The Flow of Life
Why How Things Change Matters More Than What They Are
Introduction: A Scientific Debate That Challenges Our View of Life
What if everything we thought about living systems was upside down? What if instead of focusing on the things that make up organisms—genes, proteins, cells—we should instead be focusing on the processes and flows that create and sustain them? This fundamental question lies at the heart of a fascinating scientific debate that has been unfolding in the pages of scientific journals, most recently in a reply written by Johannes Jaeger and Nick Monk to their colleagues Horsting and Hartjes.
"How scientists conceptualize the natural world shapes the questions they ask, the experiments they design, and ultimately how we understand life itself."
This isn't merely an academic exercise; how scientists conceptualize the natural world shapes the questions they ask, the experiments they design, and ultimately how we understand life itself. The shift from a substance-based perspective to a process-based perspective represents what some philosophers of science call a "paradigm shift"—a fundamental change in approach that could transform everything from how we treat diseases to how we protect ecosystems .
In this article, we'll explore this captivating scientific dialogue, unpack the key concepts of process thinking, examine the experimental evidence that supports it, and consider what it might mean for the future of biological research and beyond.
Substance Versus Process: Two Ways of Seeing the Biological World
The Traditional View: Substance Ontology
For centuries, Western science has operated primarily from what philosophers call substance ontology. This perspective views reality as composed primarily of distinct, independent objects or substances that possess certain properties. In biology, this translates to focusing on biological entities—genes, proteins, cells, organs—as the fundamental units of life 3 .
Think of it like this: if biology were a recipe, substance ontology would be primarily concerned with listing all the ingredients—flour, sugar, eggs, chocolate chips. The assumption is that if we can just identify and understand all the ingredients thoroughly enough, we'll understand the cookie.
The Emerging Alternative: Process Ontology
Process ontology offers a radically different perspective. Instead of focusing on things or substances, it emphasizes activities, relationships, and changes as the fundamental reality. From this view, what we perceive as "things" are actually temporary stabilizations in ongoing flows of matter and energy .
Returning to our recipe analogy: while substance ontology focuses on ingredients, process ontology would emphasize the mixing, baking, cooling—the dynamic interactions that transform those ingredients into something new.
The Great Debate: Understanding Jaeger and Monk's Reply
The recent exchange between these scientists began when Horsting and Hartjes published an article titled "The Substance of Process," to which Jaeger and Monk responded with "The Flow of Substance: A Reply to Horsting & Hartjes" 4 . While the technical details are complex, the core of their debate centers on how best to understand biological organization.
Jaeger and Monk, leading proponents of process thinking in biology, argue that Horsting and Hartjes have not fully embraced the implications of process philosophy. Specifically, they suggest that viewing processes as being "made of" substances misses the point entirely—in process philosophy, substances are manifestations of processes, not the other way around .
This might seem abstract, but consider a river: from a substance perspective, we might analyze the water molecules, sediment, and dissolved minerals that "make up" the river. But from a process perspective, what makes a river a river is the continuous flow of water downhill—the moment the flow stops, it ceases to be a river and becomes a lake.
Jaeger and Monk argue that similarly, living organisms are not just collections of molecules but are sustained by continuous flows of energy and matter—when these flows stop, the organism dies and begins to decompose .
In-depth Look: A Key Experiment in Process Biology
Methodology: Tracing Developmental Patterns
To understand how process biology works in practice, let's examine a representative experiment that Jaeger and colleagues might point to as evidence for their perspective. This study examines pattern formation in fruit fly embryos—a classic model system in developmental biology.
The researchers used advanced imaging techniques to track the dynamics of gene expression patterns in real-time. Rather than simply measuring which genes were present (the substance perspective), they focused on how patterns of gene expression emerged and changed over time (the process perspective) .
