Introducing Biological Energetics: How Energy and Information Control the Living World

Ecology/Energy in ecosystems
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stencohawguites.gq/map23.php But forming a sequential pathway is not adequate for many purposes. Fortunately, there are other more general ways of using enzymes to couple reactions together. How these work is the topic we discuss next. The energy released by the oxidation of food molecules must be stored temporarily before it can be channeled into the construction of other small organic molecules and of the larger and more complex molecules needed by the cell. These molecules diffuse rapidly throughout the cell and thereby carry their bond energy from sites of energy generation to the sites where energy is used for biosynthesis and other needed cell activities Figure Energy transfer and the role of activated carriers in metabolism.

By serving as energy shuttles, activated carrier molecules perform their function as go-betweens that link the breakdown of food molecules and the release of energy catabolism to the more The activated carriers store energy in an easily exchangeable form, either as a readily transferable chemical group or as high-energy electrons, and they can serve a dual role as a source of both energy and chemical groups in biosynthetic reactions. For historical reasons, these molecules are also sometimes referred to as coenzymes. We shall see that cells use activated carrier molecules like money to pay for reactions that otherwise could not take place.

When a fuel molecule such as glucose is oxidized in a cell, enzyme -catalyzed reactions ensure that a large part of the free energy that is released by oxidation is captured in a chemically useful form, rather than being released wastefully as heat. This is achieved by means of a coupled reaction , in which an energetically favorable reaction is used to drive an energetically unfavorable one that produces an activated carrier molecule or some other useful energy store.

Coupling mechanisms require enzymes and are fundamental to all the energy trans-actions of the cell. The nature of a coupled reaction is illustrated by a mechanical analogy in Figure , in which an energetically favorable chemical reaction is represented by rocks falling from a cliff. The energy of falling rocks would normally be entirely wasted in the form of heat generated by friction when the rocks hit the ground see the falling brick diagram in Figure By careful design, however, part of this energy could be used instead to drive a paddle wheel that lifts a bucket of water Figure B.

Because the rocks can now reach the ground only after moving the paddle wheel, we say that the energetically favorable reaction of rock falling has been directly coupled to the energetically unfavorable reaction of lifting the bucket of water. Note that because part of the energy is used to do work in B , the rocks hit the ground with less velocity than in A , and correspondingly less energy is wasted as heat. A mechanical model illustrating the principle of coupled chemical reactions.

The spontaneous reaction shown in A could serve as an analogy for the direct oxidation of glucose to CO 2 and H 2 O, which produces heat only. In B the same reaction is coupled more Exactly analogous processes occur in cells, where enzymes play the role of the paddle wheel in our analogy. By mechanisms that will be discussed later in this chapter, they couple an energetically favorable reaction , such as the oxidation of foodstuffs, to an energetically unfavorable reaction, such as the generation of an activated carrier molecule.

As a result, the amount of heat released by the oxidation reaction is reduced by exactly the amount of energy that is stored in the energy-rich covalent bonds of the activated carrier molecule. The activated carrier molecule in turn picks up a packet of energy of a size sufficient to power a chemical reaction elsewhere in the cell. The most important and versatile of the activated carriers in cells is ATP adenosine triphosphate. Just as the energy stored in the raised bucket of water in Figure B can be used to drive a wide variety of hydraulic machines, ATP serves as a convenient and versatile store, or currency, of energy to drive a variety of chemical reactions in cells.

ATP is synthesized in an energetically unfavorable phosphorylation reaction in which a phosphate group is added to ADP adenosine diphosphate. When required, ATP gives up its energy packet through its energetically favorable hydrolysis to ADP and inorganic phosphate Figure The two outermost phosphates in ATP are held to the rest of the molecule by high-energy phosphoanhydride bonds and are readily transferred.

The energetically favorable reaction of ATP hydrolysis is coupled to many otherwise unfavorable reactions through which other molecules are synthesized. We shall encounter several of these reactions later in this chapter. Many of them involve the transfer of the terminal phosphate in ATP to another molecule , as illustrated by the phosphorylation reaction in Figure An example of a phosphate transfer reaction. Reactions of this type are involved in more ATP is the most abundant active carrier in cells.

