Rosa Rubicondior: Unintelligent Design - A Bacterium That Goes Wrong And Self-Destructs

SAR11 bacteria comprise some 40% of marine bacterial cells, making them an essential part of our ocean ecosystems.

Image source: Smithsonian / Xiaowei Zhao.

One of Earth’s most abundant organisms is surprisingly fragile

Microbiologists at the University of Southern California (USC) have discovered that one of Earth’s most abundant species, the SAR11 bacterium, has a fundamental — and potentially fatal — ‘design’ flaw. They have just published their findings in Nature Microbiology, and it should make grim reading for any creationists with sufficient courage to read it.

When you have trillions of copies, what does it matter to ‘selfish’ genes if a few billion go wrong and end up destroying the organisms they travel through time in? For an evolved organism, it matters not one tittle or jot to its genes, because they can always produce more copies. So long as there is a sufficiently large population to keep replicating, they will continue to exist and reproduce — and they have no other ultimate function. This is all they evolved to do.

But could we say the same for an organism designed by an omniscient, intelligent designer? What would be intelligent about creating an organism that, under particular but entirely predictable conditions, attempts to reproduce but succeeds only in making repeated copies of its DNA, fails to divide, and enters a runaway cycle of replication until it becomes so disorganised that it can no longer survive and effectively self-destructs?

SAR11 dominates the surface waters of the world’s oceans and accounts for around 40% of marine bacterial cells. As such, it is a vital component at the base of the marine food chain, and is so successful partly because of a process known as genetic streamlining — the evolutionary loss of genes to reduce energy demands in nutrient-poor environments. This alone is not the main problem for creationists to explain, although it does raise the obvious question of why a designer would burden an organism with a genetic load it does not need in the first place.

The real problem is that this streamlining, as an evolved process, comes at a cost. In shedding a load of mostly surplus genes, some essential ones are lost too — including genes that regulate the cell cycle. The result is a failure to divide after genome replication, with the cell instead entering an uncontrolled loop of DNA replication without division.

How on Earth can that be regarded as intelligent design? The organism does exactly what it is ‘designed’ to do under conditions of low nutrient stress, but in doing so falls into an inescapable trap. The consequence is that populations continue to decline even when nutrients later become available again — with potentially serious knock-on effects for other species higher up the food chain.

Background^ SAR11 and Genetic Streamlining. The SAR11 clade (also known as Pelagibacterales) represents one of the most successful evolutionary strategies on Earth. These bacteria dominate the surface waters of the global oceans and are thought to account for roughly 40% of all marine bacterial cells. At any given moment, there are an estimated 10²⁸ SAR11 cells in the oceans — making them among the most abundant organisms ever to have existed. Their extraordinary success is largely due to genetic streamlining, an evolutionary process driven by natural selection in nutrient-poor environments. Over time, SAR11 bacteria have lost large numbers of genes that are not absolutely essential for survival and reproduction. This results in exceptionally small genomes, low metabolic costs, and high efficiency in scavenging scarce nutrients such as carbon, nitrogen, and phosphorus. However, streamlining is not optimisation in the engineering sense. It is a cost-cutting process without foresight. Genes are lost not because they are useless in all circumstances, but because they are dispensable *most of the time*. When environmental conditions change, those missing genes cannot be recovered. The recent findings show that some of the genes lost during streamlining are involved in cell-cycle regulation. Under certain nutrient conditions, SAR11 cells can continue replicating their DNA but fail to divide, entering a runaway replication state that ultimately leads to cellular collapse and death. From an evolutionary perspective, this is not a paradox: individual failure is irrelevant so long as the population as a whole continues to persist. This illustrates a fundamental principle of evolution that is often misunderstood or denied by creationists: natural selection favours reproductive success, not robustness, foresight, or perfection. SAR11 thrives not because it is flawlessly designed, but because its vast population size tolerates enormous losses. What looks like a catastrophic flaw at the level of the individual is simply an acceptable trade-off at the level of genes competing in a global population.

The background to the paper in Nature Microbiology is explained in a USC news item.

One of Earth’s most abundant organisms is surprisingly fragile
An evolutionary adaptation that allows one ocean bacteria to thrive could prove to be its Achilles Heel as oceans change, new study reveals.
A group of ocean bacteria long considered perfectly adapted to life in nutrient-poor waters may be more vulnerable to environmental change than scientists realized.

The bacteria, known as SAR11, dominate surface seawater worldwide and can make up as much as 40% of marine bacterial cells. Their success is tied to genome streamlining, an evolutionary process in which organisms lose genes to reduce energy costs in nutrient-limited environments.

A new study published in Nature Microbiology suggests that this extreme efficiency comes at a cost, however.

SAR11’s extraordinary evolutionary success in adapting to, and dominating, stable low-nutrient environments may have left them vulnerable to oceans that experience more change. They may have evolved themselves into a bit of a trap.

Professor Cameron Thrash, corresponding author.
Department of Biological Sciences
University of Southern California
Los Angeles, CA, USA.

