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Theory of Intelligent Design, the best explanation of Origins » Theory of evolution » Eukaryotes evolved from Prokaryotes. Really ?

Eukaryotes evolved from Prokaryotes. Really ?

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Eukaryotes evolved from Prokaryotes. Really ?

Not so simple after all. A renaissance of research into prokaryotic evolution and cell structure

Biologists have long thought that the internal workings of prokaryotes—the smallest and simplest organisms, including bacteria—are well understood, and have accordingly considered eukaryotic organisms and their cells to be more fascinating objects for study. During the past decade, however, the focus of some research has begun to turn back to prokaryotes—particularly because genomic analyses have shown the enormous flexibility and adaptability of these seemingly simple organisms. Moreover, recent structural research has shown that the cell components of prokaryotes might also be more complex than previously thought. It has long been held that prokaryotic cells lack the internal structure and organization of eukaryotic cells, which have various membrane-bound organelles, such as mitochondria, chloroplasts and the nucleus. Indeed, prokaryotes are assumed to be the predecessors of some eukaryotic organelles—permanently captured after a period of endosymbiosis.

The view that bacterial cells are structurally simpler than those of ‘higher' organisms is reflected in many text books and web sites with comments such as: “the ribosome is the only prokaryotic organelle”—if, indeed, this highly complex and sophisticated protein-synthesizing machinery is an organelle in its own right. These types of statement are correct in the sense that prokaryotes contain no membrane-bound organelles; but there is no rule that says an organelle must be enclosed by a membrane. Many eukaryotic ribosomes are freely suspended in the cytoplasm where they manufacture cytosolic proteins. Furthermore, the word ‘organelle' itself is being replaced by the terms ‘functional unit' or ‘compartment', which are increasingly used to describe coherent structures within a cell that perform clearly defined sets of tasks—such as mitochondria, which create energy by aerobic respiration, or chloroplasts, which do so by photosynthesis.

By using this definition, a series of recent discoveries show that prokaryotes also contain distinct functional units, or micro-compartments, which could reasonably be called organelles. One of the main breakthroughs was made at the University of California Los Angeles, USA, by a team led by Todd Yeates. They revealed structural details of micro-compartments in bacteria and found that these highly organized protein assemblies resemble viruses; they consist of thousands of protein subunits assembled in a viral-like structure or scaffold (Kerfeld et al, 2005).

For Yeates, the resemblance of micro-compartments to viruses is not coincidental, even if the exact evolutionary history remains uncertain. “The question remains open as to whether viruses and bacterial micro-compartments represent a case of convergent or divergent evolution,” he said. “At this point, there isn't really any substantial evidence to support either case […] If it turns out to be a case of Convergent_evolution, this will reinforce the idea that highly ordered protein assemblies occur relatively often by chance during evolution, and so have arisen multiple times independently, and in different functional contexts. If it turns out to be a case of divergent evolution—meaning bacterial micro-compartments share a common ancestry with some virus—the situation will be reminiscent of the endosymbiotic hypothesis, which holds that organelles in eukaryotes derived from prokaryotic organisms.” The endosymbiotic hypothesis is now widely accepted in the case of mitochondria and photosynthesizing organelles, which include chloroplasts in algae and plants, because comparative studies have revealed clear similarities with the genomes of relevant bacteria (van der Giezen, 2005), as well as structural similarities between some organelles and bacteria (Alcock et al, 2008).

The eukaryotic chromatin remodeling machinery, the cell cycle regulation systems, the nuclear envelope, the cytoskeleton, and the programmed cell death (PCD, or apoptosis) apparatus all are such major eukaryotic innovations, which do not appear to have direct prokaryotic predecessors. 1


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― Alan H. Linton

“Throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another... Since there is no evidence for species changes between the simplest forms of unicellular life, it is not surprising that there is no evidence for evolution from prokaryotic [i.e., bacterial] to eukaryotic [i.e., plant and animal] cells, let alone throughout the whole array of higher multicellular organisms.”

The organizational complexity of the eukaryotes is so much greater than that of the prokaryotes that it is difficult to visualize how a eukaryote could have arisen from any known prokaryote (Hickman et al., 1997, p. 39).

