Chapter 4: The Living World

Section 4.1 Hierarchical Structure

Section 4.2: Complex Organisation

Section 4.3: The Major Principles

Section 4.4: The Variety of Life

Section 4.5: Ecosystems and the Biosphere

Section 4.7: Complicated versus complexity

This chapter considers the way complex hierarchical structures are built up from the basic physical components described in the last chapter. The ability of fundamental particles to form these coherent complex structures is the basis of life. However they also live in complex environments - ecosystems and the biosphere, enabled by the conditions existing on the surface of the planet Earth.

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Section 4.1 Hierarchical Structure

The matter comprising the living world has a hierarchical structuring as follows, where we assume the bottom layers (underlying the atoms that form the chemical elements) as in the last chapter:

Hierarchical structure of life	Hierarchical structure of functioning
The biosphere	Global resource cycles
Biomes	Energy and material interchange
Ecosystems	Species interdependence
Animal populations	Competition and the food chain
Individual organisms and animals	Physiological functioning
Limbs and physiological systems	Organism homeostasis
Tissues	Growth, maintenance, repair
Cells	Growth, specialisation, death
Organelles	Cell homeostasis
Macro Molecules	Folding, recognition, binding
Building Block Molecules	Combine to form polymers
Chemical elements	Chemical binding

Table 4.1: Hierarchical nature of living systems

This Chapter will examine this hierarchical structuring, looking at the nature of what exists at each level firstly in terms of how it behaves - the kinds of concepts and behavioural patterns occurring at that level - and secondly at the diversity of what exists at that level. It will also consider how causal properties at the different levels relate to each other.

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Section 4.2: Complex Organisation

The basic laws of behaviour and composition of matter determine the structure and nature of the components that make up all natural and designed objects around us. Thus they fundamentally determine what is possible and what is not: all these interactions must obey the principles explained in the previous Chapter, in particular the First and Second Laws of Thermodynamics (i.e. conservation of energy and increase of entropy).

The particles and forces considered in the previous chapter provide the basis for complex organisation, and in particular for the functioning of living organisms, through their ability to form hierarchical structures that can store and utilise information in hierarchical feedback control systems.

The question is how the fundamental laws just discussed permit and enable the behaviour of complex objects. The way this happens is summarised beautifully in [webpage], giving an overview of the way biological complexity is organised and functions. Complex functionality is made possible by the hierarchical structuring of complex systems (motorcars, aircraft, computers, trees, animals, etc.). In particular, this is the basis of order in living systems [49], as summarised in Table 4.1.

4.2.1 Biomolecules

The great surprise has been that this applies to living beings as well as inanimate objects. Living plants and animals are based on the same material substratum as rocks and planets. Although they can reach immense complexity, all the molecules underlying life are constructed from only a few small building block molecules, in turn constructed from a few elements only (C, O, N & S), see [webpage].

Macromolecules. A fundamentally important group of biomolecules are macromolecules. These are really molecules of molecules, that is, just as simple molecules are assemblages of atoms, macro molecules are polymers: assemblages of simpler building-block molecules called monomers. The building blocks are

nucleotides (pyrimidines and purines),
amino acids,
monosaccharides (glucose and ribose),
fatty acids,
glycerol.

They are assembled together with a basic underlying repetitive pattern through carbon bonding (see [webpage] Polymers - The most important molecules of life).

Assembly is by a process known as dehydration synthesis, the net effect of which is removal of a water molecule (H₂O) for each monomer added to the chain, one molecule contributing a hydroxyl group (OH^-) and one losing hydrogen (H⁺). The process expends energy, needed to form the bonds, and only occurs through the help of organic catalysts (enzymes). They are disassembled by hydrolysis, which is essentially the reverse process: bonds between monomers are broken by addition of water molecules, a hydrogen ion from the water attaching to one monomer and a hydroxyl ion attaching to the adjacent monomer; energy i sgiven off in the process. An example is digestion of food, breaking down polymers to monomers that are then distributed via the bloodstream to the cells of the body.

The four classes of macromolecules are nucleic acids (DNA), proteins, polysaccharides and lipids (c.f. [6], pp.207-213, and [webpage]).

Nucleic acids store information. The most important are DNA, responsible for genetic information storage, and RNA, responsible for transmission of this information. DNA is constructed from four bases (nucleotides) represented by the letters A,G,C and T, attached to twin spiral backbones made of sugars, see [webpage].
Proteins are operational molecules (`molecular machines'). They are constructed from twenty amino acids; linear head-to-tail assembly of these amino acids gives rise to an immense number of different proteins, folded in complex ways. They perform all the functional operations necessary for the living state [webpage], comprising structural proteins (keratin, collagen, etc) and functional proteins (insulin, rhodopsin, myosin, etc).
Carbohydrates, including Polysaccharides, are polymers of sugars; they include starch and cellulose, taking part in energy storage and cell structure.
Lipids are formed from glycerols and fatty acids; they also take part in energy storage and cell structure. Complex lipids contain fatty acids while simple lipids (including vitamins and hormones) do not.

They are immensely complex because they are comprised of so many atoms, joined together in a way that forms very complex folding patterns (For diagrams of the molecules of life see the sources at [webpage].)

Carbohydrates are sugars and their polymers. Polysaccharides consist of long strings of covalently linked sugars (aldehydes and ketones). The most important sugar is glucose (C₆H₁₂O₆). Starch and glycogen are storage polysaccharides; cellulose is the most abundant cell-wall and structural polysaccharide.

Lipids do not mix with water. Complex lipids include fats, constructed from glycerol and three fatty acids (saturated and unsaturated), and used for energy storage; phospholipids, also made of glycerol and fatty aids but with a phosphate group replacing one fatty acid, and used in cell membranes. simple lipids include steroids, such as cholesterol, forming important hormone-like compounds, and terpenes.

Nucleic Acids include DNA and RNA. One of the most amazing information stores is the molecule DNA occurring as polymers of nucleotides, each of which is composed of three parts: a nitrogenous base bonded to a ribose (a 5-carbon sugar) bonded to a phosphate group. DNA is composed of two complementary spirals with a sugar-phosphate backbone [webpage]. To each strand is attached a sequence of the bases T (thymidine), C (cytidine), both pyramidines, and A (adenosine), G (guanosine), both purines. These bond to each other in complementary pairs, which bind only to each other: Adenine always bonds with Thymine, Guanine always bonds with Cytosine. The order in which they occur along the DNA backbone containing large amounts of digitally coded instructions for constructing living organisms.

Segments of DNA are functionally characterised as genes, coding for production of specific proteins (the process of `gene expression', controlled in a complex way by molecular mechanisms [ webpage]); genes are however separated by large sections of `junk DNA' that does not appear to code for any specific proteins. RNA is a similar but smaller molecule, with Thymine replaced by Uracil (U) and ribose by deoxyribose. When a segment of DNA is readout with the assistance of mRNA, triplets of the bases (`codons') specify one of 20 amino acids according to a universal genetic code [webpage]; these are then strung together to make a specific protein according to the sequence of codons occurring in the DNA (see [6], pp.234-237, and [webpage]). DNA replicates by separation of the twin spiral strands and then attachment of new complementary bases on each separated strand. The unique pairing of the bases (A <-->T, G <--> C) enables reliable replication of the genetic information (in complementary form) in the new strand.

Proteins are synthesized from their 20 possible amino acid components linked by peptide bonds to form a polypeptide chain, and then fold to act as either structural proteins or enzymes (catalysts). They spontaneously curl up and fold into specific stable three dimensional structures, the precise geometry of which is determined by the particular sequence of amino acids in its polypeptide chain. Thus,

· The one-dimensional information in DNA is translated into 3-dimensional macro-molecular components of living organisms by translation of DNA structure into protein structure.

Proteins may be,

· Structural proteins (e.g. alpha-keratin, collagen), providing support,

· Contractile proteins (e.g. myosin and actin), providing movement,

· Transport proteins (e.g. hemoglobin and myoglobin), transporting other substances,

· Storage proteins (e.g. ovalbumin), storing amino acids,

· Enzymes (e.g. hexokinase), regulating cell chemistry,

· Hormones (e.g. insulin, growth hormone), coordinating bodily activities,

· Antibodies, combating bacteria and viruses,

· Toxins (e.g. diptheria toxin, snake venom).

Through their folding, enzymes bind to a substrate that recognizes only them, because the active site of the enzyme molecule fits the substrate with a near perfect lock-and-key complementarity; thereby they control further reactions. They function as highly specific catalysts capable of greatly enhancing the reaction rates of specific chemical reactions. The specificity of enzymes is a particular case of specificity of molecular interactions in cells, and illustrates one of the great principles of cell biology:

· The specificity of cellular molecular reactions results from the structural complementarity of the interacting molecules.

The number of possible macro-molecules is immense, e.g. even for a small chain of 112 molecules the possibilities are about 10¹¹⁰, much greater than the numbers that characterise astronomy, which are of the order of 10⁸⁰ (the number of protons in the visible universe) and less (Elsasser, see the discussion in Stairway to the Mind by Alwyn Scott, page 20). Thus chemists will never be able to explore more than a small fraction of all organic molecules - there simply will not be enough time available. It is these immense numbers that also underlie the almost endless possibilities of structure in the living world.

Energy flows in cells are facilitated by chemical energy stored in the compound adenosine triphosphate (ATP). As ATP transfers energy to other molecules, it loses its terminal phosphate group and becomes adenosine diphosphate (ADP) - the discharged or energy-poor version of ATP. In turn ADP can accept energy again by regaining a phosphate group to become ATP, at the expense either of solar energy or of chemical energy stored in molecules such as glucose.

