See title, self explanatory 🙂

Would love to see the numbers underlying this claim:

This would scare the hell out of me if I saw it coming:

Here is my PhD thesis.

This is chapter 2 of a book on the brain I was writing in the 2010’s. The first 4 chapters are here, but I’m posting it as a single post. It tells the story of the origins of neuroscience in modern form, with Thomas Wilis and the Oxford circle making the first complete dissections of the brain, and publishing ‘cerebri anatome’.

Chapter 2 – The Anatomy of the Soul

‘Now then, listen. In order for you to fully comprehend
That minds and flimsy spirits have a birthday and an end,
I’ve spent long hours hunting the right words, and labour of love,
To set forth for you in poetry that’s worthy of
Your life’s calling. But do this favour for me just the same,
And yoke both of these concepts underneath a single name,
So that, say, when I speak of spirit, teaching that it dies,
Understand I am referring to the mind likewise,
Seeing that a single soul is formed out of their union’

Lucretius, De Rerum Natura, 1^st century BC.
Book 3, lines 417-25

Lucretius’ union

Thought found its location only gradually. It began by entertaining a hypothesis that remains astonishing to this day: that our thoughts come from an organ of the body, of physical matter. In short, that thoughts are flesh.

We begin this story over 2,000 years ago, in ancient Rome. That thought was the product of a physical structure had been inferred by the great Roman atomist philosophers, who believed that everything, however complex, was a product of the combination of the simplest of elements. One of these philosophers was Lucretius, who was quoted by Montaigne in The Essays:

‘We feel the soul is with the body born,
Grows up with it, and with it waxes old.’

Lucretius goes on, more directly:

‘That mind must be corporeal is quite plain,
Since darts and thrusts corporeal give it pain.’

So Lucretius viewed the mind as being physical 2,000 years ago, based upon simple observation, thus beginning the search for the anatomy of the soul. However, Lucretius’ linkage still leaves the nature of thought poorly defined, without mechanism or specific structure. There were two central hurdles to achieving an explanation of the mind that moved beyond this early insight.

The first hurdle was philosophical. To render the spirit physical was to render God physical, an act akin to atheism. The spirit was something deeply spiritual, religious, divine: the greatest of God’s gifts, and that gift which made us a special species. Even when people could overcome the intuitive hurdles of thinking that conscious experience arises from the brain, these religious attitudes made the quest daunting. The hostility led Vesalius, perhaps the greatest anatomist of all time, to ‘wholly abstain from consideration of the divisions of the soul and their locations’. Even today, the view that there is some separation between brain and mind is common. 

Yet for those willing to try to lay the detail onto Lucretius’ conjecture, a second major hurdle still existed, this time technical – how do you actually study the brain?

The elusive organ

‘This lax pith or marrow in man’s head shows no more capacity for thought than a cake of suet or a bowl of curds.’

Henry More, 1652, An antidote against Atheism.

The early advances in understanding the physiology of the body came from making links between structure and function. What is needed is some feature of anatomy, some pattern in the organization of the physical matter, that gives clues as to how function arises. Hearts connect to the blood vessels, lungs to the airways, stomachs to the mouth and intestine. This principle of linking anatomy to function is now at the foundation of biology, and act as a guiding light for experimental scientists. In the words of Sydney Brenner,  ‘When it’s too difficult to study function, you study structure…. Once you know anatomy you get bits of physiology for free.’ So understanding the organizational logic of physical structure helps you to see how it gives rise to function.

However, even for the heart, an organ whose form is extremely closely linked to its function, this inference was historically challenging one to make. Things that are obvious retrospectively are not so obvious at the time. Even Leonardo da Vinci himself, despite fully understanding the basic anatomy of the heart, did not realize that it implied a circulatory mechanism. Only centuries later did scientists make this link.

For the brain, the task is far harder than for other organs. The brain’s form rapidly deteriorates after death, making it hard to dissect and examine. Even removing the brain intact from the skull was not possible until the seventeenth century; investigators were left with lumps of goo rather than neat anatomical specimens. Further, even if one could extract the brain intact from the skull, the brain’s appearance does not immediately suggest that it is the organ of thought. It looks like a collection of mushy walnuts, with varying folds and bumps, and different greyish hues dispersed seemingly at random. It appears to offer few clues to the investigator. Even the clear distinctions between different brain areas shown in anatomy books are not at all obvious to the naked, unprepared eye. This mess may have been what led many medical researchers, including Galen and Da Vinci, to focus instead on the fluid-filled ventricles weaving through the brain, an area that we now know is the only brain area not directly involved in thought. 

How, then, was this impasse overcome? 

Putting nature to the torture

‘For either by this way, by Wounds and Death, by Anatomy, and a Caesarean Birth, Truth will be brought to Light, or forever lye hid.’

Thomas Willis, Preface to Cerebri Anatome, 1664

The link between the physical and mental, the ‘union’ referred to by Lucretius, was definitively demonstrated in Oxford in the seventeenth century. This was, for all intents and purposes, the beginning of neuroscience. Indeed, this was a time when science itself was new. Nature was, in the words of Francis Bacon, being ‘put to the torture’ by the new tool of inquiry – the experiment –  relentlessly probing and testing nature to reveal her secrets. 

In Oxford, a group of self-styled ‘natural philosophers’ formed a club dedicated to these experiments. This was the ‘Experimental Philosophical Club’, which later became the famous Royal Society. It grew out of the new coffee club culture, and was a social circle of investigators using natural philosophy almost as a kind of entertainment. The group would meet weekly to discuss and share demonstrations, refine and share methods, and drink that  newly-found elixir, coffee. Such luminaries as Robert Boyle, John Locke and Robert Hooke were present in these circles, working on the so-called clockwork universe, discovering laws and explanations to simplify the everyday world into mechanisms free of mystery. 

No subject was fully off limits to these men. Hooke’s law was devised, the Micrografia written, Boyle’s chemical experiments completed, all within a few short years. In secret, a futile search for the alchemical philosopher’s stone was underway, a feat that later captivated Newton. Even the properties of marijuana were investigated. Nature was indeed put to the torture. But whilst these scientists sought to uncover the clockwork universe, only one sought to uncover the clockwork mind.

