second paragraph.)

Think of an old-fashioned typewriter keyboard. When the key with the letter ‘A’ printed on it is pressed, two overall things happen. Just as with most of the other keys, the ribbon is raised into the appropriate position, by some sort of generic hinge mechanism. And by another more specific hinge mechanism a metal shape (‘a’ in reverse) strikes an inked ribbon which has been raised into position against a sheet of paper pressed against a roller. This leaves an ‘a’-shaped mark on the paper. If the shift key was pressed at the same time as the ‘A’ key, something similar would happen but a different metal shape would be pressed against the ribbon, leaving an ‘A’-shaped mark on the paper.

Antony Flew: There is a God

Antony Flew: There is a God

A fairly large subset of humans will recognise the shapes on the keys and the paper as letters which can be used to make up words. But that semantic dimension is to do with the function the machine performs, and therefore the reason it was designed the way it was. There is nothing intrinsically semantic about the mechanism itself. It has no more semantic content than two kites flying in the air would have. If you tug on one string, one kite moves; if you pull on the other string the other kite moves. The strings and kites may or may not have symbols or shapes on them, which may or may not correspond.

A single typewriter key mechanism could conceivably be used not to make an ‘a’ appear on a sheet of paper but to detonate a bullet. But in the context of a typewriter (and in the context of the normal human use of the typewriter), because of its implementation of matching shapes and rules (‘A’ key without shift creates ‘a’ on paper; ‘A’ key plus shift creates ‘A’ on paper; etc) the mechanism can be used to generate and/or transmit meaning.

The point is this. If you want to describe the mechanism in detail to show how it works, or to enable someone else to build a mechanism from the specification, you do not have to include anything about codes or languages or alphabetic characters. But if you want to explain what it is used for and how it is used, you will have to include something about codes and letters.

We can now relate this to the DNA/RNA/amino acid example. To give a full description of how the mechanism works, do we need to talk about codes or languages? I do not think we do, despite possible appearances to the contrary. I can understand the temptation to assume it is necessary, but I think that presupposes we are looking at the DNA/RNA/amino acid mechanism as something consciously designed for a particular purpose, by a mind which knows what codes and languages are. But we do not have to see it as this, and therefore we do not have to describe it in terms of codes and languages.

In a nutshell Flew’s argument seems to be this: DNA is a code; codes are semantic; minds employ semantics; therefore DNA was designed by a mind. But we must guard against metaphors. We only see it as a language-like code because we see it as something designed, as something we might have designed. So if we argue from its code-like features to the existence of a designer we are arguing in a circle.

I am not understating the size of the explanation challenge. It is huge. But I do not think the DNA mechanism has to be seen in a special semantic dimension which is not shared by other biochemical processes.

We can see it as semantic, but we do not have to. To see it as semantic we start at the protein end, at the requirement for a particular protein. Proteins are made of strings of amino acids, in a specific sequence. So if we want a specific protein we must specify the sequence. We could write it down, giving the chemical names in English. Or we could give every known amino acid a number and specify it that way: 24, 578, 3, 9003, 24, …etc. Or we could correlate each amino acid with a unique sequence of three out of four possible nucleotides (abbreviated to A, C, G and T), eg: ACT, GCA, TCC, GAT, ACT, …etc. This is seeing the nucleotide sequence primarily as a set of instructions for making proteins – because we are seeing the mechanism as something designed. It is also seeing the nucleotide sequence as implementing a code which is essentially arbitrary (Berlinski’s word): the sequence could have been specified as numbers, words, Morse code, or semaphore flags – it just happens to be specified in nucleotide trios.

But we could start at the other end, with the nucleic acid. In this picture a nucleic acid just is a sequence of nucleotides, and individual sets of three nucleotides are shaped in such a way that amino acids fit onto them. Because the amino acids are therefore brought close to each other they join up to each other to form protein molecules which then detach from the nucleic acid.

I am not speculating how this happened, or expecting anyone to take anything on trust as an explanation of how it happened. What I am trying to do is describe it as something which could have happened, and which, together with the rudimentary self-replicating properties of the nucleic acids, could have provided a basis for natural selection to operate on so as to add further ‘sophistication’. Perhaps a particular sequence of amino acids created a polypeptide or protein which somehow helped the original stretch of nucleic acid to replicate.

