Did eukaryotes evolve from prokaryotic cells ?

Did eukaryotes evolve from prokaryotic cells?

https://reasonandscience.catsboard.com/t1568-did-eukaryotes-evolve-from-prokaryotic-cells

A typical eukaryote cell consists of an estimated 40,000 different protein molecules and is so complex that to acknowledge that the "cells exist at all is a marvel… even the simplest of the living cells is far more fascinating than any human- made object" (Alberts, 1992, pp. xii, xiv).
https://christiananswers.net/q-crs/abiogenesis.html

The origin of DNA genomes and DNA replication proteins 2002
Is it possible to determine the nature of the LUCA genome from comparative analysis of modern genomes in the three domains of life? Archaeal and bacterial genomes are very similar in size, structure, replication mode and
mechanism of evolution. By contrast, eukaryal genomes are more diverse in size, and are very different from prokaryotic ones in terms of structure and organization.

Eörs Szathmáry  Toward major evolutionary transitions theory 2.0  April 2, 2015 https://www.pnas.org/content/112/33/10104
The divide between prokaryotes and eukaryotes is the biggest known evolutionary discontinuity. There is no space here to enter the whole maze of the recent debate about the origin of the eukaryotic cells; suffice it to say that the picture seems more obscure than 20 y ago.

How did eukaryotic life evolve? This is one of the most controversial and puzzling questions in evolutionary history. Life began as single-celled, independent organisms that evolved into cells containing membrane-bound, specialized structures known as organelles. What’s clear is that this new type of cell, the eukaryote, is more complex than its predecessors. What’s unclear is how these changes took place. 6

There are no true intermediates in the prokaryote-to-eukaryote transition. 5 More than 20 different versions of endosymbiotic theory have been presented in the literature to explain the origin of eukaryotes and their mitochondria. The origin of eukaryotes is certainly one of early evolution's most important topics.

“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).

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. 4

The view that bacterial cells are structurally simpler than those of ‘higher' organisms is reflected in many textbooks and websites 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

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 2

Another Missing Link Demoted 3
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.

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.

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

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.






https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-1-39

1. http://www.nature.com/cdd/journal/v9/n4/full/4400991a.html
2. https://en.wikipedia.org/wiki/Eukaryotic_chromosome_structure
3. http://creationsafaris.com/crev1103.htm
4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2267389/
5. https://royalsocietypublishing.org/doi/10.1098/rstb.2014.0330
6. https://asm.org/Articles/2018/May/the-origin-of-eukaryotes-where-science-and-pop-cul

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

Eukaryotes evolved from prokaryotes ? 

http://web.archive.org/web/20090126042355/http://darwinspredictions.com/#_1.3_Evolution’s_falsifications

Introduction
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.

Prediction
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.

Falsification
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]

Reaction
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.

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.

1) http://www.evolutionnews.org/2010/11/on_the_energetics_of_genome_co040431.html

Did eukaryotes evolve from prokaryotic cells?

https://reasonandscience.catsboard.com/t1568-did-eukaryotes-evolve-from-prokaryotic-cells

A science paper from the Royal society, published in 2015, confessed:
There are no true intermediates in the prokaryote-to-eukaryote transition.
https://royalsocietypublishing.org/doi/10.1098/rstb.2014.0330

My comment: Isn't that a REMARKABLE admission ? In the history of life, the transition from a supposed common ancestor, to eukaryotic cells, is a major transition, and there is NO evidence of transitional forms !!

They continue: More than 20 different versions of endosymbiotic theory have been presented in the literature to explain the origin of eukaryotes and their mitochondria. The origin of eukaryotes is certainly one of early evolution's most important topics.

My comment: Here we have a similar situation as in abiogenesis. There are over at least 40 different proposals and hypotheses, but , as Steve Benner wrote:

That era has produced tens of thousands of papers attempting to define processes by which “molecules that look like biology” might arise from “molecules that do not look like biology” …. For the most part, these papers report “success” in the sense that those papers define the term…. And yet, the problem remains unsolved.

So the same applies to the transition or a claimed common ancestor, to eukaryotes. So science is basically ENTIRELY in the dark in regards of the origin of eukaryotic cells.

