Friday, April 20, 2007

10 - The Persistent Gene

What is a persistent gene ?

It is a term that I have just coined to distinguish between the media and the message, the book and the story contained in the book.

One second … I have just figured out that the gene is a sequence of chemical compounds -- the A, C, T, G compounds – strung out on the thread of a DNA molecule and each gene is the recipe of a particular protein. Now is this gene persistent or transient ?

The material that creates an instance of the gene is of course transient and can decompose or be destroyed if we – say – burn the DNA but the information that it contains – the recipe, if I may say so of producing a protein – persists, in, among other thing, copies of this gene in other cells in the body, in bodies of other members of the species, or even in members of another species.

I see … just like the story of Harry Potter and the Philosophers Stone is available, not only in multiple copies of the book but also on various web pages and perhaps on DVDs ..

Not to mention the memory of individuals who know the story and can recreate them if necessary.

But there will be some deviations, some errors from the original ..

And that is exactly the point I am trying to make.

What point ?

First let us understand that when we refer to a gene we could be referring to one of the two things
* the gene – or recipe – in its physical manifestation. That exists as a physical collection of chemical compounds that can be “touched and felt” in a laboratory. This manifestation of the gene is similar to a copy of the Harry Potter book and I shall refer to it as the transient version of the gene.
* the gene – or recipe – in its abstract manifestation. This is the information that is contained in one or more collection of chemical compound, but this information cannot be “touched and felt” in a laboratory. However it can be studied, examined from an information perspective – just as we can comment and criticise a Harry Potter novel, irrespective of whether we have a copy of the book in our hand. This is the persistent version of the gene.

Is there a one-to-one connection between the transient version and the persistent version ?

For each and every transient version of the gene, there is always a persistent version of the gene. However for each and every persistent version of the gene there may or may not be a corresponding transient version, at all instants of time.

Are all persistent versions of the gene identical ?

Let me clear the air on this
* Every individual human genome has thousands of transient genes, say I number then 1 to 10,000. Each transient gene in an individual is different from the others.
+ this may not be quite correct, but I shall assume this … and it will not impact the quality of my argument.
* If you consider the mass of humanity, say 6 billion people, the persistent version of any particular gene ( say gene number 5679 ) across the population is by and large identical.
+ 5,999,999,990 are indeed identical but 10 are different and these 10 people have some feature that is different from the general population.
* For the 6 billion transient genes ( identified arbitrarily as gene 5679 ) there are 11 persistent genes at any instant of time and of these ONE greatly outnumbers the others.
+ with passage of time, the number of transient genes will change with the birth and death of individuals. However the number of persistent genes will remain constant at around 11, of which one will continue to dominate the others in sheer numbers, but the other 10 can go down with death or go up with an additional mutation happening somewhere.
* What we said for one gene ( in this case gene 5679 ) applies equally to all the other 10,000 or so other genes in the genome.

So in a population consisting of multiple members of a single species, the set of persistent genes is kind-of independent of the number of members of the species in the population.

Yes, these same 10,000 persistent genes are floating around in the population together with their individual variations. However, the same population contains variations but the number of instances of these variations ( the corresponding transient genes ) is small.

Fine, but can you tell me what these genes – persistent or transient – do ?

Thousands of things … for example, a specific gene ( say number 2346) creates an enzyme ( a protein ) that helps digest salty food, or another gene ( say number 3456 ) creates a kind of flapper between the fingers that allow the animal to swim faster … The list can go on and on .. and thousands of technical papers have been written to explain the connection between the presence of specific genes (or collections of genes ) and specific physical and metabolic functions.

This has something to do with evolution of species ?

Yes .. for example, if an animal has the correct genes, it can survive longer in a marine environment, have more offspring to which it will pass on these “good” genes. So in such an environment you would be more likely to see a larger population of these animals. Members of the same species who do not have these genes will live less and you will see fewer and fewer of them in successive generations.

You mean to say that crocodiles with webbed feet and with the ability to digest salty food will outnumber crocodiles that do not have webbed feet and who cannot digest salty food in the – say – salt water delta regions.

That is the obvious explanation … and that has been successfully used by evolutionists to explain the wide variety of animals and plants that have inhabited, and currently inhabit, the world.