In a picture like this, the nucleotide sequence replicates and therefore survives because amino acids fit onto it in a particular sequence. If a copy is made which is imperfect then either no amino acid fits where the error happened or a different amino acid might fit. If another amino acid fits that might lead to a polypeptide or protein which either hindered replication or enhanced it. If it enhanced it then the new nucleotide sequence would make more copies of itself than the original sequence.

To call a nucleotide sequence an ‘instruction’ for making a protein is therefore only a metaphor. Chemically it is operating as a catalyst. We do not familiarly call the iron used in the Haber process an ‘instruction’ to make ammonia from gaseous hydrogen and nitrogen. But we could, metaphorically. Without the catalyst, at a particular temperature and pressure, very little of the hydrogen/nitrogen mixture would convert to ammonia. Add the catalyst, and much more would be. The iron is not used up in the process – nor is the nucleic acid during protein synthesis. The nitrogen and hydrogen molecules attach themselves to the surface of the iron, as do the amino acid molecules to the nucleotide sequences. The only difference is one of complexity.

Also the nucleotide sequence is not an arbitrary code, any more than the iron in the Haber process. Amino acids are unlikely to attach to names or numbers on their own.

Of course the amino acid sequence matters, and therefore the nucleotide sequence matters. But it does not matter to anyone.

Take another, completely natural, example. Rain falls on the top of a mountain. The mountain is rocky and irregular, so because of the arrangement of ravines, cracks and gullies the water flows down the mountain in a series of streams – say four of them. 50% of the water ends up in stream 1; 30% in stream 2; 15% in stream 3; and 5% in stream 4. These proportions stay fairly constant: erosion would change the proportions by changing the structure of the mountain, but this happens very slowly. The 50%/30%/15%/5% allocation is an ordered result, like the sequence of amino acids in a protein. It is caused by the configuration of ravines and gullies, as the sequence of amino acids is caused by the nucleotide sequence. Is the structure of ravines and gullies therefore a ‘coded instruction’ to split the water 50%/30%/15%/5%? Yes – metaphorically.

Of course the nucleotide sequence looks more sophisticated, more semantic, more like a language. But the evolutionary theorist would argue that replication plus variation plus natural selection could account for such a result. And there is no a priori reason to rule out such an explanation. (Which is why I included the quote about Turing’s proof that reasoning could take a mechanical form.)

I can imagine supporters of the rival god hypothesis shaking their heads over how far-fetched this might appear. Yet again we are back to the two kinds of minds (see Another Flew over the cuckoo’s nest #7), which now seem close to exhibiting a fundamental difference of polarity. The theist sees mind as the originating cause while the evolutionary theorist sees no a priori reason why mind itself is not a result of replication plus variation plus natural selection. But I find it encouraging that those who are in a position to know most about the sheer complexity of the challenge seem least tempted to let incredulity defeat them.

Flew adds quotes from Carl Woese4 and Paul Davies5, both of which correctly stress the enormity of the challenge. But according to Flew, Davies

…emphasizes the fact that a gene is nothing but a set of coded instructions with a precise recipe for manufacturing proteins. [My emphasis.]

The ‘nothing but’ is surely unjustified. A gene is a set of coded instructions but it is also part of the physical mechanism itself. If the nucleic acids did not have the chemical properties they have, the mechanism would not work. You could say, metaphorically, that the iron in the Haber process is an ‘instruction’ for creating ammonia, but would you say it is nothing but an instruction?

A bit more on this chapter next time.

References

1 Antony Flew (with Roy Abraham Varghese), There is a god: How the world’s most notorious atheist changed his mind, HarperCollins, 2007.

2 David Berlinski, ‘On the origin of life’, Commentary, February 2006.

3 Matt Ridley, Nature via nurture, HarperCollins, 2004.

4 Carl Woese, ‘Translation: in retrospect and prospect’, RNA, 2001.

5 Paul Davies, ‘The origin of life II: How did it begin?’ http://cosmos.asu.edu/publications/papers/OriginsOfLife_II.pdf.

© Chris Lawrence 2009.

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