The endosymbiotic theory is also pseudo-scientific story telling.
If we suppose that a freeliving primordial cell engulfed another primordial cell, which formed mitochondria, then there are two considerable problems : Such a primordial cell would have to devolve from a minimal genome of 1,3million nucleotides of a freeliving organism to about 15 - 20 thousand nucleotides in mitochondria. And secondly: Mitochondria uses a different genetic Code, than the standard code. How would that transition be possible to happen?

https://royalsocietypublishing.org/doi/10.1098/rstb.2014.0330

The huge gap between prokaryotes and eukaryotes

https://reasonandscience.catsboard.com/t1568-did-eukaryotes-evolve-from-prokaryotic-cells#9234

There is a broad scientific assumption that the three domains of life, prokaryotes, and eukaryotes, had a universal common ancestor at the root of the tree of life. The mere fact, that they differ hugely in size alone, however, is a big problem to warrant common ancestry. That was acknowledged by Koonin, as he wrote: " The origin of eukaryotes is a huge enigma and a major challenge for evolutionary biology. There is a sharp divide in the organizational complexity of the cell between eukaryotes, which have complex intracellular compartmentalization, and even the most sophisticated prokaryotes (archaea and bacteria), which do not "  3 In fact, if we compare just the size alone, between the smallest prokaryote ( P.Ubique), and the smallest eukaryotic cell, the green marine alga Ostreococcus tauri, we can see the difference.  

The simplest free-living bacteria today is Pelagibacter ubique get by with about 1,300 genes and 1,308,759 base pairs and code for 1,354 proteins.  The most commonly mentioned and accepted evidence of the oldest life form is the stromatolite remains in Australia, which are remnants from cyanobacteria 16 The cyanobacteria Synechococcus LMB bulk15N as a representative comes by with 1,470,000 base pairs, 1,444 proteins 7 and 1,530 genes 23

Eukaryotic cells are vastly more complex than prokaryotic cells as evident by their endomembrane system (Gould et al. 2016). 1 

The unicellular green marine alga Ostreococcus tauri is the world's smallest free-living eukaryote known to date, and encodes the fewest number of genes. It has been hypothesized, based on its small cellular and genome sizes, that it may reveal the “bare limits” of life as a free-living photosynthetic eukaryote, presumably having disposed of redundancies and presenting a simple organization and very little noncoding sequence. 4 It has a genome size of 12.560,000 base pairs, 8,166 genes 5 and 7745 proteins 6

This speaks for itself. Ostreococcus tauri is about ten times bigger in genome size than Synechococcus LMB bulk15N . Both have very little non-coding regions.
  
The oldest eukaryotic fossil is the multicellular alga, Grypania. Coiled Grypania is found as thin films of carbon in rocks as old as 2,100 Ma in Michigan and young specimens have been recovered from 1,100 Ma rocks in China. 8 Bangiomorpha pubescens is a red alga.^[1] It is the first known sexually reproducing organism. A multicellular fossil of Bangiomorpha pubescens was recovered from the Hunting Formation in Somerset Island, Canada that strongly resembles the modern red alga Bangia despite occurring in rocks dating to 1,047 million years ago 9 Fossil evidence shows that red algae (Rhodophyta) are one of the most ancient multicellular lineages. 10 Since they have many repeats and transposable elements (TEs) and rather large genomes, they don't serve as model organisms.

There are many unique characteristics of eukaryotes:
Cells with nuclei are surrounded by a nuclear envelope with nuclear pores. This is the single characteristic that is both necessary and sufficient to define an organism as a eukaryote. All extant eukaryotes have cells with nuclei. 2
Mitochondria. Some extant eukaryotes have very reduced remnants of mitochondria in their cells, whereas other members of their lineages have mitochondria.
A cytoskeleton containing the structural and motility components called actin microfilaments and microtubules. All extant eukaryotes have these cytoskeletal elements.
Linear Chromosomes Many eukaryotic species have multiple linear chromosomes, in contrast to prokaryotic genomes which consist of a single circular chromosome.
Mitosis, a process of nuclear division wherein replicated chromosomes are divided and separated using elements of the cytoskeleton. Mitosis is universally present in eukaryotes.
Sex, a process of genetic recombination unique to eukaryotes in which diploid nuclei at one stage of the life cycle undergo meiosis to yield haploid nuclei and subsequent karyogamy, a stage where two haploid nuclei fuse together to create a diploid zygote nucleus.

