How Science Works - Not Abandonning Evolution - Refining Our Understanding Of It

A new theory of molecular evolution | University of Michigan News

A new paper in Nature Ecology & Evolution by a research team at the University of Michigan, led by evolutionary biologist, Professor Jianzhi Zhang, comprehensively, but incidentally, refutes several common creationist claims — such as that mainstream biologists are abandoning evolution because it supposedly cannot explain the evidence, that all mutations are harmful, so cannot underpin evolution, and that scientists are prevented from publishing findings that challenge orthodoxy.

The study examines a key assumption of the Neutral Theory of Molecular Evolution — namely that most amino-acid substitutions are neutral (neither beneficial nor strongly deleterious) and fix by drift rather than selection. The authors report experimental data showing that in mutational-scanning assays of over 12,000 amino-acid-altering mutations across 24 genes, >1 % of mutations were beneficial, implying a far higher beneficial-mutation rate than is conventionally assumed.

To reconcile that finding with the fact that comparative genomic data appear consistent with many substitutions being neutral, Zhang’s team propose a new model — “adaptive tracking with antagonistic pleiotropy” — in which beneficial mutations are frequently environment-specific, and when the environment changes the same mutation may become deleterious, hence failing to fix. In this way, although beneficial mutations are common, they rarely reach fixation when environments shift, and substitution patterns can appear neutral.

The paper operates fully within the framework of evolutionary theory by natural selection: it does not challenge evolution itself, but refines a subsidiary theoretical model about molecular changes. Thus, it strengthens the broader evolutionary paradigm rather than undermines it.

Average time to fixation of a mutation under different environments. To keep things simple, assume a standard Wright–Fisher population with effective size \(\small(N_e)\), diploid, with a single new copy of the allele arising in one generation.

1. Neutral mutation in a neutral environment
   A new neutral mutation starts at frequency
   \[(p_0 = 1/(2N_e)).\]
   Two classic results:
   • Probability that a neutral mutation eventually fixes: \[(P_{\text{fix, neutral}} = p_0 = 1/(2N_e)).\]
   • Expected time to fixation given that it does fix (diffusion approximation): \[(\bar T_{\text{fix, neutral}} \approx 4N_e)\ \text{generations}.\]
   
   So, for a neutral mutation that happens to win the drift lottery, the typical time-scale to drift to fixation is of order \(\small(4N_e)\) generations.
2. Mutation that is beneficial half the time and deleterious half the time
   Now suppose the same mutation experiences:
   • selection coefficient (+s) in environment A,
   • selection coefficient (-s) in environment B,
   • with the population spending 50% of generations in each environment.
   
   On average, the selection coefficient is zero:
   
   \[(\bar s = \tfrac12(+s) + \tfrac12(-s) = 0),\]
   so in a first approximation the allele is time-averaged neutral. However, it is not truly neutral – it is sometimes favoured and sometimes disfavoured. That fluctuation in selection has two important consequences:
   • The probability of fixation is typically lower than for a strictly neutral mutation, because periods in the “bad” environment (–s) tend to undo gains made in the “good” environment (+s).
   • The distribution of times to absorption (loss or fixation) is broader, and the mean time to fixation, conditional on fixation, is generally longer and more variable than the simple \(\small(4N_e)\) rule.
   
   Crucially, there is no neat closed-form equivalent to \(\small(\bar T_{\text{fix}} \approx 4N_e)\) in this fluctuating case: the mean time to fixation depends on:
   • the population size \(\small(N_e)\),
   • the magnitude of (s), and
   • how fast the environment flips between A and B.
   
   In practice, one usually estimates the fixation probability and mean fixation time in such a ±s, 50/50 scenario either by:
   • solving the diffusion (backward Kolmogorov) equations for allele frequency with a stochastic selection term, or
   • simulating a Wright–Fisher (or Moran) population in which the environment changes over time and recording how long successful mutations take to fix.
   
   

This is exactly the sort of situation considered in the Zhang et al. paper: a mutation that is advantageous in one environment but disadvantageous in another may arise fairly often, yet fail to become fixed because the population spends much of its time in the “wrong” environment.

A summary of the research is available in a University of Michigan News article.

A new theory of molecular evolution

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For a long time, evolutionary biologists have thought that the genetic mutations that drive the evolution of genes and proteins are largely neutral: they’re neither good nor bad, but just ordinary enough to slip through the notice of selection.

Now, a University of Michigan study has flipped that theory on its head.

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In the process of evolution, mutations occur which can then become fixed, meaning that every individual in the population carries that mutation. A longstanding theory, called the Neutral Theory of Molecular Evolution, posits that most genetic mutations that are fixed are neutral. Bad mutations will be quickly discarded by selection, according to the theory, which also assumes that good mutations are so rare that most fixations will be neutral, says evolutionary biologist Jianzhi Zhang.

