Before 1859 all the smallest organisms were seen as novel. They were seen as spontaneously generated under the right conditions. These organisms cannot be seen by the bare eye, so it was the invention of microscopes that made us aware of them. The first organisms that were identified through the microscope were multicellular, but better microscopes also identified single celled organisms. And eventually also bacteria, that are much smaller and simpler than eukaryotes were observed. When Luis Pasteur in an experiment in 1859 showed that their existence could be demonstrated by fermentation, he also showed that they are not spontaneously generated. This year Darwin had ready for publishing a theory based on common descent, i.e. that all life originate from one cell. His book hypothesized evolution by gradual changes. The result of evolution can be observed in present species. That does not imply that organisms representing all stages of evolution can be found among preset species, e.g. there exists no ape today which is exactly like the one that humans originate from. Chimpanzees are our closest relative, but they have evolved exactly as long as human have. If our common ancestor was more like chimpanzees, then chimpanzees must have evolved slower than humans. For certain characteristics that is probably true, such as evolution of intelligence, which has been special for the human lineage.
Bacteria are special in comparison to all other forms of life, because they evolve differently. It is evident from the forms of life that we see today that eukaryotes have evolved by constantly creating new and ingenious features. There are eukaryotes that have not participated in the latest evolution trend, multicellularity. Even though single celled eukaryotes or "protists" are much simpler than the visible, multicellular forms of life, they are very diverse and despite of their simplicity, they are still enormously more complex than bacteria.
Bacteria have not by far evolved as ingeniously as eukaryotes. Their evolution is more like adaptation to the current conditions. The bacteria that we find today represent the stage of evolution when they first occurred. No trace of any earlier stage of evolution exists, it appears as if they emerged in the way Lynn Margulis express it: "They had to emerge ALL AT ONCE, No stepwise manner is possible, all systems are INTERDEPENDENT and IRREDUCIBLE." (Can anybody tell me from which book or article this citation originate?)
When we trace evolution backward in history, then we often compare genetics of one special feature, but we can also compare the set of features that exists in a clade. The organism that originated the clade may have had the set of features that is common to the clade and maybe a few more. The same philosophy may also be used for all protists. The set of common features contains almost all the features that are present in bacteria. I may therefore seem that we could rather use the bacterial features as the origin for all eukaryotes. There are a lot of features that exist in all eukaryotes that are not found in any bacteria, so an evolution from bacteria to eukaryotes would be a great enigma from which there exists no traces. And there are two groups of bacteria, archaebacteria and eubacteria, that have so different features that they would represent a branch by themselves, branches as separate from each other as they are to the eukaryote. But there is no trunk for the branches to attach to.
Carl Woese posited spontaneous emergence of the two bacteria types, as Margulis did, but he also included eukaryotes in the process. And he used another mechanism. Instead of basing it on an intelligence, as Margulis did, he assumed that both bacteria and eukaryotes occurred through a "crystallization" process. When uses that expression it is because it should be similar to the process whereby a fluid crystallizes when it is cooled.
The evolution from protists to all multicellular eukaryotes can be traced quite well through analysis of genes found in existent organisms. Evolution before the simplest eukaryotes can however not be traced at all. If bacteria represent one stage of this evolution, then there is not much help to get in finding how the evolution happened.
How can anybody suggest that something as complex as the two types of bacteria and the eukaryotes could emerge through a crystallization process? Is the action of an intelligence the only other possibility? Margulis does not call it "design", as the Intelligent Design followers do or the action of some God, as the creationists do. Her bacteria creating intelligence is rather non-specific. But she also posits that bacterial networks represent an intelligence that controls the conditions on Earth (the Gaia theory). But that intelligence could not have created itself?
Luckily, there are other possibilities. With the Organelle Escape Theory there is no need for any intelligence or enigmatic crystallization to create bacteria. They are created by eukaryotes through the same process that creates organelles in eukaryotes. Organelles and bacteria share so many features that bacteria have been posited as sources of some of them. Margulis held bacteria as the origin of all of them, but the most accepted theory limits this to organelles that cannot regenerate in the host.
With OET all organelles were originally created in the eukaryote itself or its ancestors. Some organelles reproduce so well that they do not need any regeneration process, so this process is not in use any more. It is among these that we find most of the escaped organelles. Of cause regeneration could have been active also for commuting organelles as a safety mechanism, but with safe reproduction resident as well as commuting organelles had no use for their regeneration mechanism.
With OET there is no unconnected branches. The eukaryote branch works as branch for all bacteria through their escape. As bacteria in this model has a history as dependent organelles becoming more and more autonomous, the different features occurred at different times in the history of evolution. Some of these organelles started commuting to their environments and eventually became autonomous enough that they survived as autonomous organisms even when their host became extinct. They became the bacteria. Eubacteria and archaebacteria differ so much due to the time they established their first autonomy. The translation feature has been used as a measure in comparisons between bacteria and eukaryotes. As the archaebacteria got their translation apparatus much later than eubacteria, their apparatus is more similar to the eukaryotic system.