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First life-forms appeared at least as early as 3.5 billion years ago in the form of prokaryotes. Some of these species developed oxygenic photosynthesis, which resulted in the presence of oxygen gas in the atmosphere. Later, eukaryotes appeared and diversified through mutation and gene duplication (including mutation and duplication of master genes), which led to the rewiring of entire gene networks. The chapter shows that there is no fundamental difference between macroevolution and microevolution. It shows that making artificial life in the lab as well as transgenic life-forms would be impossible if the Intelligent Design scenario were correct. Indeed, ID posits that living systems were holistically designed and thus cannot be constructed in a piecemeal fashion.

While traditionally ecology textbooks only discuss the short term carbon cycle, the role of life has been crucial in the geological long term carbon cycle through processes such as silicate weathering. Arguments have been put forward for the co-evolution of CO₂ levels and terrestrial plants — with adaptations to lower CO₂ levels allowing large leaves to evolve. It seems clear that on Earth without the effect of life our planet would currently have a temperature which would rule out he survival of eukaryotic life. This suggests that carbon sequestration has a positive Gaian effect. However, this is probably a local conclusion which cannot be generalized to all other planets. More generally, these ideas illustrate the importance of biomass as a key feature of global ecologies. The effects of vegetation (or plankton) on carbon cycles are more directly linked to available biomass than species richness.

The Dollo parsimony method is based on the assumption that a complex character that has been lost during evolution of a particular lineage cannot be regained. When applicable, this principle leads to a substantial simplification of evolutionary analysis and provides for unambiguous reconstruction of evolutionary scenarios, which may not be attainable with other methods. In this chapter, applications of Dollo parsimony are described for the quantitative analysis of the dynamics of genome evolution. Dollo parsimony is the method of choice for reconstructing evolution of the gene repertoire of eukaryotic organisms because although multiple, independent losses of a gene in different lineages are common, multiple gains of the same gene are improbable. This contrasts with the situation in prokaryotes where the widespread occurrence of horizontal gene transfer makes multiple gains possible, thereby invalidating the Dollo principle. The chapter applies Dollo parsimony to reconstruct the scenario of evolution for the genomes of crown-group eukaryotes by assigning the loss of genes and emergence of new genes to the branches of the phylogenetic tree, and delineate the minimal gene sets for various ancestral forms. A similar analysis, with rather unexpected results, was performed to infer gain versus loss of introns in conserved eukaryotic genes. The applicability of the Dollo principle for these and other problems in evolutionary genomics is discussed.

This chapter provides a three-part introduction to sex differences, stressing both the conserved and the unique as part of Darwin's notion of descent with modification. The first section takes a step back in time and provides a broad perspective on the evolution of eukaryotes. The evolution of meiosis and syngamy (i.e., the fusion of two cells) was a precondition for the evolution of dimorphic gametes and the subsequent evolution of all other sex differences. It then outlines general causes of sex differences in animals by focusing on natural and sexual selection. The second section discusses the mechanisms that underlie sex differences in gene expression as well as the basic developmental mechanisms that produce sex differences. The third section reviews some elegant research that links evolutionary causes of and proximate mechanisms for sex differences in the brain and behavior. These examples show how sex-specific selection on behavior ultimately drives neural evolution. The chapter concludes by briefly outlining what is known about sexual differentiation of neural mechanisms in humans.

This chapter focuses on how yeast became the prime focus of eukaryotic molecular biology after 1975. It summarizes some of the major studies in yeast biology. It shows how progress in disentangling the complexity of certain features of the eukaryotic cell enabled yeast to supplant the filamentous fungi definitively as a model eukaryote.

This chapter traces the development of the baker's and brewer's yeast known now as Saccharomyces cerevisiae as a model organism. In particular, it discusses studies by Øjvind Winge, Carl Lindegren, and Boris Ephrussi.