Metabolism is the process of processing nutrients and constructing needed materials. Catabolism is the breaking down of complex nutrient molecules (carbohydrates, lipids, and proteins) to yield simpler molecules (lactic acid, acetic acid, CO₂, ammonia, urea), accompanied by the release of the binding energy of the complex molecules. Anabolism is the building up of needed macromolecules from their simple building block precursors. This takes place stepwise through many intermediary steps; each pathway consists of a sequence of enzyme-catalyzed reactions. The intermediary products of metabolism are called metabolites and the whole is called intermediary metabolism [webpage]. Altogether it is a three stage process, as summarised in the following table:

Metabolism stages

	Proteins	Polysaccharides	Lipids
Stage I	ATP --> ADP + P_i
	Amino acids	Hexoses, Pentoses	Fatty acids, glycerol
Stage II	ATP --> ADP + P_i, Pyruvate, ADP + P_i --> ATP
	Acetyl-CoA
Stage III	The Krebs cycle, ADP + P_i --> ATP
	NH₃	H₂O	CO₂

Table 4.2 Metabolism: Catabolic (biodegrading) pathways move downwards, converging to common simple end products and leading to ATP synthesis in stage III. Anabolic (biosynthesis) pathways move up, starting from a few precursors in stage III and utilising ATP energy to yield many different cell components [Lehninger Biochemistry, p.372]

The process is centred on the citric acid cycle or Krebs Cycle [webpage]. This begins after molecules of sugar produced in glycolysis are converted to a slightly different compound (acetyl CoA). Through a series of intermediate steps, several compounds (NAD and FAD) capable of storing "high energy" electrons are produced along with two ATP molecules. These compounds carry the "high energy" electrons to the next stage. This cycle occurs only when oxygen is present but it doesn't use oxygen directly. It is a universal feature of all cells.

One of the remarkable features that has been discovered through the development of molecular biology is that the molecular mechanisms are remarkably similar in all living beings. In particular,

All life is based on the same biochemical processes and on the same genetic code.

This uniformity has to be explained in evolutionary terms - there has been a common historical origin for all life- because the information in the DNA contains within itself a historical record of the evolutionary process that has led to our existence; it is our genetic heritage resulting from that process. It functions within the context of the living cell, the smallest unit of life, and replicates itself when cells divide through a process of unwinding the twin spirals of the DNA and then duplicating each separate strand through the action of remarkable molecular machines in the cell.

4.2.2 Cells

Cells [webpage] [webpage] are self-assembled arrays of biomolecules comprising all the machinery needed for functioning and replication, suspended in an aqueous environment contained within a membrane(the cell wall). They are the basis of all life:

· All living things are made from cells, the chemical factories of life ([6], p.206)

Living plants and animals are vast cooperative assemblages of cells. Numerous internal structures and thousands of feedback loops maintain each cell in its general task of supporting the chemical reactions necessary for life and the specific task of carrying out particular functions according to its type. Cells use energy to process information and communicate with each other, while the physiological macro-structure of the plant or animal ensures they receive the nutrients they need to survive and their waste products are removed. Thus the physiological systems of living animals both depend on their component cells for their functioning and nurture those cells at the same time.

Organelles :Cells contain organelles- membrane-bound structures with specialized functions [webpage]. [webpage] They carry out the basic functions needed to enable the cell to survive and reproduce [webpage]. They include

the nucleus (containing the cell's DNA),
mitochondria (provide energy needed for cell function),
the endoplasmic reticulum (an extensive membrane system, the site of steroid production and contains enzymes),
numerous ribosomes (synthesise proteins),
the Golgi body (modifies fats and proteins),
Lysosomes (contain enzymes),
Centrosomes (help form microtubules needed during cell division),
Microtubules (form the skeleton of the cell).

For excellent microscope pictures see: nucleus and microtubules [webpage], actin and microtubules [webpage], nucleus and actin [webpage], endoplasmic reticulum [webpage], golgi apparatus [webpage].

Cell Types: The major division is that Eukaryotic cells contain a central nucleus, but prokaryotic cells have no nucleus [webpage]. There are five basic cell types, corresponding to the fine main kingdoms of living things [webpage], [webpage]:

The basic cell types

· animal cells: eukaryotic cells with mitochondria, endoplasmic reticulum and ribosomes, golgi bodies and lysosomes

· plant cells: also have chloroplasts, allowing photosynthesis, a cell wall, and a vacuole (a large fluid filled space storing nutrients)

· fungi cells: eukaryotic cells forming multicellular threads with many nuclei

· protista cells: ekaryotic cells forming single-celled organisms

· prokaryotic cells: no definite nucleus, mitochondria or chloroplasts

In plants and animals, cells take a variety of forms, differentiated through the processes of developmental biology [52] as the organism grows. There are over 200 types of cells in the human body, that vary greatly in size, shape, and function (see e.g. [webpage]), with each cell specialised to perform specific functions, for example neurons are cells specialised to process information in the brain. Other cells form skin, bone, eyes, blood, and so on, the whole patterned according to positional information that is utilised in reading off from the DNA instructions to make specific proteins.

Reproduction: One of their most important properties is that they can reproduce by cell division, producing two identical cells where there was previously one in the case of mitosis [webpage] [webpage]. During this process the chromosomes, containing the genetic information for the plant or anima concerned, are copied and duplicated, so that each daughter cell has the same genetic information as the parent. During sexual reproduction, on the other hand cell division takes place by meiosis [webpage], and genetic information from two cells (one from each parent) gets mixed - playing a crucial role in the evolutionary process ([6], pp.35-237).

The crucial link: Cells form the crucial link between the micro (biochemistry) and macro (living animals and plants) by providing the environment where crucial energy utilising processes take place in a controlled way.

"The basic living unit of the body is the cell. Each organ is actually an aggregate of many different types of cell held together by intercellular supporting structures. Each type of cell is specially adapted to perform one particular function ...however all cells utilise almost identically the same types of nutrients . All cells use oxygen as one of the major substances from which energy is derived. The basic mechanisms for changing nutrients into energy are basically the same in all cells, including as a key feature the complex processes of intermediate metabolism, and all cells also deliver the end-products of their chemical reactions into the surrounding fluids".([52a], p 3)

They are indeed complete living systems. In the case of unicellular animals, they are viable on their own; in the case of multi-cellular animals, they rely on the body in which they live for their survival.

4.2.3 Tissues

Different cell types are used to make the different kinds of tissue [webpage], [webpage]: the main types are

Epithelial tissue covers body surfaces and lines body cavities,
Connective tissue, binding, supporting, and protecting ,
Cartilage, rigid connective tissue,
Bone, rigid connective tissue forming skeleton ,
Blood, connective tissue in fluid form containing red blood cells (transport oxygen) and white blood cells (functioning as part of immune system),
Muscle, made of muscle fibers, enables movement of animals. May be skeletal (striated), smooth, or cardiac,
Nervous tissue, made of neurons (cell body, axon, dendrites as discussed below) and glial cells.

The tissues form the basis for organ systems [webpage], [webpage] which together form the organism.

4.2.4 Organisms

All life around us is built on the same principle: apart from single-cell organisms such as bacteria,

Organisms are built up by combining cells into tissues which form a set of interlocking structural and physiological systems working in harmony with each other.

The complexity of what is achieved here is extraordinary: for example the human body comprises about 10¹³cells , of which about 10¹¹are in the brain [webpage]. Specifically, there

Human Physiological systems
The musculoskeletal system.	[webpage].
The integumentary system - the skin	[webpage].
The circulatory system	[webpage].
The respiratory system	[webpage]
The digestive system	[webpage]
The excretory system	[webpage]
The endocrine system	[webpage].
The nervous system and sensory system	[webpage].
The immune system	[webpage].
The reproductive system	[webpage]

Table 4.3: The main human physiological systems.

In a little more detail:

1. The musculoskeletal system.

- Basic mechanical structure and motor function through muscular and skeletal system [webpage].

2. The integumentary system - the skin

The skin provides the boundary of the body and controls interactions with the environment [webpage].

3. Transport systems: nutrients, waste products

- Circulatory system (blood): heart, arteries, veins, including regulation of blood pressure [webpage].

- Respiratory system and lungs: breathing, transport of oxygen and carbon dioxide [webpage].

- Digestive system: gastrointestinal tract and liver: eating and drinking [webpage].

- Removal of metabolic end products: kidneys, excretory system [webpage].

4. The immune system - protection against biological attack by invading organisms

- provides innate immunity, and acquired immunity through antibodies and sensitized lymphocytes [webpage].

5. The reproductive system (male and female)

- enabling continued existence of species [webpage].

There are two major control systems:

6. The hormonal system of regulation (the endocrine system)

- concerned with control of the metabolic functions of the body, controlling the rates of chemical reactions in the cells, transport of substances through cell membranes, and cell growth and secretion [webpage]. This is the first major way that top-down action takes place from the brain to all the cells in the body.

7. The nervous system and brain - cerebral function

- basically an information processing and storage system, enabled by vast numbers of neurons connected together via synapses, the specific information processing carried out by the brain being coded in a specific pattern of neuronal connections [webpage].

- functions by controlling muscles throughout the body (motor control), enabled by specific connections from the brain to individual muscles; ; this is the second major way that top-down action takes place from the brain to all the cells in the body.

- controls rapid functions of body through three major levels of function: the spinal cord (providing relatively simple reflexes and motor function), the lower brain level, and higher brain (cortical) level, providing intellectual functions (thoughts, memory, learning, consciousness) and behaviour.

- the autonomic nervous system provides the visceral functions of the body that are carried out unconsciously, for example temperature regulation.

The sensory system - information input

- the function of the nervous system and brain is enabled by information provided by the sensory system (which is perhaps a subsystem of the nervous system, but deserves recognition in its own right):

1. eyes (sight),

2. ears (hearing),

3. tongue (taste),

4. nose (smell),

5. inner ear (balance),

6. skin (pressure, texture, heat and cold, pain)

These are enabled by a variety of sensory receptors. A key element is that these channels provide a vast amount of sensory input all the time, and the brain discards vast amounts of information as irrelevant through a process of pattern-matching that selects what is important and what is not.

These systems are all interrelated through mechanical, chemical (including hormonal), and electrical interconnections, and usually work in harmony with each other under the overall supervision of the brain- an amazing engineering achievement. They enable energy storage and usage, carefully directed and timed on the basis of stored information together with current inputs of information from the environment. The functioning of life is a far from equilibrium process that is not statistical in nature. It has its own unique character.