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While we break with traditional views that simply equate organisms with biological individuals, or with living agents, we do think a sort of organism-centred view is a good start on the Problem of Biological Individuality cf. The intuitive idea behind a trait group is that demes can feature evolutionarily relevant structure wherein organisms belonging to one part of the deme are subject to causal influences that do not extend to the deme as a whole. Daniel McShea a,b; McShea and Changizi has proposed a structural hierarchy that is based on two components, the number of levels of nestedness and the degree to which the highest individual in the nesting is individuated or developed. The next distinguishing feature of organisms according to the Tripartite View, something that helps separate organisms from other living things, is that they have life cycles that allow them to form reproductive lineages of a certain kind. The challenge proposes that our studies focus not just on organisms, but instead on a variety of things that produce life through interactions. In the biosynthesis of macromolecules, this is accomplished by the transfer of phosphate groups to form reactive phosphorylated intermediates.

As one example, it is used to supply energy for many of the pumps that transport substances into and out of the cell discussed in Chapter It also powers the molecular motors that enable muscle cells to contract and nerve cells to transport materials from one end of their long axons to another discussed in Chapter But when the required product is Y and not Z, this mechanism is not useful.

A frequent type of reaction that is needed for biosynthesis is one in which two molecules, A and B, are joined together to produce A-B in the energetically unfavorable condensation reaction. The condensation reaction , which by itself is energetically unfavorable, is forced to occur by being directly coupled to ATP hydrolysis in an enzyme -catalyzed reaction pathway Figure A.

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An example of an energetically unfavorable biosynthetic reaction driven by ATP hydrolysis. A Schematic illustration of the formation of A-B in the condensation reaction described in the text. B The biosynthesis of the common amino acid glutamine. A biosynthetic reaction of exactly this type is employed to synthesize the amino acid glutamine, as illustrated in Figure B. We will see shortly that very similar but more complex mechanisms are also used to produce nearly all of the large molecules of the cell.

Other important activated carrier molecules participate in oxidation-reduction reactions and are commonly part of coupled reactions in cells. These activated carriers are specialized to carry high-energy electrons and hydrogen atoms. Later, we examine some of the reactions in which they participate. NADPH, an important carrier of electrons. A NADPH is produced in reactions of the general type shown on the left, in which two hydrogen atoms are removed from a substrate.

The hydride ion carried by NADPH is given up readily in a subsequent oxidation-reduction reaction , because the ring can achieve a more stable arrangement of electrons without it. The final stage in one of the biosynthetic routes leading to cholesterol. The difference of a single phosphate group has no effect on the electron -transfer properties of NADPH compared with NADH, but it is crucial for their distinctive roles.

The extra phosphate group on NADPH is far from the region involved in electron transfer see Figure B and is of no importance to the transfer reaction. Thus the two types of carriers are used to transfer electrons or hydride ions between different sets of molecules. Why should there be this division of labor?

The answer lies in the need to regulate two sets of electron -transfer reactions independently. NADPH operates chiefly with enzymes that catalyze anabolic reactions, supplying the high-energy electrons needed to synthesize energy-rich biological molecules.

NADH, by contrast, has a special role as an intermediate in the catabolic system of reactions that generate ATP through the oxidation of food molecules, as we will discuss shortly. Other activated carriers also pick up and carry a chemical group in an easily transferred, high-energy linkage Table For example, coenzyme A carries an acetyl group in a readily transferable linkage, and in this activated form is known as acetyl CoA acetyl coenzyme A.

The structure of acetyl CoA is illustrated in Figure ; it is used to add two carbon units in the biosynthesis of larger molecules. The structure of the important activated carrier molecule acetyl CoA. A space-filling model is shown above the structure. The sulfur atom yellow forms a thioester bond to acetate.

Because this is a high-energy linkage, releasing a large amount of free more In acetyl CoA and the other carrier molecules in Table , the transferable group makes up only a small part of the molecule. As with acetyl CoA, this handle portion very often contains a nucleotide , a curious fact that may be a relic from an early stage of evolution. It is currently thought that the main catalysts for early life-forms—before DNA or proteins—were RNA molecules or their close relatives , as described in Chapter 6. It is tempting to speculate that many of the carrier molecules that we find today originated in this earlier RNA world, where their nucleotide portions could have been useful for binding them to RNA enzymes.