The man who was addicted to the opening of heads 

‘Willis put the brain and nervous system on their modern footing, so far as that could be then done.’

Charles Sherrington, Nobel Laureate, 20^th century.

This scientist was Thomas Willis, the world’s ‘first clinical neurologist’. It is Willis who is quoted at the beginning of this book, and in the preceding section. In a series of books, first and most famously Cerebri Anatome (The Anatomy of the Brain) in 1664, he laid out a set of landmark observations about the basic organization of brains. Cerebri Anatome was the first ever neuroscience book, a catalog of the brain for the first time in history, filled with speculations and details about its working. The outcome, in Carl Zimmer’s words, was the idea of a ‘Soul Made Flesh’, a physical brain, with its structure linked to function, and its function linked to thought. 

Willis’ path to this idea was the result of the convergence of two character traits common to many great scientists. First, he had a rebellious streak, embodying the subsequent motto of the Royal Society – Nullius in verba, or Take nobody’s word for it. He described his own profession of medicine as a ‘sword in a blind man’s hand’, and openly questioned the wisdom of the ancient doctor Galen, who was still greatly revered, even idolized, in seventeenth-century England. He saw the clear conflict between Galen’s theories and his own clinical experience as a doctor, and chose to believe his own eyes.

Willis’s second crucial trait was that he not only disbelieved existing wisdom; he actively sought to overturn it with his own observations. He was a Sherlock Holmes-like figure, with a masterful eye for detail and how those details connect. Prior to working on the brain, he had already written the first case reports of influenza, and made the first link between diabetes and glucose by noticing that flies were especially attracted to the urine samples of his diabetic patients. Observation was thus a central tool for Willis, and his skill at connecting his observations was ideally suited to the problems that he was to tackle.

It was in the early 1660’s that Willis used these two traits to forge a path for the study of thought, resolving to see the brain for himself rather than trust the claims of the ancients:

‘….I determined with myself seriously to enter presently upon a new course, and to rely on this one thing, not to pin my faith on the received opinions of others, nor on the suspicions and guesses of my own mind, but for the future to believe Nature and ocular demonstrations.’

He launched vigorously into this effort, often gathering corpses from executions to fuel his investigation:

‘I betook my self wholly to the study of Anatomy: and as I did chiefly inquire into the offices and uses of the Brain and its nervous Appendix, I addicted myself to the opening of Heads.’

Through this approach, he promised that ‘the impressions, influences, and secret ways of working of the sensitive Soul itself will be discovered.’

These quotes are all from the beginning of Cerebri Anatome. Willis lived before the tyranny of journal editors and academicese had infected science, and so his writings blended his own story, his observations and his speculations. This allows us to retrace his steps as he ‘established links that are still astonishing to us 300 years on’.

Neuroscience’s Dark Side of the Moon

‘The parts of the Brain it self are so complicated and involved, and their respects and habitudes to one another so hard to be extricated, that it may seem a more hard task to institute its perfect Anatomy, than to delineate on a plain, the flexions and Meanders of some Labyrinth’

Thomas Willis, Cerebri Anatome

Yet Willis did not work alone. His ambitions combined with the spirit of collaboration in Oxford at the time, with him forging a team of young investigators to work on his task. They worked tirelessly, ‘almost no day past over without some Anatomical administration’, using Willis’ house on Merton Street in the center of Oxford as a dissection chamber.

We can envisage this crowded hall, still in place today, filled with the meetings of Willis’ investigators. We might see Richard Lower, who later performed history’s first blood transfusion, providing help through ‘his most skillful dissecting hand’, whilst Christopher Wren, of later architectural fame, was also frequently present, ‘delineat[ing] with his own most skilful hands many Figures of the Brain and Skull, whereby the work might be more exact.’ Wren’s beautiful illustrations are reprinted to this day. Willis’ group had thus unwittingly followed Da Vinci’s unpublished advice to not only dissect well, but to also draw well, in order to reveal anatomy in ways that words could not capture (Arraez-Aybar et al 2015). 

The approach that the team took differed radically from earlier scientists, enabling them to see the brain in a very different way. Willis noticed that the critical error of previous anatomists was to remove the brain from the top of the skull in pieces. The brain then lost its shape and form, such that ‘the Phaenomena arising by chance from such a dissection, they easily esteemed for true parts of the Brain’. Willis instead removed the brain intact, by breaking open the skull from the bottom. He described this innovation in some detail in his writings, testifying to its importance. 

These novel dissections revealed the brain as it had never been seen before. There, lying before this group of Oxford mavericks, was the soul in physical form. Beneath the cerebrum atop the brain lay a vast complex of structures, most of which had only been glimpsed at in previous dissections, having been disfigured by the earlier dissection method. Many of these structures were named by Willis, or after him in his honour, including the arterial Circle of Willis. To hold an intact human brain in one’s hands was Willis’ first major advance.

From this new visual perspective came one of the most famous images in the history of neuroscience: Christopher Wren’s drawing of the underside of the brain, neuroscience’s equivalent of seeing the dark side of the moon for the first time. 

Wren’s illustration of the underside of the brain, Cerebri Anatome, 1664 < I own an original first edition print of this image and can take a better version when the time comes

Willis had come a long way from his early days struggling to remove the brain from the skull, a time when he found it difficult to even discriminate between what was brain and what was not. The image had shown that the brain was not merely a ‘lax pith or marrow’, as Henry More had so derisively called it, but a layered, detailed, labyrinthine structure. It was an organ of the highest complexity.

Yet Willis still had a problem. This image alone did not appear to reveal many secrets about how the brain actually worked. The image asked much more than it answered, and thus represented a beginning, not an end, to Willis’s research. Obvious questions protruded from the lump of flesh that he had extracted. Why was the brain he saw not homogenous, a single entity matching the single entity of the soul? What was the reason for this variety of structures? If thought was not homogenous, what was the pattern of this heterogeneity? Most radically, could you link specific variation in the patterns of this flesh to specific variation in the soul? These questions were Willis’ new canvas, onto which were laid new dissections and speculations.

