A digital representation illustrating how LUCA was already under attack from viruses even at 4.2 billion years ago.
Science Graphic Design
Contrary to the Bible's laughable model of a 10,000-year-old universe consisting of a small flat planet with a dome over it, containing nothing that was unknown to the Bronze Age hill farmers whose best guess became part of the Hebrew creation myth, scientists at the University of Bristol have shown that the last universal common ancestor of all living organisms (LUCA) had evolved within 400 million years of Earth forming some 4.6 billion years ago.
They have calculated that LUCA was about as complex as a prokaryote, had already evolved an immune system and was engaged in an arms race with viruses.
Tell me about the last universal common ancestor of living organisms (LUCA) and what went before it. The Last Universal Common Ancestor (LUCA) is the most recent common ancestor of all current life on Earth. It is not necessarily the first living organism but rather the last one from which all modern organisms descend. Understanding LUCA provides insights into the origin and evolution of life.Even if they succeed in compressing all the evolution that has happened in the last 4.2 billion years into 10,000 years to try to reconcile the childish account in the Bible with the known facts, intelligent [sic] design creationists still need to account for arms races as the design of an omniscient designer, and not the obvious result of mindless, unintelligent, unplanned evolution between alliances of genes.
Characteristics of LUCA
- Genetic Code: LUCA likely had a genetic code similar to the universal genetic code seen in all modern organisms, using DNA to store genetic information.
- Metabolism: LUCA had a complex metabolism, probably capable of synthesizing proteins and nucleic acids. It may have used ATP as an energy currency.
- Cell Structure: It was likely a single-celled organism with a lipid membrane, though its exact structure is uncertain.
- Ribosomes: LUCA had ribosomes to synthesize proteins, an essential component of all living cells.
- Enzymes: It used enzymes to catalyze biochemical reactions, many of which are conserved across all domains of life (Bacteria, Archaea, and Eukaryotes).
What Came Before LUCA
Understanding what preceded LUCA involves exploring hypotheses about the origin of life, which are speculative and based on indirect evidence. Here are some key points:
- Prebiotic Chemistry: Before LUCA, there was a period known as prebiotic chemistry, where simple organic molecules formed through natural processes. Experiments like the Miller-Urey experiment have shown that amino acids and other basic building blocks of life can form under conditions that mimic early Earth.
- RNA World Hypothesis: One prevailing hypothesis is the RNA world, suggesting that early life forms used RNA both to store genetic information and to catalyze chemical reactions. RNA molecules can act as both genetic material and as enzymes (ribozymes), potentially leading to self-replicating systems.
- Protocells: These are simple, cell-like structures that could form spontaneously from fatty acids and other molecules. Protocells could encapsulate RNA or other biomolecules, creating a primitive, compartmentalized environment for chemical reactions.
- Metabolic Pathways: Early metabolic pathways might have arisen in hydrothermal vent environments, where minerals catalyzed the formation of organic molecules. This is supported by the discovery of ancient metabolic pathways that are shared by all modern life.
- Horizontal Gene Transfer: In the period leading up to LUCA, horizontal gene transfer (exchange of genes between different organisms) was likely common, complicating the tree-like representation of life's history. Early life forms may have shared genetic material more freely than modern organisms.
Evolutionary Steps to LUCA
- Abiogenesis: The process by which life arose from non-living matter, involving the formation of simple organic compounds and their assembly into more complex molecules.
- Formation of Self-Replicating Molecules: The emergence of molecules capable of self-replication, such as RNA, leading to the development of early genetic systems.
- Development of Protocells: The encapsulation of self-replicating molecules within lipid membranes, forming primitive cell-like structures.
- Evolution of Metabolic Pathways: The establishment of basic metabolic pathways that allowed these protocells to harness energy and grow.
- Emergence of LUCA: The last common ancestor from which all current life forms descend, characterized by more sophisticated cellular machinery and metabolic processes.
In summary, LUCA represents a crucial point in the history of life, the endpoint of a series of evolutionary steps that began with simple molecules and led to complex, self-replicating systems. The precise details of what came before LUCA remain a subject of ongoing research and debate, but they are rooted in the study of prebiotic chemistry, early metabolic pathways, and the properties of ancient life forms.
