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ElShamah - Reason & Science: Defending ID and the Christian Worldview

Otangelo Grasso: This is my library, where I collect information and present arguments developed by myself that lead, in my view, to the Christian faith, creationism, and Intelligent Design as the best explanation for the origin of the physical world.

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Pelagibacter Ubique is the best candidate to investigate Origin of life scenarios. Here is why

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Pelagibacter Ubique is the best candidate to investigate Origin of life scenarios. Here is why


The smallest free-living cell that is capable of synthesizing all amino acids on its own is the bacterium called Pelagibacter ubique, also known as SAR11. It is a marine bacterium that has a diameter of only about 0.1 to 0.2 micrometers, making it one of the smallest known organisms. Pelagibacter ubique is able to produce all 20 standard amino acids on its own, which is a unique feature among free-living bacteria. This is in contrast to many other bacterial species, which rely on external sources of amino acids for growth and survival. The ability of Pelagibacter ubique to synthesize all its own amino acids is thought to be a key adaptation for its survival in nutrient-poor environments, such as the open ocean. Pelagibacter ubique, like all living cells, has a gene regulatory network that controls the expression of its genes. The gene regulatory network of Pelagibacter ubique is relatively simple compared to that of other bacterial species, as it has one of the smallest known genomes of any free-living organism. However, even with its small genome size, Pelagibacter ubique has been shown to have a complex gene regulatory network that allows it to respond to changes in its environment, such as nutrient availability and temperature. The bacterium has been found to have a number of regulatory genes, including transcription factors and signal transduction proteins, which are involved in controlling the expression of its genes. These regulatory genes allow Pelagibacter ubique to adjust its metabolism and other cellular processes in response to changing environmental conditions. A gene regulatory network is essential for the function and survival of all living cells. The gene regulatory network controls the expression of genes, which in turn determines the specific proteins and other molecules that a cell produces, as well as when and in what amounts they are produced.

This regulation is critical for the proper functioning of cellular processes, such as metabolism, growth, and response to environmental cues. Without a gene regulatory network, a cell would not be able to properly respond to changing conditions, adapt to its environment, or carry out the functions necessary for its survival. The complexity of the gene regulatory network can vary greatly between different types of cells and organisms, but all living cells must have some level of gene regulation to maintain proper cellular function and survive. Yes, that's correct. A gene regulatory network and genes are interdependent, and neither has any function without the other. Genes are the basic units of heredity that contain the instructions for making the proteins and other molecules that a cell needs to function. However, the expression of genes must be properly regulated to ensure that the right molecules are produced at the right time and in the right amounts. This is where the gene regulatory network comes in - it is responsible for controlling the expression of genes and ensuring that the correct proteins and molecules are produced in response to the cell's needs and its environment. In other words, genes provide the raw material for the cell, while the gene regulatory network acts as the control system that coordinates the use of this raw material to ensure proper cellular function. Both are necessary for the cell to function properly and carry out the processes that are essential for life.

Yes, interdependence is a fundamental concept in biology. Organisms and their components, such as genes and regulatory networks, are highly interdependent and cannot function in isolation. Living organisms are made up of complex, interconnected systems of molecules, cells, tissues, and organs, and each part of the system relies on the others to function properly. For example, in order for a cell to carry out its functions, it requires a complex network of interacting molecules, including proteins, nucleic acids, lipids, and carbohydrates. Similarly, in order for an organism to survive and reproduce, it must be able to carry out a wide range of physiological and behavioral processes that are interdependent and require coordination. The study of biology seeks to understand these complex systems and the interdependencies that exist between their components, as well as the interactions between living organisms and their environment. By understanding these interdependencies, we can gain insights into how living systems work, and how they respond to changing conditions, which has important implications for fields such as medicine, agriculture, and ecology.

Life presumably started simple. This is plausible, but is an assumption. The smallest known bacteria are still rather large. One of the smallest known metabolically autonomous bacterial species is Pelagibacter ubique with about 1,400 genes (Giovannoni et al., 2005). Genome reduction of Mycoplasma mycoides by systematic deletion of individual genes resulted in a synthetic minimal genome of 473 genes (Hutchison et al., 2016). Can one consider simpler living entities?

The first life form, the supposedly Last Universal Common Ancestor (LUCA), had to be already amazingly complex. One of the smallest free living creatures we know of, Pelagibacter Ubique, for example, which is also the most abundant organism on earth, a tiny bacterium, requires 1,3 million nucleotides, the building blocks of DNA. If we suppose that an unguided event ordered the right sequence, there would have to be 10^722000 attempts to get the right sequence. There are 10^80 atoms in the entire known universe.

