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Blogger’s Code of Conduct

Posted in science on January 24, 2008| 4 Comments »

Science bloggers meeting at the North Carolina Science Blogging Conference have been debating the need for a code of conduct. You may have come across some pretty offensive and aggressive commenting from science bloggers – I know I have! (See my Commenting Policy bottom right). I think it’s a great idea. O’Reilly and others have developed a blogger’s code of conduct.

Here’s the first draft –

We celebrate the blogosphere because it embraces frank and open conversation. But frankness does not have to mean lack of civility. We present this Blogger Code of Conduct in hopes that it helps create a culture that encourages both personal expression and constructive conversation.

1. We take responsibility for our own words and for the comments we allow on our blog.

We are committed to the “Civility Enforced” standard: we will not post unacceptable content, and we’ll delete comments that contain it.

We define unacceptable content as anything included or linked to that:
– is being used to abuse, harass, stalk, or threaten others
– is libelous, knowingly false, ad-hominem, or misrepresents another person,
– infringes upon a copyright or trademark
– violates an obligation of confidentiality
– violates the privacy of others

We define and determine what is “unacceptable content” on a case-by-case basis, and our definitions are not limited to this list. If we delete a comment or link, we will say so and explain why. [We reserve the right to change these standards at any time with no notice.]

2. We won’t say anything online that we wouldn’t say in person.

3. We connect privately before we respond publicly.

When we encounter conflicts and misrepresentation in the blogosphere, we make every effort to talk privately and directly to the person(s) involved–or find an intermediary who can do so–before we publish any posts or comments about the issue.

4. When we believe someone is unfairly attacking another, we take action.

When someone who is publishing comments or blog postings that are offensive, we’ll tell them so (privately, if possible–see above) and ask them to publicly make amends.
If those published comments could be construed as a threat, and the perpetrator doesn’t withdraw them and apologize, we will cooperate with law enforcement to protect the target of the threat.

5. We do not allow anonymous comments.

We require commenters to supply a valid email address before they can post, though we allow commenters to identify themselves with an alias, rather than their real name.

6. We ignore the trolls.

We prefer not to respond to nasty comments about us or our blog, as long as they don’t veer into abuse or libel. We believe that feeding the trolls only encourages them–“Never wrestle with a pig. You both get dirty, but the pig likes it.” Ignoring public attacks is often the best way to contain them.

What do you think? Anything in that draft you wouldn’t agree with?

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How scientists give science a bad name

Posted in health, science on December 7, 2007| Leave a Comment »

The irrational claims of “scientists”

Some people claim the term “scientist” as a label of authority. It drives them crazy when people don’t accept their authority. They believe that their views are the correct views and any alternative views are wrong views. I find that attitude horrendously arrogant. And far from rational.
Sir David King, the UK government’s Chief Scientist was complaining yesterday about people who promote views which are different from his own. Specifically he was complaining about people not supporting GM crops and nuclear power but decided to throw his hat into the anti-homeopathy ring while he was at it. Here are two of the irrational claims he made against homeopathy.

First he said homeopathy was not safe. This is a very hard claim to justify if you really claim to be objective and rational. I have heard it said that homeopathy won’t be taken seriously until it kills someone. Well, two hundred years on and there’s still total failure on that one!

Drugs are not safe. An estimated 10,000 people died from serious Adverse Drug Reactions in England in one year. £466 million was spent on hospital treatment of patients suffering serious reactions to drugs.

Surgery is not safe. My trainer when I was a trainee General Practitioner said to me “Be careful and remember if you send your patient to a man with a knife he’ll use it!” It was good advice. At an inquest into the death of a patient after cosmetic surgery –

Dr Steven Chan, who conducted the inquest, did not mince his words. “I have no doubt of the determination of the deceased when she agreed to go through with major surgery,” he said, “but the point must be made that all surgery could result in complications with devastating effects. There is no safe surgery.”

Hospitals are not safe. You wouldn’t want to be in hospital unless you really had to be.

