Rosa Rubicondior: Refuting Creationism - How Our Complex Cells Evolved

Saturday, 31 October 2026

Refuting Creationism - How Our Complex Cells Evolved

How could a comparatively simple cell give rise to the elaborate internal organisation found in the cells of animals, plants, fungi and other eukaryotes? For creationists, this is another opportunity to insert a supernatural designer into an unanswered question. For scientists, it is an invitation to investigate. A new study has now brought that investigation a significant step forward by cultivating two strains of microbes belonging to one of our closest known archaeal relatives.

The research, led by Hiroyuki Imachi and Masaru K. Nobu of the Japan Agency for Marine-Earth Science and Technology, with colleagues including Satoshi Nakagawa of Kyoto University, was published in Nature on 28 October 2026. The organisms belong to Heimdallarchaeia, within the group widely known as Asgard archaea, now formally classified as Promethearchaeota.

What makes these organisms especially informative is the combination of internal simplicity and elaborate external structures. They lack a nucleus and persistent internal membrane systems, yet produce long, branching membrane protrusions. They also depend on metabolic partnerships with other microorganisms. Their biology therefore provides a way to investigate how close associations between initially separate cells could have helped set the stage for a much more intimate evolutionary partnership.

Endosymbiosis involves one organism living inside another. In the case of eukaryotic origins, a bacterial partner eventually became the mitochondrion. The outstanding questions concern how that relationship began and how it became integrated with changes in the host cell. These new findings support scenarios in which the archaeal host was still internally simple, with much of eukaryotic cellular complexity developing during or after the establishment of that partnership.

Oxygen may also have helped shape the relationship. Both cultivated strains depend on anaerobic metabolism, but one could grow in the presence of small amounts of oxygen when oxygen-consuming bacteria were also present. Protection from oxygen could therefore have been one early benefit of an association with the future mitochondrial ancestor.

These modern archaea are evolutionary relatives, not unchanged ancestors, and nobody has recreated the origin of a eukaryotic cell in a laboratory. Nevertheless, the research turns questions about ancient cellular partnerships into experimentally accessible biology. Complexity need not have appeared fully formed: relationships that initially benefited separate organisms could have provided opportunities for further evolutionary innovation. That is a hypothesis science can investigate, refine and test.

Endosymbiosis^ how a microbial partnership became part of the cell. The cells of animals, plants, fungi and other eukaryotes carry evidence of an ancient partnership. Their mitochondria — organelles that play a central role in energy metabolism — descend from bacteria that became permanent residents inside another cell. This evolutionary process is called endosymbiosis.

From neighbours to internal partners

Symbiosis is a close association between organisms of different species; it does not necessarily benefit both participants. In a mutually beneficial association, however, each partner gains something from the relationship. One microorganism might consume another's metabolic waste, for example, allowing both to obtain energy under conditions in which either would struggle alone.

Endosymbiosis takes that association inside the host. An internal partner that survives, reproduces and passes into the host's offspring can become a persistent feature of the lineage. Over evolutionary time, increasing dependence and genetic integration can transform that partner into an organelle: a specialised component of the cell.

Why do scientists think mitochondria were once bacteria?

The explanation rests on several converging lines of evidence:

They retain their own genomes.
Typical mitochondria contain a small amount of DNA, distinct from the chromosomes in the nucleus. Comparisons of mitochondrial genes reveal their bacterial ancestry.

Their protein-making machinery has bacterial roots.
Although modified by evolution, mitochondrial ribosomes and other components of their genetic machinery retain evidence of that relationship.

They grow and divide from existing mitochondria.
Their reproduction preserves features inherited from their cellular ancestors, although it is now closely regulated by the host.

They have two surrounding membranes.
This is consistent with their endosymbiotic history, although membranes alone would not establish their origin.

The strongest case comes from these observations together, particularly the molecular evidence linking mitochondria to bacteria. Chloroplasts provide a separate example: the photosynthetic organelles of plants and algae descend from cyanobacterial endosymbionts.

How does a partner become an organelle?

The transformation involves more than one cell taking up residence inside another. Genes that become unnecessary can be lost, while some genes move into the host's nuclear genome. For a transferred gene to retain its original function, the cell must also evolve the appropriate regulation and, where necessary, a way to transport its protein product back into the organelle.

Modern mitochondria consequently depend on many proteins encoded in the nucleus. The former partners have become an integrated biological system, with coordinated growth, metabolism and inheritance. Natural selection can favour intermediate stages whenever they improve survival or reproduction; it requires no foresight about the eventual outcome.

Where do Asgard archaea fit?

Evidence places the host lineage involved in eukaryotic origins among, or closely associated with, the Asgard archaea. The newly cultivated Heimdallarchaeia help researchers investigate what relatives of that host can do. Their internally simple cells, branching surface protrusions and dependence on microbial partners make them valuable experimental models.