In an evolutionary arms race, the more successful leave more descendants and so increase the pressure on their competitors to evolve solutions to their improved abilities to either resist or predate. The idea of a super-intelligent designer having an arms race with itself is ludicrous in the extreme. The fact that creationists think of it as a sign of intelligence probably explains why they are creationists.
The problem for creationists who cite the scientifically nonsensical notions of 'devolution' and 'genetic entropy', is that arms races only exist if a mutation gives an improvement in reproductive success, so can't logically be regarded as less perfect than what went before it. A 'devolutionary' mutation would simply be filtered out of the gene pool, so could not accumulate within it, as anyone with even a basic understanding of evolution could have told their inventor, Michael J. Behe.
How the team arrived at these conclusions is the subject of an open access paper in Nature Ecology & Evolution and is the subject of a press release from the University of Bristol:
Insight into one of life’s earliest ancestors revealed in new study
An international team of researchers led by the University of Bristol has shed light on Earth’s earliest ecosystem, showing that within a few hundred million years of planetary formation, life on Earth was already flourishing.
Everything alive today derives from a single common ancestor known affectionately as LUCA (Last Universal Common Ancestor).
LUCA is the hypothesized common ancestor from which all modern cellular life, from single celled organisms like bacteria to the gigantic redwood trees (as well as us humans) descend. LUCA represents the root of the tree of life before it splits into the groups, recognised today, Bacteria, Archaea and Eukarya. Modern life evolved from LUCA from various different sources: the same amino acids used to build proteins in all cellular organisms, the shared energy currency (ATP), the presence of cellular machinery like the ribosome and others associated with making proteins from the information stored in DNA, and even the fact that all cellular life uses DNA itself as a way of storing information.
The team compared all the genes in the genomes of living species, counting the mutations that have occurred within their sequences over time since they shared an ancestor in LUCA.
The time of separation of some species is known from the fossil record and so the team used a genetic equivalent of the familiar equation used to calculate speed in physics to work out when LUCA existed, arriving at the answer of 4.2 billion years ago, about four hundred million years after the formation of Earth and our solar system.
We did not expect LUCA to be so old, within just hundreds of millions of years of Earth formation. However, our results fit with modern views on the habitability of early Earth.
Dr Sandra Álvarez-Carretero, co-author
Bristol Palaeobiology Group
School of Earth Sciences
University of Bristol, Bristol, UK.
Next, the team worked out the biology of LUCA by modelling the physiological characteristics of living species back through the genealogy of life to LUCA.
The evolutionary history of genes is complicated by their exchange between lineages. We have to use complex evolutionary models to reconcile the evolutionary history of genes with the genealogy of species.
Dr Edmund R. R. Moody explained, lead-author
Bristol Palaeobiology Group
School of Earth Sciences
University of Bristol, Bristol, UK.
One of the real advantages here is applying the gene-tree species-tree reconciliation approach to such a diverse dataset representing the primary domains of life Archaea and Bacteria. This allows us to say with some confidence and assess that level of confidence on how LUCA lived.
Dr Tom A. William, co-author
Bristol Palaeobiology Group
School of Biological Sciences
University of Bristol, Bristol, UK.
Our study showed that LUCA was a complex organism, not too different from modern prokaryotes, but what is really interesting is that it’s clear it possessed an early immune system, showing that even by 4.2 billion years ago, our ancestor was engaging in an arms race with viruses.
Professor Davide Pisani, Co-author
Bristol Palaeobiology Group
School of Earth Sciences
University of Bristol, Bristol, UK.It’s clear that LUCA was exploiting and changing its environment, but it is unlikely to have lived alone. Its waste would have been food for other microbes, like methanogens, that would have helped to create a recycling ecosystem.
Timothy M. Lenton, co-author
Global Systems Institute
University of Exeter, Exeter, UK.The findings and methods employed in this work will also inform future studies that look in more detail into the subsequent evolution of prokaryotes in light of Earth history, including the lesser studied Archaea with their methanogenic representatives.
