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.

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.

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).

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.

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.

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!

So, this is as good a reason as any to wake up from my blogging hibernation/estivation that lasted almost a year, and start posting content on my web site again. What killed me this last year, was a curious lack of time (for someone who doesn't actually have any job), and a gross surplus of perfectionism. Some blog posts got begun, but never finished. And so on. And so forth.

So here we are: I'm writing a very short post today, since the link I'll post will speak for itself, literally.

I've had the pleasure, a couple of weeks ago, to talk to Paul Middlebrooks (@pgmid) who runs the fantastic "Brain Inspired" podcast. Paul is a truly amazing interviewer. He found me on YouTube, through my "Beyond Networks" lecture series. During our discussion, we covered an astonishingly wide range of topics, from the limits of dynamical systems modeling, to process thinking, to agency in evolution, to open-ended evolutionary innovation, to AI and agency, life, intelligence, deep learning, autonomy, perspectivism, the limitations of mechanistic explanation (even the dynamic kind), and the problem with synthesis (and the extended evolutionary synthesis, in particular) in evolutionary biology.

The episode is now online. Check it out by clicking on the image below. Paul also has a break-down of topics on his website, with precise times, so you can home in on your favorite without having to listen to all the rest.

Before I go, let me say this: please support Paul and his work via Patreon. He has an excellent roster of guests (not counting myself), talking about a lot of really fascinating topics.

Hello everybody. This is my first blog post. I was undecided at first. What do I write about? Where do I begin? Then, last night, I came across this article by Michael Levin and Daniel Dennett in Aeon Magazine. It illustrates quite some of the problems—both in science and about science—that I hope to cover in this blog.

"Cognition all the way down?" That doesn't sound good... and, believe me, it isn't. But where to begin? This article is a difficult beast to tackle. It has no head or tail. Ironically it also seems to lack purpose. What is it trying to tell us? That cells "think"? Maybe even molecules? How is it trying to make this argument? And what is it trying to achieve with it? Interdisciplinary dialogue? Popular science? A new biology? I think not. It does not explain anything, and is not written in a way that the general public would understand. I do have a suspicion what the article is really about. We'll come back to that at the end.

But before I start ripping into it, I should say that there are many things I actually like about the article. I got excited when I first saw the subtitle ("unthinking agents!"). I'm thinking and writing about agency and evolution myself at the moment, and believe that it's a very important and neglected topic. I also like the authors' concept of teleophobia, an irrational fear of all kinds of teleological explanations that circulates widely, not only among biologists. I like their argument against an oversimplified black-and-white dualism that ascribes true cognition to humans only. I like their call for biologists to look beyond the molecular level. I like that they highlight the fact that cells are not just passive building blocks, but autonomous participants busy building bodies. I like all that. It's very much in the spirit of my own research and thinking.

But then, everything derails. Spectacularly. Where should I start?

AGENCY ISN'T JUST FEEDBACK

The authors love to throw around difficult concepts without defining or explaining them. "Agency" is the central one, of course. From what I understand, they believe that agency is simply information processing with cybernetic feedback. But that won't do! A self-regulating homeostat may keep your house warm, but does not qualify as an autonomous agent. Neither does a heat-seeking missile. As Stuart Kauffman points out in his Investigations, autonomous systems "act on their own behalf." At the very least, agents generate causal effects that are not entirely determined by their surroundings. The homeostat or missile simply reacts to its environment according to externally imposed rules, while the agent generates rules from within. Importantly, it does not require consciousness (or even a nervous system) to do this.

AGENCY IS NATURAL, BUT NOT MECHANISTIC
 
How agents generate their own rules is a complicated matter. I will discuss this in a lot more detail in future posts. But one thing is quite robustly established by now: agency requires a peculiar kind of organisation that characterises living systems—they exhibit what is called organisational closure. Alvaro Moreno and Matteo Mossio have written an excellent book about it. What's most important is that in an organism, each core component is both producer and product of some other component in the system. Roughly, that's what organisational closure means. The details don't matter here. What does matter is that we're not sure you can capture such systems with purely mechanistic explanations. And that's crucial: organisms aren't machines. They are not computers. Not even like computers. Rosen's conjecture establishes just that. More on that later too. For now, you must believe me that "mechanistic" explanations of organisms based on information-processing metaphors are not sufficient to account for organismic agency. Which brings us to the next problem.

