Scientists describe a window into evolution before the tree of life | Oberlin College and Conservatory | EurekAlert!
In a paper published recently in the journal Cell Genomics, scientists Aaron Goldman (Oberlin College), Greg Fournier (MIT), and Betül Kaçar (University of Wisconsin–Madison) describe how they were able to study evolutionary history even before the last universal common ancestor of all living things (LUCA) emerged, and discovered that some of the genes associated with LUCA may in fact predate LUCA itself.
Creationists determined to misrepresent the process of abiogenesis often present it as a ridiculous parody in which a fully complex cell is supposed to have spontaneously assembled out of inorganic atoms and molecules. This straw-man caricature is far easier to attack than what science actually proposes: that the first population of self-replicating proto-cells arose through gradual chemical and evolutionary processes within a large and diverse population.
Within such a population, variation would inevitably occur, and whatever produced the most copies of itself would come to dominate. One of the earliest characteristics to emerge would have been rapid replication, because in a vast population with generation times measured in minutes, even “million-to-one” mutations are not rare events — they occur thousands of times a day. Under such conditions, what creationists portray as wildly improbable becomes not only plausible, but effectively inevitable over time.
Several independent evolutionary pathways could also have developed in parallel: RNA molecules coding for particular enzymes, ribosomes assembling from self-catalysing RNA, and primitive membranes forming across which chemical energy gradients could arise. Only once these components were already present could they come together within an enclosing membrane to form the first true prokaryotic cells.
The research team led by Aaron Goldman has now developed a method for determining which genes were likely present in LUCA, and which must already have been available to be incorporated when LUCA first emerged. In other words, some genes appear to predate LUCA itself, pushing parts of evolutionary history even deeper into the pre-cellular past.
What Was LUCA — and What Came Before It? The Last Universal Common Ancestor (LUCA) is often misunderstood, especially by creationists who portray it as the very first living organism. In reality, LUCA was not the origin of life, nor the first cell, nor some single creature that suddenly appeared fully formed.Their methodology is explained further in a press release from Oberlin College, via EurekAlert!.
LUCA is simply the most recent population of organisms from which all life alive today ultimately descends — bacteria, archaea, and eukaryotes alike. Crucially, LUCA already possessed a level of biochemical sophistication. Most researchers agree it likely had:
- a genetic code based on RNA and DNA
- ribosomes capable of translating RNA into proteins
- enzymes for metabolism and replication
- membrane structures maintaining internal chemistry
- the ability to exploit chemical energy gradients
This means LUCA could not have been the beginning of life. Instead, it must have been the product of a long evolutionary history that preceded it.
Pre-LUCA Evolution: A World of Competing Proto-Life
Before LUCA, early Earth was almost certainly home to a diverse population of simpler self-replicating systems — sometimes called proto-cells or pre-cellular life. These were not fully modern organisms, but chemical systems capable of reproduction, variation, and selection.
Rather than a single miraculous event, abiogenesis is best understood as an extended evolutionary process in which:
- self-replicating molecules competed for resources
- advantageous variants spread through populations
- metabolic pathways evolved gradually
- membranes formed to enclose and stabilise reactions
- genetic and protein machinery became increasingly integrated
LUCA represents the point at which one lineage became the common ancestor of everything that survived, not the moment life began.
Genes Older Than LUCA
What makes the new research so significant is the finding that some genes associated with LUCA appear to be even older — suggesting that early evolutionary innovations were already circulating in the pre-LUCA world and later became incorporated into the first universal ancestor.
This is exactly what evolutionary theory predicts: life did not begin with a fully formed cell, but with populations of evolving systems, long before anything resembling modern biology existed.
Scientists describe a window into evolution before the tree of life
All life on Earth shares a common ancestor that lived roughly four billion years ago. This so-called “last universal common ancestor” represents the most ancient organism that researchers can study.
Previous research on the last universal common ancestor has found that all the characteristics we see in organisms today, like having a cell membrane and a DNA genome, were already present by the time of this ancestor. So, if we want to understand how these foundational characteristics of life first emerged, then we need to be able to study evolutionary history prior to the last universal common ancestor.