Professor Anja Spang, co-author
Department of Marine Microbiology and Biogeochemistry, NIOZ
Royal Netherlands Institute for Sea Research
Den Burg, The Netherlands.The study also involved scientists from University College London (UCL), Utrecht University, Centre for Ecological Research in Budapest, and Okinawa Institute of Science and Technology Graduate University.Our work draws together data and methods from multiple disciplines, revealing insights into early Earth and life that could not be achieved by any one discipline alone. It also demonstrates just how quickly an ecosystem was established on early Earth. This suggests that life may be flourishing on Earth-like biospheres elsewhere in the universe.
Professor Philip C. J. Donoghue, Co-author
Bristol Palaeobiology Group
School of Earth Sciences
University of Bristol, Bristol, UK.
The research was funded by the John Templeton Foundation. The opinions expressed in this publication are those of the author(s) and do not necessarily reflect the views of the John Templeton Foundation.
Paper:‘The nature of the Last Universal Common Ancestor and its impact on the early Earth system’ by Edmund Moody et al in Nature Ecology & Evolution.
AbstractThe problem this presents creationists is one of their own making. Their entire 'argument' such as it is, is rarely more than the argument from ignorance, the god of the gaps and the false dichotomy fallacies, which they imagine means they don't need to produce any evidence for creationism; all they need do is attack science and point out what science doesn't yet know.
The nature of the last universal common ancestor (LUCA), its age and its impact on the Earth system have been the subject of vigorous debate across diverse disciplines, often based on disparate data and methods. Age estimates for LUCA are usually based on the fossil record, varying with every reinterpretation. The nature of LUCA’s metabolism has proven equally contentious, with some attributing all core metabolisms to LUCA, whereas others reconstruct a simpler life form dependent on geochemistry. Here we infer that LUCA lived ~4.2 Ga (4.09–4.33 Ga) through divergence time analysis of pre-LUCA gene duplicates, calibrated using microbial fossils and isotope records under a new cross-bracing implementation. Phylogenetic reconciliation suggests that LUCA had a genome of at least 2.5 Mb (2.49–2.99 Mb), encoding around 2,600 proteins, comparable to modern prokaryotes. Our results suggest LUCA was a prokaryote-grade anaerobic acetogen that possessed an early immune system. Although LUCA is sometimes perceived as living in isolation, we infer LUCA to have been part of an established ecological system. The metabolism of LUCA would have provided a niche for other microbial community members and hydrogen recycling by atmospheric photochemistry could have supported a modestly productive early ecosystem.
Main
The common ancestry of all extant cellular life is evidenced by the universal genetic code, machinery for protein synthesis, shared chirality of the almost-universal set of 20 amino acids and use of ATP as a common energy currency1. The last universal common ancestor (LUCA) is the node on the tree of life from which the fundamental prokaryotic domains (Archaea and Bacteria) diverge. As such, our understanding of LUCA impacts our understanding of the early evolution of life on Earth. Was LUCA a simple or complex organism? What kind of environment did it inhabit and when? Previous estimates of LUCA are in conflict either due to conceptual disagreement about what LUCA is2 or as a result of different methodological approaches and data3,4,5,6,7,8,9. Published analyses differ in their inferences of LUCA’s genome, from conservative estimates of 80 orthologous proteins10 up to 1,529 different potential gene families4. Interpretations range from little beyond an information-processing and metabolic core6 through to a prokaryote-grade organism with much of the gene repertoire of modern Archaea and Bacteria8, recently reviewed in ref. 7. Here we use molecular clock methodology, horizontal gene-transfer-aware phylogenetic reconciliation and existing biogeochemical models to address questions about LUCA’s age, gene content, metabolism and impact on the early Earth system.
