The Joy of Stats and the Visigasm

If you have never seen one of Hans Rosling's talks or videos then you need to. He is an example of how you can make the presentation of data both interesting and also clear and simple. Along with Edward Tufte he has made data visualisation an art form. The BBC have recently made a documentary about him and there is also a  Wired article about the Data Visgasm.

Peer Review Again: NASA arsenic based life and the bloggers

A critique of the Science paper by NASA investigators saying that they have discovered a new form of life that does not use phosphorous in the DNA nucleotides has been published on a Blog by a researcher in the field. The response from NASA is to put their fingers in their ears and to say they are not listening because it is not criticism from a peer reviewed journal. This is exactly the same as the authors of "The Spirit Level" who also refused to respond to criticism that was not in peer reviewed journals.

Here is a wired article discussing the NASA response and comparing it to the arguments made by the Church in pre-enlightenment times. I especially like the title - The Wrong Stuff.

The Guardian has an interesting story tracker following events

Conspiracy and Coincidence

How common is the surname Aylward?

It does not seem too common to me. I cannot remember meeting anyone who has the surname but that might reflect regional variations in surnames. My own surname is not very common outside of its ancestral home in Leicestershire, Yorkshire and Lincolnshire.

So what are the chances of the surname being involved in two major news events on the same day?

Two BBC news headlines for the 25th of October involved Aylwards.

Violetta Aylward was a nurse who accidentally switched off the life support systems of a tetraplegic man in her care leaving him with brain damage.
Rebecca Aylward was found murdered in woodland after she had been attacked by two teenage boys.

What are the chances of that happening? It did happen and there is obviously no connection but chance patterns arise all around us, and it is difficult to escape trying to read too much into them.

Dirty Tricks against Lisa Murkowski

When Lisa Murkowski narrowly lost the primary for the Republican nomination to run  for senate in Alaska to Joe Millar a Tea Party supported candidate, she decided to run a "write-in" campaign. The last time this had been successful was Strom Thurmond in 1954, and Murkowski does not have the easiest name to spell. This campaign also did not have the support of the Alaskan Republican party or the national level party who both strongly opposed the move.

Internet presence is an important part of a campaign which is going to have negative media coverage and which does not have the big money support of one of the parties or their allied groups, although her campaign still aired commercials. Accidentally I typed Linda and not Lisa Murkowski into Google trying to find her campaign, and almost all the hits pointed to the headline "Linda Murkowski: Screw you, AK Republican voters, this seat is mine". This was on five or six bulletin boards as posts mostly posted on the 19th of September, one is a disgruntled Tea Party member but more than one is a campaign. So this caught my interest and I thought I might look further.

The first place for an attack is on a candidate's wikipedia entry, as this is where many people will look for background. On the day she announced the write-in campaign her page had been vandalised by an anonymous user from 108.122.217.233. This is a Washington DC address, so I hope it wasn't a sloppy congressional staffer. Murkowski's entry was then amended to include her having failed the bar examinations four times. This was inserted by InaMaka on the 4th of October along with a citation to the Tea Party who had exposed this fact. He had been active on her page since the 20th September. After repeated warnings about bias in his submissions especially in the run-up to an election InaMaka was blocked for a week.

Feynman on Magnetism

Here is a video of Richard Feynman talking about magnetism.

Now the reason this is more interesting is the debate on Sean Carroll's Blog about whether you think Feynman is being arrogant of being honest. Now his view is similar to that from Ian Stewart and Jack Cohen in their books The Collapse of Chaos and the Science of Discworld where they talk about "lies to children".

However, the question is older than this, and is really the same on that Plato was talking about with the cave allegory in The Republic. When we give explanations do we ever give complete and definitive explanations or are they all transitory - explanations for now that will be replaced by better explanations in the future. Does knowledge depend on context?

For me Feynman was forgetting that scientists always have a duty to explain and to educate and to not assume that the level of thought of the person you are answering is far below your own. This may be the case sometimes but I prefer to find that people can manage more complex explanations than you would expect. If you get to see the Horrible Science Theatre Show then there they emphasize the problem of scientists avoiding giving explanations. In this case Feynman also cheated by making it a "why" question when it did not start out as one, but his final explanation is very good.

