Philosophy for Biologists - Part I

Why would any biologist care about philosophy?

This three-part series of blog posts is based on a talk I held at the workshop on "A New Naturalism: Towards a Progressive Theoretical Biology, " which I co-organized with philosophers Dan Brooks and James DiFrisco at the Wissenschaftskolleg zu Berlin in October 2022.

You can find part II here, and part III here.

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You may not know this (few people probably realize it) but it's true: biology urgently needs more philosophy.

After decades of rapid progress, which was mainly driven by methodological and technological progress, biology has arrived at a historical turning point. Reductionist approaches to genetic and molecular analysis are being supplemented by large-scale data-driven approaches and multi-level systems modeling. We are beginning to integrate the dynamics of gene regulatory networks with their physical context at the cellular and tissue level. We are even regaining a glimpse of the whole organism as an object of study. We can now turn our focus back on some of the deepest questions in biology: what makes a living system alive? How come it can exert agency? How does it interact with its environment? What factors shape its evolution? These questions pose a number of challenges that require not technological but conceptual progress: we need new ways of thinking to address them. And we need to re-contextualize what we already know in the increasingly complex societal and environmental circumstances we currently find ourselves in.

Philosophy can be a powerful thinking tool for biologists (or any other scientist, for that matter). It helps us better understand what we are doing when we do research: how we produce trustworthy knowledge, insights that are adequate for our times, why we ask the questions we ask, what methods we are using, and what kinds of explanation we accept as scientifically valid. It enables us to reflect on what motivates and drives our investigations. It highlights the ethical implications of our work. Moreover, we can apply philosophical approaches to address deep biological problems: philosophy can serve us to clarify concepts, to delineate their appropriate domain of application, to reveal hidden meanings or potential misunderstandings, and to provide new perspectives or angles on old questions. In brief: philosophy can help you become a better and more effective researcher.

For that, we need a specific kind of philosophy: philosophy that is tightly connected with the practice of doing research, and is informed by the latest science. Unfortunately, not all philosophy is like that. What we need is not the outdated philosophy of science that most scientists have already heard of: no positivism, Popper, or Kuhn. We also need no armchair philosophers, no far-fetched thought-experiments (on zombies, let's say), no high-level idealized simplifications and over-generalized abstractions. Instead, we need something fresh and novel: a rigorous naturalistic philosophy of biology for the 21st century, the kind of philosophy that is in tune with the latest findings in the life sciences themselves, and is adapted to the best and most realistic accounts of the production of scientific knowledge available today. Our philosophy need not be perfect, but it needs to be practical, applicable, and it needs to keep up and co-evolve with the science it is concerned with.

But even more importantly, we need more philosophical thinking within biology, a new philosophical biology. That's not philosophers thinking about biology, its concepts, methods, practices, and theories, but philosophically sound thinking applied by biologists to biological problems. It is a kind of theoretical biology, a practice within biology, but not one that necessarily involves mathematical modeling. Put simply, it's better thinking for biologists. It is the kind of biology the organicists or C.H. Waddington used to practice.

Waddington's epigenetic landscape and the work he derived from it (beautifully described in "The Strategy of the Genes") are a great example of the kind of philosophical biology I am talking about. Waddington's work radically reconceptualized the study of embryogenesis and its evolution, framing adequate explanations in terms of novel concepts such as chreodes (developmental trajectories depicted by valleys in the landscape),  canalization (structural stability of chreodes represented by the steepness of the valley slopes), and homeorhesis (homeostasis applied to chreodes or the fact that a ball rolling down the landscape would tend to stay at the bottom of a valley). The influence of genes on embryogenesis is depicted by pegs that pull on the landscape through a complex network of ropes, altering the topography in unpredictable ways when mutation alters the arrangement of pegs.

This collage of Waddington's illustrations of the landscape is taken from Anderson et al. (2020).

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Unfortunately, the century-old philosophical tradition of theoretical biology has been all but lost since the early 1970s. Some notable exceptions - torchbearers through the dark ages of molecular reductionism - are the process structuralism of my late masters supervisor and mentor Brian Goodwin (as well as others), which treated developmental processes and their evolution in terms of morphogenetic fields instead of genes as their fundamental units, Stuart Kauffman's work on self-organization in complex networks, the organization of the organism, and its consequences for open-ended evolution (especially in his "Investigations") or, more recently, Terrence Deacon's teleodynamic approach to the organization of living matter (see his "Incomplete Nature"). These researchers have revolutionized how we think about biological processes, organisms, and evolution, but they tend to work in isolation, at the fringes of biology. unnoticed by the mainstream. There would be many others worth mentioning here, but the main point is that examples of conceptually focused biological work are hard to find these days, not even mentioning what struggle it is to try and make a living as this kind of theoretician in biology today.

THE LIMITS OF TECHNOLOGICAL AND METHODOLOGICAL PROGRESS

Looking at the past sixty years or so of biology (starting with the rise of molecular biology), it is easy to convince yourself that progress in biology predominantly derives from technological and methodological advances, not from better concepts or new ideas. Indeed, we have much to show for in that regard. The rate at which we develop new techniques, produce ever more comprehensive data sets, and publish highly sophisticated technical papers appears to be increasing day by day. So what's not to like? We seem to be succeeding according to all our self-imposed metrics.