The U-M study, led by Zhang, aimed to examine whether this was true. The researchers found that so many good mutations occurred that the Neutral Theory cannot hold. At the same time, they found that the rate of fixations is too low for the large number of beneficial mutations that Zhang’s team observed.

To resolve this, the researchers suggest that mutations that are beneficial in one environment may become harmful in another environment. These beneficial mutations may not become fixed because of frequent environmental changes. The study, supported by the U.S. National Institutes of Health, was published in Nature Ecology and Evolution.

We’re saying that the outcome was neutral, but the process was not neutral. Our model suggests that natural populations are not truly adapted to their environments because environments change very quickly, and populations are always chasing the environment.

Professor Jianzhi Zhang, corresponding author Department of Ecology and Evolutionary Biology
University of Michigan
Ann Arbor, MI, USA.

Zhang says their new theory, called Adaptive Tracking with Antagonistic Pleiotropy, tells us something about how well all living things are adapted to their environments.

I think this has broad implications. For example, humans. Our environment has changed so much, and our genes may not be the best for today’s environment because we went through a lot of other different environments. Some mutations may be beneficial in our old environments, but are mismatched to today.

At any time when you observe a natural population, depending on when the last time the environment had a big change, the population may be very poorly adapted or it may be relatively well adapted. But we’re probably never going to see any population that is fully adapted to its environment, because a full adaptation would take longer than almost any natural environment can remain constant.

Professor Jianzhi Zhang.

The Neutral Theory of Molecular Evolution was first proposed in the 1960s. Previously, scientists studied evolution based on the morphology and physiology, or appearance, of organisms. But starting in the 1960s, scientists were able to start sequencing proteins, and later, genes. This prompted researchers to look at evolution at the molecular level.

To measure beneficial mutation rates, Zhang and colleagues investigated large deep mutational scanning datasets produced by his and other labs. In this kind of scanning, the scientists created many mutations on a specific gene or region of the genome in model organisms such as yeast and E. coli.

The researchers then followed the organism over many generations, comparing them against the wild type, or the most common version existing in nature, of the organisms. This allowed the researchers to measure their growth and compare their growth rate to the wild type, which is how they estimated the effect of the mutation.

They found that more than 1% of mutations are beneficial, orders of magnitude greater than what the Neutral Theory allows. This amount of beneficial mutations would lead to more than 99% of fixations being beneficial and a rate of gene evolution that is much higher than the rate that is observed in nature. The researchers realized they had made a mistake in assuming an organism’s environment remained constant.

To investigate the impacts of a changing environment, Zhang’s research team compared two groups of yeast. One group evolved in a constant environment for 800 generations (each generation lasted 3 hours), while the second group evolved in a changing environment, in this case composed of 10 different kinds of media, or solution, that the yeast grew in. The second yeast group grew in the first media for 80 generations, in the second media for another 80 generations, and so on, for a total of 800 generations as well.

The researchers found that there were far fewer beneficial mutations in the second group compared to the first. Although the beneficial mutations occurred, they didn’t have a chance to become fixed before the environment shifted.

This is where the inconsistency comes from. While we observe a lot of beneficial mutations in a given environment, those beneficial mutations do not have a chance to be fixed because as their frequency increases to a certain level, the environment changes. Those beneficial mutations in the old environment might become deleterious in the new environment.

Professor Jianzhi Zhang.

However, Zhang says there is a caveat: The data they used came from yeast and E. coli, two unicellular organisms in which it’s relatively easy to measure the fitness effects of mutations. Deep mutational scanning data collected from multicellular organisms would tell whether their findings from unicellular organisms apply to multicellular organisms such as humans. Next, the researchers are planning a study to understand why it takes so long for organisms to fully adapt to a constant environment.

Other authors of the study include former U-M graduate students Siliang Song and Xukang Shen and former U-M postdoctoral researcher Piaopiao Chen.

Publication:

Song, S., Chen, P., Shen, X. et al.
Adaptive tracking with antagonistic pleiotropy results in seemingly neutral molecular evolution.
Nat Ecol Evol (2025). https://doi.org/10.1038/s41559-025-02887-1

Abstract
The neutral theory of molecular evolution, positing that most amino acid substitutions in protein evolution are neutral, is supported by vast comparative genomic data. However, here we report that the key premise of the theory—beneficial mutations are extremely scarce—is violated. Deep mutational scanning data from 12,267 amino acid-altering mutations in 24 prokaryotic and eukaryotic genes reveal that > 1% of these mutations are beneficial, predicting that > 99% of amino acid substitutions would be adaptive. This observation demands a new theory that is compatible with both the high beneficial mutation rate and the comparative genomic data considered consistent with the neutral theory. We propose such a theory named adaptive tracking with antagonistic pleiotropy. In this theory, virtually all beneficial mutations observed are environment specific. Frequent environmental changes and mutational antagonistic pleiotropy across environments render most of the beneficial mutations seen at one time deleterious soon after and hence rarely fixed. Consequently, despite the occurrence of adaptive tracking—continuous adaptation to a changing environment fuelled by beneficial mutations—neutral substitutions prevail. We show that this theory is supported by population genetics simulation, empirical observations and experimental evolution and has implications for the adaptedness of natural populations and the tempo and mode of evolution.

