F Rosa Rubicondior: Creationism in Crisis - Scientists Show LUCA (Last Universal Common Ancestor) Lived 4.32-4.52 Billion Years Before 'Creation Week'

Friday 24 November 2023

Creationism in Crisis - Scientists Show LUCA (Last Universal Common Ancestor) Lived 4.32-4.52 Billion Years Before 'Creation Week'

Figure 1: A schematic tree of life with the primary domains, the Archaea and Bacteria shown in purple and blue, respectively and the secondary domain, Eukaryotes in green. The figure highlights key nodes in the tree of life that have been calibrated against absolute time scales of Earth history. Estimates are given in Ga referring to billions of years (or giga annum).
Looking for ‘LUCA’ and the timing of cellular evolution - NIOZ

My previous two blog posts dealt firstly with the discovery of Neanderthal art in a cave in France which had been sealed with river debris since at least 40,000 years before creationism's supposed 'Creation Week' and secondly with the discovery of fossil trilobites in Thailand in rocks independently dated to about 490 million years before 'Creation Week'.

This one is bound to send creationists into deep denialism, shouting abuse at the fact and bearing false witness against the scientists who discovered it; it is the dating of the Last Universal Common Ancestor (LUCA), i.e., the primitive free-living organism from which all life on Earth is descended, to between 4.32 and at the most 4.52 billion years ago, in other words, to soon after Earth was really formed.

This of course means that abiogenesis occurred quite quickly once Earth had coalesced from the accretion disc around the new sun and had recovered from the collision with another minor planet which gave rise to the moon and tilted Earth on its axis.

Biologists Tara Mahendrarajah of the Royal Netherlands Institute for Sea Research (NIOZ) and senior author Anja Spang discovered this, in collaboration with colleagues from Universities in Bristol, Hungary and Tokyo.

The research is published open access in Nature Communications and is explained in an NIOZ press release entitled "Looking For 'LUCA' and the timing of cellular evolution":
LUCA, the ‘last universal common ancestor’ of all living organisms, lived 4.32 to at most 4.52 billion years ago. This is indicated by a study from NIOZ biologists Tara Mahendrarajah and senior author Anja Spang, with collaborating partners from Universities in Bristol, Hungary and Tokyo, that was published in Nature Communications. What LUCA looked like is unknown, but it must have been a cell with among others ribosomal proteins and an ATP synthase. "These proteins are shared by all bacteria, archaea, and eukaryotes such as plants and animals," Spang said. Using a new molecular dating approach, the researchers were able to more accurately estimate the moment when LUCA split into bacteria and archaea, as well as when eukaryotes emerged.

Dating the root

This new dating of the primordial form of all life is not dramatically different from previous estimates. “Dating gets increasingly uncertain towards the root of the tree of life”, co-corresponding author Tom Williams of the University of Bristol explains. One of the real surprises of this research by Mahendrarajah and colleagues are further up the tree of life. "Archaea are often called ancient bacteria," says Spang. "That would suggest that they stem from an ancestor that is older than the one of today's bacteria. But with this improved dating approach, we see that the ancestor of all current archaea lived between 3.37 and 3.95 billion years ago (Figure 1). This makes the last common ancestor of known archaea younger than the one of all bacteria, which lived between 4.05 and 4.49 billion years back (Figure 1). This suggests that earlier archaea either died out, or they live somewhere hidden on Earth where we have not found them yet,” Spang hypothesizes.

We are fusions

The eukaryotes, meaning cells with a nucleus, such as all plants and animals, had their last common ancestor between 1.84 to 1.93 billion years back (Figure 1). Tara Mahendrarajah explains: "If you imagine all life on earth as a family tree, LUCA is at the base and at some point, the trunk splits into a bacterial and an archaeal branch. But eukaryotes are not a separate branch on this tree of life, but rather a fusion of two branches that came out of the bacterial and the archaeal branches. We have a bit of both in us.”

Understanding natural history

“Our new estimates for the age of the archaeal and bacterial ancestors of eukaryotes will help to improve our models on eukaryotic origins”, Edmund Moody of the University of Bristol adds. “This new way of viewing the tree of life helps us track how cells have evolved over time on Earth. It also gives us a foundation to figure out what those early microbes did in their old environments and how their evolution is linked to natural history.”

Spang further points out: “Insights into the role of both ancient and extant microbes in nutrient cycling can help to better understand and predict future biodiversification in a changing environment, including climate warming”.
My comment, for what it's worth, is that the fact that archaea appear to be younger than bacteria could be because they evolved later by a different route to that of bacteria, so could represent a second abiogenesis. Archaea and bacteria could still have fused later into eukaryotes.