The genome of P. ubique strain HTCC1062 was completely sequenced in 2005 showing that P. ubique has the smallest genome (1,308,759 bp) of any free living organism encoding only 1,354 open reading frames (1,389 genes total). The only species with smaller genomes are intracellular symbionts and parasites, such as Mycoplasma genitalium or Nanoarchaeum equitans It has the smallest number of open reading frames of any free living organism, and the shortest intergenic spacers, but it still has metabolic pathways for all 20 amino acids and most co-factors. 6

SAR11 Alphaproteobacteria (order Pelagibacterales) are the most abundant chemo-organotrophic bacteria in the oceans 1

“Sometimes we should try to ask the simplest questions. One of the simplest questions that my lab has concerned itself with over the last couple of decades is ‘how does a cell that is so simple—1.3 million base pairs, a little over 1000 genes—how does a cell that’s so simple succeed in capturing such a large part of all the organic matter entering the oceans?” 2

SAR11 is the most abundant organism on the planet! “If you go the ocean, and you go for a swim, and you accidentally swallow a mouthful of seawater, you’ve probably swallowed a million SAR11 cells.” 3

P. ubique is one of the smallest free-living cells. Tiny as it is, you may not be surprised to learn that P. ubique also has a small genome (1,308,759 bp), currently the smallest genome known for a free-living organism. The genome encodes 1,354 predicted proteins, 1 rRNA operon , and 32 tRNAs.

Genome data indicate that this bacterium possesses the complete pathways required to generate energy by respiration and also to harvest energy from the sun using proteorhodopsin, a light-dependent, retinylidine proton pump. P. ubique is also equipped with numerous high affinity nutrient transporters, consistent with a competitive strategy for nutrient scavenging. Most are ABC transporters, a large and ancient protein family noted for providing high substrate affinities at the cost of copious ATP. Clearly, the cells invest in transport to outcompete other microbes in nutrient acquisition and, based on their abundance and efficient assimilation of organic matter, they have succeeded.4.

Pelagibacter ubique, strain HTCC1062, is significantly known to be one of smallest and simplest, self-replicating, and free living cell. It is part of the SAR11 clade, which are small, heterotrophic alphaproteobacteria, equaling to ~25% of all microbial plankton cells. 5

Streamlining and Core Genome Conservation among Highly Divergent Members of the SAR11 Clade 7
SAR11 has evolved into perhaps a dozen or more specialized ecotypes that span evolutionary distances equivalent to a bacterial order. We found small genomes throughout the clade and a very high proportion of core genome genes (48 to 56%), indicating that small genome size is probably an ancestral characteristic.  In their level of core genome conservation, the members of SAR11 are outliers, the most conserved free-living bacteria known. Variation among the genomes included genes for phosphorus metabolism, glycolysis, and C1 metabolism, suggesting that adaptive specialization in nutrient resource utilization is important to niche partitioning and ecotype divergence within the clade. The SAR11 clade is the most abundant group of marine microorganisms worldwide, making them key players in the global carbon cycle. Study of isolates in culture revealed atypical organic nutrient requirements that can be attributed to genome reduction, such as conditional auxotrophy for glycine and its precursors.

Pelagibacter Ubique is the best candidate to investigate Origin of life scenarios. Here is why F2_lar12
(A) Venn diagram showing the number of OCs shared between the SAR11 subclade Ia core genome, HIMB114, and HIMB59.
(B) The relative contribution of core (blue), shared non-core (orange), and unique (red) orthologs to the pan-genome at each level of divergence. The total size of each bar is proportional to the total number of orthologs in the pan-genome. The scale bar indicates 0.2 changes per position. The tree was redrawn based on the work of Thrash et al. (6). (C) Venn diagram showing the number of shared OCs among the five strains of SAR11 subclade Ia.

At ~600 genes, the core genome for SAR11 provides an estimate of the lower limit of genes essential for maintenance of the free-living state in marine environments.

Small genomes suggest specialization, but the members of SAR11, which have small genomes, cannot plausibly be characterized as specialists, being one of the most successful and widely distributed chemoheterotrophic groups in the ocean.

Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade14 June 2011  8
Mitochondria share a common ancestor with the Alphaproteobacteria, but determining their precise origins is challenging due to inherent difficulties in phylogenetically reconstructing ancient evolutionary events.  The evidence supports a common origin of mitochondria and SAR11 as a sister group to the Rickettsiales. The simplest explanation of these data is that mitochondria evolved from a planktonic marine alphaproteobacterial lineage that participated in multiple inter-specific cell colonization events, in some cases yielding parasitic relationships, but in at least one case producing a symbiosis that characterizes modern eukaryotic life. Vital to the evolution of all known eukaryotic cells was the endosymbiotic event that resulted in the permanent acquisition of bacteria that through time were transformed into mitochondria. Even eukaryotes that were previously thought to lack mitochondria have now been shown to contain some remnants of that original endosymbiosis.  current hypotheses, making use of mitochondrial genome and proteome data, agree that the mitochondrial ancestor was most closely related to Alphaproteobacteria. The sequencing of the first Rickettsia genome provided phylogenomic evidence for the previously established theory that the mitochondrial root was within the Rickettsiales.

