Analog Science Fiction & Fact Magazine
"The Alternate View" columns of John G. Cramer

LUCA, Earth Life's Universal Common Ancestor

by John G. Cramer

Alternate View Column AV-237

Keywords: life origin, Hadean Era, evolution, prokaryotes, eukaryotes, LUCA, common ancestor

Published in the July-August-2025 issue of Analog Science Fiction & Fact Magazine;
This column was written and submitted 03/07/2025 and is copyrighted ©2025 by John G. Cramer.
All rights reserved. No part may be reproduced in any form without the explicit permission of the author.

In this AV Column we take a deep dive into the history of life's beginning and evolution on Earth, and its implications today. Earth's Hadean Era, which took place 4.6 to 4.0 billion years ago, was a time of extensive volcanic activity and heavy bombardment by meteorites, asteroids, and other celestial debris, including one colossal impact that formed the Moon. The Hadean atmosphere was composed of nitrogen with some carbon dioxide and small amounts of hydrogen and methane, but it contained no free oxygen. In some regions Earth became cool enough for pools of water to form, as today's oceans began to emerge. This chaotic and unstable environment somehow fostered the emergence of life.

The consensus view of biologists is that somewhere back in time, all existing forms of cellular life must have had a common ancestor. This view is supported by several facts: (1) the DNA-based GCAT genetic code is universal, (2) the mRNA-based GCAU protein coding and ribosome machinery is nearly universal, (3) while there are more than 500 naturally occurring amino acids, Earth life almost universally uses only the same 20 of these in producing proteins, (4) life almost universally uses only left-handed amino acids to form proteins, although their naturally occurring right-handed equivalents are available, and (5) life almost universally uses the ATP molecule (adenosine triphosphate, C₁₀H₁₆N₅O₁₃P₃) as its common energy currency.

The primordial organism of most interest in the appearance of Earth life is called LUCA, the last universal common ancestor of contemporary life. In the evolutionary hierarchy LUCA is the oldest of several cellular ancestors. The others are: LACA, the last archeal common ancestor, LBCA, the last bacterial common ancestor, LECA, the last eukaryotic common ancestor, and finally mitoLECA, the last eukaryotic common ancestor that had captured and incorporated into its metabolism a proto-mitochondrion, an ATP-generating organism that descended from a bacterium on the LCBA evolutionary branch.

There has been an ongoing debate in biology about whether LUCA was actually a true cell or instead was a primitive "protocell" that had emerged from the intense RNA activity in Earth's cooling oceans. Protocells are hypothetical simpler-than-cell organisms thought to have been a stepping stone in the evolution of life. They would not contain fully functional DNA genetic material but might contain simpler molecules (e. g., RNA) that could replicate at some level (see AV-218 in Analog May-June-2022). They should have some rudimentary metabolic processes but would lack the complexity and efficiency of cellular metabolism. They should have had primitive membrane walls made of simple lipids or other molecules but would be less effective than true cells at trans-wall substance exchange.

A team of paleobiologists, applying statistical analysis to information from fossil records along with the characteristics and DNA analysis of the vast array of contemporary organisms, have recently been able to deduce the characteristics of LUCA in some detail. They have concluded that LUCA was a not a protocell, but rather was a full-blown single cell organism, and that LUCA came into existence about 4.2 billion years ago, toward the end of the Hadean Era.

All single-cell organisms are classified as either prokaryotes or eukaryotes. LUCA was a prokaryote, a small single-cell organism with a relatively simple structure, as are modern bacteria and methane-producing archaea. Prokaryotes have a cell wall within which are unspooled circular DNA rings and some ribosomes and transcription enzymes, but few specialized organelles and no cell nucleus. Contemporary prokaryotes are often equipped with a rotating whip-like flagellum used for locomotion, and LUCA may have had one.

Eukaryotes are much larger and more structured cells, which probably evolved later. They have an internal membrane-walled cell nucleus containing DNA spooled on histones and bundled into chromosomes. They also have many organelles that perform special functions. Eukaryotes are the cells that form the basic structure of all modern plants and animals.