Examples of the type of transfer reactions catalyzed by the activated carrier molecules ATP transfer of phosphate and NADPH transfer of electrons and hydrogen have been presented in Figures and , respectively. The reactions of other activated carrier molecules involve the transfers of methyl, carboxyl, or glucose group, for the purpose of biosynthesis. The activated carriers required are usually generated in reactions that are coupled to ATP hydrolysis, as in the example in Figure Therefore, the energy that enables their groups to be used for biosynthesis ultimately comes from the catabolic reactions that generate ATP.

Similar processes occur in the synthesis of the very large molecules of the cell—the nucleic acids, proteins, and polysaccharides—that we discuss next. A carboxyl group transfer reaction using an activated carrier molecule. Carboxylated biotin is used by the enzyme pyruvate carboxylase to transfer a carboxyl group in the production of oxaloacetate, a molecule needed for the citric acid cycle. As discussed previously, the macromolecules of the cell constitute the vast majority of its dry mass—that is, of the mass not due to water see Figure These molecules are made from subunits or monomers that are linked together in a condensation reaction , in which the constituents of a water molecule OH plus H are removed from the two reactants.

Consequently, the reverse reaction—the breakdown of all three types of polymers—occurs by the enzyme -catalyzed addition of water hydrolysis. This hydrolysis reaction is energetically favorable, whereas the biosynthetic reactions require an energy input and are more complex Figure Condensation and hydrolysis as opposite reactions. The macromolecules of the cell are polymers that are formed from subunits or monomers by a condensation reaction and are broken down by hydrolysis.

The condensation reactions are all energetically unfavorable. The nucleic acids DNA and RNA , proteins, and polysaccharides are all polymers that are produced by the repeated addition of a subunit also called a monomer onto one end of a growing chain. The synthesis reactions for these three types of macromolecules are outlined in Figure As indicated, the condensation step in each case depends on energy from nucleoside triphosphate hydrolysis.

And yet, except for the nucleic acids, there are no phosphate groups left in the final product molecules. How are the reactions that release the energy of ATP hydrolysis coupled to polymer synthesis? The synthesis of polysaccharides, proteins, and nucleic acids. Synthesis of each kind of biological polymer involves the loss of water in a condensation reaction.

Not shown is the consumption of high-energy nucleoside triphosphates that is required to more For each type of macromolecule , an enzyme -catalyzed pathway exists which resembles that discussed previously for the synthesis of the amino acid glutamine see Figure The principle is exactly the same, in that the OH group that will be removed in the condensation reaction is first activated by becoming involved in a high-energy linkage to a second molecule.

However, the actual mechanisms used to link ATP hydrolysis to the synthesis of proteins and polysaccharides are more complex than that used for glutamine synthesis, since a series of high-energy intermediates is required to generate the final high-energy bond that is broken during the condensation step discussed in Chapter 6 for protein synthesis.

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There are limits to what each activated carrier can do in driving biosynthesis. In these cases the path of ATP hydrolysis can be altered so that it initially produces AMP and pyrophosphate PP i , which is itself then hydrolyzed in a subsequent step Figure An important biosynthetic reaction that is driven in this way is nucleic acid polynucleotide synthesis, as illustrated in Figure An alternative route for the hydrolysis of ATP, in which pyrophosphate is first formed and then hydrolyzed.

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This route releases about twice as much free energy as the reaction shown earlier in Figure A In the two successive hydrolysis reactions, more In the first step, a nucleoside monophosphate is activated by the sequential transfer of the terminal phosphate groups from two ATP molecules. It is interesting to note that the polymerization reactions that produce macromolecules can be oriented in one of two ways, giving rise to either the head polymerization or the tail polymerization of monomers.

In head polymerization the reactive bond required for the condensation reaction is carried on the end of the growing polymer , and it must therefore be regenerated each time that a monomer is added. In this case, each monomer brings with it the reactive bond that will be used in adding the next monomer in the series.

In tail polymerization the reactive bond carried by each monomer is instead used immediately for its own addition Figure The orientation of the active intermediates in biological polymerization reactions. The head growth of polymers is compared with its alternative tail growth. As indicated, these two mechanisms are used to produce different biological macromolecules. We shall see in later chapters that both these types of polymerization are used. The synthesis of polynucleotides and some simple polysaccharides occurs by tail polymerization, for example, whereas the synthesis of proteins occurs by a head polymerization process.

Living cells are highly ordered and need to create order within themselves in order to survive and grow. This is thermodynamically possible only because of a continual input of energy, part of which must be released from the cells to their environment as heat. The energy comes ultimately from the electromagnetic radiation of the sun, which drives the formation of organic molecules in photosynthetic organisms such as green plants.