Lee Smolin - The Trouble with Physics

The five great problems in theoretical physics

1. Combining Quantum Mechanics and Relativity in a background independent way as relativity requires a space time (background) that evolves. There is also the problems of determinism,different observational perspectives and continuity of space and time.
   
2. Resolve the foundational problems of quantum mechanics that deal with the problems of realism and determinism to avoid the problem of observers.
3. Determine whether the particles and forces can be united in a single theory. This means combining bosons with fermions with the introduction of a limited number of tuning constants.
4. Explain how the free constants of the standard model occur - why do they take their particular values?
5. Deal with the problems of dark matter and dark energy - the apparent contradictions of general relativity at the galactic scale with respect to acceleration and the need for a positive cosmological constant for the accelerating expansion of the universe.
   

Dissecting a Politician

The unlucky focus of my dissection is Nigel Lawson who was actually the MP for the constituency where I grew up. The book I wanted to take some quotes from is "An appeal to reason: A cool look at global warming".

Even before the main text starts he uses some political tricks. This is from the Foreword:

"... this book, despite being promoted by an outstanding literary agent, was rejected by every British publisher to whom it was submitted - and there were a considerable number of them.

As one rejection put it: 'My fear, with this cogently argued book, is that it flies so much in the face of the prevailing orthodoxy that it would be very difficult to find a wide marker'. The prevailing orthodoxy can be both stifling and intolerant. Those that have the temerity to question it have to become accustomed to being labelled 'deniers' - a loaded term ..." 

Now this is already loading the book for the reader. There is no sense of objectivity and reason here. This is saying here is my reasoned argument that has been rejected by closed minded orthodoxy and I am right and they are wrong. The prevailing orthodoxy might actually be correct and so it might be the right thing not to publish something that is wrong.

Next in the Introduction:

"By way of preamble, I readily admit that I am not a scientist. But then neither are the vast majority of those who pronounce on the matter with far greater certainty than I shall do here. Moreover (and this is frequently overlooked) the great majority of those scientists who speak with such certainty and apparent authority about global warming and climate change, are not in fact climate scientists, or indeed earth scientists, of any kind and thus have no special knowledge to contribute."

So, he is ignorant but that is alright because everyone else is ignorant as well. So his voice should count equally to all the others. Actually there are various levels of ignorance. If you are stuck in an isolated valley on a camping trip with a party of friends and you break a leg. None of the party are doctors, but who would you rather have treat you, your friend the vet or your friend the accountant? I might not be a climate scientist but as a scientist I know how to weigh up data and make scientific arguments and I know what limitations there are in the data. This is a use of an appeal to authority and underneath it all his authority is that he is a famous politician who now sits in the House of Lords where they debated these issues. I remember Lord Ackner giving a similar argument about his authority as head of the bar and why it should not be questioned. Authority should always be questioned.

Next in chapter one is the absolute howler:

"Nor, incidentally, does the fact that a scientific hypothesis has been published in a 'peer reviewed' learned journal provide ipso facto any evidence either that the science is 'settled', or that the hypothesis in question is likely to be proved correct. It does not even mean that the author's data and methods are available for scrutiny, or that his results are reproducible, as scientific journals, in contrast to most leading economic journals, do not require this."

That is wrong in so many ways. Firstly they do require the data and methods to be available for scrutiny. Most of the references cited come from Science and Nature which are both poor at making the methods and data available in the articles as they are in the accompanying web material as they have strict limits on article size. Real scientific journals should contain all the details. Here he is using an ad hominem argument against all science. He also cites Popper and how theories need to be refutable, but here he talks about proving a hypothesis. According to Popper you can NEVER prove a hypothesis, knowledge is always contingent.

I hate peer review as well and as he later points out it can lead to conventional wisdom dominating and a lack of  risk taking,  but if done well by open minded reviewers who take it that they might be wrong it does strenghten papers by improving the arguments. This is so long as it is not used as a political tool as it so often is. Economics is actually critiqued by Popper in the Poverty of Historicism where he says we cannot predict the future and so it is doomed to fail, as it is based purely on induction. What we observe now might not be what happens in the future.