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Section 4.3 The major principles

The great achievement in both natural complex systems and human-made ones, is reliable operation. This is true in engineering systems such as cars and aircraft, television sets and computers, and so on; and equally in living systems, which by and large grow, function, and heal themselves with a perfection of design and operation that becomes more and more astonishing the more one studies the complexity of the interlocking mechanisms at work. It is true that in both cases (engineering and natural systems) there are malfunctions and break downs when something is not working properly, particularly as they age and the parts start to wear out; but even this language emphasizes the extraordinary achievement: we expect them to function properly, and regard it as a breakdown of what should occur when this is not so. They function as expected provided the component parts are not defective, and have been connected up correctly. They have a finite lifetime, however: it has not been found possible to design complex systems that will function for ever. At a fundamental level this is because of the second law of thermodynamics, but one can also argue that death plays a fundamentally necessary role in complex biological systems: it is a required part of the natural order that the old generations give way to the new, life arising from death.

Whether this is so or not, it is not surprising that in systems of such complexity problems eventually arise; rather the present challenge is to understand how they can function at all. We are facing here the problem of synthesis: combining parts together to form a complex system that functions coherently. There are some basic principles at work in such systems allowing this to happen, allowing for the fact that they have to function within the constraints implied by their physical underpinnings, namely firstly they are subject to the laws of mechanics and secondly subject to the laws of thermodynamics. These further principles are:

Basic Principles of Complex Systems

Implications

L1: Bounded structured system with

interdependency and interrelationships

Enables identity and continuity

with specialised functions and behaviour

L2: Organised hierarchically;

- Both bottom-up and top-down action

Enables complex structure

- Enables emergent behaviour

L3: Open systems with matter and energy

internal flows and external exchanges

Enables growth and continued functioning

- Ingestion, transport, disposal

L4: Organised information/information flows

- Feedback control/homeostasis

Enables focussed and informed response

- Enables stability of systems

L5: Reproduction development and death

- the life cycle

Enables long term survival of species

- short term adaptation to environment

L6: Ecosystem Resource Cycles

Enables long term functioning of system

L7: Evolutionary origin

Historical origin of complex functionality

Table 4.4: The basic principles underlying complex systems.

These features will be discussed in turn.

4.3.1 Principle L₁: Bounded structured systems with interdependency

Living organisms are complicated and highly organised. They have definite boundaries marked by specific structures (cell walls, tree bark, animal skin), and so are bounded systems. They have structural elements (cytoskeleton, exoskeleton, skeleton) that order and maintain the basic structure. Each component of a living organism appears to have a specific purpose or function. Together these interrelated structures with specialised functions enable overall identity and continuity, with characteristic specific high level behaviour patterns. The lower level structures support and enable the higher level structure, which in turn provides the lower level systems the conditions they need in order to function.

4.3.2 Principle L₂: Hierarchical order

This order is based on the hierarchical nature of complex systems, implemented as a hierarchy of structural levels. A motorcar is made up of a set of parts (an engine, a gear box, a suspension, a chassis) each of which is made of smaller parts (the engine is made of a camshaft, four pistons, a cylinder block, and so on; the electric system is made of a generator, a battery, a wiring system, a regulator, etc.); each of these in turn is made of its components (the generator is made of a rotor, a stator, ball bearings, etc.). We can readily understand the functioning of the car through understanding this hierarchical design. The success of modern computers is based on the strict hierarchical design of both the hardware (the computer itself) and the software (the programs that run on it). Thousands of transistors, resistors and capacitors in printed circuits make up the central processing unit, the memory units, the display controller, the disk controller, and so on; these function together as a useful computer because the programming languages are arranged in a hierarchical way, the application programmes being written in high-level languages (relatively easily understood) which are based on assembly language (more difficult to read), which in turn is based on machine code (which is very hard to use for direct programming).

In each case one assembles the next layer of structure out of components whose behaviour can be understood separately; these are then connected together in a way that embodies the structural design of the system. One does not need to know the interior structure of each component in order to use it, but only has to understand it as a "black box", i.e. a component with unknown inner workings but predictable exterior behaviour. For example I do not need to know all about the internal structure of a battery in order to know how to use one in a motor car. Each component has a specific purpose, fulfilled if it has predictable behaviour as desired, and so is designed to have precisely this right behaviour. It fulfils this purpose if it is "wired in "in the right way at the right place (the battery needs to be connected in to the electrical system, not to the radiator). In this way we can build immensely complex objects such as a jumbo jet: every single part of such an aircraft has been specifically designed by someone for a particular purpose, and all the thousands of parts are integrated to work as a whole.

The function of each part can be identified and encoded in a suitable name(the wing, the engines, the undercarriage, the instrument panel, and so on);the key to understanding the whole is to focus successively on each level of design and understand it at that level, starting at the broadest level (the system as a whole) and working down to the level of detail needed. If one followed it all the way down one would need to understand the behaviour of the fundamental particles comprising the metal in the cylinder block, but in practice that level of detail is not needed: we simply need to understand that metal is a material with certain properties which we can take as given (unless we are working in metallurgy, in which case it is precisely the question of what makes some metals hard and some soft that interests us).

This principle of hierarchical organisation applies in particular to living systems [49-53]. An animal is made of many billions of cells, which together form tissues of various types, these together forming limbs and physiological systems, the whole forming the living being. As we consider each level of structure from the smallest to the largest, we come across the phenomenon of emergent order arising from the functional integration of the parts:

"With each step up in the hierarchy of biological order, novel properties emerge that were not present at the simpler levels of organisation.... we cannot fully understand a higher level of order by breaking it down into its parts", precisely because doing so destroys the integration that enables it to function as a whole (Campbell, [49] pp.2,3).

The same is true for the computer, the jumbo jet, and so on (we will not understand how a computer operates by studying a list of all its parts, even if we are given a description of what each one does, for they could be connected together in many different ways). This is made possible by the operation in complex systems of top-down action in the hierarchy, as well as bottom up action. It is this action, discussed in my article for John Wheeler's 90^thbirthday, that enables each emergent level to have its own phenomenological behaviour and so to implement its own level of emergent reality.

4.3.3: Bottom-up and Top-Down Action.

The second point is that as well as bottom-up action, as discussed above in many cases where the lower level components determine the behaviour of the higher-level structures, top-down action is ubiquitous in biology and in practical applications of classical physics, but this feature is not normally noted in physics courses because of the emphasis in physics teaching on `isolated systems'. Real physical and biological systems are not isolated. Engineers and ecologists are fully aware of this fact - it is central to their disciplines. A few examples will make the point.

Astrophysics: Nucleosynthesis. The rates of nuclear interactions depend on the density and temperature of the interaction medium. Hence their outcomes in the early universe, and then in stars and supernovae explosions, all crucial to the later formation of structure in the universe, depend in an important way on top-down action from the environment in which they occur. In each case the microscopic reactions that take place, and hence the elements produced, depend on the environment: the density of matter in the universe and its consequent rate of expansion in the first case; the atmospheric structure of the stars and supernovae, which determines which reactions will occur at what rate, in the second.

Physics: Interaction potentials. First, potentials in the Schrödinger equation, or in the action for the system, represent the summed effects of other particles and forces, and hence are the way that the nature of both simple and complex structures can be implemented (from a particle in a box to a computer or a set of brain connections). These potentials describe the summed interactions between micro-states, enabling internal top-down effects. Additionally one may have external potentials imposed in the chosen representation, representing top-down effects from the environment on the system.

Experiments and collapse of the wave function. Second, the central additional feature where top-down action takes place is in the quantum measurement process where a specific macroscopic outcome occurs through the measurement process. The experimenter chooses the details of the measurement apparatus - e.g. aligning the axes of polarisation measurement equipment - and that decides what set of microstates can result from a measurement process, and so crucially influences the possible micro-state outcomes of the interactions that happen. Thus the quantum measurement process is partially a top-down action controlled by the observer, determining what set of final states are available to the system during the measurement process.

State Preparation. The third feature where top down action takes place in quantum theory, dual to the previous one, is the choice and control of the initial state in an experiment (state preparation). This is also a choice implemented in top-down fashion by the experimenter. Thus the experimental apparatus can be described in macro (non-quantum) terms and we see top down action of the macro world on the quantum world both in the measurement process and in the prior preparation process.

The Arrow of time. This problem is discussed below (Chapter 6). The only known solution to this arrow of time problem seems to be that there is top-down action by the universe as a whole, perhaps expressed as boundary conditions at beginning of space-time, that allows the one solution and disallows the other. As there is an arrow of time in the quantum measurement process, these themes are clearly related.

Biology: Development and Reading of DNA. Top-down action is central to two main themes of molecular biology, even though the main emphasis in many texts on the subject is on the bottom-up (mechanistic) aspects.

Development of DNA codings. The first central theme of evolutionary biology is the development of particular DNA codings (the particular sequence of bases in the DNA) through an evolutionary process which results in adaptation of an organism to its ecological niche. This is a classical case of top down action from the environment to detailed biological microstructure - through the process of adaptation, the environment (along with other causal factors) fixes the specific DNA coding. There is no way you could ever predict this coding on the basis of biochemistry or microphysics alone.

Reading of DNA codings. The second central theme of molecular biology is the reading of DNA by an organism in the developmental process. Development is context-dependent all the way down, with what happens before having everything to do with what happens next. The central process of developmental biology, whereby positional information determines which genes get switched on and which do not in each cell, so determining their developmental fate, is a top-down process from the developing organism to the cell, based on the existence of gradients of positional indicators in the body. Without this feature organism development in a structured way would not be possible.

The information contained in the DNA is read in an environmentally dependent way. The reading of the DNA code is initially controlled by positional information fed the cell by morphogens that in essence tell the cell where it is in the developing animal or plant body ([6], p.225), together with information on the stage of development), and always responds to the environmental situation (e.g. plant development varies according to season and climate conditions).

Thus the functioning of the crucial cellular mechanism determining the type of each cell is controlled in an explicitly top-down way. At a more macro level, recent research on genes and various hereditary diseases shows that existence of the gene for such diseases in the organism is not a sufficient cause for the disease to in fact occur: outcomes depend on the nature of the gene and on the rest of the genome and on the environment. The macro situations determine what happens, not specific micro features by themselves, which do work mechanistically but in a context of larger meaning that largely determines the outcome. And note particularly that the macro environment includes the result of conscious decisions (a patient will or will not seek medical treatment for a hereditary condition, for example), so these too are a significant causal factor.

