Group selection

From Wikipedia, the free encyclopedia

Early explanations of social behavior, such as the lekking of blackcock, spoke of "the good of the species". Blackcocks at the Lek watercolour and bodycolour by Archibald Thorburn, 1901.

 

Group selection is a proposed mechanism of evolution in which natural selection acts at the level of the group, instead of at the more conventional level of the individual. 

Early authors such as V. C. Wynne-Edwards and Konrad Lorenz argued that the behavior of animals could affect their survival and reproduction as groups, speaking for instance of actions for the good of the species. From the mid 1960s, evolutionary biologists such as John Maynard Smith argued that natural selection acted primarily at the level of the individual. They argued on the basis of mathematical models that individuals would not altruistically sacrifice fitness for the sake of a group. They persuaded the majority of biologists that group selection did not occur, other than in special situations such as the haplodiploid social insects like honeybees (in the Hymenoptera), where kin selection was possible. 

In 1994 David Sloan Wilson and Elliott Sober argued for multi-level selection, including group selection, on the grounds that groups, like individuals, could compete. In 2010 three authors including E. O. Wilson, known for his work on social insects especially ants, again revisited the arguments for group selection. They argued that group selection can occur when competition between two or more groups, some containing altruistic individuals who act cooperatively together, is more important for survival than competition between individuals within each group. Their proposals provoked a strong rebuttal from a large group of evolutionary biologists.

Early Developments

Charles Darwin developed the theory of evolution in his book, Origin of Species. Darwin also made the first suggestion of group selection in The Descent of Man that the evolution of groups could affect the survival of individuals. He wrote, "If one man in a tribe... invented a new snare or weapon, the tribe would increase in number, spread, and supplant other tribes. In a tribe thus rendered more numerous there would always be a rather better chance of the birth of other superior and inventive members."

Once Darwinism had been accepted in the modern synthesis of the mid-twentieth century, animal behavior was glibly explained with unsubstantiated hypotheses about survival value, which was largely taken for granted. The naturalist Konrad Lorenz had argued loosely in books like On Aggression (1966) that animal behavior patterns were "for the good of the species", without actually studying survival value in the field. Richard Dawkins noted that Lorenz was a "'good of the species' man" so accustomed to group selection thinking that he did not realize his views "contravened orthodox Darwinian theory". The ethologist Niko Tinbergen praised Lorenz for his interest in the survival value of behavior, and naturalists enjoyed Lorenz's writings for the same reason. In 1962, group selection was used as a popular explanation for adaptation by the zoologist V. C. Wynne-Edwards. In 1976, Richard Dawkins wrote a well-known book on the importance of evolution at the level of the gene or the individual, The Selfish Gene.

Social behavior in honeybees is explained by kin selection: their haplodiploid inheritance system makes workers very closely related to their queen (centre).

 

From the mid 1960s, evolutionary biologists argued that natural selection acted primarily at the level of the individual. In 1964, John Maynard Smith, C. M. Perrins (1964), and George C. Williams in his 1966 book Adaptation and Natural Selection cast serious doubt on group selection as a major mechanism of evolution; Williams's 1971 book Group Selection assembled writings from many authors on the same theme.

It was at that time generally agreed that the primary exception of social group selection was in the social insects, and the explanation was limited to the unique inheritance system (involving haplodiploidy) of the eusocial Hymenoptera such as honeybees, which encourages kin selection, since workers are closely related.

Kin selection and inclusive fitness theory

Early group selection models assumed that genes acted independently, for example a gene that coded for cooperation or altruism. Genetically-based reproduction of individuals implies that, in group formation, the altruistic genes would need a way to act for the benefit of members in the group to enhance the fitness of many individuals with the same gene. But it is expected from this model that individuals of the same species would compete against each other for the same resources. This would put cooperating individuals at a disadvantage, making genes for cooperation likely to be eliminated. Group selection on the level of the species is flawed because it is difficult to see how selective pressures would be applied to competing/non-cooperating individuals.

Experiments from the late 1970s suggested that selection involving groups was possible. Kin selection between related individuals is accepted as an explanation of altruistic behavior. In this model, genetically related individuals cooperate because survival advantages to one individual also benefit kin who share some fraction of the same genes, giving a mechanism for favoring genetic selection.

Inclusive fitness theory, first proposed by W. D. Hamilton in the early 1960s, gives a selection criterion for evolution of social traits when social behavior is costly to an individual organism's survival and reproduction. This behavior could emerge under conditions such that the statistical likelihood that benefits accrue to the survival and reproduction of other organisms whom also carry the social trait. Inclusive fitness theory is a general treatment of the statistical probabilities of social traits accruing to any other organisms likely to propagate a copy of the same social trait. Kin selection theory treats the narrower but simpler case of the benefits to close genetic relatives (or what biologists call 'kin') who may also carry and propagate the trait. A significant group of biologists support inclusive fitness as the explanation for social behavior in a wide range of species, as supported by experimental data. An article was published in Nature with over a hundred coauthors.

One of the questions about kin selection is the requirement that individuals must know if other individuals are related to them, or kin recognition. Any altruistic act has to preserve similar genes. One argument given by Hamilton is that many individuals operate in "viscous" conditions, so that they live in physical proximity to relatives. Under these conditions, they can act altruistically to any other individual, and it is likely that the other individual will be related. This population structure builds a continuum between individual selection, kin selection, kin group selection and group selection without a clear boundary for each level. However, early theoretical models by D.S. Wilson et al. and Taylor showed that pure population viscosity cannot lead to cooperation and altruism. This is because any benefit generated by kin cooperation is exactly cancelled out by kin competition; additional offspring from cooperation are eliminated by local competition. Mitteldorf and D. S. Wilson later showed that if the population is allowed to fluctuate, then local populations can temporarily store the benefit of local cooperation and promote the evolution of cooperation and altruism. By assuming individual differences in adaptations, Yang further showed that the benefit of local altruism can be stored in the form of offspring quality and thus promote the evolution of altruism even if the population does not fluctuate. This is because local competition among more individuals resulting from local altruism increases the average local fitness of the individuals that survive.

Another explanation for the recognition of genes for altruism is that a single trait, group reciprocal kindness, is capable of explaining the vast majority of altruism that is generally accepted as "good" by modern societies. The phenotype of altruism relies on recognition of the altruistic behavior by itself. The trait of kindness will be recognized by sufficiently intelligent and undeceived organisms in other individuals with the same trait. Moreover, the existence of such a trait predicts a tendency for kindness to unrelated organisms that are apparently kind, even if the organisms are of a completely different species. The gene need not be exactly the same, so long as the effect or phenotype is similar. Multiple versions of the gene—or even meme—would have virtually the same effect. This explanation was given by Richard Dawkins as an analogy of a man with a green beard. Green-bearded men are imagined as tending to cooperate with each other simply by seeing a green beard, where the green beard trait is incidentally linked to the reciprocal kindness trait.

