The following excerpts come from an article on the website of Answers in Genesis about the origin of mitochondria . Although they have a different goal (related to creationism), often their analyses of contemporary science are often quite insightful. I must admit that the endosymbiotic theory has more in common with creationism than with science.
As I find as well, one of the problems with the endosymbiotic theory is that it forms a irreducibly complex systems when you look at protein transport. Proteins needs to be imported in mitochondria for their function. So the question arises, how could these multistep processes have evolved from scratch. Apparently it takes an engineer to see these things as they are hardly ever brought up by biologists, maybe becuase in essence they provide a falsification for the theory.
Complex relationships between cells and organelles
Organelles such as mitochondria and plastids have extremely integrated and complex relationships with other parts of the cell where they reside. One of those relationships is the ability to transport organelle proteins that are encoded by genes in the nucleus and formed in other parts of the cell back into the organelle where they are needed for the organelle’s proper functioning. Endosymbiotic theory proposes that the genes for organelle proteins got transferred to the nucleus as part of a reduction process by the bacteria/cyanobacteria as they became a permanent part of the cell. The problem for the cell was that it then had to “evolve” transport pathways to bring the organelle proteins (made in the cell) back to the organelle. The transport pathway is composed of many proteins that work together to bring the protein into the organelle. Each organelle has specific pathways (which differ between organelles) to accomplish this and there are typically several different pathways needed to bring a variety of proteins into the organelle. For example, five pathways have been identified so far for transport of proteins into mitochondria.2 Each pathway is composed of several proteins; some are shared among the pathways, while others are unique to a pathway.2 The case is similar for plastids.
Since mutations are the only “tool” evolution has to “work” with, and since evolutionists have yet to show how new information could be added to a genome without design, mutations cannot account for the origin of these protein-transport pathways. If there is no way to form these pathways, then the organelles would become obsolete once they started transferring their genes to the nucleus. Furthermore, if there was no pathway to return the proteins to the organelle, then the organelles would stop functioning and would no longer be selected for because they did not serve a purpose.
Another important aspects is the lack of intermediates, which has become even worse with the apparent rejection of many protists as primitive. The endosymbiotic theory has thus become a theory without mechanistic counterpart.
Intermediates not found
Unlike plants, animals and humans, where fossil evidence is used to formulate evolutionary relationships, bacteria and protists are accepted to have living “intermediates” that help elucidate these relationships. For many years, the eukaryotic protists Archezoa, a now abandoned classification, were thought to lack mitochondria and to have branched off before the mitochondrial endosymbiotic event.3 However, recent findings have shown that Archezoa have mitochondria-like structures called mitosomes or hydrogenosomes.3 They share similarities with mitochondria, such as membrane structure and protein transport machinery, but differ in function.3 So the search goes on for a eukaryote without mitochondria. But even if one were found, that still would not prove common ancestry and a later endosymbiotic event. Similarity is at best merely consistent with common ancestry.
Also a nice piece about Hatena which may be considered an intermediate is quite interesting. To every high school student it would be apparent that this does not even remotely look like the way the endosymbiotic event that created mitochondria would have occurred.
Scientists claim that Hatena, a recently discovered protist, is a “snapshot” of an endosymbiotic event that has not yet reached completion. This organism has a unique life cycle. It contains an algal symbiont, but when it divides only one of the daughter cells gets the alga.4 The other daughter cell has a feeding apparatus that allows it to engulf an alga.4 It only engulfs a certain species of alga, and the alga retains many of its cellular components, such as a nucleus4 (these are not found in plastids where endosymbiosis is thought to have reached completion). In a news article about the findings, one biologist commented, “Whatever you need to make that [the algal symbiont] a permanent part is not occurring here. Maybe in a hundred millions [sic] years it will figure it out.”