Song, S., Chen, P., Shen, X. et al.
Adaptive tracking with antagonistic pleiotropy results in seemingly neutral molecular evolution.
Nat Ecol Evol (2025). https://doi.org/10.1038/s41559-025-02887-1

© 2025 Springer Nature Ltd.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

Apart from the obvious point that the researchers show absolutely no sign of finding the Theory of Evolution unfit for purpose—let alone turning to creationism, as creationist leaders have been assuring their followers is just about to happen - for more than half a century — there are other less obvious aspects of this paper that should give creationists pause.

First, the study highlights the close relationship between the environment and whether a mutation is beneficial, deleterious or truly neutral. These terms describe how well an organism survives and reproduces under particular conditions: change the environment, and exactly the same mutation can have an entirely different effect. This is precisely what Darwin proposed.

As with all good science, the need for slight adjustment doesn't invalidate the entire science, it strengthens it. The Theory of Evolution is strengthened rather than weakened by refinements like this that improve our understanding of the details. Minor adjustments to subsidiary theories help clarify the details of how evolution works; they do not threaten the foundations of the overarching theory on which modern biology depends, and they do nothing to justify the creationist tactic of falsely presenting the dichotomy of their superstition as the only alternative choice to that of an allegedly 'failed' scientific theory, without providing the slightest scrap of testable evidence.

As Thomas Henry Huxley is reputed to have exclaimed on reading Darwin’s Origin of Species for the first time: “How stupid not to have thought of it oneself!” Nearly 170 years later, how much more foolish it is to cling to a fairy tale that explains nothing, makes no testable predictions and is unfalsifiable because it relies on magic, essentially because it happens to be the belief you were raised with, when the Theory of Evolution provides a coherent, predictive and experimentally supported account of the living world.

Refuting Creationism - Cambrian Fossils Confirm The Bible Is Wrong.

Salterella in longitudinal section, showing biomineralized outer shell (blue arrow), agglutinated material (red arrow) and the boundary between the agglutinated layer and the shell near the apex (white arrows),

Vayda PJ, Xiao S, Keller ND, et al. (2025)

Interbedded fine-grained clastic and carbonate strata of the lower Illtyd Formation, Wind River, Yukon, Canada, that locally contain Salterella.

A skeleton and a shell? Ancient fossil finally finds home on the tree of life | Virginia Tech News | Virginia Tech

As though fossils from half a billion years before their mythical “Creation Week” weren’t awkward enough for creationists, this latest find slips neatly into the tree of life and closes a small but meaningful gap in our understanding of how protective shells evolved. In doing so, it undermines more creationist claims than they might care to consider.

A research team led by Prescott J. Vayda of Virginia Tech has shown that the enigmatic fossils Volborthella and Salterella, long puzzling palaeontologists, are in fact early cnidarians — members of the group that includes corals, jellyfish, and sea anemones. These organisms are united by their stinging cells, which they use to subdue prey. Even more troublesome for creationists, the structure of the earlier Volborthella shell strongly suggests a transitional relationship with the more complex shell of Salterella, hinting at an evolutionary sequence between the two.

The team’s findings have just been published in the Journal of Paleontology.

The Cambrian period was defined by the emergence of mobility and, with it, true predation. These new ecological dynamics sparked evolutionary “arms races”, driving rapid diversification in both offensive and defensive strategies: sensory structures, spines, shells, and behaviours such as burrowing. These early cnidarians provide an important glimpse into how some of the earliest protective shells came to be.

Such evolutionary arms races also offer yet another reason to dismiss the notion of an intelligent designer. No competent designer would turn yesterday’s solution into today’s problem — yet that is precisely what we see in nature, where improvements in predators prompt improvements in prey, and vice versa. It’s exactly what one would expect from an unguided evolutionary process with no foresight, driven solely by differential survival and reproduction.

