Cell biology Evolution Intelligent Design

Eukaryogenesis: The Rise of an Emergent Superorganism

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An article published in Frontiers of Microbiology highlights the “the chasm in design between prokaryotic and eukaryotic cells.”

The Dominant Biological Paradigms of Life and Evolution

Three paradigms established in the 19th century, combined with advances in quantitative genetics in the 20th century, led to the dominant ‘textbook’ paradigm of biology where all life is cellular and descends from a common ancestor via the neo-Darwinian process of natural selection (e.g., Keeton and Gould, 1986).

Although the Modern Evolutionary Synthesis and the universal Tree of Life are very powerful paradigms, they are under challenge as several major tenets of the synthesis are being questioned (e.g., Doolittle, 1999Dagan and Martin, 2006Koonin, 2009Koonin and Wolf, 2012). One challenge is their incompatibility with endosymbiotic processes operating at the origin of the eukaryotic domain (Koonin, 2009). Since the mitochondrion initially evolved separately from the ancestor of the eukaryotic cytoplasm, it arose via a symbiotic event (i.e., saltation) rather than an autogenous incremental process expected under the Modern Evolutionary Synthesis paradigm.

The “Grand Chasm” Between Eukaryotes and Prokaryotes

The eukaryotic cell is extraordinarily distinct from the much simpler bacterial and archaeal cells of the prokaryotic domains. It possesses not only a nucleus and a mitochondrion, but also a sophisticated endomembrane system, a complex cytoskeleton and a unique sexual cycle, leaving the gap between cells of prokaryotic and eukaryotic design as the greatest chasm in biology. 

Finally, a notorious ‘queen of evolutionary problems’ related to the origin of the nucleus is the unresolved paradox of the origin of the eukaryotic sexual cycle (Bell, 1982). For the sexual cycle to function, two highly complex integrated but temporally and mechanistically unrelated processes must occur. Firstly, meiosis must occur to convert a diploid cell into four haploid daughter cells. This complex process is achieved by a single cycle of chromosomal replication generating a nucleus with 4 N ploidy and is followed by two mitosis-like cell divisions reducing the ploidy of the four daughter cells to 1 N.

The origin of this process is a paradox that has defied any generally accepted explanation for over 50 years and in part revolves around the challenge of determining which came first, meiosis that allows haploid gametes to be formed from a diploid or syngamy that allows 1 N haploid gametes to mate and create a 2 N diploid in the first place.

According to the modern evolutionary synthesis, incremental changes leading to the complex, unique and interrelated eukaryotic systems associated with the nucleus must have each provided an immediate selective advantage to an archaeal cell. Arguing these innovations were beneficial because they allowed the future evolution of complexity in the eukaryotic domain is clearly a teleological argument. It is particularly thought-provoking to explain these discontinuities in terms of incremental benefit when it appears that the eukaryotic system evolved only once in over 3.7 billion years and left no currently recognised intermediates, while the prokaryotic system remained highly efficient and conserved by the bacterial and archaeal domains for over 3.7 billion years.

In his lengthy article, Bell draws attention to evolutionary hurdles to the origin of eukaryotic cells. The “chasm” between eukaryotic and prokaryotic cells is causing a re-think of the universal common ancestor notion. Separate origins, however, of these types of cells would introduce further strain to the unguided evolution theory. Can we surmise that the evidence is more suitably consistent with intelligent design of these types of organisms?

8 Replies to “Eukaryogenesis: The Rise of an Emergent Superorganism

  1. 1
    Nonlin.org says:

    Science against fantasy. How much longer will the “evolution” fantasy be assumed true until (and even after) proven false?