Multilevel selection theory

Kin selection or inclusive fitness is accepted as an explanation for cooperative behavior in many species, but there are some species, including some human behavior, that are difficult to explain with only this approach. In particular, it does not seem to explain the rapid rise of human civilization. David Sloan Wilson has argued that other factors must also be considered in evolution. Wilson and others have continued to develop group selection models.

Early group selection models were flawed because they assumed that genes acted independently; but genetically-based interactions among individuals are ubiquitous in group formation because genes must cooperate for the benefit of association in groups to enhance the fitness of group members. Additionally, group selection on the level of the species is flawed because it is difficult to see how selective pressures would be applied; selection in social species of groups against other groups, rather than the species entire, seems to be the level at which selective pressures are plausible. On the other hand, kin selection is accepted as an explanation of altruistic behavior. Some biologists argue that kin selection and multilevel selection are both needed to "obtain a complete understanding of the evolution of a social behavior system".

In 1994 David Sloan Wilson and Elliott Sober argued that the case against group selection had been overstated. They considered whether groups can have functional organization in the same way as individuals, and consequently whether groups can be "vehicles" for selection. They do not posit evolution on the level of the species, but selective pressures that winnow out small groups within a species, e.g. groups of social insects or primates. Groups that cooperate better might survive and reproduce more than those that did not. Resurrected in this way, Wilson & Sober's new group selection is called multilevel selection theory.

In 2010, M. A. Nowak, C. E. Tarnita and E. O. Wilson argued for multi-level selection, including group selection, to correct what they saw as deficits in the explanatory power of inclusive fitness. The response was a back-lash from 137 other evolutionary biologists who argued "that their arguments are based upon a misunderstanding of evolutionary theory and a misrepresentation of the empirical literature".

David Sloan Wilson and Elliott Sober's 1994 Multilevel Selection Model, illustrated by a nested set of Russian matryoshka dolls. Wilson himself compared his model to such a set.

 

Wilson compared the layers of competition and evolution to nested sets of Russian matryoshka dolls. The lowest level is the genes, next come the cells, then the organism level and finally the groups. The different levels function cohesively to maximize fitness, or reproductive success. The theory asserts that selection for the group level, involving competition between groups, must outweigh the individual level, involving individuals competing within a group, for a group-benefiting trait to spread.

Multilevel selection theory focuses on the phenotype because it looks at the levels that selection directly acts upon. For humans, social norms can be argued to reduce individual level variation and competition, thus shifting selection to the group level. The assumption is that variation between different groups is larger than variation within groups. Competition and selection can operate at all levels regardless of scale. Wilson wrote, "At all scales, there must be mechanisms that coordinate the right kinds of action and prevent disruptive forms of self-serving behavior at lower levels of social organization." E. O. Wilson summarized, "In a group, selfish individuals beat altruistic individuals. But, groups of altruistic individuals beat groups of selfish individuals."

Wilson ties the multilevel selection theory regarding humans to another theory, gene-culture coevolution, by acknowledging that culture seems to characterize a group-level mechanism for human groups to adapt to environmental changes.

MLS theory can be used to evaluate the balance between group selection and individual selection in specific cases. An experiment by William Muir compared egg productivity in hens, showing that a hyper-aggressive strain had been produced through individual selection, leading to many fatal attacks after only six generations; by implication, it could be argued that group selection must have been acting to prevent this in real life. Group selection has most often been postulated in humans and, notably, eusocial Hymenoptera that make cooperation a driving force of their adaptations over time and have a unique system of inheritance involving haplodiploidy that allows the colony to function as an individual while only the queen reproduces.

Wilson and Sober's work revived interest in multilevel selection. In a 2005 article, E. O. Wilson argued that kin selection could no longer be thought of as underlying the evolution of extreme sociality, for two reasons. First, he suggested, the argument that haplodiploid inheritance (as in the Hymenoptera) creates a strong selection pressure towards nonreproductive castes is mathematically flawed. Second, eusociality no longer seems to be confined to the hymenopterans; increasing numbers of highly social taxa have been found in the years since Wilson's foundational text Sociobiology: A New Synthesis was published in 1975. These including a variety of insect species, as well as two rodent species (the naked mole-rat and the Damaraland mole rat). Wilson suggests the equation for Hamilton's rule:

rb > c

(where b represents the benefit to the recipient of altruism, c the cost to the altruist, and r their degree of relatedness) should be replaced by the more general equation

rb_k + b_e > c

in which b_k is the benefit to kin (b in the original equation) and b_e is the benefit accruing to the group as a whole. He then argues that, in the present state of the evidence in relation to social insects, it appears that b_e>rb_k, so that altruism needs to be explained in terms of selection at the colony level rather than at the kin level. However, kin selection and group selection are not distinct processes, and the effects of multi-level selection are already accounted for in Hamilton's rule, rb>c, provided that an expanded definition of r, not requiring Hamilton's original assumption of direct genealogical relatedness, is used, as proposed by E. O. Wilson himself.

Spatial populations of predators and prey show restraint of reproduction at equilibrium, both individually and through social communication, as originally proposed by Wynne-Edwards. While these spatial populations do not have well-defined groups for group selection, the local spatial interactions of organisms in transient groups are sufficient to lead to a kind of multi-level selection. There is however as yet no evidence that these processes operate in the situations where Wynne-Edwards posited them.

Rauch et al.'s analysis of host-parasite evolution, which even E. O. Wilson recognised as a situation where group selection was possible (1975), is broadly hostile to group selection. Specifically, the parasites do not individually moderate their transmission; rather, more transmissible variants "continually arise and grow rapidly for many generations but eventually go extinct before dominating the system."

Applications

Differing evolutionarily stable strategies

The problem with group selection is that for a whole group to get a single trait, it must spread through the whole group first by regular evolution. But, as J. L. Mackie suggested, when there are many different groups, each with a different evolutionarily stable strategy, there is selection between the different strategies, since some are worse than others. For example, a group where altruism was universal would indeed outcompete a group where every creature acted in its own interest, so group selection might seem feasible; but a mixed group of altruists and non-altruists would be vulnerable to cheating by non-altruists within the group, so group selection would collapse.

