The species debate forms a deep undercurrent in microbiology, both historically and in contemporary practice. This chapter will outline those disagreements in light of the microbial characteristics that frustrate universal species concepts and even consistent practical definitions. An environmentally oriented approach to classification is an alternative that emerges in the aftermath of these debates. It points to the causal capacities of larger functional groups of microorganisms.

Species as the unit of microbial evolution

The concept of species has a long and troubled history in microbiology. Microbiologists have made considerable efforts over the last century to find a ‘natural’ classification system. Scientists, historians and philosophers have frequently remarked about the difficulties of doing so. Without recapitulating too much of this well-known debate, I will summarize the issues and assess where microbiology is today in regard to the elusive concept of species – and more practically important, the operational definitions employed – in order to work out how much this conceptual status matters to classification practice.

A short history of species classification in bacteriology

One way of parsing the entire history of microbiology is as a history of the quest for species and the right species concept. Until the 1770s, says historian Marc Ratcliff, ‘animalcules did not exist as species, but only as specimens’ (2009: 190). Many of the most famous early observers of microorganisms, including van Leeuwenhoek, did not name a single type of microbe. Instead, they referred to the organisms they observed in only the broadest and most colloquial terms.

Microbial ecology until recently was a minor stream of microbiology. Molecular innovations have now pushed the field to the forefront of microbiological research. At the same time, these methods have generated a whole raft of conceptual issues about microbial biodiversity. These are not simply questions of how many microbial species there are, but more basic ones about whether taxa are the entities that should be the units of analysis or whether functionally interacting groups are more appropriate. Communities and ecosystems are increasingly the object of attention in microbial ecology. Analyses at these levels raise further questions about whether concepts of organism, multicellularity and reproduction should be understood in dependence on animal-based notions. Likewise, models of the distribution of microbial biodiversity and community assembly have been borrowed from large-organism ecology, but their application in microbial ecology suggests new approaches to macrobial ecology.

A brief history of microbial ecology

Most histories of microbiology do not emphasize ecological perspectives. This is at least in part because of the emphasis on laboratory-based pure culture methods and the medical applications of microbiology. However, in the early days of microbiology, when taxonomic efforts dominated, many systematists had no choice but to gather their organisms from environmental sites and even study them there, since laboratory cultures did not exist. For example, Ehrenberg – the taxonomist mentioned in Chapter 3 – collected or was sent samples from the Red Sea, the Rocky Mountains in the United States and a great variety of other aquatic and terrestrial sites (Ehrenberg 1838; O’Malley 2007). Later, as the pure culture method rose to prominence, a few microbiologists augmented their laboratory work with techniques that approximated environmental conditions. They also laid more explicit foundations for microbial ecology. These researchers argued that making ‘controlled’ approximations of natural environments was a rigorous scientific strategy that would deliver more knowledge than pure culture could (Stanier 1951).

This chapter will end the book by addressing some broad questions that arise from the more detailed discussions in previous chapters. These questions have to do with life: how microbiology puts human life into a broader biological context, what life is, and how the study of life could and should be understood by philosophy of biology.

Putting human life into a microbial context

The previous chapters have emphasized a ‘continuity of life’ perspective that sees all living things as sharing many common capacities. Living entities can be examined within shared scientific frameworks for classification, evolution and ecology, even as this common treatment enables an understanding of major differences between diverse forms of life. There is no need in this loose way of thinking about life to invoke anything such as vitalism, but there is a requirement to understand the physical processes, geology and chemistry that contribute to the origin and evolution of living things. However, despite this unobjectionable continuity view, there is still a tendency amongst philosophers and scientists to perceive humans as special – as something biologically, socially and culturally more extraordinary than the rest of life.

This chapter aims to address a question that is central to the motivation for reading (and writing) the rest of the book: why is it valuable to examine microbiology philosophically? As an initial response to this question, I will outline two microbiological case studies. One concerns major evolutionary transitions and how these need a new framework when microbial metabolism is taken into account. The other is about magnetotactic bacteria and their interpretation in philosophy of mind. These cases show in general and specific ways how philosophy can interact fruitfully with microbiology.

Philosophy vis-à-vis microbiology: two sketches

The philosophical importance of microbiology needs further argument, and I will provide a basis for this via two case studies. Each will explore certain capacities of microbes and discuss them in relation to how the science has been interpreted philosophically. One will start from a planetary perspective while the other will enter the inner mental world. The first case concerns microorganismal phototrophy or ‘light eating’ in the form of oxygen-generating photosynthesis. I will discuss the biological production of oxygen as a major transition in evolutionary history and consider whether its exclusion from the main account of evolutionary transitions is justified. The second case is focused on a microorganism that has had a curious amount of attention in philosophy: the magnetotactic bacterium. Long an example for teleosemantics, which is the philosophical study of how mental content can be explained naturalistically, further analysis of this organism challenges its exemplar status and the standard adaptationist interpretations of its magnetotactic capacities. Both cases give some insight into the ways in which microbes can be useful to philosophy.

This chapter will examine a range of the classificatory practices used to order the microbial world. Some of the categories in hierarchical classification are understood as ‘real’ and others not. Microbiology’s quest for a natural classification system has usually been thought about in regard to species. However, other levels in the ‘grand hierarchy of life’, such as kingdoms and domains, are just as problematic. I will examine several of these higher-level debates and conclude with their implications for classification in general.

