User:Gareth Leng/Life/Student Level
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What is life? Biologists use the word 'life' for the processes of living, for the things that carry out those processes, for the entire living world — the biosphere — and the history of 'life on earth'. In theory, life might include entities that exist on other planets. Just what qualities must beings have for us to call them alive? Could non-living things ever acquire those qualities? What separated the first living cells from the inanimate materials that formed them? The answers to such questions form part of the answer to that most basic of all questions in Biology: "what is life?" This article focuses on 'living'; on the things that living things do, and on what allows then to do them.
Principles of life
Molecules
All known life is built from the same set of organic molecules. Organic molecules always have a predominant structure of carbon linked to itself. In living things, organic molecules exist in pools of colloidal aqueous solutions that are bounded by lipid and protein sheets. Each pool may have a different charge, density, viscosity or osmotic pressure; these differences provide the basis for the generation of electric fields, fluid shifts, and transport of molecules. The stuff of life is carbon chains, studded with other atoms, and arranged in lagoons of fat, water, and salts.
Cells
As well as sharing a common carbon- and water-based chemistry, all living things — bacteria, oak trees, puffer fish, chimpanzees — share a common building block, the cell. Nature has produced an enormous variety of cell types that span three vast ‘domains’ of living systems: Archaea, Bacteria, and Eukarya. yet cells in all three domains have many features in common. All cells have a surrounding membrane; a physical boundary that separates them from their environment, with special properties that protect the cell from the often hostile external environment while allowing it to ingest matter, excrete waste, and communicate with other cells. Often, these functions are provided by changes in the shape or actual chemical species present on the surface — so pores, receptor molecules and protective walls are often features of the cell surface. All cells extract chemical energy from simple oxidation reactions, and convert it into other, chemical forms of energy. All cells inherit information in the form of molecules of DNA, and (with minor exceptions) the DNA of all cells use the same genetic code to produce a multitude of different proteins. All cells use those proteins to carry out diverse activities, including energy processing and conversion of carbon, nitrogen and phosphorous-containing materials into cellular structures. In the human genome, perhaps as few as 22,000 different genes lead to the production of perhaps more than a million distinct proteins that are needed by a cell.
The earth is home to a huge diversity of living organisms. Most species are just single cells; a few others are cooperative colonies of cells, but some organisms, those we think of as animals and plants, contain vast numbers of different cells, each part of a specialized subpopulation (cell types) — in a mammal, the cells that make up bone differ from those that make up muscle, and differ again from those that make up skin, for example. Humans are built from about 200 different cell types as classified by microscopic anatomy. In multicellular organisms, cells combine to make organs, the functional and structural components of the whole organism.
So what makes a single-celled organism 'alive', and do we mean the same thing when we say that an animal or plant is 'alive'? What do we really mean by 'living'?
Systems view of 'living'
To understand a living thing systematically, we might sart by making a list of its parts- the(molecules and ions; then the cells, organelles, andorgans. Then we might look at how the parts and structures are coordinated, and only then look at how the living system as-a-whole functions and behaves, and the properties that characterize it (e.g., reproduction; locomotion; cognition)
Analysising living things this way is part of the new discipline of Systems Biology. Systems biologists study, among other things, how some properties, functions, and behaviors of living systems "emerge" from the complex interactions of their parts. Emergent behaviors include such things as locomotion, sexual display, flocking, and conscious experiencing.
The intrinsic properties of a system’s components do not determine those of the whole system. What is important is how these parts are organised and how they interact. Moreover, the living system always operates in an environment that also affects the system; it is just not possible to take a living system apart and predict how it will behave by studying the parts separately.
For example, the behavior of a human kidney cell depends not only on its cellular physiology, but also on all the properties of the organ (kidney) of which the cell is a part. The kidney's structure and function influence the cell’s structure and behavior (e.g., by physical confinement and by cell-to-cell signaling), which in turn influence its intracellular organization. The kidney in turn responds to its environment, namely the individual body that it lives in, and that body responds to its environment, which includes such factors as the availability of food and water, and the ambient temperature and humidity.
The thermodynamics of 'living'
The Second Law of Thermodynamics states that:
- Heat flows spontaneously — i.e., without external help — from hotter to cooler regions, and never in the reverse direction. That is also true for other forms of energy, including electromagnetic and chemical energy: concentrations of energy disperse to lower energy levels, flowing "into the cool", so to speak.
- When heat causes a system to perform work (as in a steam engine), some heat is always wasted as ‘exhaust’. That is also true for other forms of energy; some energy is always "wasted", typically as heat. Energy conversion to work can never be 100% efficient.