1. Josip Skejo: Evidence for a Syncytial Origin of Eukaryotes from Ancestral State Reconstruction https://academic.oup.com/gbe/article/13/7/evab096/6272229
2. Organismal biology: https://organismalbio.biosci.gatech.edu/biodiversity/eukaryotes-and-their-origins/
3. Eugene V Koonin: The origin and early evolution of eukaryotes in the light of phylogenomics 05 May 2010 https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-5-209#article-info
4. Evelyne Derelle: Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features 2006 Aug 1 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1544224/
5. https://www.uniprot.org/proteomes/UP000009170
6. https://www.uniprot.org/uniprot/?query=proteome:UP000009170&sort=score
7. https://www.uniprot.org/uniprot/?query=proteome:UP000242636&sort=score
8. https://gustavus.edu/geology/nobel_display/nobel_grypania.html#:~:text=OLDEST%20EUKARYOTES&text=The%20oldest%20eukaryotic%20fossil%20is,1%2C100%20Ma%20rocks%20in%20China.
9. https://en.wikipedia.org/wiki/Bangiomorpha
10. Susan H. Brawley: Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta)

A Comprehensive Catalogue of Cellular Innovations Required for the Prokaryote-to-Eukaryote Transition

Abstract:
The evolution from prokaryotic to eukaryotic cells represents one of the most significant transitions in the history of life. This paper aims to provide an exhaustive, detailed list of all cellular components, structures, systems, and processes that would need to be created de novo or undergo substantial modifications to facilitate this transition. By examining current scientific literature, comparative genomics, and cellular biology, we present a meticulous overview of the myriad innovations required for eukaryogenesis.

1. Introduction:

The divide between prokaryotes and eukaryotes represents the most profound discontinuity in cellular organization. Eukaryotic cells are characterized by their complex internal structures, compartmentalization, and sophisticated molecular machinery. This paper seeks to elucidate every conceivable change necessary for a prokaryotic cell to evolve into a eukaryotic one.

2. Methodology:

We conducted an extensive literature review, analyzing research papers, review articles, textbooks, and databases on cellular biology, molecular evolution, comparative genomics, and biochemistry. The information was synthesized to create an exhaustive list of cellular innovations required for the prokaryote-to-eukaryote transition.

3. Results:

The following is a comprehensive list of cellular components, structures, systems, and processes that would need to be created de novo or undergo substantial modifications in the transition from prokaryotic to eukaryotic cells:

3.1 Membrane-bound organelles:

a) Nucleus:
- Double membrane envelope
- Nuclear pores and nuclear pore complexes (NPCs)
- Specific nucleoporins (at least 30 different proteins)
- Nuclear lamina (lamins A, B, and C)
- Nucleolus
- Cajal bodies
- Nuclear speckles
- Chromatin organization and condensation machinery
- Nuclear matrix
- Nuclear envelope breakdown and reassembly mechanisms

b) Mitochondria:
- Double membrane structure (inner and outer membranes)
- Cristae and cristae junctions
- Mitochondrial DNA and ribosomes
- Electron transport chain components (Complexes I, II, III, IV)
- ATP synthase complexes
- Mitochondrial fusion and fission machinery
- Mitochondrial import machinery (TIM/TOM complexes)
- Cardiolipin synthesis
- Mitochondrial calcium handling systems
- Mitochondrial-derived vesicles (MDVs)

c) Endoplasmic reticulum:
- Rough ER with associated ribosomes
- Smooth ER
- ER-associated degradation (ERAD) system
- Unfolded protein response (UPR) machinery
- ER exit sites (ERES)
- ER-Golgi intermediate compartment (ERGIC)
- ER stress granules
- ER-mitochondria contact sites

d) Golgi apparatus:
- Stacked cisternae (cis, medial, trans)
- Vesicle trafficking machinery
- Golgi matrix proteins
- Glycosylation enzymes
- Golgi pH gradient
- Intra-Golgi transport mechanisms (cisternal maturation, vesicular transport)

