Toward Process-Driven Research in Astrobiology: Stepping Away from the Binary Biogenicity Versus Abiogenicity Approach

Abstract

Biological activity has shaped environments across Earth with varying degrees of impact throughout geological time, which complicates efforts to distinguish signs of life in preserved structures. This challenge is further compounded in the ancient rock record, where diagenesis and alteration obscure biological signatures. To overcome these obstacles, it is necessary to understand the underlying processes that produce chemical and morphological features indicative of life. Traditional approaches to studying biological signatures in deep time typically focus on the binary question of “life” versus “non-life,” often guided by predefined questions. Here, we emphasize a shift toward process-driven research that explores the relationships between fundamental scientific principles that govern these features, rather than traditional outcome-focused approaches. We lay groundwork for a more comprehensive exploration of life’s role in shaping the rock record by addressing practical challenges and providing approaches for implementation.

Keywords

Abiogenic—Astrobiology—Biogenic—Biosignatures—Life detection—Physical processes

1. Introduction

1.1. The need for a shift in perspective

Throughout much of Earth’s history, life has influenced the geological record and shaped our understanding of surface, atmospheric, and subsurface processes. Traditionally, research on early life has focused on identifying evidence of life (i.e., biosignatures) in the rock record, with the assumption that a feature’s origin is biological if plausible abiotic processes are reasonably ruled out (Mustard et al., 2013). Identifying biosignatures in the early rock record, especially those that predate the Great Oxidation Event (∼2.4 Ga), is challenging due to rock alteration and limited preservation, which complicates interpretation and analysis. Early life-forms lacked hard parts, so were less likely to be preserved and were likely smaller and simpler than modern organisms, as seen in rare microfossils in Archean chert (Sugitani, 2019; Sugitani et al., 2013). The current Astrobiology Strategy (NASEM, 2019) highlights recent efforts to understand abiogenic processes that mimic biosignatures. Although valuable, these efforts continue to focus on the differentiability between life and nonlife, despite the challenges that exist in doing so, given processes such as alteration in deep time.

Here, we call for a shift in research perspective from a binary, outcome-driven approach to a process-driven approach in studying geological samples for evidence of life. A process-driven approach emphasizes an understanding of the underlying mechanisms behind potential biosignatures and explores how environmental context shapes them. By adopting this perspective, we can employ interdisciplinary methods to better constrain the processes at play. When discussing our perspective, we will use context-specific terminology to describe the potential evidence-based processes we refer to.

1.2. Challenges of separating geological and biological influences on rock samples

Suspected biosignatures in the rock record are typically assessed through morphological and geochemical evidence, informed by our understanding of modern biological processes. For instance, several studies have interpreted laminated textural structures as biogenic based on various morphological features (Allwood et al., 2006; Coffey et al., 2013; Homann, 2019; Van Kranendonk et al., 2021). Similarly, microfossils have been distinguished from abiological structures using criteria such as symmetry, size, and isotopic and spectroscopic signals (Brasier et al., 2015; McMahon and Jordan, 2022; Sugitani, 2019; Sugitani et al., 2013). A primary consideration in the application of these criteria is that any suspected biogenic structure must be located in sedimentary or metasedimentary rocks conducive for preservation and demonstrate a syn-depositional origin (deposited at the same time) with the surrounding matrix (Brasier et al., 2015).

While life interacts with and influences surface features through a range of physical and geochemical processes, confidently attributing a biological origin to many suspected biosignatures remains challenging. Over time, rocks undergo diagenesis, metamorphism, and other alteration processes, with these effects more pronounced in older and deeply buried rocks. As a result, potential biosignatures in ancient rocks are often difficult to identify or are misidentified, and initial claims of biogenicity can be controversial (McMahon and Jordan, 2022; Rouillard et al., 2021). Additionally, later biological processes can overprint evidence of abiotic or prebiotic chemical processes and create additional layers of complexity (Barge et al., 2022; McDermott et al., 2015). In such cases, determining whether life contributed to the formation of certain geologic structures is challenging, as abiotic processes can mimic or overprint biological features (Hays et al., 2017; Neveu et al., 2018; Nutman et al., 2019). For example, metamorphosed rocks can record altered sedimentary structures that resemble stromatolites (Coutant et al., 2022; Saitoh et al., 2021). Despite the need to improve the ability to decipher abiotic from biological processes, there is a noticeable paucity of published research on abiotic processes that mimic chemical or physical signs of life (García-Ruiz et al., 2003), even though this gap has become evident in the search for life beyond Earth (McMahon and Cosmidis, 2022). Understanding the formation of such abiotic signatures is crucial when searching for biosignatures on other worlds, where evidence of past life is likely even more ambiguous (Barge et al., 2022; Escamilla-Roa et al., 2022; McMahon, 2019; McMahon and Cosmidis, 2022; Nims et al., 2021; Sainz‐Díaz et al., 2021; Saitoh et al., 2021). For example, the Viking Labeled Release experiment (Levin, 1997; Levin and Straat, 1976) initially interpreted changes in ¹⁴C-labeled organics as signs of metabolic activity, but further analysis revealed that abiotic oxidants, such as formate, could produce similar signals in martian soil (Navarro-González et al., 2003). Further research into abiotic processes that mimic biosignatures will be vital for process-driven studies of biosignatures in deep time and beyond Earth.