Implications in population biology

Social behaviors such as altruism and group relationships can impact many aspects of population dynamics, such as intraspecific competition and interspecific interactions. In 1871, Darwin argued that group selection occurs when the benefits of cooperation or altruism between subpopulations are greater than the individual benefits of egotism within a subpopulation. This supports the idea of multilevel selection, but kinship also plays an integral role because many subpopulations are composed of closely related individuals. An example of this can be found in lions, which are simultaneously cooperative and territorial. Within a pride, males protect the pride from outside males, and females, who are commonly sisters, communally raise cubs and hunt. However, this cooperation seems to be density dependent. When resources are limited, group selection favors prides that work together to hunt. When prey is abundant, cooperation is no longer beneficial enough to outweigh the disadvantages of altruism, and hunting is no longer cooperative.

Interactions between different species can also be affected by multilevel selection. Predator-prey relationships can also be affected. Individuals of certain monkey species howl to warn the group of the approach of a predator. The evolution of this trait benefits the group by providing protection, but could be disadvantageous to the individual if the howling draws the predator's attention to them. By affecting these interspecific interactions, multilevel and kinship selection can change the population dynamics of an ecosystem.

Multilevel selection attempts to explain the evolution of altruistic behavior in terms of quantitative genetics. Increased frequency or fixation of altruistic alleles can be accomplished through kin selection, in which individuals engage in altruistic behavior to promote the fitness of genetically similar individuals such as siblings. However, this can lead to inbreeding depression, which typically lowers the overall fitness of a population. However, if altruism were to be selected for through an emphasis on benefit to the group as opposed to relatedness and benefit to kin, both the altruistic trait and genetic diversity could be preserved. However, relatedness should still remain a key consideration in studies of multilevel selection. Experimentally imposed multilevel selection on Japanese quail was more effective by an order of magnitude on closely related kin groups than on randomized groups of individuals.

Gene-culture coevolution in humans

Humanity has developed extremely rapidly, arguably through gene-culture coevolution, leading to complex cultural artefacts like the gopuram of the Sri Mariammam temple, Singapore.

 

Gene-culture coevolution (also called dual inheritance theory) is a modern hypothesis (applicable mostly to humans) that combines evolutionary biology and modern sociobiology to indicate group selection. It treats culture as a separate evolutionary system that acts in parallel to the usual genetic evolution to transform human traits. It is believed that this approach of combining genetic influence with cultural influence over several generations is not present in the other hypotheses such as reciprocal altruism and kin selection, making gene-culture evolution one of the strongest realistic hypotheses for group selection. Fehr provides evidence of group selection taking place in humans presently with experimentation through logic games such as prisoner’s dilemma, the type of thinking that humans have developed many generations ago.

Gene-culture coevolution allows humans to develop highly distinct adaptations to the local pressures and environments more quickly than with genetic evolution alone. Robert Boyd and Peter J. Richerson, two strong proponents of cultural evolution, postulate that the act of social learning, or learning in a group as done in group selection, allows human populations to accrue information over many generations. This leads to cultural evolution of behaviors and technology alongside genetic evolution. Boyd and Richerson believe that the ability to collaborate evolved during the Middle Pleistocene, a million years ago, in response to a rapidly changing climate.

In 2003, the behavioral scientist Herbert Gintis examined cultural evolution statistically, offering evidence that societies that promote pro-social norms have higher survival rates than societies that do not. Gintis wrote that genetic and cultural evolution can work together. Genes transfer information in DNA, and cultures transfer information encoded in brains, artifacts, or documents. Language, tools, lethal weapons, fire, cooking, etc., have a long-term effect on genetics. For example, cooking led to a reduction of size of the human gut, since less digestion is needed for cooked food. Language led to a change in the human larynx and an increase in brain size. Projectile weapons led to changes in human hands and shoulders, such that humans are much better at throwing objects than the closest human relative, the chimpanzee.

Criticism

The use of the Price equation to support group selection was challenged by van Veelen in 2012, arguing that it is based on invalid mathematical assumptions.

Richard Dawkins and other advocates of the gene-centered view of evolution remain unconvinced about group selection. In particular, Dawkins suggests that group selection fails to make an appropriate distinction between replicators and vehicles.

The psychologist Steven Pinker concluded that "group selection has no useful role to play in psychology or social science", since it "is not a precise implementation of the theory of natural selection, as it is, say, in genetic algorithms or artificial life simulations. Instead it is a loose metaphor, more like the struggle among kinds of tires or telephones."

The evolutionary biologist Jerry Coyne summarized the arguments in The New York Times in non-technical terms as follows:

Group selection isn't widely accepted by evolutionists for several reasons. First, it's not an efficient way to select for traits, like altruistic behavior, that are supposed to be detrimental to the individual but good for the group. Groups divide to form other groups much less often than organisms reproduce to form other organisms, so group selection for altruism would be unlikely to override the tendency of each group to quickly lose its altruists through natural selection favoring cheaters. Further, little evidence exists that selection on groups has promoted the evolution of any trait. Finally, other, more plausible evolutionary forces, like direct selection on individuals for reciprocal support, could have made humans prosocial. These reasons explain why only a few biologists, like [David Sloan] Wilson and E. O. Wilson (no relation), advocate group selection as the evolutionary source of cooperation.

Metabolism

From Wikipedia, the free encyclopedia

Simplified view of the cellular metabolism

 

Structure of adenosine triphosphate (ATP), a central intermediate in ENERGY metabolism

 

Metabolism (/məˈtæbəlɪzəm/, from Greek: μεταβολή metabolē, "change") is the set of life-sustaining chemical reactions in organisms. The three main purposes of metabolism are: the conversion of food to energy to run cellular processes; the conversion of food/fuel to building blocks for proteins, lipids, nucleic acids, and some carbohydrates; and the elimination of nitrogenous wastes. These enzyme-catalyzed reactions allow organisms to grow and reproduce, maintain their structures, and respond to their environments. (The word metabolism can also refer to the sum of all chemical reactions that occur in living organisms, including digestion and the transport of substances into and between different cells, in which case the above described set of reactions within the cells is called intermediary metabolism or intermediate metabolism). 

Metabolic reactions may be categorized as catabolic - the breaking down of compounds (for example, the breaking down of glucose to pyruvate by cellular respiration); or anabolic - the building up (synthesis) of compounds (such as proteins, carbohydrates, lipids, and nucleic acids). Usually, catabolism releases energy, and anabolism consumes energy. 

The chemical reactions of metabolism are organized into metabolic pathways, in which one chemical is transformed through a series of steps into another chemical, each step being facilitated by a specific enzyme. Enzymes are crucial to metabolism because they allow organisms to drive desirable reactions that require energy that will not occur by themselves, by coupling them to spontaneous reactions that release energy. Enzymes act as catalysts - they allow a reaction to proceed more rapidly - and they also allow the regulation of the rate of a metabolic reaction, for example in response to changes in the cell's environment or to signals from other cells. 

