Eukaryotes evolved from prokaryotes ?
In the nineteenth and early twentieth centuries microbiologists observed that the fundamental unit of life—the cell—was in great variety. One obvious distinction was that some cells were larger and revealed more organization, with well defined internal structures. In 1923 Edouard Chatton described these as eukaryotes and the smaller, simpler cells as prokaryotes.
With new instrumentation the twentieth century revealed the dramatic differences between the two cell types. Eukaryotic cells include an array of structures, referred to as organelles, which perform a variety of functions. Eukaryotes also have an internal skeleton, a complex system of internal folded membranes and, perhaps most notably, a nucleus. The nucleus is enclosed by a double membrane with thousands of imbedded protein machines that control the molecular traffic in and out of the nucleus. Inside the membrane is the cell’s main complement of DNA, tightly wrapped around proteins and organized into separate chromosomes. An army of protein machines are stationed around the DNA, some unzipping and copying selected genes or performing other tasks.
By contrast prokaryotes have no nucleus and are missing key organelles, such as the mitochondria—the eukaryote’s powerhouse. There are no internal folded membranes and the smaller, simpler complement of DNA is in a single, simpler chromosome.
Essentially all multicellular organisms, from the tiny amoeba to the giant redwood tree, are eukaryotic species. And the vast majority of single celled organisms, such as bacteria, are prokaryotic species. There are some single celled organisms, such as yeast, that are eukaryotic.
There is a dizzying array of prokaryote species and it was difficult for evolutionists to determine their evolutionary relationships. Nevertheless it seemed obvious that the eukaryotes had descended from the prokaryotes. As one 1971 textbook stated, “there can be little doubt that the simpler prokaryotes are the evolutionary antecedents of the more complex eukaryotes.” 
The details of how this transformation could have occurred were less clear, for the eukaryotic cell is a tremendous step from the prokaryote. As one text later admitted, “For many years biologists have wondered how eukaryotic cells evolved from prokaryotic cells.” 
Perhaps some of the eukaryote’s organelles, such as the mitochondria, evolved via a symbiotic merger of an early eukaryotic progenitor and a prokaryote. In this endosymbiotic hypothesis, the eukaryote’s mitochondria is thought to be the descendant of an ancient prokaryote that was engulfed by the eukaryote progenitor. Afterwards, a symbiotic relationship is thought to have developed between the larger cell and its new organelle. But even this hypothesis addresses only a fraction of the complexity of the eukaryote cell. (Some evolutionists considered the possibility that prokaryotes descended from eukaryotes  but leading evolutionists considered it to be unlikely.  In any case, this reverse hypothesis would have fared no better.)
Evolutionists hoped to fill in the missing details of how prokaryotes might have given rise to eukaryotes, but instead the evidence increasingly revealed that no such transformation occurred.
The most obvious problem with the prediction that eukaryotes descended from prokaryotes is the immense gap between the two designs. In decades past it was perhaps possible to imagine that the much larger eukaryotes, with their nucleus and other structures, could have somehow emerged from a precocious prokaryote lineage. But with new and better instrumentation, scientists gradually uncovered the details of how cells work, and the gap between eukaryotes and prokaryotes widened. Here are three representative conclusions made by evolutionists:
If the prokaryote-to-eukaryote transition came about by normal evolutionary mechanisms, then given the enormity of the structural and molecular differences between these two cell types, this transformation must have occurred over a very long period involving numerous intermediate species, each developing limited selective advantages and evolving certain eukaryotic characteristics. However, there is no evidence (living or fossil) for the existence of any such “intermediate” organisms, despite the great diversity of the prokaryotic and eukaryotic organisms that preceded or followed this major change. 
There are no obvious precursor structures known among prokaryotes from which such attributes could be derived, and no intermediate cell types known that would guide a gradual evolutionary inference between the prokaryotic and eukaryotic state. 
Comparative genomics and proteomics have strengthened the view that modern eukaryote and prokaryote cells have long followed separate evolutionary trajectories. Because their cells appear simpler, prokaryotes have traditionally been considered ancestors of eukaryotes. 
