That said, here are a couple of challenges noted for her own theory of endosymbiosis (some life forms evolved by swallowing others (bacteria might have swallowed mitochondria when the latter was an independent life form), which then became part of their inner workings, resulting in greater complexity):
Mitochondria and bacteria are different
1) Mitochondria are similar to bacteria in some relatively trivial ways. They both have ribosomes, and are similar in their size, single circular chromosome that lack of introns, and are bounded by a double-membrane.
2) However, there are also significant differences between the bacterium and the mitochondrion that wear down the comparison. These are in 2 general categories: structural differences and sequence differences between organelles and prokaryotes. Examples:
(a) While some regions are conserved, mitochondrial ribosomes can have very different sequences and structure and operation from bacterial ribosomes.
(b) Also similar sequences could result from other mechanisms than endosymbiosis (lateral gene transfer). Indeed, mitochondrial genomes can contain a mixture eukaryotic, archaeal and eubacterial sequences–this is different from what is expected if mitochondria are of eubacterial origin only
The mechanism of endosymbiosis is not stated
The difficult thing with the endosymbiotic theory is that it proposes no real mechanism and most textbooks show the simplistic picture of a cell that swallows another cell that becomes a mitochondrion. Unfortunately, it is not so simple as that. There is a difference between the process of endosymbiosis and its incorporation in the germline, necessitating genetic changes. What were those changes? What was the host? Was it a fusion, was it engulfment, how did the mitochondrion get its second membrane, how did two genomes in one cell integrate and coordinate? The theory is also strongly teleological, illustrated by the widely used term ‘enslavement’. But how do you enslave another cell, how do you replace its proteins and genes without affecting existing functions? The existence of obligate bacterial endosymbionts in some present eukaryotes is often presented as a substitute for a mechanism, but they remain bacteria and give not rise to new organelles. So, before we can speak of the endosymbiotic as a testable scientific theory, we need a mechanistic scenario which is lacking at the moment.
When we do try to envision a mechanistic scenario based on the endosymbiotic theory, we quickly run into problems. Genetic mutations that allow bacteria to thrive in the cytoplasm would not be strategic for survival. Anaerobic cells normally do not survive in environment that contains oxygen, while the endosymbiont would need oxygen in order to present fitness advantage. The two organisms would initially compete for energy sources since bacteria are users of ATP and do not export it. The extensive gene transfer that is needed in the endosymbiotic theory would wreak havoc in a complex genome since frequent insertion of random pieces of mitochondrial DNA would disrupt existing functions. Furthermore, gene transfer is a multi-step process were genes need to be moved to the nucleus, the different genetic code of mitochondria needs to be circumvented, the genes need to be expressed correctly, as well as imported back into the mitochondria in order to be functional. All in all, mechanistic scenarios for the endosymbiotic theory imply many non-functional intermediates or would just be plain harmful to an organism. Therefore, the endosymbiotic theory is in contrast with the concept of gradualism that forms the basis of modern evolutionary theory.
What’ endosymbiosis up against? T. Cavalier Smith is said to note: “The origin of the eukaryotic cell was the most complex transformation and elaborate example of quantum evolution in the history of life.” Since eukaryotic subcellular systems depend on each other he argues that the following 10 major suites of innovation had to occur at the same time:
(a) Endomembrane system (including budding and fusion)
(b) Cytoskeleton (including molecular motors)
(c) Nucleus (including the pore complex and RNA transport)
(d) Linear chromosomes (including pleural origins, centromeres, telomeres
(e) Cell cycle controls and mitotic segregation
(f) Sex (including meiosis)
(g) Origin of peroxisomes
(h) rRNA processing
(i) Origin of mitochondria (including import mechanisms)
(j) Spliceosomal introns