This fictional description of the destruction of much of life on Earth comes from a novel by the astronomer Fred Hoyle, co-authored with his son Geoffrey. In the story, the formation of a quasar in the centre of our galaxy leads to the destruction of all life on Earth, except at a few fortuitously sheltered locations. Quasars—first described in 1963—are colossally energetic astronomical objects with extremely high output of radio waves. The novel built on some of Fred Hoyle’s own scientific interests because in the early 1960s, along with the astrophysicist W.A. Fowler, he had predicted that the collapse of a super-massive object could form a distinctive radio source—just before the discovery of the real thing. Although Hoyle and Fowler had the theoretical head start in explaining quasars, being busy with other work they failed to follow up on this advantage, and the current best explanation for these objects is largely due to Donald Lyndon-Bell and Martin Rees. Building on the ideas of Hoyle and Fowler, they argued that a quasar is formed by a rotating super-massive black hole, fed by a disk of in-falling matter, with jets of matter flying away from the system along its axis of rotation. Like the Hoyles’ novel, this chapter focuses on ways the biosphere could end; a fitting question for the close of a book on the ecology and evolution of Earth-based life. However, any answer to a question set in the far future can necessarily be only speculative and, of course, nobody will be around to put the theory to its ultimate test. This raises a philosophical problem namely, has such a question a place in science, or should it be left to science fiction writers? We believe that such questions count as science, not least because it would be good to know the answer (especially if something could be done to postpone the end), but also because in attempting to answer the question, we can extend our understanding of processes that are currently operating. Indeed, J.B.S. Haldane, one of the greatest scientists of the past century, wrote an early essay on much the same topic we consider here.

Brett Dennen is a fine musician, but listening to his lyrics, one might be tempted to think that because we ‘do [or see] it every day’, then it does not deserve an explanation. Our book has dealt with a variety of everyday phenomena such as ageing, sex, species, a green world, and a blue sea, and we hope that by now our readers will agree that there is a reason why things are this way. Indeed, the fact that these phenomena are so commonplace makes the questions all the more important. The exciting thing is that while considerable progress has been made in each of the areas we address, we still do not have a complete answer to any of the questions we have posed. We use this short concluding chapter to pull together some common threads and to discuss some of the interrelationships between our answers. First and foremost, even the most casual reader will note that there is a close interrelationship between the ecological and evolutionary explanations we have presented. Taking the perspective of evolutionary biology, almost all of the evolutionary explanations we have proposed include an important ecological component. For example, ageing is now widely seen to arise as a consequence of there being relatively weak natural selection late in an organism’s life. Yet the primary reason for this ‘selective shadow’ is that predators and parasites are likely to have killed the organism long before it reaches an advanced stage of maturity. Likewise, one explanation for the evolution of sex is that the variation it generates allows at least some of the offspring to better compete with members of the same species, or to avoid parasitism. In a similar vein, many of the ecological phenomena we have sought to explain have evolutionary origins. For example, tropical areas may have more species because rates of speciation are greater in the tropics, or because rates of extinction are greater at high latitudes, or both. Likewise, plants have evolved secondary compounds to deter herbivory, and the presence of these compounds may go some way towards understanding why the world remains green.

Phytoplankton plays a critical role in determining light fields of the world’s oceans, primarily through absorption of light by photosynthetic pigments (see Chapters 1 to 5). Consequently there has been considerable interest from optical researchers in determining phytoplankton absorption. Conversely, from the biological point of view, this absorption assumes paramount importance because it is the sole source of energy for photosynthesis and thus should be central to direct estimates of primary production. There are two logical parts in determining this effect of phytoplankton and in estimating primary production. One is the estimation of abundance, and the other is estimation of specific effect or specific production rate. The earliest estimates of phytoplankton abundance were based on cell counts. From the time of Francis A. Richards’ Ph.D. dissertation, however, measurement of chlorophyll a concentration per unit of water volume, because of its relative ease, has assumed a central role in abundance estimation. Physiological studies and technological advances in optical instrumentation over the last decade lead me to question whether the continued use of chlorophyll a concentration to estimate phytoplankton abundance was wise either from the viewpoint of narrowing confidence intervals on estimates of absorption and production or from the viewpoint of mechanistic understanding of the processes involved. The measurement of chlorophyll a has become such a routine tool of biological oceanography, however, that the reasons for my heresy require elaboration. Some of the reasons are not too subtle. Chlorophyll a exists with other photosynthetic pigments in organized arrays associated with photosynthetic membranes. The function of these arrays is to harvest photons and transfer their energy to the specialized reaction center complexes that mediate photochemistry (see Chapter 9). The size of the arrays or packages and the ratio of chlorophyll a molecules to other light-harvesting pigments within the packages vary with phytoplankton cell size, total irradiance and its spectral distribution, as well as with other environmental parameters. It is well known that dark-adapted (= light-limited) cells increase their complements of photopigments. This plasticity in pigment packaging is evidenced in the variability of chlorophyll a-specific absorption coefficients. Simple optical models based only on chlorophyll a concentrations cannot be accurate or precise unless the effects of pigment packaging are considered.