But homeopathy is safe. Nobody has ever died from the effects of a homeopathic medicine. What people actually mean when they say homeopathy is not safe is that some practitioners who use homeopathy are not safe. Well you can say the same of doctors and surgeons, but the way to deal with that issue is training, clinical governance and regulation. The issue is the practice of unregulated or poorly regulated health care. “Where is the evidence that a homeopathically trained doctor is more dangerous than one without homeopathic training?” I recently asked the Editor of the Lancet who had claimed homeopathic practice was dangerous practice. So far, his reply is a deafening silence.

Second Sir David said there is not a jot of evidence that homeopathy works. Well, he can only say that if he hasn’t looked. There is evidence. Go here and read it for yourself. Having read and considered the evidence you might conclude that there is not enough evidence to be convincing enough to change your beliefs. But that’s not the same as saying there is no evidence. You might conclude that there is some evidence that homeopathy is more effective than placebo. Or you might critique the published research and highlight its methodological weaknesses but that’s normal in science. There isn’t a single piece of research into anything which is ‘perfect’. Every study can be, and should be, reviewed, analysed and criticised. What you can’t do is say the research doesn’t exist. What you can’t say is that “there is not one jot of evidence supporting the notion that homeopathic medicines are of any assistance whatsoever” which is what Sir David King said. Not unless you don’t know any better.

Scientists who claim to know The Truth and to tell the rest of us that they know absolutely certainly what is best for us give science a bad name. I enjoy science. It’s fascinating to explore and to learn about how things work. We need good science and good scientists. But science is increasingly showing us that life is complex and that if we want to understand how the world works we need to move away from the old habit of reductionism and simplification which promotes a two-value, unhelpful view of the world dividing everything into right or wrong, proven or unproven, true or false. Understanding and knowledge are never finished, never complete.

(thanks to mo79uk for drawing my attention to Sir David King’s remarks and for commenting –

A fair number of people, I think, have a fairly good or neutral opinion of homoeopathy because the swimming money pool of conventional medicine isn’t delivering all we hope for. And there’s no guarantee and infinite amount of time ever will. At least not for those of us living now. It’s fine to believe in conventional medicine, but when it doesn’t believe in making you better, it’s not foolish to entertain something we don’t understand.

People laughed when it was suggested the earth was round.)

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Changing perspectives. Paradoxes

Posted in from the consulting room, from the reading room, health, science on November 18, 2007| 19 Comments »

I think the only controversial principle of homeopathy is the degree of dilution of the medicines but one of the other principles that at first glance doesn’t make sense is that a smaller amount of something can have a greater effect. I think there are a number of reasons why that’s counterintuitive at first. One is that with poisons and drugs we’ve got used to the common phenomenon of bigger doses having more powerful, usually more toxic effects. You can be sure that if a small amount of a substance poisons you then a larger amount will poison you even more. In fact, it will probably kill you. That’s absolutely true. But if you reverse the direction, is it also true that a smaller amount of something will do the same as the larger amount did, but just more weakly? Strangely, the answer is……not always!

Here’s a couple of examples. Aspirin in large amounts increases body temperature. In fact, one of the signs of an aspirin overdose is hyperthermia. But a small dose of aspirin doesn’t put up the body’s temperature just a little bit. In fact it does the opposite. It lowers the body temperature, which is why we use it to treat a fever. Digoxin (from the Foxglove plant) in a high dose causes a highly irregular heart beat, but a small dose of digoxin doesn’t cause a small amount of irregularity, in fact it does the opposite. It produces a regulation of an irregular heart. An old term for this phenomenon is ‘hormesis’. It’s a term which fell into disuse but which has begun to reappear in two interesting areas.

First of all, in the area of toxicology. There’s an organisation called the International Dose-Response Society which seeks to promote research into hormesis. They distribute a newsletter from a scientific grouping which studies BELLE (Biological Effects of Low Level Exposures). You can find a radio item about this on CBC.

Secondly, Richard Bond, an Associate Professor of Pharmacology at the University of Houston, has proposed the term “paradoxical pharmacology” ( Bond, R.A.: Is Paradoxical Pharmacology a strategy worth pursuing? Trends Pharmacol. Sci 22: 273-276, 2001). This is a proposal for research to be done into the use of smaller amounts of drugs given intermittently in some situations to produce curative effects instead of the tolerances and toxicities which come from the use of large amounts constantly. His main area of interest is into the effects of beta blockers, which are drugs which are designed to block adrenaline and noradrenaline which increase the contractility of the heart. Logically, in a condition like heart failure where the body responds to the changed heart function by releasing more adrenaline and noradrenaline to increase the contractility of the heart, beta blockers should have made the situation worse. And in the short term they can do exactly that, but in the longer term they actually improve the situation. As he says –

Therefore, the paradox remains as to why impeding a contractile system results in an increase in contractility.