The sequencing of the first Rickettsia genome provided phylogenomic evidence for the previously established theory that the mitochondrial root was within the Rickettsiales5,10,12,13 (and references therein). This theory was intellectually satisfying because all known Rickettsia have extremely reduced genomes and obligate intracellular lifestyles, although there was evidence to suggest that the genome reduction in mitochondria and Rickettsia probably happened independently.

SAR11 genomes bear distinctly different evolutionary signatures from other Rickettsiales genomes, indicating that selection for a streamlined genome, rather than genetic drift, has been the path of genome reduction in these organisms. For example, the sequence of Candidatus Pelagibacter ubique HTCC1062 has few recent gene duplications, phage, transposons, or pseudogenes, has extremely small intergenic regions and is optimized for a highly efficient lifestyle, whereas organisms like Rickettsia and those of the Anaplasmataceae contain large numbers of duplications, putatively inactive genes, larger intergenic regions, and/or mobile elements, indicative of the different selective pressures of obligate intracellular life.

Modern SAR11 cells have small genomes imposed by selection for efficient replication in nutrient limited systems17, which have evolved unusual nutritional requirements that would pre-adapt them to closer dependence on other organisms.

1. https://sci-hub.ren/10.1038/nmicrobiol.2016.65
2. https://asm.org/Podcasts/MTM/Episodes/SAR11-and-Other-Marine-Microbes-with-Steve-Giovann
3. https://twitter.com/asmicrobiology/status/1209160770136813568
4. https://schaechter.asmblog.org/schaechter/2015/02/the-most-abundant-small-things-considered.html
5. https://microbewiki.kenyon.edu/index.php/Pelagibacter_ubique
6. https://alchetron.com/Pelagibacter-ubique
7. https://mbio.asm.org/content/3/5/e00252-12
8. https://www.nature.com/articles/srep00013

Pelagibacter Ubique is the best candidate to investigate Origin of life scenarios. Here is why Pelagi10

Last edited by Otangelo on Fri 17 Feb 2023 - 19:35; edited 10 times in total




Three-Dimensional Structure of the Ultraoligotrophic Marine Bacterium “Candidatus Pelagibacter ubique” 1

Transport functions dominate the SAR11 (Pelagibacter ubique) metaproteome at low-nutrient extremes in the Sargasso Sea 2
The membrane protease HflKC and the chaperone proteins GroEL, GroES and DnaK were among the most prevalent proteins detected in this study; ATP-dependent proteases FtsH. The detection of these chaperone and protease proteins suggests that protein refolding and proteolysis may be integral to bacterial survival in ocean surface water, because proteins are continually being damaged as a result of exposure to environmental stresses.

Imagine machines, that fix machines, which help to fix other machines.  All fully set up to operate in an independent, fully automated, robot-like manner. Evidently, such a process/system requires the highest sort of engineering artistry and foreknowledge of what could get wrong and how to fix the errors.

That is what we see in life.

Proteins,marvelous pieces of chemical nanoengineering, in order to become functional, must fold from linear, to specific 3-D forms. Properly folded proteins are essential for life because they conduct most of the necessary functions in a cell. If it folds into the wrong shape, a protein is useless. If the first proteins fell into these death valleys, life on Earth would never have appeared. Spontaneous folding is quite rapid (milliseconds to seconds) for many proteins, but many large, critical proteins fail to find by themselves the right shape and, without help, would become only so much molecular waste.So when a protein misfolds, other proteins, named chaperonins, help proteins fold into the right shape. They have been shown to interact with up to 30% of the cell’s proteins, so their importance is real. Now, amazingly, even these very own proteins, named GroEL, which help misfolded proteins to fold properly, can also misfold. And it has been  shown that GroES, a co-chaperone assists in folding GroEL. Amazing. Machines, that help other machines to assemble properly, are by themselves subject to errors, and life has inbuilt mechanisms to fix as well these machines that help fixing other machines !!

Molecular Chaperones Help Guide the Folding of Most Proteins

SAR11 bacteria are small, heterotrophic, marine alphaproteobacteria found throughout the oceans. They thrive at the low nutrient concentrations typical of open ocean conditions. We studied “Candidatus Pelagibacter ubique” strain HTCC1062, a member of the SAR11 clade. Its cellular dimensions and details of its intracellular organization. Frozen-hydrated cells, which were preserved in a life-like state, had an average cell volume (enclosed by the outer membrane) of 0.037 ± 0.011 μm3. Strikingly, the periplasmic space occupied ∼20% to 50% of the total cell volume in log-phase cells and ∼50% to 70% in stationary-phase cells. The nucleoid occupied the convex side of the crescent-shaped cells and the ribosomes predominantly occupied the concave side, at a relatively high concentration of 10,000 to 12,000 ribosomes/μm3. Long filaments, most likely type IV pili, were found on dividing cells. The physical dimensions, intracellular organization, and morphological changes throughout the life cycle of “Ca. Pelagibacter ubique” provide structural insights into the functional adaptions of these oligotrophic ultramicrobacteria to their habitat.