Human Volition. The last point emphasises that consciousness brings in a whole new series of effects into the causal network. When a human being has a plan in mind (say a proposal for a bridge being built) and this is implemented, then enormous numbers of micro-particles (comprising the protons, neutrons, and electrons in the sand, concrete, bricks, etc that become the bridge) are moved around as a consequence of this plan and in conformity with it. Thus in the real world, the detailed micro-configurations of many objects (which electrons and protons go where) is in fact to a major degree determined by the macro-plans that humans have for what will happen, and the way they implement them.

The existence of human volition thus causes a major difference in the causal hierarchy between the natural sciences branch on the one hand, where human action may be ignored, and the human sciences branch on the other, where volition and goal-seeking determine the course of events. Some specific socially important examples of top down action involving goal-choice are:

(i) The Internet. This embodies local action in response to information requests, causing electrons to flow in meaningful patterns in a computer's silicon chips and memory, mirroring patterns thousands of miles away, when one reads web pages. This is a structured influence at a distance due to channelled causal propagation and resulting local physical action.

(ii) Hiroshima. The dropping of the nuclear bomb at Hiroshima was a dramatic macro-event realised through numerous micro-events (fissions of uranium nuclei) occurring because of a human-based process of planning and implementation of those plans.

(iii) Global Warming. The effect of human actions on the earth's atmosphere, through the combined effect of human causation moving very large numbers of micro-particles (specifically, CFC's) around, thereby affecting the global climate. The macro-processes at the planetary level cannot be understood without explicitly accounting for human activity.

The Human Body and Brain. The foundation for all of this is the top-down action in the human body, where the brain controls the functioning of the parts of the body through a hierarchically structured feedback control system, which incorporates the idea of decentralised control to spread the computational and communication load and increase local response capacity. It is a highly specific system in that dedicated communication links convey information from specific areas of the brain to specific areas of the body, enabling brain impulses to activate specific muscles (by coordinated control of electrons in myosin filaments in the bundles of myofibrils that constitute skeletal muscles), in order to carry out consciously formulated intentions.

Furthermore, through this process there is top-down action by the mind on the body, and indeed on the mind itself, both in the short term (immediate causation through the structural relations embodied in the brain and body) and in the long term (structural determination through imposition of repetitive patterns). An example of the latter is how repeated stimulation of the same muscles or neurons encourages growth of those muscles and neurons. This is the underlying basis of both athletic training and of learning by rote. Additionally, an area of importance that is only now beginning to be investigated by Western medicine is the effect of the mind on health.

· The existence of top-down action is crucial to the way causation in hierarchical systems should be envisaged.

· The higher causal levels influence and even control the lower causal levels, even though the lower levels causally underlie what happens at the higher level through bottom-up causation.

· It is through this process that the higher levels of structure attain their causal efficacy and effective (phenomenological) behaviour.

4.3.4 Principle L₃: Open system with matter and energy flows and exchanges

Living organisms have the capacity to extract and transform energy and materials from their environment, which they use to construct and maintain their own structure. This enables growth and continued functioning, including carrying out mechanical work. It requires ingestion of nutrients, their transformation to usable form, transport of nutrients and stored energy plus oxygen needed to use them to where they are needed, and disposal of waste products. As every cell needs energy and nutrients, some kind of transport system is required to and from every cell (unless the cell is in direct contact with the external environment and obtains its energy and food for itself from that environment).

Thus living beings are open systems exchanging materials and energy with their environment, and will cease to function if either the provision of nutrients and energy (supplied by food and drink in the case of animals) or the supply of oxygen needed to utilise them ceases. In energy terms, living organisms absorb from the environment a form of energy that is useful to them and return to the environment an equivalent amount of energy in some other less useful form. Indeed, "Living organisms create and maintain their essential orderliness at the expense of the environment, which they cause to become more disordered and random" (Lehninger p. 8).

4.3.5 Principle L₄: Information flows

The third point is that the hierarchical structuring and use of materials and energy is based on, and embodies in material form, information (the shape of a bird's wing or an aircraft wing is based on information as to how air flows); and indeed information flows are the basis of organisation. This is true both in terms of the design of the system (for example plans convey information from the designer to the builder; books inform the designer of the best design strategies; computer programmes written by one group enable design of an aircraft by another), and in the fact that the functioning of any complex system takes place on the basis of flows of information within the system which guide the energy and material flows that enable its functioning.

For example a motor car is controlled by the driver sending signals continually to the engine (via the accelerator), to the wheels (via the steering wheel), to the brakes (via the brake pedal). A computer is controlled by information stored in a controlling programme; the computer reads the programme and carries out the instructions it finds there; it may also receive instructions from the operator, typing in new information which is used as programme execution proceeds. Of course the programme itself is initially typed in by an operator before it is stored for use. The same is generally true in society: myriads of information flows through newspapers, telephones, faxes, TV keep society functioning.

· Central to all complex organisation are structures that obtain, code, store, diffuse, and utilise information.

Most important of all, the information that shapes living systems is mainly incorporated in the DNA molecules that are at the centre of each cell in an organism [23,24,49]. This information, stored in terms of the genetic code and copied to every cell by intricate molecular mechanisms [webpage], is read by other molecules as the organism develops, and used to create the hierarchical structure of the functioning animal [53]. Thus an algorithm for the construction of the animal is encoded in DNA molecules, and passed on (in slightly altered form) from generation to generation. Some of this information structures the brain, and thus provides the basis of our own information processing, utilising ways of storing and processing information (possibly by neural networks, or conceivably using holographic techniques) that form the basis of how the mind and consciousness work. It is read out in a context -dependent way: for example a plant will enroll different processes and supporting molecular mechanisms if it is encountering a drought than if it is in a cold wet climate; the brain will develop different reflexes if a person undertakes different kinds of gymnastic training .

This is an example of a general principle that all information will be interpreted and used in a context dependent way. In particular vast amounts of information will be discarded as irrelevant, and attention will be focused on what are discerned to be the key variables only. During its processing and use, the same information may be represented and coded in multiple ways. Information should not be confused with specific molecular patterns or specific brain states; it is an abstract concept that can be realised in a multiplicity of physical forms.

Information flows both top-down and bottom up in biological systems, and in particular in the human body. It serves to integrate the actins of the different levels.

Hierarchical structure of information systems

In order to encode information about any complex hierarchically structured system, the information must also necessarily be hierarchically structured.

Languages provide a way of hierarchical coding of information: a set of basic units (letter of the alphabet) are strung together in sequence to code complex information. The overall meaning is given by building up parts in a hierarchical way. The standard language hierarchy is

Language Hierarchy

Book

Chapter

Paragraph

Sentence

Word

Letter

Table 4.5: The hierarchy in language.

Because one can string the basic symbols (the letters) together in an arbitrary order, one can convey arbitrary information with the same finite set of symbols. That is the magic of the technology of language. An interesting comparison is the hierarchical structuring of computer languages.

Human Heredity: Physical Hierarchy and Information Hierarchy

Nature has discovered this principle in the code used in the human genome. It has the structure of a language [webpage], as follows:

Human heredity: Physical Hierarchy

Genome: 2 pairs of 23 chromosomes

Book: combined systems give functioning human

Chromosomes (strands of DNA)

Chapter: combination of cell types

gives physiology systems

DNA: sequence of genes

plus other material

Paragraph: folded proteins determine

cell types produced

Gene: sequence of codons in DNA

Sentence: codes for proteins

(a sequence of amino acids)

Codon: Triplets of bases on DNA:

64 possibilities

Word: codes for one of 20 Amino Acids

Bases on DNA backbone:

4 possibilities (A, C, G, T)

`Letter' of DNA codes

Table 4.6: The information/structure hierarchy in human heredity

Thus the sequence of bases on the DNA, read out in a hierarchically structured way (and with starts, stops, and gaps) gives the information needed to construct the body. Vast amounts of information are stored in the DNA in this language with letters A, C, T, and G: human DNA contains about 3.2 billion base pairs. Developmental biology studies how the particular parts of DNA are chosen for reading in any particular cell: DNA is not read from the beginning sequentially, but particular parts are read depending on the position of the cell in the body and the developmental stage reached. Thus this is like reading hyper-text rather than ordinary text: the next part to be read does not follow in sequential order but rather depends on what information is required next to complete the biological tasks at hand.

The Brain

The brain is the most complex organ in the human body and indeed the most complex system known to us. To fulfil its complex information processing function, it necessarily has a complex hierarchical structure [webpage], [webpage].

Hierarchical structure of the brain		Function
The brain	Brain stem, cerebellum, neocortex, spinal cord	Consciousness
Neocortex	Frontal, Temporal, Parietal, Occipital lobes	Integration
Neural networks	10¹¹ neurons each with 10³ to 10⁵ connections	Pattern recognition
The neuron	Axons, Non-linear dendritic amplifiers, synapses	Basic computation
The nerve axon	Nerve fibre, sheath (myelin)	Signal transmission
Complex biochemical molecules	Proteins, nucleic acids	Folding and recognition
Simple organic molecules	Bases, Amino Acids, Sugars, Phosphates	Bonding
Atoms	Nucleus, electrons	Atomic structure

Table 4.7: The main brain systems.

Neurons The main functioning of the brain is via vast interconnected sets of neurons forming a neural network, interleaved with numerous glial cells that provide support functions. Intermediary neurons [webpage], [webpage] are linked to each other by dendrites that receive input signals, obtained from other intermediary neurons or from sensory neurons, which run from the various types of stimulus receptors, e.g., touch, odor, taste, sound, and vision. They combine and process these signals. If a threshold value is exceeded by the combined incoming signals they send a resulting signal down axons through which they provide output signals. Electrical signals travel down the axon to its terminal where a synaptic junction triggers the release of chemicals that stimulate the next neuron in the chain. Some intermediary neurons link to motor neurons which activate muscles and glands.

Neural Nets Neurons are often structured in layers, with numerous connections from neurons in one layer to the next. The precise pattern of connections determines the output signal that is given to an input signal, in a way that can be simulated on a digital computer. Neural nets are trained to undertake pattern recognition tasks by showing them a set of objects and rewarding them when they are correctly recognised (that pattern of connections is strengthened) but punishing them when they get it wrong (that pattern of connections is weakened). Hence simple information processing elements (neurons) can be combined in neural networks to carry out complex computations, and one has a biologically based computer processing information received from the sense and outputting signals to motor neurons as well as to itself for storage, recall, and further processing. It is the latter feedback loops that enable the build up of real complexity in the information process.

