Fundamental Constraints to the Logic of Living Systems
Following are the key factors that constrain the possibility space for life across different scales:
1. Thermodynamic constraints:
Life requires internal entropy-reducing processes coupled with processes that increase entropy in the environment (e.g., heat generation).
The Second Law of Thermodynamics states that the total entropy (disorder) of an isolated system always increases over time. Living systems are non-equilibrium systems that maintain their organized, low-entropy state by extracting energy and materials from their surrounding environment. This allows them to build up ordered biomolecular structures and maintain their metabolism. However, in doing so, the living system must increase the total entropy of the universe by dissipating energy as heat and increasing the disorder/entropy in the environment around it. So while a living organism can locally reduce its internal entropy temporarily through metabolic processes, this is always coupled to an overall increase in entropy of the system as a whole (organism + environment). The internal entropy reduction allows the organism to maintain its complex, organized structures and functional processes against the natural tendency toward disorder. But this is enabled by irreversible processes that generate heat/waste and increase environmental entropy even more. Life requires a constant flow of energy from the environment to power the creation of ordered biomolecules and organized structures within the organism, at the expense of increasing net entropy/disorder outside in the surroundings. This entropy exchange between organism and environment is a fundamental thermodynamic requirement for life.
Life must store and use energy intermediates to drive internal processes and decouple from environmental conditions, achieving thermodynamic autonomy. Internal metabolic processes must be organized around cyclic transformations.
Metabolism refers to the complex network of chemical reactions that occur within living cells/organisms. These reactions allow the organism to extract energy from nutrients, build biomolecules, and carry out biological functions. Many of the key metabolic pathways and processes are cyclic in nature, meaning they operate in a cycle or circular manner. Some examples: The citric acid cycle (Krebs cycle) - a cyclic pathway that oxidizes acetyl-CoA to release energy in the form of ATP and CO2. The Calvin cycle - the cyclic set of reactions that take place during photosynthesis to convert CO2 into organic compounds. The urea cycle - the cyclic metabolic pathway that converts toxic ammonia to urea for excretion. Cyclic regeneration of metabolic cofactors like NAD+/NADH, ATP/ADP etc.
There are advantages to having a cyclic organization: It allows the recycling and re-use of key metabolites and enzymes in the pathways. It enables greater metabolic efficiency and control. Cyclic pathways decouple the breaking down and building up processes. They prevent the depletion or accumulation of key intermediates. Non-cyclic, linear metabolic processes would rapidly get depleted or saturated without regeneration mechanisms. The cyclic nature maintains the steady-state required for metabolism by having the final products re-enter the pathway. So metabolic cycles are widespread across living systems, suggesting that cyclicity and circularity at a fundamental level are important organizational constraints that enable persistent, regulated metabolism in life.
2. Molecular information constraints:
- Linear heteropolymers formed by units (monomers) with near-equivalent energies are expected to be the substrate for carrying molecular information.
If the monomers had wildly different energies, it would make the process of accurately replicating and storing information in these polymers more error-prone and thermodynamically unfavorable. Near-equivalent energies facilitate replicating the sequence precisely. Polymers made of monomers with very different energies would tend to be unstable and prone to spontaneous breakdown or internal strain. Near-equivalent monomer energies contribute to an overall structural stability of the polymer. If incorporation energies differed too much, there would be a strong bias towards incorporating some monomers over others during polymerization. Equal or near-equal energies ensure an unbiased probability of incorporation. The vast combinatorial sequence space that allows information storage requires the ability to freely combine the monomers. Widely varying energies would restrict this flexibility. It is hypothesized that life's polymers emerged from a limited prebiotic inventory of molecules with similar energetics, rather than highly diverse and reactive monomers. Near-equivalent energies provide the goldilocks condition - not too tightly or loosely bound - that enables linear heteropolymers to robustly store information, be replicated accurately, remain stable, and explore vast sequence spaces by free combination of monomers. This facilitates their role as informational molecules driving the molecular logic of life. The physicochemical constraints associated with linearity may severely limit the repertoire of possible monomers.
3. Compartmentalization and replication constraints:
- Closed cell compartments equipped with a von Neumann replication logic are needed for self-reproducing life forms capable of evolution. The statement refers to an important principle that enables the existence of self-replicating, evolvable life forms, based on information that could also be preserved. Self-replication of life depends heavily on the existence of functional units (atoms, molecules and ions) that can be maintained, concentrated, and propagated by prevailing ambient forces. For planets like Earth, most of the material for self-replication was present in oceanic environments, where seawater supplied and circulated the basic molecular building blocks. This statement appears to signify the widespread occurrence of ancient marine conditions, which promoted the generation of substances from primal chemical elements. The compartment must concentrate required molecules and define a boundary between internal and external environments, connected by a membrane that can exploit physical instabilities. The closed container can be achieved using a specific class of molecules (amphiphiles), constraining the chemical candidates.