Ribosomes are relatively abundant in the Pelagibacter cytoplasm, considering its small volume and slow growth. The ribosome concentration of Pelagibacter is about twice as high as the concentration in slowly growing E. coli cells, although Pelagibacter grows significantly (30-fold) more slowly than E. coli.

Evolution of Divergent Life History Strategies in Marine Alphaproteobacteria 3

Pelagibacter Ubique is the best candidate to investigate Origin of life scenarios. Here is why Model-11
Figure 1 Model-based phylogenomic trees of alphaproteobacteria based on a concatenation of 60 orthologous protein sequences using the P4 Bayesian software with the NDCH and NDRH models (A), the RAxML software (B), and the PhyloBayes software with the CAT model (C). A Bayesian phylogeny using MrBayes with or without the covarion model had the same branching order as the RAxML tree. The node representing the most recent common ancestor (MRCA) of the Roseobacter and SAR11 lineages is indicated with a red dot, and the predicted gene number for the MRCA is indicated. For clarity, only the deep branches connecting the major lineages and their statistical support values are shown. The complete trees are shown in Fig. S1 in the supplemental material.

The phylogenetic birth-and-death model consistently predicted that the small extant SAR11 genomes (1,300 to 1,500 genes) evolved from a slightly larger common ancestor (~2,000 genes; Fig. 2A; see also Fig. S2A and C)

Dating Alphaproteobacteria evolution with eukaryotic fossils
We estimate that Alphaproteobacteria arose ~1900 million years (Ma) ago 10

The most recent common ancestor (MRCA) (Fig. 1B) of the SAR11 and Roseobacter lineages is predicted to have had only ~2,100 genes, suggesting only a trivial reduction to the SAR11 ancestor. If the SAR11 lineage branched off either before (Fig. 1A) or after (Fig. 1C) the marine SAR116 lineage (represented by the “Candidatus Puniceispirillum marinum” IMCC1322 genome), the MRCA genome is predicted to contain either ~3,300 or ~6,900 genes (Fig. 1A and C), with the latter most strongly supporting the hypothesis that genomic and metabolic streamlining is the primary evolutionary process influencing the content of extant SAR11 genomes. The cyanobacteria and green algae dominated the early ocean.  

Pelagibacter Ubique is the best candidate to investigate Origin of life scenarios. Here is why Ancest10
FIG 2 Ancestral genome content reconstruction using the COUNT software. The reconstruction is based on the P4-based alphaproteobacterial tree (see Fig. S1 in the supplemental material), but only the parts of the results involving marine SAR11 (A) and Roseobacter (B) are shown. The log-scale color coding represents numbers of reconstructed gain and loss events of each lineage. Numbers in parentheses are predicted gene numbers for ancestral nodes and observed gene numbers for extant lineages. The genome expansion on the Roseobacter branch leading to R37 was statistically significant based on reconstruction of randomized genome content in 100 bootstrapped replicates (see Table S3).

Alpha proteobacterium HIMB59
Number of nucleotides:       1410127
Number of protein genes:        1493
Number of RNA genes:              38

Rhodobacterales bacterium HTCC2255
Est. Genome size (bp) 4,812,704 9

Pelagibacter Ubique is the best candidate to investigate Origin of life scenarios. Here is why Gene_f11
FIG 4 Gene families gained per branch in Roseobacter versus SAR11 lineages (left) and in Roseobacter ancestral nodes R37 versus R1 to R36 (right).
 Letters represent COG categories. Asterisks indicate significant differences in proportions based on Xipe analysis (64) (P 0.01). The horizontal axis indicates the number of families gained per branch for each COG class. Cell motility families gained in SAR11 represent pilus formation genes.

Pelagibacter Ubique is the best candidate to investigate Origin of life scenarios. Here is why A_chro10
FIG 6 A chronogram of alphaproteobacteria.
Nodes with fossil record corrections are indicated with an asterisk.

According to above diagram, they put Chromobacterium violaceum ATCC 12472 ( the first at the bottom ) as the most ancient bacterium. The second is Nostoc sp. PCC 7120

The complete genome sequence of Chromobacterium violaceum reveals remarkable and exploitable bacterial adaptability 4
General Features of the Genome.
The complete genome of the C. violaceum consists of a single circular chromosome of 4,751,080 bp. The identification of such genetic resources in C. violaceum, a free-living tropical bacteria, justifies the contemplation of strategic high-throughput programs to survey further the genomes of such organisms.