Estimating the age of LUCA
Life’s evolutionary timescale is typically calibrated to the oldest fossil occurrences. However, the veracity of fossil discoveries from the early Archaean period has been contested11,12. Relaxed Bayesian node-calibrated molecular clock approaches provide a means of integrating the sparse fossil and geochemical record of early life with the information provided by molecular data; however, constraining LUCA’s age is challenging due to limited prokaryote fossil calibrations and the uncertainty in their placement on the phylogeny. Molecular clock estimates of LUCA13,14,15 have relied on conserved universal single-copy marker genes within phylogenies for which LUCA represented the root. Dating the root of a tree is difficult because errors propagate from the tips to the root of the dated phylogeny and information is not available to estimate the rate of evolution for the branch incident on the root node. Therefore, we analysed genes that duplicated before LUCA with two (or more) copies in LUCA’s genome16. The root in these gene trees represents this duplication preceding LUCA, whereas LUCA is represented by two descendant nodes. Use of these universal paralogues also has the advantage that the same calibrations can be applied at least twice. After duplication, the same species divergences are represented on both sides of the gene tree17,18 and thus can be assumed to have the same age. This considerably reduces the uncertainty when genetic distance (branch length) is resolved into absolute time and rate. When a shared node is assigned a fossil calibration, such cross-bracing also serves to double the number of calibrations on the phylogeny, improving divergence time estimates. We calibrated our molecular clock analyses using 13 calibrations (see ‘Fossil calibrations’ in Supplementary Information). The calibration on the root of the tree of life is of particular importance. Some previous studies have placed a younger maximum constraint on the age of LUCA based on the assumption that life could not have survived Late Heavy Bombardment (LHB) (~3.7–3.9 billion years ago (Ga))19. However, the LHB hypothesis is extrapolated and scaled from the Moon’s impact record, the interpretation of which has been questioned in terms of the intensity, duration and even the veracity of an LHB episode20,21,22,23. Thus, the LHB hypothesis should not be considered a credible maximum constraint on the age of LUCA. We used soft-uniform bounds, with the maximum-age bound based on the time of the Moon-forming impact (4,510 million years ago (Ma) ± 10 Myr), which would have effectively sterilized Earth’s precursors, Tellus and Theia13. Our minimum bound on the age of LUCA is based on low δ98Mo isotope values indicative of Mn oxidation compatible with oxygenic photosynthesis and, therefore, total-group Oxyphotobacteria in the Mozaan Group, Pongola Supergroup, South Africa24,25, dated minimally to 2,954 Ma ± 9 Myr (ref. 26).
Our estimates for the age of LUCA are inferred with a concatenated and a partitioned dataset, both consisting of five pre-LUCA paralogues: catalytic and non-catalytic subunits from ATP synthases, elongation factor Tu and G, signal recognition protein and signal recognition particle receptor, tyrosyl-tRNA and tryptophanyl-tRNA synthetases, and leucyl- and valyl-tRNA synthetases27. Marginal densities (commonly referred to as effective priors) fall within calibration densities (that is, user-specified priors) when topologically adjacent calibrations do not overlap temporally, but may differ when they overlap, to ensure the relative age relationships between ancestor-descendant nodes. We consider the marginal densities a reasonable interpretation of the calibration evidence given the phylogeny; we are not attempting to test the hypothesis that the fossil record is an accurate temporal archive of evolutionary history because it is not28. The duplicated LUCA node age estimates we obtained under the autocorrelated rates (geometric Brownian motion (GBM))29,30 and independent-rates log-normal (ILN)31,32 relaxed-clock models with our partitioned dataset (GBM, 4.18–4.33 Ga; ILN, 4.09–4.32 Ga; Fig. 1) fall within our composite age estimate for LUCA ranging from 3.94 Ga to 4.52 Ga, comparable to previous studies13,18,33. Dating analyses based on single genes, or concatenations that excluded each gene in turn, returned compatible timescales (Extended Data Figs. 1 and 2 and ‘Additional methods’ in Methods).
LUCA’s physiologyFig. 1: Timetree inferred under a Bayesian node-dating approach with cross-bracing using a partitioned dataset of five pre-LUCA paralogues.
Our results suggest that LUCA lived around 4.2 Ga, with a 95% confidence interval spanning 4.09–4.33 Ga under the ILN relaxed-clock model (orange) and 4.18–4.33 Ga under the GBM relaxed-clock model (teal). Under a cross-bracing approach, nodes corresponding to the same species divergences (that is, mirrored nodes) have the same posterior time densities. This figure shows the corresponding posterior time densities of the mirrored nodes for the last universal, archaeal, bacterial and eukaryotic common ancestors (LUCA, LACA, LBCA and LECA, respectively); the last common ancestor of the mitochondrial lineage (Mito-LECA); and the last plastid-bearing common ancestor (LPCA). Purple stars indicate nodes calibrated with fossils. Arc, Archaea; Bac, Bacteria; Euk, Eukarya.