With twenty-first-century hindsight, at least some of the answers to these seventeenth-century questions may seem deceptively obvious, as we are taught from a young age that different brain areas do different things. But instead of jumping to this conclusion, let’s consider what Wren’s drawing shows, and how ambiguous its interpretation could be. At the bottom of the image is the white tube of brainstem, which links seamlessly with the spinal cord. This is what feeds into your neck, and down to the rest of the body. The largest, richly folded structure, farthest from the brain stem, is the cerebrum, the walnut-like structure. So, what do they do?

<<Add diagram>>

With modern knowledge, we may see an obvious solution. The proximity of these lower brain regions to the spinal cord must surely suggest a simpler, more primitive role, whilst the richly folded cerebrum, being further away, would be a more advanced, ‘higher’ structure, serving uniquely human cognition? This inference is partly a product of hindsight bias. An equally persuasive but thoroughly wrong argument and arrangement could be devised. Might one not put the more uniquely human brain areas, the ‘soul’, deeper within the brain, to be more protected? Might the more uniform and exposed cerebrum not be a simple structure, with the deeper and varied labyrinths being the seat of higher complexity and thus of complex thought? Willis used two approaches to circumvent these uncertainties, finding a way to ask Nature questions more directly. 

A notable analogy

‘Concerning the Heads of living Creatures, in the dissection of which it happened for us chiefly to be exercised, it was observed, as to the chief parts of the Head, that there was a notable Analogy between Man and four-footed Beasts’

Thomas Willis, Cerebri Anatome

The first approach Willis used relied upon comparison with animals. Animal dissections had already formed the basis of ancient knowledge of the body. The result was a surprisingly accurate portrait of human anatomy, with some notable errors. 

Willis and his team also used animal brains extensively. The difference, however, was that Willis compared the brains of different animals with those of humans, which the ancients did not do. In doing so, Willis found a ‘notable analogy’ between them. It appeared that the brains of different ‘four-footed beasts’, by which Willis usually meant mammals, differed from one another, and from the human brain, more or less in magnitude alone:

Wherefore when the form and composition of the Brain in a Dog, Calf, Sheep, Hog, and many other four-footed beasts, were little different (the magnitude only excepted) from the figure of the same, and the disposition of the parts, in a man, I was the more satisfied to compose a certain Anatomy of the Brain by the frequent dissection of all sorts of living Creatures

Thomas Willis, Cerebri Anatome

In short, the brains of ‘beasts’ and humans were similar enough that the shape of the former could be used to inform the understanding of the latter. There was a remarkable conservation of the anatomy of the brain, such that in all of the mammals that Willis examined, he found the same set of brain areas. Even in light of our understanding of evolution, this is still somewhat counterintuitive even to this day. Generally speaking, Willis saw few fundamental differences between mammalian brains, including those of humans.

In all of them, he saw the brain connecting to the spinal cord at the base of the brain, through the brain stem. This brainstem structure then appeared to blossom into many other areas. There was the darker, richly folded little brain, or cerebellum. There was the striatum, named by willis, near the front of the brain, with streaks of white passing distinctly through it (hence, striations). There was the thalamus, the inner chamber resting at the brain’s core, and the cerebral cortex, the crowning outer structure, as well as a myriad of other areas of greatly varying size and form. For each area found in humans, an obvious parallel could be found in any mammal. The manner of brain folding was different, so that parts shifted slightly within the skull, but the deep similarity, even sameness, was striking.

Willis understood the implications of his observation. He could find nothing fundamentally different between the brains of humans and animals except size. Previously, the hearts, lungs, digestive and reproductive systems of animals and humans were known to be closely matched. Now brains were added to this list, a far more dramatic shot across the bow of human uniqueness.

So the brains of humans and animals were far more similar than a seventeenth century anatomist might have suspected. But how did they differ? 

The seat of the soul

‘The cerebrum is the primary seat of the rational soul in man, and of the sensitive soul in animals. It is the source of movements and ideas.’

Thomas Willis, Cerebri Anatome

It was in finding differences between mammalian brains that Willis began to link structure and function more precisely. In Cerebri Anatome there is another version of the Wren drawing of the underside of the brain described above. It is the same view of the brain, but this time the brain is of a sheep, not of a human, is depicted. Willis’ pioneering neuroanatomy had peered deep within the brain, where others could not reach, away from the cerebrum sitting atop the brain. Ironically though, his eyes were now drawn back to the cerebrum, where he made one of his most impressive inferences.

The cerebrum, the term Willis used for what we now usually call the cerebral cortex, is a densely folded structure in humans. It is the large, walnut-like area that covers the rest of the brain. The human cerebrum is so large in surface area that it must literally be folded up to fit in the skull. However, Willis noticed that in non-human animals, such folds were much fewer, or even absent. This seemed to be related to the extent of cognition the animals had, that is, to their intelligence. This led him to his famous proposal that the ‘cerebrum is the primary seat of the rational soul in man’. Willis confirmed this link of cognitive ability and the cerebral cortex by dissecting the brain from somebody who had suffered from severe learning difficulties from birth, including an illustration of this with the description:

‘The Effigies of an humane Brain of a certain Touch that was foolish from his birth…..the bulk of whose Brain…..was thinner and lesser than is usual’

The image shows a particularly withered Cerebrum, helping to confirm Willis’ speculation that the cerebrum was indeed the site of the higher faculties. Through detective work, comparative anatomy and clinical case studies, thought had found its place. A specific variation in a piece of flesh had been linked to the very attributes that seemed to make humans unique: their thoughts.

The rivers of animal spirits

“The animal Spirits flowing from the Brain….. irradiate the nervous System.”

Thomas Willis, Cerebri Anatome

But Willis was not quite done. He further speculated on  the functions of multiple other brain regions, including the Cerebellum (meaning little brain), which he linked, correctly, to involuntary movement. He postulated that the parts of movement that were automated, without conscious thought were delegated by the cerebrum to the cerebellum in a division of labour. We shall explore this in later chapters. For now, what emerged from Willis’s work was a picture of a split soul, a brain with ‘provinces’, each dedicated to their own part of the mental firmament.

