How A Single Metaphor Transformed Biology
René Descartes kinda ruined biology
Overview of the series
This video is the first in a series on biological agency. In this introduction, I give a very brief overview of the history of agential thinking in biology from Aristotle through to the organicists in the 1930s. In future parts, I'll look at: i) how leaving out agency (via the machine metaphor) breaks down in modern biology; ii) how goals and teleology in general can be naturalised, studied empirically, and highlight the value of taking this approach; iii) why reductionism is a flawed epistemic method and why taking many higher level perspectives (like the agential one) is useful and; iv) why once we take all over the above into consideration, it would be unreasonable to expect laws of nature in biology and other 'soft' sciences.
Further reading
Denis Walsh's book Organisms, Agency and Evolution will form the backbone of this series and the first chapter Introducing organisms provides the backbone of this video.
D. M. Walsh
There is also Bill Wimsatt's magnificent book Re-Engineering Philosophy for Limited Beings which is not super important for this video, but will be great background reading for the next ones. I also stole the idea of the "rainforest universe" from chapter 10 of Wimsatt's book (or in more philosophy-jargon terms the "tropical rainforest ontology"). We'll come back to Wimsatt later though.
And of course, there's the Stanford Encyclopaedia of Philosophy entry, which is always useful.
If you prefer watching YouTube videos/lectures, I'd start with Yogi Jaeger's series Beyond Networks, specifically these two videos:
Sources
"Organisms do things" … is a pretty uncontroversial statement. But "organisms want to do things" is a whole lot more controversial. Do plants really want to grow? Do our hearts aim to pump blood around our body? Do our cells know how to divide?
Using intentional language like this to describe non-conscious creatures in biology seems to only be useful as a metaphor. Of course our cells don't want to do anything - they're just a bundle of chemistry, they don't have brains. That said, when you watch a video like this of a white blood cell chasing a bacterium, you can't help but think that its goal is to catch it.
Source:
David Rogers (who filmed this in the late 1950s!)
Walsh, D. M. (2015). Organisms, agency, and evolution. Cambridge University Press, p. 186. https://doi.org/10.1017/CBO9781316402719
The question of whether the language of "goals," "trying," "knowing," and "wanting" belong in science or not, is the centre of a two-thousand year old debate in biology. And in this series of videos, I hope to convince you that such language is more than just a useful metaphor. Taking it seriously could be the change in perspective we need to fight cancer, develop a new theory of evolution and unlock the secrets of how our brains work.
Sources:
In De Anima (350BC), Aristotle formulated his concept of the soul in opposition to the Pre-Socratics Atomists, Democritus and Empedocles, who came before him. So indeed, the debate has been going on for at least 2022 - (-350) = 2372 years.
Walsh, D. M. (2015). Organisms, agency, and evolution. Cambridge University Press, pp. 5-6. https://doi.org/10.1017/CBO9781316402719
https://plato.stanford.edu/entries/teleology-biology/
As for the possible applications of the agential perspective:
1. Cancer
Sultan, S. E., Moczek, A. P., & Walsh, D. (2022). Bridging the explanatory gaps: What can we learn from a biological agency perspective?. BioEssays, 44(1), 2100185, p. 9. https://doi.org/10.1002/bies.202100185
2. Evolution
Walsh, D. M. (2015). Organisms, agency, and evolution. Cambridge University Press, pp. 163-247. https://doi.org/10.1017/CBO9781316402719
Chiu, L. 2022. Extended Evolutionary Synthesis. A Review of the Latest Scientific Research. John Templeton Foundation. West Conshohocken, Pennsylvania, USA. 85 pp. https://doi.org/10.15868/socialsector.40950
3. Cognition
https://aeon.co/essays/how-to-understand-cells-tissues-and-organisms-as-agents-with-agendas
Two thousand years ago, the language of purposes was at the heart of biology. It was how we respected the richness, complexity and unpredictability of the natural world. We looked at it, the way we look at a rainforest. We were astounded by its beauty and deeply unsure if we would ever be able to understand it.
Sources:
More reference to Aristotle's teleological conception of the world, with some inspiration from Bill Wimsatt's "tropical rainforest ontology." Although the use of the term 'rainforest' in this way is very much modern, I argue that Aristotle's theory is inherently a multi-level perspective, hence rainforest. Though, it is missing the process ontology we now know and love because of evolution. But hey, it's a beautiful metaphor, forgive me for reappropriating it slightly.
Wimsatt, W. C., & Wimsatt, W. K. (2007). Re-engineering philosophy for limited beings: Piecewise approximations to reality. Harvard University Press, pp. 193-240.
