Evolution

The modern theory of natural selection derives...
The modern theory of natural selection derives from the work of Charles Darwin in the nineteenth century. (Photo credit: Wikipedia)

If we accept Darwin’s theory of evolution, which I do, then we accept that we are the way we are as a result of a very period of gradual changes brought about by the pressures that our species has experienced through emergence and during process of its existence.

But let’s take a step back. All organisms have so called genetic material, stuff within them which encodes the way they are and the way that their offspring will be. The genetic material is copied as a part of the process of living, of growing and of repairing the organism if it sustains damage.


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If that were all there was to the process, then organisms would be static, with no changes and no evolution. In fact the process is not perfect and both minor and major changes to the genetic material happen all the time, by all sorts of means.

Obviously, if too many changes or major changes occur in the genetic material, then the organism may not grow properly and may not repair itself properly when damaged. Also if the genetic material is passed to the organism’s descendants, they may they may not be viable or they may be disadvantaged and be unable to thrive and reproduce.

Baby turtle, species unknown.
Baby turtle, species unknown. (Photo credit: Wikipedia)

To counter this, our bodies have mechanisms to repair our genetic material, our DNA. If our bodies did not have this ability, it is unlikely that we would last long, as our body cells could experience millions of cases of damage to our genetic material per cell per day. That’s an awful lot of damage!

As described in the Wikipedia reference above, the errors in our genetic material could result in cell death or unregulated growth resulting in tumours. The DNA repair mechanism in our cells  do a good job, but they are only effective if the DNA strands are broken or incomplete. If a change is minor, and is properly reflected on both strands of our double helices, then the repair system will not notice the change.

English: Close up of The Double Helix
English: Close up of The Double Helix (Photo credit: Wikipedia)

This allows small changes to slip through, and provided they don’t cause life threatening problems, they may get passed to our descendants. The same applies to organisms other than ourselves of course.

Some major changes do slip through and organisms may end up with extra chromosomes or with damaged chromosomes. Sometimes these issues may not cause too many problems for the organism, while in other cases the descendant organism may not survive long enough to breed.

English: Illustration of the chromosomal organ...
English: Illustration of the chromosomal organisation of haploid and diploid organisms. (Photo credit: Wikipedia)

The minor errors mentioned above may affect the descendant organism to some extent, making it more or less successful than its parent organisms. The theory of evolution suggests that if the change in the genetic material makes it more successful than its siblings who don’t have the small errors, then, over generations, organisms carrying the new DNA changes will eventually replace those who don’t carry the change.

This could lead to problems for an organism. If we consider a stable population with few pressures, that has plenty of resources, there is little that would cause any permanent changes to the population, and small genetic traits could appear and disappear over time and not have any measurable effect.

Boreray sheep - on Boreray - geograph.org.uk -...
Boreray sheep – on Boreray – geograph.org.uk – 1439988 (Photo credit: Wikipedia)

If the environment then changes, such that one trait provides a large benefit to those individuals who have this trait, then over time there will be a tendency for the trait to be found in more individuals and the number of individuals without it would fall.

If the environment changes back again, then those with the trait may be disadvantaged and those without the trait could then come to dominate the population. However if enough time had passed and all the individuals without the trait in their genetic material had died out, then the population would be stuck with the trait.

Français : Trait du Nord - Salon de l'Agricult...
Français : Trait du Nord – Salon de l’Agriculture 2010 (Photo credit: Wikipedia)

It would be extremely unlikely but not impossible for the change in the genetic material to be reversed by chance as this would require another minor error to exactly reverse the original error. In effect, evolution as reflected in the genetic material never (or astronomically rarely) reverses.

If a group of organisms gets isolated from the rest of its species, some of the genes that are present in the population at large will not be present. In addition, some of the genes in the isolated population will also die out, either by chance, or because the trait that they confer is not beneficial in the isolated environment.


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This can cause problems for the population if the environment changes dramatically to the detriment of the organisms. While the population at large may have genes which would enable the population to survive the changes, but those genes may have died out in the isolated environment, and the population may fail.

Of course, a mutation may arise which would enable organisms to survive in the new conditions, but environmental changes would almost certainly be faster than the rate of evolution through mutation.

exemples de mutations possibles sur l'ADN
exemples de mutations possibles sur l’ADN (Photo credit: Wikipedia)

Some species have different behaviours and appearance while still remaining the same species. Some of Darwin’s finches are an example. At least two varieties of one of the species feed on the Opuntia cactus, but they have different ways of feeding on them. One variety has a long beak and can punch holes in the cacti, while the other variety, with a short beak, break open the cacti to feed.

The birds can and do interbreed, so they are indeed the same species. This is similar, I presume, to the variation in skin colour in humans or the various blood types in humans. Such species have the same genes, but have slightly different versions (alleles) of it. This is called genetic polymorphism.