Creationism Refuted - Neanderthals Didn't Disappear - They Became Us

A simple analytical model for Neanderthal disappearance due to genetic dilution by recurrent small-scale immigrations of modern humans | Scientific Reports

One of the enduring myths cherished by creationists is that humans appeared suddenly, as a distinct and immutable species, untouched by the messy processes of evolution. Yet study after study continues to reveal just how fluid and interconnected the human story really is. The latest comes from three researchers - Andrea Amadei, Giulia Lin, and Simone Fattorini - who have just published a fascinating analytical model in Scientific Reports explaining how the Neanderthals did not simply “vanish,” but were gradually absorbed into the expanding population of early modern humans.

This idea is not new, as I have reported before in this blog here and here, but what is new is this analytical model that shows how easily it happened. The model shows that repeated, small-scale migrations of Homo sapiens into Neanderthal territories would have resulted in gradual genetic dilution over time, without any need for violent extermination or sudden extinction events. Their DNA lives on in our genomes today — in Europeans, Asians, and other non-African populations — a genetic signature of our shared ancestry.

This finding adds yet another layer to the mounting evidence that humanity is not the product of divine design without ancestry but of evolutionary blending and adaptation. The neat, separate categories that creationists like to imagine simply never existed. Instead, what we see is a continuum of populations interacting, interbreeding, and shaping one another’s evolutionary fate. Rather than distinct “kinds,” humans and Neanderthals were part of a dynamic, interconnected lineage shaped by migration and time — the very processes that creationist dogma denies.

Far from the simplistic tale of a single miraculous creation, the history of our species is one of mixture, movement, and gradual transformation — precisely what evolution predicts, and precisely what the fossil and genetic evidence confirms.

Refuting Creationism - The Universe Doesn't Need a God to Program It

In the film The Matrix, about a computer-simulated world, the red and blue pills symbolize a choice the hero must make between illusion and the truth of reality.

Photo by ANIRUDH on Unsplash.

UBCO study debunks the idea that the universe is a computer simulation - UBC's Okanagan News

Creationists who want to believe that science and theology are compatible often resort to a pantheistic-style argument: that although the universe clearly operates according to the laws of physics, those laws must have been set by a creator deity of some kind. A modern twist on this theme is the claim that the universe, and everything within it, is in fact a vast computer simulation — and that “God” is the programmer. This is, of course, an argument that challenges science to prove a negative: to demonstrate that the universe *isn’t* a simulation.

What creationists are doing here is trying to prise open a gap — any gap — into which they can insert their god.

Now, four scientists at the University of British Columbia believe they have effectively closed that gap by putting the “simulation hypothesis” to the test against the null hypothesis. One of the them is the renowned atheist physicist Dr Lawrence M. Krauss, author of several books and articles debunking creationist ideas, including A Universe From Nothing: Why There Is Something Rather Than Nothing, which dismantles the notion that there had to be a ‘prime mover’ for the universe to exist.

Refuting Creationism - Microbes That Create Life From Non-Life

Mud volcano

Fig. 9: Schematic of microbial succession and biogeochemical processes in serpentinite mud at the Mariana forearc.
This schematic depicts lipid biomarker transitions from pelagic sediment communities to extremophiles adapted to high pH and redox conditions in serpentinite mud. The Mariana forearc biosphere is fueled by alkaline serpentinization fluids enriched in H₂, CH₄, DIC, and organic acids, sustaining specialized microbial communities. Lipid and stable carbon isotope data reveal a shift from relict methanogenic archaea, likely engaged in hydrogenotrophic methanogenesis, to a later ANME-SRB community mediating anaerobic oxidation of methane (AOM). Changes in substrate availability likely drove this transition. Distinct lipid signatures, including unsaturated diethers, acyclic GDGTs, and ether-based glycolipids, highlight adaptations to pH stress, phosphate limitation, and fluctuating redox conditions. The presence of in-situ branched GDGTs suggests previously uncharacterized bacterial communities persisting in these ultra-oligotrophic conditions. The Mariana forearc serpentinite biosphere, shaped by episodic fluid flow and substrate shifts, provides insights into deep-sea subsurface habitability. DIC = dissolved inorganic carbon, ANME anaerobic methanotrophic archaea, SRB sulfate-reducing bacteria, AOM anaerobic oxidation of methane, GDGT glycerol dialkyl glycerol tetraether.

Kumawat, P., Albers, E., Bach, W. et al. (2025).

Fats provide clues to life at its limits in the deep sea

Researchers at MARUM – Bremen University’s Centre for Marine Environmental Sciences – have made a discovery, just published open access in the journal Communications Earth & Environment, which, properly understood, should make depressing reading for creationists.

They have found living organisms both on and within the ocean floor, surviving in conditions where normal life would be impossible. These microorganisms inhabit mud volcanoes with a pH of 14, metabolising hydrogen and carbon to form methane by drawing energy from minerals in the surrounding rock. In other words, they live entirely without oxygen and with almost no organic matter, synthesising all they need from inorganic sources.