  2. 2
    bornagain77 says:

    Eukaryogenesis: The Rise of an Emergent Superorganism – May 2022
    Excerpt: The eukaryotic cell is extraordinarily distinct from the much simpler bacterial and archaeal cells of the prokaryotic domains. It possesses not only a nucleus and a mitochondrion, but also a sophisticated endomembrane system, a complex cytoskeleton and a unique sexual cycle, leaving the gap between cells of prokaryotic and eukaryotic design as the greatest chasm in biology.
    https://www.frontiersin.org/articles/10.3389/fmicb.2022.858064/full

    Along that line,

    Endosymbiosis: A Theory in Crisis by Jeffrey P. Tomkins, Ph.D. * – Oct. 30, 2015
    Excerpt: However, now that genome sequencing is inexpensive and widespread, the evolutionary story of endosymbiosis has become increasingly clouded and controversial. As new bacterial and eukaryotic genomes are sequenced and the proteins they encode are deduced, the whole evolutionary idea of endosymbiosis has been thrown into utter confusion.
    One of the most unexpected discoveries has been the utter lack of identified genes that would support the evolutionary tale. As stated in a recent paper,
    “What was not anticipated was how relatively few mitochondrial proteins with bacterial homologs [sequence similarity] would group specifically with -Proteobacteria in phylogenetic [evolutionary tree] reconstructions: At most, only 10–20% of any of the mitochondrial proteomes examined so far display a robust -proteobacterial signal.4”
    This lack of evidence for mitochondrial genes derived from bacterial origin in both the mitochondrial DNA and the genome contained in the cell’s nucleus, where most mitochondrial genes are located, is a serious problem for the evolutionary story.,,,
    http://www.icr.org/article/end.....ory-crisis

    Information Processing Differences Between Archaea and Eukarya—Implications for Homologs and the Myth of Eukaryogenesis by Change Tan and Jeffrey P. Tomkins on March 18, 2015
    Abstract
    In the grand schema of evolution, a mythical prokaryote to eukaryote cellular transition allegedly gave rise to the diversity of eukaryotic life (eukaryogenesis). One of the key problems with this idea is the fact that the prokaryotic world itself is divided into two apparent domains (bacteria and archaea) and eukarya share similarities to both domains of prokaryotes while also exhibiting many major innovative features found in neither. In this article, we briefly review the current landscape of the controversy and show how the key molecular features surrounding DNA replication, transcription, and translation are fundamentally distinct in eukarya despite superficial similarities to prokaryotes, particularly archaea. These selected discontinuous molecular chasms highlight the impossibility for eukarya having evolved from archaea. In a separate paper, we will address alleged similarities between eukarya and bacteria.
    https://answersingenesis.org/biology/microbiology/information-processing-differences-between-archaea-and-eukarya/

    Information Processing Differences Between Bacteria and Eukarya—Implications for the Myth of Eukaryogenesis by Change Tan and Jeffrey P. Tomkins on March 25, 2015
    Excerpt: In a previous report, we showed that a vast chasm exists between archaea and eukarya in regard to basic molecular machines involved in DNA replication, RNA transcription, and protein translation. The differences in information processing mechanisms and systems are even greater between bacteria and eukarya, which we elaborate upon in this report. Based on differences in lineage-specific essential gene sets and in the vital molecular machines between bacteria and eukarya, we continue to demonstrate that the same unbridgeable evolutionary chasms exist—further invalidating the myth of eukaryogenesis.
    https://answersingenesis.org/biology/microbiology/information-processing-differences-between-bacteria-and-eukarya/

  3. 3
    martin_r says:

    The eukaryotic cell is extraordinarily distinct from the much simpler bacterial and archaeal cells of the prokaryotic domains. It possesses not only a nucleus and a mitochondrion, but also a sophisticated endomembrane system, a complex cytoskeleton and a unique sexual cycle, leaving the gap between cells of prokaryotic and eukaryotic design as the greatest chasm in biology.

    the gap between cells of prokaryotic and eukaryotic design as the greatest chasm in biology.