4. Ecological constraints:
- Ecosystem architectures are deeply constrained within a finite set of possible classes of ecological interactions, as revealed by current and past ecosystems, and supported by in silico models of evolving ecologies.
Ecosystem architectures refer to the overall structure and organization of ecosystems, including how different species interact and how energy and resources flow through the system. This suggests that there are limitations or restrictions on how ecosystems can be organized. Finite set of possible classes of ecological interactions indicate that there are only a limited number of ways in which species can interact within an ecosystem. These interactions typically include:
- Predation
- Competition
- Mutualism
- Commensalism
- Parasitism
Revealed by current and past ecosystems means that scientists have observed these constraints in both existing ecosystems and in the fossil record of ancient ecosystems. The main point is that despite the vast diversity of life on Earth and the countless ecosystems that have existed throughout history, the fundamental ways in which species interact and ecosystems are structured fall into a limited number of categories. This isn't random, but rather a result of principles that shape how organisms can coexist and interact. The widespread presence of parasites suggests they are an inevitable outcome of complex adaptive systems.
5. Reproduction constraint:
While reproduction was mentioned briefly under compartmentalization, it wasn't fully explored as a fundamental constraint. The ability to reproduce and pass on genetic information is a critical aspect of life.
6. Homeostasis constraint:
The ability to maintain internal stability and regulate internal conditions wasn't explicitly mentioned in the original list. This is a crucial aspect of living systems.
7. Growth and development constraint:
The capacity for growth and development over time wasn't included in the initial list but is an important characteristic of living systems.
8. Information processing and response constraint:
While information was mentioned in relation to molecular constraints, the broader ability of living systems to process information and respond to their environment wasn't fully addressed.
9. Hardware/software entanglement constraint:
This refers to the intricate relationship between nucleic acids (software) and proteins (hardware) in living systems, which wasn't covered in the initial list.
10. Permanence and change constraint:
The paradoxical need for both conservation and adaptation in living systems wasn't addressed in the original constraints.
11. Autonomy constraint:
The ability of living systems to maintain some degree of independence from their environment wasn't explicitly mentioned.
12. Electrical/bioelectric constraint:
The document mentions the importance of the cell's self-generated "electrome" and electrical gradients, which wasn't covered in the initial list of constraints.
These additional constraints highlight the complexity and multifaceted nature of life, encompassing aspects of information processing, stability, adaptability, and various forms of organization that weren't fully captured in the initial list.
https://www.preprints.org/manuscript/202406.0891/v1
Following are the key factors that constrain the possibility space for life across different scales:
1. Thermodynamic constraints:
Life requires internal entropy-reducing processes coupled with processes that increase entropy in the environment (e.g., heat generation).
The Second Law of Thermodynamics states that the total entropy (disorder) of an isolated system always increases over time. Living systems are non-equilibrium systems that maintain their organized, low-entropy state by extracting energy and materials from their surrounding environment. This allows them to build up ordered biomolecular structures and maintain their metabolism. However, in doing so, the living system must increase the total entropy of the universe by dissipating energy as heat and increasing the disorder/entropy in the environment around it. So while a living organism can locally reduce its internal entropy temporarily through metabolic processes, this is always coupled to an overall increase in entropy of the system as a whole (organism + environment). The internal entropy reduction allows the organism to maintain its complex, organized structures and functional processes against the natural tendency toward disorder. But this is enabled by irreversible processes that generate heat/waste and increase environmental entropy even more. Life requires a constant flow of energy from the environment to power the creation of ordered biomolecules and organized structures within the organism, at the expense of increasing net entropy/disorder outside in the surroundings. This entropy exchange between organism and environment is a fundamental thermodynamic requirement for life.
Life must store and use energy intermediates to drive internal processes and decouple from environmental conditions, achieving thermodynamic autonomy. Internal metabolic processes must be organized around cyclic transformations.
Metabolism refers to the complex network of chemical reactions that occur within living cells/organisms. These reactions allow the organism to extract energy from nutrients, build biomolecules, and carry out biological functions. Many of the key metabolic pathways and processes are cyclic in nature, meaning they operate in a cycle or circular manner. Some examples: The citric acid cycle (Krebs cycle) - a cyclic pathway that oxidizes acetyl-CoA to release energy in the form of ATP and CO2. The Calvin cycle - the cyclic set of reactions that take place during photosynthesis to convert CO2 into organic compounds. The urea cycle - the cyclic metabolic pathway that converts toxic ammonia to urea for excretion. Cyclic regeneration of metabolic cofactors like NAD+/NADH, ATP/ADP etc.
There are advantages to having a cyclic organization: It allows the recycling and re-use of key metabolites and enzymes in the pathways. It enables greater metabolic efficiency and control. Cyclic pathways decouple the breaking down and building up processes. They prevent the depletion or accumulation of key intermediates. Non-cyclic, linear metabolic processes would rapidly get depleted or saturated without regeneration mechanisms. The cyclic nature maintains the steady-state required for metabolism by having the final products re-enter the pathway. So metabolic cycles are widespread across living systems, suggesting that cyclicity and circularity at a fundamental level are important organizational constraints that enable persistent, regulated metabolism in life.