Willis, however, saw a problem in this view, and then provided the solution. How did the provinces of the brain influence one another, given their separation in space? To answer this, Willis spoke of ‘animal spirits’, which he imagined as travelling like the ‘explosion of gunpowder’ between brain regions. He was arguing that there was a nonphysical element of the mind that flowed between brain areas to carry thought.

It was not in the spirit of the Experimental Philosophy Club to settle for these mystical explanations, however. Instead, Willis theorised that these ‘spirits’ needed a method for travel. To work out how this could happen, he investigated a ‘simple’ type of thinking: vision. He started with the eyes. Here, he traced fiber-like pathways from the eyes to the middle of the brain, concluding that they were ideally suited for carrying the animal spirits from the eye to the brain. Willis could not prove this directly, but we now know that cutting these fiber projections leads to an incurable and total blindness. This means that those tiny fibers, scarcely a few millimetres in width, have provided the pathway for the entirety of the visual experience of your life. Everything you have ever seen has passed through two threads of biological string. 

Willis wanted to prove that these rivers of animal spirits were not unique to vision, but were a general organizing principle underlying the exchange of thoughts within brains. To do this, he used another clinical case, this time involving a movement disorder. Willis obtained the body of a patient who, in life, had had severe problems with movement on only one side of their body, offering the ideal chance to track down the pathways of movement. If he could find a difference between the left and right side of the brain, he reasoned, he could isolate the change underlying the one-sided dysfunction. Willis and his team meticulously dissected the extracted brain, poring over each part for hints of asymmetry. They eventually found that a pathway from the top of the brain, the cerebral cortex, down to the bottom, the brainstem, was selectively and severely damaged, and on one side only. This part, the cerebral peduncle, we now definitively know to be the major conduit for signals from our motor cortex to our brainstem motor control areas. When you decide to move, signals flow down this pathway to your brainstem and onward, driving movement. The individual whose body Willis dissected was part-paralysed not because they could not think about making movement, but because those thoughts were forever trapped high in the brain, unable to pass down to the site of movement execution. The patient was unilaterally trapped.

These varied insights combined to form a simpler image as Willis saw and delineated these same tube-like pathways all over the brain. The different brain areas appeared to be linked in an elaborate web: the brain was a network for the flow of the animal spirits, which move along tiny fibrous pathways as they carry thoughts back and forth.

The doctrine of the nerves

Marcus Aurelius asks in Meditations, ‘If souls survive after death, how has the air above us found room for them all since time began?’ Willis’ answer, which Aurelius may have suspected, is that the soul is flesh, and thus rots away with our bodies. There is no paradox.

But Willis’ contribution was far more than this. He found poetic explanations of thought in the brain where others had found only an amorphous confusion. From Willis’ insights we can extract the fundamentals of neuroanatomy, what he called his ‘Doctrine of the nerves’. A simple distillation of his insights and his doctrine is as follows: thought comes from the physical brain, which is split into parts. Each part is specialized for a particular function, with a progressive elaboration of the higher brain areas: those closest to the tops of our heads are correlated with increased intelligence. The physical connections between these areas are what allows our thoughts to spread, and the pattern of these connections is crucial for determining what an area does. It is a theory of networks, of specializations, of flow. 

The rest of this book is an examination of, and derivation from, Willis’ core insights. The fundamental approach of anatomizing, then understanding the connections and interactions between the resulting brain elements, is the basic logic of neuroscience. We must now turn our focus toward the question of the ‘animal spirits’: what they are, and what carries them.

Obviously DALLE-2 is incredible, as is Imagen. I’ll post on them separately, which reminded me to go ahead and publish an old draft here that was kept as a private post.

https://www.scientificamerican.com/article/an-ancient-greek-astronomical-calculation-machine-reveals-new-secrets/ Possibly the most amazing thing from the ancient world – an ancient analogue computer. we only know of it due to a single example. what else are we missing?

https://www.smithsonianmag.com/science-nature/snake-infested-island-deadliest-place-brazil-180951782/ About a small island where, due to a quirk in evolution, the dominant species is snakes who prey on migrating birds. Hence, ‘snake island’, which people are banned from visiting due to how completely snake infested it is.

https://twitter.com/buitengebieden_/status/1471607067093970953?s=20

I recently found a pdf of an important biography of Omori Sogen, the most important zen master of the 20th century, at least in the Rinzai Lineage. Meido Roshi, my teacher, refers to it in this YouTube video. I encourage you to listen to if you are interested in Zen. Meido is in the lineage of Sogen via his Sogen’s Dharma heir Hosokowa Roshi (who wrote the book below) and then one of Hosokawa’s dharma heirs Miller Roshi after Hosokawa retired.

The book itself is hard to get hold of, and cannot be shipped outside the US, so I decided to post the PDF here in case it is of help.

I’ll post some notes later. Its a fascinating read about the life of an unusual zen master who spent most of his life as a lay person in the real world – most zen masters begin their training in their teens or early twenties (such as Meido).

“Having adjusted your body in this manner, take a breath and exhale fully, then sway your body to left and right. Now sit steadfastly and think not-thinking. How do you think not-thinking? Beyond thinking. This is the essential art of zazen.”

This is my favourite translation of my favourite introduction to zen meditation, a kind of poem to introduce the central practice of zen: sitting meditation (Zazen). This is also one of my favourite pieces of writing, full stop. Dogen is the key figure in Japanese Soto Zen, which is the most prominent zen branch in the west. People who hear I went on a retreat often ask for a pointer to an introduction to meditation, so here it is.

The words here are largely not meant to be understood literally. They are poetic, as is the case in most zen writings. The key instruction of ‘think non thinking’ is also not meant to be a readily followed instruction – a little like learning to ride a bike, the task of meditation is to learn to find the meaning in the instructions yourself. You may notice contradictions in the writing – zen is full of this. A contradiction is a concept, a thought – part of zen is about seeing through these patterns of thought and seeing they are creations of the mind.