In eukaryotes the mitochondria produce most of the cell’s ATP (anaerobic glycolysis also produces some) and in plants the chloroplasts can also service this function. The mitochondria produce ATP in their internal membrane system called the cristae. Since bacteria lack mitochondria, as well as an internal membrane system, they must produce ATP in their cell membrane which they do by two basic steps. The bacterial cell membrane contains a unique structure designed to produce ATP and no comparable structure has been found in any eukaryotic cell (Jensen, Wright, and Robinson, 1997).

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Eukaryotes evolved from prokaryotes ?’s_falsifications


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.” [1]

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.” [2]

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 [3] but leading evolutionists considered it to be unlikely. [4] 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. [5]

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. [6]

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. [7]

Or in other words, as one reviewer summed up our knowledge of prokaryotes and eukaryotes, “The saltational difference cannot be overstated.” [8] 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. [9] 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.” [10] "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.” [9]


The evidence does not indicate an obvious evolutionary pathway leading to eukaryotes so, not surprisingly, evolutionists have produced a wide spectrum of hypotheses. [11] 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. [6]

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. [5]

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.


1.    Quoted in [8]; Gunther Stent, Molecular genetics: An introductory narrative (San Francisco: W.H. Freeman, 1971).

2.    Kenneth R. Miller, Joseph Levine, Biology 4th ed (Upper Saddle River, NJ: Prentice Hall, 1998), 349.

3.    K. A. Bisset, “Do bacteria have a nuclear membrane?,” Nature 241 (1973): 45.

4.    R. Y. Stanier, “Some aspects of the biology of cells and their possible evolutionary significance,” In H. P. Charles and B. C. Knight (ed), Organization and control in prokaryotic cells: Twentieth Symposium of the Society for General Microbiology (Cambridge, England: Cambridge University Press, 1970), 1-38.

5.    R. S. Gupta, “Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes,” Microbiology and Molecular Biology Reviews 62 (1998): 1435-1491.

6.    T. M. Embley, W. Martin, “Eukaryotic evolution, changes and challenges,” Nature 440 (2006): 623-630.

7.    C. G. Kurland, L. J. Collins, D. Penny, “Genomics and the irreducible nature of eukaryote cells,” Science 312 (2006): 1011-1014.

8.    J. Sapp, “The prokaryote-eukaryote dichotomy: Meanings and mythology,” Microbiology and Molecular Biology Reviews 69 (2005): 292-305.

9.    E. Pennisi, “The Birth of the nucleus,” Science 305 (2004): 766-768.

10.  J. A. Lake, “Disappearing act,” Nature 446 (2007): 983.

11.  W. F. Doolittle, J. R. Brown, “Tempo, mode, the progenote, and the universal root,” Proceedings of the National Academy of Sciences 91 (1994): 6721-6728.

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Alberts, Molecular biology in the cell:

Bacteria carry their genes on a single DNA molecule, which is often circular. This DNA is associated with proteins that package and condense the DNA, but they are different from the proteins that perform these functions in eucaryotes. Although often called the bacterial "chromosome," it does not have the same structure as eucaryotic chromosomes, and less is known about how the bacterial DNA is packaged. Therefore, our discussion of chromosome structure will focus almost entirely on eucaryotic chromosomes.

Compared to prokaryotic chromosomes, eukaryotic chromosomes are much larger in size and are linear chromosomes.

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Below, a classical " just so " story , a  example of pseudo science about how transition from Prokaryotic to Eukaryotic cells could have happened. That scenario is not tenable for several reasons exposed here and here and here

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The Darwinian Basis of the Prokaryote-to-Eukaryote Transition Collapses 1

The question of the evolution of eukaryotic cells from prokaryotic ones has long been a topic of heated discussion in the scientific literature. It is generally thought that eukaryotes arose by some prokaryotic cells being engulfed and assimilated by other prokaryotic cells. Called endosymbiotic theory, there is some empirical basis for this. For example, mitochondria contain a single circular genome, carry out transcription and translation within its compartment, use bacteria-like enzymes/components, and replicate independently of host cell division and in a manner akin to bacterial binary fission.