    I can imagine :))))) Darwinists believe in miracles …

  4. 4
    martin_r says:

    and this is brutal:

    Finally, a notorious ‘queen of evolutionary problems’ related to the origin of the nucleus is the unresolved paradox of the origin of the eukaryotic sexual cycle (Bell, 1982). For the sexual cycle to function, two highly complex integrated but temporally and mechanistically unrelated processes must occur. Firstly, meiosis must occur to convert a diploid cell into four haploid daughter cells. This complex process is achieved by a single cycle of chromosomal replication generating a nucleus with 4?N ploidy and is followed by two mitosis-like cell divisions reducing the ploidy of the four daughter cells to 1?N.

    The origin of this process is a paradox that has defied any generally accepted explanation for over 50?years and in part revolves around the challenge of determining which came first, meiosis that allows haploid gametes to be formed from a diploid or syngamy that allows 1?N haploid gametes to mate and create a 2?N diploid in the first place.

    Darwinism is a scam …. no doubts …

    PS: i was wondering, how Darwinists will ever be able to replicate such processes by heating and cooling down some flasks … this is crazy …. i said it before, but the one who created the cell did not use a common chemistry. That is for sure. Obviously, there have to be some undiscovered means of how to work with molecules … obviously, you can’t work like that … you can’t create sophisticated chemical systems where billions of molecules work together for a purpose by mixing some chemicals in flasks then cooling it down or heating it up … we are missing something …

  5. 5
    ET says:

    Yes, eukaryotes are much more than a prokaryote with a new organelle. Evolutionists love to pretend otherwise. From 2006- can evolution make things less complicated:

    Instead, the data suggest that eukaryote cells with all their bells and whistles are probably as ancient as bacteria and archaea, and may have even appeared first, with bacteria and archaea appearing later as stripped-down versions of eukaryotes, according to David Penny, a molecular biologist at Massey University in New Zealand.

    Penny, who worked on the research with Chuck Kurland of Sweden’s Lund University and Massey University’s L.J. Collins, acknowledged that the results might come as a surprise.

    “We do think there is a tendency to look at evolution as progressive,” he said. “We prefer to think of evolution as backwards, sideways, and occasionally forward.”

  6. 6
    Silver Asiatic says:

    Although it is widely taught that all modern life descended via modification from a last universal common ancestor (LUCA), this dominant paradigm is yet to provide a generally accepted explanation for the chasm in design between prokaryotic and eukaryotic cells.

    There’s no “generally accepted” exxplanation.
    They not only cannot explain the origin – but they don’t explain why there’s this chasm of design between the two.
    What was the supposed selection pressure that caused this “gap”? Bacteria couldn’t find enough food so they had to evolve a nuculeus and new logic-based processes?

    A virus initiated the eukaryogenesis process by colonising an archaeal host to create a virocell that had its metabolism reprogrammed to support the viral factory.

    Reprogramming.

    Subsequently, viral processes facilitated the entry of a bacterium into the archaeal cytoplasm which was also eventually reprogrammed to support the viral factory.

    Then more reprogramming. Then a factory is built and the virus does a great job supporting the factory to make sure that the program is working correctly. Otherwise there would be big problems and nobody wants that to happen.

    As the viral factory increased control of the consortium, the archaeal genome was lost, the bacterial genome was greatly reduced and the viral factory eventually evolved into the nucleus.

    The factory increases control over all the elements, because otherwise it would be messy in there. Then, it got rid of some things and evolved a nucleus. There was probably some excellent reprogramming here also.

    It possesses not only a nucleus and a mitochondrion, but also a sophisticated endomembrane system, a complex cytoskeleton and a unique sexual cycle, leaving the gap between cells of prokaryotic and eukaryotic design as the greatest chasm in biology.

    It left a gap that is not explained.

    However, the alternative must also be considered: the unattested ‘proto-eukaryotes’ or ‘progenotes’ may be purely hypothetical constructs required by the neo-Darwinian paradigm of incremental descent from LUCA and thus may never have existed at all.

    Really? You mean evolutionists just fantasized about the existence of proto-eukaryotes and called that “science”?