For the sense of beauty of the universe, that's expressed in Plato's allegory of the cave, and our inability to understand the universe in Socrates.
https://en.wikipedia.org/wiki/I_know_that_I_know_nothing
https://en.wikipedia.org/wiki/Allegory_of_the_cave
But somewhere along the way, we replaced this thriving world with a dead one. We took all the life out of it, and looked at it like a machine. It was reducible to its parts. It ticked away like clockwork, dictated by natural laws. And it was devoid of all purpose.
Sources:
A reference to the rise of the mechanical philosophy in the seventeenth century, pushed by Descartes in particular.
https://plato.stanford.edu/entries/descartes/
https://en.wikipedia.org/wiki/Mechanical_philosophy
https://twitter.com/Sara_Imari/status/1565564272075149312?s=20&t=8nqQO-TqCe2460xIP4ptTg
So how did we get here? How did we lose sight of the rainforest universe? How did the machine metaphor infect biology?
Around 350 BC, Aristotle wrote his treatise De Anima, a comprehensive account of the biological soul. This soul, or anima in Latin, was nothing like the Christian concept of the soul that exists today. It wasn't a physical 'thing', nor could it be separated from the body it was located in. Rather, Aristotle described the anima as the collection of active abilities possessed by the organism. So for instance, a plant's anima is made up of its ability to grow and reproduce. But a human's anima is more complex since it also includes our ability to think and reason.
Source:
https://plato.stanford.edu/entries/ancient-soul/
This way of thinking about life is called teleology. It's the idea that organisms have goals or purposes. They're not just the product of atoms bumping together. They actually strive to do things. They're … alive.
To our modern ears, talk of trees wanting to grow upwards sounds pretty foreign and it would be easy to dismiss it as nonsense. But let's entertain the idea for a second. You have to remember that this is a time before science or Christianity. There's no theory of natural selection yet. So without the anima, the Greeks would have to explain, how an apple tree manages to produce apples consistently, purely in terms of the random movement of atoms.
Source:
https://plato.stanford.edu/entries/democritus/
Walsh, D. M. (2015). Organisms, agency, and evolution. Cambridge University Press, pp. 5-6. https://doi.org/10.1017/CBO9781316402719
Quite rightly, Aristotle says that this just seems way too improbable. Clearly the coordination of our body parts or a tree's form is hardly accidental. And Aristotle argues that to explain these regularities, we have to look to the organism's goals.
We have a mouth because we have to eat. And a tree grows apples because it needs to reproduce. As Denis Walsh puts it:
For Aristotle, 'way of life' explains the arrangement of parts and not the other way around.
Sources:
Walsh, D. M. (2015). Organisms, agency, and evolution. Cambridge University Press, pp. 5-7. https://doi.org/10.1017/CBO9781316402719
Hankinson, R. J. (1998). Cause and explanation in ancient Greek thought. Clarendon Press, pp. 125-159. https://doi.org/10.1093/0199246564.001.0001.
Gotthelf, A. (1997). Understanding Aristotle’s teleology. Final causality in nature and human affairs, pp. 71-82. https://doi.org/10.1093/acprof:oso/9780199287956.003.0003.
This goal-driven way of looking at organisms was certainly useful. And it gave many Arab and European thinkers the tools for understanding the regularities of life for, over two thousand years.
Source:
https://plato.stanford.edu/entries/ibn-rushd-natural/
https://plato.stanford.edu/entries/aquinas/
But in the seventeenth century, a very different perspective of the world was beginning to gain ground.
René Descartes is a French philosopher living in the Netherlands. In 1618, while on military duty in Breda, Descartes meets the craftsman Isaac Beeckman who introduces him to some revolutionary ideas.
Whilst Descartes' scholastic education in France was dominated by Aristotle's philosophy, here in the Netherlands with Beeckman, Descartes is free to theorise as he pleases and be as creative as he wants to. And so together with Beeckman, he begins to formulate what will become known as the mechanical view of the universe.
This is the idea that the world is no more than a clock. So to understand it, we have to take it apart into its smaller pieces. And once we do that, we find that the pieces don't have any self-organising goals like Aristotle suggests. They're just physical matter ticking away.
From this central metaphor, Descartes believes that we can study the world in the same way that we study clocks. That is, by looking at how matter moves according to set laws. We don't need any more than that. No anima required*.
So for Descartes the universe was dead. There were no internal goals, no wanting, no striving, no thinking. (Actually he makes an exception for us humans, that's his famous 'I think therefore I am'). But everything else was dead.
Animals were just machines. All of their behaviour could be understood by simple matter in motion. Therefore, we shouldn't feel guilty for killing them or cutting them open alive as this is just the same as taking apart a clock. Animals, for Descartes, were not really alive.
Sources:
https://plato.stanford.edu/entries/descartes/
But how then to answer the question that puzzled Aristotle? If everything is just dead matter in motion, why are living things so well organised?
Descartes attempted to give some preliminary mechanical explanations to account for how animals managed to breathe and circulate blood. But it still left the question of why these mechanisms existed in the first place.