e) Lysosomes and peroxisomes:
- Single membrane-bound structures
- Specific sets of hydrolytic enzymes for each organelle
- Lysosomal membrane proteins (LAMPs)
- Peroxisomal targeting signals (PTS1, PTS2)
- Peroxisomal import machinery
- Autophagy-lysosome pathway components

f) Vacuoles (in plant cells):
- Large central vacuole
- Tonoplast membrane
- Vacuolar H+-ATPases
- Vacuolar storage proteins
- Vacuolar sorting receptors

g) Chloroplasts (in photosynthetic eukaryotes):
- Double membrane structure
- Thylakoid membranes
- Chloroplast DNA and ribosomes
- Photosynthetic machinery (Photosystem I and II, cytochrome b6f complex)
- Carbon fixation enzymes (Calvin cycle)
- Chloroplast division machinery
- Chloroplast import machinery (TIC/TOC complexes)

h) Other specialized organelles:
- Melanosomes
- Weibel-Palade bodies
- Secretory lysosomes
- Glyoxysomes

3.2 Cytoskeleton:

a) Microfilaments (actin filaments):
- Actin monomers (multiple isoforms)
- Actin nucleation factors (Arp2/3 complex, formins)
- Actin-binding proteins (e.g., profilin, cofilin, gelsolin)
- Myosin motor proteins (at least 35 classes)
- Actin-based cellular processes (e.g., cytokinesis, endocytosis, cell migration)

b) Intermediate filaments:
- Various intermediate filament proteins (e.g., keratins, vimentin, desmin, neurofilaments, lamins)
- Intermediate filament-associated proteins
- Tissue-specific intermediate filament networks

c) Microtubules:
- α- and β-tubulin subunits (multiple isoforms)
- γ-tubulin and microtubule organizing centers (MTOCs)
- Centrosomes and centrioles
- Microtubule-associated proteins (MAPs)
- Kinesin and dynein motor proteins
- Microtubule plus-end tracking proteins (+TIPs)
- Microtubule-severing proteins (e.g., katanin, spastin)

d) Septins:
- Multiple septin proteins
- Septin filament assembly and regulation

e) Cytoskeletal crosslinking and regulatory proteins:
- Plectin
- Spectrin
- Ankyrin
- Filamin

3.3 Endomembrane system:

a) Vesicle trafficking machinery:
- COPI, COPII, and clathrin-coated vesicles
- Adaptor protein (AP) complexes
- SNARE proteins (at least 60 in humans)
- Rab GTPases (over 60 in humans)
- Arf and Arl GTPases
- Tethering factors (e.g., exocyst complex, TRAPP complex)
- Coat proteins (e.g., clathrin, COPI, COPII)

b) Sorting and targeting mechanisms:
- Signal peptides
- Receptor-mediated endocytosis machinery
- Retromer complex
- Sorting nexins
- Endosomal sorting complexes required for transport (ESCRT)

c) Membrane fusion and fission machinery:
- Dynamin family proteins
- BAR domain proteins
- SNARE regulatory proteins (e.g., NSF, α-SNAP)

d) Lipid trafficking and metabolism:
- Phosphoinositide kinases and phosphatases
- Lipid transfer proteins
- Flippases, floppases, and scramblases

3.4 Genomic organization and expression:

a) Linear chromosomes:
- Telomeres and telomerase
- Shelterin complex
- Centromeres and kinetochores
- Sister chromatid cohesion proteins

b) Chromatin structure:
- Histones (H2A, H2B, H3, H4, and variants)
- Histone chaperones
- Nucleosomes and higher-order chromatin structures
- Chromatin remodeling complexes (e.g., SWI/SNF, ISWI, CHD, INO80)
- Histone modifying enzymes (e.g., HATs, HDACs, HMTs, HDMs)

c) Transcriptional regulation:
- Enhancers and silencers
- Insulators and boundary elements
- General transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH)
- RNA polymerase II and associated factors
- Mediator complex
- Transcription factors and coactivators
- Epigenetic modifications (e.g., DNA methylation, histone modifications)
- Long non-coding RNAs (lncRNAs)