The metabolic system of a particular organism determines which substances it will find nutritious and which poisonous. For example, some prokaryotes use hydrogen sulfide as a nutrient, yet this gas is poisonous to animals. The basal metabolic rate of an organism is the measure of the amount of energy consumed by all of these chemical reactions. 

A striking feature of metabolism is the similarity of the basic metabolic pathways among vastly different species. For example, the set of carboxylic acids that are best known as the intermediates in the citric acid cycle are present in all known organisms, being found in species as diverse as the unicellular bacterium Escherichia coli and huge multicellular organisms like elephants. These similarities in metabolic pathways are likely due to their early appearance in evolutionary history, and their retention because of their efficacy.

Key biochemicals

Structure of a triacylglycerol lipid

 

This is a diagram depicting a large set of human metabolic pathways.

 

Most of the structures that make up animals, plants and microbes are made from three basic classes of molecule: amino acids, carbohydrates and lipids (often called fats). As these molecules are vital for life, metabolic reactions either focus on making these molecules during the construction of cells and tissues, or by breaking them down and using them as a source of energy, by their digestion. These biochemicals can be joined together to make polymers such as DNA and proteins, essential macromolecules of life. 

Type of molecule	Name of monomer forms	Name of polymer forms	Examples of polymer forms
Amino acids	Amino acids	Proteins (made of polypeptides)	Fibrous proteins and globular proteins
Carbohydrates	Monosaccharides	Polysaccharides	Starch, glycogen and cellulose
Nucleic acids	Nucleotides	Polynucleotides	DNA and RNA

Amino acids and proteins

Proteins are made of amino acids arranged in a linear chain joined together by peptide bonds. Many proteins are enzymes that catalyze the chemical reactions in metabolism. Other proteins have structural or mechanical functions, such as those that form the cytoskeleton, a system of scaffolding that maintains the cell shape. Proteins are also important in cell signaling, immune responses, cell adhesion, active transport across membranes, and the cell cycle. Amino acids also contribute to cellular energy metabolism by providing a carbon source for entry into the citric acid cycle (tricarboxylic acid cycle), especially when a primary source of energy, such as glucose, is scarce, or when cells undergo metabolic stress.

Lipids

Lipids are the most diverse group of biochemicals. Their main structural uses are as part of biological membranes both internal and external, such as the cell membrane, or as a source of energy. Lipids are usually defined as hydrophobic or amphipathic biological molecules but will dissolve in organic solvents such as benzene or chloroform. The fats are a large group of compounds that contain fatty acids and glycerol; a glycerol molecule attached to three fatty acid esters is called a triacylglyceride. Several variations on this basic structure exist, including alternate backbones such as sphingosine in the sphingolipids, and hydrophilic groups such as phosphate as in phospholipids. Steroids such as cholesterol are another major class of lipids.

Carbohydrates

Glucose can exist in both a straight-chain and ring form.

 

Carbohydrates are aldehydes or ketones, with many hydroxyl groups attached, that can exist as straight chains or rings. Carbohydrates are the most abundant biological molecules, and fill numerous roles, such as the storage and transport of energy (starch, glycogen) and structural components (cellulose in plants, chitin in animals). The basic carbohydrate units are called monosaccharides and include galactose, fructose, and most importantly glucose. Monosaccharides can be linked together to form polysaccharides in almost limitless ways.

Nucleotides

The two nucleic acids, DNA and RNA, are polymers of nucleotides. Each nucleotide is composed of a phosphate attached to a ribose or deoxyribose sugar group which is attached to a nitrogenous base. Nucleic acids are critical for the storage and use of genetic information, and its interpretation through the processes of transcription and protein biosynthesis. This information is protected by DNA repair mechanisms and propagated through DNA replication. Many viruses have an RNA genome, such as HIV, which uses reverse transcription to create a DNA template from its viral RNA genome. RNA in ribozymes such as spliceosomes and ribosomes is similar to enzymes as it can catalyze chemical reactions. Individual nucleosides are made by attaching a nucleobase to a ribose sugar. These bases are heterocyclic rings containing nitrogen, classified as purines or pyrimidines. Nucleotides also act as coenzymes in metabolic-group-transfer reactions.

Coenzymes

Structure of the coenzyme acetyl-CoA.The transferable acetyl group is bonded to the sulfur atom at the extreme left.

Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer of functional groups of atoms and their bonds within molecules. This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions. These group-transfer intermediates are called coenzymes. Each class of group-transfer reactions is carried out by a particular coenzyme, which is the substrate for a set of enzymes that produce it, and a set of enzymes that consume it. These coenzymes are therefore continuously made, consumed and then recycled.

One central coenzyme is adenosine triphosphate (ATP), the universal energy currency of cells. This nucleotide is used to transfer chemical energy between different chemical reactions. There is only a small amount of ATP in cells, but as it is continuously regenerated, the human body can use about its own weight in ATP per day. ATP acts as a bridge between catabolism and anabolism. Catabolism breaks down molecules, and anabolism puts them together. Catabolic reactions generate ATP, and anabolic reactions consume it. It also serves as a carrier of phosphate groups in phosphorylation reactions. 

A vitamin is an organic compound needed in small quantities that cannot be made in cells. In human nutrition, most vitamins function as coenzymes after modification; for example, all water-soluble vitamins are phosphorylated or are coupled to nucleotides when they are used in cells. Nicotinamide adenine dinucleotide (NAD⁺), a derivative of vitamin B₃ (niacin), is an important coenzyme that acts as a hydrogen acceptor. Hundreds of separate types of dehydrogenases remove electrons from their substrates and reduce NAD⁺ into NADH. This reduced form of the coenzyme is then a substrate for any of the reductases in the cell that need to reduce their substrates. Nicotinamide adenine dinucleotide exists in two related forms in the cell, NADH and NADPH. The NAD⁺/NADH form is more important in catabolic reactions, while NADP⁺/NADPH is used in anabolic reactions. 

The structure of iron-containing hemoglobin. The protein subunits are in red and blue, and the iron-containing heme groups in green. From PDB: 1GZX​.

Minerals and cofactors

Inorganic elements play critical roles in metabolism; some are abundant (e.g. sodium and potassium) while others function at minute concentrations. About 99% of a mammal's mass is made up of the elements carbon, nitrogen, calcium, sodium, chlorine, potassium, hydrogen, phosphorus, oxygen and sulfur. Organic compounds (proteins, lipids and carbohydrates) contain the majority of the carbon and nitrogen; most of the oxygen and hydrogen is present as water.