This is not the branch of zen my teacher is in, and the meditation here is different to the breath counting meditation more prominently used in Rinzai Zen, but for beginners like myself and probably for you these differences are not relevant.

Dogen, 1227, Japan – Recommending Zazen to all people

The real way circulates everywhere; how could it require practice or enlightenment?

The essential teaching is fully available; how could effort be necessary?

Furthermore, the entire mirror is free of dust; why take steps to polish it?

Nothing is separate from this very place; why journey away?

And yet, if you miss the mark even by a strand of hair, you are as distant as heaven from earth. If the slightest discrimination occurs, you will be lost in confusion. You could be proud of your understanding and have abundant realization, or acquire outstanding wisdom and attain the way by clarifying the mind. Still, if you are wandering about in your head, you may miss the vital path of letting your body leap.

You should observe the example of Buddha Shakyamuni of the Jeta Grove, who practiced sitting up straight for six years even though he was gifted with intrinsic wisdom. Still celebrated is Master Bodhidarma of the Shaolin Temple, who sat facing the wall for nine years although he had already received the mind seal. Ancient sages were like this; who nowadays does not need to practice as they did?

Hence, you should stop searching for phrases and chasing after words. Take the backward step and turn the light inward. Your body-mind of itself will drop off and your original face will appear. If you want to attain just this, immediately practice just this.

For zazen, a quiet room is appropriate. Drink and eat in moderation. Let go of all involvements and let myriad things rest. Do not think good or bad. Do not judge right or wrong. Stop conscious endeavor and analytic introspection. Do not try to become a buddha. How could being a buddha be limited to sitting or not sitting?

In an appropriate place for sitting, set out a thick mat and put a round cushion on top of it. Sit either in the full or half-lotus posture. Loosen the robes and arrange them in an orderly way. Then place the right hand palm up on the left foot, and the left hand on the right hand, lightly touching the ends of the thumbs together.

Sit straight up without leaning to the right or left and without bending forward or backward. The ears should be in line with the shoulders and the nose in line with the navel. Rest the tongue against the roof of the mouth, with lips and teeth closed. Keep the eyes open and breathe gently through the nose.

Having adjusted your body in this manner, take a breath and exhale fully, then sway your body to left and right. Now sit steadfastly and think not-thinking. How do you think not-thinking? Beyond thinking. This is the essential art of zazen.

The zazen I speak of is not learning meditation. It is simply the dharma gate of enjoyment and ease. It is the practice-realization of complete enlightenment. Realize the fundamental point free from the binding of nets and baskets. Once you experience it, you are like a dragon swimming in the water or a tiger reposing in the mountains. Know that the true dharma emerges of itself, clearing away hindrances and distractions.

When you stand up from sitting, move your body slowly and rise calmly, without haste. We understand from past precedents that going beyond ordinary and sacred, where sitting and standing are effortless and boundless, depends solely on the power of zazen.

Furthermore, bringing forth the turning point by using a finger, a pole, a needle, or a mallet, or leading people to enlightenment with a whisk, a fist, a stick, or a shout cannot be understood by discriminatory thinking. How can it be understood by the use of supernatural powers? Zazen is an awesome presence outside form and color. How is it not the path preceding concept?

Thus, do not be concerned with who is wise and who is stupid. Do not discriminate the sharp from the dull. To practice whole-heartedly is the true endeavor of the way. Practice-realization is not defiled with specialness; it is a matter for every day.

Now, in this world and in other worlds, in India and China, buddha ancestors equally carry the buddha seal and teach the practice of sitting immersed in steadfastness. Although circumstances may vary in a thousand ways, whole-heartedly practice Zen, giving yourself fully to the way. Why give up the sitting platform of your own house and wander uselessly in the dust of a remote land? Once a wrong step is taken, you depart from the way.

Having received a human life, do not waste the passing moments. Already upholding the buddha way, why would you indulge in the sparks from a flint? After all, form is like a dewdrop on the grass. Human life is like a flash of lightning, transient and illusory, gone in a moment.

Honored practitioners of Zen, please do not grope for the elephant or try to grasp the true dragon. Strive to hit the mark by directly pointing. Revere the mind that goes beyond study and surpasses all doings. Experience the enlightenment of the buddhas, correctly inheriting the samadhi of the ancestors. Practice thusness continuously, and you will be thus. The treasury will open of itself for you to use as you wish.

Reddit comments on this that I liked:

The translation comes from a book I own, but rather than retype I found it online and copy pasted. Here are comments from the original reddit: both touch on the thing that is often so difficult to understand about zen – you are not adding anything to your mind, you are not grasping some external truth, but rather clearing obstacles that your mind creates. It is only after 3-4 days of near continuous meditation at Sesshin that I felt this long enough for it to be anything but a fleeting sensation, but it is perhaps the most striking state I have ever entered. It cannot be explained in words.

“Zazen is practical self improvement. In that when you practice it becomes obvious that you are improving

This obviousness is what Dogen is speaking to. To chase external mysteries or mysticism is to miss what is right here already, the inner mysteries of ourselves”

“Are you different when you zazen? No. Do you do something different when you zazen? Perhaps but not really. Do you do zazen because you like or dislike it? No neither; it’s just what you do. Why do you do it then? Enlightenment itself.

It’s hard to talk about. When people see Dogen and say they see contradictions or are confused it’s because of this delusion of like and not like, right and wrong or enlightened or enlightened etc. that we are all very fond of holding on to. Dogen in his writing took a step beyond the writing of his ancestors in describing zen in the most non dualistic way possible.”

“The power of the unaided mind is highly overrated. Without external aids, memory, thought, and reasoning are all constrained. […] The real powers come from devising external aids that enhance cognitive abilities.” Don Norman

NB: ‘The Knowledge Illusion: Why we never think alone’ by Sloman and Fernbach- is a good book to read to understand how little you actually internally know, how reliant on the outside world you are.

