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Researcher claims to have simplified account of eukaryote origin

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Strikes blow against “ominous specter of irreducible complexity”

Archaeal ancestors of eukaryotes are not so elusive any more, says Eugene V. Koonin,

Thus, eukaryotes show a qualitatively different level of cellular organization from that of archaea and bacteria, and there are no detectable evolutionary intermediates. Comparative analysis of eukaryotic cells and genomes indicates that the signature advanced functional systems of the eukaryotic cells were already present in the last eukaryotic common ancestor (LECA). These ancestral features include the actin and tubulin-based forms of cytoskeleton, the nuclear pore, the spliceosome, and the ubiquitin signaling network, to mention only several aspects of the inherent organizational complexity of eukaryotic cells [12]-[16]. The emergence of these fundamental facets of advanced cellular organization presents a challenge of such scale that Darwin’s famous scenario for the evolution of the eye looks like a straightforward solution to an easy problem. To some, the enigma of eukaryogenesis can appear so perplexing that the infamous concept of ‘irreducible complexity’ has sneaked into the scientific mainstream [17], although debunking of these ideas has not been long in coming [18]. Below I discuss the recent advances in evolutionary genomics that make the origin of eukaryotes much less mysterious than it appeared even recently.

Also dumps on Tree of Life:

The newly achieved clarity in our understanding of these key aspects of eukaryogenesis calls for reassessment of some of the most general concepts in biology. The first one is the representation of the entire history of life as a single evolutionary tree, a grand idea that goes back to the famous single illustration of Darwin’s Origin of Species[70]. The symbiogenetic scenario of eukaryogenesis flatly defies this concept because under this scenario, a major kingdom of life, the eukaryotes, emerged in a non-tree-like manner, through fusion of different, distant branches of the tree. The importance of trees for understanding the evolution of individual genes, gene ensembles and major taxa, especially those that encompass multicellular eukaryotes, is undeniable [71]. However, the new findings on the origin of eukaryotes as well as the origin of archaeal phyla [72] indicate that major transitions in evolution often, perhaps typically, occur through the fusion of cells and/or genomes of distantly related organisms. The second, not unrelated general theme is the number and nature of the primary domains of life. In the late 1980s, based on the rRNA trees, Woese and colleagues developed the three-domain scheme (Fig. 1a) [19]. The placement of eukaryotes within the archaeal branch that has been clinched by the discovery of Loki refutes this scheme and shows that the only consistent interpretation of the phylogeny of the universal (primarily informational) genes involves two primary domains: bacteria and archaea (with eukaryotes included) (Fig. 1b) [45].

Wanna bet the Tree of Life will still be in the textbooks a dozen years from now? Here’s why, probably.

Here’s the abstract:

The origin of eukaryotes is one of the hardest problems in evolutionary biology and sometimes raises the ominous specter of irreducible complexity. Reconstruction of the gene repertoire of the last eukaryotic common ancestor (LECA) has revealed a highly complex organism with a variety of advanced features but no detectable evolutionary intermediates to explain their origin. Recently, however, genome analysis of diverse archaea led to the discovery of apparent ancestral versions of several signature eukaryotic systems, such as the actin cytoskeleton and the ubiquitin network, that are scattered among archaea. These findings inspired the hypothesis that the archaeal ancestor of eukaryotes was an unusually complex form with an elaborate intracellular organization. The latest striking discovery made by deep metagenomic sequencing vindicates this hypothesis by showing that in phylogenetic trees eukaryotes fall within a newly identified archaeal group, the Lokiarchaeota, which combine several eukaryotic signatures previously identified in different archaea. The discovery of complex archaea that are the closest living relatives of eukaryotes is most compatible with the symbiogenetic scenario for eukaryogenesis. (Open access) – BMC Biology 5 October 2015, 13:84 | doi:10.1186/s12915-015-0194-5

Yes, but this was the same guy who was willing to accept the multiverse as a means of eliminating the problem of vast complexity in life forms.

So I wouldn’t bet anything I needed on his current suggestions making “the origin of eukaryotes much less mysterious than it appeared even recently.”

When a researcher wants to discredit something (irreducible complexity, in this case) this badly, he is apt to swat at just anything whistling past. When he uses terms like “ominous specter” and “much less mysterious” to describe his battle, we can be fairly certain of one thing: The next round of conundrums and complexities will blow the speculations high.

