A paper recently published in Science Advances by an international team led by researchers at Heinrich Heine University Düsseldorf (HHU) will make disappointing reading for any creationist with enough courage to read a scientific paper—especially those pinning their hopes on science never closing their favourite gap: the gap between geochemistry and the first living systems.
Leaving that gap permanently open would allow them to declare, “God did it!”, without providing a scrap of supporting evidence or explaining how their preferred god supposedly made chemistry and physics behave in ways that they could not have done unaided. This combination of the god-of-the-gaps argument and a false dichotomy—either science already has a complete explanation, or magic must have been responsible—is standard creationist fare in the absence of positive evidence for a creator.
The new research does not, as some headlines might suggest, show that abiogenesis occurred twice independently. Instead, it presents evidence that the genetic code and a core metabolic network had a single origin before the ancestral lineage divided into Bacteria and Archaea, but that the two lineages subsequently completed the transition to free-living cells independently. As senior author William F. Martin expressed it, the findings point to “one origin of the genetic code, but two origins of life”—with “life” here referring specifically to autonomous, free-living cellular life.
The findings therefore do not overturn universal common ancestry. Both Bacteria and Archaea still trace their ancestry to the last universal common ancestor, or LUCA. What the researchers propose is that LUCA was not yet a fully independent cell equipped with enzymes for every essential metabolic reaction. It remained partly dependent on inorganic catalysts supplied by the hydrothermal environment in which its metabolism had evolved. Only after the bacterial and archaeal lineages had diverged did each independently evolve the remaining enzymes needed to become free-living.
Eukaryotes appeared much later and are descended from an archaeal lineage that entered into an endosymbiotic association with a bacterium. That bacterium eventually became the mitochondrion, while the resulting partnership gave rise to the common ancestor of all known eukaryotic organisms. The new findings therefore refine the earliest stages of common descent rather than replace common descent with multiple, unrelated creation events.
The research team, whose lead author was HHU biologist Natalia Mrnjavac, examined the network of 420 chemical reactions used by cells to manufacture amino acids, nucleotides and cofactors from substances available on the early Earth, including hydrogen, ammonia and carbon dioxide. The reactions themselves are almost universally conserved, but the enzymes catalysing them are not. From comparisons of genomes, protein structures and chemical reactions, the researchers inferred that LUCA possessed enzymes for only about half of this metabolic network. Many of the remaining reactions could have been catalysed by naturally occurring metals in hydrothermal vents.
The team reconstructed four broad stages in the evolution of metabolism: an initial network catalysed by metals; a hybrid system employing both metals and enzymes in LUCA; divergence into the bacterial and archaeal lineages; and the independent replacement of environmental catalysts by enzymes in each lineage. In several cases, Bacteria and Archaea evolved structurally different enzymes to catalyse the same essential reaction—parallel evolutionary solutions to the same chemical problem.
Laboratory experiments also identified a possible early source of metabolic energy. The researchers found that phosphite, a reduced form of phosphorus found in serpentinising hydrothermal systems, could drive phosphorylation reactions in water when palladium acted as a catalyst. Under these conditions, phosphite and palladium could perform functions now carried out by complex enzymes and ATP-based biochemical machinery.
The important distinction is therefore between the common origin of the fundamental biochemical system and the later, independent evolution of cellular autonomy. The shared genetic code is evidence of inheritance from common ancestry, while the different bacterial and archaeal enzymes show that evolution can produce more than one molecular solution to the same biochemical requirement. Far from revealing the work of a genetic programmer, the pattern is precisely what descent with modification, environmental dependence and evolutionary divergence would be expected to produce.
The research does not demonstrate that life arose independently from non-living chemistry twice, so it cannot legitimately be used to calculate the probability of abiogenesis. It does, however, suggest that one crucial transition—from an environmentally supported biochemical system to a self-sufficient cell—was completed independently in two lineages. That is hardly comforting for creationists who insist, without any rational statistical basis, that natural processes could not produce biochemical complexity even once.
