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Archive for the ‘science’ Category

Wondering while wandering

Posted in from the dark room, photography, science, tagged on July 23, 2008| 6 Comments »

butterfly
butterfly and bee

While wandering around yesterday I stumbled across this lovely butterfly. It’s not easy to get a photo of a butterfly cos they don’t stay still for very long, but this one seemed to be taking its time more than the others. It got me wondering. What do butterflies eat? And how do they fly the way they do? Their flight seems most erratic, apparently lacking the consistency of movement that you see in bird flight for example. I realised I don’t know very much about butterflies at all! I certainly don’t know anything about butterfly classification! What “kind” of butterfly is this?

Well, when I got back home I checked out wikipedia. Turns out butterflies only eat liquids which they suck up through their long, tube-like “probosci”. They live on nectar and they can drink water from puddles. I would have guessed they lived on nectar but I hadn’t realised they had a fluid only diet. As for how they fly, well, that’s even more interesting…….it turns out nobody understands it. Their mechanism of flight – the aerodynamics and the physics of it – has never been fully explained. About four different ways of flying have been described but they don’t provide a full explanation and nobody knows how they manage to switch between the different flight modes so quickly.
I’m quite happy about that. I do like to learn but I also enjoy having that feeling of wonder and amazement. What I like best is a mixture of understanding and marvel. Butterfly life fits the bill!

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What constitutes evidence in the practice of medicine?

Posted in from the consulting room, health, science, tagged on July 13, 2008| Leave a Comment »

Clinical epidemiology has been cleverly spun into something referred to as “Evidence Based Medicine” (“EBM”). It’s such a powerful spin that we are seeing the term “evidence based” being used widely now to justify any decision made by any authority – whether that be politicians, civil servants, educators or scientists. In fact, the phrase is thrown around so freely and unthinkingly that it’s quickly losing its original meaning, instead becoming a code term for “fact” or undeniable Truth. “Evidence based” is a label now which is supposed to convey that the statement to which it is attached has a high value. The idea of “evidence based” as promoted by those who use the term is founded on the belief that what constitutes “truth” is, however, almost exclusively, the physical and the measurable. Let me quote from  Maya Goldenberg, who wrote about this in Social Science and Medicine. Volume 62, Issue 11, June 2006 –

Reflecting on how the popular idea of “patient-centred care” remains largely unrealized in clinical practice, Van Weel and Knottneurus (1999) note that while physicians are encouraged to make diagnoses in physical, psychological, and social terms, “the EBM that is currently promoted either restricts itself to physical evidence alone, or casts such evidence at the top of a hierarchy that tends to devalue any evidence ‘lower down’”. The hierarchy of evidence promotes a certain scientistic accounting of the goals of medicine, which, the worry goes, is incommensurable with the proposed reorientation of medical practice toward the patient’s search for meaning in the illness experience. The bridging of scientistic “measure” and existential “meaning” has received some attention in the critical EBM literature with the general consensus that we need an “integrated” model of evidence that properly reflects modern health care’s constitution by diverse academic traditions—including the humanities, social sciences, and the pure and applied sciences—that rely on equally diverse notions of evidence. While EBM values evidence that is statistical in nature and general in its application, and therefore places quantitative data derived through the application of recognised study designs at the top of its pre-graded hierarchies of evidence, the phenomenological approaches rooted in hermeneutics, ethnography, sociology, and anthropology, regard evidence as primarily narrative, subjective, and historical in nature. Unlike the impersonal and generalisable measures undertaken in EBM, this conception of evidence is illustrated in case histories, clinical encounters, and qualitative studies such as in-depth interviews and focus groups. The features of the medical encounter and the illness experience emphasised by medical phenomenologists and proponents of a more “humane” medicine suggest the need to reconsider what constitutes the goals of medicine and flip EBM’s hierarchy of evidence on its head. The quantitative measures and generalisations that come out of controlled trials and biostatistical analysis are not conducive to the questions of meaning that medical phenomenology wants to address and make central to medicine.