Aristitotle's Causes

1. Material cause - what is the object made of


2. Formal cause - the definition of the object - ontological argument - Wittgenstein's pictorial logic


3. Efficient cause - how the object was produced


4. Final cause - why the object exists

Ethics 101

Aristotle

Good and bad are not opposites - good is the mean between excess or deficiency. So between rashness and cowardice lies courage or boldness, between miserliness or profligacy lies generosity.

Mill and Utilitarianism

The best acts produce the most happiness, but to restrain hedonism and selfish personal happiness different pleasures had different values. The problem is that this leads to intellectual snobbery. The problem of high art that you can see in James Martin's book.

Trolley Problem

A runaway railway trolley will kill five people if it continues down the track or one person if it goes down the alternative track. Should we change the signal? That by a simple calculus of utility suggests we should switch the tracks. What about if the one person is a world famous neurosurgeon? Now imagine there is a bridge over the track with a large man and you can stop the trolley by pushing the large man onto the track and save the five. Should you push them?

Metaphysics 101

Kant's left handed universe

Is space absolute or relative? Newton thought that it was but Leibniz argued that if you created another universe but with everything translated then it would be the same, as only the distances between particles (internal coordinates) matter.

Kant created a thought experiment to show Newton was right and Leibniz wrong by imagining a universe that contains only a left hand. Then if you create another universe this time with an identical left hand then while all the internal distances are the same these two universes are clearly not the same as they are mirror images of each other.

Now we have general relativity that shows that space is like a plastic sheet that folds and so the space we see are all those points that share the same time. The bending is caused by gravity and acceleration, which are equivalent.

The reason why relative and absolute are important comes when we consider,

Laplace's Demon

If the universe is composed of atoms (using atoms in the broadest sense to mean particles), and these are governed by the laws of physics then if there is a super intelligent demon that knows the positions and velocities of all the particles at a particular time. Then they can calculate the positions and veolicities for any other time and the future would be completely determined. There would be no possibility of having free will other than as an illusion. We would be destined to have the life we have.

Some argue that quantum mechanics removes this rigid determinism but this was the root of Einstein's famous saying that "God does not play dice". He means that the probabilities of quantum mechanics cannot apply to determinism and in particular the theory must retain causality. Events cause future events to happen. If causality is broken then there are no laws. Chaos is another example of what seems like random behaviour but it still maintains rigid determinism, it just requires an even higher standard of knowledge for the Demon.

Ryle's Ghost in the Machine

Descartes introduced the idea of dualism, i.e. mind stuff is different to physical stuff. This causes problems with understanding how the two interract. Gilbert Ryle thought this was the wrong view. For him they are an undivided whole and the body and its activities comprises the mind - a way of describing the machine's activities. In more modern terms we can imagine that mind "emerges" from the components of the body.

Epistemology 101

Epistemology

Epistemology is the theory of knowledge. The philosophy of understanding which determines the limitations of knowledge. The foundations of science depend on epistemology. Important questions are what is truth? How do we know? Absolutists such as Plato think that there is some perfect knowledge, an absolute truth that exists although we might never discover it. Relativists deny that there is an absolute truth and argue that knowledge depends on context.

Hume and Induction

The value of science is that it makes predictions about the future, usually these are based on past experiences. This assumes that the past is representative of the future. This process is called inductive inference. The question is have we observed all of the possibilities, so that our predictions are likely to be correct or are there any unknowns, either known or even worse might their be unknown unknowns (see Rumsfeld)? Hume said that it was not logically justified but this is how we actually operate.

Popper and Falsification

Popper argued that science cannot procede by induction and suggested that it develops by "conjecture and refutation". Scientists propose models of the world (theories and hypotheses) which are they then seek to falsify.  We cannot prove a hypothesis true, but any theory that cannot be falsified cannot be a part of science. This is a way of undermining pseudo-science such as astrology which does not try to provide a falsification.