Bacteria and Archaea^ Similar Cells, Different Domains. Bacteria and Archaea are both predominantly single-celled microorganisms whose cells lack a nucleus. They were consequently once grouped together as “prokaryotes”, but molecular comparisons revealed that they represent two fundamentally different evolutionary lineages. Indeed, much of the archaeal machinery for processing genetic information resembles that of eukaryotes more closely than it resembles the corresponding bacterial machinery.The paper in Science Advances was accompanied by a news release from HHU:
Feature Bacteria Archaea Cell membrane Usually composed of unbranched fatty acids joined to glycerol by ester bonds. Composed of branched isoprenoid chains joined to a chemically different form of glycerol by stronger ether bonds. Some archaeal membranes form a single molecular layer rather than a bilayer. Cell wall Most have walls containing peptidoglycan, although there are exceptions. Do not have bacterial peptidoglycan. Many possess a protein or glycoprotein surface layer, while some have pseudomurein or other polymers. Transcription Use a comparatively simple RNA polymerase and bacterial transcription factors. Use a more complex RNA polymerase and transcription machinery resembling those of eukaryotes. DNA packaging Package their DNA with bacterial nucleoid-associated proteins. Many package their DNA around histone proteins resembling the histones of eukaryotes. Protein production Possess bacterial ribosomes and translation machinery targeted by many familiar antibiotics. Possess ribosomes of similar overall size, but their components and translation machinery differ and share several features with those of eukaryotes. Motility Many swim using bacterial flagella powered by ion gradients. Some swim using archaella. Although these superficially resemble flagella, they are assembled differently and are not evolutionarily equivalent structures. Metabolism Display enormous metabolic diversity, including photosynthesis, fermentation, nitrogen fixation and aerobic or anaerobic respiration. Are equally diverse in their energy metabolism. Methanogenesis—the biological production of methane—is found exclusively among Archaea. Relationships with humans Include numerous disease-causing species, as well as countless harmless or beneficial members of the human microbiome. Occur in the gut, mouth and on the skin, but no archaeal species has yet been definitively established as a human pathogen, although some have been associated with disease.
Not merely organisms of extreme environments
Archaea were initially discovered in highly saline, acidic or extremely hot environments, leading to the mistaken impression that they were all “extremophiles”. Many do thrive under such conditions, partly because of the stability of their distinctive membranes and proteins, but Archaea are also abundant in ordinary soils, oceans, sediments and animal digestive systems.
What the two domains have in common
Despite their differences, Bacteria and Archaea share the same genetic code, use DNA to store inherited information, transcribe DNA into RNA and translate RNA into proteins using ribosomes. They also share a core network of metabolic reactions. These common features are evidence that both lineages inherited fundamental biochemical machinery from a common ancestral population.
The differences lie largely in the molecular equipment subsequently evolved to perform those shared functions. This is the pattern examined in the new study: an ancestral metabolic network that was still partly dependent on environmental metal catalysts, followed by the independent evolution of different bacterial and archaeal enzymes capable of completing the same essential reactions.
Archaea and the origin of complex cells
Eukaryotic cells—including those of animals, plants and fungi—arose much later through a partnership between an archaeal host cell and a bacterium. The bacterium became the mitochondrion, while the archaeal host supplied much of the genetic and cellular machinery of the resulting eukaryotic lineage. Every human cell therefore preserves evidence of this ancient union between the two great prokaryotic lineages.
Two origins of life
How and where did the first forms of life arise? These are the main questions driving research at the Institute of Molecular Evolution at Heinrich Heine University Düsseldorf (HHU). In a new publication in Science Advances, an international team led by Düsseldorf biologists uncovers pioneering insights into the network of chemical reactions that the very first cells used to make the building blocks of life and which sources of energy they used to drive those reactions. They retraced the origin of enzymes during life’s earliest divergence into bacteria and archaea, and found evidence for two independent origins of life for free-living cells.