Informed creationists will recognise that these organisms directly refute their frequent assertion that life cannot arise from non-life — because producing life from non-life is precisely what these microorganisms are doing.

This also contradicts the biblical claim that all living things were created for the benefit of humans, since there is no conceivable way these organisms could serve any human purpose. Of course, to be fair, the authors of the Bible were completely ignorant of microorganisms, deep-ocean mud volcanoes, and chemosynthetic metabolism. They could only attempt to explain the larger creatures that lived in the limited region around their homes in the Canaanite hills.

And, as any informed creationist should also understand, these are exactly the sort of extreme conditions that biologists believe may have fostered the emergence of the earliest living organisms during the origin of life on Earth — once again undermining any claim that abiogenesis is impossible.

Background^ Chemosynthetic Extremophiles. Chemosynthetic extremophiles are microorganisms that survive in environments too hostile for most known life. Instead of relying on sunlight for energy (as photosynthetic organisms do), they extract energy from chemical reactions involving inorganic compounds such as hydrogen, methane, ammonia, or sulphides.

These organisms thrive in extreme conditions — high pressure, intense heat or cold, high salinity, or extreme acidity or alkalinity — where oxygen and organic nutrients are scarce or absent. They are commonly found around deep-sea hydrothermal vents, cold seeps, and mud volcanoes, as well as in acidic mines and alkaline lakes.

Chemosynthesis typically involves oxidising inorganic molecules (e.g. hydrogen sulphide, hydrogen, or iron) to obtain energy, which is then used to convert carbon dioxide or methane into organic compounds. This allows entire ecosystems — such as those around black smokers on the ocean floor — to exist entirely independent of sunlight.

These extremophiles are of major interest to biologists and astrobiologists because they demonstrate that life can originate and persist in conditions once thought uninhabitable. Their existence supports hypotheses that early life on Earth, and potentially elsewhere in the universe, may have begun in similar environments where energy was derived chemically rather than from sunlight.

The research is explained in a Universität Bremen news item.

Fats provide clues to life at its limits in the deep sea

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Researchers use lipid biomarkers to reveal survival strategies in extreme ecosystems

Diverse life forms exist on and within the ocean floor. These primarily consist of microbes, tiny organisms that can cope with extreme environmental conditions. These include high pressures and salinities, as well as extreme pH values and a limited supply of nutrients. A team of researchers has now been able to detect microbial life in two newly discovered mud volcanoes with very high pH values. Their findings have been published in the professional journal Communications Earth & Environment.

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Blue serpentinite mud from a newly discovered mud volcano in a gravity core. The samples have been studied by a team in order to decipher the survival strategies of microorganisms.

Photo: SO292/2 Expedition Science Party

In their study, first author Palash Kumawat of the Geosciences Department at the University of Bremen and his colleagues used lipid biomarker analyses to decipher the survival strategies of the microbes in this harsh ecosystem. The high pH value of 12 here is especially challenging for deep-sea life; This is one of the highest known value so far in ecosystems. In order to detect life at all, the researchers had to resort to special methods of trace analysis. In this situation, the detection of DNA can be ineffectual where there is a low number of living cells.

But we were able to detect fats. With the help of these biomarkers we were able to obtain insights into the survival strategies of methane- and sulfate-metabolizing microbes in this extreme environment.

Palash Kumawat, first author
Faculty of Geosciences
University of Bremen
Bremen, Germany.

Microbial communities metabolize carbon in the deep sea and thereby contribute to the global carbon cycle. However, the communities that the team describe in the publication draws its energy from minerals within rocks and gases such as carbon dioxide and hydrogen to produce methane, for example, an important greenhouse gas. These processes initially take place independently of the ocean above. The lipids also provide clues to the age of the microorganisms. If the cellular biomolecules are intact, they represent a living or recently dead community. If they are not intact, they are geomolecules, which means that they are fossil communities from the past. According to Kumawat, the combination of isotopes and the lipid biomarkers indicates that multiple microbial communities now live in this inhospitable habitat and have lived there in the past.

This distinction helps us when working in areas with extremely low biomass and nutrient deficiency.

Palash Kumawat.

Dr. Florence Schubotz, organic geochemist at MARUM – Center for Marine Environmental Sciences at the University of Bremen and co-author of the study, adds:

What is fascinating about these findings is that life under these extreme conditions, such as high pH and low organic carbon concentrations is even possible. Until now, the presence of methane-producing microorganisms in this system has been presumed, but could not be directly confirmed. Furthermore, it is simply exciting to obtain insights into such a microbial habitat because we suspect that primordial life could have originated at precisely such sites.