English: Trumpeter Finches (Bucanetes githagin...
English: Trumpeter Finches (Bucanetes githagineus), Valley of the kings, Egypt. Español: Camachuelos trompeteros (Bucanetes githagineus), Valle de los reyes, Egipto. (Photo credit: Wikipedia)

A species, like the finches, has to adapt. If its environment changes and it is unable to respond, then it will die out as innumerable species have done and are still doing. However, a species needs time to respond to environmental changes. For instance, polar bears may die out because the sea is is not freezing over as it usually does, and as a result there are no seals for the bears to hunt.

Whether or not you attribute the warming to mankind’s actions or not, the lack of freezing is a fact, and the bears are so far unable to adapt to the new conditions, and are often becoming a nuisance to arctic communities.

Computers and cells

English: "U.S. Army Photo", from M. ...
English: “U.S. Army Photo”, from M. Weik, “The ENIAC Story” A technician changes a tube. Caption reads “Replacing a bad tube meant checking among ENIAC’s 19,000 possibilities.” Center: Possibly John Holberton (Photo credit: Wikipedia)

(Oops! One day late this week!)

A computer has some similarities to living organisms. Both produce something from, well, not very much. A computer program has data input from various sources, and produces output to various sinks or targets. A living organism takes in nutrients from various sources, and produces branches, leaves, fur, bones, blood and other organs.

Of course there are differences. A computer is much, much simpler than a living being, even single celled organism. A computer in general only has a relatively small number of parts, but the “parts” in a living organism number in the billions. And of course, living organisms reproduce, but that may change in the foreseeable future.

English: The heterolobosean protozoa species A...
English: The heterolobosean protozoa species Acrasis rosea Olive & Stoian. Photographed at the Biology of Fungi Lab, UC Berkeley, California. (Photo credit: Wikipedia)

Some animals are sentient, but I’m not going to discuss that here. Maybe in another post.

A computer has hardware, software and operates on data. The data is either part of the software or read from buffers in the hardware. It stores its calculations in “memory”, which is special hardware with particularly fast access speeds.

English: 1GB SO-DIMM DDR2 memory module
English: 1GB SO-DIMM DDR2 memory module (Photo credit: Wikipedia)

The computer produces results by placing data into buffers in the hardware. This results in things happening in the real world, such as printing a letter or number on paper, or more frequently these days, on some sort of screen. It may also do many other things, such as control the flow of water by moving a valve or other control mechanism.

Computers communicate with other computers, by placing data in an output piece of hardware. The hardware is connected to a distant piece hardware of the same sort which puts the data into a buffer accessible to another computer. This computer may be a specialised computer that merely passes on the data. Such computers are called routers (or modems, or firewalls).

Railway network in Wrocław
Railway network in Wrocław (Photo credit: Wikipedia)

Computers, specialised only in their usage, are found in washing machines, cars, televisions, and we all these days have multi-functional computers in our pockets, our cellphones. It would be hard to find a piece of electronic equipments these days that doesn’t have some sort of computer embedded in it. Very few of these computers are completely isolated – they chatter to one another all the times by various mechanisms.

Internet
Internet (Photo credit: Wikipedia)

(Incidentally, I came across a bizarre example of connectivity of things the other day – a wifi teddy bear. Say you are sitting in the lounge and you want to send a message to your child who is in her bedroom. You pick up your tablet and send a message to a “cloud” web site. This sends a message to your child’s tablet which is in her bedroom with her. The teddy bear, which is connected to the child’s tablet by wifi, growls the message to the child. No doubt scaring her out of her wits.)

So in the current technological world everything is connected to everything else. Much like all the cells in a living being are connected to all the other cells in the organism, directly or indirectly. So how far can we take this analogy, where the organism is the network and the individual cells as the computers. (Caveat emptor – I am not a biology expert, so don’t take what I might say from here on as gospel).


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A computer consists of hardware, software, and operates on data. A cell is sort of squishy, so “hardware” can only be a relative term, but a cell does have a relatively small number of organelles, such as mitochondria. The nucleus, which contains most of the genetic material, acts as the control centre of the cell, much as the CPU is the control centre of a computer.

The function of the nucleus is to maintain the integrity of these genes and to control the activities of the cell by regulating gene expression—the nucleus is, therefore, the control center of the cell.

In the cell, the genetic material is in some sense the software of the cell. It contains all the necessary information to create the cell itself or more interestingly the information needed to cause the cell to split into two identical daughter cells. This information is generally encoded in the DNA of the chromosomes.

Information flows between DNA, RNA and protein...
Information flows between DNA, RNA and protein. DNA -> protein is another special transfer, but it is not found in nature. (Photo credit: Wikipedia)

The cell also contains, within the nucleus, an organelle called the nucleolus. This organelle (which is part of the nucleus organelle) seems from my reading to mostly relate to RNA, while the rest of the nucleus mostly relates to DNA, very roughly. RNA and DNA perform a complex dance called protein synthesis in organelles called ribosomes.

