Sunday, January 17, 2016

Anatomy of open-source education: A paraview of "Adventures in human being" by Gavin Francis

An anatomical drawing from "De Humani Corporis Fabrica" by Andreas Vesalius, published in 1543

Traveling through time in Florence : 

A thin fog hangs low on the Arno river in Florence, framing the picturesque bridge of Ponte Vecchio in a nice photographic effect.  Inhaling the chill of the early winter air, I walk by the rows of shops selling jewelry and trinkets on the bridge. As the evening sets in, the throngs of tourists are gone, along with the artists, street food vendors and the peddlers of souvenirs chasing them.There is a faint smell of wood smoke, perhaps coming from a pizza getting baked somewhere.

As I absorb this moment of tranquility, my mind is occupied by a man who lived here five and a half centuries ago - Leonardo Da Vinci. I am reading "Adventures in human being", a book by a young Scottish doctor and clinician Gavin Francis, and Leonardo is a central character in the book.  Partially autobiographical,  the book narrates the author's experiences in his medical practice and explores the idiosyncrasies of  the various organs of the human body and how they are discovered in the history of medicine. Leonardo Da Vinci - the great artist and engineer, the maker of the Mona Lisa and the flying parachute - also helped humankind discover the most fundamental of objects, their own faces. He is the first person in history to study facial expressions in a scientific manner - how the muscles stretch and deform the skin, and how human emotions are translated into smiles and frowns on the face.  As I pass by the tourists and Florentine citizens, I wonder how Leonardo would have looked at their faces. Would he have read the emotional history of their lives in one glimpse ? Would he have seen in X-Ray vision the anatomy of muscles beneath the skin ? As I wonder, I begin to suspect if Leonardo is the answer to the greatest question of history: how did our human civilization enter the modern age of scientific investigation ? And why did this happen first in Florence, Italy ?

Once the cultural capital of the world, Florence now resembles a museum opened inside out - a dissected corpse of European renaissance. It is as if the vibrations of a furious energy from several centuries past spilled the masterpieces of art onto the pavements and gateways, with museums and galleries unable to hold them within closed doors.

Museo Galileo is an unassuming building behind the famous Uffizi gallery, which is dedicated to telling the story of how modern science began. I visited this museum a few years ago and saw its fantastic historical relics. Now I play a game in my mind,  trying to recollect where behind the walls of this building they lie: the first telescopes, microscopes, astronomical charts, sundials, mechanical clocks, navigational compasses, and the first instruments for measuring electricity. Walking through those exhibits was like traveling through time, with each successive era bringing in greater standards of precision in measurement. Apart from the myriad scientific instruments, there were two sets of objects that piqued my interest then. The first were a set of demonstrators illustrating specific scientific principles - for example, the parabolic path of a projectile discovered by Galileo. The second were a set of anatomical models showing advances in medical science - for example, tools for delivering babies in complicated pregnancies. On first sight, these anatomical models showing messy biology stood awkwardly different from the clean instruments of physics. But there is a link between the two, though this fine museum fails to show it within its modest premises.  That missing link now lies in the British Library in London, in the notebooks of Leonardo Da Vinci. They demonstrate that anatomy was the first modern science and physics followed afterwards.

The great physicist Ernest Rutherford said
All science is either physics or stamp collecting. 
This disdain runs deep in our academic establishment, with physics at the top of the pecking order of departments.  Many fields try to ape physics in their methodology, aiming for overarching theories which condense the "truth" into a small set of equations. But are we doing it completely wrong ?

 In this blog, I will narrate a short history of the science of anatomy -  the original harbinger of precision in modern science. I will argue that we scientists should aim to mimic anatomy instead of physics. By that I mean, we need to pay attention to detail even without any pretence for an overarching theory. This is not mere stamp collecting, but an art of map making that is necessary to understand a complex and dynamic subject, such as the human body. I believe this is particularly important for the field of my own study - computer science, which is arguably leading us into a new scientific age. I once related on this blog a lecture by Michel Serres, where he used the word bouleverser  to describe what computers are doing to our society - destroying everything and remaking them in a brand new fashion: politics, culture, education, economy, science, everything. This radical transformation is comparable to only two preceding moments in human civilization: the inventions of writing and printing.  As we try to step into such a new scientific age, we should understand how this happened before, 500 years ago in Florence.

Awakening of the science of anatomy: 

(Left) An anatomical drawing based on "Anathomia Corporis Humani" by Mondino de Luizi, written in 1316. The drawing is from a later print in 1541. Contrast with the lack of detail as compared to Vesalius, above. (Right) The cover of the book showing practice of dissection for anatomical studies.