Dr. Florence Schubotz, co-author
MARUM – Center for Marine Environmental Sciences
University of Bremen
Bremen, Germany.

The samples for the study come from a sediment core that was retrieved by the Research Vessel Sonne in 2022 during Expedition SO 292/2. Not only were the scientists able to discover the previously unknown mud volcanoes of the Mariana forearc during this cruise, but also to sample them.
The samples were obtained as part of the Cluster of Excellence “The Ocean Floor – Earth's Uncharted Interface.” Palash Kumawat and his colleagues are now planning to cultivate organisms in an incubator to find out more about their nutrient preferences in inhospitable environments.

Publication:

Kumawat, P., Albers, E., Bach, W. et al.
Biomarker evidence of a serpentinite chemosynthetic biosphere at the Mariana forearc. Commun Earth Environ 6, 659 (2025). https://doi.org/10.1038/s43247-025-02667-6

Abstract
Present-day serpentinization systems, such as that at the Mariana forearc, are prominent sources of reduced volatiles, including molecular hydrogen (H₂) and methane (CH₄), and are considered analogs for chemosynthetic ecosystems on early Earth. However, seepage of serpentinization fluids through mud volcanoes at the Mariana forearc seafloor is defined by high pH, and nutrient scarcity, creating challenging conditions for microbial life. We present geochemical and lipid biomarker evidence for a subsurface biosphere shaped by episodic substrate availability, highlighting microbial persistence across steep geochemical gradients within serpentinite mud. Light stable carbon isotope compositions from diagnostic lipids reveal a temporal shift from hydrogenotrophic methanogenesis to sulfate-dependent anaerobic methane oxidation. Membrane adaptations, including unsaturated diether, acyclic and branched tetraether, and ether-based isoprenoidal and non-isoprenoidal glycosidic lipids, reflect microbial strategies for coping with this extreme environment. Our findings establish the Mariana forearc as a unique serpentinite-hosted biosphere, where life operates at the fringes of habitability.

Introduction
The subseafloor biosphere is estimated to harbor up to 15% of the global biomass¹. Recent advances in deep biosphere research have improved our understanding of the distribution and diversity of microbial life in the rocky oceanic crust, especially around hydrothermal vents^2,3. This subseafloor biosphere has to adapt to limited carbon and nutrient availability, accompanied by harsh environmental conditions such as high temperature and pressure, elevated salinity, and/or extreme pH levels⁴. Serpentinization of mantle rocks by seawater can generate high levels of H₂^5,6 that, in turn, drives the abiotic reduction of carbon to form CH₄ and other organic compounds⁷, which can be oxidized by chemosynthetic organisms^8,9,10, forming the foundation for a serpentinite biosphere¹¹. The type locality for such a serpentinite biosphere is the Lost City hydrothermal vent field near the Mid-Atlantic Ridge, where hydrothermal fluids fuel microbial communities in active and inactive vent structures¹². Methanogenic archaea there are found in active brucite-calcite vents, whereas older carbonate chimneys host a syntropic consortium of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) that perform the anaerobic oxidation of methane (AOM)^13,14.

The process of serpentinization takes place in a range of geotectonic settings, including rifted continental margins, mid-oceanic ridges, transform faults, and convergent margins. Among the latter, the forearc of the Mariana subduction system is of particular interest because it provides access to serpentinization products from within an active subduction zone. There, dewatering of the subducting Pacific Plate leads to serpentinization of the mantle wedge of the overriding Philippine Sea Plate. Faults reaching 10–25 km deep into the forearc allow serpentinite, together with fluids derived from the subducting slab, to buoyantly rise and form large ‘serpentinite mud volcanoes’ on the seafloor^15,16 (Fig. 1a, c). Fluids venting from the mud volcanoes are cold (<3.5 °C), hyperalkaline (pH up to 12.6), and enriched in H₂ and CH₄ (both up to ~1 mM)^17,18 and slab-derived sulfate (SO₄²⁻; up to 28 mM)¹⁹. These fluids are also enriched in short-chain organic acids like acetate (0.04 mM) and formate (0.1 mM), contributing ~20–30% of the dissolved organic carbon (DOC)²⁰, and in methanol (0.03 mM)^20,21. The δ¹³C of CH₄ (−37‰ to 2‰), acetate (−8‰), formate (4.8‰) and methanol (2.3‰) point to their abiotic formation^17,21. While these serpentinization fluids sustain chemosynthetic life at the seafloor^22,23, the functioning and extent of the chemosynthetic microbial biosphere below the seafloor remains largely unknown. Cell counts in the serpentinite mud are variable, but overall low (101 to 106 cells cm−3)^20,24, presumably because of the high pH and intermittent fluid seepage^13,16. Extremophilic archaea are believed to perform AOM as inferred from the detection of phospholipid-derived diphytanyl diethers and reduced sulfur species in the formation fluids18. Metabolic transcripts for denitrification and AOM were interpreted as evidence for nitrate-dependent AOM within the serpentinite mud volcanoes²⁴. Although AOM is considered thermodynamically favorable here^19,25, direct evidence for AOM and its associated microorganisms is still lacking. Methanogenesis is a common metabolic strategy in serpentinization systems¹³, but since CH₄ formation at the Mariana forearc is dominantly abiotic, the extent of microbial methanogenesis remains uncharacterized.