LUCA was rod-shaped, had a cell wall made of phospholipids, and had a large DNA genome composed of at least 2.5 million base pairs containing genes that coded for ~2,600 proteins. For contrast, human mitochondria have DNA rings (mtDNA) that have 16,569 base pairs coding for 37 genes, and the human nuclear DNA chromosomes have 3.2 billion base pairs coding for 20,000 to 25,000 genes. LUCA also possessed an early CAS-based immune system that defended it from invading viruses.

LUCA was sustained by a metabolism that depended on the availability of H₂ (molecular hydrogen gas) and probably occupied two distinct habitats: (1) deep ocean where hydrothermal vents provided a source of H₂, and (2) ocean surface where the atmosphere would have provided a source of H₂ derived from volcanoes and ongoing chemical changes in surface rocks and minerals. The latter environment would be somewhat hostile because of damage done by ultraviolet (UV) radiation in sunlight, but there are hints that LUCA had proteins that repaired UV damage.

LUCA's acetogenic (acetyl-producing) metabolism worked like this: inputs of H₂, CO₂, and CO from atmospheric or sub-oceanic sources were internally combined with pre-existing CoenzymeA (C₂₁H₃₆N₇O₁₆P₃S) via complicated metabolic pathway that generated acetyl-CoenzymeA, which then proceeded to liberate free acetate (C₂H₃O₂⁻) molecules and ATP for energy, recycling the CoenzymeA for further metabolism. In this pathway, two molecules of CO₂ were reduced and combined to form an acetyl group.

The overall analysis suggests that LUCA came into existence toward the end of the Hadean Era, very early in Earth's formation, perhaps while the Late Heavy Bombardment (see AV-151 in Analog March-2010) was still in progress and well before Earth had well defined continents, oceans, and a stable atmosphere. This can be taken as encouragement that alien life, in at least primitive forms, may be quite common in our galaxy, because there should be many exoplanets that resemble the conditions of Hadean Earth, while very few of them are expected to resemble Earth's present conditions.

Of the organelles that LUCA had in its cytoplasm, a presently common one was missing: the mitochondrion. Mitochondria are the powerhouses of living cells. They are tiny bacteria-like organelles that reside within the cytoplasm of a cell and provide it with energy, busily converting food-derived molecules like glucose into ATP, the fuel that cells actually use to meet all of their energy needs. Each ATP molecule can supply ~0.32 eV of energy. For comparison, it requires 3 to 5 eV to break a typical biochemical covalent bond, and a photon of green light contains ~2.25 eV of energy.

The emergence of mitochondria, which require the availability of oxygen for their ATP production, has an interesting history. About 2.7 billion years ago during the Archaean Era, cyanobacteria (also known as blue-green algae) evolved to perform photosynthesis, producing oxygen as a metabolic byproduct. During the later Paleoproterozoic Era, (2.5 to 1.6 billion years ago) as stable continents formed, the oxygen content from the flourishing cyanobacteria increased dramatically in Earth's oceans and atmosphere, in an event called The Great Oxidation. That occurred about 2.4 billion years ago, and it was essential for the subsequent evolution of aerobic (oxygen-using) life forms.

About 1.8 billion years ago, toward the end of the Paleoproterozoic Era, a "capture miracle" occurred. Some random eukaryote cell in Earth's oceans captured a passing prokaryote that was actively producing ATP and incorporated this useful "visitor" into its metabolic processes. That cell is now called mitoLECA, the common ancestor of all of Earth's animal, plant, and fungus life forms. The captured ATP-producing prokaryote evolved into the mitochondria in today's eukaryote cells. In the Paleoproterozoic competition among eukaryotes, mitoLECA became the dominant organism because its internal prokaryotes supplied it with far more ATP-based energy than was available to any of its competitors.

