Stable Instability

Stable Instability

Introduction.
Experiment.
Molecular Regularities.
Role of Sexual Reproduction.
Multi-Staged Evolutionary Complication of Reproduction.
Quiz.
Conclusions.

1. Introduction.

(1)
This articles contains generalized analysis of role of sexual reproduction from point of biological evolution and intracellular chemistry, especially in the respect of ease of formation of combination of chromosomes which can be predictably severely disruptive for organism (without direct influence of mutations).

(2)
How does this article relates to knowledge of everything.
This subject is, actually, about one of the questions that constitute knowledge about everything, but more correct question should be: how does biology concern knowledge of everything from point of generalized basic understanding of the universe.
And the answer is that, roughly speaking, it doesn't.
The matter is that biology is significantly higher level than physics and chemistry.
And the (next level) problem is that in its correct, more or less perfect state that provides understanding and predictability of observable biological processes, it is much more complex than physics and chemistry, because they are here just a basic and you have to deal with much higher complexities (of interacting atoms, molecules, cells and etc. up) based on that basis.

Obviously, this question can be solved, in its more or less perfect state, only by [super]computers, which can do correct layered computations from atoms to molecules to cells and up.

This is the idea of what to expect from this, and some other articles (like previous about chemistry and biology), at this site.
There was statement about neutron (about it absence), it is very basic statement with very basic attendant descriptions, and it had "absoluteness" label.
The rest, with advance to higher levels (to chemistry and higher to biology), has some/high degree of approximations and abstracting, or even just thoughts and assumptions.

(3)
I just had fleeting thought about how do some of these things work at a level of cells and organisms,
spent a few of time thinking about it and came to some generalized conceptual conclusions,
and it's not a problem to share it.

And the thought, or question, was the following: how does initial combination of chromosomes (that came from different organisms) affect development of a body (especially) from point that it can very easy form combination that is very destructive for organism, and what's the reason and source of such drastic (and predictable) instability (or destructiveness).

The subject of role of sexual reproduction in evolution was already the results and conclusions, second part of them, besides the initial goal of analysing intracellular chemical characteristics for the described problem.

2. Experiment.

I'll start from the case I had chance to observe long ago, when I was young.

One of our neighbours had a cat. Actually almost all of our neighbours had cats, and I had a cat, and there was nothing peculiar about that exact mentioned cat.
That cat was female and at some point had kittens.
They kept one of the kittens (male), and gave away the rest, so they had two cats at home.
The kitten grew up.
And after a while, I noticed they had kittens again.
I instantly noticed one (strange) thing about those kittens.
They looked like an ordinary cats, but there back parts were like half frozen.
Their hind legs had ability to move at the very best of 20% of an ordinary cat should have.
I did not see them for long, most likely they were deadened as severely ill.

The whole thing initially looked strange, from the fact that they kept one cat of the offspring with opposite sex at a home.
I studied biology at school.
I, at least at a level of basic regularities, clearly new that there exist such things like plants/animals selection, and that close relatives cannot mate because of high possibility of defects.

It was pretty pathetic, but... stuff happens, and life goes on.
Well... almost.
In about half a year or a year later this exact situation repeated.
All, or most, (at least all that were not lying, but trying to walk) kittens from their second brood had the same defect.

Plain logical question: wtf?
It was pretty shocking because even children know about such things.
Obviously they did not know it even close, and probably were keeping it at the level "gods punish us for our sins" (or "gods of our cats punish them for their sins"),
but, as I found out later, advanced biology was forbidden in Soviets, so they simply were not taught such things,
what partially justifies their unintentional experiments.

3. Molecular Regularities.

The other question is not to owners of that cats, but to molecular mechanisms.
Why, and how.

Initially the problem narrows to chromosomes, as they should be the only things that are taken from male cell.

One of the functions of chromosomes is to generate building blocks and other components used in cell, besides that they can/should divide themselves.

