Is the 'Randomness' of Evolution Really Random?

[Wellwisher]

Let me ask a few questions, that can help me understand. I am not a biologist but rather a chemist. I understand physical biochemistry; water and biomaterials, but I am weak on statistics in biology.

The first question is how hard would it be to create a new gene, from scratch, that can do something useful such as allow my body to make hydrogen gas..? This gene has to made from scratch without copying. The approach can use a trial and error strategy or a chemical logic strategy; reverse engineering from an ideal aqueous enzyme.

The next question is how easy would it be to mess up a gene, for an enzyme, by changing a base or two or three?

The point of the questions is to determine if these could balance out in terms of time. Or whether I could destroy thousands of genes, in the time needed to finish a working hydrogen generator gene.

Trial and error would lose but a logical plan might stay ahead of destruction. I am not sure so I will ask.

 

[BillTre]

This gene has to made from scratch without copying.

This is not how mutations usually work.
Copying of genes is not uncommon in biology. Ruling that out is not biological. See previous posts.

1) It seems that you are not considering that mutations are not constantly pummeling genes with changes that will mess them up.
Mutations are kind of infrequent:

rates of human genomic mutation at ~2.5×10−8 per base per generation.[12] Using data available from whole genome sequencing, the human genome mutation rate is similarly estimated to be ~1.1×10−8 per site per generation.

2) One of the hallmarks of biological entities is that they reproduce, in excess of what is needed to replace the current population with new offspring. This makes (often) many copies of all the original genes (some fish can lay more than a million eggs for example). This overproduction in a population is then trimmed back as most are destined to die without reproducing. This is an insight from Malthus which was important to Darwin's conceiving of natural selection. The copies of the mutated genes in the original parent are distributed to offspring according to the rules of genetics (depends on what kind of organism you are considering).

3) Each generation, the collection of new mutations (in either a gene or the whole genome (all the genes)) is (usually) in some way scrambled around, so that a large number of different combinations are inherited by different offspring of a given individual. This results in variability in the genetics of the offspring of a given individual.

4) Due to the elimination of the overproduced offspring from the breeding population, the most deleterious mutations will be eliminated from a population. Many mutations will not have much effect on an organism (because the organism can tolerate the changes due to a variety of mechanisms). Some mutations could be beneficial.
Breeding populations can be from hundreds of individuals to billions or more.

5) New generation of survivors accrues new mutations and reproduces. In some cases, new mutations could affect a gene previously mutated, but usually not (probability of a mutation in the same gene would be the square of a single event).
Over the long run, mutations will accumulate until an equilibrium is reached of new mutations occurring and old mutations being eliminated (by various means).

I have done many mutageneses where organisms are treated to greatly increase the rate of mutation to find new mutants for research purposes. We would aim for something like a 1/1,000 mutation rate in a particular gene (used to tune the mutagenic rate to the proper level). Too many mutations give confusing results (more than one mutation per animal is difficult to figure out quickly). Too few are boring.

The point is that natural mutation rates are not particularly high. The reproduction rate and losses from each generation can eliminate a lot of the deleterious mutations you are worried about.

In early organisms, genes might have had to be generated from non-genes in a base by base manner, but in recent organisms there is a lot of other starting material for new genes (in other genes) and many mechanisms for making copies of them. Doubling of all the genes in an organism is now well known in evolution. Copies of single genes are not uncommon. Parts of different genes can be combined (by a variety of processes) to make mozaic genes that combine functional pieces of two different genes. Creating new genes from simple point mutations (a change of a single base pair in the DNA) is also possible but would be much slower and is therefore (probably) at a kinetic disadvantage compared to copying of a gene followed by point mutations that differentiate it from the original version.

 

[Drakkith]

The first question is how hard would it be to create a new gene, from scratch, that can do something useful such as allow my body to make hydrogen gas..? This gene has to made from scratch without copying. The approach can use a trial and error strategy or a chemical logic strategy; reverse engineering from an ideal aqueous enzyme.