Eventually, such theorists will get around to addressing the enigma of information. But don’t cancel any engagements in anticipation; they have hardly begun to speculate yet. 😉

See also: In a Darwinian multiverse, Eugene Koonin could be both right and wrong an infinite number of times

The multiverse: Where everything turns out to be true, except philosophy and religion

Multiverse cosmology: Assuming that evidence still matters, what does it say?

In search of a road to reality

9 Replies to “Researcher claims to have simplified account of eukaryote origin

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    bornagain says:

    Of related note:

    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
    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.

    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.

    Besides the gargantuan gap between single celled Archaea, Bacteria, and Eukarya there is also a gargantuan gap between single celled organisms and multicellular creatures:

    Challenging Fossil of a Little Fish
    Excerpt: “I think this is a major mystery in paleontology,” said Chen. “Before the Cambrian, we should see a number of steps: differentiation of cells, differentiation of tissue, of dorsal and ventral, right and left. But we don’t have strong evidence for any of these.” Taiwanese biologist Li was also direct: “No evolution theory can explain these kinds of phenomena.”

    “We go from single cell protozoa. which would be amoeba and things like that. Then you get into some that are a little bit bigger, still single cell, and then you get aggregates, they’re still individual cells that aggregate together. They don’t seem to have much in the way of cooperation,,, but when you really talk about a functioning organism, that has more than just one type of cell, you are talking about a sponge and you can have hundreds, thousands, tens of thousands of cells. So we don’t really have organisms that function with say two different types of cells, but there is only five total. We don’t have anything like that.”
    – Dr. Raymond G. Bohlin – quote taken from 31:00 minute mark of this following video
    Natural Limits to Biological Change 2/2 – video

    From one cell to many: How did multicellularity evolve? January 25, 2014
    Excerpt: Indeed, no matter how it is defined, scientists agree that multicellularity has occurred multiple times across many clades. Defined in the loosest sense, as an aggregation of cells, multicellularity has evolved in at least 25 lineages. However, even when defined more strictly — requiring that cells be connected, communicate, and cooperate in some fashion or another — it has still notably evolved once in animals, three times in fungi, six times in algae, and multiple times in bacteria.,,,

    That Conference On The Evolution of Multicellularity Revealed The Usual Problems – Cornelius Hunter – December 25, 2013
    Excerpt: “The emergence of multicellular animals or metazoans from their single-celled ancestors is one of the most important evolutionary transitions in the history of life. However, little is known about how this transition took place.”,,,
    “That is nowhere more true than with the miracle of multicellularity which, if evolution is true, must have independently evolved more than, err, twenty-five times.”

    So unguided evolution somehow now did the ‘miracle’ of multicellularity 25 times?

    The experimental evidence certainly does not suggest that such a transition from single cell aggregates to multicellular organisms is possible. To highlight the monumental problem that unguided Darwinian processes face going from a single cell organism to a multicellular creature, it is important to note the extreme (empirically established) difficulty in obtaining just two protein-protein binding sites,,

    “The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable.”
    Michael J. Behe PhD. (from page 146 of his book “Edge of Evolution”)

    To give a small glimpse at the monumental challenge this poses to unguided Darwinian processes, Dr. Behe, on Table 7.1 on page 143 of Edge Of Evolution, finds that a typical ‘simple’ single cell might have some 10,000 protein-binding sites. Whereas a conservative estimate for protein-protein binding sites for a multicellular creature is,,,

    Largest-Ever Map of Plant Protein Interactions – July 2011
    Excerpt: The new map of 6,205 protein partnerings represents only about two percent of the full protein- protein “interactome” for Arabidopsis, since the screening test covered only a third of all Arabidopsis proteins, and wasn’t sensitive enough to detect many weaker protein interactions. “There will be larger maps after this one,” says Ecker.

    So taking into account that they only covered 2%, of the full protein-protein “interactome” in the plant, then that gives a number, for different protein-protein interactions in the plant, of 310,000. Thus, from my very rough ‘back of the envelope’ calculation, we find conservatively that some 300,000 different protein/protein binding sites would have to be generated for each multicellular creature to ’emerge’ from some single cell creature.
    Therefore, from my very rough calculation, it certainly appears to be a vastly impossible step that unguided ‘bottom up’ material processes cannot possibly make to go from a single cell to a multicellular creature.