If we could go back 4 billion years in time and watch as the first cells emerged on Earth, what would we see?
Metabolism of the first cells. Starting compounds are shown at the left, they are converted by metabolism into the building blocks of life. The 420 enzymatic reactions are indicated as circles, chemical metabolites as diamonds, lines connect reactions having common metabolites. Circles shown in magenta shading indicate reactions that could have been catalysed by inorganic compounds in the environment where metabolism of the first cells arose.Image: HHU/Nadja Hoffmann.
We would see two very different kinds of cells emerging, pioneer bacteria and pioneer archaea, making their first attempts at life outside the confines of a hydrothermal vent.
Natalia Mrnjavac, lead author
Institute of Molecular Evolution
Faculty of Mathematics and Natural Sciences
Heinrich Heine University Düsseldorf
Düsseldorf, Germany.
There, Mrnjavac and an international team of scientists report investigations of genomes, protein structures and chemical reactions that probe the very earliest phases of microbial evolution before there were free living cells.
These comparisons are giving us unprecedented insights into the phase of evolution when metabolism catalysed by enzymes was arising from spontaneous reactions catalysed by metals in the Earth’s crust.
William Martin, senior author.
Institute of Molecular Evolution
Faculty of Mathematics and Natural Sciences
Heinrich Heine University Düsseldorf
Düsseldorf, Germany.
The approach that the team took differs from all previous investigations of early evolution by looking at the entire set of chemical reactions that cells use to make the building blocks of life (amino acids, RNA bases and vitamins) from compounds present on the early Earth: hydrogen gas, ammonia and CO2. This set of 420 chemical reactions is called metabolism. The chemical reactions themselves are as universally conserved as the genetic code.
The surprise is that the enzymes that catalyse those reactions are not conserved across the evolutionary divide that separates bacteria and archaea. We found that the last universal ancestor of all cells, LUCA, possessed enzymes for only about half of the reactions of metabolism. The other half was catalysed by metals in the environment where LUCA arose.
William Martin.
Metals that naturally occur in hydrothermal vents can replace a surprisingly large number of enzymes in metabolism.
Harun Tüysüz, co-author
Department of Heterogeneous Catalysis
Max-Planck-Institut für Kohlenforschung
Mülheim an der Ruhr, Germany. And the IMDEA Materials Institute
Madrid, Spain.The closer we look, the more clearly we can see that early biochemical evolution was a hybrid of enzymatic and metal catalysts.
Joseph Moran, co-author
Department of Chemistry and Biomolecular Sciences
University of Ottawa
Ottawa, Canada
[Joseph Moran is] an international leader in the use of metals to catalyse metabolic reactions, replacing enzymes and cofactors.
A big step forward in the present study was that the team could reconstruct four phases of early evolution of catalysis: metal-only, a metal-enzyme hybrid in LUCA, followed by divergent evolution towards the ancestors of the bacteria and archaeal lineages. In those lineages, new enzymes were arising, replacing inorganic catalysts provided by the environment where metabolism arose.
We can see cases where the ancestors of bacteria and archaea independently evolved structurally distinct enzymes to catalyse the same essential metabolic reaction. Such parallel inventions could have paved the way to the independent emergence of free-living bacteria and archaea.
Natalia Mrnjavac.
And where did the energy come from to drive these reactions forward? Today the energy in metabolism mainly comes in the form of ATP, but ATP is a complicated molecule, made by enzymes, not a compound that was lying around for free in hydrothermal vents.We have identified a new source of energy at metabolic origin. When we react phosphite, a form of phosphorus that naturally occurs in hydrothermal vents, with organic compounds, we get metabolic phosphorylation reactions overnight in water. Phosphite and palladium replace ATP and enzymes; it’s amazing, and it makes early evolution a lot easier to grasp.
Manon L. Schlikker, co-lead author.
Institute of Molecular Evolution
Faculty of Mathematics and Natural Sciences
Heinrich Heine University Düsseldorf
Düsseldorf, Germany.