That's not how evolution works in modern* organisms. The overwhelming majority of change is driven by copying and/or modifying preexisting genetic material. This is by far the easiest way since it is far easier to modify an existing template to do something else than to build an entirely new gene from scratch without having it mess up the organism somewhere along the way. The construction of a gene from scratch just doesn't really happen.

*See the bottom two paragraphs for more on what I mean.

The next question is how easy would it be to mess up a gene, for an enzyme, by changing a base or two or three?

Hard to say. It all depends on the details of what the gene does, how its encoded, which mutations are happening, what the gene codes for, etc. For example, the amino acid leucine has not one, not two, but six different codons (a trio of base pairs that encodes information) that code for it: UUA, UUG, CUU, CUC, CUA, and CUG. So a gene that is used to build a protein that is made up of a large number of leucine amino acids could undergo a substantial amount of mutation without it ever affecting anything as long as those mutations changed the existing codons into another that coded for leucine.

But in other cases a single change can be devastating, if not fatal. So it really depends on the details.

In early organisms, genes might have had to be generated from non-genes in a base by base manner, but in recent organisms there is a lot of other starting material for new genes (in other genes) and many mechanisms for making copies of them.

That's a very good point. There's a reason that it took 2-3 billion years for complex multicellular life to evolve, and I'd venture that a large part of that was the fact that it took that long to build up the required variation and complexity that 'fuels' evolution. The more variation and complexity, the larger the pool of genetic material that evolution can build off of, which accelerates the evolution process.

Early life was almost certainly very, very simple and because it is extremely difficult to build up genes 'from scratch' it took billions of years to get to the point to where life really took off on an evolutionary race.

 

[Wellwisher]

Thanks, l learned something new, which now raises new questions. If the mutation rate is so low, how is it possible for humans, for example, to show so much superficial variety, such as facial and body features, or finger prints and unique eyes for computer ID scans?

It almost suggests another mechanism, beyond mutations, that leads to variety, that can all be selected. Does the brain have a role in this mechanism, providing feedback for cellular differentiation control, from our unique POV.

I was left handed as a small child, but since left handed baseball gloves were rare, I became right handed for throwing. I can no longer throw left handed with any accuracy or distance. To the outsider, they would assume I have right handed genes. I can write left handed, because there were left handed pencils back then and the taboo of left handed writing was being lifted. The taboo of left, had been a type of selection process that the brain conformed to.

Brain cells or rather neurons never replicate after an early age. They are wired to most of the cells of the body, which can and do replicate. Do they help to regulate replication in other cells and therefore help control mutation rates? If you cut your hand, you slice through nerves and the local skin cells lose process control. They replicated faster until wired back up, with the scar leaving a trace of change, due to loss of process control.

 

[FactChecker]

The number of possible combinations from the male/female pairing immediately gives a lot of variation. Also, the number of DNA components involved in many single visible characteristics adds another variation multiplier.

 

[Drakkith]

Thanks, l learned something new, which now raises new questions. If the mutation rate is so low, how is it possible for humans, for example, to show so much superficial variety, such as facial and body features, or finger prints and unique eyes for computer ID scans?

I believe most of that is due to genetic recombination during meiosis. The material for these variations already exists in the genome of an individual, and is one reason multiple children from the same parents don't look identical.

It almost suggests another mechanism, beyond mutations, that leads to variety, that can all be selected. Does the brain have a role in this mechanism, providing feedback for cellular differentiation control, from our unique POV.

Not as far as I know. Note that cellular dfferentiation is not evolution and mutations have nothing to do with this process.

I was left handed as a small child, but since left handed baseball gloves were rare, I became right handed for throwing. I can no longer throw left handed with any accuracy or distance. To the outsider, they would assume I have right handed genes. I can write left handed, because there were left handed pencils back then and the taboo of left handed writing was being lifted. The taboo of left, had been a type of selection process that the brain conformed to.

That presumes that handedness is based on a certain combination of genes, which I'm not sure it is. It might be a natural product of the normal development of the brain and mostly independent of different alleles. Even if it is determined by your genes, this is only evidence that the brain is very flexible in what it can do.