[this is a rough draft, to be turned into a fuller post once I’ve experimented with the system]

Imagine if that image, times 100, was a map of your thoughts, of a lifetime of research. Not just separate facts, pieces of information, but how they relate. How you could dip into one part, and quickly find all the other connecting parts over decade. To me that’s a dream, and the topic of this experiment and blog post. That topic is known as a Zettelkasten.

This Christmas I finished reading a book I hope will hold part of a solution to a range of related research challenges I’ve been toying with since I was an undergraduate. Here I briefly explain what this is, why I am starting one myself, and, mostly importantly, provide an index of resources on the topic, both for myself and for others. I do not attempt to summarise the system myself as others have done it well. I will add my own experiences as I use it over the coming months,.

The book I finished is a book about Zettelkasten’s by Sonke Ahrens, and is called ‘How to take smart notes’. Whilst I cite a range of resources to explore, none come close to explaining what is so attractive about this system and the theory underlying it.

The need for a ‘second brain’

One of the keys to the small amount of academic success I had was to apply simple techniques to address innate cognitive deficiencies that most of us have. Without these I might have got a grade or two lower at University.

I wrote previously about Deep Work in my post giving advice about working in lockdown. I’ll write shortly about another – spaced active recall and memory palaces. Together these address focus and improving memory of isolated facts, and together they addressed key points I needed to be strong at but was not naturally good at.

But there was a major gap in this I’ve been trying to fill since I was undergraduate, and I think I may have found a simple system to address it, just as Deep Work and Spaced Active Recall addressed key points for me.

I always worked in fields where accumulating large amounts of data points, such as results and observations, and then weaving them together, was paramount. This was something I was relatively good at, unlike focus + recall of isolated facts.

If you adopt a strategy of having a broad canvas, of trying to understand disparate areas and weaving them together, you run into a problem over time. Your memory fails, and so does your external memory system such as notebooks.

This is not a problem over a period of a year, and especially not when following a curriculum. As an undergraduate I could keep word docs of key papers and observations, based loosely on the categories I was given by tutors. Likewise, for a narrow topic given at work, you can study for that and keep notes together.

But what about study over 5 or 10 years? You begin to forget where your earlier observations are. You forget they existed. Links you might make between disparate subjects are lost. This is not such an issue if you work serially on a series of topics. But it becomes a big wasted opportunity if you want to work in a much more integrative way.

Most note-taking methods separate knowledge from use of knowledge. A notebook, for example, might have notes on a wide range of things ordered by time. To get around this, you could order your notes by topic. But what if the topic isn’t clear at the time, and will only grow later? And what if an observation is of use to a wide range of topics? Linear writing is not good for developing webs of knowledge.

An intro the Zettelkasten:

This is what the Zettelkasten system addresses. I was attracted to it as it seemed to achieve a number of things I’d been trying to evolve a system to do by trial and error. Zettelkasten centres on the connections between notes, ie how knowledge fits together to form a greater whole. Its not really just a knowledge management system – it is a thinking system where the thinking itself is done in the knowledge system. This is explained well by Sonke Ahrens in his book.

Zettelkasten is German for slip box. It is also a phrase for a note-taking, writing, study, and research system that purports to be both extremely simple and extremely effective.

This is a physical Zettelkasten (image from Wikipedia). I will be using a paper one, as I try to avoid computers as much as I can as I find them impossibly distracting and difficult to think whilst using, and also bad for health as they seem to alter your breathing. I cannot be calm whilst using a computer.

A key reason I was attracted to it is it was developed by Luhmann, a highly productive and influential sociologist who had a ‘rag to riches’ story to which he credited this system he made.

Here is an intro:

Here is a selection of links to intros/deep dives – I recommend reading through before picking which one to follow. Again, none is a substitute for the brilliant book by Ahrens (itself written using Zettelkasten), which is a wonderful exploration of how we may wrongly think of research and writing (never plan!).

3 good intro pieces:

Here is a good written summary – https://kadavy.net/blog/posts/how-to-take-smart-notes-summary/ and that author’s own experiences using Zettelkasten – https://kadavy.net/blog/posts/zettelkasten-method-slip-box-digital-example/

And here is a more practical, example-based introduction to how the system should be used, including ‘writing your first Zettelkasten’: https://medium.com/@rebeccawilliams9941/the-zettelkasten-method-examples-to-help-you-get-started-8f8a44fa9ae6 Important suggestion of converting fleeting notes->literature notes on the same day they are made. This resonates with my own experiences. EDIT APRIL 2022: this is the guide most likely to be of use in my opinion, rereading it having experimented with the system for a little while.

Another good intro piece: https://writingcooperative.com/zettelkasten-how-one-german-scholar-was-so-freakishly-productive-997e4e0ca125

Zettelkasten.de seems to be the best living blog on the topic of Zettelkasten, with explorations of particular points of detail:
https://zettelkasten.de/posts/overview/ < Very good online detail of the system.
https://zettelkasten.de/posts/collectors-fallacy/ < Collectors Fallacy. Gathering knowledge without processing and using it as a work pitfall we often fall into.
https://zettelkasten.de/posts/idea-index-journal-fiction/ < A piece on indexing your work + others.
 https://zettelkasten.de/posts/use-real-notebook/ An argument for using real notebooks, not index cards, for the original pre-zettel note stage: This can work with the explanation the YouTube video has, in which the bibliography has a single index card that could ‘point’ to the relevant page in the notebook.

https://notes.andymatuschak.org/Zettelkasten ‘It’s an unusual system for developing ideas over long periods of time by slowly iterating on thousands of atomic slips of paper, all densely linked to each other. Over time, it evolved into what Luhmann considered to be an independent thought partner in his research, capable of carrying on a conversation with him and eliciting ideas which genuinely surprised him.’