Goldenberg helpfully nails down the key issues – “ While EBM values evidence that is statistical in nature and general in its application, and therefore places quantitative data derived through the application of recognised study designs at the top of its pre-graded hierarchies of evidence, the phenomenological approaches rooted in hermeneutics, ethnography, sociology, and anthropology, regard evidence as primarily narrative, subjective, and historical in nature” – The EBM approach is a statistical approach. It tells us something about probabilities, derived from studies of large, supposedly homogenous groups. It doesn’t give us certainty about either effectiveness of a treatment, or about prognosis, in any individual patient. Nor does it give us any insights into either the experience of illness, or the experience of therapeutic recovery for patients.
The use of clinical epidemiology alone in the application of health policy or therapeutic practice is neither rational nor sensible. Health and illness are experiential. Human experiences can only be conveyed by human beings. If we want a more humane form of medical practice which is a closer fit with individual reality then we need to develop our phenomenological understanding and give such research considerably greater consideration than we currently do instead of dismissing the unquantifiable as irrelevant.

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The Petabyte Age – pattern discovery sheds a light on everything

Posted in from the reading room, life, philosophy, science on July 12, 2008| Leave a Comment »

Chris Anderson of Wired magazine has published an interesting and provocative article about how “more is different”. It’s difficult to even visualise huge amounts of data, let alone analyze enormous data sets, but emerging technologies are giving us the tools to be able to interact with bigger and bigger datasets. A petabyte is 2 to the power of 50 (ie 1,125,899,906,842,624). This can be approximated to 10 to the power of 15 (1,000,000,000,000,000). Whilst this is truly a mind-bogglingly large number, Google servers process this much information every 72 minutes! But wait, it gets even more amazing! There are bigger numbers. An “exabyte” for example is 1,024 petabytes, and a “zetabyte” is 1,024 exabytes. Let’s not even go there yet! We can process such vast amounts of information by using large networks of computers and algorithms which handle the datasets as “clouds”. I like the “cloud” idea. You might already be familiar with it through the tool known as “tag clouds“. However, let’s get back to Chris Anderson’s article.

Anderson says that science has proceeded until now by making models then testing to see how well the models fit the data -“hypothesize, model, test”. This enables scientists to uncover the links between events which show us how those events come about (causation) and then make predictions about the future. This is a powerful method and has greatly increased human understanding. However,

There is now a better way. Petabytes allow us to say: “Correlation is enough.” We can stop looking for models. We can analyze the data without hypotheses about what it might show. We can throw the numbers into the biggest computing clusters the world has ever seen and let statistical algorithms find patterns where science cannot.

In other words, the ability to handle such vast amounts of information directly, allows us to uncover the correlations which exist and thereby to see patterns emerge right out of the data without pre-selecting the data with a hypothesis and a model.

Anderson has pushed this idea provocatively to claim this means the end of science as we know it and a lot of commentators have reacted to this with strong disagreement. The points made both by Anderson in his original article and by the commentators are stimulating and thought provoking.

George Dyson says

The massively-distributed collective associative memory that constitutes the “Overmind” (or Kevin’s OneComputer) is already forming associations, recognizing patterns, and making predictions—though this does not mean thinking the way we do, or on any scale that we can comprehend. The sudden flood of large data sets and the opening of entirely new scientific territory promises a return to the excitement at the birth of (modern) Science in the 17th century, when, as Newton, Boyle, Hooke, Petty, and the rest of them saw it, it was “the Business of Natural Philosophy” to find things out. What Chris Anderson is hinting at is that Science will increasingly belong to a new generation of Natural Philosophers who are not only reading Nature directly, but are beginning to read the Overmind.

This feels right to me. These new methods are not the death of science but are the beginning of scientific methods which will change the way we understand the world. Kevin Kelly says more along this line of thought

My guess is that this emerging method will be one additional tool in the evolution of the scientific method. It will not replace any current methods (sorry, no end of science!) but will compliment established theory-driven science. Let’s call this data intensive approach to problem solving Correlative Analytics. I think Chris squander a unique opportunity by titling his thesis “The End of Theory” because this is a negation, the absence of something. Rather it is the beginning of something, and this is when you have a chance to accelerate that birth by giving it a positive name. A non-negative name will also help clarify the thesis. I am suggesting Correlative Analytics rather than No Theory because I am not entirely sure that these correlative systems are model-free. I think there is an emergent, unconscious, implicit model embedded in the system that generates answers.