Brain cells or rather neurons never replicate after an early age. They are wired to most of the cells of the body, which can and do replicate. Do they help to regulate replication in other cells and therefore help control mutation rates?

Good question. I'm not sure how nerve cells affect the replication of other cells. But when we talk about mutation rate, we usually talk about the number of mutations per cell division. Hence why it's called a rate.

If you cut your hand, you slice through nerves and the local skin cells lose process control. They replicated faster until wired back up, with the scar leaving a trace of change, due to loss of process control.

I'm not sure what this means. The healing process is very complicated and I'm not sure I see how nerves come into the picture.

 

[Ophiolite]

If the mutation rate is so low, how is it possible for humans, for example, to show so much superficial variety, such as facial and body features, or finger prints and unique eyes for computer ID scans?

In addition to several pertinent points by others, your own example of changing handedness for baseball illustrates that many variations are environmental: nurture, not nature.
(As a point of general interest former World No. 1 tennis player Rafael Nadal, though naturally right handed, learned to play left handed, since this gives an advantage over right handed players.)

 

[BillTre]

If the mutation rate is so low, how is it possible for humans, for example, to show so much superficial variety, such as facial and body features, or finger prints and unique eyes for computer ID scans?

How to generate gene driven morphological variety: Billions of mutations, recombined in many billions of possible combinations, are tested by natural selection, each generation, for their ability to survive and reproduce, in their environment. Many of the variants that you might find in a population will not be strongly selectively advantageous or disadvantageous, so there will not be a strong selection for or against them, and they will be found in future generations. This can result in a lot of variability.

Nature vs. Nurture: There have been many analyses of how much variability in organisms is due to their inherited genetic instructions as opposed to other causes (usually considered nurture, meaning events specific to their life, affecting how they develop).
Realizing genetically identical organisms have a degree of variability among themselves, makes it possible to calculate a ration of effects on a final phenotype by comparing the variability of the trait in identical siblings with the variability among unrelated individuals with a "similar" genetic complement (like non-identicle twins or siblings).
There are many studies. Seems like they are usually around 50%-50% in the effect of Nature vs. Nurture on different traits, but there's a lot of variability.
There are cases were it will be all nature (a mutation in a gene product directly causing a phenotype, like sickle cell) and some that can be caused or strongly influenced by environmental influences (like loss of an appendage or modifying the color of fish by what you feed them).

The environmental variability can be attributed to many things:
For example, Development: Not all processes in development (going from a fertilized egg to an adult) are genetically determined at a molecular level. There are many cases in development where systems of operation are set-up and let run (such as sets of cells at certain locations in a developing embryo, they produce, release bind, and respond to small amounts of communication molecules to signal among themselves). A cell here and there may die, get misplaced, not get a signal, or not respond normally and the system can adapt and still produce a functionally useful product (adult form, able to reproduce).

These kinds of adaptive processes are repeated, over and over during development, as structures generated by one developmental process (like gastrulation endoderm, mesoderm, and ectoderm), are used as a basis for the generation of another level of structural detail (like the generating the nervous system).
Small changes in earlier stages can cascade into larger changes in later stages, like gastrulation problems, can lead to later developing nervous system problems, like spina bifida. The later structures are contingent on earlier structures.

Their communication system let's the developing system (higher level than cells) adapt to its different situation. It should be noted that in the axon and synapse do more than just release neurotransmitters. There a lot of signals going in both directions among the players interacting in this situation. In times of disturbance (wounding) the signals will change, cells will respond by changing their physiology and which genes they are expressing and how that is controlled.
Cells are not just dumb little bags. They are sophisticated information processors that can sense things around them, respond physically and biochemically, and move change position and their OS.
These kinds of adaptive processes also allow a developmental process to control greater numbers of cells (in a larger space, in a larger organism) without having to individually programming each individual cell (cells in an animal can excede the number of base pairs in the genome).

From a selection point of view, there would be no selection against a system that operates this way, unless it did not work well and produced bad results (fewer reproducing offspring). Perhaps there would be a burden of the building and maintaining the signalling systems in the various different types of cells involved (but these singnalling systems are found in many other cellular systems). Selection in favor of such a mechanism could be attributed to its greater robustness in the face of environmental challenges.