d) mRNA processing:
- 5' capping enzymes
- Splicing machinery (spliceosome, over 150 proteins)
- Alternative splicing regulators
- 3' polyadenylation machinery
- mRNA editing enzymes

e) Nuclear export of mRNA:
- Nuclear pore complexes (over 30 different nucleoporins)
- mRNA export factors (e.g., TAP/NXF1, REF/Aly)
- TREX complex

f) Translational control:
- Cap-dependent translation initiation factors (at least 13 eIFs)
- Internal ribosome entry sites (IRES)
- microRNAs and RISC complex
- Poly(A)-binding protein (PABP)
- Nonsense-mediated decay (NMD) pathway

g) Ribosome biogenesis:
- Eukaryotic ribosomal proteins (79 in humans)
- rRNA processing and modification enzymes
- Ribosome assembly factors

3.5 Cell cycle regulation:

a) Complex cell cycle control:
- Cyclins (at least 29 in humans)
- Cyclin-dependent kinases (CDKs)
- CDK inhibitors (CKIs)
- Anaphase-promoting complex/cyclosome (APC/C)
- Checkpoint proteins (e.g., p53, ATM, ATR, Chk1, Chk2)
- DNA damage response pathways

b) Mitotic apparatus:
- Mitotic spindle
- Kinetochores and spindle assembly checkpoint
- Centrosomes and centrioles
- Cohesin and condensin complexes
- Aurora kinases
- Polo-like kinases

c) Cytokinesis machinery:
- Actomyosin contractile ring
- Centralspindlin complex
- Septins
- Exocyst complex
- Abscission machinery (ESCRT-III complex)

3.6 Protein targeting and sorting:

a) Signal recognition particle (SRP) and receptor
b) Protein import/export systems for organelles:
  - Mitochondrial import (TIM/TOM complexes)
  - Chloroplast import (TIC/TOC complexes)
  - Peroxisomal import (PEX proteins)
  - Nuclear import/export (importins, exportins, Ran GTPase cycle)
c) Vesicle-mediated protein transport
d) Post-translational modifications for targeting (e.g., glycosylation, lipidation)

3.7 Energy metabolism:

a) Compartmentalization of metabolic pathways
b) Oxidative phosphorylation in mitochondria:
  - Complex I (NADH:ubiquinone oxidoreductase)
  - Complex II (Succinate dehydrogenase)
  - Complex III (Cytochrome bc1 complex)
  - Complex IV (Cytochrome c oxidase)
  - ATP synthase (Complex V)
c) Photosynthesis in chloroplasts (for plant cells):
  - Light-harvesting complexes
  - Photosystem I and II
  - Cytochrome b6f complex
  - ATP synthase
d) Pentose phosphate pathway
e) Fatty acid oxidation
f) Lipid biosynthesis
g) Amino acid biosynthesis and degradation pathways
h) Nucleotide biosynthesis and salvage pathways

3.8 Cell signaling:

a) G protein-coupled receptors (GPCRs) - over 800 in humans
b) Tyrosine kinase receptors
c) Serine/threonine kinase receptors
d) Second messenger systems:
  - cAMP and cGMP
  - Phospholipase C and inositol phosphates
  - Calcium signaling
e) Nuclear receptors
f) JAK-STAT pathway
g) MAPK cascades
h) PI3K-Akt pathway
i) NF-κB pathway
j) Wnt signaling pathway
k) Notch signaling pathway
l) Hedgehog signaling pathway
m) TGF-β signaling pathway

3.9 Cell adhesion and communication:

a) Cell junctions:
  - Tight junctions (claudins, occludins, ZO proteins)
  - Adherens junctions (cadherins, catenins)
  - Desmosomes (desmogleins, desmocollins, desmoplakins)
  - Gap junctions (connexins, innexins)
b) Extracellular matrix components:
  - Collagens
  - Proteoglycans
  - Glycoproteins (e.g., fibronectin, laminin)
c) Cell surface receptors for cell-cell and cell-matrix interactions:
  - Integrins
  - Selectins
  - Immunoglobulin superfamily cell adhesion molecules (IgCAMs)
d) Focal adhesions and hemidesmosomes

