Notes: Interlude: The Embrace

Chapter notes for “Interlude: The Embrace”

Notes

¹ Daniel Mills, quoted in Michael Marshall, “How these strange cells may explain the origin of complex life,” Science News (December 11, 2025). The sentiment reflects the long-standing assumption in evolutionary biology that eukaryogenesis was extraordinarily improbable.

² R.B. Pedersen et al., “Discovery of a black smoker vent field and vent fauna at the Arctic Mid-Ocean Ridge,” Nature Communications 1:126 (2010).

³ Anja Spang, quoted in Marshall (2025). Spang’s work at Uppsala University was foundational to identifying Lokiarchaeota.

⁴ Burak Avcı, quoted in Marshall (2025).

⁵ Hiroyuki Imachi et al., “Isolation of an archaeon at the prokaryote–eukaryote interface,” Nature 577 (2020): 519–525. This paper, years in preparation, presented the first cultured Asgard archaean and proposed the “entangle-engulf-endogenize” model based on the observed tentacle morphology.

⁶ The term “syntrophy” describes metabolic cooperation where neither organism can survive independently — a form of obligate mutualism that is thermodynamically favored in certain environments.

⁷ T. Rodrigues-Oliveira et al., “Actin cytoskeleton and complex cell architecture in an Asgard archaeon,” Nature 613 (2023): 332–339.

⁸ Anja Spang, quoted in Marshall (2025).

⁹ Marshall (2025), summarizing the shift in scientific consensus.

¹⁰ Spang, quoted in Marshall (2025).

¹¹ D.B. Mills et al., “A reassessment of the ‘hard-steps’ model for the evolution of intelligent life,” Science Advances 11 (2025). This paper challenges the assumption that major evolutionary transitions were extraordinarily improbable single events.

¹² Euglenids acquired their plastids through secondary endosymbiosis — absorbing a green alga that itself had acquired photosynthesis through an earlier primary endosymbiotic event with a cyanobacterium. Multiple independent secondary and tertiary endosymbioses are now documented across diverse eukaryotic lineages. See Patrick J. Keeling, “The endosymbiotic origin, diversification and fate of plastids,” Philosophical Transactions of the Royal Society B 365 (2010): 729–748.

¹³ Pedro Leão et al., “Asgard archaea defense systems and their roles in the origin of eukaryotic immunity,” Nature Communications 15:6386 (2024). The study identified 2,610 complete defense systems across Asgardarchaeota and demonstrated that eukaryotic viperin proteins derive from Asgard viperins, while both eukaryotic and bacterial Argonaute proteins appear to have originated in Asgardarchaeota.

¹⁴ Carter, C.W. and Wills, P.R., “Interdependence, Reflexivity, Fidelity, Impedance Matching, and the Evolution of Genetic Coding,” Molecular Biology and Evolution 35 (2018): 269-286. Carter and Wills demonstrate that the genetic code itself bears the signature of ancient peptide-RNA cooperation: the aminoacyl-tRNA synthetases that enforce the code divide into two complementary classes whose ancestral forms were short peptides, each dependent on the other and on RNA for function. The coding system could not have arisen from RNA alone or protein alone — it required both, cooperating from the start.

¹⁵ Kathryn E. Appler, James P. Lingford, Xianzhe Gong, Kassiani Panagiotou, Pedro Leão, Marguerite V. Langwig, Chris Greening, Thijs J. G. Ettema, Valerie De Anda, and Brett J. Baker, “Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor,” Nature (2026). DOI: 10.1038/s41586-026-10128-z. Analysis of 404 Asgardarchaeota metagenome-assembled genomes (including 136 new Heimdallarchaeia) revealed that the closest archaeal relatives of eukaryotes encode electron transport chain Complex IV, haem biosynthesis, reactive oxygen species detoxification, and novel respiratory membrane-bound hydrogenases with Complex I-like subunits. The authors propose that both hydrogen production and aerobic respiration were present in the Asgard-eukaryotic ancestor, shifting eukaryogenesis models from a simple hydrogen-for-shelter exchange to a partnership between two bioenergetically sophisticated organisms. This is an ancestral inference drawn from living descendants, not a direct observation of the host that acquired the mitochondrial ancestor. Notably, Pedro Leão — who co-authored the Asgard archaeal defense systems study (note 13)—also contributed to this work, connecting the bioenergetic and immunological strands of the eukaryogenesis story.