Maybe the contribution I’ve enjoyed most, however, is that made by Bruce Sterling, which begins this way –

I’m as impressed by the prefixes “peta” and “exa” as the next guy. I’m also inclined to think that search engines are a bigger, better deal that Artificial Intelligence (even if Artificial Intelligence had ever managed to exist outside science fiction). I also love the idea of large, cloudy, yet deep relationships between seemingly unrelated phenomena—in literature, we call those gizmos “metaphors. ” They’re great!

As is so often the case, Bruce Sterling puts his finger right on what’s interesting. He highlights the relationship between this way of viewing data sets and the way we use language. Metaphors are incredibly powerful tools. They can feel like a kind of magic, producing sudden, potentially profound insights, literally in moments. It’s exciting to think that the “petabyte age” will bring us similar tools to engage with a wide range of phenomena.

Finally, Oliver Norton brilliantly manages to make these mind-bogglingly large computations suddenly seem not so overwhelming at all by saying –

And I guess my other point is “petabytes—phwaah”. Sure, a petabyte is a big thing—but the number of ways one can ask questions far bigger. I’m no mathematician, and will happily take correction on this, but as I see it one way of understanding a kilobit is as a resource that can be exhausted—or maybe a space that can be collapsed—with 10 yes or no questions: that’s what 2 [10] is. For a kilobyte raise the number to 13. For a petabyte raise it to 53. Now in many cases 53 is a lot of questions. But in networks of thousands of genes, really not so much.

The complexities of life can seem overwhelming but I feel pretty excited by our human capacity to perceive patterns using all kinds of tools from “clouds” to “metaphors”. The drive to make sense of life, to find meaning and purpose, is a core human quality. Science, its new methods and its old ones, is one way of responding to this drive.

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Scaling changes everything

Posted in from the reading room, perception, science on June 24, 2008| Leave a Comment »

I don’t think you can understand anything unless you see it in its’ context. The tricky thing about that is that everything exists in multiple contexts, so depending on the context which you choose to consider (the perspective you take), whatever it is you are considering can be understood in different ways. I like that. It means you can never FULLY know ALL there is to know about anyone.

During a consultation with a patient I think it’s important to consider several contexts. I drew myself a simple diagram to illustrate this – I’ve described it in the post about the “Human Spectrometer“.

Today I came across a great flash animation which really makes you think about how scaling up or down totally changes the relevant contexts. Try it out. It’s interactive, informative and fun.

It reminded me of the scale of ten project where a series of images are presented, each one being a magnification ten times greater than the previous one. Here’s one version of that from youtube …….

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The life force

Posted in health, life, philosophy, science on June 17, 2008| 15 Comments »

The concept of a “life force” fascinates me. What is it that enlivens a creature? What changes in that moment between life and death? I vividly remember the first time I had to certify that someone had died. That person was an old man who had died peacefully in a geriatric ward in the middle of the night. As a young doctor this was a diagnosis I absolutely wanted to get right. I took my time and completely convinced myself that this old man had indeed passed away. Perhaps because I spent so long over this, I found myself thinking long and hard about that borderline between living and dying. What changes in a moment? As I sat next to this man’s lifeless body, what had gone? How exactly do we die? Of course, as a doctor I’d learned about the stopping of the heart, about the ceasing of the lungs and about “brain death”, but the closer I looked the harder it seemed to me to discern the exact moment of death. Life and death seem two such absolute states. There isn’t really a transitional zone that is neither life nor death. Even “half-dead” is still life! All these years later I’m no closer to understanding exactly how to pin down the moment of death or to understand what disappears or dissipates at the end of life.

The “life force” (or the “vital force”) is an old concept to try and capture what it is that enlivens us, what it is that is present when we are alive, but gone when we are dead. In fact, for a long time the life force was believed to be an entity, but when the anatomists dissected human bodies and couldn’t find any such entity, the concept lost a lot of ground. Science, it seemed, had shown that no such entity existed and materialistic understandings of the human being became much more accepted than “vitalist” one.

It’s fascinating, therefore, to see the re-emergence of the life force in a totally new guise. Modern systems theory, and complexity science, both show that complex systems have certain characteristics which are remarkably like the old “life force”.

