Rosa Rubicondior: Refuting Creationism - The Long Pre-'Creation Week' Evolutionary History of Bacteria

Refuting Creationism

The Long Pre-'Creation Week' Evolutionary History Of Bacteria

The Great Oxidation Event

AI-Generated Image (ChatGPT4o)

Machine learning helps construct an evolutionary timeline of bacteria - UQ News - The University of Queensland, Australia

A helpful analogy employed by Richard Dawkins in Unweaving the Rainbow illustrates the vastness of evolutionary time:

Fling your arms wide in an expansive gesture to span all of evolution from its origins at your left fingertip to today at your right fingertip. All the way across your midline to well past your right shoulder, life consisted of nothing but bacteria. Multi-celled invertebrate life flowers somewhere around your right elbow. The dinosaurs originate in the middle of your right palm and go extinct around your last finger joint. The whole story of Homo sapiens and our predecessor Homo erectus is contained in the thickness of one nail-clipping.

We can construct such a timeline because, although microbial life leaves few conventional fossils, it does leave behind chemical signatures in ancient rocks—clues to how bacteria lived, metabolised, and evolved.

By correlating this geochemical record with genomic data, a multinational collaboration – led by researchers from the Okinawa Institute of Science and Technology, Japan, the University of Bristol, UK, Queensland University of Technology, Australia and the University of Queensland, Australia, has used machine learning to reconstructed an evolutionary tree of bacterial lineages. This allows us to trace how different taxa adapted to major environmental changes, such as the Great Oxidation Event (GOE). Remarkably, this study suggest that some microbes had already evolved the capacity to utilise oxygen even before it became abundant during the GOE.

The disturbing fact for creationists is not the evidence of common origins and descent with modification that this study reveals, but the fact that it all happened billions of years before their mythical 'Creation Week' when their god allegedly created a small flat planet with a dome over it in the Middle East. But then this is hardly surprising, since 99.9975% of the history of life on Earth happened before that alleged act of magic.

How the team of scientists conducted this study, and their conclusions are the subject of a research paper in Science and a news item from the University of Queensland, Australia:

What information do you have on the geological evidence for the presence of bacteria/archaea before during and after the GOE?

The geological evidence for the presence of bacteria and archaea before, during, and after the Great Oxidation Event (GOE) — which occurred roughly 2.4 to 2.0 billion years ago — comes from multiple lines of evidence: isotopic signatures, stromatolites, microfossils, and molecular biomarkers. Here's a structured summary:

Before the GOE (~>2.4 billion years ago)

Microfossils and Stromatolites

Stromatolites — laminated microbial structures formed by cyanobacteria — date back to at least 3.5 billion years ago (e.g., Warrawoona Group, Western Australia). These structures suggest the presence of photosynthetic microbial mats well before the GOE.
Microfossils from similar-aged rocks also support the early presence of prokaryotic life.

Isotopic Evidence

Carbon isotopes (δ¹³C): Fractionation patterns consistent with biological carbon fixation (especially the Calvin cycle) are found in rocks older than 3.5 Ga, suggesting microbial activity.
Sulphur isotopes (Δ³³S anomalies): Prior to the GOE, large mass-independent fractionation (MIF) of sulphur isotopes occurs in sedimentary rocks. This is only possible in an anoxic atmosphere, confirming that Earth had little or no free oxygen.

Biomarkers

Certain hydrocarbon molecules, such as hopanes, have been interpreted as biomarkers for bacteria, although their preservation and interpretation in ancient rocks (e.g., 2.7 Ga rocks from the Pilbara Craton) remain debated due to possible contamination.

During the GOE (2.4–2.0 Ga)

Atmospheric and Ocean Chemistry Changes

The GOE marks a significant rise in atmospheric O₂, likely due to the activity of oxygenic photosynthesising cyanobacteria.
Oxidised iron formations (Banded Iron Formations, or BIFs) begin to decline toward the end of the GOE, indicating a shift in ocean chemistry from anoxic to more oxygenated conditions.

Sulphur Isotope Shift

A disappearance of MIF sulphur signals in sediments after ~2.4 Ga provides strong geochemical evidence for a major atmospheric oxygenation event.
This transition indicates that atmospheric oxygen levels crossed a threshold (~10⁻⁵ PAL), altering the atmospheric photochemistry.