The abundant inorganic elements act as ionic electrolytes. The most important ions are sodium, potassium, calcium, magnesium, chloride, phosphate and the organic ion bicarbonate. The maintenance of precise ion gradients across cell membranes maintains osmotic pressure and pH. Ions are also critical for nerve and muscle function, as action potentials in these tissues are produced by the exchange of electrolytes between the extracellular fluid and the cell's fluid, the cytosol. Electrolytes enter and leave cells through proteins in the cell membrane called ion channels. For example, muscle contraction depends upon the movement of calcium, sodium and potassium through ion channels in the cell membrane and T-tubules.

Transition metals are usually present as trace elements in organisms, with zinc and iron being most abundant of those. These metals are used in some proteins as cofactors and are essential for the activity of enzymes such as catalase and oxygen-carrier proteins such as hemoglobin. Metal cofactors are bound tightly to specific sites in proteins; although enzyme cofactors can be modified during catalysis, they always return to their original state by the end of the reaction catalyzed. Metal micronutrients are taken up into organisms by specific transporters and bind to storage proteins such as ferritin or metallothionein when not in use.

Catabolism

Catabolism is the set of metabolic processes that break down large molecules. These include breaking down and oxidizing food molecules. The purpose of the catabolic reactions is to provide the energy and components needed by anabolic reactions which build molecules. The exact nature of these catabolic reactions differ from organism to organism, and organisms can be classified based on their sources of energy and carbon (their primary nutritional groups), as shown in the table below. Organic molecules are used as a source of energy by organotrophs, while lithotrophs use inorganic substrates, and phototrophs capture sunlight as chemical energy. However, all these different forms of metabolism depend on redox reactions that involve the transfer of electrons from reduced donor molecules such as organic molecules, water, ammonia, hydrogen sulfide or ferrous ions to acceptor molecules such as oxygen, nitrate or sulfate. In animals, these reactions involve complex organic molecules that are broken down to simpler molecules, such as carbon dioxide and water. In photosynthetic organisms, such as plants and cyanobacteria, these electron-transfer reactions do not release energy but are used as a way of storing energy absorbed from sunlight.

Classification of organisms based on their metabolism

Energy source	sunlight	photo-			-troph
	Preformed molecules	chemo-
Electron donor	organic compound		organo-
	inorganic compound		litho-
Carbon source	organic compound			hetero-
	inorganic compound			auto-

The most common set of catabolic reactions in animals can be separated into three main stages. In the first stage, large organic molecules, such as proteins, polysaccharides or lipids, are digested into their smaller components outside cells. Next, these smaller molecules are taken up by cells and converted to smaller molecules, usually acetyl coenzyme A (acetyl-CoA), which releases some energy. Finally, the acetyl group on the CoA is oxidised to water and carbon dioxide in the citric acid cycle and electron transport chain, releasing the energy that is stored by reducing the coenzyme nicotinamide adenine dinucleotide (NAD⁺) into NADH.

Digestion

Macromolecules such as starch, cellulose or proteins cannot be rapidly taken up by cells and must be broken into their smaller units before they can be used in cell metabolism. Several common classes of enzymes digest these polymers. These digestive enzymes include proteases that digest proteins into amino acids, as well as glycoside hydrolases that digest polysaccharides into simple sugars known as monosaccharides. 

Microbes simply secrete digestive enzymes into their surroundings, while animals only secrete these enzymes from specialized cells in their guts, including the stomach and pancreas, and salivary glands. The amino acids or sugars released by these extracellular enzymes are then pumped into cells by active transport proteins.

A simplified outline of the catabolism of proteins, carbohydrates and fats

Energy from organic compounds

Carbohydrate catabolism is the breakdown of carbohydrates into smaller units. Carbohydrates are usually taken into cells once they have been digested into monosaccharides. Once inside, the major route of breakdown is glycolysis, where sugars such as glucose and fructose are converted into pyruvate and some ATP is generated. Pyruvate is an intermediate in several metabolic pathways, but the majority is converted to acetyl-CoA through aerobic (with oxygen) glycolysis and fed into the citric acid cycle. Although some more ATP is generated in the citric acid cycle, the most important product is NADH, which is made from NAD⁺ as the acetyl-CoA is oxidized. This oxidation releases carbon dioxide as a waste product. In anaerobic conditions, glycolysis produces lactate, through the enzyme lactate dehydrogenase re-oxidizing NADH to NAD+ for re-use in glycolysis. An alternative route for glucose breakdown is the pentose phosphate pathway, which reduces the coenzyme NADPH and produces pentose sugars such as ribose, the sugar component of nucleic acids. 

Fats are catabolised by hydrolysis to free fatty acids and glycerol. The glycerol enters glycolysis and the fatty acids are broken down by beta oxidation to release acetyl-CoA, which then is fed into the citric acid cycle. Fatty acids release more energy upon oxidation than carbohydrates because carbohydrates contain more oxygen in their structures. Steroids are also broken down by some bacteria in a process similar to beta oxidation, and this breakdown process involves the release of significant amounts of acetyl-CoA, propionyl-CoA, and pyruvate, which can all be used by the cell for energy. M. tuberculosis can also grow on the lipid cholesterol as a sole source of carbon, and genes involved in the cholesterol use pathway(s) have been validated as important during various stages of the infection lifecycle of M. tuberculosis.

Amino acids are either used to synthesize proteins and other biomolecules, or oxidized to urea and carbon dioxide as a source of energy. The oxidation pathway starts with the removal of the amino group by a transaminase. The amino group is fed into the urea cycle, leaving a deaminated carbon skeleton in the form of a keto acid. Several of these keto acids are intermediates in the citric acid cycle, for example the deamination of glutamate forms α-ketoglutarate. The glucogenic amino acids can also be converted into glucose, through gluconeogenesis (discussed below).

Energy transformations

Oxidative phosphorylation

In oxidative phosphorylation, the electrons removed from organic molecules in areas such as the protagon acid cycle are transferred to oxygen and the energy released is used to make ATP. This is done in eukaryotes by a series of proteins in the membranes of mitochondria called the electron transport chain. In prokaryotes, these proteins are found in the cell's inner membrane. These proteins use the energy released from passing electrons from reduced molecules like NADH onto oxygen to pump protons across a membrane.

Mechanism of ATP synthase. ATP is shown in red, ADP and phosphate in pink and the rotating stalk subunit in black.

 

Pumping protons out of the mitochondria creates a proton concentration difference across the membrane and generates an electrochemical gradient. This force drives protons back into the mitochondrion through the base of an enzyme called ATP synthase. The flow of protons makes the stalk subunit rotate, causing the active site of the synthase domain to change shape and phosphorylate adenosine diphosphate – turning it into ATP.