    But ‘vastly impossible’ never stopped true Darwinians from believing in Darwinism before, and I certainly don’t expect such ‘vastly impossible’ odds to dent their blind faith in unguided material processes now.

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    tjguy says:

    I went to the site and noticed that at least his article was listed as an opinion. So, gotta give ’em credit for not claiming this as fact.

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    Dionisio says:

    tjguy @4

    I went to the site and noticed that at least his article was listed as an opinion. So, gotta give ’em credit for not claiming this as fact.

    Thank you for sharing your observation here.

    As indicated in the comments referenced @1 & @2 in this thread, even if their findings were factual, they would only be (1) passive genomic descriptions, rather than (2) hypothetical functional processes underlying the required changes of developmental cellular/molecular choreographies within a given biological system (X/Y) in order to get another biological system (Y/Z).
    There’s a HUGE* gap between the former (1) and the latter (2) cases.
    Those who daydream about crossing that gap on their hypothetical ‘canoes’ are doomed to a frustratingly unpleasant experience, filled with shocking/intriguing/unexpected/surprising discoveries in the days ahead, as ongoing research will keep shedding more light (at an accelerated pace) on the elaborate cellular and molecular choreographies orchestrated within the biological systems.
    It is well known to all that only intelligent design can produce that kind of information-processing systems at such a complexity level. At least we are not aware of another source of it.
    To many folks out there matter and energy is all there’s, hence they are willing to take their ideas through all kinds of acrobatic pirouettes for the sake of sticking to their worldview positions.
    However, to some of us, the Ultimate Reality is summarized in this sentence: “In the beginning was the Word”. It’s all settled. Hence we delight in the knowledge of the marvelous creation and wonder like children.
    These are fascinating times to see what true science is discovering. I encourage young people to pursue careers in exciting research fields like biology.

    (*) in this case HUGE is a gross understatement, but my poor vocabulary lacks better terms.

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    bornagain says:

    semi related:

    In Allaying Darwin’s Doubt, Two Cambrian Experts Still Come Up Short – October 16, 2015
    Excerpt: “A recent analysis of disparity in 98 metazoan clades through the Phanerozoic found a preponderance of clades with maximal disparity early in their history. Thus, whether or not taxonomic diversification slows down most studies of disparity reveal a pattern in which the early evolution of a clade defines the morphological boundaries of a group which are then filled in by subsequent diversification. This pattern is inconsistent with that expected of a classic adaptive radiation in which diversity and disparity should be coupled, at least during the early phase of the radiation.”
    – Doug Erwin
    What this admits is that disparity is a worse problem than evolutionists had realized: it’s ubiquitous (throughout the history of life on earth), not just in the Cambrian (Explosion).

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    bornagain says:

    [dih-spar-i-tee] noun, plural disparities.
    1. lack of similarity or equality; inequality; difference:

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    bornagain says:


    COMPASS method points researchers to protein structures – October 15, 2015
    Excerpt: Searching for the precise, complexly folded three-dimensional structure of a protein can be like hacking through a jungle without a map: a long, intensive process with uncertain direction. University of Illinois researchers developed a new approach, dubbed COMPASS, that points directly to a protein’s likely structure using a combination of advanced molecular spectroscopy techniques, predictive protein-folding algorithms and image recognition software.,,,
    “We’ve taken a process that would take months and brought it down to hours,”,,,
    For COMPASS, the researchers rely on a single spectrum measurement using a spectroscopic technique called nuclear magnetic resonance, which gives a molecular “fingerprint” – no two protein structures have the same spectrum.
    The COMPASS platform looks at the possible structures generated by the predictive models, projects a spectrum for each one, and uses advanced image-recognition software to compare each projected spectrum with the spectrum collected from the experimental sample.
    “We call it COMPASS because we’re using a magnetic field to hopefully point us in the right direction of which protein structure is the right one out of all these options,” Rienstra said.
    The researchers compared COMPASS results of 15 proteins to the structure information determined from traditional methods, and found that COMPASS was successful in correctly determining the proteins’ structures.

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