Or in other words, as one reviewer summed up our knowledge of prokaryotes and eukaryotes, “The saltational difference cannot be overstated.”  This observed difference between prokaryotes and eukaryotes is reinforced by a more subtle difficulty in trying to draw an evolutionary path between the two: the respective DNA and protein sequences do not reveal an evolutionary pathway.
An interesting side story is that in the 1970s the prokaryotes were found to sub divide into two major categories. Typical bacteria fell into one category while bacteria that are tolerant of certain extreme environments, such as high temperatures, fell into the other category. These extreme environments are thought to be more representative of early earth conditions so this category is referred to as Archaea.
More important for our purposes is the fact that the molecular comparisons between these three categories were ambiguous. The three different cell types were sufficiently different that they could not have evolved from each other. Evolutionists postulated that the three lineages must have had evolved from a single progenitor, as Fig. 4 illustrates below.
The eukaryotes were now envisioned not to evolve from prokaryotes (bacteria) or archaea, but rather all three evolved from an unknown ancestor. Having a single progenitor evolve in three different directions would explain how the three lineages could have substantial similarities yet also did not have any direct evolutionary relationship between them. The problem, however, is that the new model was motivated less by the scientific evidence than by the conviction that evolution is true. Not only do the data not suggest such an evolutionary arrangement, the data do not reveal any particular evolutionary pathway. We may interpret the data according to evolution, but the expectation that eukaryotes descended from prokaryotes was not fulfilled
In fact, this new model places a substantial burden on the unknown progenitor and unknown evolutionary processes, in order for it to produce both prokaryotes and eukaryotes. In particular, evolutionists increasingly realize that the progenitor would have to be highly complex. Evolutionists at a recent conference concluded that they had underestimated the complexity of the eukaryotic cell’s precursor. The ancestral cell, they realized, must have had more genes, more structures, and more diverse biochemical processes than previously imagined.  The evolutionary quandary about how the eukaryote cell arose has substantially been pushed back onto its ancestor.
The new model is not a minor, empirically motivated, adjustment to the prediction that eukaryotes descended from prokaryotes. The new model is a substantial departure. The ingredients needed to make a eukaryote were not found in prokaryotes and no evolutionary pathway was evident. So the lineages were separated. Their connection to an unknown ancestor is not a theory-neutral inference, but is based on an evolutionary view. The old model provided specific hypotheses. The prokaryote genome was expected to lead toward the eukaryote genome. The new model allows for a wide range of observables. The relationship between the eukaryote and prokaryote is far more arbitrary and their evolution less compelling. As one leading evolutionist admitted, the evolution of eukaryotes is “one of the greatest enigmas in biology.”  "It’s like a puzzle," remarked another. “People try to put all the pieces together, but we don’t know who is right or if there is still some crucial piece of information missing.” 
The evidence does not indicate an obvious evolutionary pathway leading to eukaryotes so, not surprisingly, evolutionists have produced a wide spectrum of hypotheses.  As one review explained:
There are no obvious precursor structures known among prokaryotes from which such attributes could be derived, and no intermediate cell types known that would guide a gradual evolutionary inference between the prokaryotic and eukaryotic state. Accordingly, thoughts on the topic are diverse, and new suggestions appear faster than old ones can be tested. 
Practically every permutation has been suggested on the basic model of an ancestor splitting three ways to give rise to bacteria, archaea and eukaryotes. As Figure 5 illustrates, perhaps the archaea split off from the eukaryote lineage, or perhaps the bacteria split off from the archaea lineage. Perhaps the bacteria split off from the eukaryote lineage, or perhaps the archaea and bacteria lineages produced a fusion that led to eukaryotes. The problem is that none of the solutions are strongly supported. Very different evolutionary relationships are indicated by different molecular sequences, so it is difficult to choose among them. 
In addition to a plethora of evolutionary relationships, evolutionists have also resorted to a variety of new processes or events to explain this early evolution. Genetic annealing, genetic integration, various fusion events and symbiotic relationships have all been proposed. Even viruses have been hypothesized to stimulate the origin of the different cell types.
The scientific evidence does not fit evolution very well, and not surprisingly there is a dizzying array of hypotheses for the origin of the eukaryotes, greatly complicating the theory of evolution. One hypothesis that is not popular, however, is that eukaryotes descended from prokaryotes.
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