Iron Formations

BIFs reflect a time when ferrous iron (Fe²⁺) in oceans was oxidised by O₂ to form insoluble ferric iron (Fe³⁺) and precipitated out, a process linked to cyanobacterial oxygen production.

After the GOE (Post-2.0 Ga)

Microbial Evolution and Niches

Oxygen levels remained relatively low (estimated 0.001–0.1% of present atmospheric levels) for hundreds of millions of years after the GOE, a period known as the "oxygen overshoot" or "oxygen plateau".
Aerobic respiration evolved, offering more efficient energy production pathways and enabling more complex metabolisms.
Anoxygenic phototrophs and anaerobic archaea (e.g. methanogens) continued to thrive in oxygen-poor niches (e.g., sediments, deep sea).

Redox-Sensitive Elements

Shifts in the abundances and isotopic compositions of redox-sensitive elements (e.g. molybdenum, uranium, chromium) in marine sediments provide evidence of fluctuating oxygen levels.
These proxies suggest a stepwise oxygenation of Earth’s surface, oceans, and eventually the deep ocean, continuing through the Neoproterozoic Oxidation Event (~800–540 Ma).

ChatGPT4o [Response to user request]
Retrieved from https://chatgpt.com/

Information Continually updated

Machine learning helps construct an evolutionary timeline of bacteria
University of Queensland scientists have helped to construct a detailed timeline for bacterial evolution, suggesting some bacteria used oxygen long before evolving the ability to produce it through photosynthesis.
The multinational collaboration – led by researchers from the Okinawa Institute of Science and Technology, the University of Bristol, Queensland University of Technology and UQ – focused on how microorganisms responded to the Great Oxygenation Event (GOE) about 2.33 billion years ago, which changed Earth’s atmosphere from mostly devoid of oxygen to one that allows humans to breathe. Professor Phil Hugenholtz from UQ’s School of Chemistry and Molecular Biosciences said establishing accurate timescales for how bacteria evolved before, during and after the GOE had been difficult until now, because of incomplete fossil evidence.

Most microbial life leaves no direct fossil record, which means that fossils are missing from the majority of life’s history on Earth. But we know ancient rocks hold chemical clues of how bacteria lived and fed, and we were able to address the gaps by concurrently analysing geological and genomic records. The key innovation was using the GOE as a time boundary, assuming that most aerobic branches of bacteria are unlikely to be older than this event unless fossil or genetic signals suggested otherwise.

Professor Philip Hugenholtz, co-author.
The University of Queensland
School of Chemistry and Molecular Biosciences
Australian Centre for Ecogenomics
Brisbane, Queensland, Australia.

The team first estimated which genes were present in ancestral genomes. They then used machine learning to predict whether or not each ancestor used oxygen to live.

To best utilise fossil records, the researchers included genes from mitochondria (related to alphaproteobacteria) and chloroplasts (related to cyanobacteria), which allowed them to use data from early complex cells to better estimate when events happened.

Results show that at least 3 aerobic lineages appeared before the GOE – by nearly 900 million years – suggesting that a capacity for using oxygen evolved well before its widespread accumulation in the atmosphere. Evidence suggests that the earliest aerobic transition occurred around 3.2 billion years ago in the cyanobacterial ancestor, which points to the possibility that aerobic metabolism occurred before the evolution of oxygenic photosynthesis.

Professor Philip Hugenholtz.

Lead author Dr Adrián Arellano Davín said the combined approach of using genomic data, fossils and Earth’s geochemical history married together cutting-edge technologies to clarify evolutionary timelines.

By using machine learning to predict cell function, we can not only predict the aerobic metabolisms of ancestral bacteria but also start to take incomplete genomes to try to predict other traits that could impact the world now, such as whether certain bacteria might be resistant to antibiotics.

Dr. Adrián A. Davín, lead author.
The University of Queensland
School of Chemistry and Molecular Biosciences
Australian Centre for Ecogenomics
Brisbane, Queensland, Australia.
Publication:

Adrián A. Davín et al.
A geological timescale for bacterial evolution and oxygen adaptation.
Science 388, eadp1853 (2025). DOI:10.1126/science.adp1853.