Browsing through wikipedia, I discovered a peculiar quirk from history that connects three great scientists. The anatomist Andreas Vesalius was born in 1514 and died in 1564. The astronomer Galileo Galilei was born in 1564 and died in 1642. The physicist Isaac Newton was born in 1642 and died in 1726. Tibetans who believe in reincarnation might very well say that the ghost of the scientific spirit successively reincarnated in these three people. The last of the three, Newton was born on 25th December 1642, which gave rise to a recurring annual joke amongst atheists during Christmas time, that "Of course, we need to celebrate the birth of Newton". Newton revolutionized physics by bringing it into the ambit of mathematics: his glorious three laws of motion. Many school children grow up thinking that this mathematical insight occurred to Newton while he was dozing off under an apple tree when lo, an apple popped on his head. Of course, this story is a myth and not true, but so is the myth that physics was the centre of modern science. To understand what motivated Newton, we need to understand Galileo and his fellow pioneers in precise astronomical observation, such as Johannes Kepler. And to understand what motivated Galileo, I believe we need to understand Vesalius and his fellow pioneers in precise anatomical observation.

By the time of Vesalius, the science of human anatomy was already mature. Crucially, it was Europe that held the advantage in anatomical knowledge as opposed to other great civilizations such as China, India or Arabia. These other civilizations stood superior to Europe in many other fields such as mathematics or astronomy. Scholars of history keep arguing why the awakening of modern empirical science, requiring precise experimental observation, arose in Europe and not in other places. There are many theories, but I believe the answer lies with anatomy, where Europe and specifically Italy, held a distinct superiority over other places. Dissecting the human body was a cultural taboo in many civilizations, as it is still today in many contexts. Ancient India had a vast knowledge in medicine, but cutting the human body was banned due to religious reasons. Instead, Indian anatomists let the body decompose naturally and peeled off the layers using Kusa grass. This was not as effective as using precise surgical instruments for studying anatomy as practised later in Europe. Ancient China had a cultural emphasis on holistic medicine that required studying the entire body, as opposed to observing each organ in detail. This resulted in a lack of a demand for anatomical knowledge. It is not clear whether Arabs performed dissections, but the strong prohibition in Islam of representing the human body in artistic form resulted in a shortcoming of anatomical knowledge.

A strong contrast to all these civilizations is the popularity in Europe of the artistic description of the human form. Sculpture and fine-arts have been valued highly by the Greeks and pursued with equal gusto by the Romans. It can be argued that Greek science and philosophy have stagnated during Roman times, but the arts of sculpture, painting and architecture have advanced immensely. As the artistic standards  rose for the description of human form, many painters and sculptors realized that they needed to understand the underlying muscular structure of the human body. However, the Roman empire prohibited the dissection of the human body, again due to religious reasons. The Greek physician Galen, working in Rome in 2nd century AD, obtained his anatomical knowledge by observing the injured gladiators. When this didn't give sufficient knowledge, he compensated for this by dissecting animal cadavers. For many centuries, his work remained the standard in Europe as further progress was stunted by the ban on dissection. A remarkable element was that the delivery of human babies was studied by dissecting sheep, so much so that amnion - the scientific word for the placental membrane  - comes from the Latin word for lamb. Obviously, this extrapolation from animal studies to human bodies resulted in several errors, which were not corrected until  the 16th century by Vesalius.

Before Vesalius could achieve his mastery of the human anatomy, the gates needed to be opened for scientific investigation of the human body by dissection . The first advantage was given by Christianity. Although it required the proper burial of the bodies of believers,  Christianity removed the sharp prohibition on dissection present in pagan Rome. The atmosphere was sufficiently relaxed by 13th century AD, when an Italian physician named Mondino de Liuzzi was able to perform public dissection of human cadavers. He wrote a text named "Anathomia Corporis Humani" which is considered to be the first true anatomical text, based on observations of the human body.

The later physicians in Italy regularly performed dissections and improved anatomical knowledge. Thus, the text of Vesalius with its detailed anatomical drawings is the outcome of a gradual evolution. The publication of this text was greatly aided by the invention of the printing press by Johannes Gutenberg (born 1398, died 1468). But the science of anatomy was already in the ascendancy by this time. Apart from physicians, sculptors and artists in Italy studied anatomy in a rigorous manner. The teacher of Leonardo Da Vinci (born 1452, died 1519) in Florence, Andrea del Vercocchio (born 1435, died 1488) was a master of human facial anatomy, as can be seen in his drawing below.