Animals obtain their energy by eating these organic molecules and oxidizing them in a series of enzyme -catalyzed reactions that are coupled to the formation of ATP—a common currency of energy in all cells.

The Biological Notion of Individual

To make possible the continual generation of order in cells, the energetically favorable hydrolysis of ATP is coupled to energetically unfavorable reactions. In the biosynthesis of macromolecules, this is accomplished by the transfer of phosphate groups to form reactive phosphorylated intermediates. Because the energetically unfavorable reaction now becomes energetically favorable, ATP hydrolysis is said to drive the reaction. Polymeric molecules such as proteins, nucleic acids, and polysaccharides are assembled from small activated precursor molecules by repetitive condensation reactions that are driven in this way.

Other reactive molecules, called either active carriers or coenzymes, transfer other chemical groups in the course of biosynthesis: NADPH transfers hydrogen as a proton plus two electrons a hydride ion , for example, whereas acetyl CoA transfers an acetyl group. By agreement with the publisher, this book is accessible by the search feature, but cannot be browsed.

Turn recording back on. National Center for Biotechnology Information , U. Garland Science ; Catalysis and the Use of Energy by Cells. Figure Order in biological structures. Cell Metabolism Is Organized by Enzymes The chemical reactions that a cell carries out would normally occur only at temperatures that are much higher than those existing inside cells. One of the most general of these issues is what we will call the Problem of Biological Individuality cf.

Clarke , , and we can express it in a number of different questions:. As will become apparent, addressing the Problem of Biological Individuality does not require an essentialist answer according to which biological individuals form a kind individuated by a set of singly necessary and jointly sufficient properties.

Indeed, biological essentialism is a view with little credibility in discussions of species and more generally amongst philosophers of biology Hull ; Sober ; cf. Responses to the Problem of Biological Individuality should clarify what relationship s hold between the category of biological individuals and the related categories of living thing, organism, evolutionary individual, developmental individual, and so on. For example, are biological individuals just organisms? Is there a nesting or some other hierarchical relationship between biological individuals and living agents?

Although there are semantic decisions to be made about how these terms will be used, those uses should also be assessed in part by the plausibility of the implications they hold for scientific methodology, evidence judgments, and prediction and explanation. To take a simple example, suppose someone proposes that all evolutionary individuals also called units of selection are organisms. Measuring fitness values to help predict trait frequencies of populations of evolutionary individuals in the future would then involve counting just all the relevant organisms.

This methodology will produce misleading predictions and evidence judgments about the course of natural selection, however, if groups in some contexts or genes in other contexts are also evolutionary individuals, as many have argued. Detecting the poor predictions or judgments would then tell against the initial claim that all evolutionary individuals are organisms.

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Taking biological individual as a quite general category that may subsume several kinds of biological individuals e. The first concerns individuality in general—what it is that makes anything an individual of any kind. The second aspect concerns biology in particular—what it is that makes an individual biological rather than, say, chemical or sociological.

When philosophers of biology discuss individuality they understand individuals to be distinct from other entities such as properties, processes, and events, even if certain say properties and processes are constitutive of some forms of individuality. Biological individuals have three-dimensional spatial boundaries, endure for some period of time, are composed of physical matter, bear properties, and participate in processes and events. Biological processes such as photosynthesis and biological events such as speciation lack such a suite of features.

A further feature often associated with individuals is agency: The sense in which biological individuals are agents is compatible with their also playing a more passive role in biological processes, or with their functioning as products rather than as causes of the evolutionary processes they are involved in. For instance, this notion of agency allows that some species and even larger clades are on some views of speciation and taxa ontology biological agents. This deflationary notion of agency is weaker and less controversial than the notion of agency that Peter Godfrey-Smith has challenged through his critique of rationalizing and optimizing approaches to explanation within evolutionary biology, approaches exemplified by Dawkins' [] classic appeal to selfish genes.

In fact, the conception of agency that we draw on is compatible with recognizing that the vast majority of biological agents are not psychological agents at all. It remains an interesting question as to why the use of cognitive metaphors in describing biological agency is widespread, if not ubiquitous R. Related issues that likewise are worth pursuing elsewhere include whether the agency of some biological individuals is determined partially by their context or relations to other things R.