Global structure The brain itself integrates this all together.

It consists of the spinal cord plus three main parts.

· The brain stem handles body regulation (automatic tasks such as breathing, heartbeat, and digestion) and arousal.

· The cerebellum handles timing and prediction.

These are the primitive parts of the brain;

· The neo-cortex is more recent in origin and handles higher functions.

The neo-cortex in turn consists of

· Parietal lobes (handling judgements of weight, size, shape, and feel),

· Occipital lobes (handling vision),

· Temporal lobes (handling language and perception of sound), and

· Frontal lobes (governing voluntary movements and some logical processes).

Three points should be made here. First, through modern brain scanning techniques we are discovering more and more about which brain regions control which cerebral functions and so for example learning more and more about the processes of cognition. Second, despite this wealth of detailed knowledge about the electro-chemical functioning of the brain, we have no idea how consciousness comes about, for example how we come to experience sight, sound, and time. Indeed we don't even know how to seriously approach that topic - the `hard problem of consciousness studies. Third, in all animal types this complex structure leads to complex behavioural patterns that represent extraordinary high level responses to the internal needs and environmental challenges facing each species.

4.3.6 Feedback control

The further point in the implementation of information use in complex systems is feedback control [46-48], enabling homeostasis. To see why it is necessary, consider a computer operating in a strictly mechanistic pre-programmed fashion. It will (unless some error occurs)do precisely what it is programmed to do; for it is an essentially reliable machine, so that for example we place in its care the safety of passengers in an aircraft, and the keeping of accounts in a bank or building society. However this totally pre-programmed mechanistic approach is also the reason why present day computers are often so stupid, being unable to correct the simplest errors. If a small error is made in a command entered by the operator, the computer may do something quite different from what was intended, or (more often) will refuse to do anything at all (the screen will say "Command Error", or something similar); if the programme itself is wrongly written, the computer will not do the right thing even if the right data is entered; and if both are correct, it will do what is wanted provided nothing takes place that was unforeseen by the programmer. The problem is that the computer proceeds in a purely mechanical way, assuming that the results of the actions taken are exactly as planned; but this may not be so. The consequence is that for example an aircraft may crash into a hill even if it is computer controlled if positional errors due to cross-winds accumulate until the aircraft is far from its planned position, even thought the pre-planned course has been accurately followed.

The missing element is feedback control, which underlies the successful functioning of all purposive systems.

· The essential principle of feedback control is:

- continually monitoring what is happening,

- comparing it with the chosen goals,

- taking corrective action if things go wrong.

This can be illustrated by considering how you control the temperature of water in a shower. Essentially, you choose a desired temperature T (say, 28 degrees), and compare it with the actual temperature T₁ of the water in the shower (to do so you put a hand in and feel how hot the water is). If they are the same, no action is required; however it may be that the water is too hot (T₁ is greater than T, say 30 degrees). Then you turn the hot water tap down by an amount you believe is sufficient to cool the water to the right temperature, and (after a minute)feel it to see the result. If it is now too cool, you turn the tap the other way to make the water hotter. By repeating this process several times, you attain the right temperature.

The essentials of the process are that we compare the actual situation with the desired situation, and if they differ an error message is generated ("The water is too hot"); this is the information used to actuate a controller (the tap) by an amount estimated to be just right to correct the situation (the corrective information is "fed back" to the controller, hence the name feedback control). This process is repeated until the right result is attained. A similar process occurs as we steer a motor car down the road. We observe the direction we are heading, compare it with the direction we want to go, and if they differ, we use the amount and direction of this difference (the error signal) to determine how to turn the wheel (the corrective action to make the real situation accord with our wishes). As we drive we continually repeat this process; and we do the same with the speed, monitoring the real speed to see if it is within acceptable limits or not.

This fundamental process is the way we attain any goals in a purposive way, and engineering systems routinely use it to ensure successful accomplishment of their task (for example, in the control of speed of an engine or of the temperature of water). The same process underlies biological purposive action and functioning; an impressive example being the temperature controls in the human body which are so accurate that we can detect ill-health by measuring deviations of our temperature by only one degree from the expected value. There are many thousands of feedback loops in operation in every living cell, and all the major physiological systems in the body are feedback control systems [webpage], enabling homeostasis - the dynamic maintenance of equilibrium conditions, for example control of blood pressure and body temperature. An immensely complex example is the immune system that makes our bodies resistant to attack by a host of hostile micro-organisms; and one of the most impressive is the molecular mechanism by which DNA is copied.

One strand of DNA is used as a template to make a new strand, the series of four bases that form the genetic code (occurring in complementary pairs) being read to form a complementary strand (containing the identical information). Once in every 10,000 times an error occurs: the pairing of bases is done wrongly. However the DNA polymerase that does the assembly checks the copying for correctness; if a wrong base has been added, it is removed and replaced with the correct one, before the next one is added. After this check has been performed, there is an error only once every billion times. Without this mechanism, life would not be possible.

As well as being fundamental in natural and engineering systems, feedback control is an essential element in human society, underlying the successful running both of organisation of all kinds [11,46,47] and of personal life [54],hence being the basis of attaining basic welfare and adequate quality of life[55,56]. It is also the underlying principle of the basic learning cycle (see[11]) and of scientific discovery. Whenever feedback mechanisms are missing or ineffective, sooner or later things are bound to go wrong, because the basic mechanism needed to correct errors is missing.

Feedback takes place both within levels in the hierarchical system, and between levels. Thus it stabilizes both the individual levels, and the relationships between the levels.

4.3.7 L₅: Reproduction development and death - the life cycle

"The most extraordinary attribute of living organisms is their capacity for precise self-replication, a property that can be regarded as the very quintessence of the living state" (Lehninger, p.4) This takes place through structural replication at the lower levels, for example DNA and cell replication, followed by the processes of developmental biology based on positional information that generate higher level structures by top-down control of the functioning of the lower level biological functions. This leads to the entire life cycle of each species, with birth, growth and development to maturity, and a reproductive phase, eventually ending in death as the long-term viability of the interlocking systems begins to fail. Overall this entire process enables long term survival of species together with short term adaptation to the environment.

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Section 4.4 The diversity of life

4.4.1 The Variety of life

There is an extraordinary variety of life [53a] [webpage]. Apart from viruses [webpage], living things can be split into five kingdoms [53b]:

Prokaryotes: all the bacteria, including germs and archaeans [webpage]: Single celled organisms that reproduce asexually.
Protoctista: micro-organisms such as algae, slime molds, protozoa (stem eukaryotes) [webpage]
Fungi: eukaryotes that form spores [webpage]
Plants: life that is usually able to photosynthesize, comprising non-vascular plants and non-seed vascular plants [webpage] and vascular seedplants [webpage]), and without an active method of locomotion.
Animals: the vast array of vertebrates and invertebrates (including sponges, planktons, worms, insects, fishes, birds: [webpage], [webpage], [webpage], each with some method of locomotion

The first kingdom contains only prokaryote cells, the other four only eukaryotes. Each kingdom is split into phyla, classes, orders, families, genera, and species. Classifying life forms [webpage] used to be done on the basis of appearance, this then moved to function, and then to evolutionary origins. The latter is now preferred, with molecular biology techniques able to classify life according to genetic resemblance, which in turn is based on evolutionary origins.

About 1.75 million species have been named, about 75% of which are insects. It is probable there are between 13 and 14 million species, most being insects and microscopic life forms living in the tropical regions.

4.4.2 Plants and Trees

Many of the same needs are met in plants and trees as in animals but in slightly different ways, as briefly suggested in the following table [webpage], [webpage].

Plant Physiological systems compared with vertebrate animals
Trunk, branches, roots	Basic support: the skeletal system.
Bark	External barrier : the skin
Translocation system	Nutrients to cells: the circulatory system
Photosynthesis: Leaves	Supply of oxygen: The respiratory system
Roots	Source of nutrients; the digestive system
Evaporation system: Leaves	Getting rid of waste: The excretory system
Plant growth substances	Control of development: The hormonal system
Immune functions	The immune system
Flowers/ fruits	The reproductive system

Table 4.8: The main plant physiological systems.

Energy comes form photosynthesis and nutrients from the roots, rather than both being obtained by the digestion of food. The leaves function as an analogue of the lungs in terms of exchanging oxygen and carbon dioxide with the atmosphere. However plants have no locomotion or nervous systems; consequently the hormonal system does not provide top-down control of cells as in the case of the human. They have feedback control systems of many kinds, with rudimentary information sensors, but genuine information processing capability as in the case of animal brains. They cannot store information, recall it, consider, and act on the basis of a resulting decision.

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Section 4.5 Ecosystems and the Biosphere

4.5.1 Ecosystems and Biomes

The totality of living beings in an area forms a complex interacting network called an ecosystem [58,59] [webpage]. The interacting sets of ecosystems in a region with given physical characteristics form a biome. The biosphere is the name given to the ecosystem of all living things on Earth. Each animal needs energy to function [because of the second law of thermodynamics!], and so has to consume food and produces waste. In an ecosystem there will be animals and plants living off each other in a food chain [webpage], with herbivores living off plants, carnivores living off herbivores, and so on, with the larger and more complex animals occupying the higher levels (trophic levels) in the food chain [webpage]. The whole is powered by sunshine, whose energy is captured by plants through the process of photosynthesis, and stored by them in chemical form. This chemical energy is then utilised by animals that eat the plants, and by successive predators that prey on other animals in the food chain [35,58]. Thus we have energy flows [webpage] [webpage] and matter flows [webpage] in the ecosystem. In the natural system the waste products and dead plants and animals get recycled, the organic elements C,H,N P, O, and S becoming available again in various forms to be reused by later generations of plants and animals. The usable energy is eventually reduced to heat, this waste energy being radiated away to space (if this did not happen, the earth would rapidly warm up and become so hot that life would be impossible [34]; thus the Earth is held in an overall energy balance through its gains and losses of heat). The soil plays a crucial role in ecosystem functining [webpage]

An example of ecosystem analysis is the university of Maryland's network analysis of south Florida's wetland biotic communities [webpage]. We can attain some understanding of the ecosystem dynamics by running computer simulations [webpage]

The ecosystems function in the context of the major terrestrial biomes, classified as the world's major communities, classified according to the predominant vegetation and characterized by adaptations of organisms to that particular environment" (Campbell) [webpage]. Different kinds of ecosystems are viable in these different contexts. They can be classified as follows:

Terrestrial Biomes
aquatic	[webpage], [webpage]
forests	[webpage], [webpage]
deserts	[webpage], [webpage].
grasslands	[webpage], [webpage]
tundras	[webpage], [webpage]

Table 4.9: The main biomes on earth.