Fig. 1: Study area and geological context of serpentinite mud volcanism in the Mariana subduction system.

a Bathymetry map of the Mariana subduction system showing the incoming Pacific Plate, the overriding Philippine Sea Plate, the Mariana Trench, and a subset of the known serpentinite mud volcanoes on the forearc seafloor. Stars mark the locations of the Pacman and Subetbia mud volcanoes investigated in this study. Bathymetry from GEBCO Compilation Group¹²⁵. b Bathymetry map showing the Pacman mud volcano and the location of gravity core GeoB24917-1 retrieved during expedition SO292/2. Bathymetric data collected during expedition SO292/2²⁶. c Schematic of serpentinite mud volcano formation, following serpentinization of the mantle wedge by slab-derived fluids, formation of H₂ and CH₄, and the rise of serpentinite mud and fluids through deep-seated faults towards the seafloor.

This study documents AOM coupled to sulfate reduction as a key metabolic process in the Mariana forearc, indicating the importance of methane cycling for the indigenous microbial community. Our findings also provide evidence of relict methanogenesis in the serpentinite mud, where its temporal distribution is possibly controlled by variable substrate availability. We present a comprehensive lipid biomarker and isotopic record from the Pacman and Subetbia mud volcanoes, providing insights into the habitability and survival strategies of extremophilic chemosynthetic life in this serpentinite biosphere.

Kumawat, P., Albers, E., Bach, W. et al.
Biomarker evidence of a serpentinite chemosynthetic biosphere at the Mariana forearc. Commun Earth Environ 6, 659 (2025). https://doi.org/10.1038/s43247-025-02667-6

Copyright: © 2025 The authors.
Published by Springer Nature Ltd. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Creationists often insist that “life cannot come from non-life,” claiming that the origin of life through natural processes — abiogenesis — is impossible. Yet these microorganisms thriving deep beneath the ocean floor undermine that argument completely. They demonstrate that life does not require sunlight, oxygen, or organic nutrients. Instead, it can sustain itself entirely through chemical reactions involving inorganic matter, precisely the kind of chemistry that would have been available on the early Earth long before photosynthesis or complex ecosystems evolved.

These microbes survive by harnessing energy from the oxidation of minerals and gases such as hydrogen and carbon, producing methane as a by-product. In doing so, they show that biological systems can indeed emerge and persist using nothing more than inorganic chemistry and environmental energy sources. If life can continue this way today — in conditions strikingly similar to those thought to exist on the early Earth — then it is perfectly reasonable to infer that the same processes could once have given rise to life itself.

Creationists’ claim that life from non-life violates natural law is based on a false analogy with modern life, which relies on pre-existing organic systems. But these extremophiles illustrate that the boundary between “non-living” chemistry and “living” biochemistry is not a rigid wall — it is a continuum. The metabolic reactions that sustain these organisms are direct chemical extensions of the mineral and geochemical reactions occurring in their surroundings. Life in such places does not appear magically; it emerges naturally from the physical and chemical conditions of its environment.

Far from being a problem for evolutionary science, discoveries like this one strengthen the case for a natural origin of life. They show that even today, the chemistry of life and the chemistry of rocks remain intimately connected. To deny that such chemistry could, under the right conditions, cross the threshold into life is to deny the very evidence creationists claim to seek — evidence that life can, and demonstrably does, arise from the non-living world through the workings of natural law.

Sadly, the same creationists who continue to parrot the 'no life from non-life' fallacy won't have understood a word of that and will continue to make proven false claims.

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Refuting Creationism - Diverging Sloth Genomes - Just As The TOE Predicts

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Deforested genomes: scientists find signs of environmental degradation in the genomes of the endangered Maned Sloths - Leibniz Institute for Zoo and Wildlife Research

The discovery fits seamlessly within the framework of Darwinian evolution. Two once-connected populations became isolated and exposed to different ecological conditions, followed their own evolutionary paths. Over time, their genomes accumulated distinct mutations reflecting adaptation, genetic drift, and local environmental pressures. The result is two clearly defined species whose divergence can be explained entirely by natural processes acting over generations — a textbook demonstration of evolution in action.