Defining a satisfactory biosignature has historically been challenging (Hartz and George, 2022; Neveu et al., 2018; Rouillard et al., 2021). Some definitions rely on falsifying an abiotic origin (Awramik and Grey, 2005), which complicates our understanding of the boundaries between abiological and biological chemistry due to limited, conclusively agreed-upon representations of both in the rock record (McMahon and Jordan, 2022). For instance, establishing multiple lines of evidence for life while ruling out abiotic factors is difficult for Archean rocks, which have undergone billions of years of metamorphism and overprinting by both abiotic and biotic processes (Allwood et al., 2018; Nutman et al., 2016, 2019; Zawaski et al., 2020). Furthermore, processes once thought to be predominantly abiotic, such as the formation of carbonates in continental settings and geyserite in hot springs, have been shown to have biological influences (Blyth and Frisia, 2008; Brasier et al., 2015; Cady and Farmer, 1996; Campbell et al., 2015; Guido et al., 2019; Murphy et al., 2021). Similarly, research on purported ancient stromatolites and microfossils has led to the recognition that some of these structures are abiogenic in origin (Allwood et al., 2018; Gong et al., 2022). Experimental models that have replicated biogenic sedimentary structures have also shown that they can have abiotic origins (Grotzinger and Rothman, 1996; Yee et al., 2003). As a result, the assumption that life-like signatures in the rock record can be categorized as strictly biological versus abiological is problematic (Fig. 1a).

FIG. 1.

Conceptual approaches to investigating potential biosignatures in the rock record. (A) The traditional binary approach frames investigations as an “either-or” outcome of biotic versus abiotic, limiting interpretive flexibility. This traditional model emphasizes classification and can treat biosignatures as discrete isolated features. The linear nature of the circles is not intended to represent the order of process but is organized in this manner to highlight the distinction between the two approaches. (B) The process-driven approach advocated here integrates geological, chemical, and biological data in a web of interactions that help assess how complex systems shape biosignatures. Rather than focusing on binary outcomes, this framework considers a spectrum of interacting processes shaped by environmental context. This visualization illustrates a multimodal framework that emphasizes the network of possible factors in the rock record.

While most studies have focused on a binary assessment of a feature’s biogenicity, many signatures of life on Earth reflect a complex interplay between geological and biological processes (Della Porta et al., 2022; Murphy et al., 2021). Suspected biosignatures in the rock record rarely yield straightforward, indisputable interpretations as being either biogenic or abiotic. Instead, they often represent a spectrum of interactions that range from minimal biological influence to features predominantly shaped by life (Brasier et al., 2006) (Fig. 1b). Therefore, a binary approach does not adequately encapsulate the realities faced when attempting to determine the biogenicity of features produced by the interplay of life and non-life processes in either the rock record or modern surface settings (Havig et al., 2021). In the search for life beyond Earth, remote sensing, sample collection, and analytical limitations will further complicate efforts to distinguish biotic from abiotic structures (Nordheim et al., 2022). While new information and additional scientific scrutiny are important, in these instances, a binary approach becomes limiting and counterproductive to assess definitively the origin of a feature of interest. We propose that there is a need to shift away from a dichotomous line of questioning and focus instead on multi-modal assessment of general processes that dictate the complex abiologic and biological relationships that contribute to the formation of geologic structures.

2. A Process-Driven Perspective

Here, we call for a shift in perspective from a binary approach toward process-driven research that focuses on assessing evidence of life’s influence on a geological sample while placing a strong emphasis on environmental context. We define process-driven research as an understanding of the underlying mechanisms that govern a particular phenomenon. In contrast to outcome-driven assessments, where the primary goal is to obtain specific results or answers to predefined questions, process-driven research utilizes interdisciplinary, iterative, and exploratory approaches to reveal how the context shapes outcomes by integrating insights and methods from various fields. A process-driven approach to studying geological materials requires a practical and theoretical methodology, each of which takes into consideration abiotic and biotic information. A practical methodology rooted in comprehensive field observations, laboratory experiments, and analytical tests provides a baseline for inferring the inherent characteristics of a given sample. Concurrently, a theoretical approach that incorporates modeling of the fundamental physical and chemical processes that led to the formation of specific geologic structures, irrespective of the presence of biogenic influence(s), can help ground working hypotheses.