Two major principles emerge in the functioning of ecosystems and biomes: resource cycles, and interdependence.

4.5.2 Principle L₆: Resource cycles

Unlike all other biological systems, ecosystems are largely closed - there is relaqtively little energy and material transport across their boundaries, for that is what characterises them as a `system' with its own unique properties - and the biosphere, taken as including the interactin with the geological system, is completely closed. Because material resources are conserved and are limited, any such system depends ultimately on recycling the resources at its disposal. Thus in any ecosystem there are local carbon, nitrogen, oxygen and water cycles that interact with the global resource cycles and maintain the whole in operation. For the carbon cycle, see [webpage], [webpage]; for the hydrological cycle, see [webpage], [webpage]; for the nitrogen cycle, see [webpage], [webpage]. The existence of these cycles corresponds to the fundamental role that carbon, nitrogen, oxygen, and hydrogen play in organic molecules. Each of these materials spends some time free in the environment, then is taken up by living organisms and incorporated in their bodies, and (perhaps after being released into the environment again for a while) eventually is taken up by some new organism. It is literally true that we are lent the materials for our bodies for a while, these same materials(which may have already been used by many thousands of organisms before us) being later incorporated in other living beings. Understanding these resource cycles is the basis of sustainable development and in particular sustainable agriculture [60,61], for it makes crystal clear that trees and vegetables can only grow by incorporating such materials into their bodies; if these elements are not replenished in the earth when crops are harvested, new generations of plants and trees cannot grow for very long. Furthermore not only must there be a sustainable source of energy and materials for the ecosystem with provision for recycling of the needed elements but also a sustainable way of disposing of its waste products so that they do not accumulate and poison the system.

In both the case of the materials for life and the energy that enables its functioning, the underlying reason for the existence of these cycles and channelling is the underlying physical conservation laws, previously discussed. In particular they underlie the fact that, since available material and non-renewable energy resources on the surface of the Earth are strictly finite, once these resources have been used they will be gone forever (for practical purposes). This is the essential foundation of the need for conservation policies, this issue being relevant to all of us because of our interrelatedness.

4.5.3 Principle L₁ revisited: Interdependence and complexity

The beings in an ecosystem are not as tightly bound together as the components of an organisam. Nevertheless in their separate lives they develop intimate relationships between each other, resulting in complex interdependence between them (flowers feed butterflies which pollinate the plants; foxes depend on eating rabbits who depend on eating carrots and similar vegetables; the air is breathed by animals and recycled by plants and trees; microbes decompose dead bodies, making their materials available again for future use), and also with the physical environment of the ecosystem. This provides the basic food web through which minerals and energy are cycled in each ecosystem [webpage] enabling its ongoing biological productivity [webpage], with many plants and animals specialised to undertake specific functions within the context of the rest of the life forms present food chain. Thus

· All life is interconnected, sharing in energy, resource, and information flows ([6], pp. 260-266).

Indeed each life form fills a specific ecological niche - an opportunity space for a specialised animal or plant, see [webpage], [webpage], [webpage], [webpage], determined by all the other life forms present with which it interacts, as well as by the physical surroundings; see for example a great discussion of the causes of tides and how they affect sea animals, thus demonstrating the kinds of linkages that take place in ecosystems, at [webpage] (select `tides'). In this context, the fact that an animal is small does not mean it is unimportant. On the contrary, bacteria for example (one-cell organisms) are very important in ecosystems because there are so many of them, and they fulfil the vital role of decomposing waste matter, as well as being crucial in animal digestive systems. Indeed as a result of the hierarchical structure of flows of energy and materials in ecosystems, there will always be many more tiny organisms than large ones. The further up the food chain you are, the less of you there are.

Interference with one component of an ecosystem can lead to unexpected consequences in quite different components, because of these dependencies. While we can try to estimate these effects by use of mathematical models, three sources of uncertainty make this difficult.

Firstly, it is usually difficult to get the needed data (how many foxes are there in England? How many whales in the Antarctic ocean? What is the birth-rate for albatrosses in different age groups?) Secondly, the equations in this case represent an average statistical behaviour, rather than a precise physical law, so they only give an approximate description of what is likely to happen (unlike the case of physics where the laws are precise laws enabling us for example to predict future planetary positions with great accuracy). Thirdly, the very complexity of the interactions makes it difficult to solve the resulting equations accurately. In particular, non-linear interactions in the system can lead to chaotic behaviour [64], when very small changes in initial conditions lead to very large changes in the resultant behaviour. This can lead to large uncertainty in prediction of future growth patterns of interacting populations, because we cannot know the initial data to infinite accuracy.

Furthermore problems of chaotic behaviour affect weather forecasting, despite the fact that in this case the underlying equations are well founded, for these equations lead to deterministic chaos(despite the equations being deterministic, their results are unpredictable).

4.5.4 Stability of ecosystems

While feedback mechanisms work to maintain stability in ecosystems, they are not so well ordered and precise as in a single organism, because they result from the interaction of many independent living entities, often in competition with each other for the same limited resources. As a consequence, they are not always successful in maintaining a balance [57]. An important issue is water supply and waste disposal. The weather is crucial in terms of rain and drought; proper treatment of both solid and fluid waste is crucial in terms of preventing the system becoming poisoned in the long term. Indeed the aim of long-term sustainability should be a key concept in terms of analysing present and future ecosystem conditions. This involves using non-reusable resources carefully, developing as much recycling of resources as possible and sustainable systems for renewable resources, and long term plans for handling waste products that cannot be recycled.

It is important to mention a particular case where previously existing control mechanisms no longer operate effectively, leading to a presently operative instability of major significance that will affect us all because of our interdependence. This is the exponential population growth that has occurred in the past few hundred years, and is still taking place in many parts of the world (see below).

4.5.5 The biosphere

The totality of all ecosystems on the earth forms the biosphere [webpage] - the interdependent whole which both comprises and sustains life. The local ecosystems interact with each other and with the global resource cycles of the key elements carbon, nitrogen, hydrogen, and phosphorus. The nature of the atmosphere is controlled by interactions between the atmosphere, sea, and continents, with the water cycle ([6], pp.196-201) and atmospheric cycle ([6],pp.202-205) crucially interacting with each other and - in the long term - with the rock cycle ([6], pp.193-196).

The temperature is controlled by the balance of incoming and outgoing radiation, strongly affected by the composition of the atmosphere which controls its opacity at different wavelengths. Global warming, with consequent drastic effects on weather and agriculture, can result when human activity interferes on the one hand with the composition of the atmosphere at high altitude, and in particular when this results in ozone depletion, and on the other with the global oxygen cycle by depleting natural vegetation. A complex of interacting factors affect these processes [webpage].

The threats that human pose to the long term sustainability of the biosphere are in the end driven by uncontrolled global human population growth [webpage], [webpage] (the present size of the world's population is estimated at [webpage]). Long term sustainability will not be attained until the size of the total human population is stabilised on the one hand, and ever-increasing demands for resource use are contained in the context of a long-term resource use plan on the other. Because of limited resource availability, see [57,62] and [webpage],

· The resource consumption and waste generation associated with a rapidly growing population are major threats to the future well-being of humanity and to the ecology of the planet.

They are the underlying force behind the looming large-scale environmental and ecological problems facing us – in particular ([6], pp.267-274),

· the hole in the ozone layer,

· acid rain,

· the greenhouse effect,

· depletion of non-renewable resources.

These issues simply did not arise when the population was small. They are exacerbated by massive over-consumption by a minority of the world's total population (this being associated with major global inequity in resource distribution and use), which can be countered by more caring and conservation-centred resource use policies, associated with a more equitable distribution of wealth. They can also to some extent be compensated by technological advances, and indeed both measures are needed to improve the situation. However by themselves these steps cannot solve the problems arising from unchecked population growth, which will in the end swamp any gains we can make by such methods. The issue will have to be tackled directly in order to stabilise the overall situation of humanity on earth, and to prevent continual exacerbation of the regional problems occurring from massive local population concentrations [57,62,63].

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Section 4.6 Evolution

Apart from understanding in more detail how complex systems work, the major question remaining is how they came into being. In the case of man-made objects, the answer is obvious: they were designed that way, and then manufactured according to that design.

4.6.1 The historical evolutionary process

Living plants and animals are immensely more complex than anything men or women have ever designed. How has this been achieved? All the evidence points to a process of evolution, whereby single cell animals developed out of carbon-based molecules thousands of millions of years ago, and then evolved to multi-cellular organisms of higher and higher levels of complexity [webpage], culminating in the existence of the human race ([49,65-67], [webpage]).

Life started as single cell animals and then evolving through small multi-cellular animals to fish to mammals (with some dead-ends occurring, like the dinosaurs that once used to dominate the Earth but then died out completely, in a mass extinction whose cause is still open to debate). Thus the highest levels of complexity and order that we know of were created, leading eventually to humanity and the evolution of consciousness.

· Humankind evolved through an evolutionary chain in which complex functionality developed over time from the first life single-celled life forms.

· The first true humans appeared in Africa about 50,000 years ago and then spread by migration to the rest of the world

This interpretation is supported both by a large variety of data:

· Observations of the distribution of related plant and animal populations (Darwin’s original method);

· The fossil record which gives time-scale to the evolutionary process [webpage] through the early paleozoic [webpage] to the late paleozoic [webpage] and the mesozoic (the epoch of cycads and dinosaurs) [webpage], and the data on hominids [webpage], [webpage], [webpage],

· Present-day observation of evolution taking place in populations of flies, bacteria, viruses, and animals (dog-breeding and horse-breeding is nothing other than evolution of these species, assisted and guided in a specific direction by the breeders)

· Evidence from developmental biology, where the embryos of humans and of many animals are found to be virtually indistinguishable for the first few weeks of their growth;

· Evidence from molecular structure, where the same molecules and molecular mechanisms (for example the Krebs cycle) are known to occur in all living cells. In particular

· The genetic code is virtually universal, controlling the development of fish and birds, of frogs and elephants, of monkeys and men [49,53,65,66], allowing us to trace the evolutionary history of plant sand animals by studying DNA relationships.