By the early 1990s, it was becoming clear that the commonly used five kingdom classification schemes were oversimplified and simply inadequate for describing the major divisions of life. At this critical point in time, when morphological data from electron microscopy was beginning to be supplemented with information from DNA sequences, Chris Humphries organized a Linnean Society conference entitled “Modern Views of Kingdoms and Domains” in the spring of 1994 to discuss the new, emerging picture of eukaryotic relationships. This chapter reviews the general history of the debate over the eukaryote tree of life and describes the progress that has been made since that historic conference. When Carl Linnaeus presented the catalog of all life using his binomial system of nomenclature in 1758, he described two kingdoms: Plantae and Animalia. The unicellular eukaryotes were discovered approximately 300 years ago by Antony van Leeuwenhoek, who considered them to be tiny animals that he called simply “animalcules.” This chapter also describes Opisthokonta, Amoebozoa, Archaeplastida, alveolates and stramenopiles, Rhizaria, and excavates.

This chapter reviews the literature on speciation experiments, identifies neglected questions that could be addressed by new experiments, and suggests general guidelines for such experiments, focusing exclusively on sexually reproducing eukaryotes—that is, those with meiosis and syngamy at some stage of the life cycle. It first defines key concepts used in the speciation literature and gives an overview of the questions that have been, or could be, addressed by experimental evolution approaches. The chapter then suggests questions that have been mostly neglected in past experiments, but which are ripe for further investigation, and finally gives some general guidelines for future laboratory experiments on speciation.

This chapter explains what the book is about and highlights the range of processes and questions to be considered. The central thesis is that species represent more than a unit of taxonomy, they are a model of how diversity is structured and how groups of organisms evolve. All organisms live in diverse communities with hundreds of other species. Knowledge of what species are, how they form, and the genetic and ecological interactions among them is therefore vital both for understanding where diversity comes from and for predicting contemporary and future evolution. It is time for evolutionary biology to embrace the diversity of life.

Ever since life’s debut on the earth, biotic evolution has been a near-balancing act. On virtually every level, competition and cooperation, shifting endlessly between foreground and background, have tugged and teased evolving systems as they have wobbled through time along the edge of chaos. The emergence of cellular life from the world of complex carbon-based chemistry appears to have happened only once in the primordial dreamtime of planet Earth. Scientists base this conjecture on a number of virtually universal distributions of chemical structures and processes across the spectrum of living organisms. Despite their perhaps tenuous hold on life, the earliest cells, primitive bacteria and archea, possessed the keys to the opening of new potential for matter and energy—the capabilities of self-replication, controlled energy transduction, directed locomotion, and the regulation of an internal environment. Out of this cellular Big Bang there arose a totally new force field on planet Earth superimposed over the physical, chemical, and geological, but with tendrils pervading all of those realms. It was the beginning of the biosphere. Life pervaded and began to transform the lithosphere, hydrosphere, and atmosphere. The chapter highlights transitions of prokaryote to eukaryote via endosymbiosis. Also featured are: biofilms, bioluminescence, coral reefs, and ecological succession.

This chapter describes evolution as a long-running algorithm that has designed all species on Earth. Evolution, a process discovered by Charles Darwin, has been working for more than four billion years to obtain, at first, simple unicellular organisms (prokaryotes) and, later, much more complex life forms, based on eukaryotic cells. Evolution worked not with bits stored in a computer memory, but with replicators that are digital sequences written in very long DNA molecules, the genomes. Complex cells, which are the results of this optimization algorithm, eventually organized themselves in vast multi-cellular complexes, leading to the multicellular organisms in existence today and, ultimately, to humans and the human brain, the most complex information processing device we know.