More technical detail is given in the team's open access paper in Nature Communications:

The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and rooting the tree of life. We reconstruct the evolutionary history of ATP synthases using an expanded taxon sampling set and develop a phylogenetic cross-bracing approach, constraining equivalent speciation nodes to be contemporaneous, based on the phylogenetic imprint of endosymbioses and ancient gene duplications. This approach results in a highly resolved, dated species tree and establishes an absolute timeline for ATP synthase evolution. Our analyses show that the divergence of ATP synthase into F- and A/V-type lineages was a very early event in cellular evolution dating back to more than 4 Ga, potentially predating the diversification of Archaea and Bacteria. Our cross-braced, dated tree of life also provides insight into more recent evolutionary transitions including eukaryogenesis, showing that the eukaryotic nuclear and mitochondrial lineages diverged from their closest archaeal (2.67-2.19 Ga) and bacterial (2.58-2.12 Ga) relatives at approximately the same time, with a slightly longer nuclear stem-lineage.
Fig. 3: Maximum-likelihood tree of all ATP synthase headpiece subunits identified in sampled Archaea (red), Bacteria (blue), and Eukaryotes (yellow).
A Homologs corresponding to each subunit form monophyletic clusters for each protein family. Catalytic subunits (cF1 and cA1V1) and non-catalytic subunits (ncF1 and ncA1V1) cluster together on either side of the root. The alignment contains 1520 sequences and was trimmed with BMGE v1.12 (settings: -m BLOSUM30 -h 0.55)110 (alignment length = 350 amino acids). The maximum-likelihood tree was inferred using IQ-TREE2 v2.1.2 with the LG+C50+R+F model, selected using the best-fitting model (chosen by BIC)111,123,132. The scale bar corresponds to the expected number of substitutions per site. The Walker-A motif from ancestrally reconstructed sequences123 are shown at their respective nodes. B Conserved protein motifs for each subunit derived from the same alignment.

Fig. 4: ATP synthase evolutionary scenarios.
A Overview of possible ancestral ATP synthase acquisition in LECA from the putative prokaryotic hosts; the A/V-type derived from the archaeal host, and F-type ATP synthases derived from bacterial endosymbionts. B Evolutionary proposal supporting an F-type-like ancestral ATP synthase present pre-LUCA with subsequent divergence consistent with the split between Bacteria and Archaea and early transfers of A/V-type ATP synthases into the bacterial stem, and late HGT of F-type ATP synthases to Archaea. C Evolutionary proposal supporting an F-type-like ancestral ATP synthase and pre-LUCA duplication and divergence of at least the head components of the F- and A/V-type subunits with subsequent loss of the F-type components along the archaeal stem. The cartoon of the ATP synthase was drawn manually in Adobe illustrator.

Fig. 5: Timing of cellular evolution across the tree of life based on a cross-braced dated ribosomal species tree and ATP synthase gene tree.
A Suggested timing of key evolutionary events based on a schematic ribosomal species tree. B Suggested timing of key evolutionary events based on a schematic ATP synthase gene tree. C Dated cross-braced ribosomal species tree (Edited2, see Methods) including nuclear, mitochondrial, and plastid eukaryotic homologs. See Methods for inference of the maximum-likelihood concatenated ribosomal species phylogeny and constraints (Edited2). The alignment contained 863 sequences and was trimmed with TRIMAL129 (alignment length = 2133 amino acids), and the maximum-likelihood phylogeny was inferred using IQ-TREE2 v2.1.2 the LG+C60+R+F model111,122,123. Abbreviations: b braced, nb non-braced, MAncL shared ancestor of mitochondria and closest alphaproteobacterial sister lineage, AAnc: shared ancestor of eukaryotic host lineage and closest asgardarchaeal sister lineage; Hod, Hodarchaeales; PAnc, shared ancestor of plastid and closest cyanobacterial sister lineage; c catalytic; nc non-catalytic; F F-type ATP-synthase; AV AV-type ATP-synthase.

Regardless of the debate about whether archaea were the ancestors of bacteria or evolved by a different pathway from simple self-replicating molecules, the fact remains that both were present several billion years before creationists think Earth existed and fused to form the first eukaryote cells that went on to form all multicellular organisms including humans.

Once again, we see science revealing that key events in the history of life on Earth happened in that vast expanse of time before 'Creation Week'.

And there will undoubtedly be more bad news for creationists on that score in the days to come. And still there is no sign of the abandonment of the Theory of Evolution in favour of creationists' childish superstition by mainstream biologists, as has regularly been predicted by creationist frauds, and swallowed hook, line and sinker by their credulous dupes, for some 20 years or more.

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