Wilson , whether such agency is determined partially by our values or conventions Butler ; Keller ; Kitcher , and whether biological agency and reality can come in degrees Sober ; Godfrey-Smith ; Clarke With individuals understood as agents in our sense, what makes for distinctly biological individuals? Historically, however, there has been lumping together of or slides between three categories: One legacy of this has been a historical privileging of organisms in reflection on biological individuals more generally.

Consider two recent challenges to this privileging:. These are challenges to particular ways in which organisms have been thought special. Heeding what we think is right in these challenges, we next begin to articulate an answer to the Problem of Biological Individuality that proposes a different special place for organisms in reflection on biological individuals more generally. While we break with traditional views that simply equate organisms with biological individuals, or with living agents, we do think a sort of organism-centred view is a good start on the Problem of Biological Individuality cf.

Jagers op Akkerhuis On this view biological individuals include exactly:. We call this an organism-centred view because each of its three parts reference organisms cf. Pepper and Herron It allows that many biological individuals—for example, hearts and populations—are not themselves organisms. And it allows us to recognize a thing as a biological individual even when we are not sure whether it is an organism, or a part of an organism e.

Organism-centered views of biological individuality seem widely, if implicitly, endorsed, though confusing choices of terminology can conceal this.

Cell Metabolism Is Organized by Enzymes

To see how an organism-centred view captures something striking about organisms without running afoul of A and B , take those challenges in turn. A 's challenge to historical privileging of organisms addresses the methodological question of how to study life. The challenge proposes that our studies focus not just on organisms, but instead on a variety of things that produce life through interactions. This methodological prescription is based on answers to other questions, e.

How Energy and Information Control the Living World

Although an organism-centered view and Challenge A directly address different questions, they in fact can be viewed as fitting together nicely. Both are based on rejecting the ideas that only organisms are biological individuals, that only organisms are alive, and that only things that are alive are biological individuals. The methodological reorientation that A proposes does little by way of challenging an organism-centered view of biological individuals. Challenge B raises the question of which biological individuals are paradigmatic.

Based on the number of traditionally excluded things this lets in, and on the differences between those and organisms themselves, an organism-centred view could allow that organisms are no longer paradigmatic biological individuals. It is simply that, conceptually or metaphysically, all biological individuals either are organisms or are importantly related to them on one of the two ways specified: For this reason, understanding the nature of organisms and their relations is central to understanding biological individuality even if organisms represent just a fraction of the biological individuals there are, or are an idiosyncratic subset of biological individuals.

As promising as an organism-centred view of biological individuality is, its initial formulation does not specify which parts of organisms are biological individuals and which are not; likewise for groups of organisms. And it says nothing about what an organism is. We need to address these issues. To do so we must first reflect on the heterogeneity one finds in the biological world. At the outset we emphasized the diverse variety of biological individuals.

One can think of this diversity as consisting in significant differences between kinds of biological individuals. But striking diversity in the living world also exists within biological kinds. Within the category organism , for instance, there is astonishing diversity. Likewise within other putative kinds of biological individual: This diversity within biological kinds has been labeled intrinsic heterogeneity because it seems part-and-parcel, and distinctive, of those kinds and how they are theorized in the biological sciences R.

Intrinsic heterogeneity is manifest most clearly in the centrality of population thinking in evolutionary biology. Natural selection acts on variation within a population of individuals. As Elliott Sober has argued , in the physical sciences and in pre-Darwinian biology, variation was understood as deviation from a natural or normal state, whereas in the post-Darwinian era, and especially through the Evolutionary Synthesis, variation came to be viewed as prodigious and itself crucial to the underlying causal mechanisms at the heart of biological stasis and change.

Rather than being explained away, variation goes all the way down and does much explaining. But intrinsic biological heterogeneity isn't restricted to evolutionary biology. The geophysicist Walter Elsasser drew this out in his Atom and Organism with the contrast between physical and biological kinds see also Elsasser , Roughly put, the chief idea is that if you've seen one electron or quark or boson you've seen them all.

Although there are differences between instances of any two individuals in accord with Leibniz's Law , these are differences that do not matter for physical kinds. What physicists and chemists do is abstract away from such differences, treating any instance like any other. By contrast, this is not true in the biological sciences. If you've seen one tiger or vertebrate or coral reef you have not seen them all, for there are differences between instances of any of these biological kinds that remain significant in some cases, central for the articulation of biological knowledge.