Some of the known facts about sexual reproduction:

Close relatives can produce rough defects in offspring.
Pure lines.
These are the specimens of offspring who survived after application of item 1 above.
They are usually characterized by low(er) variation inside chromosomes, and partial, or in general, depressed functionality.
Heterosis.
Burst of activity of processes in offspring when different pure lines are crossed.
It's characterized as having high diversity inside chromosomes.

Now this has to be mapped to (for now generalized approximate) intracellular molecular regularities,
luckily initially narrowed to activities of pretty uniform and primitive components like chromosomes (in the light of complexity of the whole cell),
as source of the current question.

The basic physical law we're going to employ, and which actually pretty clearly and in straightforward way (almost entirely) explains the essence of the question, is the following:
chemical forces are based on force of attraction.
For molecules, force of interconnection of molecules is dependent on fitness of molecules, what is based on (a) fitness of exact (close) atoms, and (b) the spatial structures of molecules. (Under fitness is implied ability to form stronger bonds)

The translates to the following basic rule at the level of chromosomes:
ability to replicate (completely or partially/locally) is dependent on exact combination of sub-components at exact places of molecules in the respect of (average) force of interconnection of (parts) of strands.

This is all of the mystery.

The rest is probabilities and statistics, and a few of local technics based on the rule above (possibly like formation of local unconnected loops from (one side) with their possible later elimination, and other existing descriptions of phenomenons like chromosomal translocations, deletions... etc).

Pure-lining (the cats in that experiment were force to do) vs Heterosis,
or simply the basic regularity in the respect of successive alterations of chromosomes during sexual reproduction,
in a nutshell is the following:

Diverse chromosomes are (most/more likely) badly fitted and thus form on average weaker general connections between molecules and as a result have higher rate of replication (of self and/or of parts).
During recombination of DNAs in gametes (where divided chromosome is more prone to alterations than more stable for current case multiline molecule) local alterations tend to use/replace better fitted components, what is directly based on higher forces of attraction of such components (together with chaotic motion of surrounding components as the other mean of this mechanism), thus leading to higher average forces of interconnection across whole molecule and as a result lower subsequent replication rate.

This also shows that rate of local replications can vary depending on strength of connections at that region.
What matter for cell (in the respect of chromosomes) is the resulting total output of products with exact structure, not exact position where they are generated, or amount of points at chromosome capable of effectively generating such products.

The conclusions for evolutionary development is the following:
Without introduction of chromosomal diversity, replicating activity of chromosomes (gradually) fades (with each next recombination at gamete) (only during fertilization? looks like mainly yes, if it's most vulnerable point because of divided state of chromosomes) till some stable state,
or it destroys this line/group if reduction of replicating activity leads to degrade of functions necessary for survivability below critical threshold, (what may be dependent not on the ability to replicate entire strand, but on more narrow bottleneck, like rate of production of exact crucial components/sub-parts).

Pretty fundamental distinction of changes introduced by sexual reproduction from mutations is that they (a) have gradual influence during development of an organism and (b) are based more on deficit/excess of exact products, than on initially predefined strict structural changes.
In other words, even if such changes are vital, in main part its expressed as indirect influence of secondary traits.
That mentioned cats did not have two heads, or fifth spare extremity, but just partially underdeveloped functionality.

Some of the Characteristics of Natural Distribution of Chromosomal Diversity.

There was shown very nice characteristic regarding distribution of diversity inside chromosomes per species:
low chromosomal diversity is characteristic for species at top of consumption pyramid of ecosystem (lions, polar bears, cheetah), high for bottom.

Primary reason for such characteristic of vertical distribution of diversities is obvious and it's size of population, where higher number of species provides higher number of mutations, and as a result higher chromosomal diversity,
but for species at top more probable could be appearance of successful chromosomal combination not through intraspecies extensive selection,
but selection as introductory threshold for appearance of species (since there's no room for wide selection).

Another thought:
lesser chromosomal diversity across population (on average) should require larger chromosomes to provide the same level of activities that can do smaller chromosomes with bigger chromosomal diversity across population,
though this should have reversed dependency on rate of growth (/replication of the whole chromosome).