Despite such evidence, however, when assessing the causal sufficiency of unguided processes, they -- predictably -- come up short. After all, it is all-too-easy to lapse into a long-discredited Lamarckian "inheritance-of-acquired-characteristics" mentality. It is important to bear in mind that, even if a cooperative assemblage of prokaryotes did by some fluke of luck arise, such an arrangement is of no evolutionary significance unless there is a genetic basis to ensure its propagation.

A second problem with this scenario is that mitochondria use a slight variation on the conventional genetic code (for example, the codon UGA is a stop codon in the conventional code, but encodes for Tryptophan in mitochondria). This implicates that the genes of the ingested prokaryotes would need to have been recoded on their way to the nucleus. The situation becomes even worse when one considers that, in eukaryotic cells, a mitochondrial protein is coded with an extra length of polypeptide which acts as a "tag" to ensure that the relevant protein is recognised as being mitochondrial and dispatched accordingly. The significant number of specific co-ordinated modifications which would be required to facilitate such a transition, therefore, arguably make it exhibitive of irreducible complexity.

A few weeks ago, a review paper was published in the prestiguous journal, Nature, by the internationally renowned scientists and authors, Nick Lane and Bill Martin.

The abstract reports as follows:
All complex life is composed of eukaryotic (nucleated) cells. The eukaryotic cell arose from prokaryotes just once in four billion years, and otherwise prokaryotes show no tendency to evolve greater complexity. Why not? Prokaryotic genome size is constrained by bioenergetics. The endosymbiosis that gave rise to mitochondria restructured the distribution of DNA in relation to bioenergetic membranes, permitting a remarkable 200,000-fold expansion in the number of genes expressed. This vast leap in genomic capacity was strictly dependent on mitochondrial power, and prerequisite to eukaryote complexity: the key innovation en route to multicellular life. The paper's chief concern is with regards to the energy costs of what they describe as "the most intense phase of gene invention since the origin of life." The problem is that bacterial cells are highly unlikely to possess the technology necessary to facilitate such a transition.

How is one to resolve this paradox? The authors explain:

The answer, we posit, resides ultimately in mitochondrial genes. By enabling oxidative phosphorylation across a wide area of internal membranes, mitochondrial genes enabled a roughly 200,000-fold rise in genome size compared with bacteria. Whereas the energetic cost of possessing genes is trivial, the cost of expressing them as protein is not and consumes most of the cell's energy budget. Mitochondria increased the number of proteins that a cell can evolve, inherit and express by four to six orders of magnitude, but this requires mitochondrial DNA. How so? A few calculations are in order. The paper's authors then present a discussion of the energy costs associated with the processing of eukaryotic DNA, and find that this value is far greater than that which can be produced by a bacterial cell. They thus conclude that the ATP required for the processing of eukaryotic DNA necessitates the presence of mitochondria, the powerhouse of eukaryotic cells.

Moreover, this mitochondrion needed to contain just the right set of genes and possess just the right gene density. The mitochondrion also required thousands of copies of the said genes, with each copy located in close enough proximity to the respective machinery such that the required energy could be produced at a fast enough rate.

The authors conclude by saying,
The transition to complex life on Earth was a unique event that hinged on a bioenergetic jump afforded by spatially combinatorial relations between two cells and two genomes (endosymbiosis), rather than natural selection acting on mutations accumulated gradually among physically isolated prokaryotic individuals. Given the energetic nature of these arguments, the same is likely to be true of any complex life elsewhere.
It gets worse, of course. Even if one presumes a sufficient supply of ATP from mitochondrial processes (such as oxidative phosphorylation and the electron transport chain), no traction is given to the causal sufficiency of undirected mechanisms in accounting for the origin of novel genes and proteins which are required for eukaryotic life. One might just as easily say that purchasing a bigger power supply for your computer will cause the computer to magically be programmed to perform more complex calculations and activities! Obviously, such power would be useless without the input of novel programming script -- information -- to appropriately harness the available power.