EVOLVED COMPUTER METAPHORS

We've covered quite some ground so far, but haven't even arrived at the main two flaws of the article. The first of these is the central idea that organisms are some kind of evolved information-processing machines. They "exploit physical regularities to perform tasks" by having "long-range guided abilities," which evolved by natural selection. Quite fittingly, the authors call this advanced molecular magic "karma." Karma is a bitch. It kills you if you don't cooperate. And here we go: in one fell swoop, we have a theory of how multicellularity evolved. It's just a shifting of boundaries between agents (the ones that were never explained, mind you). Confused yet? This part of the article is so full of logical leaps and grandstanding vagueness that it's really hard to parse. To me, it makes no sense at all. But that does not matter. Because the only point it drives at is to resuscitate a theory that Dennett worked on throughout the 1970s and 80s, and which he summarised in his 1987 book The Intentional Stance. 

THE INTENTIONAL STANCE

The intentional stance is when you assume that some thing has agency, purpose, intents in order to explain it, although deep down you know it does not have these properties. It used to be big (and very important) in the time when cognitive science emerged from behaviourist psychology, but nowadays it mostly applies to rational choice theory applied in evolutionary biology. For critical treatments of this topic, please read Peter Godfrey-Smith's Darwinian Populations and Natural Selection, and Samir Okasha's Agents and Goals in Evolution. Bottom line: this is not a new topic at all, and it's very controversial. Does it make sense to invoke intentions to explain adaptive evolutionary strategies? Let's not get into that discussion here. Instead, I want to point out that the intentional stance does not take agency serious at all! It is very ambiguous about whether it considers agency a real phenomenon, or whether it uses intentional explanations as purely heuristic strategy that explicitly relies on anthropomorphisms. Thus, after telling us that parts of organisms are agents (at least that's how I would interpret the utterly bizarre "thought experiment" about the self-assembling car) they kind of tell us now that it's all just a metaphor, this agency thing. What is it, then? This is just confusing motte-and-bailey tactics, in my opinion.

AGENCY IS NOT COGNITION!!!

So now that we're all confused whether agency is real or not, we already get the next intellectual card trick: agency is swapped for cognition. Just like that. That's why it's "cognition all the way down." You know, agency is nothing but information processing. Cognition is nothing but information processing. Clearly they must be the same. There's just a difference in scale in different organisms. Unfortunately, this renders either the concept of agency or the concept of cognition irrelevant. Luckily, there is an excellent paper by Fermín Fulda that explains the difference (and also tells you why "bacterial cognition" is really not a thing). Cognition happens in nervous systems. It involves proper intentions, the kind you can even be conscious of. Agency, in the broad sense I use it here, does not require intentionality or consciousness. It simply means that the organism can select from a repertoire of alternative behaviours when faced with opportunities or obstacles in its perceived environment. As Kauffman says, even a bacterium can "act on its own behalf." It need not think at all.

PANPSYCHISM: NO THANK YOU

By claiming that cells (or even parts of cells) are cognitive agents, Levin and Dennett open the door for the panpsychist bunch to jump on their "argument" as evidence for their own dubious metaphysics. I don't get it. Dennett is not usually sympathetic to the views of these people. Neither am I. Like ontological vitalism, panpsychism explains nothing. It does not explain consciousness or how it evolved. Instead, it explains it away, negating the whole mystery of its origins by declaring the question solved. That's not proper science. That's not proper philosophy. That's bullshit.

SO: WHAT'S THE PURPOSE?

What we're left with is a mess. I have no idea what the point of this article is. An argument for panpsychism? An argument for the intentional stance? Certainly not an argument to take agency serious. The authors seem to have no interest in engaging with the topic in any depth. Instead, they take the opportunity to buzzword-boost some of their old and new ideas. A little PR certainly can't harm. Knowing Michael Levin a little by now, I think that's what this article is about. Shameless self-promotion. Science in the age of selfies. A little signal, like that of the Trafalmadorians in The Sirens of Titan that constantly broadcasts "I'm here, I'm here, I'm here." And that's bullshit too.

To end on a positive note: the article touches on a lot of interesting topics. Agency. Organisms. Evolution. Philosophical biology. Reductionism. And the politics of academic prestige. I'll have more to say about all of these. So thank you, Mike and Dan, for the inspiration, and for setting such a clear example of how I do not want to communicate my own writing and thinking to the world.