These organisms are modern relatives, not unchanged ancestors. Nor are their cultivated partnerships examples of mitochondria forming: their usual partners in these cultures are methane-producing archaea living outside the cells. The relevance lies in the opportunities they offer to study cell contact, metabolic dependence and possible starting conditions for closer integration.

What remains unresolved?

The bacterial ancestry of mitochondria is firmly established. The precise sequence of events that produced the first eukaryotic cells remains under investigation: how the bacterial partner entered the host, what initially sustained the association, and when the nucleus and internal membrane systems developed.

Uncertainty about that sequence does not erase the evidence for endosymbiosis. It identifies the questions that new cultures, experiments and genetic comparisons can help answer.

The Heimdallarchaeia cultivation study.
Kyoto University's research summary.
Endosymbiotic gene transfer and the integration of organelle genomes.

The finding reported in Nature is also described in a Kyoto University news release:

Capturing our closest archaeal relatives offers clues to the origin of eukaryotes

Successful isolation and growth of two strains of Heimdallarchaeia
A collaborative research team led by Hiroyuki Imachi and Masaru K. Nobu of the Japan Agency for Marine-Earth Science and Technology (JAMSTEC), and including Satoshi Nakagawa of Kyoto University, has for the first time isolated and cultivated two strains of Heimdallarchaeia, a group of archaea that are among the closest known archaeal relatives of eukaryotes – the organisms that include humans and other animals, as well as plants and fungi. By examining their cells and lifestyles directly, the team has gained the clearest picture yet of what the archaeal ancestor of eukaryotes may have looked like and how they lived.
How complex eukaryotic cells emerged remains one of the biggest mysteries in biology. A leading hypothesis is that they emerged when an archaeal cell belonging to Promethearchaeota formed a close partnership with a bacterium that eventually became the mitochondrion. In 2020, the JAMSTEC team first cultivated a member of this group, strain MK-D1, from deep-sea sediment. Based on its cell structure and metabolism, the team proposed the E3 model for the origin of eukaryotes.

Studies of environmental DNA later suggested that Heimdallarchaeia, a lineage within Promethearchaeota, are the closest archaeal relatives of eukaryotes. Some researchers proposed that they might already have complex internal structures and/or the ability to use oxygen, like eukaryotes. However, because they had never been grown in the laboratory, their cell organization and physiology remained unverified. In this study, the team successfully cultivated two strains and examined them directly.

The researchers found that the internal structure of both strains was simple, lacking membrane-bound organelles such as a nucleus. Instead, the cell surface was complex, extending multiple long, branching membrane protrusions. These protrusions facilitated attachment to other microorganisms and formation of symbiotic partnerships. Although both strains were oxygen-independent (anaerobic) microorganisms, one had several systems to protect itself from oxygen and could grow even when small amounts of oxygen were initially present, as long as oxygen-utilizing (aerobic) bacteria were also present.

What separates eukaryotes from archaea is their complex internal structure and internal symbiosis with a former bacterium, yet how these two manifested remains enigmatic. First, the presented findings suggest that the archaeal ancestor of eukaryotes may have remained simple on the inside. Second, the team further discovered surface structure-mediated symbioses as the first biological connection between structural complexity and symbiosis in archaea.

This supports the idea that the internal complexity of eukaryotic cells developed through surface structure-mediated symbiosis with the bacterial ancestor of mitochondria. Third, the results also suggest that this early partnership may have begun in an environment with low levels of oxygen and the partner may have helped the anaerobic archaea cope with oxygen. One of these archaea may have eventually taken the bacterial ancestor of mitochondria into its cell, leading to major changes in its cellular structure and metabolism and ultimately evolving into an ancient eukaryote.

The newly cultivated Heimdallarchaeia provide experimental models for studying the origin of eukaryotes. By investigating their cell structures and interactions with microbial partners, the researchers hope to better understand how a simple archaeal cell gave rise to the complex cells of eukaryotes.

Evolutionary relationships between Promethearchaeota and eukaryotes, and electron micrographs of cultured strains.
The diagram on the left shows the evolutionary relationships between eukaryotes and groups within Promethearchaeota, an archaeal lineage of particular interest for understanding eukaryotic origins. Heimdallarchaeia, the group to which strains HC1 and SC1 isolated in this study belong, are the closest archaeal relatives of eukaryotes. The electron micrographs on the right show cultured archaea extending long protrusions from their cell surfaces. White arrows indicate their symbiotic partners, methane-producing archaea. The electron micrograph of strain B35 is reproduced from Rodrigues-Oliveira et al., Nature (2023), doi: 10.1038/s41586-022-05550-y

Publication:
Imachi, H., Nobu, M.K., Ishii, S. et al. Eukaryotes’ closest relatives are internally simple syntrophic peptidotrophic archaea. Nature (2026). https://doi.org/10.1038/s41586-026-11170-7