Step-by-step procedure:
- Embryos were genetically modified to include fluorescent markers attached to specific proteins
- Using time-lapse microscopy, researchers captured images of the embryos every minute for several hours
- Advanced computational methods tracked the movement and concentration of these proteins
- Mathematical models were applied to identify patterns of flow and organization
- Perturbation experiments tested how the system responded to interruptions
Results and Analysis: The Dynamics of Development
The results were striking: rather than appearing fully formed, the body patterns of the developing flies emerged gradually through a series of dynamic flows and waves of gene expression. Specific findings included:
- Protein gradients formed through continuous flows rather than static concentration differences
- Patterns self-organized through feedback loops between different genes and proteins
- The system showed resilience to minor perturbations—able to return to normal developmental patterns despite interruptions
These findings support the process view by demonstrating that the dynamic interactions between biological components, rather than the components themselves, are primarily responsible for reliable development .
| Observation | Substance Interpretation | Process Interpretation |
|---|---|---|
| Gradient formation | Static concentration differences | Continuous flow and redistribution |
| Pattern stability | Fixed genetic blueprint | Dynamic maintenance through feedback loops |
| Response to perturbation | Breakdown of mechanism | Adaptive reorganisation of processes |
The Scientist's Toolkit: Research Reagent Solutions in Process Biology
Process biology requires specialized methods and tools designed to capture dynamics rather than just snapshots. Here are some key approaches and their functions:
| Method/Tool | Function | Why It's Important for Process Studies |
|---|---|---|
| Live-cell imaging | Real-time visualization of cellular processes | Captures dynamics rather than static states |
| Fluorescent biosensors | Tagging molecules to track their movement | Allows following flows and changes in location |
| Computational modeling | Simulating system dynamics over time | Tests how processes might unfold under different conditions |
| Microfluidics devices | Controlling environmental flows | Manipulates process parameters to test their effects |
| Perturbation analysis | Temporarily interrupting normal processes | Reveals how systems maintain patterns despite change |
Live Imaging Technologies
Advanced microscopy techniques allow researchers to observe biological processes in real time, capturing the dynamic nature of living systems rather than static snapshots.
Computational Models
Sophisticated algorithms and simulations help researchers understand how complex patterns emerge from simple interactions over time.
Beyond the Debate: Broader Implications of Process Thinking
The substance-process debate extends far beyond theoretical biology. Embracing process thinking could transform how we approach many practical challenges:
Medicine and Health
A process perspective shifts our view of health from mere absence of disease to maintenance of healthy processes. Diseases become disruptions in the normal flow of biological processes rather than simply damaged parts. This could lead to treatments focused on restoring healthy dynamics rather than just targeting specific molecules .
Environmental Conservation
Process thinking emphasizes that ecosystems are not just collections of species but complex networks of energy and material flows. Conservation efforts would then focus on maintaining these flows—like nutrient cycles and energy pathways—rather than just protecting specific species 2 .
Understanding Ourselves
Even our understanding of human identity might be transformed by process thinking. Rather than seeing ourselves as static entities, we might come to appreciate that our bodies and minds are sustained by continuous processes of renewal—literally flows of substance that make us who we are 3 .
Conclusion: The Flow Continues
The scientific reply from Jaeger and Monk to Horsting and Hartjes represents more than just an academic disagreement; it's part of a larger shift in how we understand the natural world. From the dance of subatomic particles to the grand cycles of ecosystems, reality appears to be less like a collection of static objects and more like a complex symphony of flows and processes.
This doesn't mean that the traditional substance perspective is wrong—clearly, identifying biological components has yielded tremendous insights. But by complementing this with process thinking, scientists may gain a more complete understanding of life's dynamics .
"As the debate continues, one thing is certain: how we conceptualize the biological world shapes not only what we know but how we interact with it."
As the debate continues, one thing is certain: how we conceptualize the biological world shapes not only what we know but how we interact with it. Perhaps by learning to see the flows as well as the things, we'll develop a deeper appreciation for the continuous processes that sustain us and our world.
As Jaeger and Monk might say: everything flows, and understanding those flows may be the key to understanding life itself.
| Domain | Substance Approach Focus | Process Approach Focus | Integrated Perspective |
|---|---|---|---|
| Biology | Genes, proteins, cells | Developmental pathways, metabolic flows | How components enable processes |
| Medicine | Disease-causing organisms, genetic defects | Disruptions in physiological processes | Treatments that restore healthy dynamics |
| Ecology | Species counts, resource quantities | Nutrient cycles, energy flows, migrations | Protecting both components and their interactions |
| Psychology | Brain structures, neurotransmitters | Learning processes, cognitive development | How neural structures support mental processes |