Putting the organism back into biology

2 November 2022

Biology studies organisms. This seems to be a truism. But is this assumption really correct? Some scientists and philosophers hold that it is not. Developmental biologist Brian Goodwin, for example, states:  

“Organisms have disappeared as fundamental entities, as basic unities, from contemporary biology because they have no real status as centres of causal agency. Organisms are now considered to be generated by the genes they contain… This is the sense in which organisms have disappeared from biology” (Goodwin 1999: 230).

Goodwin argues that especially evolutionary biology is to blame for this situation, where in the course of the 20th century genes and populations, but not organisms, have become the central target of researchers’ concerns. Goodwin is not alone with this opinion. Since the 1980s, many attempts to expand or replace the central population genetic framework of evolutionary theory – the so-called ‘Modern Synthesis’ – argued for reestablishing the ‘organism’ as a central unit in evolutionary biology (see Depew and Weber 2013). For example, for evolutionary biologist Stephen J. Gould (1980: 129) a reformed theory of evolution should, among others, reintroduce “to biology a concept of organism”. Philosophers of science Elliot Sober (1980: 334) once stated: “The population is an entity, subject to its own forces, and obeying its own laws. The details concerning the individual who are part of this whole are pretty irrelevant… In this important sense, population thinking involves ignoring individuals”.  

In last three decades we see more and more voices demanding to put organisms back into evolutionary biology. These calls for a ‘return of the organism’ (Nicholson 2014) have been stirred through new findings in fields such as evolutionary developmental biology (evo-devo), epigenetics, microbiome research, and niche construction theory. In these field researchers try to reestablish the organism as a central unit in evolutionary biology. This new “organism-centered perspective” (Laland et al. 2015) argues that the level of the organisms is crucial to not only understand evolutionary relevant dynamics in (gene-)regulatory processes during embryogenesis, but also to study developmental plasticity, non-genetic channels of inheritance, and constructive behaviors that shape organisms’ niches and selection pressures.

This new framework – sometimes labeled the ‘Extended Evolutionary Synthesis’ (Pigliucci and Müller 2010, Laland et al. 2015) – defends two cornerstones of organism-centered evolution:

(1) Contextualizing genes:

Scientists should highlight organismal and developmental contexts of gene activity, and study the impact of these contextual ‘wholes’ in shaping evolutionary processes (rather than abstracting from these organismal contexts when measuring changes in gene-frequencies).

(2) Recognizing organisms’ actions in their environment:

Scientists should understand evolution as the result of organism-environment reciprocal interaction, rather than of external environmental factors causing changes in gene-frequencies and population dynamics.

In short, the organism should be seen as the central, causally efficacious, autonomous, and active unit that modulates inwardly the activity of genes in development, and outwardly its environment and thus its own selection pressures. Taking up these both organismal perspectives should better explain the ‘arrival of the fittest’, i.e. is how variation emerges that then, later, is selected. Philosopher Denis Walsh summarizes this organism-centered view as follows: “The evolutionary biology of our own century suggests that the exclusive reliance on the dynamics of populations ushered in by the Modern Synthesis must be augmented, or perhaps even replaced, by an account of the ways that organisms participate in and direct the process of evolution” (Walsh 2021: 281).   

In other words, this organism-centered biology argues that organisms are not only endpoints of adaptive processes, but also causal starting point of evolutionary trajectories. As biologist and dialectical thinker Richard Lewontin once summarized this position:

“Organisms have constructed environments that are the conditions for their further evolution and reconstruction of nature into new environments. Organisms within their individual lifetimes and in the course of their evolution as a species do not adapt to environments; they construct them. They are not simply objects of the laws of nature, altering themselves to bend to the inevitable, but active subjects transforming nature according to its laws” (Lewontin 1982: 163).

This approach argues that organisms can bias or drive evolution by controlling the availability of variation (inwardly) and modulating selection pressures (outwardly; for Lewontin’s view, see Prieto and Fábregas-Tejeda forthcoming) during development. It rejects views claiming that “allele frequency change [in populations] caused by natural selection is the only credible process underlying the evolution of adaptive organismal traits” (Charlesworth et al. 2017). 

But if the 20th century was a ‘century of the gene’ (Keller 2000) and the 21st will be a ‘century of the organism’ for biology, what does this shift actually mean? What at all is the unit of the organism? How can we link developmental and evolutionary perspectives through a focus on the organism? What kind of biological individual is the organism that legitimizes its allegedly special causal status? How should we conceptualize the organism-environment relation? How can we rightfully say that organism-centered explanations of a particular evolutionary phenomenon are better than gene-centered ones? What consequences does this perspective have on understanding ourselves as human beings, how we relate to our environment and which role we play in evolution? And: Which biomedical consequences does the new emphasis on organismal development and organism-environment relations have?