- Work can produce organization in a system, but only by exporting disorganizing heat to its surroundings. Scientists have learned how to measure the disorder of a system, and they refer to it as entropy. Water vapor, with its molecules distributed nearly randomly, has a higher entropy than liquid water, with its molecules distributed less randomly, and a much higher entropy than ice, with its molecules organized in a crystal array. Left to itself, ice will melt and water will evaporate: order tends to disorder, unless something keeps it ordered.
The Second Law says that energy and order will tend to disippate over time. Given this, how do some animals ever develop from a very simple embryo to become large, highly complex organisms? How do they escape the Second Law?
They don’t: they only seem to. Like a steam engine, they import energy and order, and convert it, to the work of internal organization. But all along they emit enough 'exhaust' to increase the disorder and entropy of their surroundings, so that the total entropy of the living system and its surroundings increase, in keeping with the Second Law.
Biological cells are non-equilibrium thermodynamic systems in that they consume energy to live, and export unusable energy. Living things can store energy and perform work both on themselves and their environment; only after a living thing dies do all parts relate to each other according to spontaneous physical and chemical processes. Non-equilibrium thermodynamic systems, can display unexpectedly complex behaviors when maintained far from equilibrium, and one very remarkable behavior that can result is self-organization.
Evolutionary aspects of 'living'
|
Last Paragraph of Charles Darwin’s Origin of Species (1859) "It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us. These laws, taken in the largest sense, being Growth with Reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the external conditions of life, and from use and disuse; a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less-improved forms. Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." |
In poetry and imagination, fires and storms have often been given the status of living things. Although tornadoes or the flames of candles, are, like living things, non-equilibrium open thermodynamic systems, they lack other essential qualities. Fire may spread and tornadoes may split, but tornadoes and candle flames cannot 'reproduce' themselves, as cells and organisms can. When a living system reproduces itself, its offspring inherit its properties, but with variations introduced by chance (including mutations). Some variations make some of the offspring less able to reproduce than others, and other offspring more able, sometimes better even than their parents. Some of these variations are variations in the inherited genetic recipe (DNA), and will be passed on to the offspring. Accordingly, some variations will spread in a population over generations, while others will die out. Biologists call this "evolution by natural selection", and regard it as the most important way whereby living systems evolve over geological time. The earth has harboured life for nearly 4 billion years, and, over that vast time, all life today descended with modification from an ancient ancestral community of microorganisms.
Viruses have only a few of the characteristics of living systems, but they do have a genotype and phenotype, making them subject to natural selection and evolution. Accordingly, descent with modification is not only a characteristic of living systems. Beyond the scope of this article, we find descent with modification in memes and the artificial life of computer software, such as computer viruses.
We might say that:
| A living system can remain for a time as an organized system, made possible by the influx of energy and matter. It can also take part in the evolution of the species to which it belongs in adapting to changing environments. |
Self-organization
Cells, in an important sense, are systems that organize themselves. Self-organization emerges in part from the chemical properties of the proteins encoded in their genes. Those proteins are produced by a machinery for translating the genetic code, which itself emerges from the chemical properties of proteins and other molecules. We can view the genome as a 'computer program' that guides construction of the components of the cell that then arrange themselves according to their chemical properties. That arrangement, with the tinkering comprising local trial-and-error and evolution’s handiwork, can then carry out ('compute')functions that are not explicitly encoded in the genome.
Self-organized systems need no behind-the-scene 'master controller', and no recipes that specify the structure and dynamics of the system. Instead, those patterns emerge from the interactions among the components of a system, dictated by their physical properties, and dynamically modified by the emerging organization, which is itself modified by the environment. The single-celled zygote organizes itself into a multicellular living system as the genetically encoded proteins interact, responding to changing influences from the changing environment generated by growing multicellularity — becoming a network of many cell-types working cooperatively. That biological systems self-organize has led one prominent biologist to say they are products of a "blind watchmaker".[2]
Self-organization tends to breed greater complexity of self-organization. One important aspect of self-organization in cells rests on the tendency for lipids with polar (water-loving) and non-polar (water-shunning) ends to line up side-by-side to form bilayers in an aqueous solution, each unit of the bilayer with two lipid non-polar ends mutually attracted in the center and the polar ends surrounded by water. Membranes thereby form. Proteins can span the bilayer membrane, or selectively straddle only one or the other side of the membrane and its aqueous surrounding, according to their specific amino-acid sequence and side-groups. Other aspects of self-organization: Genes express not only proteins that organize themselves into a functional unit, but also proteins that organize themselves to regulate that unit, as in transcription regulatory circuits. Protein networks interact in a self-organizing way to produce networks of networks with complex levels of coordination, as in metabolic pathways. Cells communicate with other cells, either in free-living cellular communities or in multicellular organisms, and those communication activities self-organize by virtue of the properties of the cells, selected for fitness by evolutionary mechanisms, and subject to downward effects by the systems' organization and environmental influences on the systems.