Cyanobacterium Anabaena sp. Strain PCC 7120 5
Nostoc sp. PCC 7120 The genome of Anabaena consisted of a single chromosome 6,413,771 bp.  Both, chromobacterium, and Anabaena, are far bigger genomes than Pelagibacter Ubique.

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss 6
Reductive genomic evolution, driven by genetic drift, is common in endosymbiotic bacteria. Genome reduction is less common in free-living organisms, but it has occurred in the numerically dominant open-ocean bacterioplankton Prochlorococcus and “Candidatus Pelagibacter,” and in these cases the reduction appears to be driven by natural selection rather than drift. 

Nature offers numerous examples of “reductive evolution,” where simple organisms derive from more complex ancestors. This phenomenon is typified by macro- and microscopic parasites and symbionts, particularly those that reside inside their hosts

The highly abundant but streamlined marine heterotrophic bacterium “Ca. Pelagibacter ubique” has lost the genes required for assimilatory sulfate reduction, which are present in all other known aerobic marine bacteria. As a consequence, “Ca. Pelagibacter ubique” is dependent on external sources of reduced sulfur for growth 8

New rRNA Gene-Based Phylogenies of the Alphaproteobacteria Provide Perspective on Major Groups, Mitochondrial Ancestry and Phylogenetic Instability 2013 Dec 11  7
Alphaproteobacteria, which has received considerable attention because it contains many important taxa, including the ancestor of the mitochondria. The Alphaproteobacteria contains members that are pathogens of humans, such as Rickettsia, and livestock, such as Ehrlichia, as well as agriculturally valuable species, such as Rhizobium radiobacter (formerly Agrobacterium tumefaciens), and several highly abundant marine groups such as Roseobacter, SAR116, and SAR11.  The commonly accepted alphaproteobacterial orders are the Rhizobiales, the Rhodobacteriales, the Caulobacteriales, the Parvularculales, the Sphingomonadales, the Rhodospirillales, the Rickettsiales and the recently validated Magnetococcales.  In 2007, Williams et al. used a thoroughly selected set of 104 protein-encoding genes and found that Candidatus Pelagibacter ubique (P. ubique) was basal in the Rickettsiales and that mitochondria were sister to the Rickettsiaceae and Anaplasmataceae. The key nodes in the alphaproteobacterial tree, such as the branch leading to modern mitochondria, are very ancient (dating to >2 billion years ago;

Pelagibacter Ubique is the best candidate to investigate Origin of life scenarios. Here is why Tree_i10
The earliest diverging clade is the Magnetococcales, represented by Magnetococcus marinus. One of the subsequent clades has the Pelagibacterales subtending the Anaplasmataceae, Midichloria mitochondrii, the Rickettsiaceae and the mitochondria (if present). Pelagibacteraceae are the sister clade to the mitochondria.

Pelagibacter Ubique is the best candidate to investigate Origin of life scenarios. Here is why Pone.0083383.g005
Proposed subclasses of the Alphaproteobacteria.
The three proposed subdivisions are the Magnetococcidae, the Rickettsidae and the Caulobacteridae. Furthermore, the Holosporaceae should be removed from the Rickettsiales, however the identities of the family-level subdivisions of the Holosporales, such as the Holosporaceae (marked with an asterisk), are beyond the scope of this work. Under this scheme the Rickettsiales are comprised solely of the Rickettsiaceae, Anaplasmataceae and Midichloriaceae. The protomitochondrion (†) is an extinct organism that gave rise to the mitochondrial organelles of eukaryotes.

Magnetococcus marinus gen. nov., sp. nov., a marine, magnetotactic bacterium that represents a novel lineage (Magnetococcaceae fam. nov., Magnetococcales ord. nov.) at the base of the Alphaproteobacteria 01 March 2013
The magnetotactic cocci are ubiquitous in freshwater, marine water and mud samples collected from natural habitats, and are the most commonly observed morphotype of magnetotactic bacteria from these environments. Strain MC-1T is capable of fixing nitrogen under both autotrophic and heterotrophic conditions. The genome of strain MC-1T appears to consist of a single, circular chromosome of about 4.7 Mb

My comment: Having 4.700,000 nucleotides means this bacteria is FAR more complex than Pelagibacter ubique. And therefore, not a good candidate as the first most simple life-form.