In a new article published in the journal Cell Genomics, scientists Aaron Goldman (Oberlin College), Greg Fournier (MIT), and Betül Kaçar (University of Wisconsin-Madison) describe a method to do just that. “While the last universal common ancestor is the most ancient organism we can study with evolutionary methods,” said Goldman, “some of the genes in its genome were much older.” The authors describe a type of gene family known as a “universal paralog,” which provides evidence of evolutionary events that occurred before the last universal common ancestor.
A paralog is a gene family that has multiple members in the same genome. For example, in our own genome, we have eight versions of hemoglobin genes, which encode proteins that bind to oxygen and carry it through the blood. All of these paralog genes descended from an ancient globin gene that existed as a single copy about 800 million years ago. The paralogs were created by repeated duplications of that gene through DNA copying errors, with each copy then evolving its own distinct features over millions of years.
Universal paralogs are a rare, special type of paralog that have at least two copies in the genomes of all or nearly all organisms alive today. This broad presence indicates that the duplication of an original gene must have taken place before the last universal common ancestor, with multiple copies inherited by its descendants, all the way to the present day.
For this reason, the authors argue that universal paralogs provide an indispensable, but underutilized, target for understanding the earliest history of life on Earth, especially as tools for such research improve with the arrival of new AI-based techniques and AI-optimized hardware.
While there are precious few universal paralogs that we know, they can give us a lot of information about what life was like before the time of the last universal common ancestor.
Aron D. Goldman, lead author.
Department of Biology
Oberlin College and Conservatory
Oberlin, OH, USA.
The history of these universal paralogs is the only information we will ever have about these earliest cellular lineages, and so we need to carefully extract as much knowledge as we can from them.
Gregory P. Fournier, co-author
Department of Earth, Atmospheric and Planetary Sciences
Massachusetts Institute of Technology
Cambridge, MA, USA.
In their article, Goldman, Fournier, and Kaçar, survey all known universal paralogs. These universal paralogs are all associated with the production of proteins or the movement of different molecules across cell membranes. These two features of the cell were therefore among the earliest characteristics of life to have evolved.
The authors also recommend deeper descriptions of the ancient ancestral genes themselves. For example, Goldman’s own lab at Oberlin studied a universal paralog family that is responsible for embedding enzymes and other proteins into cell membranes. Using common techniques of evolutionary biology and computational biology, they reconstructed the protein encoded by the original ancestor of this protein. They found that the simpler, ancient version of this protein was still able to perform functions like binding to the membrane and binding to the protein synthesis machinery, and could have assisted simple proteins in implanting themselves into an early cell membrane.
Ultimately, the authors hope that increasingly sophisticated computational tools will allow researchers to discover new universal paralog families and describe their ancient ancestors in greater detail.
By following universal paralogs, we can connect the earliest steps of life on Earth to the tools of modern science. They provide us a chance to transform the deepest unknowns of evolution and biology into discoveries we can actually test.
Betül Kaçar, co-author
Department of Bacteriology
University of Wisconsin-Madison
Madison, WI, USA.
They envision painting a more detailed picture of evolution prior to the last universal common ancestor, when life as we know it first emerged.
Publication:
What this research demonstrates, yet again, is that creationist caricatures of origins collapse the moment they are compared with what science actually proposes. Abiogenesis is not the fairy tale of a modern cell assembling itself by chance in a single improbable leap, but the far more plausible and evidence-based picture of chemistry giving rise to populations of replicators, and those replicators undergoing selection long before anything recognisable as a true cell existed.
The idea that some of LUCA’s genes predate LUCA itself is not an embarrassment for evolutionary biology — it is exactly what one would expect if early life emerged gradually through a long continuum of evolutionary experimentation. Evolution does not begin with perfection. It begins with variation, competition, and incremental refinement, leaving traces of earlier stages embedded in what comes later.
And this is precisely what makes such findings so devastating for creationism. A model of special creation has no explanatory framework for why life should contain molecular relics older than its supposed first ancestor, nor why the deepest foundations of biology point not to sudden manufacture, but to a long history of shared descent and pre-cellular evolution stretching back into the earliest chapters of Earth’s history.
Once again, reality stubbornly refuses to conform to the creationist requirement for instant, fully formed beginnings. Instead, it tells the same consistent story written throughout biology: life is ancient, life is connected, and life emerged through natural processes unfolding over immense spans of time — not through the snap of supernatural fingers a few thousand years ago.
The deeper we look, the further back evolution is waiting for us.
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