Cells produce chemicals, which can be consider analogous to computer outputs and receive chemicals from other cells, and so cells communicate, in a sense, with each other. Since all cells are equal genetically, it follows that a cell’s type, liver, skin, lung or brain neurone is determined by factors in its environment.

The model of an artificial neuron as the activ...
The model of an artificial neuron as the activation function of the linear combination of weighted inputs (Photo credit: Wikipedia)

This only loosely true as each cells is the daughter of another cell and inherits its type, but in the early days of an organism’s life, before organs are formed cells do differentiate. Just as when computers were new, they were all very similar, keyboard, monitor, and beige case.

As the computer-sphere evolved, special types of computer evolved, such as routers and modems, and firewalls. Not to mention phones. Computers became specialised. Similarly cells become differentiated, some going on to become liver cells for example, and others brain cells (neurones).

English: Front side of a Juniper SRX210 servic...
English: Front side of a Juniper SRX210 service gateway Deutsch: Vorderseite eines Juniper SRX210 Service Gateways (Photo credit: Wikipedia)

When an organism is young and a cell divides both cells are the same type, but when the organism is very young there is no differentiation. The DNA in the cell contains the necessary information to determine the cell type and tissues and organs are created in the more complex animals.

This process obviously can’t be random, otherwise cells of the various tissue types would be all mixed up. It seems to me, maybe naively, that while the “program” for creating cells is in the DNA, some factors in the environment convey such information as how old the organism is, and what type of cell needs to be created.

an example of a Program
an example of a Program (Photo credit: Wikipedia)

We know from investigations into fractals that a simple equation can result in the creation of an image that looks very much like a tree or grasses and that small changes to the equation can lead to different tree or grass shapes. It is tempting to think that a similar process takes place in organisms – a general rule is given which results in the right sort of cells being produced in the right places.

The problem with the fractal idea is that it only creates simple shapes. An arm with fingers, skin and so on is beyond the capabilities of a fractal process so far as I know. Fractals don’t stop. Again, so far as I know there’s no way to iteratively create a tree structures with leaves.


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So the “software” of the cell, the “program” embedded in the DNA doesn’t appear to be analogous to a simple computer program that draws fractals. Of course that doesn’t mean that we can never describe a simple organism completely in fractal terms, and create analogous distinct individuals.

It seems that a long as the analogy is not pushed too far, computers in a distributed network are reasonably similar to living organisms. Please note I am note referring to the fractal type computer programs, but am talking about the way that computers themselves in a network are somewhat analogous to living organisms. Primitive ones!

Sample oscillator from hexagonal Game of Life.
Sample oscillator from hexagonal Game of Life. (Photo credit: Wikipedia)

Growing up, down and sideways, and George Clooney.

Ginkgo seedling 1
Ginkgo seedling 1 (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.

Bonsai IMG 6396
Bonsai IMG 6396 (Photo credit: Wikipedia)

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.

Genetics diagram: Punnett square describing on...
Genetics diagram: Punnett square describing one of Mendel’s crosses, between parents that are heterozygous for the purple/white color alleles. Category:Punnett squares (Photo credit: Wikipedia)

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.

English: George Clooney at the Toronto Interna...
English: George Clooney at the Toronto International Film Festival 2011. (Photo credit: Wikipedia)

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.

A black-bodied peppered moth (Biston betularia...
A black-bodied peppered moth (Biston betularia f. carbonaria) in the Ahlenmoor, a hill moor in northern Lower Saxony, Germany. (Photo credit: Wikipedia)

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.

English: Capsella bursa-pastoris, Brassicaceae...
English: Capsella bursa-pastoris, Brassicaceae, Shepherd’s Purse, flowers and fuits; Karlsruhe, Germany. The fresh aerial parts of the blooming plant are used in homeopathy as remedy: Capsella bursa-pastoris (Thaspi.) Deutsch: Capsella bursa-pastoris, Brassicaceae, Gewöhnliches Hirtentäschel, Blüten und Früchte; Karlsruhe, Deutschland. Die frischen, oberirdischen Teile der blühenden Pflanzen werden in der Homöopathie als Arzneimittel verwendet: Capsella bursa-pastoris (Thaspi.) (Photo credit: Wikipedia)

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.

POOR SOIL, DAMAGED BY ACCUMULATED SALT, IS EXA...
POOR SOIL, DAMAGED BY ACCUMULATED SALT, IS EXAMINED BY MEXICAN FARMER, GILBERTO BUITIERREZ BANAGA, NEAR MEXICALI… – NARA – 549083 (Photo credit: Wikipedia)

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.

English: Edge of a ditch on a gravelly, lime-r...
English: Edge of a ditch on a gravelly, lime-rich soil at eastern Jutland, near the Kattegat. Dansk: Grøftekant på gruset, kalkrig jordbund i Djursland, nær Kattegatkysten. (Photo credit: Wikipedia)

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.

Male and female Gold Molly. Watch the Gonopodi...
Male and female Gold Molly. Watch the Gonopodium of the left fish. Its the male. Left is the female fish. (Photo credit: Wikipedia)

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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