Kuhn's Scientific Revolutions

In the structure of scientific revolutions Kuhn argued that "normal science" takes place in the context of scientific paradigms (fundamental world views) which define how we create our models/hypotheses. Sometimes these paradigms fail during revolutions which follow a period of crisis when existing science faces an increasing number of paradoxes. One example is the Copernican revolution in astronomy. The fluid model of electrical conduction is another important example as is the move to quantum mechanics from classical mechanics. At the minute both physics and biology are facing a period with an increasing number of puzzles and paradoxes and so it is possible that we are entering another paradigm change.

Pragmatism

This is the view of William James. The question we should always ask is "What practical difference does it make?" If the answer is none then the alternatives can be implied to be the same. So a belief is true if if helps us practically - is it useful, helpful applicable. This is the nature of Truth. Probably this is close to how most scientists think. Is it also applicable to religion? Can we just believe certain tenets of faiths because they make a practical difference to our experience of our lives?

Rumsfeld on unknown unknowns

Baggini gives a version of Rumsfeld's speech, which he points out to be philosophically correct but in a context that I cannot find on videos of the speech. I cannot find a video of the section "Reports that say that something hasn't happened are interesting to me, because as we know there are ...". All the videos I can find show Rummy to be evasive and suggest he does not merit the benefit of the doubt he is given by Baggini, as he ends the interview saying I am not going to tell you which they are (known unknowns or unknown unknowns).

The video is here but it might be edited:
Most complete - starts at "There are .."
He also seems to have used the same speech more than once.
Here is another video.


Here is the official transcript version used by Baggini:

Rumsfeld: Reports that say that something hasn't happened are always interesting to me, because as we know, there are known knowns; there are things we know we know. We also know there are known unknowns; that is to say we know there are some things we do not know. But there are also unknown unknowns -- the ones we don't know we don't know. And if one looks throughout the history of our country and other free countries, it is the latter category that tend to be the difficult ones.

This is the problem of induction and the weakness of positivism. We just cannot know what we do not know. The typical example is swans are white, and experience said this was true until we found black swans. You can never prove a hypothesis you can only falsify it - see Karl Popper on refutations.

The term was used by the US military before Rumsfeld in giving guidance for war games and suggesting unknown unknowns should be incorporated into games so that they were unfair, because real life is unfair. For the Star Trek geeks an example of this is Kirk's response to the Kobayashi Maru simulation from the
Wrath of Khan.

Fallacies: from J Baggini - Do They Think You're Stupid.

If I don't do it somebody else will

"If we want to stop the defence industry in this country, we can do so. The result incidentally would be that someone else supplies the arms that we supply."

Tony Blair

If you carry out the action then you are directly responsible. You cannot be held less responsible because it was inevitable. This confuses cause and responsibility

Existentialist Fallacy

This is the confusion of can or ought with must. Just because someone carries out an action or expresses an opinion, this just means that it is a legitimate choice. It does not follow that everyone should make the same choice.

Susan Greenfield - Stephen Hawking is like the Taliban

So says Prof Susan Greenfield. Now we all make heat of the moment comments and I also get tired of the excessive rants of the atheists who forget about pragmatism, not because they are necessarily wrong, but because they go the wrong way about making their point. But here is a nice article showing Prof. Greenfield's past track record.

Tom Chivers in the Times

Then there is her difficulties with the Royal Institution reported in the Guardian. In the end she did a deal to end the Sex Discrimination case - as also reported in the Guardian. The Telegraph was less sympathetic and argued that she should have been sacked.

If you want to see live updates of Prof. Greenfield's controveries then watch the Ben Goldacre twitter feed and the Bad Science blogs where she makes a regular appearance. Although she did decline to meet Goldacre for a debate at a literary festival.

Common Sense and the Common Cold

In his book "Do they think you're stupid" Julian Baggini takes Edzard Ernst to task over something he said about homeopathy.

"If you study medicine and pharmacology, you know that [homeopathy] can't work" - Edzard Ernst
'The alternative professor' Sarah Boseley Guardian 25th Sept 2003.