And it explains why elephants and giraffes still exist whereas dinosaurs have disappeared from the face of the earth.

As I said, that is the simplistic explanation … but there is a far deeper significance.

What is that ?

We have traditionally viewed natural selection – the process by which organisms which are more efficient or successful in a specific physical environment, become more numerous and get to dominate that physical environment – as a competition between species.

That is correct. Mammals exist today because they were more efficient and successful than dinosaurs were in world.

And tigers who can handle a salty diet are the only ones that exist in the Sunderbans delta.

Yes it is either a competition between species or a competition between sub-species within a species that leads to wide diversity of biological life.

But let me challenge you with this statement : The competition is NOT between the organisms – the members of the species – but instead, it is a competition between their respective genes !!

But the genes are synonymous with the animals .. are they not ?

The physical genes – the transient genes – are synonymous with the physical organism, the persistent genes are not synonymous at all.

Please explain ..

If you go back to the example of the salt-diet gene (to which I gave an arbitrary number 2346). If we look at the population of tigers in the delta … there would have been say 3 variations of this gene – let us say 2346A, 2346B, 2346C and initially there could have been an equal number of tigers with these genes. Then the land got flooded and the water turned salty. Now tigers with 2346A – which is best for salty diets – are more successful. They feed better, do not suffer from nausea, are more healthy, can fight the others better and in the long run have more offspring.

So what happens next ?

After three or four generations .. you will see that the ratio of the three persistent genes is heavily biased towards the A variety. In a population of 100 tigers, a good 95 will be carrying the 2346A gene. Thus it is not that salt-friendly tigers are more successful than salt-averse tigers BUT it is the salt-friendly gene that is more successful than the salt-averse gene.

What is the difference ?

Our focus has moved away from the physical gene – the transient gene, and towards the information content of the gene – the persistent gene.

This is semantics, there is a close correlation between the persistent gene and the transient, physical gene. Between the genome – the total collection of all the genes – and the physical animal.

Not quite, because the same gene – or its close variant – could be found ACROSS different species !!

You mean a man and chimpanzee could have the same gene ?

Of course, they would .. if you lay out the entire genome of a man and chimpanzee, you would find that they are identical to the extent of 97% of the patterns – that is how the proteins that make your eyeballs and that of the chimpanzee are similar. So is true for so many other physical features.

Goodness gracious ! and what about behavioral features ?

Perhaps they are not discussing genetics at the moment .. but they would behave the same way as we would if there was a big sound or a flash of light, or if they are hungry and find food !

And what does that imply ?

If we go back to our salty-friendly gene, it means that all mammals that have gene 2346A – whether they are tigers or they are deer – would be more comfortable, successful and hence more numerous than their peers who have 2346B and 2346C.

But tigers may eat deer and deplete their number.

Fine … but whatever may be the final number of tiger and deer ( which can depend on so many other ecological parameters ) one thing is certain : the proportion of 2346A gene will be higher than the proportion of the other two in the total biological population of the region.

So the competition is not between the members of the species .. it is between the genes that reside, or are carried inside, the members of the species.

Exactly … and that is the theory of the persistent gene or the Selfish Gene.[1]

Why selfish ?

Because the persistent gene does not really care if the member of the species that is carrying its current transient version succeeds ( survives, proliferates) or not. What matters is that the persistent gene should succeed, survive and proliferate.

Is it not the same ?

In many cases it is true. Which is why we in our mind get mixed up between the persistent and the transient gene .. but in some cases that is not the case.

Can you give an example when that is not the case ?

That will be a big detour and will not serve to illustrate what I am trying to say here, but for the sake of completeness, let me say that there are cases where the persistent gene can cause the death of the physical animal to serve its larger purpose of preserving and perpetuating itself – but that is another story. Let us stop here and focus on the persistence and not on the selfishness.

Fine, let us stick to the persistent gene.

So our first step was to replace the concept of competition among species with the concept of the competition of among persistent genes. The next step is to replace the concept of the evolution of the species with the parallel concept of the evolution of the genome.

What do you mean by that ?

You see it is quite common to draw the process of evolution along time as a tree – the evolutionary tree.

I know … and we begin with a trunk that is far away in time and as we move upward ( or rather forward in time , we have the trunk dividing into branches which in turn subdivide into branches – and at each fork where the branches break out .. we say that vertebrates separated from invertebrates and then the vertebrates broke up into reptiles, fishes, birds, mammals and so on ..