Rather than isolating individual signatures, this approach seeks to understand system dynamics and thus offers a comprehensive view of how various signals could interact within the rock record (Fig. 2). For example, larger-scale processes (Fig. 2, outer yellow circle) relate to chemical, biological, and geological interactions (Fig. 2, middle green circle), which are inferred from individual signals within a rock feature (Fig. 2, inner blue circle). These signals are further shaped by environmental context and later biological activity that can overprint geologic features over time (Fig. 2, center). As systems progress through time, interactions between life and its environment, such as biofilm formation, biomineralization, and changes in redox or chemistry gradients, can progressively obscure or modify original rock textures and geochemical patterns (Mateos-Carralafuente et al., 2023). This biological overprinting can complicate interpretations of the origin of a feature by introducing secondary biosignatures or altering primary ones. A focus on the underlying processes enables researchers to distinguish system-level characteristics and provides a framework for interpreting the processes that could have led to similar features on other worlds.

FIG. 2.

Conceptual diagram illustrating the interconnected processes that influence a structure of interest. At the center, time, environmental context, and biological activity continuously shape the sample and may modify or obscure original features. The inner blue circle depicts signatures that may be observable in the rock record. The green circle shows processes inferred from those signals. The outermost yellow circle reflects larger-scale geological and chemical processes inferred from patterns in the inner circles. This diagram presents non-exhaustive examples and emphasizes how overlapping processes interact to influence interpretations.

2.1. Environmental context in rock formation

Understanding the environmental context of rock formation is crucial for interpreting the origin of ancient rocks and their preserved features. While the same laws of physics apply to all environments, not every environment works in the same way (e.g., water currents are not the same in oceans as in rivers). Just as sedimentary structures are shaped by the paleocurrent active during sediment consolidation, the composition of a rock is influenced by structural and geochemical changes that occur during compaction, cementation, and lithification of the original sediment (e.g., sandstone, composed mainly of quartz grains). Features in the rock record are preserved through deposition, lithification, and fossilization, which scientists can identify and often link to environmental information, including chronology. For instance, Precambrian oceans had high silica concentrations, which promoted silicification and created conditions ideal for preserving biogenic structures, whereas in Phanerozoic assemblages, silicified microbes are mainly restricted to continental silicification in thermal springs (Xiao, 2021) or arise from pH changes in eutrophic waters (Conley et al., 1993). Understanding the underlying environmental and chronological context is essential for accurately interpreting the rock record. Once this context is established, the processes that influence observable geologic features can be more effectively investigated.

When material is deposited, a range of textures and mineralogies can be preserved. The distribution of these textures is directly linked to the energy and sediment-carrying capacity of the transport agent (i.e., water, wind). Typically, transport agents exhibit the highest energy near the sediment source and gradually lose energy as they move away. As a result, coarser sediments and bedforms are deposited closer to the source, while finer sediments with low-energy structures accumulate in sink areas (Dasgupta, 2017). In addition to sediment transport, biological processes can also shape observable textures. Microbial organisms excrete substances that bind to sediment grains, creating substrates for further community growth. These organisms also influence water chemistry and geochemical conditions through their metabolic processes, which can lead to biologically induced textures with signatures indicative of specific sub-environments. These signatures are shaped by factors such as energy, water availability, and geochemistry (Dupraz et al., 2009). The interaction between these physical, chemical, and biological influences can be measured or modeled. For example, depositional models for travertines and silicic hot springs offer fine-scale transects that help reconstruct the processes behind the final textures (Capezzuoli et al., 2014; Guido and Campbell, 2011). These studies, based on geographic transects, have enriched our understanding of the distribution of biological textures and provided deeper insights into how to interpret them in the fossil record. Ultimately, the combined geological and biological processes at the time of deposition are responsible for producing the features observable in the rock record today.