He cites the use of stimulants such as amphetamines to treat hyperactivity in children and skin irritants such as retinoic acid and benzoyl peroxide are used to treat acne, which is an inflammatory skin condition as other such paradoxical examples. (it’s also known than giving sedative antihistamines, like ‘phenergan’ to children who don’t sleep makes them more awake!) His potential explanation for these effects is interesting –

acute and chronic effects of drugs often produce opposite effects. This is particularly true for receptor-mediated events. For example, acute agonist exposure can produce activation of receptors and increased signaling, whereas chronic exposure can produce desensitization and decreased signaling

We tend to think of the chronic effects of something as just being a linear extension of the acute situation but that’s actually not true. Here’s his rather startling conclusion –

if acute versus chronic responses are often opposite in nature, and if the contraindications [of drugs] have been made based on the acute effects, there is a suggested list of where basic research can begin to look for clues to investigate paradoxical pharmacology. It is the list under ‘Contraindications’ because the opposite of contraindicated is indicated. This is the list where one would have found β-blockers in CHF just a short time ago. I suggest we test the first precept of medicine, ‘do no harm’, and determine its validity by performing basic research with paradoxical pharmacology. If medicine and pharmacology behave as other areas where short-term discomfort produces longer-term benefit, it might well be that we have paid a high price for accepting a presumption.

This is really another example of the non-linear nature of reality. You can’t take a simplistic notion like more of something will do more of the same so less of something will just do less of what more is, and declare it as a Truth. Life, it turns out, is more complex, and way more interesting! It’s Good Science.

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Componential explanations. Thin explanations.

Posted in books, from the reading room, philosophy, science on November 6, 2007| 1 Comment »

I understand the value of focusing on only the part of something to try and understand it better. It’s an essential part of the way we make sense of our world. BUT we must never lose sight of the fact that we CANNOT understand the whole by understanding the parts when we deal with complex adaptive systems.

My own area of medical practice is holistic and that’s not a New Age concept – it’s a focus on the person, rather than just a part of the person which is damaged (the pathological lesion).

A couple of authors I’ve read recently have used other vocabularies to address this issue. Robert Solomon describes a focus on parts as “thin” – it lacks “richness” and “depth”. That strikes me as very true. There’s too much left out of explanatory models which are reductionist. So much left out in fact that they fail to help us understand real life complexity. And Andy Clark uses the term “componential explanation”. Somehow this immediately makes sense to me. He shows how this only works when “the parts display the relevant behaviour even in isolation from each other.” Otherwise, we try a “connectionist explanation” similar to that described so beautifully by Barabasi in Linked. But, he points out, even a focus on the connections is not enough and he describes another model – “emergent explanation” (as explored in Dynamical Systems Theory). This is a good explanatory model for real life complexity and includes a study of “collective variables, control parameters, attractors, bifurcation points and phase portraits”.

Now doesn’t that sound much richer than the reductionist approach?

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How to be a superhero – get connected!

Posted in from the reading room, life, science on October 25, 2007| 7 Comments »

Here’s an interesting study published in the Journal of Statistical Mechanics: Theory and Experiment …..woah!! Hold on there! Bear with me! I know that sounds a desperately uninteresting journal, but what this author, Gleiser, a physicist, has done is to study the characters in Marvel comics – you know, the superheros, the villains, and the others – 6486 characters in 12942 comics! Now I know you’re probably thinking what on earth are physicists studying Marvel comics for? Well, this is where it gets really interesting. There’s an increasing amount of interest in complex networks – we find them in all walks of life – physical systems, neuropsychological, biological and social systems. Gleiser used a collaborative networks model to analyse the Marvel characters. Basically, each character is a node and then the nodes are connected with lines to represent the relationships between the characters. It’s presented graphically which makes it instantly easy to understand – you’ll need to look at the original article to see that.

