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I'm not quite sure what this paper is saying, but it doesn't seem to be "mutations are non-random".
This one does, but it's talking about cancer, not reproduction, which offers fundamentally different challenges. We know the mutations that lead to cancer are not entirely random; that's how we can classify certain things as carcinogenic or not!
That's because biologists have given up on mutations as concerning reproduction long ago in real life versus imaginations of the mind. The only place mutations were studied as respecting reproduction is in plant and animal husbandry. Where every single biologist involved agreed mutations were not viable as a new source of information. Where every single experiment failed to produce the outcomes expected.
http://www.weloennig.de/Loennig-Long-Version-of-Law-of-Recurrent-Variation.pdf
Because this randomness is, to some extent, conserved. It's not like the whole genome fluctuates wildly with every generation. Keep in mind we're talking about populations, not individuals, and at a population level, some mutations will be selected against and some mutations will be kept. Although even in vastly simplified models, where such things as gene conservation are not taken into account, you will still get consistent nested hierarchies, as the CDK007 video makes perfectly clear.
No, we are talking about individuals - not populations. A random mutation would occur in an individual - and not be passed on to the rest of the population unless that individual or its descendants mate with every single other one - or all the others die off and only those with the mutation survive. Don't try those strawmen please, I have asked you this several times. Random mutations do not spread to the population by magic. If someone in LA had a random mutation - at most it would only pass to their descendants - leaving those in New York completely unaffected. In a population of billions, the random mutation will always be limited to those who belong to that particular family line and will never become fixed in the general population.
So at the beginning, we have one population. This population undergoes various mutations. Then, that population splits, and all of the mutations thus far are conserved by each of the two groups. Then, each of these groups undergoes various mutations. Now, consider a separate group, which started with the same genetic material but was completely distinct from the start. It undergoes random genetic mutation. Will its genetics appear similar to the other group? No. Given the random nature of the mutations themselves, similar mutations might be selected for (assuming these groups had the same selection pressure), but you will not end up with the same pattern of similarities and differences that you would among the first group, or its divergent branches. However, those divergent branches will show a pattern of similarities, because they both got those specific mutations from their shared ancestor.
No, in the beginning we have two breeds - one male, one female - each one containing half the genetic code for everything that exists or will exist. Some may be lost through the ages - but nothing new is ever added. What already exists is merely transcribed into a new dominant or recessive order. There was no mutation involved - merely the recombination of genes and new dominant and recessive traits as observed in every single reproduction experiment performed in plant and animal husbandry. (above citation)
This is a large part of why this:
"when nested hierarchies are observed to occur in breeding pairs"
Is not a viable model. These nested hierarchies occur far, far above the level where your proposed mechanism would work
And yet we see exactly those nested hierarchy's at exactly the level of breed mating with breed. You observe them nowhere else but at the family level, no matter how much you might dream it to be otherwise.

You can make all the claims you want - but in the end they are just claims and wishful thinking - countered by the direct empirical evidence. Only when two things mate - does a hierarchy tree come into existence. No tree exists from one individual anywhere on the planet.
The fact that we can observe this nested hierarchy throughout all of nature, and that it concords with morphology, with individual genes, with embryology, with ERVs... All of this is empirical observation that points to one thing and one thing only: common ancestry. Yes, in the last few hundred years that we've been looking, we haven't seen massive divergences in morphology. We wouldn't expect to. But to claim that there is no empirical observation of common ancestry as a result is completely wrong and ignores the strongest and most important evidence evolution has to offer.
You have no choice but to expect large divergences - just look at your claimed whale evolution for example. There's nothing gradual about it. So now you go against your own claims - when gradual changes is what is expected from mating pairs as genes recombine into new dominant and recessive traits - gradual as in the picture above - only minor differences between parent and offspring.
Abiogenesis is a field in its infancy; actually establishing what the first lifeforms looked like is almost impossible, given that they were almost certainly microscopic soft cells that would not leave much in terms of fossils. Brooker is right; the origin of life is still largely an unknown. This does nothing to detract from the theory of evolution, which deals with life after it has started to exist.
So now you are promoting spontaneous generation?
https://en.wikipedia.org/wiki/Abiogenesis
"Belief in the present ongoing spontaneous generation of certain forms of life from non-living matter goes back to Aristotle and ancient Greek philosophy and continued to have support in Western scholarship until the 19th century. This belief was paired with a belief in heterogenesis, i.e., that one form of life derived from a different form (e.g., bees from flowers). Classical notions of spontaneous generation, which can be considered under the modern term abiogenesis, held that certain complex, living organisms are generated by decaying organic substances."
https://en.wikipedia.org/wiki/Spontaneous_generation
"Spontaneous generation or anomalous generation is an obsolete body of thought on the ordinary formation of living organisms without descent from similar organisms.
So now you propose the decent of living organisms without the descent from similar living organisms????? Are evolutionists really that lost, that they would resurrect an obsolete body of thought to defend their falsified theory? All you have done is changed bees from flowers into humans from chimps.
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