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Abstract
Eukaryotes are theorized to have an origin associated with the archaeal phylum Promethearchaeota (formerly Asgard archaea)^1,2,3. The first cultured representatives revealed valuable insights^4,5 but are still distantly related to eukaryotes, leaving many unknowns regarding eukaryogenesis. Here we report the isolation of two strains, HC1 and SC1, that belong to the archaeal lineage that branches closest to eukaryotes (Heimdallarchaeia);^6,7,8 these isolates are members of a pure co-culture and a tri-culture with methanogenic partners. Both are obligately anaerobic, syntrophic, peptide-degrading and mesophilic archaea that produce protrusions and vesicles but lack persistent internal membrane structures, like Promethearchaeales^4,5. All Promethearchaeota isolates demonstrate behaviour focused on cell construction and membrane structures rather than division, in contrast to typical prokaryotes⁹. Strain HC1 possesses genes associated with aerobic lifestyles (such as cytochrome c oxidase (Cox)) but co-cultures cannot grow under (micro)oxic conditions. Meanwhile, the strain demonstrates growth under microoxic conditions when in the presence of aerobes, suggesting that Cox supports oxygen detoxification rather than respiration. Comparative genomics provides evidence that, like HC1, Cox-possessing Heimdallarchaeia studied to date probably do not respire oxygen. The wide conservation of anaerobiosis, cell structure without persistent intracellular membranes and membrane protrusions across Promethearchaeota suggest that the archaeal ancestor of eukaryotes may have had such physiological features. In this cultivation-informed scenario for eukaryogenesis, the archaea–eukaryote transition would involve a steep transition in cell structure and physiological shift from anaerobiosis to (facultative) aerobiosis¹⁰, with early interactions between the archaeal host and mitochondrial ancestor probably occurring under low-oxygen conditions and at least partially mediated by oxygen detoxification.

Fig. 2: Microscopy characterization of HC1

a–e, SEM images showing single (a), dividing (b), protrusion-producing (c) and methanogen-attached (d) cells, and a magnified view of the image in d (e). f, QFDE image. g,h, Ultrathin section. i, Fluorescence image of cells stained with DAPI (blue) and hybridized with nucleotide probes targeting the rRNA of HC1 (green) and Methanocalculus (red) (Extended Data Fig. 7). j, Immunofluorescence image of cells stained with SYBR Green I (yellow/green) and labelled with an HC1 actin-specific antibody (red) (Extended Data Fig. 4). k–n, Cryo-electron tomogram (cryo-ET) slices (k,m) and corresponding 3D volume segmentations (l,n). Intracellular vesicle-like structures were infrequently observed in the images in m and n. Red, ferritin-like granules; yellow, actin filaments; blue, cell membrane; light blue, intracellular vesicle-like structure. The images c, f, h and i–n were obtained from cultures in the late-exponential phase, and the others were obtained from cultures in the mid-exponential phase. SEM, QFDE, ultrathin section, FISH and immunofluorescence images are representatives of n = 98, 48, 60, 21 and 36 recorded images, respectively. Cryo-ET images were obtained from 11 recorded tilted cryo-EM images. The white arrows indicate Methanocalculus sp. strain MC2 cells. Scale bars, 1 µm (a–j) and 500 nm (k,m).

Imachi, H., Nobu, M.K., Ishii, S. et al. Eukaryotes’ closest relatives are internally simple syntrophic peptidotrophic archaea. Nature (2026). https://doi.org/10.1038/s41586-026-11170-7

Copyright: © 2026 The authors.
Published by Springer Nature Ltd. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

What makes this research significant is not that scientists have recreated the origin of complex cells, but that they have brought another part of that ancient transition within reach of experimental investigation and reduced the size of another gap so beloved of creationists. Living relatives of the probable host lineage can now be examined directly, allowing ideas about cellular structure, metabolic partnerships and responses to oxygen to be tested against observations. The picture remains incomplete, but its missing details are becoming research questions with practical ways to investigate them.

For intelligent design creationism, the difficulty is that cellular complexity carries evidence of evolutionary history. Mitochondria retain traces of their bacterial ancestry, while their dependence on proteins encoded in the nucleus reflects the integration of formerly separate organisms. The new cultures add evidence relevant to how such a partnership could have begun. An association that initially benefited its participants could have provided opportunities for further adaptation, without either organism anticipating the eventual outcome.

None of this requires us to pretend that every step is settled. These archaea are not our unchanged ancestors, their present partnerships are not mitochondria in the making, and the route from external association to internal integration remains under investigation. Those distinctions are strengths of the scientific account: they separate what the evidence establishes from what researchers still need to discover. Invoking a designer supplies neither the missing sequence nor a testable mechanism.

Once again, evolutionary biology is providing the framework for productive research into a question creationists would prefer to declare insoluble. Science advances by identifying what it does not yet understand and finding ways to investigate it. A gap in our knowledge is a starting point for that work, not evidence that a god occupies it.

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