  1. Self-organisation. Complex systems (specifically, complex adaptive systems) have the ability to self-organise. They are made of many, many components, connections and systems, which co-ordinate with each other to maintain overall defence, to adapt and maintain homeostasis of the inner environment, and to be self-repairing.
  2. Autopoiesis. Living systems have the unique characteristic of “self-making capacity”. This is a term coined by Maturana and Varela. Autopoietic organisms can make and maintain themselves.
  3. Emergence. This is a fairly new term which captures that characteristic of being able to produce new, previously unwitnessed, behaviours.
  4. Consciousness. Finally, let me add the phenomenon of consciousness. Not every living creature has consciousness. However, consciousness is a phenomenon which, like the old “life force”, is actually not an entity but a behaviour, or an experience. OK, I know, this is way too simplistic a description of consciousness and clearly it isn’t the same as the life force (think of persistent vegetative states for example). But it strikes me that the life force is a similar kind of phenomenon.

I am repeatedly impressed with the strength of the life force in the patients I see. It seems to me that it’s the basis of their ability to cope, to grow, and to shine. It’s the basis of the fight to overcome disease and to say to Death, “not yet”. Without it, there is, indeed no life at all.

I’m reading Antoine Sainte-Exupery’s “Citadelle” at the moment. Here’s the line I read today which set me off thinking about this post –

The tree is more than first a seed, then a stem, then a living trunk, and then a dead timber. The tree is a slow, enduring force straining to win the sky.

That captures it for me. Aren’t we all the slow, enduring force of life straining to win the sky? The life force flows through us, maintains us, repairs us, and drives our growth. Amazing, isn’t it?

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The intimate connectedness of life

Posted in from the dark room, from the reading room, philosophy, photography, science on May 29, 2008| 4 Comments »

the spider and the flower

I was photographing this lovely yellow flower when suddenly I noticed a bit of it was moving…….then I saw the little spider!

Look at it! See how the yellow of its body so PERFECTLY matches the yellow of the flower! Goodness! How does that happen? Isn’t it astonishing!

One of my favourite philosophers is Deleuze. He emphasises not thinking of discrete objects. He rejects the typical “arboreal” system of thought where we set every organism into a specific branch in a taxonomic tree. Instead he suggests we think in terms of the connections and borders and interactions. He emphasises a “rhizome” model (like grass, which has no single centre, but is, instead more like a vast web). I’ve always found that idea appealing because it rejects labelling and putting things into boxes. Instead it emphasises dynamic change. That’s why I have the byline at the top of my blog – “becoming not being…..”

When you think in terms of becoming, not being, you focus on the interactions, the connections and the development of organisms. After all, can we really understand either this flower or that spider without considering how, together, they make a little functioning unit, a little ecosystem?

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Seed

Posted in creativity, from the dark room, life, photography, science on May 28, 2008| 3 Comments »

I was sitting sipping a coffee at an outside table in the cafe at the market the other day and I saw this seed lying on the table.

seed

I thought I’d capture it and share it with you.

Isn’t it amazing? If you look closely, there are two capture devices built into it! At the left end, there’s a tiny, wee hook-shaped hair for grabbing onto something and, at the other end is this delicate and exquisite brush of fine, fair hairs for carrying it far in the wind.

Seeds have always been a source of wonder to me. How can such a tiny object turn into a flower, or a bush, or a tree? I guess if you are knowledgeable about such things you’ll know what this seed might become – I’m afraid I don’t! One of the subjects which enthralled me at university was embryology. How on earth can a single, fertilised cell turn into all the diverse types of cell in the human body and grow in the right places?! Awesome!

Do you think this seed might become a great tree somewhere? Like these ones?

forest sky

I also went to a garden festival and one of the stalls sold seed pods. Look at their diversity!

seedpods
seedpods
seedpods

So, there’s two things that amaze me about Nature – creativity and diversity. These are such important features of human beings too, aren’t they? How little we guess about the potential of a baby! How little we know about his or her uniqueness! Amazes me every time I think about it!

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4 verbs which make us human?