This category would include things like your wound scenario.

Does the brain have a role in this mechanism, providing feedback for cellular differentiation control, from our unique POV.

Do they help to regulate replication in other cells and therefore help control mutation rates? If you cut your hand, you slice through nerves and the local skin cells lose process control. They replicated faster until wired back up, with the scar leaving a trace of change, due to loss of process control.

Influence of the nervous system on injury responses: There are some cases where injured nerves have been shown to release substances that promote regeneration/repair responses. This usually affects things involved things like regenerating a limb or promoting cell division to repair a wound.
At a cellular level, a neuron can tell a regenerating muscle cell where to put its part (post-synaptic side) of the synapse.

Influence of somatic mutations on evolution:
In animals, any mutations of somatic cells (cells of the body (soma) that will not be genetically involved in reproducing) are not going to contribute to evolutionary change of the breeding population because mutations in cells in the body will not end up in the next generation. To get new mutations into the next generation, the cells with the mutations will have to be in the gonads (ovaries and testes), and only some of those cells will be the reproductive germ cells. The others will just be there to keep the germ cells happy (physiologically speaking).
However, mutations in somatic cells may cause cancer.
The germ cells are usually a protected set of cells (selected to be protected because they are the seat of genetic transmission (to the next generation)). Their lineage is usually separated from the rest of the cells in the body and under go relatively few cell divisions until the animal starts reproducing.

There are primitive animals where the germ cell lineages are not separated from those of somatic cells (sponges, coelenterates). Some can also reproduce by budding, when somatic mutations could transmit to the next generation. Their reproductive cells are endodermally derived pluripotent stem cells. These kinds of animals can regenerate from having their bodies cut in half, so germ cell distribution would be adaptive.

Do they help to regulate replication in other cells and therefore help control mutation rates?

Regulating replication and mutation rates are two separate things.
I suppose an overly rapid rate of division could result in cell division before DNA copying is done or before chromosomes are properly lined up and separated, but normally there are lots of molecular mechanisms in cell division (mitosis) to prevent these things.

Brain cells or rather neurons never replicate after an early age.

Yes, but:
A few cases are now known (for >20 years) where new brain cells have been produced in mammals. Its not the brain cells dividing however, its precursor cells dividing and making new baby neurons.

 

[Wellwisher]

My interest is based on the water side of life. Water offers another way to look at the same things. I’ll also impacts how one sees randomness.

Life is composed of organics and ions working together within an aqueous continuum. Contemporary wisdom tries to explain life and life processes in an organic-centric way. However, none of the organic configurations and processes will work properly without water. You cannot replace water with any other solvent, or else nothing will work since randomness will increase in term of folding. Water limits randomness in cells since the free energy needs of water dominate. This means everything has a sweet spot in terms of configuration and position; water and oil affect.

How the brain controls replication and differentiation of cell, is not based on an organic explanation. Rather the brain can control the aqueous environment outside the cells, thereby impacting their internal aqueous equilibrium. When cell cycles happen the membrane potential lowers due to ion reversal caused by the fluidity of the membrane. This impacts internal aqueous equilibrium; replication mode. Neurons have the highest membrane potential of all cells and they do not replicate. The nerve connection will inhibit the cell cycle because the control cell’s membrane potential is held hostage. It can’t formed the correct internal aqueous equilibrium mode to replicate freely.

The large size of dinosaurs was probably due to their smaller brains unable to inhibit body cell replication. Their brain could maintain differentiation control; internal equilibrium, but not fully inhibit replication. Since the cells of the dinosaur body were dominant, growing, the brain cells would see a potential to replication. The brain grew.

One of the benefits of neurons never replicating is this allows memory to perpetuate. Cell cycles cause cellular structures to dissociate so they can be divided. This material will reform through bulk aqueous equilibrium processes. If a neuron did this, you would lose memory detail during bulk reformation. Is is likely the growing dinosaur brain would sort reboot as it grew, back to a base mode; loss of memory. This helped build the basic equilibrium foundations of consciousness; instinctive impulse

 

[Drakkith]

I stand by what I said previously, and I think you're just making stuff up now.

