Gene – Me on the net

[Ooops! Late again.]

The seed pod of milkweed (Asclepias syriaca) (Photo credit: Wikipedia)

Most living things come from seeds or eggs. A fertilized egg or seeds has all the information in it to generate the organism that springs from it. All the organs of the organism are implicit in the egg or seed, but minor details, like freckles or fingerprints are not encoded in the egg.

The environment and chance play a part in the final shape of an organism. A seed may fall in a good environment or it may fall in a less favourable environment and the shape of the organism can be totally different in the two environments, to the extent that an unwary botanist may categorise them as two different species.

This property of plants was used by the writer of the Christian gospel in the Parable of the Sower (Matthew 13:3-23). Interestingly this comes just before the part where the Gospel writer expounds on Jesus’ reasons for teaching in parables.

Some plants and animals change significantly as they mature. Lancewood is so different as a mature plant from its juvenile form. The juvenile leaves are narrow and spiky while the mature leaves are broader and softer, and while there are competing theories as to why this is, my favourite theory is that the juvenile plants had to discourage browsing by animals, and in particular the extinct bird called the Moa. Since the Moa is extinct this theory cannot be tested!

Japanese horticulturists have used this feature of organisms to fit themselves to the environment to create miniature trees in a pot. Basically the tree is grown in a small container which obviously can’t maintain a full sized tree and as a result a perfectly formed miniature tree can be formed with care, sometimes over long periods of time.

It would seem obvious that you can’t produce bonzai human beings, but in fact this can be done. Whenever a drought or famine hits a country the children who grow up there are small and underdeveloped (as well as having other deficiency problems.

When researching this topic I came across an article on the Internet which discusses this topic, and the authors state in part:

Therefore, by coding for proteins, genes determine two important facets of biological structure and function. However, genes cannot dictate the structure of an organism by themselves. The other crucial component in the formula is the environment.

This overstates the role of the environment a little, I feel, as in most cases the organism’s structure is determined in the most part in its genes, so that it looks much like any other member of the species. It is only when the environment is unfavourable (as in the case of the bonzai trees) that the gene expression leads to significantly differently formed individual. Droughts and poor soils will also leads to significantly differently formed individuals, but those are deficiency effects.

Early succession on poor, sandy soil at Øer, D... — Early succession on poor, sandy soil at Øer, Djursland, Denmark. (Photo credit: Wikipedia)

This is more clearly true in the case of organisms like humans. Unless the environment in which a human grows up is very extreme, there is actually little difference between individuals, and those differences, race, eye colour, hair colour and things like the tendency to myopia are almost certainly genetic.

So I am arguing that genes result in the major characteristics of any organism, except in certain rare cases. Somewhere in the human genome the number of fingers and toes are coded for, and only rare individuals with genetic variations have more or less digits. We don’t all speak the same language, but that is not a genetic trait, though the ability to learn and speak a language may be genetic.

Genes are interesting things. As mentioned in the article, genes can code for structural proteins or for enzymes which affect the chemical reactions in the cell. I suspect that the line between the two is pretty blurred as building the structure of the cell is after all a chemical reaction.

Of course, not only must a cell’s genetic mechanism build and maintain its own organisation, but a cell is part of a tissue, and in, for example, the liver, a cell must maintain itself as a liver cell. Similarly for cells in other organs.



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It appears that, as the genetic material is identical across the whole organism, that there must be some way for a cell to “know” that it should develop as liver cell and not as a brain cell. This is done by switching genes on and off, but I don’t understand how this happens in multi-cellular organisms. It seems that there are environmental influences within the organism and within the tissues that determine this.

It’s likely that these environmental influences are based on something like chemical gradients. Otherwise, when a bone is created there would be no way of telling the process of bone creation when to stop. It is evident that it is an approximate influence because fruit flies have different numbers of eye cells between left and right eyes (about 1000). If it were an accurate influence then the number of eye cells would be the same in both eyes.



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Apparently scientists do not know exactly how it work either. In this web page, “10 Questions Still Baffling Scientists“, the claim is made that not even the experts know. Of course these Internet lists of things may or may not be accurate, but it is an interesting link.

Of course fractal generation programs can be used to generate pretty good imitations of the structures of trees, and changing a few parameters fed to the fractal generation programs can change the shape of the “tree” from a bushy structure to an extended poplar type structure.

Some similar mechanism might be involved here. Fractal programs are simple, can produce a wide range of shapes. The trouble with fractals is that there is usually no way to stop the shape generation, so any stopping mechanism is probably not part of any possible fractal method for generating. Some other method for stopping the growth of an organ once it is the right size and shape most likely exists.

From the link above it is possible that this mechanism is not yet known, but it does appear that organ growth and shape is encoded in the genes, and is effected by switching genes on and off. Some fractal type mechanism might be involved.

English: Apprentice. Man and boy making shoes. (Photo credit: Wikipedia)

Often a plant seed will end up in a place that is not particularly suitable for it. In particular it may end up in a gravel path or similar where there is little real soil. Or it may end up in sand which drains quickly and may, if near the sea, contain high amounts of salt.

