Aquatic phototrophs have a remarkable ability to cope with variations in a range of environmental factors, such as light, temperature, pH and salinity. However, some environmental conditions are beyond what are considered the normal limits for growth and can thus be considered as extreme. Focusing on algae and cyanobacteria, we discuss the capacity of extremophilic organisms to cope and even thrive in extremes of temperature ranging from hot springs to snow and ice algae, under extremes of pH and in situations where water is in short supply, such as in biological soil crusts and on man-made surfaces such as buildings and statues. Many of the mechanisms that allow algae to cope with these extremes are common across different situations and involve, for instance, processes to dissipate excess light energy and deal with reactive oxygen species. Algae and cyanobacteria enter symbiotic associations with other organisms, such as lichens and corals. They are also found as intracellular symbionts in plants, other algae and various protists and metazoans. There are looser associations where algae grow on animals such as gastropods, seals and terrestrial animals such as sloths. We also discuss the retention of active chloroplasts by phagotrophs in the process of kleptoplasty.

Facilitative interactions include mutualisms, in which both species benefit, and commensalisms, in which only one species benefits and the second species is unaffected by the interaction. The commercially important pollination mutualism between honeybees and plants is under assault by a mysterious emerging disease, CCD. Mutualistic species play critical roles in biological communities, including coral and their algal symbionts that are the foundations of coral reef communities, and the mycorrhizal association between plant roots and their fungal symbionts that is essential for most plant communities. A facilitative interaction can benefit species either directly, or indirectly by its effect on another species. There is usually some cost to each mutualistic species; thus, mutualism is most likely to evolve if the benefits exceed the costs, and if each species can ensure that its mutualistic partner provides the appropriate benefit. Facilitation may be more common in stressful environments, where the benefits of facilitation are greater than they might be in more benign environments. Some facilitative interactions, such as the interaction between the great spotted cuckoo and the carrion crow, are beneficial under some conditions and detrimental under other conditions.

In recent times, self-interest has been seen as the main driving force of behaviour and function in organisms. This is particularly evident in the concept of the selfish gene. However, as elaborated in this book, living systems strongly depend on cooperative behaviour, which is found everywhere in nature. All the way from millions of minute bacteria cooperating in the way they feed and grow, to massive whales talking with each other across oceans, organisms communicate with each other, and that communication is used as the glue of cooperation, even between distinct species. The idea of nature as ‘red in tooth and claw’ is at best a distorted perspective of the entirety of nature. However, in the grand scheme of things, both cooperation and competition are part of the story, and – whether wittingly or unwittingly – organisms form part of and interact with their ecosystems.

The view of living systems as machines is based on the idea of a fixed sequence of cause and effect: from genotype to phenotype, from genes to proteins and to life functions. This idea became the Central Dogma: the genotype maps to the phenotype in a one-way causative fashion, making us prisoners of our genes.

Living systems are characterised by intelligence. Treating organisms as gene-driven automata, blindly reacting to events, does not take account of their social or ecological being. Living systems anticipate the actions and reactions of other living systems. As in a chess game, anticipation can consider many options. Nevertheless, the chess analogy only gets us part of the way to understanding this characteristic of life. It is more like a chess game in which the players can create the rules, much as happens in a game of poker, in which anticipation is the key to success, including assessment of the other’s power of anticipation. Life is rule-creating, rather than rigidly rule-following. This does not mean there is no logic to what happens or how organisms behave; there is, and often it involves a clear strategy. But this is not regulated by genes. Much behaviour may be programmed, and much is learned; the logic, however, is situational (that is, dependent on circumstances) and subject to change. The ability to adapt to circumstances is an example of evolved functionality. Therefore, dogmatic models of life, seeking to reduce behaviour to little more than a set of algorithms, misunderstand the intelligence of organisms.

Where is the living mind that thinks? Culture is the matrix of the mind. Organisms owe their social and mental abilities to the ‘nesting’ of causation between all levels of their functioning. Higher levels mould what the lower levels can do. This is how living systems can use their flexibility, from cultural and linguistic variability to the water-based jiggling around of their molecules, to enable the evolution of rational and ethical social organisation. It is within this purposiveness that genuine freedom and responsibility are to be found.

Artificial intelligence (AI) is a tool created by living organisms, us humans. Like the hydraulic robots of the seventeenth century which inspired Descartes’ mechanical view of organisms, AI has become the latest in a list of mechanical metaphors for life. Yet it is just as limited, just as much a mistaken view of organisms. It views life as just processing further and further information faster and faster. Computers exist to process rapidly. That is their function, given to them by the humans who created them. Organisms use processing to help them create objectives, purpose.