Structured Abstract

INTRODUCTION
Microbial life dominates the biosphere, but a timescale of early microbial evolution has proven elusive as a result of an inadequate fossil record. The lack of maximum age calibrations—the earliest point in time at which a given group might have emerged—is particularly problematic. However, the geochemical record bears the imprint of microbial metabolism through time, providing a complementary source of information. A pivotal event in this history was the Great Oxidation Event (GOE) ~2.43 to 2.33 billion years ago (Ga), which marked a substantial increase in atmospheric oxygen. This transition, driven by the evolution of cyanobacterial oxygenic photosynthesis and carbon burial, transformed the biosphere from predominantly anoxic to oxic, causing widespread adaptation to oxygen. In this study, we used the temporal link between atmospheric oxygenation and the evolutionary spread of aerobic metabolism to calibrate the phylogeny of the bacterial domain.

RATIONALE
To date the bacterial tree, we introduced multiple new maximum age calibrations by linking the GOE to the age of aerobic lineages. We used a Bayesian approach that assumes that aerobic nodes are unlikely to be older than the GOE but can predate it given sufficient evidence from fossils or sequence divergence. To implement this approach, we integrated phylogenetic reconciliation with machine learning to map transitions from anaerobic to aerobic lifestyles onto the bacterial tree. By aggregating signals across the genome, we could robustly infer aerobic and anaerobic phenotypes from incomplete ancestral gene repertoires.

RESULTS
We identified 84 anaerobic to aerobic transitions on a species tree of 1007 bacteria. Most transitions occurred after the GOE and were driven by horizontal acquisition of respiratory and oxygen tolerance genes. However, despite the GOE calibration, at least three transitions predated this event, suggesting that aerobic respiration evolved before widespread atmospheric oxygenation and may have facilitated the evolution of oxygenic photosynthesis in cyanobacteria. Our molecular clock analyses estimated that the last bacterial common ancestor lived in the Hadean or earliest Archaean era (4.4 to 3.9 Ga), whereas bacterial phyla originated in the Archaean and Proterozoic eras (2.5 to 1.8 Ga); most bacterial families are as old as land plants and animal phyla, dating back to the late Proterozoic (0.6 to 0.75 Ga).

CONCLUSION
We infer that the earliest aerobic bacteria emerged in the Archaean, predating the GOE by 900 million years. After the GOE, aerobic lineages experienced faster diversification than their anaerobic counterparts, highlighting the impact of atmospheric oxygenation on bacterial evolution. The approach developed here provides a framework for linking microbial traits to Earth’s geochemical history, offering a pathway for exploring the evolution of other phenotypes in the context of Earth’s history.

An integrated approach to date bacterial evolution and reconstruct the history of oxygen adaptation.
We inferred a bacterial timetree by integrating genomic, fossil, and geochemical data and linking oxygen tolerance and aerobic metabolism to the GOE. Colors denote anaerobic (blue) and aerobic (red) states, whereas shades of purple show the fraction of aerobic lineages within extant bacterial phyla. Mitochondria and plastids were included to leverage the more extensive eukaryotic fossils. Land plants and animals are indicated for temporal comparison.
Abstract
Microbial life has dominated Earth’s history but left a sparse fossil record, greatly hindering our understanding of evolution in deep time. However, bacterial metabolism has left signatures in the geochemical record, most conspicuously the Great Oxidation Event (GOE). We combine machine learning and phylogenetic reconciliation to infer ancestral bacterial transitions to aerobic lifestyles, linking them to the GOE to calibrate the bacterial time tree. Extant bacterial phyla trace their diversity to the Archaean and Proterozoic, and bacterial families prior to the Phanerozoic. We infer that most bacterial phyla were ancestrally anaerobic and adopted aerobic lifestyles after the GOE. However, in the cyanobacterial ancestor, aerobic metabolism likely predated the GOE, which may have facilitated the evolution of oxygenic photosynthesis.

Adrián A. Davín et al.
A geological timescale for bacterial evolution and oxygen adaptation.
Science 388, eadp1853 (2025). DOI:10.1126/science.adp1853.

© 2025 American Association for the Advancement of Science.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

As is often the case, this research presents several inconvenient truths that creationists are likely to ignore, distort, or dismiss.

First, there is no indication whatsoever that the authors of the Bible had any awareness of microbes—let alone an understanding of their genetics or evolutionary origins.

Second, the evolutionary developments described in this research occurred billions of years before those authors composed their highly imaginative version of history.

Thirdly, the authors of the study show no signs of concluding that anything other than the Theory of Evolution is needed to explain their results. No role for magic was found in the data.

Finally, the geological record provides clear evidence of transitional stages in microbial evolution—evidence that directly contradicts the central creationist claim that such transitions do not exist.

Advertisement

Amazon