Maxwell's demon revisited

In his book (reference 1), Davies, first noticed at reference 5 and who does quantum physics in his day job, makes much of Maxwell’s demon, a little chap invented well over a hundred years ago, who does battle with the second law of thermodynamics, the one that says everything tends to decay to a sort of grey soup. A demon who continues to attract much interest & debate and Wikipedia, at reference 2, tells us lots about him. And for readers with bigger appetites there is also reference 3.

He does this battle by using the random thermal motion of the molecules in a gas to sort them into hot molecules in one compartment and cold molecules in another, so creating a temperature gradient which can be exploited to do work. In fact, more or less a perpetual motion machine, a sort of machine which is not permitted at all. Davies suggests that one way to balance the thermodynamical books is to add a term to the relevant equation for information; to allow the conversion of information to and from energy.

Davies also tells us that various people are now making such demons, albeit on a very small scale. While he goes on to tell us about life, and I follow him here in noticing a sort of demon which works at a rather larger, if still microscopic, scale.

Figure 1

Notice which takes the form of a story, with some foundation in truth, about the construction of proteins.

We suppose we have a eukaryotic cell, the building brick of much of life, floating around in a turbulent, watery sea of chemicals of various sorts. A unicellular animal.

We use the metaphor of the wall of a medieval city. A rough, circular stone wall (blue), punctuated at intervals by gates (red), through which traffic into and out from the city is regulated. A stone wall which is under continual attack from the outside world, attack which necessitates continual repair.

So this city wall is the cell membrane, the boundary between the interior of the cell and what to it is the outside world, a semi-permeable membrane which is largely built of proteins. Inside we have a relatively calm, watery lagoon full of the twenty or so of the amino acids used by animals to build the proteins they use to build and maintain their bodies. All milling around in the watery medium which is warm enough that all these acids have plenty of thermal energy and do indeed mill around, but not so warm that they all disintegrate into their constituent parts.
We also have lots of proteins milling around, awaiting their turn in the wall.

Figure 2

Then we have a chromosome, a portion of which is illustrated above. One of the functions of this chromosome is to provide recipes for the proteins, in the form of asterisk separated sequences of codes for amino acids, these proteins being made up of sequences of amino acids. Given that there are around 20 such acids, we can use letters for these codes. So in the figure above we have two complete such sequences (aka genes) and fragments of two more. While in the real world, proteins can be made up of thousands of amino acids.

Sometimes the cell decides that it needs more of some particular protein and activates the relevant portion of the chromosome. We leave aside the details of how exactly this happens.

Figure 3

The idea now is to build the desired protein, one amino acid at a time, stepping through the instructions which have been coded into the gene.

Figure 4

In Figures 1 and 2, we have expressed this coding as letters, there being enough letters for this particular purpose. However, the metaphor of shapes is nearer the truth, with each amino acid being represented above by a shape code, corresponding to the actual shapes of the molecules concerned. Some of this is suggested in Figure 3 above.

Now the stepping, or more precisely this binding of successive amino acids onto the growing tip of the protein, needs to be facilitated by enzymes.

Figure 5

We suggest such an enzyme in the figure above. At the top end we have the male end of the female code top left in the previous figure, Figure 4, enabling the enzyme to lock onto the right place in the chromosome. At the bottom end we have the female shape for the amino acid which has been coded for. These enzymes, in twenty or so different varieties, express the map between the blue codes top and the brown acids bottom.

We suppose that there are lots of these enzymes inside our city walls.

Step 1 is for the enzyme to lock onto the appropriate amino acid. This will happen fast enough, given all the thermal jostling that is going on.

Step 2 is for the loaded enzyme to lock onto the appropriate place on the chromosome.

Figure 6

Step 3 is for the enzyme’s load, the amino acid, to be tagged onto the end of the growing protein. Note that the protein is much bigger, much longer, than the segment of chromosome which codes it. Chromosome coding is space efficient and there is also much less to go wrong, handy when it comes to copying them.

Step 4 is for the now empty enzyme to go off in search of another amino acid.

Eventually the protein is completed and released and the chromosome can be reset.
And if we further suppose that other areas of our chromosome have management functions, our demon will so arrange things that the manufacture of proteins needed to keep the city walls in good repair carries on as long as there are supplies of the necessary amino acids.

With another of the demon’s functions being to arrange for those supplies to come in through the city gates. And if the demon fails, the city wall will eventually disintegrate and the city, that is to say the cell, will die.

Otherwise, gradually, we will draw proteins out of our undifferentiated soup of water and amino acids; a march uphill against the forces of thermodynamics which go for undifferentiation.
All of which might be summarised in the figure which follows.

Figure 7

Top left we have the city wall, made up of bound proteins, themselves made up of bound amino acids. Right we have the free proteins and the free amino acids milling around the city. And in the middle we have our chromosome, using enzymes to build proteins from amino acids.
So what we have here is a biologically flavoured version of Maxwell’s demon, with the forces of life, using the information about proteins coded into the chromosome, doing battle with the second law of thermodynamics, doing battle with the chaos of the outside world. with most of the energy needed being drawn from the thermal energy & the continual mixing of the molecules involves. With the resultant reactions reminding me of the energy and mixing going into the student dances of my youth, with all kinds of interesting results, not needing intermediary action by dating agencies or websites. The chromosome might also be said to have invented symbols and agency, at least agency of a sort.

This engineering of proteins with information from chromosomes has been around, more or less unchanged, for a very long time, for several billion years. A version of the demon which pre-dates Maxwell by a very long time and which can be thought of as a very early form of computing.

Figure 8

The Davies argument is that this is very different from the sort of thing that non-life processes can manage. A non-life process might make a complex thing like the large snowflake snapped above, but this involves nothing like the orchestrated action-at-a-distance sketched above. The construction of a snowflake can be completely explained by relatively simple, local processes. One might try to argue that the construction of the snowflake is coded into the electrical arrangement of the interior of the water molecule. Which may well be true, but the reply is that this coding is more or less immutable and is built into every molecule of water. Nothing can fiddle with those electrical laws and arrangements to give us different kinds of snowflakes. There is no central store of data being drawn on by the snowflake as a whole. We have physics rather than biology.

References

Reference 1: The demon in the machine – Paul Davies – 2019.

Reference 2: https://en.wikipedia.org/wiki/Maxwell%27s_demon.

Reference 3: Engineering Maxwell’s Demon – Zhiyue Lu, Dibyendu Mandal, Christopher Jarzynski – 2014. An article from ‘Physics Today’.

Reference 4: https://psmv4.blogspot.com/2019/02/trivia.html. The last post mentioning Davies.

Reference 5: https://psmv4.blogspot.com/2019/02/paul-davies.html. The first post mentioning Davies.