Here’s what he found –

All the superhero have loads of connections to other characters. In network theory they are “hubs” – in fact they are super-connected to many other characters. On the hand, the villains are very poorly connected. You can actually pick out the superheroes and the villains really easily from the network map. The reason for the poor connected-ness of the villains is apparently the rules by which the Marvel comic stories were constrained. They weren’t allowed to make villains attractive or to make evil appealing!

I think this is such an interesting piece of work for two reasons –

Firstly, it’s a great demonstration of the applicability of network science.

Secondly, it’s shows you one of the key characteristics of superheroes – get connected!

If you’d like to read more about network science I recommend your read Linked, by Barbarsi.

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Improving health by aiming at something else….

Posted in education, from the consulting room, from the living room, health, life, science, Uncategorized on October 18, 2007| 1 Comment »

 Now, here’s an interesting study. It’ll soon be published in the November issue of the American Journal of Public Health. There’s a way of considering the amount of health benefit from an intervention. It’s to assess the number quality-adjusted life-year gains per dollar invested. That is, not just benefits in terms of greater life expectancy, but also a measure of quality of life in those years. It’s a cost benefit analysis so the economic payoff is measured by assessing how much the intervention costs so you can work out how much it would cost to get the benefit of the better, longer lives. These researchers claim to have found an intervention which brings greater payoffs in these terms than most other interventions. What amazing new drug is this? Or is it a life-style change?

Nope.

You’re going to be surprised.  It’s reducing class sizes at school!

The class size reduction was from 22 – 25 kids per class, down to 13 – 17. From kindergarten through to Grade 3. The better education, produced better educational outcomes leading to better, less hazardous jobs and the ability to move out of poorer housing etc. I won’t bother you with the details of the figures here (you can follow the link and read more yourself if you like). But what I think makes this study especially fascinating is thinking out of the box.

These days we hear endless claims for technological fixes – from wonder drugs, to vaccines, to new claims for possible genetic engineering. But, historically, the greatest improvements in the health of populations do not come from medical interventions, they come from things like improving water supplies, sanitation, reducing overcrowding and so on. There’s been an enormous movement towards looking at smaller and smaller parts over the last couple of hundred years – reductionism. In the future we’ll see the greatest health gains by focusing holistically, considering the environments and contexts in which individuals are embedded and studying what happens within these systems instead of exclusively studying what happens at molecular levels.

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Linked

Posted in from the reading room, health, life, science, Uncategorized on October 17, 2007| 23 Comments »

Smart World starts by acknowledging the work of two others – Albert-Laszlo Barabasi and Andy Clark. I’ve just read Linked by Barabasi. (ISBN 0-452-28439-2) It’s a fascinating book about the rather young science of networks. I agree with the author, that understanding how networks are created and function is going to be absolutely key to our future direction in science.

A network, quite simply, is made up of nodes and links. One example is social networks. Think of a piece of paper with the names of several individuals on it and lines drawn between the names of people who know each other. It’s remarkable how quickly information can spread around such a network. Maybe you came across the movie “Six Degrees of Separation” – a story based on the premise that there are only an average of six links between any two human beings on the planet. Turns out that idea, which apparently came from a Hungarian short story, is pretty accurate. But there’s a twist…….sometimes the number of links is way less than six (even between people who don’t know each other). Other kinds of networks you are familiar with are the maps of flight routes you see published in airline magazines, the power grid, and, yes, our dear World Wide Web. In fact, everywhere you look, you’ll see networks. Everything is connected. Nothing exists in isolation.

To try and understand how networks develop and how they function, Barabasi takes you on a journey through the world of mathematicians, physicists, social scientists and engineers. It’s quite fascinating. In the process he describes a very clear evolution of this new science. Intially, complex networks were thought to be completely random. But randomly created networks produced by computer modeling turn out not look like real world networks. Real world networks don’t have random distribution of nodes. Some nodes are way more connected than others. Barabasi calls these hubs. Once you introduce the concept of hubs, the mathematical modeling of networks reveal what are known as “power laws” (this is a bit beyond me I’m afraid – maybe Phil can help explain these?) but, as I understand it, if you take a single quality or characteristic in nature, say, height of individual human beings, you’ll get a bell curve. Bell curves look symmetrical and they have steep sides ie there aren’t many “outliers”. Complex, natural networks however have node distributions which can’t be described by bell curves. Instead you get a small number of highly connected nodes (hubs) and a huge number of less connected ones. This characteristic produces incredibly resilient and fast networks.