Baggini says that this is an example of the fallacy that if there is no rational explanation then it cannot be true. He then gives the example of Lord Kelvin saying that heavier than air flying machines were not possible, to show how our knowledge of the world changes and that just because there is no rational explanation today, this does not mean that there will not be one tomorrow.

Now this is true to a certain extent, but truth is a rather deceptive and tantalising (in the historical meaning of the word) concept. There are some things we know and we can know that our models will not be supplanted by some alternatives - flat Earthers are not credible any more. Kelvin is actually not a very good example as he was actually wrong pretty often - he showed the world could not be ancient or the core would have cooled completely and so gave the creationists plenty of ammunution against Darwin. He also said at the end of the 19th Century there were only two clouds (problems to be solved) before physics would be complete. Sadly the clouds lead to relativity and quantum mechanics and the end of his view of physics. In the case of heavier than air flying machines he just had to look at birds - they are a bit heavier than air.  Anyway too much digression back to Ernst. What Ernst means is that if you know medicine and pharmacology you know that there is no mechanism that can possibly allow homeopathy to have an effect. So you do not need to carry out the experiments as Baggini suggests. As these are harder to carry out unequivocally to deal with the placebo effect.

Anyway a much bigger mistake is his dealing with common sense and why it is often wrong. His example is the common cold and he cites Lewis Wolpert who uses the example of your mum telling you to wrap up properly and to dry yourself properly or you will get a cold. I know of doctors who share my mum's view, although my brother spent most of his youth trying to show she was wrong. The common cold is a virus and so being damp or cold has no effect, but being inside keeping warm with virus carriers does (this is why we get more colds in winter). Baggini cites this as true but this is the exact same mistake that Ernst made. Has anyone done the experiment to see whether it is true? In this case the virus is the mechanism for getting the cold but could we expand on this mechanism?

What are the effects of getting cold or of going about with wet hair and not dried properly?

• Your body takes action to protect your temperature.
• You shiver.
• You get goose bumps.

Could any of these factors "cause" a cold?

Now I use cause in the broadest sense. Are any of these factors contributing to increase the likelihood of you getting the virus? Now I can make some thought models - I can do what Kelvin should have done. Here are some hypotheses:

1. When I am cold my body has to warm me up by generating more internal heat and burning more fuel, this takes more oxygen and so I breath more deeply and more frequently increasing the chances of taking one of those viral particles into my lungs and so "causing" my cold.
2. By using energy to keep warm I cannot use that energy in my defence mechanisms such as my immune system which is constantly fighting the ever present virus. So as I get "run down" in my weakened state it is more likely that I get a cold.
3. Colds and flu are more frequent in the winter months and we do not change our patterns of behaviour sufficiently to explain this difference just because of being indoors more, and so this correlation must hide a true causative effect that we have not discovered yet.

Now all of these are reasonable arguments that could be true - so maybe common sense should not be discounted in this case.

The deCode Genetics Story

deCode Genetic was an Icelandic Company set-up to investigate the genetic factors that contribute to diseases. Iceland is a perfect place to study inherited diseases because of its extensive historical records and its limited population. The problem is the limited population size means that privacy becomes an issue and also you have a narrower range of disease diversity. In the end the company went bankrupt in 2009 after 11 years of research.

Guardian 2002 article - reporting the downside of the boom
Bankruptcy
New deCode - after bankruptcy

Intellect does not equal culture

There was an article in the Guardian about the lack of modern intellectuals, and that now it is all about trivia. Not surprisingly this was written by an old liberal arts academic.

What he meant was that there has been a steady neglect of the old cultural standards. His view of culture is no longer appreciated. I agree with him that our culture is based on a preoccupation with body disfiguring and with growing social rifts, but I do not see that the past was any better. Now is not worse - just different.

There is plenty of intellect but the new intellectuals do not share the same views and concerns as past generations.

In the end his viewpoint translates to - there are no longer many academics who share the same views as he does, particularly amongst the young.

I spy with my little eye scientists acting deceitfully

In my last post I said that highly cited papers become a stronger part of the literature than less cited papers and those that are never cited. I also said that the porportion of uncited papers now is similar to that in 1973 but here are some interesting graphs created by Scopus rather than from looking at citations in Google Scholar, which had suggested this 40-50% level of uncited articles.

