Mike Hosken's

"Hinges and Loops"

CHAPTER FOUR

INTRIGUING BIOLOGY

  1. Information
  2. Causes and Effects
  3. The Code in the Zygote
  4. The Code in the Embryo
  5. The Code in Action
  6. Summary and Coda
  7. Conclusion
Of all the countless wonderful things that go on in the world of living things I want to follow just one major and significant story through in a fair amount of detail. It concerns what is usually called the "genetic code".

We ourselves are biological systems, and we largely take ourselves for granted except when we are ill. So the wonder of living things in general is something which has to be drawn to our attention. To my taste, a really nice example - of extremely limited philosophical significance - concerns brewers' drays! Traditionally these were drawn by cart-horses but the role has largely been taken over by diesel lorries. However, there are nowadays some pretty potent arguments being put forward for the return of the horse-drawn dray in the very competitive context of inner city distribution.
  • Lower capital, fixed and running costs than any lorry.
  • Environmentally friendly:
    • Relatively very low capital energy input in rearing and training a colt compared with the manufacture of a lorry.
    • Uses renewable fuels.
    • Produces useful waste products.
    • Non-polluting -
      • Non-toxic exhaust free of carbon monoxide and lead.
      • Quiet.
    • Can react to verbal commands.
    • Exempt from many official regulations concerning both vehicle and driver.
    • But the literally wonder-ful aspect is that horses are living machines which are capable of self-reproduction. It is as if lorries could couple and produce vans which, given care and fuel, would grow into brand new lorries. Each lorry - or pair of lorries at any rate - would have to include all the necessary mechanisms and information to behave as a lorry AND as a lorry factory. It is extremely unlikely that the raw material could be milk, grass, hay and the occasional apple, though those are enough in the case of the horse which is provided with the full set of instructions for the production of a complete new horse.

§4.1 Information

But to consider more everyday examples, how does an acorn know that it's an oak tree in the making? Why does a chicken's egg hatch into a chicken and not into a giraffe? - let alone into an oak tree? The generations can be physically separated: acorns and eggs can be transported beyond all possible influence of the parents and into a wide variety of environments without losing any of their blueprint information. We have no alternative but to conclude that there is something about an egg and an acorn which carries the full specification of the bird or the tree. And that specification is quite detailed:
  • If the egg came from parents of the Light Sussex breed then the chick produced will mature to be similar, chicken-sized rather than turkey- or sparrow-sized, with mainly white feathers but black tips here and there.
  • Similarly, a Quercus robur (the ordinary English oak) can reliably be expected to produce the normal oak-shaped leaves but the indentations will not be as deep as those of a Quercus cerris (Turkey oak), though the leaves will be shed each autumn unlike the evergreen habit of Quercus ilex (Holm oak).
Looking at it from a different point of view, how does a daffodil know when and how to bloom? How does a house martin know how to construct a house-martin-type nest?

If we go right down to a fundamental level we have to realise that there are very few ways in which information can get into a living system:
  • GENETIC: the information itself is coded in some way in the fertilised egg of animals or ovule of plants.
  • ACQUIRED: the genetic make-up is not rigid: it includes some element of plasticity or elasticity for greater versatility.
    • Being able to learn, preferably (if I may be allowed a value judgement at this stage) allied with intelligence. This is largely an attribute of animals. But grass plants might be said to "learn" to keep their heads down in a lawn situation, mown weekly, where the oak tree would succumb at the first or second decapitation.
    • Reacting to various environmental influences. A seedling "knows" how to produce roots and it reacts to gravitational information in making that growth go downwards: it goes to pot in a spacecraft! Most mushroom type growth is upwards against that same gravity, but green plants need extra information about light for stems and leaves to grow in the needful direction. All the sense data discussed in Chapter One are informational inputs from the environment.
I can think of no other way in which information can get into a living system.