The paper describes the invention of new protein folds in eukaryotes as being "the most intense phase of gene invention since the origin of life." The problems associated with the chance-based origin of novel genes is only accentuated by the bioenergetic dilemma described here. Granting a satisfaction of the energy demands required for those new genes and protein folds, does neo-Darwinism gain any traction? It seems very clear that it does not.


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7 Another Missing Link Demoted on Thu Jan 28, 2016 3:37 pm


Another Missing Link Demoted

The microscopic protozoan Giardia may be the bane of hikers who like to drink creek water, but it has been the boon to evolutionists as their missing link between prokaryotes and eukaryotes – until now.  New findings “mark a turning point for views of early eukaryotic and mitochondrial evolution,” report Katrin Henze and William Martin in the Nov. 13 issue of Nature1, summarizing work by Tovar et al.2 in the same issue: “Giardia’s place as an intermediate stage in standard schemes of eukaryotic evolutionary history is no longer tenable.”  They comment that this paper “will surprise many people.”
    What happened?  Central to the missing-link idea was the belief that Giardia lacked mitochondria, the ATP-energy factories common to eukaryotes (cells with nuclei, as opposed to prokaryotes, which lack them).  Lo and behold, the researchers found tiny mitochondria, dubbed mitosomes, had been present in the little germs all along.  And they are not just shriveled up versions of the big ones.  They have a unique biochemical path that produces ATP without oxygen, required for their anaerobic environment.  They build iron and sulfur clusters and then organize them into oxidation-reduction transport machinery.
    So it seems evolutionists have to start over in their search for a new candidate to bridge the gap between the two kingdoms.  But all is not lost by the finding; it helps shed light on alternative mitochondria, ones that don’t need oxygen:

We know that mitochondria arose as intracellular symbionts in the evolutionary past.  But in what sort of host?  That question still has biologists dumbfounded.  In the most popular theories, Giardia is seen as a direct descendant of a hypothetical eukaryotic host lineage that existed before mitochondria did.  But Tovar and colleagues’ findings show that Giardia cannot have descended directly from such a host, because Giardia has mitosomes.  So our understanding of the original mitochondrial host is not improved by these new findings, but our understanding of mitochondria certainly is.  In its role as a living fossil from the time of prokaryote-to-eukaryote transition, Giardia is now retired.  But it assumes a new place in the textbooks as an exemplary eukaryote with tiny mitochondria that have a tenacious grip on an essential — and anaerobic — biochemical pathway.

1Katrin Henze and William Martin, “Evolutionary biology: Essence of mitochondria,” Nature 426, 127 - 128 (13 November 2003); doi:10.1038/426127a.
2Tovar et al., “Mitochondrial remnant organelles of Giardia function in iron-sulphur protein maturation,” Nature 426, 172 - 176 (13 November 2003); doi:10.1038/nature01945

Also of interest in this report is Henze and Martin’s admission that the whole story of eukaryote evolution is slightly less than watertight: “The prokaryotes came first; eukaryotes (all plants, animals, fungi and protists) evolved from them, and to this day biologists hotly debate how this transition took place, with about 20 different theories on the go.”  Hate to break it to them on an already bad day, but the endosymbiont theory is not as watertight as they assume, either (see a rebuttal by Don Batten.)
    Even assuming their assumption, Tovar et al. admit that whatever this endosymbiont was, it was not a simple clod: “Thus, the original endosymbiont must have possessed the capacity to synthesize Fe–S clusters and to assemble them into functional redox and electron transport proteins.”  If you don’t know how to do that, don’t expect that a germ figured it out millions of years ago.

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Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases

The core enzymes of the DNA replication systems show striking diversity among cellular life forms and more so among viruses. In particular, and counter-intuitively, given the central role of DNA in all cells and the mechanistic uniformity of replication, the core enzymes of the replication systems of bacteria and archaea (as well as eukaryotes) are unrelated or extremely distantly related. Viruses and plasmids, in addition, possess at least two unique DNA replication systems, namely, the protein-primed and rolling circle modalities of replication. This unexpected diversity makes the origin and evolution of DNA replication systems a particularly challenging and intriguing problem in evolutionary biology.

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