Yet this same process now drives both species along a far more perilous trajectory. As their habitats continue to shrink and fragment, their populations are losing genetic diversity and becoming increasingly inbred. Evolution has no foresight or purpose; it cannot plan for the future or reverse the consequences of environmental destruction. The very mechanism that once diversified life on Earth can, under relentless human pressure, just as readily lead to extinction.

There is no sign of “intelligent design” in this grim reality — only the blind, natural workings of selection, drift, and chance operating within a degraded environment. If a designer were guiding life towards some higher purpose, it would hardly produce a situation where its own creations are being driven to extinction by the ecological collapse of their habitats. The plight of the maned sloths stands as a vivid reminder that life’s diversity, beauty, and tragedy arise not from supernatural intent, but from the impersonal and unyielding logic of evolution.

As world leaders prepare for COP30 in Brazil, the message from the maned sloths’ genomes could not be clearer: conservation must be guided by evolutionary science and ecological understanding, not by comforting myths of divine oversight. Only by recognising the true, natural processes that shape life can we hope to protect what remains of it.

Refuting Creationism - Another of Those 'Living Fossils' For Creationists To Misrepresent

Adult marine shell-boring spionid polychaete.

Vasily Radishevsky/
Far Eastern Branch of the Russian Academy of Sciences

Spionid traces on fossilized bivalve shells.

Javier Ortega-Hernandez/Harvard University.

Half-billion-year-old parasite still threatens shellfish | UCR News | UC Riverside

It’s Coelacanth time for creationist disinformers again.

Hilariously, I’ve known creationists claim that the 'fact' that coelacanths haven’t changed for 200 million years somehow proves the “evilutionists” are wrong and that Earth is only 6,000–10,000 years old. How they managed to examine the genome of a 200-million-year-old fossil remains a mystery, but DNA appears to play no part in a creationist’s definition of evolution.

So, for an alternative fallacious argument, here’s an even older fossil that’s still around today, apparently in much the same form as it was almost half a billion years ago. It’s a parasitic worm that attacks oysters. The details have just been published in the journal iScience by scientists led by University of California, Riverside palaeobiologist Karma Nanglu, with colleagues from Harvard.

The parasitic, soft-bodied bristle worm belongs to a group called the spionids. It’s common in today’s oceans and feeds on the shells of mussels and oysters, leaving a characteristic question mark-shaped track in their shells. Their parasitism doesn’t kill the shellfish but probably shortens their lifespan.

Refuting Creationism - 300,000 Years Of Stone Technology In Africa - Over 2 Million Years Before 'Creation Week'

Fig. 1: Map of Turkana Basin with the Namorotukunan Archeological Site and timeline of currently known events in the Plio-Pleistocene.

a Geographical context of the Koobi Fora Formation (red stripes), the paleontological collection area 40 (green square), and the location of the site of Namorotukunan (black dot); [map produced Natural Earth and NOAAA ETOPO 202295]; b Stratigraphic context of the Koobi Fora Formation highlighting members and key volcanic ash marker levels, yellow bars refer to the age of archeological horizons (tephrostratigraphy after McDougall et al.⁹⁶); c A chronology of key Plio-Pleistocene hominins from the East African Rift System (EARS)^11,74,97,98 d A chronology and key localities associated with hominin lithic technology^3,6,12 (images of Nyayanga provided by E. Finestone; images of Lomekwi and BD1 based on 3D models; artifact images are for representation and not to scale) and the investigations at Namorotukunan: red arrows represent the artifact levels in the archeological excavations (photos DRB), and colored circles (lettered A-G) represent geologic sections investigated to develop a synthetic stratigraphic column (presented in Figs. 2 and 3).

Braun, D.R., Palcu Rolier, D.V., Advokaat, E.L. et al (2025)

Stone Tools Through Generations: 300,000 Years of Human Technology | Media Relations | The George Washington University

The story of our origins is written in the ground of Africa. It is real, tangible, and objective — a record that doesn’t rely on belief or interpretation, but on physical evidence left behind by our ancient ancestors. A fresh chapter of that record has just been described in a new open-access paper in Nature Communications, authored by an international team of palaeoanthropologists led by Professor David R. Braun of the Center for the Advanced Study of Human Paleobiology at George Washington University, and the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

By comparison, the origins narrative found in Genesis reflects the worldview and assumptions of people who believed the Earth was small, flat, and covered by a solid dome. It is astonishing that, even today, some treat that ancient cosmology as a more reliable account of human history than the rich and expanding fossil and archaeological record in Africa. Yet such individuals continue to seek influence over policy, law, morality, and social institutions, grounding their authority not in evidence, but in pre-scientific tradition — a worldview formed long before the wheel, let alone modern science.