In our research group ROTO (The Return of the Organism in the Biosciences: Theoretical, Historical and Social Dimensions, https://rotorub.wordpress.com/) at Ruhr University Bochum we seek to address this set of questions.  This project investigates these recent developments from a perspective of integrated history and philosophy of science. It focuses on biotheoretical and conceptual, historical, as well as social and anthropological dimensions of today’s ‘return of the organism’. Especially, it aims at offering solutions for theoretical and societal challenges of organism-centered biosciences in the 21st century.

This concerns the problem that while organisms are increasingly recognized as units that actively construct their own development and their environments, large genomic datasets also reveal that they are inextricable linked with and fully embedded in their material (and social) environment. This ambiguous new character of the individual – to stand out and at the same time to disappear – leads to various methodological and explanatory challenges. This complex current situation can better be understood when compared to periods in the history of biology, especially in the early 20th century, in which the organism category took a, so far, unparalleled strong position in biological theory.

Driven by a rapidly increasing number of new empirical findings and experimental results on the one side, and a lack of conceptual and theoretical frameworks on the other, in the early 20th century (especially in the UK and German speaking contexts) scholars reflect upon the basic concepts that underpin biology (Nicholson and Gawne 2015, Peterson 2016). A central idea was to interlink developmental biology and embryology with evolutionary biology though a unified conceptual and methodological framework that highlights the organism (Baedke 2019, Fábregas-Tejeda et al. 2021). This movement, which included different organicist, holistic and dialectical approaches, had many names: ‘organicism’ (John Scott Haldane), ‘organismalism’ (William Emerson Ritter), ‘organismic biology’ (Ludwig von Bertalanffy), and ‘organismic basic conception’ (Julius Schaxel), to name a few. In our group, we seek to understand how and why this organicist movement defended the view that the concept of organism should be the explanatory starting point of biology, and whether its conceptual framework can provide fruitful stimuli for today’s similar debates.

Finally, what ROTO also investigates is how current (anti-)individualistic developments in biology drive trends in personalized medicine and public health debates. This includes, for example, debates about suitable targets of policy interventions, individuals or collectives, to combat diseases such as cancer and obesity. Here, we recently see a trend to return to racial classifications for studying disease susceptibilities of environmentally embedded individuals, for example, in epigenetics and microbiome research (see Baedke and Nieves Delgado 2019, Nieves Delgado and Baedke 2021).

Looking inward and outward from the organism

Let me pick out two central conceptual challenges that both past and present approaches to organism-centered (evolutionary) biology share. In line with the central two tenets above, let us call them the (a) ‘inward challenge’ and (b) ‘outward challenge’. They concern the questions (a) what the internal organization of the organism is that constitutes its individuality, and (b) how we can separate organisms from their environment, despite the fact that both are deeply intertwined. Answers to both challenges allow clarifying the organism’s internal make-up and organization as well as its border to the external environment. In short, these challenges concern how organisms affect (evolutionary relevant) causal pathways inside of them and in their environment.

To solve the inward challenge means identifying a characteristic intrinsic pattern of organization that is organismal in kind. One traditionally influential view, organism-centered biology commonly draws on, conceptualizes organisms as individual living systems in which the reciprocal interaction of their parts creates and maintains them as functional wholes, which goes back to at least Immanuel Kant. A reoccurring theme in this account is the idea of organismal self-maintenance and self-organization, which has taken many different forms over the years, from metabolic and thermodynamic accounts to views of autopoiesis and operational closure (von Bertalanffy 1937, Schrödinger 1944, Maturana and Varela 1984, Mossio and Moreno 2010). In line with this view of self-maintenance, recently organisms have been characterized as ‘persisters’ (Godfrey-Smith 2013).

While this influential philosophical tradition surely allows grasping some important organizational characteristic of organisms, one might wonder whether it is precise enough. How do we distinguish the self-maintained organizational status of organisms from that of other biological individuals, as this characterization seems to be applicable also to other functionally integrated, self-organizing individuals (wholes) on different levels of organization (e.g., cells, holobionts, colonies)? Thus, it seems that this approach could lead to an inflationary understanding of organismality and cannot clarify which explanatory roles the organism plays in biology. Admittedly, it echoes a common understanding of organisms introduced in the end of the eighteenth century that uses the concepts of organism, life form and biological individual as interchangeably (i.e. organisms are paradigmatic living beings or biological individuals). But one might wonder whether the general self-organizing and -maintaining properties of organisms are exactly those properties that will allow biologists to single out organisms as central explanatory and methodological starting point to study evolution, in contrast to other units. In short, are there any evolutionary-relevant, organizational features that only organisms have and other individuals or life forms do not? An organism-centered biology should be able to answer this question affirmatively.  