3.10 Specialized cellular processes:

a) Apoptosis machinery:
  - Caspases
  - Bcl-2 family proteins
  - Apoptosome
  - Death receptors and ligands
b) Autophagy systems:
  - ATG proteins
  - LC3/GABARAP family proteins
  - ULK1 complex
  - PI3K complex
c) Cell differentiation mechanisms:
  - Lineage-specific transcription factors
  - Epigenetic regulators
  - Cell fate determination pathways
d) Sexual reproduction and meiosis:
  - Synaptonemal complex
  - Meiosis-specific cohesins
  - Homologous recombination machinery
e) Cellular senescence:
  - Telomere shortening mechanisms
  - Senescence-associated secretory phenotype (SASP)
f) Stress responses:
  - Heat shock proteins
  - Unfolded protein response (UPR)
  - Antioxidant systems
g) Cellular polarity:
  - Par complex
  - Crumbs complex
  - Scribble complex

3.11 Immune system components (in multicellular eukaryotes):

a) Innate immune system:
  - Pattern recognition receptors (PRRs)
  - Complement system
  - Phagocytosis machinery
b) Adaptive immune system:
  - T cell receptors (TCRs)
  - B cell receptors (BCRs) and antibodies
  - Major histocompatibility complex (MHC)
  - V(D)J recombination machinery

3.12 Specialized organelles and structures in certain eukaryotic lineages:

a) Flagella and cilia:
  - Basal bodies
  - Axoneme structure (9+2 or 9+0 arrangement)
  - Intraflagellar transport (IFT) machinery
b) Contractile vacuoles (in some protists)
c) Eyespots (in some algae)
d) Hydrogenosomes and mitosomes (in some anaerobic eukaryotes)
e) Plastids other than chloroplasts (e.g., chromoplasts, amyloplasts)
f) Symbiosomes (in legumes)

4. Discussion:

The transition from prokaryotic to eukaryotic cells requires an extraordinary number of innovations and modifications. This exhaustive list highlights the immense complexity of eukaryotic cells and the vast array of cellular components, structures, and systems that would need to evolve for this transition to occur.

Key challenges in explaining this transition include:

1. The origin and evolution of membrane-bound organelles, particularly the nucleus, mitochondria, and endomembrane system.
2. The development of the complex cytoskeleton and its various components.
3. The transition from circular to linear chromosomes and the associated telomere/centromere machinery.
4. The emergence of intricate gene regulation mechanisms, including chromatin organization and mRNA processing.
5. The evolution of sophisticated cell cycle control and the mitotic apparatus.
6. The development of complex signaling pathways and cell communication systems.
7. The origin of sexual reproduction and meiosis.

The endosymbiotic theory provides a partial explanation for the origin of mitochondria and chloroplasts. However, it does not account for the majority of eukaryotic innovations. The lack of intermediate forms between prokaryotes and eukaryotes in both the fossil record and extant species further complicates our understanding of this transition.

5. Conclusion

The transition from prokaryotic to eukaryotic cells represents one of the most significant evolutionary leaps in the history of life on Earth. This exhaustive list of required innovations underscores the immense complexity of eukaryotic cells and the vast array of cellular components, structures, and systems that would need to evolve for this transition to occur.

The sheer number and intricacy of these innovations pose significant challenges to our understanding of eukaryogenesis. While some aspects, such as the origin of mitochondria and chloroplasts, can be partially explained by endosymbiotic events, the majority of eukaryotic features require alternative explanations.

Future research should focus on:
1. Identifying potential intermediate forms or "missing links" between prokaryotes and eukaryotes.
2. Investigating the order and interdependence of eukaryotic innovations.
3. Exploring the role of horizontal gene transfer and symbiotic relationships in driving eukaryotic evolution.
4. Developing more sophisticated computational models to simulate the evolution of complex cellular systems.
5. Conducting experimental evolution studies to recreate aspects of eukaryogenesis in laboratory settings.

Understanding the prokaryote-to-eukaryote transition remains one of the greatest challenges in evolutionary biology. This comprehensive catalogue of required innovations serves as a roadmap for future research and highlights the remarkable complexity of eukaryotic life.