"Genetics" Revisited.

In the light of conclusions made above, I should acknowledge that some of the things of "genetics" in some part concern reality,
but taking into consideration drastic shouting incorrectness of the very basis, which postulates that some of the molecules contain inside of themselves other molecules/information (what was the source of my (maybe sometimes not very rightfully) increased critic),
often in such cases it should be just accidental coincidences.

Two (main) things to (re)consider are the following:

Level of activity of parts of chromosome may vary across chromosome.
In the respect of methods, there should be a bit opposite direction this subject (of rate of generation of exact products by chromosomes) has to be approached at, because the fact that organism survived means that it already has necessary level of chromosomal activities along the whole line (that allowed it to grow to acceptable size with acceptable level of internal processes), and the defining distinction (in this respect) should be searched at a level of amount of difference in production of different components which is enough to trigger some process or which is enough for acceptable distinguishing of traits/processes (at macro-level).
Functioning of a cell is actually dependent on (averaged) exact number of exact molecules (products of chromosomes),
but the whole thing here is almost entirely about the resulting number of products at a level of outputs of chromosomes, and not about exact positions inside of chromosomes which generate such products or their number.

Also it should be noted that there is/may be no direct/proportional correspondence between
(1) number of atoms in chromosome and number and rate of generated materials by chromosomes (not including here chromosomes themselves), and
(2) rate of replication of chromosomes and number and rate of generated materials by chromosomes,
because one of the main parameters here is exact combination of sub-parts, what defines average force of connection at exact region and average force of connection along the whole line, and as a result (average probable) time of replication, of sub-part or total for the whole line.

4. Role of Sexual Reproduction.

The main fact is already obvious and it's the following:

From point of existence of exact species, and representatives of this species which are to be born, sexual reproduction is (in its significant part of outcomes) (extremely) destructive for both, exact species and species as the whole.
Only the specimens who were born without defects imposed by sexual reproduction are indifferent to this trait.
From point of evolutionary development, as it was known long ago, this is useful feature.

Taking into consideration that lots of people do not know basic rules of selection,
for all other organisms this is pretty standard part of outcomes.

Asexual reproduction provides unbelievably higher stability of outcomes, but at the same time unbelievably lower dynamics of changes/adaptation (in environment with pretty high rate of mutations per organism).

I think most of species would vote for more stable development,
but what matters for evolution is not exact individual, but general statistics of survival (in this context more at a level of species),
so sexual reproduction "unintentionally" has become very widespread because of benefits (for interspecies competition) expressed at higher resulting statistical outputs (with basic tools in form of higher dynamics of changes and adaptation and as result domination),
disregarding the fact that it (potentially) is very destructive for both, exact individual and species (because of possibility of providing combinations of chromosomes which in free environment cannot be resolved back to more stable and more pure lines, thus leading to possible gradual degrade of survivability and possible disappearance).

There's also (possible) situation when more complex forms are dependent on more simple, reproducible asexually, and disregarding of the fact that development of higher forms is much more dynamical, lower forms will be more ubiquitous/numerous as representatives of lower layer of consumption pyramid.
Though relation more complex/less complex above may be omitted and it can be just dependency "sexually reproducing" depend on "asexually reproducing".

In the previous articles was considered (unbiased/indifferent) appearance of sexual reproduction at a level of mutations,
but, above/after the fact of its appearance,
further analysis of the dynamics of development (in the conditions of existing mutations / at higher level) still can be very useful,
and one of the most interesting and unexpected conclusions in this respect is that:

sexual reproduction at low (time) scale of existence is (extremely) unfavourable for exact individuals, as carrying almost nothing except possibility of problems (for offspring), (and can be destructive for the whole species, though with low probability for large population).

Evolution has spent billions of years to develop complex species, like that cats.
This is amazing process and outcome.
But the fact that elementary permutations of representatives of species can make their ordinary and basic processes (reproduction) non-functional and (mostly) destructive for offspring is not less interesting and amazing.