Adaptation with a flaw for SAR11 marine bacteria

The researchers analyzed hundreds of SAR11 genomes and discovered that many lack the genes normally required to control the cell cycle, a process that coordinates DNA replication and cell division. In most bacteria, these genes are essential for healthy growth. Under changing environmental conditions, that missing regulation appears to cause serious cellular problems for SAR11.

An analysis of hundreds of SAR11 genomes revealed that changes to their environment led to abnormal cell division.

Image: Courtesy of the Thrash Lab.

Their sensitivity to environmental changes has been observed before by scientists. What surprised the researchers was how SAR11 cells responded to stress. Rather than simply slowing growth, many cells continued copying their DNA while failing to divide.

Their DNA replication and cell division became uncoupled. The cells kept copying their DNA but failed to divide properly, producing cells with abnormal numbers of chromosomes. The surprise was that such a clear and repeatable cellular signature emerged.

Chuankai Cheng, lead author.
Department of Biological Sciences
University of Southern California
Los Angeles, CA, USA.

These abnormal cells, which carried extra chromosomes, often became enlarged and eventually died. As a result, overall population growth slowed even when nutrients were plentiful, a finding that challenges common assumptions about microbial growth.

The findings also help explain why SAR11 populations often decline during the later stages of phytoplankton blooms, when organic matter increases.

We have known for a long time that these organisms are not particularly well suited to late stages of phytoplankton blooms. Now we have an explanation: Late bloom stages are associated with increases in new, dissolved organic matter that can disturb these organisms, making them less competitive.

Professor Cameron Thrash.

What’s next for SAR11 bacteria

The study has broader implications for understanding climate change and marine ecosystems. SAR11 bacteria play a major role in ocean carbon cycling, and their sensitivity to warming and nutrient pulses could reshape microbial communities as oceans become more variable.

This work highlights a new way environmental change can affect marine ecosystems, not simply by limiting resources, but by disrupting the internal physiology of dominant microorganisms. As environmental stability declines, he added, organisms with greater regulatory flexibility may gain an advantage.

Chuankai Cheng.

Researchers say future work will focus on uncovering the molecular mechanisms behind these disruptions. Their work will help improve our understanding of SAR11’s role in marine carbon cycling, an effort made critical by the organism’s sheer abundance.

About the study

In addition to Cheng and Thrash, the study’s authors include Brittany Bennett, Pratixa Savalia, Hasti Asrari, Carmen Biel and Kate Evans at USC Dornsife; and Rui Tang of the University of California, San Diego.

Publication:
Cheng, C., Bennett, B.D., Savalia, P. et al.
Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation.
Nat Microbiol 11, 551–565 (2026). https://doi.org/10.1038/s41564-025-02237-8

Abstract
Genome streamlining is hypothesized to occur in bacteria as an adaptation to resource-limited environments but can result in gene losses affecting fundamental aspects of cellular physiology. The most abundant marine microorganisms, SAR11 (order Pelagibacterales), exhibit canonical genome streamlining, but the consequences of this genotype on core cellular processes such as cell division remain unexplored. Here, analysis of 470 SAR11 genomes revealed widespread absence of key cell cycle control genes. Growth experiments demonstrated that although SAR11 bacteria maintain a normal cell cycle under oligotrophic conditions, they exhibit growth inhibition and aneuploidy when exposed to nutrient enrichment, carbon source shifts or temperature stress. Detailed growth measurements and antibiotic inhibition experiments showed that these phenotypes resulted from cell division disruption with continuing DNA replication, leading to heterogeneous subpopulations of normal and polyploid cells. This vulnerability raises questions about microbial genome evolution and the evolutionary trade-offs between adaptation to stable nutrient-limited conditions and physiological resilience.

Cheng, C., Bennett, B.D., Savalia, P. et al.
Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation.
Nat Microbiol 11, 551–565 (2026). https://doi.org/10.1038/s41564-025-02237-8

© 2026 Springer Nature Ltd.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

What this study exposes, yet again, is the gulf between how living systems actually work and how creationists wish they worked. SAR11 is not a finely engineered machine designed with foresight and resilience in mind; it is a statistical success story, held together by numbers, redundancy, and the ruthless indifference of natural selection to individual failure. When conditions are right, it flourishes. When they are wrong, vast numbers die — and evolution does not care in the slightest.

This is precisely what we expect from an evolved system driven by gene-level competition over deep time. Genes that maximise replication will spread, even if they occasionally doom the organisms that carry them. There is no mechanism in evolution that rewards robustness for its own sake, nor any requirement that organisms be safe, elegant, or even particularly sensible. Survival is not guaranteed; persistence is.

By contrast, the Intelligent Design narrative demands foresight, optimisation, and intentional constraint. Yet SAR11 displays none of these. It contains a failure mode that is not merely inefficient but actively self-destructive under predictable environmental conditions — a flaw that no competent designer would introduce, and certainly not leave unmitigated in one of the most ecologically important organisms on the planet.

Once again, biology delivers exactly what evolutionary theory predicts and exactly what Intelligent Design cannot explain. Far from pointing to an omniscient designer, SAR11 instead stands as another reminder that life was not engineered — it was filtered.

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