Source:
https://plato.stanford.edu/entries/descartes/
Grosholz, E. R. (1991). Cartesian method and the problem of reduction. Oxford University Press, pp. 117-132. https://doi.org/10.1093/acprof:oso/9780198242505.003.0007
William Paley would give the clearest answer to this question two centuries later in his magnum opus Natural Theology. He extended Descartes' watch metaphor to say that if the world and everything in it operated like clockwork, then there must have been a watchmaker to put it all together. That watchmaker being God.
So why do animals have lungs to breathe in oxygen and hearts to pump blood? Well, because God designed them to be that way.
The nature of this answer is actually pretty teleological. It gives a purposeful explanation for why things are the way they are. But here, the why's are externally imposed onto organisms, not internally generated by an anima as Aristotle had imagined it two thousand years before. The universe was still a machine, it just happened to be God's machine.
So although our digestive system follows certain mechanistic laws based on our physiology, the reason it's so perfectly designed is because God created it for us. There’s no need for an internal soul to do all the organising, when God has designed everything already.
The mechanisms explain the how and God explains the why.
Source:
Paley's argument is pretty controversial today amongst biologists because of its association with the intelligent design movement. That said, in 1986, Richard Dawkins showed how the watchmaker analogy had actually survived into modern biology. But rather than an intentional, purposeful watchmaker, we have a blind watchmaker - natural selection.
So when biologists stumble across some beautiful adaptation in nature like the streamlined body shape of a fish, they're less likely to say "Wow, look at what God has made!" and instead opt for "Wow, isn't natural selection crazy?"
It's crazy. I love natural selection.
Source:
Dawkins, R. (1986). The blind watchmaker: Why the evidence of evolution reveals a universe without design. Norton & Company, Chapter 1. https://en.wikipedia.org/wiki/The_Blind_Watchmaker
https://ncse.ngo/william-paley-1743-1805
In taking the place of 'God the designer', natural selection gives biologists a way to talk about purposes, functions and other teleological ideas in the natural world. We really can say that: "cactuses have spines for the purpose of deterring herbivores." Because this is just shorthand for "in an environment with lots of cactus-eating herbivores, cactuses with spines tended to get eaten less and were favoured by natural selection to survive and reproduce." Yeah that's a mouthful and is why the shorthand is so common.
Source:
Okasha, S. (2018). Agents and goals in evolution. Oxford University Press, pp. 18-21. https://doi.org/10.1093/oso/9780198815082.001.0001
Mayr, E. (1998). The multiple meanings of 'teleological'. History and philosophy of the life sciences, 20(1), 35-40.
But we're still a long ways off from what the Aristotelian universe looked like. The cactus is still not really alive. It's not an active player in control of its own fate, it's just an object formed by natural selection. The universe is still dead.
Source:
Lewontin, Richard C. (1983). The Organism as the Subject and Object of Evolution. Scientia 77 (18):65. http://joelvelasco.net/teaching/systematics/Lewontin 83 - organism as subject and object .pdf
Many people are entirely happy with this picture of the world. For instance, Nobel prize winning biologist François Jacob celebrated the fact that 'we no longer study life in our laboratories.' But this quip ignores the problems of the machine worldview.
Source:
Jacob, F. (1970). La logique du vivant. Gallimard, p. 320. https://archive.org/details/lalogiqueduvivan0000jaco/page/320/mode/2up?q=+&view=theater
On n'interroge plus la vie aujourd'hui dans les laboratoires.
If we simply think of organisms like machines and reduce them to their genetic parts, we can seriously oversimplify the world. We can begin to think that race, behaviour and sexuality are all just a product of our genes. That we're just computers, programmed by our genetic code. That evolution is just the changing of gene frequencies. That the whole organism can be derived from just its molecular parts.
Sources:
https://mercatornet.com/the-hunt-for-the-gay-gene-continues/77114/
Schaffner, K. (1969). The Watson-Crick Model and Reductionism. British Journal for the Philosophy of Science 20, pp. 326–327. https://www.jstor.org/stable/686260
None of these things are true. The genetic approach is a useful map for navigating some of the biological world, but it's become so widespread that the map has become the world.
Sources:
Lewontin, R. C. (1972). The apportionment of human diversity. In Evolutionary biology (pp. 381-398). Springer, New York, NY. https://www.vanderbilt.edu/evolution/wp-content/uploads/sites/295/2022/04/lewontin1972.pdf
Ganna, A., Verweij, K. J., Nivard, M. G., Maier, R., Wedow, R., Busch, A. S., ... & Zietsch, B. P. (2019). Large-scale GWAS reveals insights into the genetic architecture of same-sex sexual behavior. Science, 365(6456). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7082777/
Winther, R. G. (2020). When maps become the world. University of Chicago Press. https://press.uchicago.edu/ucp/books/book/chicago/W/bo45713064.html
This isn't a new realisation. There was immediate resistance to Descartes' machine metaphor, with many biologists insisting that organisms were more than machines. There was one problem in particular, that seemed to defy mechanistic explanations.