Well, there is a growing and legitimate concern that this frantic acceleration of technological and methodological progress, this flood of big data, is not always a good thing. First and foremost, the current cult of productivity that comes with this kind of acceleration has a negative impact on researchers (especially young ones), who struggle to keep up with ever increasing demands for a successful career. More generally, it has led to a general neglect (even some disdain) for purely theoretical work in biology. I think this may be the main reason philosophical biology has been obscured in the past few decades. Questions that are not immediately accessible to empirical investigation are dismissed as idle speculation. One such example is the nature of the organism and its role in evolution. Technological progress is so fast that we can always keep ourselves busy with the latest new methodology instead, be it single-cell sequencing, 3D cell culture, or CRISPR gene editing, and the next big technological breakthrough is always just around the corner. Contextualizing our empirical findings within a broader view of life seems unnecessary, as all those intractable theoretical problems will surely become tractable through technological progress in the very near future.

This kind of techno-optimism leads to a dangerous loss of context, a sort of technological tunnel vision. There is a worrisome gap that is opening between our power to manipulate living systems and our understanding of the complex consequences of these manipulations. Take the possibility of gene drives in uncontrollable natural environments as an example. Higher-order ecological effects will be inevitable in this case and almost certainly won't be harmless or benign. In fact, this is an example where we are running at increasing speed through the dark woods, blindly. And in the middle of this, we have hit a solid wall in terms of understanding some of the most fundamental concepts and problems in our field, among them the concept of "life" itself. This severely distorts our understanding of our own place in the world. We are drowning in data, yet thirsting for wisdom as E.O. Wilson once so aptly put it.

To address these pressing issues, we need to urgently relearn to ask the big questions. François Jacob wrote in his "Logic of Life" in 1975 that "biologists no longer study life." This sounds a little crazy but it is essentially true. Yet, we have not really solved the problem of life (as Jacob implies). The truth is that we have not even confronted it. We simply skirted around it, explained it away by reducing organisms to metaphorical programs and machines. We no longer need to worry about such difficult questions. Life as a biologist is so much easier that way. That may be a smart move in a way, but it's not based on any solid grounding. Granted, it enabled us to better focus on those aspects of living systems that were tractable given whatever technological and conceptual capabilities we had at the time. Still, this kind of reductionism is simply bad philosophy, tainted by poor and outdated metaphysical commitments. It looses the forest for the trees.

In fact, it is not too far-fetched to make the claim that we understand what life is (and what it is worth) less than ever before in human history. In other words, we have never been more wrong about life than with our current mechanistic-reductionist approach and its machine view of the organism. The core problem is that we have been carried so far away by the breakneck pace of technological progress that we have started to view the whole world (including all living beings) through the lens of our most advanced technology. We treat life as if it was a computational device that we can fully understand, predict, manipulate, and control. We have forgotten that this machine view of the world is only a metaphor, and not a good one at that. This is dangerous hubris, pure and simple. If we don't take a little time-out to stop and think, we will wipe ourselves from the face of the planet by the mechanistic application of increasingly powerful interventions to complex systems we are not even beginning to understand. We are in danger of losing track of our own limitations. We're on a straight path to oblivion if we let our technological might outpace our wisdom this way. Reconceptualizing life is an important first step, not only towards a deeper understanding of living systems, but also towards a healthier, more sustainable, and less exploitative attitude for humanity towards nature.

A NEW ATTITUDE TOWARDS LIFE?

Thus, the first conclusion I will draw here is that it is essential that we change the way we study and understand living systems. This is a philosophical problem. It requires new ways of thinking, instead of new technology. Unfortunately, the kind of reflection required for such conceptual change is all too often considered a waste of time in our frenzied academic research environments. We are too busy publishing and perishing. Yet, we urgently need to reconsider what we are doing, we must take the time to reexamine our concepts and practices if we are to continue making progress towards understanding life, ourselves, and our place in the universe. What are we collecting data for? Do any of us even remember? Of course, we do. And there are examples where conceptual progress is being made all across the life science. Yet it remains too disconnected and isolated to be truly effective. What is needed is a broader movement towards conceptual change, a much broader confrontation of these issues that is grounded in the most solid and powerful philosophical ideas we have available today.

Such a movement needs a new philosophy of biology that is actually taught and known to practicing researchers, shaping the questions they ask, the methods they use, and the kinds of explanations they consider appropriate. We need to reintroduce philosophy as an essential part of a well-rounded scientific curriculum at our institutions of higher education. In addition, we also need a philosophical kind of theoretical biology that biologists actively engage with in their practice because it is useful to them. The alternative is for us to be buried under rapidly growing heaps of impressive but increasingly incomprehensible data, to wastefully burn through our vast (yet limited) funds and resources, and to end up as ignorant about life as we've ever been. Organisms are not machines. But what are they instead? We currently have no idea.

This, broadly put, is why I believe philosophy is so important to contemporary biology. These are exciting times to be a biologist. We are on the cusp of great discoveries that will revolutionize our discipline, but the revolution won't be achieved without better concepts, better questions, and better theories. For the first time in decades, biology needs conceptual change to drive progress. The time is ripe to teach biologists philosophy again: no condescending preaching from the philosophical pulpit, but a kind of philosophy they will like, find plausible, and which they can put to work in their own research practice. Where do we start?

In the next post, I will examine what I think is the proper naturalist philosophy of biology for the task. Then, in the final part of this trilogy, I will give you a number of examples that illustrate the philosophical kind of theoretical biology we may want to resurrect in order to tackle some fundamental biological challenges of our current age. Stay tuned!