If Elsasser's general contrast obtains, then we should expect to find manifestations of intrinsic heterogeneity throughout the biological sciences. Various forms of pluralism have become increasingly popular approaches to handling intrinsic heterogeneity, responding to the difficulty that intrinsic heterogeneity presents for characterizing some kind K by moving on to characterize finer-grained, more determinate kinds.

If K seems too diverse to characterize, split it into diverse sub-kinds and characterize each of those. A ramet is what we might readily identify as an individual plant; a genet is a collection of ramets that propagate, as is often the case, through the clonal growth of a particular ramet. How many plants there are, in many cases, depends on whether we mean ramets or genets. For example, while each of the trees in an aspen grove that forms clonally is a ramet, collectively they typically form a single genet. A pluralist might prefer a description cast in terms of ramets and genets over any attempt to answer the question of how many plants or organisms per se there are in this case.

One reason to instead or additionally explore monistic approaches to biological individuality is that intrinsic biological heterogeneity should lead us to suspect that the pluralistic splitting of concepts will simply turn up more heterogeneity. This may be why pluralism in biology seems never to end conceptual disputes Clarke ; cf. A second reason to do so is the frequently overlooked fact Brigandt that monist and pluralist approaches are often compatible, even complementary. Monists can quite happily recognize as correct, useful, or legitimate, multiple categories that result from splitting K , while still attempting to elucidate K as an umbrella or genus category or even a less neatly related category.

Splitting the category tools into hammers , saws , and others doesn't thereby impugn tools as a category. The two pluralism-compatible ways in which we advocate monism concern, respectively, approaches to concepts of biological individuality in general, and to the concept of organism in particular. Regarding the first, we encourage attempts to retain concepts of biological individuality when apparent counterexamples to their definitions arise from intrinsic heterogeneity.

To see this, consider a particular concept of biological individuality, Godfrey-Smith's notion non-marginal evolutionary individual. Ereshefsky and Pedroso interpret Godfrey-Smith as implying a certain necessary condition on being such an individual: A genetic bottleneck event is a narrowing between generations. Any human individual, for example, is typically the product of such a bottleneck, as he or she develops from a single cell a zygote in which maternal and paternal genetic material is combined.

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Ereshefsky and Pedroso marshal biofilms as a putative counterexample to this necessary condition on being a non-marginal evolutionary individual. Biofilms, they argue, are non-marginal evolutionary individuals despite not satisfying the bottleneck condition. A pluralist might accept this as a counterexample, then consequently move from non-marginal evolutionary individual to two finer-grained concepts, one associated with genetic bottlenecks and the other with cases like biofilms. But the ecumenical monist option is to allow that a pluralistic focus on more specific concepts may be fruitful, while denying that biofilms are a counterexample.

Put differently, the monist can retain the initial concept of non-marginal evolutionary individuality while conceding that such individuality can be realized in more than one way. This is an attractive option when there is some good theoretical reason for retaining the initial concept. In the present case, Godfrey-Smith argued for the bottleneck condition on the basis that non-marginal individuals are the kinds of things that form populations in which selection can produce evolutionary novelty.

Production of such novelty is important enough, he contends, that whatever mechanism enables this should count as a constitutive factor one satisfied to degrees of being a non-marginal evolutionary individual. We can agree with both this, and with Ereshefsky and Pedroso's insistence that bottlenecks are not the only novelty-creating mechanism.

They are not the only such mechanism because biofilms enjoy novelty creation by lateral gene transfer rather than bottlenecks. What is right about pluralism here is that there are at least two distinct mechanisms rather than one. What is right about monism is emphasizing that the two mechanisms play the same theoretically important role—helping generate evolutionary novelty.

This role helps distinguish the concept non-marginal evolutionary individual that the monist retains as theoretically important, while encouraging pluralist exploration of distinct mechanisms.

Pluralism and monism of these sorts are not just compatible, but complementary as well. The exploration of mechanisms helps us better articulate their shared role and the concept of non-marginal evolutionary individual; in turn, this helps guide further exploration of associated mechanisms. This is one way in which interplay between conceptual and empirical work, exemplified in our introduction, is manifest when exploring various sorts of biological individuality. In the next section we elaborate the second way we advocate monism.