§4.2 Causes and Effects

When I want to track down the cause of any particular aspect of a living thing I have got to find out where that cause got its information from.
  • Blueprint, inheritance, genetics, or pedigree or any such term. The feature in question is either determined or has its limits set by an information system carried in the zygote (the biologist's name for the animal's fertilised egg or the plant's pollinated ovule).
  • Some other cause which comes before the effect, like the gravitationally controlled direction of root growth. This is the concern of the physiologist - the biological scientist whose interest lies in working out relationships and mechanisms, both within the living organism and between the environment and the plant or animal. It need concern us no further in this context.
  • A less clear-cut division is the class of relationships where the cause seems to come after the effect; an action happens apparently in order to achieve some purpose or goal. We could easily get into deep philosophical waters here, especially about "teleology" - purposive causes. I don't want to go off on that particular tack at the moment but I think we must just appreciate one distinction:
    • A tremendous amount of sloppy science is explained in terms of purpose as if that provided a full and sufficient explanation. The plant sends its roots down in order to search(!) for water. That sparrow over there collected that bit of straw in order to build its nest in order to have a home in which to raise its brood in order to help perpetuate the sparrow species. All these and a myriad other examples make convenient shorthand correlations but they don't actually provide anything that could be regarded as an explanation of how those things came to be. It is almost like saying that a stream runs down its course in order to join the river, which continues the journey in order to reach the sea.
    • So far as I can deduce causes must always come before effects. The only thing that can have a purpose as a cause is a conscious being. Again we must not tarry too long, but I think a few examples are called for.
      • Being at the top (so far) of the evolutionary tree we human beings can indeed use our intelligence and insights to plan courses of action designed specifically to achieve desired ends. The way you may enrol for an Open University course in order to work towards a qualification is quite different, though, from the mechanism which keeps young children in regular attendance at school. The whole subject of motivation is a matter of carrots coming at the end as well as threatening sticks to be avoided. And such things are effective only if the conscious being is aware of them before the action is decided on. So even here it is really the case that the cause must come before the effect.
    • But what about wild nature: can't we see evidence of purpose there? When pack animals like wolves and lions are hunting they "obviously" work co-operatively in order to catch prey. This involves weighing-up the terrain and anticipating the actions of the prey animal as well as monitoring the movements of the other members of the hunting party. But although these activities are apparently so refined it is clear that each young pack animal has to learn its craft: hunting skills are a matter of social learning building on a genetic potential. And that all has to come before an effective hunt: it is not enough for the animal simply to know the purpose of the exercise. So again the cause of its running in this direction or that must come before the resulting action.
    • To broaden the scope a bit the case of an ant colony is worth mentioning. Again there is "pack" behaviour, especially with some of the more horrendous tropical species. But ant behaviour is almost entirely instinctive, even to the extent of sometimes being self-sacrificial for the general good of the colony. But the cause of that self-sacrifice is the inbuilt programming of instinct (which comes before the act) and not the good of the colony (which comes later, if at all).
    • Slightly higher up the evolutionary tree, a bee returning from a successful nectar-hunting expedition performs its well-known dance because it is programmed to do so, not from some altruistic wish to help its hive-mates with their navigation.
So where does this leave us? I think we can now draw a significant conclusion:

Information in zygotes fixes the shapes, colours and many actions of plants and animals.
Any action which cannot have been learned must have a genetic cause.

§4.3 The Code in the Zygote

We are going to be having a look at the mechanisms of DNA. Nearly all proteins (see the side of your breakfast cereal packet) are large molecules: some are positively gargantuan with millions of constituent atoms, usually arranged as a long and complex chain. Such formations are possible because carbon, almost but not quite uniquely, is capable of forming both rings and chains in which carbon atoms join neighbouring carbon atoms - by what can perhaps best be thought of as holding hands!

There are some organic (carbon-containing) units called bases which include adenine, guanine, cytosine and thymine: we shall abbreviate them to their initial letters, A, G, C and T. Each can be attached to a sugar unit: the sugar we are concerned with here is not the sucrose we stir into our tea nor the glucose beloved of athletes but ribose. The combined sugar-base unit is called a nucleotide.

Phosphate bonds can link nucleotides into protein chains. Deoxyribonucleic acid - DNA - is not just a single protein of constant composition. Although the pattern is fixed by the nature of the molecule the succession of A, G, C and T is variable and it is indeed this which stores the genetic information. In physical structure, DNA takes the form of a double helix - easiest to visualise as two intertwined parallel spiral staircases: there is one base on each step of each staircase, with the framework being provided by the sugars and phosphates.

Where one staircase has base G the complementary one has base C.
And vice versa.
Where one staircase has base A the complementary one has base T.
And vice versa.