Now if we replace the various species and sub-species on this tree diagram with their corresponding genomes ..

You obviously do not mean the individual genomes of each individual member of the species .. that will be too cumbersome.

No – I mean the part of the genome of each individual member of a species which is by and large common to all members of the species at that point of time ..

Fine ..

So once I have replaced the species on the tree, with the persistent genome of the species on the tree there are some very interesting things that you will notice …

What ?

If you go back to the trunk at the base of the tree, there is only version of the genome – and this genome is the genome of what is referred to as LUCA – the Last Universal Common Ancestor .. and for some reason, that organism is generally referred to as a female though there is no logical reason for that.

Fine we have the genome of LUCA and as we move away from it, we have genomes that break away and become different from each other.

And each branch of this genome tree has some genes that are different from the genes that are found in branches that represent other genomes.

So we have genomes that have evolved – changed, mutated – over a period of time.

Yes and in this case, the time periods over which a genome mutates and changes are typically an order of magnitude larger than the time period over which a species mutates and changes.

So effectively, our focus has shifted FROM the change, mutation and evolution of physical organisms that are members of a species TO the change, mutation and evolution of the non-physical, persistent genome.

Yes … and that is the crux of the matter : That persistent genes compete with other genes in seeking to perpetuate their own existence beyond the individual body OR the species that currently houses them in their physical or transient form and
* just as members of a species compete with each other and with members of another species
* just as one species competes with another species
* So do genes compete with other genes
* and the principle of the “survival of the fittest” applies to the gene ( or the genome – the gene collection ) as well

Why is all this important for us ?

Just think back for a moment and see what we have in our hand – we have this transient genome[2], which in a sense is something abstract and yet it has a very close relationship with the structure and behavior of a living, conscious and sentient organism.

Yes ..

And it is this genome that has been evolving over time .. from the time it represented some insignificant and semi-conscious entity like a bacteria or something even less life like ..

OK ..

And with the passage of time, of thousands of years it has now come to represent a highly competent, capable and conscious entity like a human being. And how has this happened ?

How ?

By responding to events and stimuli from the environment that has been changing around it ?

Why do you say so ?

Evolution is dictated by the environment – the land got flooded and so the salt-friendly genes got the upper hand – and so in a sense, this evolution is dictated by the cues and stimuli that the genome has been picking up from the environment.

But this reminds me of something – the Atman ?

Yes … you are right. The genome – the collection of persistent genes – is without form, without shape and cannot be directly accessed by our senses. And yet it is immortal over time … it does not die, it does not decay with time as is true for any physical entity .. it continues on and on but changes the physical environment that houses it – the sequence of chemical compounds located temporarily in a physical body. It evolves and changes over time.

But the genome reminds me of something else as well … the UTM[3] !

Exactly .. the UTM, though it is a mathematical construct, is something very similar. It begins at a very primitive state and then it picks up cues from the environment and improves – in its ability to understand and react to the environment. And with the passage of time it becomes sophisticated.

But in an earlier chapter we had modeled the human cognitive process on the mathematics of the UTM and were left wondering where in the world would we find the UTM to implement this model.

So here you have the UTM that is so important for us … that the UTM that we were looking for.

[1] The Selfish Gene, Richard Dawkins

[2] Ya Devi Sarvabhuteshu, Jati-roopena Sangsthita, Namastasyai Namastasyi Namastasyai Namoh Namaha – Salutations to the Devi who abides in all beings in the form of Genus or Species

[3] ‘Nobody realizes it at the time, least of all Turing, but he is probably closer to the mystery of life than anybody else. Heredity is a modifiable stored program; metabolism is a universal machine. The recipe that links them is the code, an abstract message that can be embodied in a chemical, physical or even immaterial form’ – Genome, Matt Ridley, page 15

1 comment:

leprechaun said...

Wow! So genes are our soul?!

That's an intriguing idea!

So maybe that explains why Dawkins calls them "our parasites", which sounds weird.

I am reading just now "The blind watchmaker", then I will proceed with "The selfish gene" in order to understand this better!

So we're getting to the singular point... let's move ahead to Love instead! :)