To estimate the physiology of LUCA, we first inferred an updated microbial phylogeny from 57 phylogenetic marker genes (see ‘Universal marker genes’ in Methods) on 700 genomes, comprising 350 Archaea and 350 Bacteria15. This tree was in good agreement with recent phylogenies of the archaeal and bacterial domains of life34,35. For example, the TACK36 and Asgard clades of Archaea37,38,39 and Gracilicutes within Bacteria40,41 were recovered as monophyletic. However, the analysis was equivocal as to the phylogenetic placement of the Patescibacteria (CPR)42 and DPANN43, which are two small-genome lineages that have been difficult to place in trees. Approximately unbiased44 tests could not distinguish the placement of these clades, neither at the root of their respective domains nor in derived positions, with CPR sister to Chloroflexota (as reported recently in refs. 35,41,45) and DPANN sister to Euryarchaeota. To account for this phylogenetic uncertainty, we performed LUCA reconstructions on two trees: our maximum likelihood (ML) tree (topology 1; Extended Data Fig. 3) and a tree in which CPR were placed as the sister of Chloroflexota, with DPANN sister to all other Archaea (topology 2; Extended Data Fig. 4). In both cases, the gene families mapped to LUCA were very similar (correlation of LUCA presence probabilities (PP), r = 0.6720275, P < 2.2 × 10−16). We discuss the results on the tree with topology 2 and discuss the residual differences in Supplementary Information, ‘Topology 1’ (Supplementary Data 1).
We used the probabilistic gene- and species-tree reconciliation algorithm ALE46 to infer the evolution of gene family trees for each sampled entry in the KEGG Orthology (KO) database47 on our species tree. ALE infers the history of gene duplications, transfers and losses based on a comparison between a distribution of bootstrapped gene trees and the reference species tree, allowing us to estimate the probability that the gene family was present at a node in the tree35,48,49. This reconciliation approach has several advantages for drawing inferences about LUCA. Most gene families have experienced gene transfer since the time of LUCA50,51 and so explicitly modelling transfers enables us to include many more gene families in the analysis than has been possible using previous approaches. As the analysis is probabilistic, we can also account for uncertainty in gene family origins and evolutionary history by averaging over different scenarios using the reconciliation model. Using this approach, we estimated the probability that each KEGG gene family (KO) was present in LUCA and then used the resulting probabilities to construct a hypothetical model of LUCA’s gene content, metabolic potential (Fig. 2) and environmental context (Fig. 3). Using the KEGG annotation is beneficial because it allows us to connect our inferences to curated functional annotations; however, it has the drawback that some widespread gene families that were likely present in LUCA are divided into multiple KO families that individually appear to be restricted to particular taxonomic groups and inferred to have arisen later. To account for this limitation, we also performed an analysis of COG (Clusters of Orthologous Genes)52 gene families, which correspond to more coarse-grained functional annotations (Supplementary Data 2).Fig. 2: Probabilistic estimates of metabolic networks from modern life that were present in LUCA.
In black: enzymes and metabolic pathways inferred to be present in LUCA with at least PP = 0.75, with sampling in both prokaryotic domains. In grey: those inferred in our least-stringent threshold of PP = 0.50. The analysis supports the presence of a complete WLP and an almost complete TCA cycle across multiple confidence thresholds. Metabolic maps derived from KEGG47 database through iPath109. GPI, glycosylphosphatidylinositol; DDT, 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane.Fig. 3: A reconstruction of LUCA, within its evolutionary and ecological context.