1. https://aem.asm.org/content/83/3/e02807-16
2. https://www.nature.com/articles/ismej200883
3. https://mbio.asm.org/content/mbio/4/4/e00373-13.full.pdf
4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC208814/
5. https://academic.oup.com/dnaresearch/article/8/5/205/418978
6. https://mbio.asm.org/content/3/2/e00036-12
7. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3859672/
8. https://mbio.asm.org/content/3/2/e00036-12
9. http://www.roseobase.org/Species/htcc2255.html
10. https://www.biorxiv.org/content/10.1101/2020.09.08.285460v1.full

Last edited by Otangelo on Mon 1 Mar 2021 - 13:41; edited 7 times in total


3Pelagibacter Ubique is the best candidate to investigate Origin of life scenarios. Here is why Empty 'The All-Species Living Tree' Project Wed 17 Feb 2021 - 19:10



Earliest known life forms


'The All-Species Living Tree' Project
'The All-Species Living Tree' Project is a collaboration between various academic groups/institutes, such as ARB, SILVA rRNA database project, and LPSN, with the aim of assembling a database of 16S rRNA sequences of all validly published species of Bacteria and Archaea. 1

'The All-Species Living Tree' Project 2
Five international partners together with the journal Systematic and Applied Microbiology (SAM) started “The All-Species Living Tree" Project (LTP) to provide a valuable resource particularly for microbial taxonomists.


Earliest known life forms 4
The earliest known life forms on Earth are putative fossilized microorganisms found in hydrothermal vent precipitates. A December 2017 report stated that 3.465-billion-year-old Australian Apex chert rocks once contained microorganisms, the earliest direct evidence of life on Earth.

Evidence for early life in Earth’s oldest hydrothermal vent precipitates 5
Here we describe putative fossilized microorganisms that are at least 3,770 million and possibly 4,290 million years old in ferruginous sedimentary rocks, interpreted as seafloor-hydrothermal vent-related precipitates, from the Nuvvuagittuq belt in Canada. There are no confirmed microfossils older than 3,500 million years (Myr) on Earth, probably because of the highly metamorphosed nature of the oldest sedimentary rocks1 . Therefore, studies have focused almost exclusively on chemical traces and primarily on the isotopic composition of carbonaceous material,which has led to controversies regarding the origin of isotopically light reduced carbon2 . Schists from the approximately 3,700-Myr-old Isua supracrustal belt in southwest Greenland contain up to 8.8 wt% graphitic carbon that is depleted in 13C, and this depletion has been attributed to biological activity.  Modern hydrothermal Si-Fe vent deposits host communities of microorganisms, some of which are Feoxidizing bacteria that form distinctive tubes and filaments

Potentially biogenic carbon preserved in a 4.1 billion-year-old zircon 6
the microfossil record only extends to ∼3.5 billion years (Ga), the chemofossil record arguably to ∼3.8 Ga, and the rock record to 4.0 Ga. Detrital zircons from Jack Hills, Western Australia range in age up to nearly 4.4 Ga. From a population of over 10,000 Jack Hills zircons, we identified one >3.8-Ga zircon that contains primary graphite inclusions.

As for life on land, in 2019 scientists reported the discovery of a fossilized fungus, named Ourasphaira giraldae, in the Canadian Arctic, that may have grown on land a billion years ago, well before plants were living on land

Early fungi from the Proterozoic era in Arctic Canada 7
Fungi are crucial components of modern ecosystems. They may have had an important role in the colonization of land by eukaryotes, and in the appearance and success of land plants and metazoans1–3 . Nevertheless, fossils that can unambiguously be identified as fungi are absent from the fossil record until the middle of the Palaeozoic era4,5. Here we show, using morphological, ultrastructural and spectroscopic analyses, that multicellular organic-walled microfossils preserved in shale of the Grassy Bay Formation (Shaler Supergroup, Arctic Canada), which dates to approximately 1,010–890  million years ago, have a fungal affinity. 

Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origin 8
Establishing a unified timescale for the early evolution of Earth and life is challenging and mired in controversy because of the paucity of fossil evidence, the difficulty of interpreting it and dispute over the deepest branching relationships in the tree of life.  We find the last universal common ancestor of cellular life to have predated the end of late heavy bombardment (>3.9 billion years ago (Ga)). The Great Oxidation Event significantly predates the origin of modern Cyanobacteria, indicating that oxygenic photosynthesis evolved within the cyanobacterial stem lineage. Modern eukaryotes do not constitute a primary lineage of life and emerged late in Earth’s history (<1.84 Ga), falsifying the hypothesis that the Great Oxidation Event facilitated their radiation. The symbiotic origin of mitochondria at 2.053–1.21 Ga reflects a late origin of the total-group Alphaproteobacteria to which the free living ancestor of mitochondria belonged.

My comment: This is interesting. If Alphaproteobacteria, to which Pelagibacter Ubique belong, came about 2 billion years ago, then this is much later than Cyanobacteria, which are considerably more complex.