This way involves developing an account of being an organism that accommodates intrinsic heterogeneity by drawing on the Homeostatic Property Cluster HPC view of kinds. This view has been widely discussed with respect to biological species Boyd a,b; Griffiths , ; R. Ereshefsky ; Ereshefsky and Matthen , but has also been introduced in accounts of higher taxa, homology, and cell types Assis and Brigandt ; Rieppel a, b, ; Wilson, Barker, and Brigandt Although this view of kinds fits with some forms of pluralism, it is motivated by a distinctive response to intrinsic heterogeneity.

Confronted by Elsasser's point that intrinsic heterogeneity is something about biological kinds to be captured rather than overcome, the HPC view responds with naturalistic humility: Our account of being an organism is called the Tripartite View of Organisms R. At its core are the explicit claim that organisms are a type of living thing or individual or agent , and the implicit claim that this kind is central to the biological sciences.

Additionally, organisms are distinguished from other living agents by two properties: In summary, the Tripartite View holds that any organism is physically continuous and bounded and is:. Empirical facts and findings continually inform the definition and to see what a good definition might look like consider the following structural, functional, and relational properties possessed by living things. The fundamental, general feature of HPC views of kinds concerns how an HPC kind term is defined by a cluster of properties rather than any one property. No one property in the definitive cluster need be possessed by any individual belonging to the kind, but each individual must have one of the n -tuple of properties in the cluster that is sufficient for belonging to the HPC kind.

What features or implications of the HPC view of kinds are important for understanding its application to the case of living things? First, defining a kind term by a property cluster , rather than a single property, as HPC views do, acknowledges a complexity to the structure of entities that fall under the biological kind living thing. While the view allows that there may though needn't be some properties in the defining cluster that all living things share e. Second, implying that no one of the properties in a given definitive cluster is strictly necessary for an individual to belong to the corresponding HPC kind recognizes the intrinsic heterogeneity of entities subsumed under living thing.

For instance, this accommodates biological individuals that don't reproduce e. Third, the HPC view doesn't conceptualize a definitive cluster of properties as simply those properties that each kind member typically coinstantiates. Rather, coinstantiation of properties in the cluster is reliably underwritten by specific causal mechanisms and constraints.

This gives definitive clusters their homeostatic character, and ensures the causal structure of the world plays a significant role in determining what is and what is not an HPC kind. Consequently, whether something is a living thing is determined in significant measure by how the mind-independent world is, rather than simply by our conventions and categories for thinking about the world Wilson, Barker, and Brigandt This is one thing that distinguishes the HPC view from Wittgensteinian family resemblance accounts of concepts and from subjective taxonomies, such as pheneticism about species Sokal and Sneath ; Sokal and Crovello Suppose that organisms are living agents, and that we accept the HPC view of living agency.

This tells us something significant about what organisms are. But as section 4 suggests, it would be a mistake simply to identify organisms with living agents. Doing so would have problematic implications, chief among them being that only organisms are living agents. Implying that only organisms are living things is hopeless in light of counter-examples, namely, entities that form parts of organisms. These include cells and the organelles they contain such as mitochondria and ribosomes , bodily organs such as the heart or kidney , and bodily systems such as the digestive system or the circulatory system.

Such entities have the structural, functional, and relational properties specified in the HPC definition given above, but they are not themselves organisms. Closest to our commonsense thought is the second of these, where we readily speak of an organ that is available to be transplanted from a dead person to living recipient as living or alive. Once a reactant molecule absorbs enough energy to reach the transition state, it can proceed through the remainder of the reaction.

Activation energy and reaction rate. The activation energy of a chemical reaction is closely related to its rate. Specifically, the higher the activation energy, the slower the chemical reaction will be. This is because molecules can only complete the reaction once they have reached the top of the activation energy barrier. The higher the barrier is, the fewer molecules that will have enough energy to make it over at any given moment. Why do some molecules have more energy than others?

At a particular temperature, individual molecules in a sample will have a range of different kinetic energies — temperature is just an average value. This means that some fraction of molecules in a population will be able to make it over an activation energy barrier, but if the barrier is high, this fraction may be tiny. In this case, the reaction will be very slow: Many reactions have such high activation energies that they basically don't proceed at all without an input of energy. For instance, the combustion of a fuel like propane releases energy, but the rate of reaction is effectively zero at room temperature.

To be clear, this is a good thing — it wouldn't be so great if propane canisters spontaneously combusted on the shelf!