While the historical occurrence of evolution is beyond reasonable doubt, the biological trend to order proceeds directly counter to the trend to disorder(entropy growth) that is one of the most fundamental characteristics of macroscopic physical systems. At a certain level this is answered by stating hat the animals accumulate this order by doing so at the expense of their surrounding environment, so the total system (the animal plus its environment)does indeed obey the entropy law: overall the trend to disorder is obeyed. However this does not explain the mechanisms leading to the increasing order: the source of apparently purposive design.

4.6.2 Principle L₇: Natural Selection

It is clear that as mutations occur in a population, those animals with a greater ability to survive (because of a greater breeding ability, a greater survival capacity of those born, or both) will tend to dominate the population more and more, while those with a lesser ability to survive will tend to die out. Thus the accepted explanation of evolution is

· Evolutionary development of living beings takes place via Darwin's mechanism of natural selection ("survival of the fittest"), based on

- variations produced by random mutation, followed by

- selection based on reproduction and survival rates,

· taking place over extremely long stretches of time [65].

The animals that have best survival rates reproduce most effectively and come to dominate the population. Those traits that enabled them to survive fit them to the environment in which they live better than any of their competitors. Thus feet, lungs, teeth, fingers, eyes, brains all evolved in order to improve survival fitness. They gave competitive advantage in the struggle for survival. This is a powerful feedback mechanism, however with the goal not of production of any particular type of animal, but rather simply of an increase of survival rates; the resulting control process acts as a purposive directional device to increase fitness for survival, with an impressive ability to lead to functional design of living organisms, see [webpage], [webpage], and [webpage]. Evidence comes from the similarity across life forms of the molecules of life and of cellular architecture, as well as from the historical record left to us in fossils - the remains of ancient life forms imbedded in rock, leading to a powerful picture of how different life forms existed in the past (dinosaurs, for example) and how the different present animal lineages evolved from each other ([6], pp. 252-257), despite features such as mass extinctions.

Additionally evolution provides a central explanatory paradigm used throughout present day biology. Thus

· All forms of life evolved by natural selection ([6], pp.243-257).

The question that remains is whether purely random mutations are a source of variation able to provide a complete explanation of all we see. We do not fully understand the interaction between mutations occurring at the genetic level(which must be their location) and the resulting changes in the animal population. This may be associated with the question of ``punctuated equilibria", where some of the fossil record seems to indicate long periods of very slow change, followed by short bursts of rapid evolution. The situation is complicated by ``piggybacking", where some feature which is very dominant in the appearance of an animal, and so is the obvious feature to focus on, was not the feature that led to selection, but came along also as a by-product of some other feature that was the real evolutionary determinant leading to improved survival. The apparent changes of rate of evolution might simply be due to selection effects (which determine what fossils are actually available to us for examination, as remnants from the many millions of creatures that have lived in the past). Certainly conclusive discussion of such issues is hindered by gaps in the fossil record, forcing us to guess what the situation was from a fraction of the evidence that might in principle be available to us.

A key point is whether evolution of complex structures, for example a wing, can in every case be achieved in the available time by a route involving many thousands of small purely random mutations, in which every step of the way leads to an improved survival rate, despite the fact that until it is developed enough to actually enable it to fly, a developing wing is probably a hindrance rather than a help to the animal in its fight for survival; indeed local maxima could be evolutionary dead-ends. Dawkins [65] strongly argues that natural selection based on purely random mutations suffices, but his argument is not backed up by estimates of the probabilities involved. The alternative is that not all steps in the process are completely random; some kind of direction is given to mutations that take place, so the process is not purely based on chance. This could occur for example if the nature of physical and chemical potentials preferred particular biological structures to others (which certainly is the case when elementary biological molecules form from some primeval soup of chemicals; the question is how far this effect extends). That this is so is suggested by the time-scale problem: estimates of the numbers of possibilities involved show that random choice would not have time to explore the full space of molecular possibilities since the origin of the universe, because this number is immense (much greater than 10¹²⁰) and hence is very much larger than astronomical numbers (of order 10⁸⁰). Purely random mutations don't have time to create what we see since the start of the universe (this case has been strongly made by Fred Hoyle, for example).

The answer is probably provided by Haken's idea of autocatalytic hypercycles: that is cycles of cycles, in each of which the mechanisms in operation produce a catalyst that then speeds up the cycle. That there are indeed preferred developmental pathways is already implied by the known biochemistry; the proposal is that they provide powerful positive-feedback mechanisms that rapidly develop preferred chemical pathways. Then development is to some degree guided rather than random.

The origin of life Perhaps most difficult of all is the question of how life first arose [webpage]. There are a series of sticking points in the evolution of living systems, overcoming of each of which is difficult to explain; perhaps the most difficult of all being the origin of the first functional cell, complete with sufficient DNA and RNA to replicate plus all the myriad cellular mechanisms that support them in this task [webpage]. Ingenious suggestions have been made, such as Manfred Eigen's proposal that natural selection can operate in particular inorganic systems in such a way as to lead to living systems, or the idea that silicates could provide a `scaffold' on which complex organic molecules could then form. The issue again is introducing some kind of direction into the process so that it will proceed more certainly than purely random variations. However none of these ideas has achieved universal acceptance; essential steps remain unresolved [65,68].

In any case, this line of questioning does not doubt the existence of evolution, or the functioning of the mechanism of natural selection, but queries whether all the mutations that take place are completely random, or whether rather they are in some sense directional towards their final product(for whatever reason).

Possibility Space: Given that evolution has taken place, it is interesting [65] to think of the space of all possible animals allowed by the laws of physics and chemistry (that is, all the animals that could possibly exist and function), and then the subspace of that space that has been actualised through the historical process of evolution. That subspace is very large (cf. the enormous variety of animals around us [49]); however the whole space of possibilities may be enormously greater. In any case, one of the most spectacular achievements has been the evolution of consciousness and language, and subsequently of social and economic systems, the whole nature of evolution changing with the advent of consciousness. Intimately tied in with this is the fundamental question of the mechanisms underlying evolution of ethics and morality, and of a sense of aesthetics. These lie in the province of the speculative and controversial theory of evolutionary psychology. Debate continues, with evolutionary game theory being proposed as a major tool for understanding these issues.

The Future: A final intriguing question is the future of evolution: what is its future, given human interference in the biosphere? What evolutionary future is there for human beings? The interference of human intelligence with the natural mechanism creates an entirely new situation. The outcome is unclear.

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Section 4.7 Complicated versus complexity

As remarked in the previous Chapter, although mountain chains are complicated, they are not complex as in the case of living systems - they do not display the kinds of complex organisation characteristic of living systems.

The principles underlying natural structures have been characterised in the previous chapter as P₁ to P₆ and those for living systems in this chapter as L₁ to L₇. We now consider briefly the differences in the principles underlying complex and complicated structures.

4.7.1 Physical Principles

All physical systems including living systems must be subject to the physical principles P₁ to P₆ but they are not all equally directly relevant to complex systems. We consider them in turn.

P₁: Relativity Theory does not at first seem relevant to the functioning of living systems. However a consequence of special relativity in combination with quantum theory is electron spin, which leads to fine structure in electron energy levels in atoms that affect some chemical energies. Thus the essential human micro-nutrient Vanadium would have different chemical properties if special relativity were not valid.

P₂: Quantum theory is crucial to life firstly in underlying atomic stability and secondly in underlying the nature of the periodic table through the Pauli exclusion principle. However the interesting question is whether genuinely quantum effects are apparent in biology. There are some cases where this seems to be so: for example quantum tunnelling affects oxygen transport by haemoglobin, and single photons can be detected by the eye. The most interesting question is highly contested: do genuinely quantum effects occur in the brain, for example to do with memory or with neuron function? Stapp, Penrose, Squires and others have suggested this is so, but most neuro-physicists do not agree. However an interesting philosophical issue is at stake here: if evolution is as powerful as some have suggested (Dawkins, Dennett for example) then surely it should have discovered truly quantum effects such as entanglement and collapse of the wave function, and have exploited them? From this viewpoint it would be most surprising if they did not occur in the brain.

P₃: The variational principles and symmetry principles of fundamental physics seem far removed from the complexities of biology. However there is one remnant of great importance: namely chiral symmetry is vital in biology - some molecules are right-handed and some left-handed and biological activity depends crucially on having molecules of the same chirality interact with each other. Drugs for example will not function if of the wrong chirality.

P₄: Conservation laws of atoms, energy, and momentum are all vital to the world of biology. They underlie global resource cycles and weather patterns as well as the need for energy and material transport systems in animals and plants, and indeed all aspects of animal and plant functioning.

P₅: The Second Law of Thermodynamics is true in extended form in living systems, as shown by Prigogine et al, but does not have the consequences it has in non-living systems. They do not tend to greater disorder, although they do by the order they attain at the expense of the environment. That fact underlies a great deal of issues in conservation biology and sustainable development.

P₆: Laws of large numbers do not apply to living systems, even though they involve huge numbers of atoms, molecules, and cells, because they are open systems that are far from equilibrium. However some of the consequences of these laws in terms of gas pressures etc. are important to living systems.

4.7.2 Complexity Principles

Considering the Principles of Complex Systems L₁ to L₆, as discussed above they are fundamental to living systems. To what degree do they apply to complicated systems?

L₁: Bounded structured system with interdependency and interrelationships Abiotic systems are often not clearly bounded. They have structure, but it is not functional in the sense of living systems - there is no purpose or function in their relationships, in the same sense that an eye is for seeing and an ear is for hearing. Interdependence is true only in a passive sense - there is no food chain, existence of functional niches, etc.

L₂: Hierarchical structuring applies in both cases, as demonstrated above. However the emergent levels of order and meaning in the abiotic world are passive rather than active. This is because the other principles of complex systems do not apply there.

Bottom-up and top-down action applies in both cases also, e.g. rock types and mineral types are determined by large-scale geological processes. Again this fact is important but by itself only leads to complication rather than complexity.

