1) Complexity: The scientists are unable to work out some of the aspects of gene phylogeny in their labs. How could these develop randomly, spontaneously and unaided? - Vidqun
You have linked this comment to a scientific paper that describes in astonishing detail how genes were transferred from chloroplasts - previously free-living cyanobacteria - to the nucleus of plant cells and how enzymes coded by those genes are returned to chloroplasts.
The level of information in that paper and the detail of the very specific genetic interactions as a direct result of endosymbiosis that is described by Wm Martin and Reinhold Herrmann in that paper is astonishing. Could you possibly ask for any stronger evidence of the evolutionary history of plant cells?
In the paragraph you refer to Martin & Herrmann have just described the phylogeny of key genes and then they comment that in the case of other nuclear genes their phylogeny cannot be stated with certainty. This sort of modesty should inspire confidence but you pick out thins sentence and try to use it to cast doubt on the entire theory of evolution. That is truly desperate.
2) Amoebal Immunity: This is a simple immunity mechanism integral to Amoebae, similar to our more complicated immune response. This is not a random process and cannot develop spontaneously. It has been designed that way. In addition, there’s a huge chasm between Amoebal immunity and mammalian immunity, as I remarked earlier. - Vidqun
This time you refer to the concluding sentence from a paper by Kwang Jeon describing the way that production of a specific enzyme is switched to an alternative gene in the amoebae when it is has a symbiont bacteria. The paper is not about an immune response. Did you even read the paper or did you just quote-mine from the conclusion? Did you understand the paper?
The work of Jeon shows that endosymbiosis does occur and does lead to gene transfer. It was a case of a prokaryote invading an amoebae - a prokaryote. The event that led to eukaryotic cells involved a prokaryote and and an archaea. There were still a few million years of evolution to go before mammalian immune systems made an appearance.
3) Human cancer cells remain human even though their nuclear material had been altered (not a new species) - Vidqun
Again you don't provide any link to your source so I don't know the context. Regardless of that, your comment is a total red herring. A virus that causes cancer has nothing at all to do with endosymbiosis.
4) Natural selection: Interestingly, the xD amoebae have not been improved. Their chances of survival have been considerably reduced. No super or improved organism with the proses of endosymbiosis, I’m afraid. - Vidqun
You seem to keep mixing up an event that took place millions of years ago involving a prokaryote and an archaea with one that happened in Jeon's lab in the 60s when a bacteria invaded a eukaryote.
The evidence for the fact that mitochondria were once free-living bacteria is beyond sensible dispute. If you look at the OP you will see a summary of some of it. Jeon's work is an interesting bit of evidence. It proves that endosymbiosis happens. Whether or not Jeon's amoebae were "improved" is irrelevant. Earlier you accepted the fact of endosymbiosis. Have you changed your mind?
5) Theoretically then, super or improved organisms should result from the following processes, even in the lab. We see, this is not the case. - Vidqun
Now you refer to the abstract of an article entitled "Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes".
Access to the full paper is by payment so I assume you haven't read it. From the abstract it provides evidence that...
"DNA is transferred from organelles to the nucleus at frequencies that were previously unimaginable. ...This relentless influx of organelle DNA has abolished organelle autonomy and increased nuclear complexity."
Could there be any better evidence for endosymbiosis?
Organelles swapping genes with host cells to their mutual benefit is "ubiquitous". I have not got a clue what you mean "super or improved organisms" and I am sure you don't either.
You are building the case for the symbiotic origin of mitochondria but you don't seem to notice. Strange.
6) The sentence reads: "Members of the recA/RAD51 family have functions that have differentiated during evolution." The next sentence reads: "However, the evolutionary history and relationships of these members remains unclear." Isn't that accepting things at face value without evidence? - Vidqun
It just keeps getting better and better.
Now you cite another abstract (no link of course) called "Origins and evolution of the recA/RAD51 gene family: evidence for ancient gene duplication and endosymbiotic gene transfer."
If you read the article you would have seen that it presents pages of evidence comparing homologs of a specific gene in prokaryotes, archaea and eukaryotes. The authors unpick a very complex history involving differentiated during evolution.
Why you think a paper presenting detailed evidence for endosymbiosis is somehow evidence to the contrary is a mystery.
7) Mitochondria and Chloroplasts: If things took place randomly and spontaneously, Why did chloroplasts not find their way into the animal and human genome? - Vidqun
This actually qualifies as a dumb question. It is exactly like asking why zebras don't have wings. Plants stay still and use chloroplasts to absorb energy from the sun to produce hydrocarbons. Animals move and consume these hydrocarbons turning them into ATP via mitochondria. Different economies.
8) Again, the fossil record is full of gaps and do not support symbiogenesis as the principal mechanism of developing life forms. - Vidqun
Now you cite an article called "Gene transfer to the nucleus and the evolution of chloroplasts".
The abstract begins by pointing out that the fossil record is not the place to look for evidence for the phylogeny of chloroplast genes. Why should that surprise you? Why are you pretending that supports your case?
A typical eukaryote is about a tenth of a millimeter across and it is a poor candidate for fossilisation. The paper is specifically about the DNA evidence for the evolution of chloroplasts.
Coming from a professional scientist this is just bizarre.
9) Unnatural Gene Manipulation by Researchers: If it was an open, random, spontaneous process to begin with, why is it now a closed process that can only be manipulated with the help o the genetic engineers? - Vidqun
Finally you refer to another paper by Wm Martin called "Gene transfer from organelles to the nucleus:Frequent and in big chunks"
The paper describes the study of plant genomes to calculate the percentage of nuclear genomes that originated in organelles. Experiments described in the paper are for the purpose of studying the mechanism of gene transfer. You have totally drawn the wrong conclusion as if you didn't actually read the paper.
Every one of you so-called objections are based on a total misreading of the papers you misuse to support them.
You are either being dishonest or you actually don't understand what you are reading. Perhaps it's a combination of both. Copy-pasting chunks from scientific papers in an attempt to impress the casual reader is intellectually dishonest.
Normally I would simply disregard this sort of tactic but you started by boasting about your professional qualifications so I decided to invest the time to respond.
I will explain more about the process of and evidence for endosymbiosis in part two.