That's all there is to it - except that each double staircase is a modest few hundred million steps high! Such a DNA strand can also be thought of as a chromosome, which is the name given to a string of linked genes - characteristics of the final product.

§4.4 The Code in the Embryo

Now the starting point for our argument is that the genetic information is all contained in the zygote. But the zygote is a single cell. [Yes, the egg you have for breakfast is the largest single cell you will ever come across.] All the plants and animals that we are interested in are multi-cellular, made up of millions upon millions of cells in most cases. If the genetic message is to influence all parts of the mature living thing then the information in the zygote has got to be duplicated countless times as the embryo develops. And total reliability is essential: a few fuzzy copyings could spell disaster.

This duplication of the information is achieved by replication of the DNA, ahead of each actual cell division. It starts at a particular place on each chromosome, known as the replication origin. This is where the two spiral staircases start to come apart, where the DNA begins to unzip, exposing its hitherto paired complementary bases. It is the function of an enzyme in the cell, called DNA polymerase, to collect appropriate units from the chemicals available inside the cell to assemble the complements.

Base G exposed: complementary base C is added.
And vice versa.
Base A exposed: complementary base T is added.
And vice versa.

So, starting at the replication origin and zipping away in both directions, a staircase 1 is built onto staircase 2 and a staircase 2 is built onto staircase 1: we now have two identical double helix chromosomes, each consisting of half-original and half-complementary material. Clever, eh? (Any more modern-technological system of duplication would involve some vulnerable intermediate stage, like a photo negative or the electrostatic charge on the drum of a photocopier.)

§4.5 The Code in Action

So that seems to be fine so far: the information can be passed on to successive cells as the zygote becomes an embryo, as the embryo grows to independence, as the organism matures to adulthood. But to what end? How does the code actually do anything? Where and how is the code interpreted and acted upon?

First point is that only the complementary-base helix (what we called staircase 2) is actually used, surprising at it may seem at first. The so-called initiation site is different from the replication origin, but again it sets about an unzipping - but only temporarily this time. Another vital difference is that from now on any A (adenine) exposed has a complementary uracil (U not T) added. So as it unzips a new enzyme, RNA polymerase this time, supervises the formation of a new complementary molecule known as ribonucleic acid (RNA not DNA).

Base G exposed: complementary base C is added.
And vice versa.
Base A exposed: complementary base U is added.
Base T exposed: complementary base A is added.

The DNA re-unites as a double helix once each section has been dealt with. (There may be some uncopied DNA at either end since the copying stops when it reaches a transcription termination site.) The new strand is in fact a copy of "staircase 1", having used "staircase 2" as the template, except for having a U in place of every T. So this time we finish up with the original DNA unchanged, plus a brand new single staircase/helix known as messenger RNA.

We can now take a slightly closer look at the code itself. What we have got in messenger RNA is a single but seemingly endless string of A, G, C and U bases. Geneticists have worked out that they function in groups of three: the whole genetic code is made up of three-letter words. Each such group of three is known as a codon. For example A-U-G behaves as the RNA start codon: the corresponding stop codon may be U-G-A or U-A-A or U-A-G.

It is perhaps worth realising that the four types of bases can be combined into three-base codons in just 64 different ways. Try it! AAA, AAG AAC AAU, AGG ACC AUU, AGA ACA AUA, ... If we discount the ones used to control the system such as the stop and start codons we are not left with all that many with which to code the entire diversity of the natural world! Nevertheless, virtually all heredity is based on this system: it is not the case that there are different systems for each class of organisms.

Be that as it may, the next question is, how does a codon come to signify anything specific? Well, inside cells there are chemical-manufacturing facilities, commonly located in structures called ribosomes. Now the ordinary proteins which go to make up our bodies, or a butterfly or a daffodil are built up from just twenty different components called amino acids. So to make any specifiable protein the cell needs to assemble a long sequence of particular amino acids. The pattern is derived from the messenger RNA by different types of transfer RNAs. Whereas messenger RNA is a vastly long staircase each transfer RNA is much more modest in size: it recognises its particular three-base codon and brings from the cellular soup a molecule of its particular amino acid for inclusion in the body-protein that is being assembled.