So this suggests that actually only a very small percentage of articles are not actually cited and that over time this approaches nearly 0% for Bioinformatics and BMC Bioinformatics. This seems a little bit odd given the previous results. So what happens if Nature and Science are added to the chart?

Nature and Science have a similar number of uncited papers as the 1973 study and the study using Google Scholar. So what is happening that the Bioinformatics journals are more highly cited than Nature and Science? There are two possibilities:

1. Scopus is incorrectly calculating the citations for the Bioinformatics journals (but how can this be if it does it right for Science and Nature).
2. The scientists are fiddling the results to make sure that their papers are cited at least once by citing it themselves - maybe as a conference report or in a non-peer reviewed journal. Citations make careers and an uncited and unloved paper is no use on a curriculum. 

So scientists have learned to play the system, but only those who publish in the discipline specific journals seem to be playing. The big names who get the Nature and Science articles don't care. This is a response to the way Tenure is earned in the States and many other countries and the way funding is calculated by the RAE in the UK.

Citation and confidence - Bioinformatics as an example

How do you know an article is a good article?

We know that peer review is flawed and that it can let through bad articles while blocking actually good work. So how can we be confident about a piece of research? The more an article is cited, the more this article has become important to the community. This can either be citations by those who disagree but most often with those who agree with the work. So highly cited papers even if they are shown in the future to be flawed, have become a significant part of the literature.

As a little experiment I took the articles from 2001 in Bioinformatics of which there are about 819 including editorials and comments and lookd at the number of times they have been cited using Google Scholar. Only about 300 articles have ever been cited. So 500 have never been cited. Of those articles that have been cited the most cited has over 6500 citations and there are 10 articles with more than 500 citations.

This means that in the eight and a half years since the end of 2001 less than 40% of articles have been cited. This agrees with the results reported in Ziman - Reliable Knowledge for 1973 (p 130), where less than 50% of articles were cited within the first year after they were published. This is slightly surprising with the advent of the internet and the increase in open source publication which makes access to the literature wider, but this also reflects the massive growth of the literature in the last 40 years.

Cyril Cleverdon and Document Retrieval

Cyril Cleverdon is one of those people you will not see mentioned in the news. He was a librarian at Cranfield. In the 1950s he wrote some of the pioneering work about document retrieval and most importantly defined the terms precision and recall.

Precision is the fraction of retrieved documents relevant to the search.

Precision = no. of retrieved relevant documents / no. of retrieved documents

Precision is the number of true positives relative to false positives successfully retrieved. The is a measure of the type I error.

Recall is the fraction of documents that are relevant to the query that are succesfully retrieved.

Recall = no. of relevant documents retrieved / no. of relevant documents

Recall is the number of true positives retrieved out of the total number of positives, and is a measure of the type II error. This is much harder to measure or infer than the type I error, as we cannot be sure of the total number of relevant documents except in cases where we use synthetic data.

Peer Review Again

The New Scientist has an article about peer review and how science is failing. It shows how psuedo-science can end up as part of the public record as it was introduced to Parliament by Davd Tredinnick. Tredinnick was quoting a University study that "showed" that homeopathic treatment can kill cancer cells. This article had been peer reviewed and now it has been clearly debunked but it still has not been withdrawn. Peer review is failing. The problem is that this undermines confidence and belief in science. Science is about giving answers and more fundamentally about giving us rational grounds for making decisions. Faith in science can easily be destroyed, when poor scientists let their internal views and convictions over-ride their actual experiments. There are two ways errors like this can occur.

1. Intentional deception.
2. Accidental mistake.

The first we can deal with by applying ethics policies and reviewing our processes but the second is harder to deal with. Even the greatest scientists are sometimes wrong because they have world views that turn out to be wrong. Einstein never accepted quantum mechanics, Mach never accepted atomic reality etc. Then there are scientists who make mistakes with their experiments or analysis, often this is the abuse of statistics. Mendel fiddled his statistics and got the right answer, Fleishman and Pons did not perform the correct measurements in their cold-fusion experiment, but there was no intention to deceive.