Energy from inorganic compounds

Chemolithotrophy is a type of metabolism found in prokaryotes where energy is obtained from the oxidation of inorganic compounds. These organisms can use hydrogen, reduced sulfur compounds (such as sulfide, hydrogen sulfide and thiosulfate), ferrous iron (FeII) or ammonia as sources of reducing power and they gain energy from the oxidation of these compounds with electron acceptors such as oxygen or nitrite. These microbial processes are important in global biogeochemical cycles such as acetogenesis, nitrification and denitrification and are critical for soil fertility.

Energy from light

The energy in sunlight is captured by plants, cyanobacteria, purple bacteria, green sulfur bacteria and some protists. This process is often coupled to the conversion of carbon dioxide into organic compounds, as part of photosynthesis, which is discussed below. The energy capture and carbon fixation systems can however operate separately in prokaryotes, as purple bacteria and green sulfur bacteria can use sunlight as a source of energy, while switching between carbon fixation and the fermentation of organic compounds.

In many organisms the capture of solar energy is similar in principle to oxidative phosphorylation, as it involves the storage of energy as a proton concentration gradient. This proton motive force then drives ATP synthesis. The electrons needed to drive this electron transport chain come from light-gathering proteins called photosynthetic reaction centres or rhodopsins. Reaction centers are classed into two types depending on the type of photosynthetic pigment present, with most photosynthetic bacteria only having one type, while plants and cyanobacteria have two.

In plants, algae, and cyanobacteria, photosystem II uses light energy to remove electrons from water, releasing oxygen as a waste product. The electrons then flow to the cytochrome b6f complex, which uses their energy to pump protons across the thylakoid membrane in the chloroplast. These protons move back through the membrane as they drive the ATP synthase, as before. The electrons then flow through photosystem I and can then either be used to reduce the coenzyme NADP⁺, for use in the Calvin cycle, which is discussed below, or recycled for further ATP generation.

Anabolism

Anabolism is the set of constructive metabolic processes where the energy released by catabolism is used to synthesize complex molecules. In general, the complex molecules that make up cellular structures are constructed step-by-step from small and simple precursors. Anabolism involves three basic stages. First, the production of precursors such as amino acids, monosaccharides, isoprenoids and nucleotides, secondly, their activation into reactive forms using energy from ATP, and thirdly, the assembly of these precursors into complex molecules such as proteins, polysaccharides, lipids and nucleic acids. 

Organisms differ according to the number of constructed molecules in their cells. Autotrophs such as plants can construct the complex organic molecules in cells such as polysaccharides and proteins from simple molecules like carbon dioxide and water. Heterotrophs, on the other hand, require a source of more complex substances, such as monosaccharides and amino acids, to produce these complex molecules. Organisms can be further classified by ultimate source of their energy: photoautotrophs and photoheterotrophs obtain energy from light, whereas chemoautotrophs and chemoheterotrophs obtain energy from inorganic oxidation reactions.

Carbon fixation

Plant cells (bounded by purple walls) filled with chloroplasts (green), which are the site of photosynthesis

 

Photosynthesis is the synthesis of carbohydrates from sunlight and carbon dioxide (CO₂). In plants, cyanobacteria and algae, oxygenic photosynthesis splits water, with oxygen produced as a waste product. This process uses the ATP and NADPH produced by the photosynthetic reaction centres, as described above, to convert CO₂ into glycerate 3-phosphate, which can then be converted into glucose. This carbon-fixation reaction is carried out by the enzyme RuBisCO as part of the Calvin – Benson cycle. Three types of photosynthesis occur in plants, C3 carbon fixation, C4 carbon fixation and CAM photosynthesis. These differ by the route that carbon dioxide takes to the Calvin cycle, with C3 plants fixing CO₂ directly, while C4 and CAM photosynthesis incorporate the CO₂ into other compounds first, as adaptations to deal with intense sunlight and dry conditions.

In photosynthetic prokaryotes the mechanisms of carbon fixation are more diverse. Here, carbon dioxide can be fixed by the Calvin – Benson cycle, a reversed citric acid cycle, or the carboxylation of acetyl-CoA. Prokaryotic chemoautotrophs also fix CO₂ through the Calvin – Benson cycle, but use energy from inorganic compounds to drive the reaction.

Carbohydrates and glycans

In carbohydrate anabolism, simple organic acids can be converted into monosaccharides such as glucose and then used to assemble polysaccharides such as starch. The generation of glucose from compounds like pyruvate, lactate, glycerol, glycerate 3-phosphate and amino acids is called gluconeogenesis. Gluconeogenesis converts pyruvate to glucose-6-phosphate through a series of intermediates, many of which are shared with glycolysis. However, this pathway is not simply glycolysis run in reverse, as several steps are catalyzed by non-glycolytic enzymes. This is important as it allows the formation and breakdown of glucose to be regulated separately, and prevents both pathways from running simultaneously in a futile cycle.

Although fat is a common way of storing energy, in vertebrates such as humans the fatty acids in these stores cannot be converted to glucose through gluconeogenesis as these organisms cannot convert acetyl-CoA into pyruvate; plants do, but animals do not, have the necessary enzymatic machinery. As a result, after long-term starvation, vertebrates need to produce ketone bodies from fatty acids to replace glucose in tissues such as the brain that cannot metabolize fatty acids. In other organisms such as plants and bacteria, this metabolic problem is solved using the glyoxylate cycle, which bypasses the decarboxylation step in the citric acid cycle and allows the transformation of acetyl-CoA to oxaloacetate, where it can be used for the production of glucose.

Polysaccharides and glycans are made by the sequential addition of monosaccharides by glycosyltransferase from a reactive sugar-phosphate donor such as uridine diphosphate glucose (UDP-glucose) to an acceptor hydroxyl group on the growing polysaccharide. As any of the hydroxyl groups on the ring of the substrate can be acceptors, the polysaccharides produced can have straight or branched structures. The polysaccharides produced can have structural or metabolic functions themselves, or be transferred to lipids and proteins by enzymes called oligosaccharyltransferases.

Fatty acids, isoprenoids and steroids

Simplified version of the steroid synthesis pathway with the intermediates isopentenyl pyrophosphate (IPP), dimethylallyl pyrophosphate (DMAPP), geranyl pyrophosphate (GPP) and squalene shown. Some intermediates are omitted for clarity.

 

Fatty acids are made by fatty acid synthases that polymerize and then reduce acetyl-CoA units. The acyl chains in the fatty acids are extended by a cycle of reactions that add the acyl group, reduce it to an alcohol, dehydrate it to an alkene group and then reduce it again to an alkane group. The enzymes of fatty acid biosynthesis are divided into two groups: in animals and fungi, all these fatty acid synthase reactions are carried out by a single multifunctional type I protein, while in plant plastids and bacteria separate type II enzymes perform each step in the pathway.