So there is, for example, a particular transfer RNA which recognises G-A-U. When it finds a G-A-U somewhere along the length of the messenger RNA it metaphorically drags an aspartic acid - one of the amino acids - along to join onto the new protein. There is not quite a one-to-one relationship: G-A-C fetches aspartic acid in the same way that G-A-U does.

Ah! But I hear you object, "How does it know that, for example, it really is a G-A-U codon? That G may be the end of a codon going north and the A-U the start of a different one going south." The answer is that besides the transfer RNAs for the twenty amino acids there is an initiator RNA which recognises the start codon (A-U-G): this is enough to set up the triplet pattern so that the sequence is then dealt with correctly without codon overlap. Similarly, it is the function of the stop codon to free off the newly assembled protein. The long-chain messenger RNA can then break up into base units for re-use in another cycle.

§4.6 Summary and Coda

Chromosome = double helix genetic code + complement = "spiral staircase 1" + complementary "spiral staircase 2"

REPLICATION
Chromosome unzips
DNA polymerase assembles a new staircase 2 onto staircase 1
DNA polymerase assembles a new staircase 1 onto staircase 2

TRANSCRIPTION
Chromosome opens, sectionally and temporarily
Using staircase 2 as a template RNA polymerase assembles messenger RNA

TRANSLATION
Transfer RNAs key on to the codon sequence of messenger RNA
They assemble amino acids into a protein chain

That only leaves us to question the control system. If every active or growing cell has all these protein production facilities how is it that they do not go on growing indefinitely? Not too surprisingly, there are several forms of control. Some genes are known to control others: they can affect rate of growth, for example, and final body size. Chemicals in the cell may act as inhibitors so that the transfer RNAs can't function: in converse cases the RNAs need activator chemicals without which they will not be effective. It is all a matter of balance. Cancer is one of the more serious possible results when that balance is upset: growth and cell division run amok.

§4.7 Conclusion

All the genetic information in living things is digital in nature. We have all, from our experience of digital clocks and watches, come to know the technical meaning of "digital" in informational terms: items are either totally absent or fully present. In the case of those watches the "items" are the succession of numbers: some time plus forty-seven seconds is followed by that time plus forty-eight seconds, not 47.1 and then 47.11 and 47.236183... and all the other possible times. So that is different from an analogue watch where a photograph of the sweep hands could be measured to as many places of decimals as the measuring system allows.

The genetic code is simply a digital succession of A, G, C and T (or U) units: each unit is either totally absent or fully present. So the difference between a rook and a crow is not the result of their having slightly different amounts of control chemicals or anything like that: it is all a matter of differing patterns of A, G, C and T units.

But at the end of §4.2 we had reached the conclusion that any action which cannot be learned must have a genetic origin. Let us take a few example cases and see where that gets us.
  • Virtually all young mammals can suckle. Call it instinct or innate ability or just a predisposition, whatever it is if it appears without tuition then it must have been coded in the zygote. If it was coded in the zygote then it must have taken the form of a digital pattern of A, G, C and T.
  • Nearly all birds build nests. The structure and shape of those nests is, rather like the language of calls and cries, characteristic for each species. It is possible, of course, that since the young are reared in nests each spent its infancy examining and memorising the nest and working out how it must have been sited, started and structured - while keeping an ear to learning the parental language. That may strike you as improbable, but the only other alternative requires unlearned behaviour and total A, G, C, T coding.
  • As our archetypal example, what of the cuckoo? The adult lays its fertilised eggs in other birds' nests. Hatching and rearing are carried out entirely by foster-parents. So how does a young cuckoo know that its "song" must be 'cuckoo'? And how is it to react to the passing of the seasons by flying away? - and why to Africa? - and how does it know when it has got there? The answers can lie only in the appropriate succession of As and Gs, of Cs and Ts.
Oh dear! The early sections of the Chapter seemed to hold logical water alright. And the whole business of the biochemistry of inheritance is now orthodox mainstream biology. But put the two together and what do you get? A credibility gap? You would not be the only one of that opinion.

So we can't leave it all there. We shall come back to it for a different view later on, in Chapter Six.

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Please contact Mike Hosken at
[email protected]
with your observations, comments, criticisms and suggestions, or to request an A5 printed copy of "Hinges and Loops".
The next chapter concerns the Physical World.
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