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
Here’s a suggestion:
http://www.uncommondescent.com.....ent-583227
Here’s an observation:
http://www.uncommondescent.com.....ent-583240
Of related note:
Besides the gargantuan gap between single celled Archaea, Bacteria, and Eukarya there is also a gargantuan gap between single celled organisms and multicellular creatures:
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,,
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,,,
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.
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.
tjguy @4
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.
semi related:
disparity
[dih-spar-i-tee] noun, plural disparities.
1. lack of similarity or equality; inequality; difference:
OT:
The state of affairs over two years later.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5557255/pdf/13062_2017_Article_190.pdf
http://mmbr.asm.org/content/81/3/e00008-17
http://www.pnas.org/content/114/42/11018
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5507279/pdf/pone.0180827.pdf