Terpenes and isoprenoids are a large class of lipids that include the carotenoids and form the largest class of plant natural products. These compounds are made by the assembly and modification of isoprene units donated from the reactive precursors isopentenyl pyrophosphate and dimethylallyl pyrophosphate. These precursors can be made in different ways. In animals and archaea, the mevalonate pathway produces these compounds from acetyl-CoA, while in plants and bacteria the non-mevalonate pathway uses pyruvate and glyceraldehyde 3-phosphate as substrates. One important reaction that uses these activated isoprene donors is steroid biosynthesis. Here, the isoprene units are joined together to make squalene and then folded up and formed into a set of rings to make lanosterol. Lanosterol can then be converted into other steroids such as cholesterol and ergosterol.

Proteins

Organisms vary in their ability to synthesize the 20 common amino acids. Most bacteria and plants can synthesize all twenty, but mammals can only synthesize eleven nonessential amino acids, so nine essential amino acids must be obtained from food. Some simple parasites, such as the bacteria Mycoplasma pneumoniae, lack all amino acid synthesis and take their amino acids directly from their hosts. All amino acids are synthesized from intermediates in glycolysis, the citric acid cycle, or the pentose phosphate pathway. Nitrogen is provided by glutamate and glutamine. Amino acid synthesis depends on the formation of the appropriate alpha-keto acid, which is then transaminated to form an amino acid.

Amino acids are made into proteins by being joined together in a chain of peptide bonds. Each different protein has a unique sequence of amino acid residues: this is its primary structure. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a huge variety of proteins. Proteins are made from amino acids that have been activated by attachment to a transfer RNA molecule through an ester bond. This aminoacyl-tRNA precursor is produced in an ATP-dependent reaction carried out by an aminoacyl tRNA synthetase. This aminoacyl-tRNA is then a substrate for the ribosome, which joins the amino acid onto the elongating protein chain, using the sequence information in a messenger RNA.

Nucleotide synthesis and salvage

Nucleotides are made from amino acids, carbon dioxide and formic acid in pathways that require large amounts of metabolic energy. Consequently, most organisms have efficient systems to salvage preformed nucleotides. Purines are synthesized as nucleosides (bases attached to ribose). Both adenine and guanine are made from the precursor nucleoside inosine monophosphate, which is synthesized using atoms from the amino acids glycine, glutamine, and aspartic acid, as well as formate transferred from the coenzyme tetrahydrofolate. Pyrimidines, on the other hand, are synthesized from the base orotate, which is formed from glutamine and aspartate.

Xenobiotics and redox metabolism

All organisms are constantly exposed to compounds that they cannot use as foods and would be harmful if they accumulated in cells, as they have no metabolic function. These potentially damaging compounds are called xenobiotics. Xenobiotics such as synthetic drugs, natural poisons and antibiotics are detoxified by a set of xenobiotic-metabolizing enzymes. In humans, these include cytochrome P450 oxidases, UDP-glucuronosyltransferases, and glutathione S-transferases. This system of enzymes acts in three stages to firstly oxidize the xenobiotic (phase I) and then conjugate water-soluble groups onto the molecule (phase II). The modified water-soluble xenobiotic can then be pumped out of cells and in multicellular organisms may be further metabolized before being excreted (phase III). In ecology, these reactions are particularly important in microbial biodegradation of pollutants and the bioremediation of contaminated land and oil spills. Many of these microbial reactions are shared with multicellular organisms, but due to the incredible diversity of types of microbes these organisms are able to deal with a far wider range of xenobiotics than multicellular organisms, and can degrade even persistent organic pollutants such as organochloride compounds.

A related problem for aerobic organisms is oxidative stress. Here, processes including oxidative phosphorylation and the formation of disulfide bonds during protein folding produce reactive oxygen species such as hydrogen peroxide. These damaging oxidants are removed by antioxidant metabolites such as glutathione and enzymes such as catalases and peroxidases.

Thermodynamics of living organisms

Living organisms must obey the laws of thermodynamics, which describe the transfer of heat and work. The second law of thermodynamics states that in any closed system, the amount of entropy (disorder) cannot decrease. Although living organisms' amazing complexity appears to contradict this law, life is possible as all organisms are open systems that exchange matter and energy with their surroundings. Thus living systems are not in equilibrium, but instead are dissipative systems that maintain their state of high complexity by causing a larger increase in the entropy of their environments. The metabolism of a cell achieves this by coupling the spontaneous processes of catabolism to the non-spontaneous processes of anabolism. In thermodynamic terms, metabolism maintains order by creating disorder.

Regulation and control

As the environments of most organisms are constantly changing, the reactions of metabolism must be finely regulated to maintain a constant set of conditions within cells, a condition called homeostasis. Metabolic regulation also allows organisms to respond to signals and interact actively with their environments. Two closely linked concepts are important for understanding how metabolic pathways are controlled. Firstly, the regulation of an enzyme in a pathway is how its activity is increased and decreased in response to signals. Secondly, the control exerted by this enzyme is the effect that these changes in its activity have on the overall rate of the pathway (the flux through the pathway). For example, an enzyme may show large changes in activity (i.e. it is highly regulated) but if these changes have little effect on the flux of a metabolic pathway, then this enzyme is not involved in the control of the pathway.

Effect of insulin on glucose uptake and metabolism. Insulin binds to its receptor (1), which in turn starts many protein activation cascades (2). These include: translocation of Glut-4 transporter to the plasma membrane and influx of glucose (3), glycogen synthesis (4), glycolysis (5) and fatty acid synthesis (6).

 

There are multiple levels of metabolic regulation. In intrinsic regulation, the metabolic pathway self-regulates to respond to changes in the levels of substrates or products; for example, a decrease in the amount of product can increase the flux through the pathway to compensate. This type of regulation often involves allosteric regulation of the activities of multiple enzymes in the pathway. Extrinsic control involves a cell in a multicellular organism changing its metabolism in response to signals from other cells. These signals are usually in the form of soluble messengers such as hormones and growth factors and are detected by specific receptors on the cell surface. These signals are then transmitted inside the cell by second messenger systems that often involved the phosphorylation of proteins.

A very well understood example of extrinsic control is the regulation of glucose metabolism by the hormone insulin. Insulin is produced in response to rises in blood glucose levels. Binding of the hormone to insulin receptors on cells then activates a cascade of protein kinases that cause the cells to take up glucose and convert it into storage molecules such as fatty acids and glycogen. The metabolism of glycogen is controlled by activity of phosphorylase, the enzyme that breaks down glycogen, and glycogen synthase, the enzyme that makes it. These enzymes are regulated in a reciprocal fashion, with phosphorylation inhibiting glycogen synthase, but activating phosphorylase. Insulin causes glycogen synthesis by activating protein phosphatases and producing a decrease in the phosphorylation of these enzymes.