Posted in life, narrative, neuroscience, perception, personal growth, philosophy, psychology, science on May 20, 2008| 3 Comments »

Let’s consider four verbs which highlight essential characteristics of human beings.

SENSING

All living creatures are sensate. All have sensory organs to pick up stimuli from the environment – light, sound, odours, temperature and so on. As human beings we have a particularly elaborate sensory system, possibly THE most elaborate of all creatures, however, being sensate is a characteristic we share with all animate beings.

FEELING

I have a large hardback copy of Gray’s Anatomy on my bookshelf. I bought it when I was studying anatomy at Medical School back in 1973. I still find it fascinating. The section on the nervous system and the brain shows something incredibly striking. All the nerves which carry the signals from the sensory organs travel first of all to what is termed “the old brain”, the “limbic system” more or less. That always amazed me. Why do all the sensory signals go there? This particular area of the brain is the main emotion generating and processing centre. It’s responsible for those feelings you get of fear, of arousal, of anger, and so on. Modern techniques of brain imaging are helping us to understand this better. It seems that we have developed in a way which allows signals from our sensory equipment to first of all create emotional states. This has a survival advantage. For example, we can quickly develop the “fight or flight” response to successfully deal with any threats around us. Obviously emotions are considerably more elaborate than this. Anthony Damasio is really interesting to read about this subject. “Descartes’ Error: Emotion, Reason and the Human Brain” is a good starting point. But I can also recommend his “The Feeling of What Happens” and “Looking for Spinoza”. You might also like “Consciousness Explained” by Daniel C Dennett and “Emotional Intelligence” by Daniel Goleman. What all of these authors show us is how this particular function of the brain allows us to respond to stimuli from the environment far, far more quickly than we could if we had to become aware of everything consciously first, then figure out what to do about it. That thinking thing comes next! Although it’s not possible to really know the emotional content of another creature’s mind, from observing behaviour patterns it would seem that other animals also have emotions.

THINKING

Those two great parts of the brain known as the cerebral hemispheres are responsible for what we term “cognition”…….thinking. In its entirety, the human brain is THE most complex structure in the known universe. Amazing, huh? And it’s inside your head! There’s way too much involved in thinking for me to explain here but it involves memory, imagination, awareness, concentration and systems of assessment. Once signals have been processed in the old brain (and acted upon!), this “new brain” picks up the trail and processes what’s going on. It’s thinking that let’s us make choices. Some other creatures think too, but, as far as we know, not to nearly the same extent as human beings do. One of the things we’ve done with these capacities is to develop language which gives us the ability to handle and manipulate symbols and to think both abstractly and synthetically. And that leads to the fourth verb – the one which seems to be uniquely human –

MEANING-SEEKING

We don’t just pick up signals, we don’t just generate feelings, we don’t just think about the signals and the feelings to make choices, we do something else. We try to make sense of things. We are always asking the questions “Why?” and “How come?” We are insatiably curious but we are also insatiably trying to understand the world and our experiences. The way we do this is by telling stories. We put everything together and attribute values and meanings to weave narratives which enable us to make sense of the world and of ourselves. We do this in a host of complex ways. Viktor Frankl showed how this is one of our most fundamental drives. See his “Man’s Search for Meaning”. Richard Kearney shows how we use storytelling for this purpose, and Owen Flanagan shows how we inhabit “spaces of meaning” to create our distinct worldviews and narratives.

So, there you have it. Four verbs which make us human – sensing, feeling, thinking and meaning-seeking.  Let me just add one further level of complexity. I’ve presented this is a logical, step-wise way – inspired by those evolutionary biologists – but on a moment to moment basis, these activities of the human being are continuously active and interactive. What sense we make of something influences what we sense and vice versa. Feelings influence thoughts and vice versa. And so on.

What do you think? Do you agree that these four verbs capture what it is to be human? Have you any others you think I should add?

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The reductionism vs holism debate

Posted in books, from the reading room, science on April 11, 2008| 4 Comments »

I’ve just finished reading Michio Kaku‘s “Hyperspace” – it’s a book I’ve had on my shelves for years but didn’t get round to reading (I’ve got LOADS like that – but I’m still convinced I’ll read them ALL eventually!). It’s about multi-dimensional thinking in physics and maths, and I read it because of a dream I had. It’s a fabulous book, which really does make difficult concepts understandable. I highly recommend it.