     Pelagibacter Ubique is the best candidate to investigate Origin of life scenarios. Here is why A_tree11
Pelagibacter Ubique is the best candidate to investigate Origin of life scenarios. Here is why A_tree12

A tree combining uncertainties from approaches using uncorrelated and autocorrelated clock models and different calibration density distributions. 
Tip labels are shown for Eukaryota (grey), Archaeabacteria (red) and Eubacteria (blue). The purple bars denote the credible intervals for each node. Red dots highlight calibrated nodes, and corresponding black dots highlight the age of the minimum bound of its corresponding calibration. The phylogenetic relationships of the mitochondrion within Alphaproteobacteria are still debated56,74–76, and it is unclear whether the free-living ancestor of the mitochondrion was a crown or stem representative of this group. The red bar above the crown eukaryote node denotes the time period during which the mitochondrial endosymbiosis may have occurred. The green bar denotes the time during which the plastid endosymbiosis may have occurred. Important events in Earth and life history are indicated along the base of the figure. Mesoprot., Mezoproterozoic; Neoprot., Neoproterozoic.

Recent environmental genomic surveys indicate that metabolisms using the Wood–Ljungdahl pathway to fix carbon minimally evolved in stem archaebacteria and might have been a characteristic of LUCA. The Great Oxidation Event (GOE; ~2.4Ga) was perhaps the most significant episode in the Proterozoic, fundamentally changing the chemistry of Earth’s atmosphere and oceans, and probably altering temperature. It has been causally associated with the evolution of Cyanobacteria, as a consequence of their oxygen release.   Our timescale indicates that crown Cyanobacteria and crown Eukaryota significantly postdate the GOE. Crown Cyanobacteria diverged 1,947–1,023Ma, precluding the possibility that oxygenic photosynthesis emerged in the cyanobacterial crown ancestor. However, the Cyanobacteria separated from other eubacterial lineages  including the non-photosynthetic sister group of the Cyanobacteria Melanibacteria in the Archaean, before the GOE, consistent with the view that oxygenic photosynthesis evolved along the cyanobacterial stem49, and compatible with a causal role of the total-group Cyanobacteria in the GOE. Crown Eukaryota diverged considerably after both the Eukaryota–Asgardarchaeota split and the GOE, in the middle Proterozoic (1,842–1,210Ma). Our study strongly rejects the idea that eukaryotes might be as old as, or older than, prokaryotes, and agrees with a number of other studies that date the last eukaryote common ancestor (LECA) to the Proterozoic (~1,866–1,679Ma) Within eukaryotes, the main extant clades emerged by the middle Proterozoic, including Opisthokonta (~1,707–1,125Ma), Archaeplastida (~1,667–1,118Ma) and SAR (stramenopiles (heterokonts), alveolates and Rhizaria; ~1,645–1,115Ma). The symbiotic origin of the plastid occurred among stem archaeplastids (~1,774–1,118Ma), and our 95% credibility interval for the origin of the plastid overlap with the results of other recent studies

The search for the earliest fossil evidence of life on Earth has created more heat than light. Although the fossil record remains integral to establishing a timescale for the Tree of Life, it is not sufficient in and of itself. Our integrative molecular timescale encompasses the uncertainty associated with fossil, geological and molecular evidence, as well its modelling, allowing it to serve as a solid foundation for testing evolutionary hypotheses in deep time for clades that do not have a credible fossil record.

The crown clades of the primary divisions of life, Archaebacteria and Eubacteria emerged over one billion years after LUCA in the Mesoarchaean–Neoarchaean. The earliest conclusive evidence of cellular life (Strelley Pool Formation, Australia falls within the 95% credibility intervals for the ages of the last common ancestors of both clades, indicating that these fossils might belong to one of the two living prokaryotic lineages.

Eubacteria (blue)

Kosmotoga olearia 
The complete K. olearia genome consists of 2,302,126 bp in a single circular chromosome, making it one of the largest sequenced Thermotogales genomes. 9

Rickettsia bellii
The 1,552,076 base pair–long 10

1. https://en.wikipedia.org/wiki/%27The_All-Species_Living_Tree%27_Project
2. https://www.arb-silva.de/projects/living-tree
3. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2
4. https://en.wikipedia.org/wiki/Earliest_known_life_forms
5. http://eprints.whiterose.ac.uk/112179/1/ppnature21377_Dodd_for%20Symplectic.pdf
6. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664351/
7. https://sci-hub.ren/10.1038/s41586-019-1217-0
8. https://sci-hub.ren/10.1038/s41559-018-0644-x
9. https://jb.asm.org/content/193/19/5566
10. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1458961/








The first life form, the supposedly Last Universal Common Ancestor (LUCA), had to be already amazingly complex.