Implementing a Zettelkasten using Roam Research – https://betterhumans.pub/the-complete-guide-for-building-a-zettelkasten-with-roamresearch-8b9b76598df0

LessWrong posts on it: 

https://www.lesswrong.com/posts/T382CLwAjsy3fmecf/how-to-take-smart-notes-ahrens-2017  – an excellent LessWrong introduction to Zettelkasten
https://www.lesswrong.com/posts/NfdHG6oHBJ8Qxc26s/the-zettelkasten-method-1
This is an hour long deep dive on the Zettelkasten method. “

Your first note doesn’t need to be anything important — it isn’t as if every idea you put into your Zettelkasten has to be “underneath” it. Remember, you aren’t trying to invent a good category system. Not every card has to look like a core idea with bullet points which elaborate on that idea, like my example in the previous section. You can just start writing whatever. In fact, it might be good if you make your first cards messy and unimportant, just to make sure you don’t feel like everything has to be nicely organized and highly significant.”

One aspect of digital I will miss is the ability to make maps of your own knowledge like this below (from https://medium.com/@rebeccawilliams9941/the-zettelkasten-method-examples-to-help-you-get-started-8f8a44fa9ae6) – this uses obsidian, a promising looking digital implementation of the Zettelkasten – https://obsidian.md):

Updates – this isn’t readable – its a prompt for myself to add the next stage of this piece.

5th Feb 2022

I’ve begun this, and got around 100 cards. I’ve also found index cards are fantastic for keeping a notebook focussed on quality. Notebooks accumulate many wonderful/interesting thoughts/ideas/sections, but this can get cluttered out by the detritus of everyday reminders etc (another way to handle this is to put reminders in pencil, quality thoughts in pen).

Whats working/note working….

Good:
1) the index cards feel like a much better way of organising information than notebooks. Conversely, they are not as good for detailed thinking or writing drafts. They are complementary tools.
2) they promote a sense of flow somewhat better than working on a computer, for obvious reasons.
3) they are very easy to use.
Bad:
1) I haven’t found a good way to transport index cards to work and back. Most boxes I can find are too big to carry in a box. I briefly thought of using digital, but this means I have to have my laptop open at times when I am trying to have it off……….
2) they are a little slower than digital, but I don’t think long-term that’s a problem as that slowness promotes quality of thought.

One key error has been to fall into converting it into an index, with title cards such as ‘politics’ or ‘Japanese cooking’. This is the role of a bibliography, not the Zettelkasten, and misses its key role- it is an organiser of ideas, identifying links between them. I won’t start from scratch, but will try to convert the existing slides I’ve got into that format.

Update April 2022

https://forums.getdrafts.com/t/zettelkasten-usage-analog-or-digital/10740/6 a useful back and forth on digital vs analog notes…. https://www.reddit.com/r/Zettelkasten/comments/fga4km/paper_or_software/

As in the 5th Feb update, my original sorting of my ZK into clear headings was a major mistake. It has got me trapped inside the index level approach. I’m weighing up the right way to fix this.

To add later: https://medium.com/@ethomasv/the-folgezettel-conundrum-20b14dc986ec, https://medium.com/@ethomasv/understanding-zettelkasten-d0ca5bb1f80e, https://www.youtube.com/watch?v=U2hxygqjx2k, https://www.youtube.com/watch?v=sSM0CZZEDYQ, https://www.youtube.com/watch?v=eMJGKZ7n9hE&t=2s, ZK’s as an antidote to ageing, a wisdom machine, etc.

An example Zettel, from https://zettelkasten.de/introduction/#the-paper-based-zettelkasten:

Luhmann’s slip box notes: https://luhmann.surge.sh/communicating-with-slip-boxes

To add later – video of Sonke Ahrens

ANNEX

“Many famous authors and artists used index cards in their work. The Russian-born American novelist Vladimir Nabokov wrote his last novel The Original of Laura (subtitled A Novel in Fragments) on a set of 138 cards that were put together and published after his death. He also used index cards for his (in)famous Lolita. ” from – https://www.taskade.com/blog/zettelkasten-method-software-remote-work/ Note this is also how ‘Zen and the art of motor cycle maintenance’ was written, as outlined in its sequel.

https://users.speakeasy.net/~lion/nb/book.pdf – This link was recommended by one of the LessWrong posts as an alternative system to this – I have yet to study but will try to look at it before I get too deep into Zettelkasten – (I have tried briefly reading but it is incredibly irritatingly written, as though the author was on cocaine at the time)

Not been keeping track of online quirkiment lately… hence the delay.

@Rainmaker1973 is quickly becoming one of my favourite twitter feeds… a reliable source of enwonderment.

A reminder that you can go to the zoo and experience a time machine of sorts:

Adding this 1st October:

Note: “At the core is the view that the control of the somatic location of attention within the self could be a critical part of health and cognition.” This is the overarching theme of these notes, and should be testable with both animal and human experiments.

Here are all 3 parts as a single pdf:

Here are the first three pdfs as separate files, as well as the intro below:

Some quotations…..

‘Of the essentials of preserving life, nourishing the breath has no peer. When the breath is exhausted, the body dies, when the people are downtrodden, the nation collapses.’
Zen Master Hakuin Ekaku, Letter to a Sick Monk, 18th century Japan, Yampolsky translation.

‘This elixir field, located in the sea of vital energy, the lower back, the legs, the soles of the feet –  it is all my true and original face. How can that original face have nose holes?’
First line of the Naikan Koan, Zen Master Hakuin, Yasen Kanna (Appendix to Wild Ivy, Waddell Translation), 18th century Japan

‘Breathing to the heels: The true person of ancient times slept without dreaming and woke without care. Their food was plain. Their breathing was deep. The true person breathed to their heels. Most people breathe to their throats. Bent and tight, they quarrel and vomit words. Their desires are old and deep, but they are shallow when it comes to knowing the opportunities of heaven.’
Zhuangzei, one of the two founding books of Chinese Taoism along the Tao Te Ching, 4th century BC
(Translation in Story 44, ‘The wisdom of the Tao’, Deng Ming-Dao)

“As you breathe in, experience the whole body,
As you breathe out, experience the whole body.”