Standard evolutionary theory represents genes as the target of evolution. But organisms may functionally develop without alterations in their DNA, and they may also buffer changes in the DNA to retain function. It is organisms that are the agents in the process of evolution. Outside a living system, DNA is inactive, dead. Furthermore, many significant transitions in evolution have not depended on new DNA mutations. They arose from the fusion or hybridisation of organisms with existing but different DNA. All the molecular processes in a living system are constrained by its purpose. Viewed this way, genes are the most constrained elements in organisms. Evolution of different species has occurred through extraordinarily creative and varied processes that include cooperation and fusion of existing species and the exchange of DNA and organelles. It is much more like nature using preformed tried and tested functionality than through slow gradual mutation. Evolution can occur in leaps and bounds.

If the dichotomy between replicator and vehicle is wrong, then what is it that replicates? The purpose of reproduction is not replication, at least not exactly. Reproduction brings about change. It shakes up the templates and provides new avenues to explore in adapting to a changing environment. It creates and propagates variation. But it also provides a way for the lessons learned in one generation to be passed on to the next. Reproduction is sensitive to the environment of the parent generation and enables change through the germ line.

We are writing this book as agents with a purpose. Agency and purposeful action is a defining property of all living systems. Yet modern science has presented a reductionist, gene-centred view of life, where life is reduced to biochemistry, particularly DNA and proteins. It has even carved out its own areas of study – genomics and proteomics – as if these components can be understood in isolation from the organisms themselves. But they cannot. The gene-centric view of life creates a fundamental problem. If all action can be reduced to genes, or is controlled by them, then purposeful agency cannot exist. Indeed, it has been referred to as an illusion. At best, modern science gives this problem to philosophers, assuming that the answer does not lie in biology itself. This is a mistake. Casting the issue aside ignores the most creative aspect of living things: problem-solving and the agency of organisms.

In the preceding chapters, we showed why the idea that living organisms are really driven by their genes is a profound misunderstanding of how living systems work. On the contrary, they are open systems at all levels of organisation. How things work at the molecular level is constrained and regulated at the cellular level. The interaction of cells is regulated at the tissue level, and tissues at the organ level, and organs at the system level. The system is regulated by the behaviour of the organisms, and organisms by social and ecological interactions. The psychosocial level is unique. If there is a privileged level of causation, then it lies at the psychosocial level and not at the level of genes. This is the level at which wilful agency is initiated and organisms can be genuinely selfish or altruistic. In truth you cannot be selfish if you do not have the choice to be altruistic, which is why selfishness cannot be applied at a genetic level, neither metaphorically nor literally.

Our bodies are home to a vast sea of microorganisms. They reside inside us and on all our body surfaces. There are as many cells of these microbial partners as there are cells inside our bodies. The word microbiota describes all the organisms that are on our body surfaces as well as inside us. The important role of these partners of ours in our health and fitness has only been realized in the past ten years. They are invisible and do not receive the attention they deserve. The microbiota are a key component of our physical reserve and are vital to our health and fitness. The microbiota influence all of our organ systems, assist in digestion, disease resistance, contribute to metabolism, and are critical for the maintenance of health and fitness. A vital feature of the microbiota is their diversity of organisms—a wide variety of organisms are normally present. Our history with the microbiota is best described by the word coevolution - we evolved with them, and they evolved with us.The good news about the microbiota is that it is relatively easy to change bacterial populations in the gut through diet. Ways to do this are comprehensively outlined in the book.

According to ancient Hebrew tradition, human beings are soil that is divinely animated. This suggests that humanity cannot thrive apart from the earth that inspires and nurtures its life. Recent discoveries in soil science and human physiology indicate that the necessity and intimacy of humanity’s attachments to soil are greater than we might suppose. People are “rooted” beings. This chapter explores what the lives of plants have to teach us about the character of this rootedness, and thus argues that human life is not only animal but also plant in its nature. This is not a reduction of humans to plants but an opening to rethinking what is required of people if they are to live long and well in their places.

We argue here that Tarski’s conception of “the mathematical” is paradigmatic for model theory, moving foward from Tarski’s work into contemporary practice. The question of when a piece of natural language mathematics has a natural syntax or a natural logic is considered, also in the context of Shelah’sPresentation Theorem. The possibility of laying down a methodology providing a mathematically direct conceptualisation of mathematical content is argued for. The seocnd order logic vs set theory debate is considered, especially focussing on previous attempts to separate the two. Symbiosis is discussed at length as providing a solution to the problem of the entaglement of second order logic with set theory.