In such an environment it may grow stunted or may be deformed. For instance Bonsai trees are kept in a small container and kept relative short of nutrients so that stay small and become gnarled and twisted. They may even have their roots trimmed.

One can imagine a society of concerned individuals fighting against the sustained torture of the trees treated in such a manner, but strangely, I’ve never heard of one. Maybe it is because trees can’t scream?

All members of a species have the same genetic make up, the same genotype. All individuals grow in much the same way, to produce similar adult individuals. This is termed the phenotype.

There may be sexual dimorphism, where the female of the species differs from the male of the species, but in most ways, all members of one sex are pretty similar to one another. I am not too dissimilar from George Clooney. My wife is much like Angelina Jolie.

Of course individuals are not identical. I’m slightly taller than George, for instance. This difference can be genetic, or it may be environmental. My genes may be the cause of the difference, or maybe the environment when we were growing up has slightly affected our growth. Our good looks are almost certainly genetic.

Sometimes a plant grows in a particular way in one environment will look completely different in another environment. Also a young specimen of a plant may look different from a mature specimen of the same species. Lanceword (Pseudopanax crassifolius) has a juvenile form so different from the mature form that it was initially thought to be two different species.

The environmental effect on the phenotype or expressed shape can be seen in genetically identical twins. One would expect their phenotypes to be identical at all ages, however, while “identical twins” look very very similar there are detectable differences.

English: Comparison of typical zygote developm... — English: Comparison of typical zygote development in monozygotic identical and dizygotic twins. (Photo credit: Wikipedia)

For instance if one twin had suffered a serious illness at a critical stage of growth, then their adult sizes may be significantly different. If one twin had a rich diet and the other twin a restricted diet that also might affect their sizes and expectations of longevity. Scientists can tell a lot about the processes of growth and development by studying genetically identical twins.

A more subtle variation in the phenotype can be seen when populations are considered rather than individuals. A population of moths that lives on darker surfaces may tend to be darker in colour than the same species that lives on lighter surfaces. Since this effect happens slowly, over many generations, it appears to be a genetic change or shift. However this change to the genotype is at a lower level than the species as the lighter moths and the darker ones can interbreed.

Some plants look completely different if grown in different environments. The weed that grows in gravel may look completely different from the weed that grows a metre away in a more favourable environment. It’s as if a switch has been thrown which turns on a totally different way of “building” the plant, as it may well be something like that.

If the genome of the organisation is a “program” to “build” the plant, it is perfectly feasible that a lack of resources at an early stage in the plant’s life might well kick in a different path in the developmental process from the path that it would take if resources were abundant.

if (abundant_resources == true)

then build_good_version

else build_poor_version

This is a simple branching process in a computer program, but the process is almost certainly a lot more complex in real life. However the principle is sound, I believe.

A simple iterative process can be used to generate complex shapes that look a lot like real plants. Minor changes to the process can cause significant changes to the end results. Tall thin shapes can morph into shorter bushier ones with a few changes to fixed numbers (constants) in the iterative process.

The phenotype of a plant of a particular species will be similar in all individuals. If an individual has leaves, stem, flowers of a particular sort then the phenotype of an individual in a different (eg poorer) environment, will most likely have similar parts, though some differences will be obvious.

Maybe the stem into of being long and flexible, it may be a lot shorter and stiffer. Maybe the leaves will be a lot thicker and fleshier in the poor environment plant and may therefore be able to retain water which will be scarcer in the poor environment. Perhaps the flower will be more robust in the harsher environment.

One would expect such variations of phenotype, the poor and the rich, to be implicit in the genome if the wider environment is patchy, with areas of rich soil mixed up with areas where the soil is poor. Otherwise, the ability of the genome to be expressed in multiple ways would likely be bred out of the population, as nature always goes for the simpler rather than the more complex.

The flexibility of the genome is something that the organism benefits from its whole life. For example there are some fish which live in groups of one male and several females. If the single male is killed by another fish, an octopus or a human being, one of the females will change sex and become male, taking the place of the missing male fish.

I’ll not speculate on how that happens in detail, but it seems that it must be implicit in the genome. The trigger is the absence of the male fish, but how the “genetic program” detects this, I don’t know, but once is does it transforms the largest female into a male, presumably by triggering changes in the genetic organs. That’s bound to be a complex process.

The central idea in this post is that the genome is much like a computer program and that the environmental influences are like the parameters to such a program. This is probably an over simplification in many ways, but by considering it as a program can explain why the same genome can produce such different individuals.

A computer program can be controlled by inputs while it is running, and similarly the environment can shape an organism while it is growing and after it has reached maturity. The idea of organism as computer controlled machine is not new, but I like to bring it out and have another look at it now and again.



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Tag: Gene

10 fingers and 10 toes

Growing up, down and sideways, and George Clooney.