Real life networks are highly resistant to damage and they adapt to change. You can take out lots of nodes and not make much difference to the functioning. To really damage them you have to go for the hubs. Take them out and you bring the system down catastrophically. So, the structure of networks provides both their greatest strength and their greatest weakness.

Barabasi gives masses of great examples, from epidemiological spread of viruses like HIV, to the functioning of international economic markets, to the spread of ideas throughout civilisations. But one of his most interesting analyses is his critique genetics.

How often do you read about “breakthroughs” in mapping the genetic “origins” of various diseases – all with the promise of predictive genetic tests and of treatments based on what is known as pharmacogenomics – finding which genetic precursors determine the responses to which particular drugs. He dismantles this reductionist view very effectively and promotes a network model instead – making what I find to be a convincing argument that the genetic bases of diseases won’t be found in mapping the genome but in mapping the networks of genes.

This shift in perspective is crucial. It drives us away from a reductionist consideration of elements and parts towards a holistic consideration of system function by understanding nodes and their connections. He even terms this “postgenomic biology”. I like it! However, it’s at this point that he suddenly disappoints. His chapter 13 is very odd. It’s entitled “Map of Life” and in it he takes this idea of postgenomic biology and applies it in a bizarrely reductionist way, predicting that the future of medicine will be in tests and highly individualised drugs based on eliciting these genetic maps. He thinks you won’t need consultations with doctors any more, just simple blood tests which will be computer analysed and targetted, tailored drugs will then be kind of published on demand and delivered to your door and, voila! you have your own special cure!  I’m sorry, but I don’t buy this. I mean, I believe that if we could produce a new generation of highly specific drugs rather than the blunderbust ones we use now that would be great, but what happened to this idea of the science of networks, and how they would change our understanding of everything? Suddenly Barabasi leaps into a reductionist model of disease and healing which is predicated on the idea that each individual is indeed an island. Hasn’t he just spent the rest of the book showing us the importance of mapping connections? Isn’t every individual in fact massively connected not only to other individuals but to all kinds of environments. Isn’t it impossible to understand an individual as context-free?

However, don’t let chapter 13 put you off. He really is onto something extremely important here. Once you start to think this way you see networks everywhere and you begin to understand the inescapable importance of connections, and, interestingly, of hubs. We’re at the beginning of this science and I think it’s pretty exciting.

Those of you who have read other posts on this blog will be familiar with my references to Deleuze. His philosophy of networks – he preferred the model of the rhizome – predates this scientific development and has probably been one of the important nodes from which this area of study has grown. You’ll also be familiar with the concept of the Complex Adaptive System which I believe is the best model we have so far for understanding human health and illness.

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Goethe’s science

Posted in from the dark room, from the reading room, philosophy, photography, science on October 12, 2007| Leave a Comment »

From Brian Broom’s Meaning-full Disease –

Goethe showed science a new approach…..of seeing the whole world symbolised in a flower, an animal, a pebble, the human eye, the sun; and to construct the world from

this flower flower

this pebble pebble

that is to create anew and to investigate things not by analysing, but by placing them in the context of the whole.

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Sloppy thinking or sloppy reporting?

Posted in from the consulting room, health, science on October 4, 2007| Leave a Comment »

A study into herbal medicine hit the headlines in the UK today. It was conducted by a researcher at the Peninsula Medical School, Dr Peter Carter. What his team did was trawl through the world literature to see what randomised clinical trials into “tailored” herbal treatments – this means the practice of a consultation with a herbalist who makes up a particular prescription of herbs for each individual patient. They only found three studies and only one of the three showed the herbal treatment to be better than the placebo. Now, I’ve no knowledge or experience of herbal medicine, and I’ve no axe to grind for or against (although I would declare that the belief that herbs are safe because they are natural is a silly belief which could kill you!).

I don’t have something to say about herbal medicine but what strikes me about this report are the conclusions and/or the way they are reported.