Juan A. G. Ranea et al.: Protein Superfamily Evolution and the Last Universal Common Ancestor (LUCA) 31 May 2006
We know that the LUCA, or the primitive community that constituted this entity, was functionally and genetically complex. Life achieved its modern cellular status long before the separation of the three kingdoms. we can affirm that the LUCA held representatives in practically all the essential functional niches currently present in extant organisms, with a metabolic complexity similar to translation in terms of domain variety.   The true genetic and functional content of the LUCA has, with all probability, been underestimated. Even if the ancestral domain set in the LUCA was much larger than the set considered here, the functional analysis of this selected sample reveals that the LUCA comprised functions for (i) replication, transcription, and translation; (ii) the use of glucose and other sugars; (iii) the assimilation of amino acids and nucleosides/ bases; (iv) the synthesis of ATP both by substratelevel phosphorylation and through redox reactions coupled to membranes; (v) signal transduction and gene regulation; (vi) protein modification; (vii) protein signal recognition, transport, and secretion; (viii) protein folding assistance; and (ix) cell division. In our view, the LUCA was faced with two important challenges associated with the source of amino acids and purine/pyrimidine bases or nucleosides. Most of these compounds need complex pathways to be synthesized and our analyses suggest that these are not present in the LUCA. Based on that, we are more in favor of amino acids and nitrogenous bases being present in a possible primitive soup rather than being synthesized by the LUCA.

My comment: That would require LUCA to have complex import and incorporation mechanisms of nucleotides and amino acids, and membrane import channel proteins able to distinguish and select those that are used in life, from those that aren't. There is no known abiotic non-enzymatic biosynthesis pathway nor availability of these building blocks known.  But even IF that would be the case, that would still not explain how LUCA made the transition from external incorporation to acquire the complex metabolic and catabolic pathways to synthesize nucleotides and amino acids. 

De novo Nucleotide synthesis: All in all, not considering the metabolic pathways and enzymes required to make the precursors to start RNA and DNA synthesis requires at least 26  enzymes.   In total, 57 enzymes.
De novo Amino Acid synthesis A minimum of 112 enzymes are required to synthesize the 20 (+2) amino acids used in proteins.
The above does not account for the essential origin of catabolism, recycling mechanisms of building blocks, and of two enzymes essential for the recovery of purine and pyrimidine bases and nucleosides— nucleoside phosphorylase and base-phosphoribosyl transferase—is highly relevant. LUCA required as well the biogenesis of membrane and wall structures associated with them, machinery to carry out redox reactions coupled to electron transfer and synthesis of ATP. Also essential is the presence of chaperones to help carry proteins to different destinations, and help malformed proteins to gain the right shape. Domains involved in protein-protein recognition, signal transduction, gene regulation, cell division, protein signal recognition, and transport.

Pelagibacter Ubique (SAR11)  is known as one of, if not the smallest and simplest, self-replicating, and free-living cell, a tiny bacterium.  Its genome has the smallest genome (1,308,759 base pairs) of any free-living organism, encoding for 1,354  proteins, and 32 tRNAs. The phylogenetic birth-and-death model consistently predicted that its small extant genomes devolved from a slightly larger common ancestor (~2,000 genes). Pelagibacter is an alphaproteobacterium. In the evolutionary timescale, its common ancestor supposedly emerged about 1,3 billion years ago. The oldest bacteria known however are Cyanobacteria,  living in the rocks in Greenland about 3.7-billion years ago.  With a genome size of approximately  3,2 million base pairs ( Raphidiopsis brookii D9) they are the smallest genomes described for free-living cyanobacteria. This is a paradox. The oldest known life-forms have a considerably bigger genome than Pelagibacter, which makes their origin far more unlikely from a naturalistic standpoint.  The unlikeliness to have just ONE protein domain-sized fold of 250 amino acids is 1 in 10^77. That means, to find just one functional protein fold with the length of about 250AAs, nature would have to search amongst so many non-functional folds as there are atoms in our known universe ( about 10^80 atoms).   We will soon see the likeliness to find an entire functional genome of Pelagibacter with 1,3 million nucleotides, which was however based on the data demonstrated above, not the earliest bacteria....
The chance to get its entire proteome would be 10^722,000.  The discrepancy between the functional space, and the sequence space, is staggering.

Steve Meyer: Signature in the Cell, chapter 10:
Taking this into account only causes the improbability of generating the necessary proteins by chance—or the genetic information to produce them—to balloon beyond comprehension. In 1983 distinguished British cosmologist Sir Fred Hoyle calculated the odds of producing the proteins necessary to service a simple one-celled organism by chance at 1 in 10^40,000 . At that time scientists could have questioned his figure. Scientists knew how long proteins were and roughly how many protein types there were in simple cells. But since the amount of functionally specified information in each protein had not yet been measured, probability calculations like Hoyle’s required some guesswork. Axe’s experimental findings suggest that Hoyle’s guesses were pretty good. If we assume that a minimally complex cell needs at least 250 proteins of, on average, 150 amino acids and that the probability of producing just one such protein is 1 in 10^164 as calculated above, then the probability of producing all the necessary proteins needed to service a minimally complex cell is 1 in 10^164 multiplied by itself 250 times, or 1 in 10^41,000.




Cultivation and genomics of the first freshwater SAR11 (LD12) isolate

Pelagibacter Ubique is the best candidate to investigate Origin of life scenarios. Here is why Pelagi11


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