The Intelligent Design of LUCA

Pseudoscience at the Root of Biology

Darwin’s 1837 sketch of the ‘tree of life’ — an idea drawn before evidence, much like LUCA reconstructions today.

In September 2024, Nature Ecology & Evolution published a major paper reconstructing LUCA by Edmund R. R. Moody, Tom A. Williams, Nick Lane, Ziheng Yang, Davide Pisani, Philip Donoghue, Timothy Lenton, and others. The authors presented LUCA as a “prokaryote-grade anaerobic acetogen” with primitive immune defenses and metabolic pathways, claiming to locate it ~4.2 billion years ago.

What the paper actually does is construct LUCA from the start and then describe the imposed figure as if it were discovered.

The paper begins by defining LUCA into existence as the node from which Archaea and Bacteria diverge, then reconstructs its genome and metabolism by back-projecting modern organisms. The conclusion, that LUCA existed, is built into the premises. It’s like a lottery where the winning number is chosen first and all the tickets are printed afterward to fit it.

The authors state: “the common ancestry of all extant cellular life is evidenced by the universal genetic code, machinery for protein synthesis, shared chirality of amino acids, and use of ATP. LUCA is then defined as “the node on the tree of life from which the fundamental prokaryotic domains diverge.”

This is circular reasoning — the kind Darwin himself warned against, yet ultimately still used. Darwin conceded that analogy is “a deceitful guide,” yet he immediately relied on it to argue that all life descended from “one primordial form.” The LUCA paper makes the same mistake in technical language. The scientists are designing LUCA themselves, inadvertently showing that the better analogy is intelligent design. They labor through elaborate thought experiments — picking genome size, pathways, and timelines by deliberate choices and calibration constraints — then present the result as if it were discovered. In truth, what they describe are sophisticated natural technologies already embedded in life, technologies so advanced they remain beyond full human understanding, while imagining how those technologies engineered themselves.

— Charles Darwin

The paper estimates LUCA’s genome at ~2.7 Mb and ~2,600 proteins, “comparable to modern prokaryotes.” But this figure is produced “by using modern prokaryotic genomes as training data.” In other words, LUCA’s genome is projected backward from present life. Even within this construct, the reconstruction is incomplete: “reconstructions of metabolic pathways [are] incomplete due to phylogenetic noise and other limitations.” LUCA’s genome is not evidenced. It is like averaging all modern languages and then insisting you’ve rediscovered the first language. What you’ve really done is build a composite from modern forms, not found any evidence that they all came from one.

The authors infer that LUCA used the Wood–Ljungdahl pathway — a carbon-fixation process used by some modern anaerobic microbes to turn CO₂ and hydrogen into acetate. They base this on a subset of 399 KEGG gene families with ≥0.75 probability across domains. Yet they admit: ‘our interpretation of LUCA’s metabolism relies on inference of pathways, not individual genes.’ Pathways are stitched together from fragments of modern organisms under the assumption of descent. They have to know this isn’t evidence, but they present it anyway — because the system demands they keep publishing.

LUCA is dated to ~4.2 Ga by molecular clocks calibrated with fossils. The authors concede: “Dating the root of a tree is difficult because errors propagate from the tips to the root … information is not available to estimate the rate of evolution for the branch incident on the root node.” But what ‘root node’? It’s the one they assumed into existence when they defined LUCA at the start.

Even more speculative are the maximum-age constraints: the paper discards the Late Heavy Bombardment as “should not be considered a credible” and instead relies on the Moon-forming impact at 4.51 Ga. Thus, even LUCA’s age is based on hypothetical planetary events opportunistically chosen to maintain the narrative.

If LUCA lived in aquatic settings at ~4.2 Ga, it requires stable oceans. Yet materialist cosmology holds that water was delivered later by comet impacts during the Late Heavy Bombardment (~3.8–3.9 Ga). It’s a telling omission: they discard a major cosmological event because it would make their LUCA date impossible.

The paper also claims LUCA was part of an “established ecological system.” Yet it concedes: “By definition, we cannot reconstruct LUCA’s contemporaries using phylogenomics.” The ecology is pure speculation stacked on admitted impossibility.

But even if we granted LUCA, the problem only gets worse. Darwin’s model requires a gradual climb from single cells to multicellular animals. The record shows no such climb — it jumps straight from single-celled organism to thousands. That chasm makes LUCA irrelevant, and I’ve explained why in detail here: The Missing Transition Overlooked by Science.

Notably, the LUCA paper is not an exception but an example of a wider pattern. Materialist origin theories contradict themselves on their own but even more so when combined. The contradictions are always resolved by discarding one timeline to preserve another. This paper is only one piece of a larger failure that has turned into a paradigm of authoritative pseudoscience. This is why I argue for Natural Technology — a comprehensive theory of technology in nature that explains what evolutionary narratives can’t.