Drawing of St Jerome by Andrea del Vercocchio, the teacher of Leonardo Da Vinci

Another great master of human anatomy is the sculptor Michelangelo (born 1475, died 1564). This analysis of human anatomy flourished in Florence and spread from there to the whole of Italy and Europe.  Specifically, Leonardo Da Vinci depicted bone structure and musculature in significant detail, as shown below.

Anatomical drawings of Leonardo Da Vinci from his notebooks

Apparently, Leonardo was so curious to study facial expressions that whenever he saw particularly ugly or grotesque looking people, he followed them around the town in the hope of catching their facial expressions under different emotions. His systematic analysis of the human face is the secret behind his masterpieces - such as the Last Supper and Mona Lisa, with their precise and enigmatic facial expressions.

It is sometimes acknowledged that the year 1543, with the publication of the book De Humani Corporis Fabrica by Vesalius, is the beginning of  the scientific revolution. Another significant event in the same year is the publication of Nicolas Copernicus about the heliocentric theory of the universe (something already discovered by several ancient astronomers). However, we have to note that the work of Vesalius is not the beginning, but a significant milestone of maturity for the science of anatomy. In terms of scientific investigation and experimentation, the other sciences caught up only much later.

The scientific study of anatomy revolutionized surgery, and medicine in general. In his book "Adventures in Human Being", Gavin Francis describes the Victorian medical school building in central Edinburgh in Scotland as follows.

Carved into the stone lintel of the entrance was "SURGERY ANATOMY PRACTICE OF PHYSIC"  The greater weighting given to the word ANATOMY was a declaration that the study of the body's structure was of primary importance, and the other skills we were engaged in learning - those of surgery and practice of physic (medicine) were secondary. 

Edinburgh has a unique and significant place in the history of anatomy. The physician and artist Charles Bell was born and practised here. Francis narrates how Bell was inspired by the drawings of Da Vinci and by his analytical detail in the depiction of facial musculature. Bell described in detail the different facial nerves that animate the human facial expression. One of the medical pathologies that is studied by Bell is that of facial paralysis, now known as Bell's palsy. The complexity of the facial anatomy in the human has led Bell to proclaim that humans are unique with respect to the other animals in how complex their facial expressions are. This model was later criticized by Darwin who also studied in Edinburgh. But Darwin expressed a great fondness for the anatomical work done by Bell and by his predecessor Da Vinci, which undoubtedly influenced the later development of his theory of evolution. Even the observations of Charles Bell on the uniqueness of human facial expression remain relevant to this day, as  facial expression mirrors the complexity of emotional states in the human brain, which is substantially superior to that of the other animals. In more recent times, psychological research by Paul Ekman and others has investigated how the facial expressions in different human cultures, including traditional tribal societies, are remarkably similar to each other and exhibit similar complexity. The synthesis of virtual human characters in films and computer games derives greatly from this work in psychology and anatomy. 3D face modelling for visual effects is also my window into this fascinating field.

Another significant advance in the study of anatomy is the work by Henry Gray, whose classic "Gray's Anatomy: Descriptive and Surgical" first published in 1858, remains an important reference to this day. Many scientists working in other fields have relied on this book to extend their findings to the field of medicine. This open scientific investigation, structured on an open understanding of the human body, has greatly benefited mankind. This is arguably one of the most important gifts of science: in addition to the discoveries of evidence based medicine through randomized controlled trials, and that of antibiotics such as Penicillin. These advances in medicine have saved countless number of lives and alleviated the pain of several more people. In this sense, even from a practical and utilitarian point of view, medicine (and specifically, anatomy) is a greater role model for sciences than physics.

Open source education of anatomy: 

With the advances in body imaging technologies and computational medical sensors, we now have a unique opportunity to extend the understanding of anatomy to the general public. Unlike X-rays and CAT scans, novel imaging technologies such as Ultrasound Imaging and Magnetic Resonance Imaging (MRI and fMRI)  do not use harmful ionizing radiation. Thus, in principle, they can be used extensively for acquiring a lot more data about the human bodies than what we have today. But in practice, they remain extremely expensive and have not yet realized economies of scale. Very few people have deep knowledge of their own bodies, as captured by the latest medical imaging technology. Why is this ?

