Life/Student Level


 * Elementary commentary for beginners relating to the topic of Life.

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 &mdash; the biosphere &mdash; and the history of 'life on earth'. In theory, life might include entities on other planets. Just what qualities must those 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? These questions form part of that most basic of all questions in Biology: "what is life?"

Molecules
All known life is built from organic molecules. Organic molecules all 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 &mdash; bacteria, oak trees, puffer fish, chimpanzees &mdash; 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 properties that protect the cell while allowing it to ingest matter, excrete waste, and communicate with other cells. Often, these functions are provided by changes in the shape or chemical species present on the surface &mdash; 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 different 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) &mdash; 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 at least 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 start by making a list of its parts- the molecules and ions; then the cells, organelles, and organs. Then we might look at how the parts and structures are coordinated, and then look at how the living system as-a-whole functions and behaves, and the properties that characterize it. Analysing living things this way is part of the new discipline of Systems Biology. Systems biologists study, among other things, how properties of living things "emerge" from the complex interactions of their parts. Emergent behaviors include such things as locomotion, sexual display, flocking, intelligence and conscious experience.

The intrinsic properties of a system’s components do not determine those of the whole system, what matters is how the parts are organised and how they interact. Moreover, a 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, how a kidney cell behaves depends on the properties of its cells, but also on all the properties of the organ (kidney) to which the cells belong. 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 internal organization. The kidney in turn responds to its environment, - the body that it lives in, and that body responds to its environment, which includes things like the availability of food and water, and the ambient temperature and humidity.

We might begin simply by saying that:

The thermodynamics of 'living'
The Second Law of Thermodynamics says that:




 * Heat flows spontaneously &mdash; i.e., without external help &mdash; 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, so how can animals develop from a 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 its parts surrender to spontaneous physical and chemical processes. Non-equilibrium thermodynamic systems, can display unexpectedly complex behaviors.

We might say that:

Evolutionary aspects of 'living'
In poetry and imagination, fires and storms have often been given the status of living things. Although tornadoes or the flames of candles are non-equilibrium open thermodynamic systems, they lack other essential qualities of living things. 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 likely to reproduce, and other offspring more likely to, sometimes more so 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 die out. Biologists call this "evolution by natural selection", and regard it as the most important way whereby living systems evolve over generations. The earth has harboured life for more than 3 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, so descent with modification is not only a characteristic of living systems. We also can recognize descent with modification occurring in memes and in the artificial life of computer software, such as computer viruses.

We might say that:

Self-organization
Cells, in an important sense, can organize themselves, partly because of the chemical properties of the proteins encoded by their genes. Those proteins are produced by a machinery for translating the genetic code, which itself emerges from the properties of proteins and other molecules. The genome is like a 'computer program' that guides construction of the components of the cell, which 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 additional functions that are not directly encoded in the genome.

Self-organized systems need no behind-the-scene 'master controller', and no recipes for the structure and dynamics of the system. Instead, those patterns emerge from the interactions among the components, dictated by their physical properties, and modified by the emerging organization, which is itself modified by the environment. The single-celled zygote organizes itself into a multicellular living system as its genetically encoded proteins interact, responding to influences from the changing environment &mdash; becoming a network of many cell-types working cooperatively. Living systems are, in the words of one biologist, the products of a "blind watchmaker".

Self-organization tends to breed ever more complex organization. For example, lipid molecules with polar (water-loving) and non-polar (water-shunning) ends tend to line up side-by-side to form bilayers in an aqueous solution. Each unit of the bilayer has two lipid non-polar ends mutually attracted in the center and polar ends surrounded by water, forming membranes. They don't have to be "programmed" to do this, it happens naturally, and once a membrane is formed, proteins can interact with it. Some can span the membrane, allowing communication between one side and the other.

Genes express not only proteins that organize themselves into a functional unit, but also proteins that regulate that unit. Protein networks organize themselves 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 by evolutionary mechanisms, and subject to "top-down" influences of the systems' organization and to environmental influences.

We might say that:

Autonomous agents
To understand how molecules can replicate themselves, imagine an enzyme that can enable two smaller molecules to bind together to make 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 more enzyme. However, the replication will stop when all of the "motor" molecules have been used up, so some external energy &mdash; perhaps from light impinging on the system &mdash; must repair the broken bond, re-energizing the motor. A new cycle of replication can then begin, if enough energy and 'food' (sub-components of the enzyme) is available.