The Satipatthana Sutta’s meditation guidance, attributed to the Buddha in India.
Translation from ‘Breathing through the whole body’ by Will Johnson

“I wanted to change the world. But I have found that the only thing one can be sure of changing is oneself.”
Aldous Huxley

“Hence, you should stop searching for phrases and chasing after words. Take the backward step and turn the light inward. Your body-mind of itself will drop off and your original face will appear.”
Dogen, 13th Century Zen Master and Founder of the Soto school of Zen,  Recommending Zazen to all people

‘….. wanting good government in their states, they first established order in their own families; wanting order in the home, they first disciplined themselves.’
Confucius, born 551 BC, The Great Digest

Background to these notes

These research notes concern circle around some speculative ideas regarding the physiology of parts of how the brain and body are controlled, and a research project I have been undertaking on myself about things we might be missing in our current understanding of this, that led to me learning to see in 3D. Its mainly a collection of mostly forgotten historical observations from history, anthropology, zen, ethology, neuroscience etc. I thought it would be good to share some of this so others who might be interested can pick up threads, and also consolidate my thoughts. I mostly gathered these notes together from old notebooks during my easter break whilst pondering some questions, so they are not at all polished, and won’t make full sense until the rest is written. 

For the past 5 years I have become interested in some questions around different views of health, zen buddhism & eastern medicine, breathing, the brain:body connection, and their links to my neuroscience work. I hinted at this in the prologue to my book in 2018, a ‘Semi-Monocular I’ – “[My operation], and two other experiences around then, fundamentally changed my sense of self, my thoughts as a scientist, and ultimately this book….  We shall come to this question of embodiment and the mind:body link.” One of those experiences was seeing in 3D for the first time.

The narrative of my book (An Emergent I) in part concerns how I taught myself to see in 3 dimensions (having been born with a cataract) and largely cured an illness I had, that was thought to be genetic but never showed up in whole genome sequencing (prologue of book here). 

However, I figured it will be some time until I can write this up fully as I am currently preoccupied, so I thought I would post some of my notes in rough form now.

These are just a loosely organised set of notes (a small subset) that I intend to use to finish writing that book. This is not intended as a fully polished version or a clear narrative with lots of explanation and links to neuroscience – that will come later as much of it is strewn across various old notebooks, as will some of the specific experiments I think this hints at. Some of the most interesting parts (to me) of this journey relate to why the notes below (as well as others) held the secret to learning to see in 3D, and how I found this path, but that is for the book itself! I also need to learn to draw well to illustrate this properly, which I am trying to do……

(For any eager minded readers who have read the prologue to my memoir, think why the mental habit I described on page 9/10 of the pdf version of ‘A semi-monocular I’, of consciously correcting the displacement between my two eyes, would lead to sickness if the bulk of the thoughts in the notes below are true, and why learning to see in 3D would correct this sickness.)

This is the first of at least 10 sets of notes in this area, which I will then combine, along with neuroscience & AI notes, with my own story of learning to see in 3D, and experimental predictions, in my book. They are one narrative.

At the core is the view that the control of the somatic location of attention within the self could be a critical part of health and cognition.

A couple comments, in part to try to assuage concerns I have gone completely mental in posting this…..

1. First, these are just notes and not intended to be compelling/scientific yet. One must venture to the edges to see where the center might need to go to find explanations for experiences that current paradigms don’t explain well.

2. Second, we explore things which appear at face value to make little sense in terms of modern science, but are conserved across several traditions. Its worth noting that practices like fasting are conserved across many traditions from millenia ago, but until recently were ridiculed or at least dismissed by western science. Now fasting’s effects for health are being unravelled. Likewise with meditation (currently largely) for mental health. I think the same may be true of some of the historical practices/methods in this series of notes – they offer experiences potentially hinting at as-yet unknown mechanisms in Physiology – per Da Vinci: ‘Although nature commences with reason and ends in experience it is necessary for us to do the opposite, that is to commence with experience and from this to proceed to investigate the reason.” We have largely forgotten the notion of consilience in science, that multiple independent sources converging on similar conclusions is itself evidence absent any single piece being ‘scientific’. I’ll post notes on later on causal inference, especially in the context of the COVID19 pandemic.

As you cannot see the value of controlling the breath without practicing meditating for some time, so too I think with these practices. Some may be false paths, but some might lead to something interesting. I don’t claim any of it is true yet, experiments are needed! But just because something does not fit in our current scientific paradigm does not mean it is not true. This also hits on different epistemological approaches in east and west:  ‘What is meant by eastern wisdom is never a mere condensation of theoretical knowledge but the fruit of ripe experience, confirmed and proved by faithful, patient practice.’ (pg. 9, Durckheim). I intend to make as much of it scientific as truth allows, but this will take time, and other endeavours exist also…..

These notes are disorganised, incomplete, partly redundant – some parts could equally well go in other sections/other note collections for instance. This is for use in writing a book, legible enough for me to read whenever I can immerse myself in said pursuit… throughout the text, sections in photos highlighted with pencil are usually the parts to be read. This text is not meant to be well written – no attempt to have a strong narrative, control tension etc I made.

Pilecki is someone I find particularly inspiring, and who I try to mention to people when the opportunity comes up. I’ll update this post over time, but thought I’d gather a few videos/pictures here to point people to who might want to learn more about him. When I was ill I found his example particularly inspiring. I’ll write a fuller blog later. If I could make even 0.1% of the difference he made, and have 0.1% of his courage, I would be very happy.

“I tried to live my life in such a fashion that in my last hour I would look back and feel not sad but happy. In this realisation I found strength within me, from knowing that the fight was worth it”.
Witold Pilecki upon the announcement of his death sentence at a communist show trial.

This short video explains some of what he did. Video I first watched in 2013. The music is ‘Polski Drogi’ (Polish roads).

Books

Pilecki used to carry Thomas Kempis’ ‘The Imitation of Christ’ with him wherever he went including Auschwitz, and gave his copy to Eleanora, his wife, just prior to his execution, asking her to read from it every night to their children once he was gone.

Here is a shorter, earlier report written from within auschwitz and smuggled out:

Here is a short book about Pilecki:

From an interview with his child: “My father always taught me one thing: when you start doing something, do it well and to the end. If you think you’re not good enough, do not even start. It’s a wise word. Throughout my life I have tried to live by this principle.”