The headline to this piece on the BBC news website is

Tailored herbal medicine ‘futile’

I read the article thoroughly and can’t find the word “futile” anywhere. Is it in the original study? It’s not anywhere in the BBC’s own report. So does the study show herbal treatment is futile? Actually, it doesn’t. It shows that if you look for randomised controlled trials of herbal treatments against placebo you’ll find only three and only one of them shows statistical superiority of the herb vs the placebo. Well you certainly can’t conclude from that evidence that herbal treatments work but you can hardly claim that the fact that almost nobody has bothered to study the subject scientifically means that herbal treatment is “futile”! This study doesn’t tell you that.

This is either sloppy thinking or sloppy reporting. As doctors say “There’s a lot of it about!” Remember this?

Have you come across any other articles or studies which make claims way beyond what the original research actually shows?

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Good science

Posted in life, philosophy, science on September 30, 2007| 13 Comments »

I’ve always had a bit of a passion for science. But what does that mean? What is science? There’s a lot of talk these days about anti-science, as if it were some kind of political party or team to be opposed, or about bad science, which, strangely, tends not to be a discussion about either the philosophy of science or about more or less effective methodologies. In fact, people do tend to apply labels to the experiences of life and those labels, unfortunately, more often stop thought than promote understanding.

So, let me say what I mean when I use the word science. My understanding of what science is owes a lot to the philosopher, Gilles Deleuze. He said there were three ways to think about experience – science, philosophy and art. You can read more about that here. He said science was thinking about function. That makes a lot of sense to me. A scientific approach to a phenomenon is one of curiosity, one of wonder; it’s driven by a hunger to understand. Specifically, it’s about a hunger to understand how something works – whether that be the brain, evolution, or the weather. Indeed it’s about a way of trying to make sense of some aspect of the world. There are two important consequences to the Deleuzean definition for me – one is that science is only one way of thinking about the world, and the other is that it is the main way to think about how something works.

But there are other factors to consider when thinking about science. Popper’s famous principle of “falsification” really hit the mark too. The scientific method is not one of proving things; it’s one of attempting to disprove things. In brief, what Popper said was that we form a hypothesis (an explanatory theory of something) and then, as scientists, we conduct experiments to try to disprove that hypothesis. The more we fail to do that, the stronger the hypothesis becomes. In other words, good science is a process of never ceasing to doubt. A good scientist never says he or she has worked everything out and there’s nothing more to be discovered here. A good scientist must be humble, open-minded, curious and never cease to wonder. When you read the writings of a scientist who claims to be the holder of The Truth, or who claims to be absolutely certain of their position, beyond doubt, you know you’ve found a scientist who’s lost the plot. Scientists aren’t gods. They are people. When they get hooked on certainty conversation with them becomes uncomfortable or even downright unpleasant. That’s not a function of science though, because a scientific approach necessitates a perspective of doubt which should humble.

There’s another quality which is often mentioned in relation to science. One definition I read, (and I confess I can’t right at this moment remember where!), was that science is the study of what can be measured. Well, I’m not entirely comfortable with that definition but I can see where it’s coming from. It’s impossible for us to lead a value-free life. Everything we think and experience and do and influenced by our values. In the scientific approach, there is a tendency to value the physical over the non-physical and that’s what tends to lead to a view that science is about what can be measured. For example we can easily measure the physical dimensions of red patch on the skin of a patient with eczema but we can’t measure their itch, and we can’t measure their emotional experience of their eczema. If we dismiss what can’t be measured we dismiss the experience of eczema (as Cassell would call it, the “illness”) and focus only on the physical changes which are measurable (Cassell again – the “disease”)

So, let me say again. I’m passionate about science. Why? Because I am insatiably curious! I love to explore and discover. I love to understand the world, my life and the people I meet. I know that understanding is an eternal process. It has no stopping point. It’s never finished. It has no conclusion. So, for me, science is a way of understanding life better. That said, philosophy and the arts are equally important ways of understanding the world and each will shed a very special light which the other ways of thinking won’t.

I am equally passionate about philosophy and the arts.

I titled this post “Good science” because I want to highlight a positive conception of science – insatiably curious, constantly developing, continuously humble, practised with an intention of building our knowledge and understanding.

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