We might say that:
| A living system can remain, for a time, in a stable state as a self-organized system. The organization is enabled by the influx of energy and matter. A system can also take part in the transgenerational evolution of the species to which it belongs in adapting to changing environments. |
Autonomous agents
To understand how molecules can replicate themselves, imagine an enzyme that can catalyze the binding of two smaller molecules into a copy of itself. Suppose the energy to produce the enzyme comes from a neighboring molecule, by breaking an energy-rich bond, thus the neighbor molecule is a 'motor' for producing excess enzyme. But the replication will stop whwn all of the "motor" molecules have been used up, so some external energy — perhaps from light impinging on the system — must repair the broken chemical bond, re-energizing the motor. A new cycle of replication can then begin, given both external energy and 'food' (sub-components of the enzyme). .
Importantly, interactions among the components of a system have effects that help organize and coordinate its processes, allowing the replication to proceed. Kauffman conceives, then, of an autocatalytic molecule in a network of molecules that has cycles of self-replication driven by external energy and materials. The network has a self-replication process as a subsystem, and a motor, namely, the breakup of an energy-rich molecule, supplying energy that drives the self-replication, and its re-energizing repair by transduction of external energy. Such a network is a 'molecular autonomous agent' because, given external energy (e.g., photons) and ample materials (the molecules needed to assemble the autocatalytic enzyme), the network perpetuates its existence;. The network is autonomous because it is not controlled by outside forces even though it depends on outside energy and materials. The 'agent' is the system doing work; in this case, the work of self-replication. (That's what 'agents' do; they do work.) In this example, the agent survives by ‘eating’ outside materials and energy. Work gets done because the system remains far-from-equilibrium: as energy flows through the system, the system does its work, and in so doing dissipates the energy gradient, but it temporarily constrains the rate of dissipation by storing energy in its internal organization. Kauffman argues that cells, and indeed all living systems, qualify as autonomous agents, constructed from molecular autonomous agents.
So we might say that:
| A living system can remain for a time in a stable state as a self-organized system. It works autonomously to offset responses to perturbations, and to reproduce itself, enabled by the influx of energy and matter, exploiting a far-from-equilibrium state. Finally, it takes part in the transgenerational evolution of the species to which it belongs in adapting to changing environments. |
Networks
The science of networks provides another useful perspective. Networks ‘re-present’ a system as 'nodes’ and ‘interactions’ among the nodes (also referred to as ‘edges’ or ‘arrows’ or ‘links’). For example, in a spoken sentence, nouns and phrases are the nodes, and the interconnections between them are the links. Intracellular molecular networks represent specific functions in the cell; molecules make up the nodes, and their interactions with other nodes make up the edges or arrows.
Networks are everywhere in biology, from intracellular signaling pathways, to social networks, to ecosystems. We all belong to many social networks of people working (more or less) to a common purpose, families, friends, colleagues; a mobile phone is a network of electronic parts; networks of sentences and paragraphs express messages, including this very article. Researchers view the World Wide Web as a network, and study its characteristics and dynamics.
Cellular networks, like many human engineered networks, how 'modularity', 'robustness', and 'motifs':
- Modules are subnetworks with a specific function and which connect with other modules often only at one input node and one output node. Modularity facilitates adaptation to a changing environment, as, to produce an adaptation, evolution need tinker with just a few modules rather than with the whole system. Evolution can sometimes 'exapt' existing modules for new functions that contribute to reproductive fitness. For example, the swim bladder evolved as an adaptation for control of buoyancy but was exapted as a respiratory organ in various groups of fish.
- Robustness describes how a network can maintain its functionality despite environmental perturbations that affect the components. Robustness also reduces the range of network types that researchers must consider, because only certain types of networks are robust.
- Network motifs offer economy of network design, as the same circuit can have many different uses in cellular regulation. Nature selects motifs in part for their ability to make networks robust, so systems use motifs that work well in many different networks. In several biological networks, the abundance of network motifs — small subnetworks — correlates with the degree of robustness. Networks, like those in cells and those in neural networks in the brain, use motifs as basic building blocks, like multicellular organisms use cells as basic building blocks. Motifs offer biologists a level of simplicity of biological functionality for their efforts to model the dynamics of organized hierarchies of networks.