A side note: a plant analog of this "capture miracle" event occurred once again about 1.2 billion years ago with eukaryote plant cells. One of them captured and incorporated a photosynthetic cyanobacterium, providing the host cell with the ability to perform photosynthesis, i. e., convert sunlight into chemical energy (glucose) while releasing oxygen as a byproduct. Over time, the captured cyanobacteria evolved into chloroplasts, the basis of modern plant photosynthesis.

Over the passing eons, the prokaryote's mitochondrial DNA genome "slimmed down" from ~2.5 million base pairs coding for ~2,600 genes to ~16.5 thousand base pairs coding for a few dozen genes. Some of the needed coding moved to the nuclear DNA of the host eukaryote cell. There is a good reason for this evolutionary change: the environment of mtDNA is made very hostile by the organelle's highly-active ATP production machinery, which can crank out ~10⁸ ATP molecules per second while it generates ROS oxidizing radicals that easily damage mtDNA. This causes the rate of unrepaired point-substitution and sequence-deletion mutations in mitochondrial DNA to be about 100 to 1,000 times higher than that in the cell's nuclear DNA. The high mitochondrial mutation rate creates evolutionary pressure to move all but the most essential and immediately needed genetic coding elsewhere.

In the evolution of mitochondria-bearing prokaryote cells, there have been parallel but independent developments in the DNA-repair mechanisms for mitochondrial and nuclear DNA, with those for nuclear DNA being far more effective. Mitochondria provide base excision repair (BER) to fix oxidative lesions but lack most other repair mechanisms. For example, one common genome failure is that during the replication of a DNA sequence some random event causes the replication enzyme to "skip" a length of the DNA sequence that can be thousands of base pairs long, creating a deletion mutation. For nuclear DNA there are repair mechanisms for fixing this damage, but the only way the mitochondrion has of dealing with the damage is to eject an entire nucleoid capsule containing the deletion-damaged genome and perhaps several other mtDNA rings.

The consequence of these damage and repair differences is that over time the mitochondrial DNA accumulates unrepaired damage much faster than does nuclear DNA. This is partly compensated by the fact that cells have many mitochondria, which in turn contain 2-10 or more copies of their mtDNA rings. Nevertheless, the ultimate consequence of this accumulated mitochondrial DNA damage is that critical components of the ATP-production machinery are not being synthesized and provided as needed for ATP production, which ultimately slows to a halt, depriving the myriad of vital cell process of the energy they need to function normally.

It is believed that this mitochondrial degeneration is the root cause of the age-based degeneration in long-lived vertebrates like humans. So it turns out that the "miracle capture" of the first mitochondrion by mitoLECA was a two-edged sword: our cells have lots of energy, but over time the energy flow shuts down, leading to the decrepitude and diseases of old age. (See AV-233 in Analog Nov-Dec-2024 for a fix for this problem.)

John G. Cramer's 2016 nonfiction book describing his transactional interpretation of quantum mechanics, The Quantum Handshake - Entanglement, Nonlocality, and Transactions, (Springer, January-2016) is available online as a hardcover or eBook at:
http://www.springer.com/gp/book/9783319246406 or https://www.amazon.com/dp/3319246402 .

SF Novels: John's 1^st hard SF novel Twistor is available online at: https://www.amazon.com/Twistor-John-Cramer/dp/048680450X. His 2^nd and 3^rd novels, Einstein's Bridge and its new sequel Fermi's Question, are now available as eBooks from Baen Books at: https://www.baen.com/einstein-s-bridge.html and https://www.baen.com/fermi-s-question.html .

Alternate View Columns Online: Electronic reprints of 237 or more of "The Alternate View" columns written by John G. Cramer and previously published in Analog are currently available online at: http://www.npl.washington.edu/av .

Reference:

E. R. R. Moody, et al, "The nature of the last universal common ancestor and its impact on the early Earth system," Nature Ecology & Evolution 8, 1654–1666 (2024); arXiv:2412.14265v1.

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This page was created by John G. Cramer on 03/08/2025.