Let us now turn to the ‘outward challenge’. In today’s new focus on the organism in evolutionary biology, scholars increasingly question the way the organism-environment relationship and, as a consequence, that of adaptation is constructed. Lewontin (1980: 244-245) once described his version of this critique as follows: “the very use of the notion of adaptation inevitably carries over into modern biology the theological view of a preformed physical world to which organisms were fitted”. Rather than viewing the environment as something external that forces selective pressures on passive organisms, in recent years, biologists and philosophers of science have argued that evolutionary theory should incorporate more seriously the idea of ‘reciprocal causation’ (see Buskell 2019, Baedke 2019, Fábregas-Tejeda and Vergara-Silva 2018, Baedke et al. 2021, Prieto and Fábregas-Tejeda forthcoming). This notion refers to feedback loops whereby organisms actively alter their surroundings, which then act back on the organisms. In these loops, in particular niche constructing activities are central, since in this case organisms can alter selection pressures acting on them, which can affect their evolutionary trajectories.

This view of reciprocal organism-environment interaction that drive evolutionary change is not new. Several advocates of organism-centered perspectives in early 20th century, like John Scott Haldane, Jakob von Uexküll, and Conrad Hal Waddington, defended this view. Unfortunately, studying the interconnectedness of organism and environments in developmental and ecological settings let many of these scholars to also adopt the view that both interacting units ultimately cannot be distinguished from one another. They claimed that the idea of a boundary between organism and environment has to be rejected altogether, as it is impossible “to distinguish separately the factors concerned” (Haldane 1935: 12). Unfortunately, the same tendency can be found in recent attempts to reciprocal causation in evolutionary biology, as biologists and philosophers of biology increasingly reject the idea of a boundary between organism and environment (e.g., see Baedke et al. 2021).   

Somewhat paradoxically, this leads to a conceptual tension between wanting to highlight the organism as crucial autonomous and active unit that causes evolutionary change and, at the same time, understanding the organism as inextricably interwoven and indistinguishable from its environment. The latter position can easily lead to methodological problems as the organism becomes intractable or harder to assay in empirical studies. Thus, future empirical and philosophical work needs to show that the idea or causal reciprocity is in fact able to highlight the organism as identifiable driver of evolution, without losing the organism as a causally efficacious and autonomous unit. To meet this challenge, we recently put forward a model that allows maintaining meaningful boundaries between organism and environment despite their interconnectedness by separating their causal contribution in complex scenarios of niche construction (Baedke et al. 2021).   

The future of organism-centered biology

To see what will be the future for organism-centered biology, we have to understand its past. In 1919, the embryologist and dialectical materialist Julius Schaxel complained:

(Schaxel 1919: 2, German original; picture from the archives of the Ernst-Haeckel-Haus, Jena)

Biology loses its own reasoning, wants to be physics and chemistry of the living, collects immeasurable individual knowledge, hypotheses proliferate uncontrolled, self-reflection, methodology remains undone. Contemporary biology is in a state of crisis.

These worries about increasing specialization and fragmentation of biology were widely shared by Schaxel’s contemporaries. They were triggered by new methodological advances and experimental techniques that let to various new insights into the genetic and cellular nature of organisms, but also into their plasticity, robustness, regeneration, morphology as well as inheritance. However, the interpretation of this complex net of new data became increasingly difficult. Many argued that biology needs a thorough debate on its conceptual and theoretical foundations, in order to structure and guide its different methodological approaches and interlink new empirical findings. For many, the answer to these questions was the organism. The concept of organism should allow interlinking developmental biology and embryology with evolutionary biology and establish a unified framework that highlights organismal processes as the starting point of biological research.

As we have seen, however, developing an organism-centered biology is not an easy task – it wasn’t back then, and it isn’t today. The older organicist movement adopted two different strategies to flash out the nature of the organism. One focused on spelling out internal characteristics of organisms, the other external relationships with the environment. Not least due to the serious challenges these inward and outward looking strategies faced when highlighting the role of the organism in evolution, these approaches were never able to penetrate mainstream evolutionary reasoning. Ultimately, after WWII, they were replaced by more gene-centered approaches.

It seems that not much has changed in the last 100 years. The current calls for a ‘return of the organism’ – which, similar to Schaxel’s complain, criticize the lack of a suitable theoretical framework for evolutionary biology – still follows these two strategies. As a consequence, however, it faces the same challenges. We still see conceptual tensions between individualistic and anti-individualistic perspectives in this movement and scientists still struggle with describing the individual organism as an autonomous and discrete unit and, at the same time, as inextricably interwoven with its environment. Despite these challenges, establishing an organism-centered biology is a worthy endeavor. It is full of promise and rich in history. It may open the door to more pluralist views on biological processes, especially by (re)connecting development and evolution and by avoiding research biases through overly gene-focused approaches. At the same time, as already the organicist movement in the early 20th century learned, there is no obvious way paved by the organism. The concept of organism does not unambiguously stipulate how to move from genes to organisms, how to individuate organism in their environments, or how organisms can figure in evolutionary theory. It’s about time biologists and philosophers jointly pave this way, once and for all.


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