    As a result, the existence of ‘proto-eukaryotes’ transitional between archaea and eukaryotes remains an unsupported hypothesis within the 2D neo-Darwinian paradigm.

    Well the great thing about evolution is that everybody has their opinion. That’s what makes it more certain than gravity and proves there are no weaknesses in evolutionary theory. The fact that everybody has different false ideas about it just proves how strong the theory really is.

    An unanswered puzzle is how and why would a nuclear pore evolve to export mRNA or import RNA polymerase across a membrane in an archaeon before a nuclear membrane existed? This is particularly challenging since archaea possess a perfectly adequate system of coupled transcription and translation where mRNA already interacts directly with the translational apparatus (Benelli and Londei, 2011). Alternatively, how could a nuclear membrane evolve in an archaeon before nuclear pores were functional? Without nuclear pores, mRNA could not be exported from the nucleus and no RNA polymerase could be imported to the nucleus and thus, the nucleus could not function.

    What they mean by “unanswered puzzle” is that we don’t have 100% certainty – but of course, nothing in science is 100% certain so what’s the big problem here? Puzzles are good. Otherwise, evolution would be boring. As for all of those questions that indicate the illogic and absurdity of evolutionary claims, evolutionists certainly already have answers to all of that. We can be sure of it since they never admitted that there are any open questions at that most fundamental level which would put the entire evolutionary enterprise at risk. They made sure, under force of law, nobody could question evolutionary theory. So, certainly, a nuclear membrane evolved and was functional before the complex logic of membrane pores existed. The membrane just worked very nicely without the pores which allowed nutrients into the cell, blocked toxins and expelled waste. But then one day, the cell membrane needed pores – so they evolved.

    Finally, a notorious ‘queen of evolutionary problems’ related to the origin of the nucleus is the unresolved paradox of the origin of the eukaryotic sexual cycle (Bell, 1982). For the sexual cycle to function, two highly complex integrated but temporally and mechanistically unrelated processes must occur.

    There are no weaknesses in evolutionary theory. Sure there are unresolved paradoxes that are inexplicable and contradictory, but there’s nothing wrong with that. “Highly complex integrated but unrelated processes” were created by blind unintelligent causes. That happens so often there’s no need to even demonstrate how it’s possible. Who could question it?

    As for “the queen of evolutionary problems” – that just means “on the top of the stack of all of them”. Taking the effort to actually compile the entire list of evolutionary problems is far too much work for any Darwinian researchers to actually produce. Instead, it’s a lot easier to first deny that there are any problems at all, and then when one might be able to become a little famous by coming up with a novel solution, then proclaim that there’s actually a “queen” of problems and whole ranks of problems under that.

    To complete the sexual cycle and restore diploidy, mating between two haploid cells of opposite mating types must occur which requires both gamete recognition and a fusogen to fuse the haploid cells together to generate a diploid cell. The origin of this process is a paradox that has defied any generally accepted explanation for over 50?years and in part revolves around the challenge of determining which came first, meiosis that allows haploid gametes to be formed from a diploid or syngamy that allows 1?N haploid gametes to mate and create a 2?N diploid in the first place.

    The origin of this process by Darwinian mechanisms is a “paradox” which has “defied” explanation.
    These guys are strangely honest and transparent.

    Arguing these innovations were beneficial because they allowed the future evolution of complexity in the eukaryotic domain is clearly a teleological argument.

    Well, yes – but come on. What would evolution be without teleological assumptions and claims?
    Haven’t we all learned that evolution does things because it can foresee beneficial effects in the future? It just creates some things – useless at the time – and then holds on to them for when they’re going to be needed later.

  7. 7
    Fred Hickson says:

    ID theorists should step in and propose their explanation.

  8. 8
    Silver Asiatic says:

    ID gives evidence of intelligent design in nature. We know what intelligence can produce.
    This particular article undercuts claims that we know that natural causes did produce it.

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