Very often, it is too late when doctors perform clinical diagnosis of harmful tumours, bone fractures or misalignments in the body. This results in costly late procedures or even in the death of patients. This is terrible, but there is a greater problem that is not apparent to people who are not aware of the possibilities of computational medicine.

It is now possible to capture and analyse the human body throughout its  metabolism, and obtain a detailed understanding of its processes of digestion, locomotion or cognitive control. Obviously, all these bodily processes depend on the exact physical structure and anatomy of the patient, as well as his lifestyle. So the medical advice can be tailor-made to the exact needs and requirements of the patient. This can be achieved by computational analysis of the sensor readings from one patient, and putting them in relation to the statistics from large human populations. All of this computational analysis needs to be grounded on the anatomy of the human body.  Another grounding factor is the DNA of the patient. If we have an open model to represent this knowledge, this can facilitate the development of personalized drugs as well as lifestyle recommendations, which can be prescribed by the doctor in coordination with experts in many different fields. These recommendations can be as detailed as the posture of the body, the cognitive tasks during the day, or how to organize one's home or furniture. This will be in stark contrast to the one-size-fits-all drugs that we currently have in the pharmaceutical market. In fact, future generations will look back at our current medical practice in dismay, similar to how we look at the ancient Roman physicians who delivered human babies on the basis of sheep anatomy.

However, medical diagnosis is not solely a computational problem and we can never replace the role of the clinician. Reading the book of Gavin Francis made me realize this very strongly. There is an underlying strand of compassion and empathy that runs throughout the book, across the various medical cases that he describes. This empathy cannot but be obtained from a dedicated clinical practice. It is the job of the clinician to explain the alternatives to the patient and convey the information in a manner that he can understand. Very often the problems are not clear cut and there is no easy solution. In this sense, the role of the clinician is not much different from that of a teacher. What we now have is a problem of educating the general public, and making them understand their own bodies in a more profound manner.

Despite the great advances in technology, our societal understanding of the human body has not progressed much from the era of Leonardo Da Vinci. We need a new model for anatomy that corresponds to the computational understanding of the human body. We need a method of communicating this model between experts and the general public, in a way similar to how printed books communicated the anatomical drawings of Vesalius. Without these models of communication, we will not be able to exploit the advances of medical imaging technologies and computational medicine. In fact, the situation is far worse. These advances will be used by the nefarious powers on the market who will exploit the gullible public similar to how livestock animals are exploited. The disaster in the food industry, which keeps churning out addictive sugar loaded products, is a case in point. Another disaster is unfolding in the industry of medical supplements and pain medicine, which make the human users addicted to them. Many people use legal drugs such as nicotine and alcohol as pain relief. But the human exploitation is not limited to food or drugs. All social and cognitive activities will be analysed with respect to how they affect the human body, and thus they will be exploited. An important avenue of exploitation, based on advances in neuroanatomy and physiology, is that of our digital lives on the internet,which now hosts a significant chunk of the economy.

How can we have an open-source education of computational anatomy for the general public ? This is not an easy question to answer. In fact, the question is deeply tied to how we communicate computational objects in general. Most people do not understand computers. Even trained computer programmers do not understand complex software. This is the case even for "open-source" software, where the source-code is made public for anyone to see. For most people, this is illegible and a foreign, alien language. If we are not able to communicate relatively simple computational objects like web pages, how can we communicate complex biological models to the public ?

We need to go back to the roots of anatomy and decipher how those artists sketched the human form and musculature. In fact, an anatomical drawing follows a complex aesthetic of visualization. When the body is dissected, the important nerves and muscles are drawn out and presented in a visually comprehensible manner. This is necessary even for medical students, and more so for patients. If we want to show the metabolism of the human body in motion, we need to develop a similar language of aesthetic. Crucially, this language should be able to represent the computational aspects of the metabolism that are relevant for diagnosis. This might seem like a daunting task, but we have a great starting point, which is that people are motivated to know about their own bodies, and they can start from the static anatomical drawings aligned to their medical images. However,  we cannot avoid the job of educating the public. In this regard, we need the effort of artists similar to Leonardo Da Vinci, who can bridge the elite world of scientists to the lay person.

We still have many cultural taboos about anatomical images. Most people associate bone skeletons and inner body images with corpses. Very few people see them as masterful creations of nature, depicting all the dynamics of life. In Germany, there is a traveling exhibition of plasticized human and animal anatomy, known as Körperwelten (Body Worlds) which keeps running foul of  religious groups. Part of the appeal to such anatomy exhibitions is their shock factor and morbid  element. However, we need to grow out of this shock and understand our human bodies in their true dynamic form. We need artists who can bridge this gap.