The view of the cell as an overlay of mathematically-definable dynamic networks can reveal how a living system can be an improbable, intricate, self-orchestrated dance of molecules. The 'overlay of networks' view also suggests how the concept of self-organized networks can extend to all higher levels of living systems.
We might thus say that:
| A living system has the ability to remain for a time in a near steady-state as a self-organized system of hierarchical robust modular networks. It works autonomously to offset responses to perturbations and to reproduce itself, enabled by the influx of energy and matter and by a more than compensatory efflux of waste, thereby exploiting a far-from-equilibrium state. Finally, it can take part in the transgenerational evolution of the species to which it belongs in adapting to changing environments. |
Information processing
The word 'information' comes from the verb 'to inform', originally meaning to put form in something: the seal in-forms the wax, and the wax now contains in-formation. A random collection of particles or other entities has no form, nothing has given it form, and it contains no in-formation. Biological systems contain in-formation: something has happened to 'form' the parts into an improbable state.
The flow of energy into a cell feeds it, enabling it to work to gain form, raising its information content.
Thus a living system is an information processing system. It receives information from energy and materials in its environment, fueling and supplying the machinery that builds and sustains information-rich organization; it generates new information inside itself, as in embryonic development; and it transmits information within and outside itself, as in transcription regulation and exporting pheromones. From its parent, it inherits information that establishes its developmental potential and scripts its realization — including information that enables it to reproduce itself.
Viewing living systems as information banks, enables one to see all life as a vast, complex, naturally-selected, self-sustaining, evolving communication network. Recently (on the timescale of the history of life) that network produced the human brain, an organ capable of communicating with other humans using networks of symbols. That led to the emergence of cultural evolution, a whole new domain of self-reproducing entities ('culturgens', 'memes') and descent with modification. That in turn led to the emergence of another vast communication network: books, wikis, and other technologies of information generation and exchange.
We might now consider another closely related perspective, a ‘cognitive’ perspective. Because networks resist common perturbations (e.g., by their robustness, and by ‘homeostasis’), one might think of them as containing a representation of their environment and of how it might vary. As networks self-organize through interactions between proteins, any 'representation’ of its environment must derive from the genetic information that determines those proteins. The genetic information comprises a molecular code, and the process that transforms that information into proteins describes an algorithm — the transcription-translation algorithm. As these algorithms evolved through natural selection, one can view evolution as selecting for cognitive functionality in the genome — the ability to ‘represent’ the cell’s environment and, more generally, to remember and anticipate.
The genetic information has the form of a digital code, one that can jump-start cellular processes, including the processes that lead to self-organization of networks that regulate execution of the genetic code — the gene regulatory networks. A separate digital code also has a central role in the operation of those gene regulatory networks: the code adjacent to a gene determines which transcription regulating factors can bind there, and thereby controls gene activity. In other words, a digital code, separate from the code that specifies the proteins of the gene regulatory networks, gives specificity to the behavior of those networks and to their regulation of the genetic code. Generally, we learn how to "crack£ digital codes, so someday we might be able to read the message of living and find ways to edit it.
Further elaborating beyond the thermodynamic, evolutionary, self-organizational, autonomous agent and network perspectives we might say that:
| A living system has the informational content and information-processing faculty to remain in a near steady-state as a self-organized system of robust modular networks. It works autonomously to offset responses to perturbations and to reproduce itself, enabled by the influx of energy and matter. Finally, it takes part in the transgenerational evolution of the species to which it belongs in adapting to changing environments. |
Organic chemistry as informatics
Why does carbon have such a the central place in the chemistry of living things? The physical chemistry of carbon allows it to bond with many other elements, especially hydrogen, oxygen, nitrogen and phosphorus, and, even to form carbon-to-carbon bonds. The avidity for carbon to bond to itself allows carbon atoms to form long chains and closed rings; and allows small organic molecules (such as sugars, amino acids and nucleotides) to join into huge macromolecules that are remarkably stable. These macromolecules contain the information that is used by living things.
The variety of carbon bonds vary in strength as well as in 3-D conformation; adding a dynamic quality to many organic molecules. The simplest set of bonds that carbon can form is that of a tetrahedron, or pyramid. Other types of bonds involve more than one shared electron, and for that reason are called double, and triple bonds; importantly, these different bonds constitute three entirely different geometries. Changing from one type of carbon-to-carbon bond to another type, as when a double bond is reduced to a single bond, will cause energy changes but without destroying the molecule. Such changes not only affect free energy, but also affect the actual shape of the molecule and the particular side groups attached to it. In this way, for at least some organic molecules, the 'pulse of life' is represented at an atomic level.