a, A representation of LUCA based on our ancestral gene content reconstruction. Gene names in black have been inferred to be present in LUCA under the most-stringent threshold (PP = 0.75, sampled in both domains); those in grey are present at the least-stringent threshold (PP = 0.50, without a requirement for presence in both domains). b, LUCA in the context of the tree of life. Branches on the tree of life that have left sampled descendants today are coloured black, those that have left no sampled descendants are in grey. As the common ancestor of extant cellular life, LUCA is the oldest node that can be reconstructed using phylogenetic methods. It would have shared the early Earth with other lineages (highlighted in teal) that have left no descendants among sampled cellular life today. However, these lineages may have left a trace in modern organisms by transferring genes into the sampled tree of life (red lines) before their extinction. c, LUCA’s chemoautotrophic metabolism probably relied on gas exchange with the immediate environment to achieve organic carbon (Corg) fixation via acetogenesis and it may also have run the metabolism in reverse. d, LUCA within the context of an early ecosystem. The CO2 and H2 that fuelled LUCA’s plausibly acetogenic metabolism could have come from both geochemical and biotic inputs. The organic matter and acetate that LUCA produced could have created a niche for other metabolisms, including ones that recycled CO2 and H2 (as in modern sediments). e, LUCA in an Earth system context. Acetogenic LUCA could have been a key part of both surface and deep (chemo)autotrophic ecosystems, powered by H2. If methanogens were also present, hydrogen would be released as CH4 to the atmosphere, converted to H2 by photochemistry and thus recycled back to the surface ecosystem, boosting its productivity. Ferm., fermentation.
The problem there is that their argument gets weaker with every gap that closes and every gap-shrinking discovery shrinks their ever-decreasing little god, and this discovery is no exception. Now we have a pretty good idea of what LUCA was like and the evidence of parasitism that there was no intelligence behind its appearance of design, we can work out what changes were necessary to turn a self-replicating strand of RNA and/or a simple membrane-bound self-replicating proto-cell into something we would recognise as LUCA.
And of course, the evidence of parasitism also means that, far from being near impossible there was more than one evolutionary process at work producing a diversity of living organisms, some of which, viruses, had evolved in the presence of other organisms with the same genetic code, and providing the means to add new genetic information into the evolving genome.
Time for the creation cult to begin work on some new gaps of their own creation.
Viruses are indisputably the oldest life forms having existed since the early part of the Precambrian era, called the Hadean. The atmosphere of this early earth was anaerobic, suffocating, unbreathable, so these earliest life forms were obligate anaerobes and were designed to live in such inhospitable conditions. Planet earth is 4.6 billion years old, an almost unimaginable expanse of time, also called Deep Time. For us humans it's hard to imagine millions to billions of years. A mere 5 years or 10 years is considered a long time for many people. But what is 10 years compared to the 4.6 billion years of earth prehistory? It's just a drop in a swimming pool, its just a blink of an eye by geological standards.
ReplyDeleteThe middle part of the Precambrian era is known as the Archaean, and the late Precambrian is known as the Proterozoic. The awesome immensity of the Precambrian era is mind boggling and awe inspiring. We're talking about a time span from 4.6 billion years ago to 545 million years ago. This is a lot older than Dinosaurs and this was before even Arachnids and Insects existed! Cyanobacteria and Stromatolites were dominant life forms in the Precambrian and produced oxygen but the oxygen level during this time was hypoxic and unbreathable because iron absorbed all the oxygen, and because there was a much higher level of carbon dioxide, and because this was before large plants and trees existed. The oxygen in this early Precambrian earth failed to build up to a breathable level.
Jellyfish, sponges, anemones, and very strange and primitive aquatic animals existed during the late Precambrian. The question is did these very early and very primitive life forms have the capacity to suffer? I dont know but it's possible to take an educated guess. In my opinion, from what I know, the capacity to suffer physically came about sometime during the middle to late Paleozoic era, either during the Devonian period, or Carboniferous period, or Permian period, with early fish, amphibians, and reptiles. Obviously suffering increased as animals became more physically complex during the Mesozoic era with the Dinosaurs and especially during the Tertiary period when modern reptiles, mammals, and birds appeared.
The fact that LUCA was being attacked by viruses 4.2 billion years ago illustrates the great antiquity of Natural evil. The world was always a cruel, dangerous place right from the getgo. There was no idyllic Garden and no peaceable kingdom as the ignorant author of Genesis mentions. Genesis is so vague, ambiguous, unclear, and contradictory its impossible to even interpret what it's saying. We need to look at science for the truth.