Among the metals that naturally occur in hydrothermal vents are palladium, an excellent catalyst known and used by chemists for a century.
The study is the first focused investigation into the reaction set called metabolism. That reaction set is a highly interconnected network of 420 reactions, with many compounds participating in multiple reactions. Such networks can be mathematically challenging to deal with. But among the authors are Prof. Mike Steel, from the University of Canterbury in New Zealand, and Prof. Daniel Huson from the University of Tübingen. Experts when it comes to networks, they devised a new method to order metabolic reactions from the simplest to the most complex, possibly recapitulating the order in which metabolic reactions arose at origins.
The first question is whether or not a unique order exists for these reactions. Once we could prove that there is one, the algorithm to order them became tractable.
Professor Mike Steel, co-author
Biomathematics Research Centre
University of Canterbury
Christchurch, New Zealand.
It is part of our human condition to want to know about our origins, where we come from, where life started and how the first cells on Earth made a living. And what is the larger significance of the new findings?The new data leave only one conclusion. The bacteria and archaeal lineages made the transition to the free-living state independently. Only free-living cells are alive. Let’s call it by name: we are looking at one origin of the genetic code, but two origins of life.
William Martin.
In addition to researchers from HHU, the international team included scientists from the Universities of Canterbury (New Zealand), Rostock, Constance, Ottawa (Canada), Strasbourg und Tübingen, the Max-Planck-Institute for Terrestrial Microbiology in Marburg and the Max-Planck-Institut für Kohlenforschung in Mülheim/Ruhr plus the IMDEA Materials Institute in Madrid (Spain).
Background: Bacteria and Archaea
Biologists divide life forms into two categories: Eukaryotes – advanced cells with a cell nucleus – and the more ancient cells lineages without a nucleus: the prokaryotes. The prokaryotes comprise the two primordial lineages of life: Bacteria and Archaea. Many prokaryotes can survive in extreme conditions such as high temperatures, acid or alkaline environments. Many inhabit hydrothermal vents on the ocean floor where, in some theories, life is thought to have arisen.
Publication:
This research does not claim to have reproduced the origin of life or established every stage by which geochemistry became biology. What it does is replace another part of that supposed impenetrable mystery with a testable scientific model—one constructed from comparative genomics, protein structures, metabolic networks and laboratory chemistry.
Instead of a fully formed cell appearing suddenly with a complete complement of enzymes, the evidence indicates a gradual transition. Naturally occurring metals first catalysed reactions in a hydrothermal environment; enzymes then assumed some of those functions; LUCA employed a mixture of biological and inorganic catalysts; and, following their divergence, the bacterial and archaeal lineages independently evolved different enzymes to complete their metabolic machinery and become free-living cells. Complex biochemical systems did not need to appear all at once: they could be assembled incrementally from simpler processes already supplied by their environment.
The resulting pattern is exactly what evolutionary common descent predicts. The shared genetic code and conserved metabolic reactions point to common ancestry, while structurally different enzymes performing the same tasks record the subsequent independent evolution of the bacterial and archaeal lineages. An unidentified designer explains neither pattern and makes no testable prediction about why the similarities and differences should be distributed in this particular way.
Significantly, the researchers did not regard their findings as a crisis for evolutionary biology or as evidence that supernatural intervention must be inserted into the remaining uncertainties. They used evolutionary theory to formulate their questions, reconstruct the sequence of changes and interpret the results. Their findings refine our understanding of the earliest evolution of cells without requiring a single magical creation event.
Creationists can, of course, retreat into whatever parts of the process have yet to be explained and declare that their god must be hiding there. But an unanswered scientific question is not evidence for any answer someone cares to invent. As this study illustrates once again, the abiogenesis gap is not a secure refuge for a creator; it is a collection of research questions that science is steadily turning into chemistry. The gap contains no evidence of a god—only natural processes still waiting to be understood, and retreating into the god of the gaps and false dichotomy fallacies simply emphasised the intellectual and moral bankruptcy of creationism.
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