That's where the name of the articles comes from.

Stability of general evolutionary development with instability at a level of (sexually reproducing) exact species and individuals.

5. Multi-Staged Evolutionary Complication of Reproduction.

Information in this topic is obvious after the previous articles, but it can be useful to repeat a few of things in the context of sexual reproduction.

Simplest organisms can create exact copies.
More complex require some significant additional growth after separation to become full-fledged organism and be ready to survive in free environment.

For more complex number of stages increase further:
gamete → pre-natal development → post-natal development.

Each stage is not abstraction, but directed addition/supply of materials/information to the developing organism to develop it to basic intendant state.

The basic axiom here is the following (what's basically simply is physical law of conservation):
the more complex organism is, the less information about it is represented in gamete.

Unicellular (or more simple) organisms have 100% of information about them encoded in the new born organism, for more complex this number is lesser, and, roughly/directly speaking, is proportional to the mass of full-fledged organism.

The key thing here is that post-natal development for complex species (like mammals) is almost exactly the same as pre-natal.

For such primitive species like fish, embryo + egg may be enough for development of full-fledged organism because of primitive hardcoded behaviour.

New born mammal, roughly speaking, can compete only with vegetables.
It still requires directed supply of unbelievable amount of materials/information to make necessary physical changes to complete formation of organism with necessary basic traits and behaviour.

The process of learning (for instance to hunt of cheetahs) physically is the same directed development of organism as it was at pre-natal stage, and exactly the same important, and without this stage this vital for survival information in small cheetahs will not appear out of nowhere.

The role of gamete in reproduction for (such) complex organisms is almost negligible.

6. Quiz.

Just was clarifying a few things while writing this articles and came across interesting fact: unravelled DNA can reach moon.
Now, take a look at (1) picture of replication of DNA (at wikipedia, or its copy at previous article) and (2) length (time) of division of chromosomes (what is only part of time of division of cell), and calculate speed the "helicase" should have ))
I would also note that its path is non-linear and would ask how does it change direction (correctly), and how it supports/restores that directional speed after collisions, and (!!) what's the reason of such directional motion (currently it all looks like severe violation of basic physical laws of conservation), or other physical particularities of that process, like side effects of friction at such speed, but this is going to be quiz number two.

From point of correct biological views based on correct chemistry, an ordinary chaotic motion (of free components) with natural (dynamical/changing) restrictions inside of a cell is plain enough, with lots of replicating and other processes going in parallel along one complex component/molecule
(and, actually, at most times it should be possible only in parallel/collective way, since sufficiency for most cases of simple involvement of single molecule would tend to prove instability that (far) exceeds observable, while start/completion of complex processes, or division of complex organelles, that requires passing some threshold of applied forces that can be provided by exact positioning of exact molecules along component, and completion of reaction based on exact superposition of influences of exact srrounding molecules, is more probable from point of sustaining both, complexity and (acceptable) stability, or, more nicely put: stability of complex processes,
and this is partially covered by more generalized descriptions like recognition of molecular patterns and replication).
So, the time of completion of some intracellular process is basically based on two main parameters: (1) average speed of components, (2) concentration of exact components.
The result in such environment, or average possibilities of appearance of exact components in exact places, in its main part is pretty predictable/calculable thing.

7. Conclusions.

The following topics were considered and clarified:

Molecular mechanisms of outer expression of activity of chromosomes (as amount of generated products, including self-replication), and their relation to (a) chromosomal diversity, (b) sexual reproduction, and (c) evolutionary development.
Evolutionary role of sexual reproduction at each level of the tree: biological evolution at a level of species as elements of development → intraspiceis influence → organism.

One of the most nice things of the whole story in this article is that:

there appeared to be clear (and straightforward/primitive) basic substantiation/understanding of one of the major means of biological evolution (sexual reproduction) of complex multicellular organisms at the level of molecular interactions of a cell (at chromosomes, what is defining governing point for the current subject).