Organic macromolecules are capable of containing tremendous 'banks' of information coded in their structure. Not only can each of the constituent molecules be huge, but several categories of chemicals, like nucleotides or amino acids, that contain several different species, can be ordered so that the possible combinations are effectively limitless. All of these molecules are involved in the molecular-interaction networks of cells. Amogst these networks of interactions are those that enable cells to import and transform energy and energy-rich matter from the environment and that enable cells to grow, survive and reproduce.
Elsewhere in the universe, where conditions differ greatly from earth’s, other elements may hold a central place in life. Silicon, carbon's close relative on the periodic table, also forms bonds with itself, but they are not stable under conditions compatible with life as we know it. In places in the universe where physical conditions might favor silicon-based macromolecules, life might be based on silicon instead.
Identifying the different scientific perspectives on life
The different perspectives biologists use in viewing living systems can be identified as follows:
- Living systems import energy, matter, and information from their environment, and export waste. This flow enables living systems to organize and maintain themselves, and thus to delay (for their lifetime) the dictate of the Second Law of Thermodynamics, that organized systems ultimately degrade to a state of randomness;
- The basic building blocks of all living systems are cells; the basic (genetic) information that generates cells comes as part of their starting materials. This information, in the form of DNA, encodes many different types of proteins that interact to assemble an organization that can import energy and export waste. Cells inherit this information from ‘parent’ cells, raising two as yet unanswered questions: how did cells arise in the first place? and how did they acquire stores of information?
- The molecular interactions are governed by the laws of physics and chemistry; those laws, together with the inherited information, enable a self-organizing system that can work autonomously for survival and reproduction, and allow unexpected properties to emerge.
- The activities of a living system have no 'master controller'; they need only a type of organization that maintains the system far-from-equilibrium, which can yield self-organized structures and activities.
- Living things cannot escape from changing external conditions, so they must be robust in their organization and they must be adaptable. Robustness and adaptability derive from the properties of a hierarchical network of subnetworks of molecular circuits;
- Living systems must produce enough reproductive variability to allow evolution through natural selection, which guides the continuation of a 3.5 billion year history of Earth’s living world. By evolution, living systems generate increasing varieties of living systems, occupy an extreme spectrum of environments, create their own environments, and permit enough complexity to enable them to process information in a way that lets them ‘experience’ themselves.
Synthesis of perspectives on what constitutes Life
The activity of living, depends on the ability of a system to maintain a stable state of organized function. The system achieves that in part because of its location in the path of a downhill gradient of flowing energy. It imports some of the energy flowing past it, and exports unusable energy and material.
Those principles seem to apply to all living systems: single cells, multicellular organs and organisms, and multi-organism demes and ecosystems.
The building block and working unit of all living systems is the cell. For cells to use energy and achieve order, they must have, from the outset, some informational content. That enables the cell to produce components that can respond to the imported energy and material to organize themselves. That organization comprises modular networks of molecular interactions, and networks of interacting networks — self-organized and coordinated functional interactions. The properties of the networks and those of the hierarchy of networks enable the system to perpetuate itself, and to maintain its steady-state despite fluctuations in environmental factors. That principle, too, applies to all living systems. Any organism, plant or animal, comprises a network of organs working autonomously, maintaining its steady-state functioning far from equilibrium in response to environmental perturbations — physiologists refer to that as homeostasis.
The networks that regulate the flow of information through the cell were 'designed' by natural selection and other evolutionary processes. That is, the codes that evolved by natural selection were those which produced molecules that could interact in ways that contribute to self-organization of those networks that enable a cell to sustain and reproduce itself. The collaboration of natural selection and physico-chemical laws perpetuates living systems not only in real-time but also in geological, or ‘evolutionary’, time. From common ancestors — however they may have arisen (see Evolution of cells) — informationally-guided, self-organizing, autonomous network dynamics enabled generation of the diversity of all living systems on the planet, over a period of more than three billion years. Living systems perpetuate living systems, exploiting free energy on its inexorable path to dissipation and degradation, and harvesting energy in developing systems organization by a more than counterbalancing dis-organizing of the larger system in which it is embedded.
References
Citations and Notes
- ↑ from Robinson R (2007) Both barriers and trait complementarity govern pollination network structure. PLoS Biol 5(2): e54 doi:10.1371/journal.pbio.0050054
- ↑ Dawkins R (1988) The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe Without Design. New York: W.W. Norton & Company, Inc. ISBN 0393304485