2. Molecular information constraints:
- Linear heteropolymers formed by units (monomers) with near-equivalent energies are expected to be the substrate for carrying molecular information.
If the monomers had wildly different energies, it would make the process of accurately replicating and storing information in these polymers more error-prone and thermodynamically unfavorable. Near-equivalent energies facilitate replicating the sequence precisely. Polymers made of monomers with very different energies would tend to be unstable and prone to spontaneous breakdown or internal strain. Near-equivalent monomer energies contribute to an overall structural stability of the polymer. If incorporation energies differed too much, there would be a strong bias towards incorporating some monomers over others during polymerization. Equal or near-equal energies ensure an unbiased probability of incorporation. The vast combinatorial sequence space that allows information storage requires the ability to freely combine the monomers. Widely varying energies would restrict this flexibility. It is hypothesized that life's polymers emerged from a limited prebiotic inventory of molecules with similar energetics, rather than highly diverse and reactive monomers. Near-equivalent energies provide the goldilocks condition - not too tightly or loosely bound - that enables linear heteropolymers to robustly store information, be replicated accurately, remain stable, and explore vast sequence spaces by free combination of monomers. This facilitates their role as informational molecules driving the molecular logic of life. The physicochemical constraints associated with linearity may severely limit the repertoire of possible monomers.
3. Compartmentalization and replication constraints:
- Closed cell compartments equipped with a von Neumann replication logic are needed for self-reproducing life forms capable of evolution. The statement refers to an important principle that enables the existence of self-replicating, evolvable life forms, based on information that could also be preserved. Self-replication of life depends heavily on the existence of functional units (atoms, molecules and ions) that can be maintained, concentrated, and propagated by prevailing ambient forces. For planets like Earth, most of the material for self-replication was present in oceanic environments, where seawater supplied and circulated the basic molecular building blocks. This statement appears to signify the widespread occurrence of ancient marine conditions, which promoted the generation of substances from primal chemical elements. The compartment must concentrate required molecules and define a boundary between internal and external environments, connected by a membrane that can exploit physical instabilities. The closed container can be achieved using a specific class of molecules (amphiphiles), constraining the chemical candidates.
4. Ecological constraints:
- Ecosystem architectures are deeply constrained within a finite set of possible classes of ecological interactions, as revealed by current and past ecosystems, and supported by in silico models of evolving ecologies.
Ecosystem architectures refer to the overall structure and organization of ecosystems, including how different species interact and how energy and resources flow through the system. This suggests that there are limitations or restrictions on how ecosystems can be organized. Finite set of possible classes of ecological interactions indicate that there are only a limited number of ways in which species can interact within an ecosystem. These interactions typically include:
- Predation
- Competition
- Mutualism
- Commensalism
- Parasitism
Revealed by current and past ecosystems means that scientists have observed these constraints in both existing ecosystems and in the fossil record of ancient ecosystems. The main point is that despite the vast diversity of life on Earth and the countless ecosystems that have existed throughout history, the fundamental ways in which species interact and ecosystems are structured fall into a limited number of categories. This isn't random, but rather a result of principles that shape how organisms can coexist and interact. The widespread presence of parasites suggests they are an inevitable outcome of complex adaptive systems.
5. Reproduction constraint:
While reproduction was mentioned briefly under compartmentalization, it wasn't fully explored as a fundamental constraint. The ability to reproduce and pass on genetic information is a critical aspect of life.
6. Homeostasis constraint:
The ability to maintain internal stability and regulate internal conditions wasn't explicitly mentioned in the original list. This is a crucial aspect of living systems.
7. Growth and development constraint:
The capacity for growth and development over time wasn't included in the initial list but is an important characteristic of living systems.
8. Information processing and response constraint:
While information was mentioned in relation to molecular constraints, the broader ability of living systems to process information and respond to their environment wasn't fully addressed.
9. Hardware/software entanglement constraint:
This refers to the intricate relationship between nucleic acids (software) and proteins (hardware) in living systems, which wasn't covered in the initial list.
10. Permanence and change constraint:
The paradoxical need for both conservation and adaptation in living systems wasn't addressed in the original constraints.
11. Autonomy constraint:
The ability of living systems to maintain some degree of independence from their environment wasn't explicitly mentioned.
12. Electrical/bioelectric constraint:
The document mentions the importance of the cell's self-generated "electrome" and electrical gradients, which wasn't covered in the initial list of constraints.
These additional constraints highlight the complexity and multifaceted nature of life, encompassing aspects of information processing, stability, adaptability, and various forms of organization that weren't fully captured in the initial list.
https://www.preprints.org/manuscript/202406.0891/v1