2.2. Post-depositional alterations and preservation processes

The interconnected relationship between geology and biology is fundamental to processes such as fossilization and biomineralization. Prokaryote fossilization primarily occurs through casting and molding, where chemical bonds form between organic functional groups in prokaryotic cell walls and substances such as silicic acids, phosphate groups, pyrite, or clay minerals. These interactions produce molds and casts; they enable exceptional microorganism preservation if recrystallization is inhibited (Barlow et al., 2024; Xiao, 2021). Additionally, photosynthesis and carbon dioxide-concentrating metabolic activities can drive biologically induced calcite mineralization (Riding, 2006). These processes generate a continuum of geological structures, from bona fide fossils to biologically mediated mineral and mineraloid deposits, as well as trapped organic remains and substances. Much of our understanding of these mechanisms comes from field observations and taphonomic experiments that replicate geological conditions to study the preservation of fossils or organic matter (Konhauser et al., 2003). The intricate interplay among geology, chemistry, and biology governs the formation and preservation of diverse signatures. Although these signatures are not always definitively identifiable, the environmental processes that facilitate their preservation can often be observed and tested.

Later processes such as diagenesis and metamorphism can obscure those linked to deposition and fossilization by altering original textures and chemistry. These processes involve crystallization and recrystallization, which modify molecular structures, rock morphology, and chemistry. Diagenesis, an early alteration stage, may preserve original textures as minerals grow around preexisting structures. With increasing temperature and pressure, metamorphism produces distinct alterations, including new minerals (e.g., chlorite, muscovite, biotite) and textures (e.g., foliation, banding, veins) that overprint original signals. Examining mineralogy, textures, and geochemical changes caused by metamorphism (e.g., cross-cutting veins, mineral overgrowths) helps assess the extent of secondary alterations. Minerals such as quartz, apatite, pyrite, and calcite, commonly associated with fossilization, reflect their formation conditions (Auer et al., 2017; Planavsky et al., 2010). Deviations in chemical signatures, such as trace element profiles (e.g., rare earth element + yttrium plots) or isotopic ratios (e.g., U-Pb or Ca clumped isotopes), indicate metamorphic overprinting (Reynard et al., 1999). Geochemical data from modern sedimentary environments (e.g., lakes, reefs, oceans) are crucial for distinguishing depositional and diagenetic signals. While metamorphic and metasomatic processes may produce distinct textures, their chemical compositions can converge. In situ fine-scale measurements tied to texture are essential to disentangle overprinting and reconstruct depositional processes. For example, macro- and micro-textures, rare earth geochemistry, and U-Pb isotopes have been used to differentiate depositional and early diagenetic signals in phosphorite from metamorphic overprints (O’Sullivan et al., 2021). Thus, multi-scale observations are crucial for interpreting diagenetic and metamorphic processes and their contributions to the observable rock record.

3. Conclusion

The study of early life on Earth through potential biosignatures has historically relied on binary distinctions between biotic and abiotic origins. However, this approach oversimplifies the complex interplay between geological and biological processes. Geological, chemical, and biological activities collectively shape the rock record; this makes it unrealistic to classify any biosignature as exclusively biotic or abiotic. Instead, potential biosignatures should be examined as products of interconnected processes over time. A process-driven perspective emphasizes the environmental context and the dynamic interactions that shape rocks. Features formed during deposition and fossilization may be altered by diagenesis and metamorphism, but these changes reveal valuable insights into a rock’s history. By linking observations to fundamental physical and chemical principles, researchers can disentangle overlapping processes and establish the environmental and chronological context of biosignatures. Addressing these complexities requires interdisciplinary teams capable of integrating geological, chemical, and biological expertise, as collaborative and multimodal approaches are essential for investigating these intricate interactions. Moving beyond binary thinking not only enhances our understanding of Earth’s geological history but also equips us to tackle the challenges of identifying life on other planets.

Footnotes

Acknowledgments

The authors would like to thank all members of the STROMATOLITE Syndicate for engaging in thoughtful and critical discussions regarding the topic presented here. They would especially like to thank Michaela Dobson, whose foundational efforts were instrumental in organizing the initial development of this article. They would also like to thank Dr. Laurie Barge for her helpful comments and feedback. Their work would not have been possible without their affiliations and funding sources.

Author Disclosure Statement

No competing financial interests exist.

Funding Information

S.R.B. was supported by the National Science Foundation Graduate Research Fellowship. GAS was supported by the NASA FINESST award (80NSSC20K1365). A.J.S. was supported by FONCyT (PICT 2020-SERIE A-02000). B.L.T. conducted her portion of the work at the Jet Propulsion Laboratory, California Institute of Technology under a contract with the National Aeronautics and Space Administration (80NM0018D0004). E.V.B. was supported by an appointment to the NASA Postdoctoral Program at Pennsylvania State University and the Laboratory for Agnostic Biosignatures, administered by Oak Ridge Associated Universities under contract with NASA, and by NASA Astrobiology NfoLD grant (80NSSC18K1140). G.G.S. conducted her portion of the work while at the College of Earth and Mineral Sciences, Pennsylvania State University.

Data Availability Statement

There is no data affiliated with this article.

Associate Editor: Christopher P. McKay

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