6. Evolutionary Mechanisms and Hypotheses:

To further explore the prokaryote-to-eukaryote transition, it's important to consider various evolutionary mechanisms and hypotheses that have been proposed to explain the origin of eukaryotic features:

6.1 Endosymbiotic theory:
- Primary endosymbiosis: explaining the origin of mitochondria and chloroplasts
- Secondary and tertiary endosymbiosis: explaining the diversity of plastids in different eukaryotic lineages
- Hypothetical endosymbiotic origins for other eukaryotic features (e.g., peroxisomes, nucleus)

6.2 Viral eukaryogenesis hypothesis:
- Potential role of large DNA viruses in the origin of the nucleus
- Contribution of viral genes to eukaryotic genomes

6.3 Syntrophy hypothesis:
- Metabolic interdependence driving the initial association between archaeal and bacterial ancestors of eukaryotes

6.4 Autogenous origin hypotheses:
- Gradual evolution of internal membranes from prokaryotic ancestors
- Spontaneous emergence of compartmentalization in primitive cells

6.5 Evolutionary mechanisms:
- Gene duplication and divergence
- Exon shuffling and domain recombination
- De novo gene origin
- Horizontal gene transfer
- Symbiogenesis
- Neutral evolution and constructive neutral evolution
- Adaptive evolution and natural selection

7. Comparative Genomics and Molecular Evolution:

A deeper understanding of the prokaryote-to-eukaryote transition can be gained through comparative genomics and molecular evolution studies:

7.1 Comparative analysis of prokaryotic and eukaryotic genomes:
- Identification of eukaryotic signature proteins (ESPs)
- Tracing the evolutionary history of key eukaryotic genes
- Analysis of gene family expansions in eukaryotes

7.2 Molecular clock studies:
- Estimating the timing of key eukaryotic innovations
- Calibrating the eukaryotic tree of life

7.3 Reconstruction of ancestral genomes:
- Last eukaryotic common ancestor (LECA)
- First eukaryotic common ancestor (FECA)

7.4 Analysis of early-branching eukaryotes:
- Excavates (e.g., Giardia, Trichomonas)
- Amoebozoa (e.g., Dictyostelium)
- Archaeplastida (e.g., red algae, green algae)

7.5 Study of prokaryotic relatives of eukaryotes:
- Asgard archaea and their eukaryotic-like features
- Analysis of bacterial contributors to the eukaryotic genome

8. Experimental Approaches:

While the prokaryote-to-eukaryote transition occurred billions of years ago, experimental approaches can provide insights into the process:

8.1 Synthetic biology:
- Bottom-up approaches to create minimal synthetic cells
- Engineering prokaryotic cells with eukaryotic-like features

8.2 Experimental evolution:
- Long-term evolution experiments with prokaryotes under various selective pressures
- Directed evolution of specific eukaryotic-like traits in prokaryotes

8.3 In vitro reconstitution:
- Reconstruction of key eukaryotic cellular processes using purified components
- Study of self-organization in minimal systems

8.4 Single-cell analysis:
- Investigation of cellular heterogeneity and compartmentalization in prokaryotes
- Study of primitive eukaryotes and their cellular organization

9. Implications and Future Directions:

Understanding the prokaryote-to-eukaryote transition has far-reaching implications:

9.1 Astrobiology and the search for extraterrestrial life:
- Assessing the likelihood of eukaryote-like life on other planets
- Refining our understanding of the conditions necessary for complex cellular life

9.2 Synthetic biology and biotechnology:
- Designing artificial cells with enhanced capabilities
- Engineering novel cellular compartments and functions

9.3 Medical research:
- Insights into the evolution of human diseases
- Identification of novel drug targets based on eukaryote-specific features

9.4 Environmental and ecological studies:
- Understanding the role of eukaryotes in global biogeochemical cycles
- Predicting the impact of environmental changes on eukaryotic diversity

9.5 Philosophical and societal implications:
- Refining our understanding of the nature of life and its complexity
- Ethical considerations in creating synthetic life forms

In conclusion, the prokaryote-to-eukaryote transition represents a fundamental shift in the organization and complexity of life on Earth. This comprehensive analysis of required innovations serves as a foundation for future research, highlighting the immense challenges and opportunities in understanding one of the most significant evolutionary events in the history of life.