Anatomy of open-source education: 

The media theorist Marshall McLuhan has theorized in the 1960s that  modern media is fundamentally reshaping our human consciousness. He profoundly influenced many computer scientists who wanted to achieve a fundamental transformation in human society through computational thinking. In order to qualify as a medium for thinking, a computer should not be restricted to an elite set of programmers or engineers, but used by everybody. In other words, this should be as versatile as a book. This vision and dream was the driving force of the pioneering work in personal computing by scientists such as Seymour Papert and Alan Kay. We now have the technological means to provide personal computers for all human beings. However, the way we are using computers today is a complete disaster, and a total sell out of the original dream.

Most people use their computers (now hidden inside their mobile phones or home appliances) as livestock tethered to a pole. In other words, they are willing slaves to an overarching system of control. With repetitive use, they are conditioned to think and behave like captive animals. In this regard, computers and internet are much worse than books, and closer to chemically addictive substances. A loose analogy to the situation today is most people using books entirely to write confession material to the pastor in the church, and never for reading anything, not even the bible. If books were used like that, they would have resulted in a slave society in complete thrall to the powers in the dark. The invention of the printing press by Gutenberg would have simply exacerbated the situation. In reality, this did not happen. The fundamental reason is that the elite scientists have found a way to communicate their knowledge to the general public. This started with the science of anatomy. Today, we face a similar task in computational sciences. I believe we can draw similar inspiration from anatomy, building the first applications in health and environmental sciences, where there exists a significant minority of passionate people eager to know more. These people can be trained to think in a computational manner through applications that visualize the hidden anatomy of the human bodily processes or of the environmental processes. Much as the underlying neural and cardiovascular structure describes the health of the human body, the threads of biodiversity and natural resources describe the health of the environment,

These applications need a method for communicating computational media that can be easily  interpreted and visualized by the general public, which over the course of interaction, reveals the computational intricacies to the user. In other words, we need to decouple how the media is programmed with how it it reacts to the user. But at the same time, we need a guarantee that the user interface produces the same level of computational control as a full-fledged programming language. The work of Alan Kay, the original inspiration behind the movie Tron, remains a hallmark in this regard. Snippets from this inspiring work are now available in the programming languages of Smalltalk and Squeak. Another  example is the work of Bill Atkinson at Apple, who developed Hypercard (eulogized here by Douglas Adams). Although limited in its computational expressiveness, this pioneering work was far ahead of the World Wide Web developed by Tim Berners Lee, in terms of user expressibility. The web, in turn, is far more expressive than the disastrous world of apps we have today. In terms of computational education of the general public, we have regressed tremendously.

In today's world (in 2016),  my personal hopes for an open data format for  educating the general public to think in a computational manner are with iPython notebooks. At present, these notebooks are used extensively by researchers in computational sciences and machine learning to display scientific data sets. With a little bit of prodding, they might be developed to communicating computational data  to the general public. Taking another cue from clinical medicine, we can develop applications to help the users understand their own bodies or lifestyles in an analytic manner. It is very easy to develop apps that make money by getting the users addicted via some psychological weakness. It is much harder to develop apps that don't make as much money, but will educate the public. Without conscious effort from programmers, these will never happen.

What is a paraview : 

This blog post is inspired by my reading of the book by Gavin Francis. However, it also draws from my own personal experiences in my  life and my perspectives as a computer scientist. In this sense, it is something more than a review of the book. I am expressing my inspiration by using the equivalent of anatomy in the human language: etymology, to coin a new word.

In Greek, the prefix "para" refers to something "beyond" or "by the side of". Interestingly, this is one of the prefixes that applies equally to Greek and Sanskrit. Examples in English that use this prefix include paragraph, parallel, parapsychology, paranormal, parachute (first imagined by Da Vinci). I coin the word "paraview" to refer to a "view beyond the subject". I think this is a very useful word to describe a detailed comment enriched with one's own experience or perspective. Ideally, our expressions of the digital lives on the internet should be connected to one another as paraviews, and not organized in a hierarchical list. This imposition of hierarchy on human thought by the world wide web is one of the complaints of Ted Nelson, the originator of the ideas of hypertext and hyperviews. At present, we do not yet have a hyperview browser to inspect the anatomy of online content, as envisioned by Ted Nelson. But at the least, we can try to express paraviews, instead of mere appendages in a hierarchy.

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