It was the question of how organisms could develop from relatively simple forms, to immensely complex ones. It almost seemed like magic.
Source:
http://www.janvanijken.com/films/becoming/
Nothing else in the universe seemed to behave the way life did here. I mean, if I plant a rock in some soil, it doesn't just turn into a full organism. Clearly something special was going on.
The solution was to posit that there was some kind of mysterious force, directing the chemicals inside living things around, causing them to become more complex. This force went by many different names over the years, but they all fell under the umbrella term vitalism.
Vitalism was a very different philosophy to Descartes' because, vitalists saw the biological world as being directed by non-physical forces. But their belief in these forces wasn't based on mere speculation or religious convictions. They were grounded in concrete, empirical observation.
Source:
McLaughlin, P. (2014). The Impact of Newton on Biology on the Continent in the Eighteenth Century. The Reception of Isaac Newton in Europe, Londres, Continuum, à paraître. https://www.uni-heidelberg.de/fakultaeten/philosophie/philsem/md/philsem/personal/mclaughlin_newton_biology.pdf
In 1891, a 24-year old German embryologist Hans Driesch was working in Naples on sea urchins. One day, Driesch takes a 16-cell sea urchin embryo and cuts it in half.
Taking the mechanical philosophy seriously, if the embryo contains the complete information needed to make an organism, then each of these halves should only contain enough information to make half an organism. Makes pretty good logical sense.
But to his surprise, each of these halves managed to develop into whole sea urchin larvae. This was a very unexpected and seemed to defy the mechanistic view. You can't split a machine into its parts and watch them turn back into whole machines again.
For the next seven years, Driesch carried out experiment after experiment to work out what was going on here but by the early 1900s he didn't think that there would be a mechanistic solution to the problem. He claimed that there must be a kind of vital force guiding the sea urchin embryos to organise themselves.
Source:
Allen, G.E. (2005). Mechanism, Vitalism and Organicism in Late Nineteenth and Twentieth-Century Biology: The Importance of Historical Context. Studies in the History and Philosophy of Biology and the Biomedical Sciences 36: 261–283 https://www.researchgate.net/profile/Garland-Allen-2/publication/24176290_Mechanism_vitalism_and_organicism_in_late_nineteenth_and_twentieth-century_biology_The_importance_of_historical_context/links/5a660836a6fdccb61c590b23/Mechanism-vitalism-and-organicism-in-late-nineteenth-and-twentieth-century-biology-The-importance-of-historical-context.pdf
No process in late nineteenth or early twentieth-century biology remained more of a bastion for metaphysical explanations than that of fertilization of the egg by a sperm and the subsequent developmental events that it triggered.
The vitalists never managed to provide conclusive evidence for their vital forces and eventually vitalism would be abandoned for being too unscientific, but Ernst Mayr rightly points out that:
It would be ahistorical to ridicule vitalists. When one reads the writings of one of the leading vitalists like Driesch one is forced to agree with him that many of the basic problems of biology simply cannot be solved by a philosophy as that of Descartes, in which the organism is simply considered a machine... The logic of the critique of the vitalists was impeccable.
Source:
Mayr E (2002) The Walter Arndt Lecture: The Autonomy of Biology, adapted for the internet, on "BOTANY ONLINE: Ernst MAYR: Walter Arndt Lecture: The Autonomy of Biology". Archived from the original on 2006-09-26. Retrieved 2006-09-24.
In fact, in the early 20th century, a small group of biologists known as the organicists, took on the spirit of vitalism without its extra metaphysical baggage.
They argued that most biological phenomena arose out of the reciprocal interactions between different parts and levels of the organism. So instead of a linear reduction to atoms, organisms ought to be studied as complex wholes, completely irreducible to their molecular parts. More importantly, to understand why the parts do what they do, we have to look to the goals of the organism. A very Aristotelian idea.
And with that, the organicists brought goal-seeking back into biology, without having to invent mystical vital forces.
Source:
Herring, E., & Radick, G. (2019). Emergence in Biology: From organicism to systems biology. In The Routledge Handbook of Emergence (pp. 352-362). Routledge.
https://eprints.whiterose.ac.uk/138755/3/Truly Final EMERGENCE IN BIOLOGY 0418 (2).pdf
The organicist movement has been all but forgotten amongst modern biologists, but by re-examining their approach, we can see two paths forward for biology. We can continue along the path set out by Descartes in viewing organisms as machines or we can jump back onto the one envisaged long ago by Aristotle which views organisms as agents that pursue goals.
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