In the last chapter of the book, Michio tackles the reductionism vs holism issue, because in Physics, apparently, there are two very different groups of adherents to each of these viewpoints. He has an interesting exposition of the more extreme forms of these two groups, referring to the reductionists as “Belligerent science” and holists and “Know-nothing science” – OK, I know, both extremely judgmental and controversial terms but read this paragraph where he describes them –

Belligerent science clubs the opposition with a heavy, rigid view of science tht alienates rather than persuades. Belligerent science seeks to win points in a debate, rather than win over the audience. Instead of appealing to the finer instincts of the lay audience by presenting itself as the defender of enlightened reason and sound experiment, it comes off as a new Spanish Inquisition. Belligerent science is science with a chip on its shoulder. Its scientists accuse the holists of being soft-headed, of getting their physics confused, of throwing pseudoscientific gibberish to cover their ignorance. Thus belligerent science may be winning the individual battles, but it is ultimately losing the war. In every one-to-one skirmish, belligerent science may trounce the opposition by parading out mountains of data and learned PhDs. However, in the long run arrogance and conceit may eventually backfire by alienating the very audience that it is trying to persuade.

Know-nothing science goes to the opposite extreme, rejecting experiment and embracing whatever faddish philosophy happens to come along. Know-nothing science sees unpleasant facts as mere details, and the overall philosophy as everything. If the facts do not seem to fit the philosophy then obviously something is wrong with the facts. Know-nothing science comes in with a preformed agenda, based on personal fulfillment rather than objective observation, and tries to fit in the science as an afterthought.

I recognise these attitudes clearly. I have been on the receiving end of classic “belligerent science” communications – some of it so offensive, I just delete it straight after reading it (and wish I’d never read it in the first place!) “Belligerent scientists” clearly don’t like homeopathy! In fact, the tone of some of the comments I have received to posts I put up concerning homeopathy, led me to create a “Commenting policy” which you can read at the bottom of the right hand sidebar of this blog. On the other hand, I’ve read plenty of comments from the other extreme end of this axis. I find this latter group to be a lot nicer than the belligerent crowd I must say, but often not any easier to have a discussion with.

I confess to having a strong affiliation to holistic perspectives on the world, but science has always been a fascination for me and it thrills me to understand how things work so I see a real value in reductionist thinking too.

How to reconcile these two viewpoints? Well, you could read Kaku’s final chapter, but essentially he argues for taking a higher perspective and seeing that both methods are appropriate in different circumstances.

One contemporary philosopher who has considered this issue is Mary Midgely.

She argues against reductionism or the attempt to impose any one approach to understanding the world as the only right way to see things. She suggests that there are “many maps, many windows” on reality and argues that “we need scientific pluralism – the recognition that there are many independent forms and sources of knowledge – rather than reductivism, the conviction that one fundamental form underlies them all and settles everything” and that it is helpful to think about the world as “a huge aquarium. We cannot see it as a whole from above, so we peer in at it through a number of small windows … We can eventually make quite a lot of sense of this habitat if we patiently put together the data from different angles. but if we insist that our own window is the only one worth looking through, we shall not get very far”

I like that. I like it a lot.

Here’s to an understanding of the value of different viewpoints, and different methods in diverse circumstances. I think we could advance the lot of humankind so much more if we attempted to engage with, and understand, each other, rather than bashing each other about the heads! In particular, less arrogance and conceit would be good!

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The use of music to understand scientific experiments

Posted in from the reading room, science on February 12, 2008| 2 Comments »

Sometimes scientific experiments and findings can be really beautiful. When this happens we see a real cross-over from science to art. I recently came across a rather technical study from the field of quantum mechanics. Researchers have used a laser to study the wave patterns of movement of nuclei inside hydrogen molecules. As well as producing amazing colourful images which clearly show exactly the phenomena revealed in the experiment, the scientists produced an acoustic version relating the frequencies at the subatomic level to frequencies which we can hear, so letting us understand what’s going on using the musical analogy of notes and chords. The whole experiment is reported here. Do scroll down to reference 2 which gives a clickable link to a short movie file where you can see and hear what happens.

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