L₃ Open system with matter and energy internal flows and external exchanges Geological systems are open in more or less the same way that ecosystems are. There is nothing like the directed storage and transfer of energy and materials that exist in biosystems, but the global cycles do provide internal and external matter flows, in particular rivers serve as vehicles for matter transport and exchange in the natural world. Energy exchange is mainly through electromagnetic radiation received and emitted and weather patterns, plus the flow of molten magmas, earthquakes, lightning, and a contribution from radioactive decay. Fires have some effect but they are based in the biotic kingdom resident on the surface of the earth rather than in natural materials, none of which burn at the temperatures usual on the earth's surface. Indeed there is vary little usable chemical energy in the abiotic world, and what there is (e.g. petroleum) is in fact a residue from the biotic world.

L₄: Information storage and processing only happens in a passive way in the abiotic world. Each rocklayer does in deed contain a record of its history but it can't be recalled and processed. Here is a crucial difference between the two types of system.

Feedback control processes do not occur in the abiotic world, but abound in living systems. This is a crucial difference. It leads to `purposeful' action which does not occur in the natural world.

L₅ Reproduction development and death - the life cycle On long time scales there is reproduction of a kind and indeed lifecycles in the natural world (minerals, rocks, mountains), but they do not correspond in any way to the storage and readout of genetic information as occurs in the biotic world. They lead to reasonably consistent patterns in natural landscapes but these are the result of blind forces at work in similar circumstances, rather than directed use of energy and materials controlled by developmental processes reading stored genetic information.

L₆: Resource cycling takes place in the long term but only at the ecosystem level and above. The relatively short term cycles are all to do with living systems, and presumably would not occur in a lifeless planet. The point is that rocks, mountains, etc do not need a resource flow to keep functioning. They just exist. The case where this is not true is the water cycle - rivers and rain would cease to exist of there were not recycling of water.

L₇: Evolution? There is nothing approaching Darwinian adaptation in the natural world. There is `survival of the fittest' in the tautological sense that what survives survives, and therefore was fittest. But there is no adaptation through reproduction and variation because there is no short-term process of reproduction.

Overall we see the essential differences between the states are centred in use of information, feedback control circuits, and reproduction based on heredity leading to `design without design’. Hence complicated systems such as mountains (requiring vast amounts of information to describe their state in detail) do not represent true complexity. They have no emergent functionality - just emergent existence.

4.7.3 Reductionist explanation

Finally, it should be commented that when it comes to complex systems, as has been emphasized particularly by Harold Morowitz and by Alwyn Scott, the principle of bottom-up explanation of higher level behaviour rapidly fails in practice; and indeed the way higher levels behave is apparently largely independent of the lower level structure - there is an autonomy at the higher levels - so that one cannot even in principle determine the higher level from the lower level behaviour. Rather one has to add in higher level phenomenological relationships that characterise the higher level behaviour. They cannot be reduced to lower level principles or directly explained form those lower level principles alone.

In particular one runs into a combinatorial explosion when trying to go from physics to real chemistry, biomolecular dynamics is based on non-linear classical physics rather than linear quantum theory, and the Hodgkin-Huxley equation for nerve impulses cannot be derived from the laws of physics and chemistry: "There are new laws appropriate to the science of electrophysiology, which is removed by several hierarchical levels from atomic physics" (Alwyn Scott, Stairway to the Mind, p. 182). This corresponds to what happens in quantum physics in phenomena such as superfluidity and the quantum Hall effect, see the Nobel lecture by R B Laughlin in Reviews of Modern Physics quoted in the previous Chapter, where again the macroscopic behaviour cannot in fact be deduced from the microscopic behaviour.

This corresponds to the fundamental issue that emerges from the above considerations:

· The principles of complexity L₁ to L₇ cannot be deduced from the physical principles P₁ to P₆. They are emergent principles characterising the higher levels of organisation.

The lower levels allow those higher levels of organisation, but do not imply them. A deep question is why the lower levels do indeed allow such independent higher levels of organisation to emerge. Not all kinds of conceivable lower level physics would lead to such an outcome. Thus this must be due to the particular particles that exist and the specific nature of the interactions between them, as discussed in the last Chapter. Particular particle masses, charges, and interactions make emergent complexity possible.

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References for Chapter 4: The structures around us

The Applications of physics to the daily world is discussed in

[39] David MacCauley: The Way things work (Dorling Kindersley, 1990)

[40] K Schmidt-Nielsen: How animals work (Cambridge University Press,1972)

and the way it underlies the development of modern society in

[41] J Bronowski: The Ascent of Man: (BBC, London, 1976).

The implications of energy and entropy limits are discussed in [35,36] and

[42] P Colinvaux: Why big fierce animals are rare: An ecologist's perspective (Princeton University Press, 1979)

[43] W F Baxter: People or penguins: the case for optimal pollution (Columbia University Press, 1974)

[44] Georgescu Roegen: The Entropy law and the Economic Process (Harvard University Press, 1976)

[45] H E Daly: The economic growth debate: what some economists have learned but many have not, Journal of Environmental Economics and Management14: 323-336 (1987).

The issue of Hierarchical organisation is presented in

[46] Stafford Beer: Platform for Change (Wiley, 1978)

[47] Stafford Beer: Brain of the Firm (Wiley, 1981)

[48] R L Flood and E R Carson: Dealing with complexity (Plenum Press,1990).

Biology is discussed in

[49] N. A. Campbell: Biology (Benjamin Cummings, 1990),

(a magnificent general text), and specific aspects in

[50] C Grobstein: The Strategy of Life (W H Freeman, 1974)

[51] F C Steward: Plants at work (Addison Wesley, 1965)

[52] L Cudmore: The centre of life: A Natural History of the cell (Quadrangle, 1977)

[52a] A C Guyton: BasicHuman Physiology: Normal Function and mechanisms of disease (W B Saunders1977)

[53] L Wolpert: The Triumph of the Embryo (Oxford University Press,1991).

The variety of life is discussed in

[53a] M Fingerman: Animal Diversit y(Holt Rhinehart and Winston:1976)

[53b]: L Margulis and K Schwartz: Five Kingdoms: An Illustrated guide tothe phyla on earth.(Freeman, 1988).

Application of feedback control to organisational issues is discussed in [11]and [46-48], its functioning in personal life in

[54] Scott Peck: The road less travelled(Arrow Books, 1990)

and its role in general determination of quality of life in

[55] G F R Ellis: An overall framework for quality of life evaluation, in Social development in the Third World, Ed. J G M Hilhorst and M Klatter (Croom Helm, Beckenham, Kent, 1985), 48-62.

[56] G F R Ellis: The dimensions of poverty. Social Indicators Research 15: 229-253 (1984).

The dynamic feedback systems controlling the atmosphere and biosphere are described in

[57] J Lovelock: Gaia (Gaia Books Ltd., 1991).

The nature of Ecology is discussed in

[58] E J Kormendy: Concepts of ecology (Prentice-Hall, 1969)

[59] R E Ricklefs: The economy of nature (Chiron, 1976).

Practice of agriculture with a long-term future is discussed in

[60] Jim Mollison: Permaculture One: A perennial Agriculture for human settlements (Tagari Publications, 1990)

[61] Jim Mollison: Permaculture Two: Practical design for Town and country (Tagari Publications, 1990),

and the nature of long-term resource limitations in

[62] P R Ehrlich and A H Ehrlich: Population Resources Environment: Issues in Human Ecology(Freeman, 1974)

[63]Managing Planet Earth, Readings from Scientific American (Freeman,1990).

The unpredictable behaviour envisaged by chaos theory is discussed in

[64] I Stewart: Does God Play Dice? The new mathematics of chaos (Penguin Books, 1990).

The nature of Evolution, and evidence for the theory, are presented in [49]and

[65] R Dawkins: The Blind Watchmaker (Penguin Books, 1986)

[66] M A Edey and D C Johansen: Blueprints (Oxford University Press,1990)

[67] S M Stanley: Earth and Life through Time (Freeman, 1989)*.

The problem of the origin of life is discussed in [49,65] and

[68] A Scott: The Creation of Life(Blackwell, 1986).

The nature of the Earth is presented in

[75] J Mitchell (Ed.):Anatomy of the Earth (Mitchell Beazley, 1976).

The forces at action in shaping the Earth's surface are examined in [67] and

[76] V Fuchs (ed.):Forces of Nature (Thames and Hudson, 1977).

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[Version 2002-08-06].

Chapter 4 of The Universe Around Us by George Ellis

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Chapter 4: The Living World

Section 4.1 Hierarchical Structure

Section 4.2: Complex Organisation

4.2.1 Biomolecules

Metabolism stages

4.2.2 Cells

4.2.3 Tissues

4.2.4 Organisms

Section 4.3 The major principles

4.3.1 Principle L1: Bounded structured systems with interdependency

4.3.2 Principle L2: Hierarchical order

4.3.3: Bottom-up and Top-Down Action.

4.3.4 Principle L3: Open system with matter and energy flows and exchanges

4.3.5 Principle L4: Information flows

Hierarchical structure of information systems

The Brain

4.3.6 Feedback control

4.3.7 L5: Reproduction development and death - the life cycle

Section 4.4 The diversity of life

4.4.1 The Variety of life

4.4.2 Plants and Trees

Section 4.5 Ecosystems and the Biosphere

4.5.1 Ecosystems and Biomes

4.5.2 Principle L6: Resource cycles

4.5.3 Principle L1 revisited: Interdependence and complexity

4.5.4 Stability of ecosystems

4.5.5 The biosphere

Section 4.6 Evolution

4.6.1 The historical evolutionary process

4.6.2 Principle L7: Natural Selection

Section 4.7 Complicated versus complexity

4.7.1 Physical Principles

4.7.2 Complexity Principles

4.7.3 Reductionist explanation

References for Chapter 4: The structures around us

4.3.1 Principle L₁: Bounded structured systems with interdependency

4.3.2 Principle L₂: Hierarchical order

4.3.4 Principle L₃: Open system with matter and energy flows and exchanges

4.3.5 Principle L₄: Information flows

4.3.7 L₅: Reproduction development and death - the life cycle

4.5.2 Principle L₆: Resource cycles

4.5.3 Principle L₁ revisited: Interdependence and complexity

4.6.2 Principle L₇: Natural Selection