Microbes versus macrobes; pragmatic versus natural classification

This book is about a vaguely defined type of life form: the microorganism. The label ‘microbe’ or ‘microorganism’ is used to describe any organism too small to be seen without a microscope. Conventionally, this category includes bacteria, archaea (which also used to be called bacteria), protists and many fungi. Microbiology textbooks usually include viruses and virology within the remit of microbiology (e.g., Madigan et al. 2008), although many microbiologists and virologists do not count viruses as microbes (e.g., van Regenmortel 2011). Although microscopic size is an undeniably important feature of microorganismal life, it is also a very problematic criterion. Many of these supposedly microscopic organisms are quite visible to the naked eye, due to their habit of clustering together in large, sometimes colourful, single-taxon colonies (for example, moulds and filaments) or ubiquitous multitaxon biofilms (slimy accretions of microbes). There are even some bacteria that are visible as single cells. One of these is the spherical sulphur bacterium, Thiomargarita namibiensis, which is found in seafloor sediments off the coast of Namibia. It can have a diameter of up to 750 μm (1000 μm = 1mm) and now tops the growing list of giant bacteria, all of which have enormous amounts of DNA due to genome duplication (Angert 2012).

The microbial world has major implications for how evolution is theorized and researched. Philosophy of biology has focused on the evolutionary theory developed for animals and plants. This chapter will examine what happens to philosophical analyses of evolution when prokaryote evolution is taken into account. I will do this by focusing on several evolutionary processes that are often claimed to distinguish microbial evolution from macrobial evolution. The chapter will conclude with reflections on the ways in which microbial evolution might be the more encompassing way of thinking about and investigating evolution in general.

Microbes and the modern synthesis of evolutionary biology

It is now commonly thought that microbes should fit into the modern synthesis of evolutionary biology, either as simpler versions of multicellular sexually reproducing organisms, or – in the case of prokaryotes – as somewhat anomalous phenomena that do not greatly perturb evolutionary theory. However, this has not always been the case in the history of evolutionary biology. Even now, a number of contemporary microbiologists and other biologists are more inclined to embrace the idea that ‘bacteria are different’ (Levin and Bergstrom 2000: 6981). They give several reasons for this claim. Prokaryotes and many other unicellular organisms do not need to recombine genomes to reproduce. They commonly multiply themselves through binary fission, thereby giving rise to genetically identical clonal lineages. Because prokaryote genomes are not in a nucleus or specialized germ cell, they are often argued to be ‘more directly exposed to environmental influences than the germline DNA of animals’ (Sharp and Agrawal 2012: 6142). This exposure makes prokaryote genomes more vulnerable to DNA damage and thus more mutable. Bacteria in particular are known to possess ‘mutator’ genes, which allow elevated rates of mutation. Prokaryote genomes are also more open to the introgression (incorporation) of foreign DNA.

This chapter investigates the way in which microbes have been used in general biological research. Microbial model systems have served as the material and epistemic bases for several incarnations of molecular biology, as well as experimental evolution and ecology. Microbes have been used to exemplify general theoretical accounts and concepts, pertinent to all life, and they do this via capacities for representation and tractability. Microbial model systems also illuminate philosophical analyses of classification, evolution and ecology. I suggest as a conclusion that philosophy should start with microbes as the entry point into biological reflection and only subsequently focus on larger organisms.

Microbes as model molecular systems

The idea that microorganisms could be used to understand any life form has important roots in the late-nineteenth century. Beijerinck – whom we met in the ecology and classification chapters – argued alongside founding geneticist William Bateson (1861–1926) that bacteria should be understood as genetic and biochemical model systems. He thought they were both experimentally tractable and representative of all forms of life (Beijerinck 1900–1901; Bateson 1907, in Summers 1991). Beijerinck’s research focused on how different bacterial physiologies could be understood as adaptations to environmental conditions. He believed that microbiology could contribute to a universal theory of life that would be built on the new science of heritability and variation (1895, in Theunissen 1996; van Iterson et al. 1983 [1940]). This science eventually would be known as genetics, and Beijerinck predicted that enzymes would form the material basis of inheritable ‘genes’.

Philosophy of microbiology might seem like a highly specialized and even esoteric subfield of philosophy of biology. However, there are many good reasons to think that in fact microbes form the basis of all things biological and thus have major contributions to make to philosophy of biology. This chapter, and the book in general, will make that case.

The grounds for a philosophy of microbiology

Microbes are the most important, diverse and ancient life forms on our planet. The science of these organisms, microbiology, is the science of the most significant living entities and their influence on all the rest of life. Many philosophers will need to be persuaded of these claims, and this book will try to do that. Every scientific field has philosophical aspects, from how the objects of study are conceptualized to the ways in which those objects are known, but microbiology’s philosophical issues have only just begun to attract sustained attention from philosophers of biology. These philosophical aspects have driven many debates in microbiological research itself. This book will set out some central philosophical issues in microbiology, along with suggestions for how microbiological insight contributes to and even transforms philosophy of biology. I will start by making a case for philosophy of microbiology based on a general appreciation of the microbial world and its significance for all life. If the world we inhabit is indeed a microbial world, then many of the standard philosophical ways in which we conceive biological phenomena and how they are investigated will have to be rethought. Each of the following chapters deals with a particular aspect of that rethinking.