So we have 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, (the 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, although it depends on outside energy and materials. The 'agent' is the system doing work; in this case, the work of self-replication. 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 slows the rate of dissipation by storing energy in its internal organization.

So we might say that:

Networks


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 sentence, the nouns and phrases are 'nodes', and the interconnections between them are 'links'. Inside every cell, molecular networks carry out specific functions; the molecules are nodes, and their interactions with other molecules are links.

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 increasingly complex messages, including this very article, and the World Wide Web is a giant network of networks.

Cellular networks, like many human engineered networks, have 'modules' and 'motifs', and they display 'robustness.'
 * Modules are subnetworks with a specific function and which connect with other modules. Modularity makes it easier to adapt to a changing environment, because, to produce an adaptation, evolution need tinker with just a few modules rather than with the whole system. Evolution can also sometimes 'exapt' modules for new functions: for example, the swim bladder evolved as an adaptation for control of buoyancy but was exapted as a respiratory organ in some groups of fish.
 * Network motifs are the basic building blocks of networks, just as multicellular organisms use cells as basic building blocks. Motifs allow networks to be built "economically", as the same circuit can have many different uses.
 * Robustness describes how a network can keep working despite environmental disturbances. A "perfect" network is no good in a living system if it an be easily broken or thrown off balance. Usually a living system is robust because each of the problems that it faces is addressed in several different ways - by complex co-ordinated networks.

This view of the cell shows a living system as an 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:

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 feeds the cell, enabling it to work to gain form, raising its information content.

Thus a living system receives information from energy and materials in its environment, fueling and supplying the machinery that sustains information-rich organization. It also generates new information inside itself, as in embryonic development; and it transmits information within and outside itself, as in transcription regulation and secreting hormones. From its parent, it inherits information that establishes its developmental potential and scripts its realization &mdash; including information that enables it to reproduce itself.

Thus all life can be seen as a vast, complex, naturally-selected, self-sustaining, evolving communication network. Recently (in 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.

Because networks resist common perturbations, one might think of them as containing a representation of their environment and of how it might vary. For a living system, any 'representation’ of its environment must derive from genetic information - a molecular code. The process that transforms that code into proteins describes an algorithm &mdash; the transcription-translation algorithm. As these algorithms evolved through natural selection, one can view evolution as selecting for cognitive functionality in the genome &mdash; the ability to ‘represent’ the cell’s environment and, more generally, to remember and anticipate.

The genetic information has the form of a code that can jump-start cellular processes, including the processes that lead to self-organization of networks that regulate execution of the genetic code &mdash; the gene regulatory networks. Another digital code also has a central role in those 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. Generally, we learn how to "crack£ digital codes, so one day we might be able to read the message of living and find ways to edit it.

So we might say that:

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 ability 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 very 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 bonds involve more than one shared electron, and so are called double and triple bonds; importantly, these different bonds havethree entirely different geometries. Changing from one type of bond to another, as when a double bond is reduced to a single bond, will cause energy changes but without destroying the molecule. Such changes affect the 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 can contain huge 'banks' of information coded in their structure. Not only can individual molecules be huge, but some 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. Some of these networks enable cells to import and transform energy and energy-rich matter from the environment and enable cells to grow, survive and reproduce.

Elsewhere in the universe, where conditions differ 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; but 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

 * Living systems import energy, matter, and information from their environment, and export waste. This enables them to organize themselves, and to delay (for their lifetime) the dictate of the Second Law of Thermodynamics, that organized systems ultimately degrade to randomness;
 * The basic building blocks of all living systems are their 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 proteins that interact to assemble an organization that can import energy and export waste. Cells inherit this information from ‘parent’ cells, raising two further 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 only need 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 and 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 range 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
A living system must be able to maintain a stable state of organized function. It achieves that in part by being 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.

Cells are the building blocks and working units of all living systems. For cells to use energy and achieve order, they must have, from the outset, some information content. That initial information 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 &mdash; self-organized and coordinated functional interactions. These enable the system to perpetuate itself, and to maintain its steady-state despite environmental disturbances. Any organism, plant or animal, comprises a network of organs working autonomously, maintaining its functioning in response to environmental disturbances.

The networks that regulate the flow of information through the cell were 'designed' by natural selection and other evolutionary processes. Codes evolved to produce molecules that interact in ways that contribute to the self-organization of those networks that enable a cell to survive 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 (see Evolution of cells) informationally-guided, self-organizing, autonomous network dynamics generated the diversity of all living systems on Earth, over more than three billion years.