Evolution

Evolutionary tree showing the common ancestry of organisms from all three domains of life. Bacteria are colored blue, eukaryotes red, and archaea green. Relative positions of some of the phyla included are shown around the tree.

 

The central pathways of metabolism described above, such as glycolysis and the citric acid cycle, are present in all three domains of living things and were present in the last universal common ancestor. This universal ancestral cell was prokaryotic and probably a methanogen that had extensive amino acid, nucleotide, carbohydrate and lipid metabolism. The retention of these ancient pathways during later evolution may be the result of these reactions having been an optimal solution to their particular metabolic problems, with pathways such as glycolysis and the citric acid cycle producing their end products highly efficiently and in a minimal number of steps. The first pathways of enzyme-based metabolism may have been parts of purine nucleotide metabolism, while previous metabolic pathways were a part of the ancient RNA world.

Many models have been proposed to describe the mechanisms by which novel metabolic pathways evolve. These include the sequential addition of novel enzymes to a short ancestral pathway, the duplication and then divergence of entire pathways as well as the recruitment of pre-existing enzymes and their assembly into a novel reaction pathway. The relative importance of these mechanisms is unclear, but genomic studies have shown that enzymes in a pathway are likely to have a shared ancestry, suggesting that many pathways have evolved in a step-by-step fashion with novel functions created from pre-existing steps in the pathway. An alternative model comes from studies that trace the evolution of proteins' structures in metabolic networks, this has suggested that enzymes are pervasively recruited, borrowing enzymes to perform similar functions in different metabolic pathways (evident in the MANET database) These recruitment processes result in an evolutionary enzymatic mosaic. A third possibility is that some parts of metabolism might exist as "modules" that can be reused in different pathways and perform similar functions on different molecules.

As well as the evolution of new metabolic pathways, evolution can also cause the loss of metabolic functions. For example, in some parasites metabolic processes that are not essential for survival are lost and preformed amino acids, nucleotides and carbohydrates may instead be scavenged from the host. Similar reduced metabolic capabilities are seen in endosymbiotic organisms.

Investigation and manipulation

Metabolic network of the Arabidopsis thaliana citric acid cycle. Enzymes and metabolites are shown as red squares and the interactions between them as black lines.

 

Classically, metabolism is studied by a reductionist approach that focuses on a single metabolic pathway. Particularly valuable is the use of radioactive tracers at the whole-organism, tissue and cellular levels, which define the paths from precursors to final products by identifying radioactively labelled intermediates and products. The enzymes that catalyze these chemical reactions can then be purified and their kinetics and responses to inhibitors investigated. A parallel approach is to identify the small molecules in a cell or tissue; the complete set of these molecules is called the metabolome. Overall, these studies give a good view of the structure and function of simple metabolic pathways, but are inadequate when applied to more complex systems such as the metabolism of a complete cell.

An idea of the complexity of the metabolic networks in cells that contain thousands of different enzymes is given by the figure showing the interactions between just 43 proteins and 40 metabolites to the right: the sequences of genomes provide lists containing anything up to 45,000 genes. However, it is now possible to use this genomic data to reconstruct complete networks of biochemical reactions and produce more holistic mathematical models that may explain and predict their behavior. These models are especially powerful when used to integrate the pathway and metabolite data obtained through classical methods with data on gene expression from proteomic and DNA microarray studies. Using these techniques, a model of human metabolism has now been produced, which will guide future drug discovery and biochemical research. These models are now used in network analysis, to classify human diseases into groups that share common proteins or metabolites.

Bacterial metabolic networks are a striking example of bow-tie organization, an architecture able to input a wide range of nutrients and produce a large variety of products and complex macromolecules using a relatively few intermediate common currencies. 

A major technological application of this information is metabolic engineering. Here, organisms such as yeast, plants or bacteria are genetically modified to make them more useful in biotechnology and aid the production of drugs such as antibiotics or industrial chemicals such as 1,3-propanediol and shikimic acid. These genetic modifications usually aim to reduce the amount of energy used to produce the product, increase yields and reduce the production of wastes.

History

The term metabolism is derived from the Greek Μεταβολισμός – "Metabolismos" for "change", or "overthrow".

Aristotle's metabolism as an open flow model

Greek philosophy

Aristotle's The Parts of Animals sets out enough details of his views on metabolism for an open flow model to be made. He believed that at each stage of the process, materials from food were transformed, with heat being released as the classical element of fire, and residual materials being excreted as urine, bile, or faeces.

Islamic medicine

Ibn al-Nafis described metabolism in his 1260 AD work titled Al-Risalah al-Kamiliyyah fil Siera al-Nabawiyyah (The Treatise of Kamil on the Prophet's Biography) which included the following phrase "Both the body and its parts are in a continuous state of dissolution and nourishment, so they are inevitably undergoing permanent change."

Application of the scientific method

The history of the scientific study of metabolism spans several centuries and has moved from examining whole animals in early studies, to examining individual metabolic reactions in modern biochemistry. The first controlled experiments in human metabolism were published by Santorio Santorio in 1614 in his book Ars de statica medicina. He described how he weighed himself before and after eating, sleep, working, sex, fasting, drinking, and excreting. He found that most of the food he took in was lost through what he called "insensible perspiration". 

Santorio Santorio in his steelyard balance, from Ars de statica medicina, first published 1614

 

In these early studies, the mechanisms of these metabolic processes had not been identified and a vital force was thought to animate living tissue. In the 19th century, when studying the fermentation of sugar to alcohol by yeast, Louis Pasteur concluded that fermentation was catalyzed by substances within the yeast cells he called "ferments". He wrote that "alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells." This discovery, along with the publication by Friedrich Wöhler in 1828 of a paper on the chemical synthesis of urea, and is notable for being the first organic compound prepared from wholly inorganic precursors. This proved that the organic compounds and chemical reactions found in cells were no different in principle than any other part of chemistry. 

It was the discovery of enzymes at the beginning of the 20th century by Eduard Buchner that separated the study of the chemical reactions of metabolism from the biological study of cells, and marked the beginnings of biochemistry. The mass of biochemical knowledge grew rapidly throughout the early 20th century. One of the most prolific of these modern biochemists was Hans Krebs who made huge contributions to the study of metabolism. He discovered the urea cycle and later, working with Hans Kornberg, the citric acid cycle and the glyoxylate cycle. Modern biochemical research has been greatly aided by the development of new techniques such as chromatography, X-ray diffraction, NMR spectroscopy, radioisotopic labelling, electron microscopy and molecular dynamics simulations. These techniques have allowed the discovery and detailed analysis of the many molecules and metabolic pathways in cells.