 

[Wellwisher]

I stand by what I said previously, and I think you're just making stuff up now.

You are partially correct. These are predictions based on decades of studying and pondering hydrogen bonding and water and how these interface to biomaterials. This aqueous side of life is not taught so I try to teach it.

For example, there is a double helix of water within the DNA double helix, yet the DNA is rarely shown this way, in any textbook. The DNA will not work without it, yet this is ignored and never taught. I bet if textbooks showed the DNA with the water helixes, new questions would be raised and new doors would open.

I remember years ago wondering why some of the bases of DNA has more hydrogen bonding hydrogen than it used. It turned out these were ear marked for the water helixes.

 

[BillTre]

Just having "another way to look at the same things" does not mean that makes any sense.
If you have some new way of explaining things you want someone else to take interest in, you should show:

• how it explains things that are not explained well
• show its is still compatible with other unchallenged concepts in the field

You are not doing this.
You also seem to have zero support (based upon you inability to find any thing published anywhere that supports your claims).

This stuff is getting really confused:

Rather the brain can control the aqueous environment outside the cells, thereby impacting their internal aqueous equilibrium. When cell cycles happen the membrane potential lowers due to ion reversal caused by the fluidity of the membrane.

Any control the brain might have on "the aqueous environment outside the cells" would be through controlling the water and ion flew in and out of the body. this is completely different from any membrane caused changes in ion content during cell division.

The nerve connection will inhibit the cell cycle because the control cell’s membrane potential is held hostage. It can’t formed the correct internal aqueous equilibrium mode to replicate freely.

This is your unsupported conjecture. I don't thing there is any proof of this.
If there is please reference or link to it.

The large size of dinosaurs was probably due to their smaller brains unable to inhibit body cell replication.

This is fantasy.

Their brain could maintain differentiation control; internal equilibrium, but not fully inhibit replication. Since the cells of the dinosaur body were dominant, growing, the brain cells would see a potential to replication. The brain grew.

It is hard to make any sense out of this.

These are predictions based on decades of studying and pondering hydrogen bonding and water and how these interface to biomaterials. This aqueous side of life is not taught so I try to teach it.

I beg to differ.
In the 1980's I took a physical biochemistry course what covered exactly these kinds of phenomena.
Not something new.
Your teaching is completely unconvincing without any kind of referencing.

I remember years ago wondering why some of the bases of DNA has more hydrogen bonding hydrogen than it used.

Would not having a more distinctive binding structure for the two different sets of base pairs be enough? Proper binding (which having a distinction of a 2 vs. 3 H-bond recognition surface might conceivably strengthen) is basic to all maintaining of genetic information and would be strongly selected for.

It turned out these were ear marked for the water helixes.

Does this mean that there was a plan before DNA was made for the water molecules to be in particular places?

 

[Drakkith]

For example, there is a double helix of water within the DNA double helix,

Unless this is composed of ice, then there is no water helix, since liquid water doesn't form a solid structure like the DNA molecule is.

These are predictions based on decades of studying and pondering hydrogen bonding and water and how these interface to biomaterials. This aqueous side of life is not taught so I try to teach it.

This is nonsense. The interaction of water with other molecules inside the cell is extremely important to biochemistry, and it is ludicrous that it isn't taught where it is needed. You might be right in that it isn't taught in a lower level biochemistry class (I don't know if it is or isn't), but you can be certain that the scientists working on understanding protein folding and other advanced topics understand how water functions in the cell.

I think the issue is that you're elevating water's function in the context of evolution without really having a valid reason for it. As I already said, these details just aren't that important to the general principles of evolution. Are they important for the details of how life on this planet formed and functions? Absolutely. But whether it's water or something else, the general ideas of biological evolution still apply.

We don't talk about water when talking about evolution for the same reasons we don't talk about the properties of sulfur-based molecules inside the cell. Or any other specifics. They are simply different topics. Biochemistry isn't evolution, even though the two are obviously related.

 

[berkeman]

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