So how can we make peer review better? Certainly making it public and not anonymous would help people to behave more honestly and ss competitively. What we need is a fundamental change in the way scientists behave. Science has to have less ego and reputation which makes it more likely for scientists to maintain views that even they realise are not as rigorous as they claim.

Formal Systems Modelling

The following diagram is adapted from "Why Critical Systems Need Help to Evolve" B. Cohen and P. Boxer, Computer Magazine, IEEE, May 2010, p56-63. This is a systems model that divides the system using three cuts. The first Endo-exo divides the systems behaviour from its surroundings, the Cartesian cut then divides the identity of the behaviour from its manifestation and the final Heisenberg cut divides supply from demand/need.

Pre-print archives arXiv and snarXiv

One way that science is becoming more open is the setting up of online repositories of pre-print (not yet peer reviewed) articles. One of the first pre-print archives was for theoretical physics and is called arXiv. There is also a newer alternative archive snarXiv.

For an interesting comparison of the two different archives you should look at the arXiv vs snarXiv page.

Another interesting and similar example can be found in the discussions of the Social Text affair (this is also known as the Sokal affair). Sokal's paper discussing the Social Text paper.

Teleology - Plato's Final Cause

Most people have never heard of the word teleology but is a very important idea. It is one of the oldest ideas and also one of the most controversial. It is intimately linked to the concept of Truth and its opposites are the more relativistic theories of knowledge. It is as fundamental to the way we think as religion or atheism. The problem is that many people (myself included) who believe they oppose it strongly actually often fall into the trap of supporting it.

The question of teleology rather than its contradiction of the bible account of creation is what made Darwin's Origin of the Species so controversial. Darwin introduced a two step process. In the first there was variability and in the second there was selection by reproductive success. The problem is this variability, as it does not have either cause or direction. In the Origin there is no need for progress and if there is no progress then there is no move toward some final perfection of the universe and so there is no ultimate cause, no reason for the universe to exist.

The modern synthesis of Darwinian Evolution as presented by Richard Dawkins in books like the Blind Watchmaker forgets this idea. While I am pretty sure that Prof. Dawkins would reject teleology completely from a philosophical viewpoint it does creep into his work. The problem is that it is very hard for us not to feel that we are superior to the rest of the world about us and so we instinctively talk of ourselves as a higher species that has evolved from more primitive species and this in turn implies progress. This rising to perfection is the argument for design. Now teleology can either be "designed" internally as a result of the behaviour of the system or externally as the result of a designer. So this is the fundamental difference between the teleology of Dawkins and that of religion.

Teleology applied more generally to science makes it very hard for us not to think that science will finally give us an absolute answer to everything and that this answer will be true. Plato wrote extensively in the Republic about this idea. Can there be a truth that we can discover? At first our ideas are mere shadows on the cave wall but can science discover the actual truth? Can we come out of the cave and see the world as it really is. Once we discover truth then there is no further for us to go. This would be the final aim of science - the ultimate cause of our investigations. Among educationalists teleology also creeps in where teachers think that there should be a convergence between pupil and teacher so that in the end the student will find the truth of the master's view.

Two modern proponents of teleology are John Barrow and Frank Tipler who wrote "The Anthropic Cosmological Principle". This uses lots of probability arguments to suggest that life is incredibly unlikely (in much the same way as the intelligent design argument) and so the world must have been created in the way it has just for us. I have paraphrased a very long and difficult book that I have not managed to complete in over 20 years. In effect they go back to the view of the world of Genesis where the Earth was the centre of the heavens but in this new world view humans are at the centre of the universe. The question of Why? has an answer.

For me this sort of teleology is an incredible arrogance but then I am also caught by the paradox that my rejection of teleology also becomes teleological. It is just something you should always be careful of when you make an argument. Am I falling into the trap of teleology? On the other hand what do wishy-washy relativisitic views of knowledge mean? So I bend towards relativism but I am sympathetic to some of the teleological thinkers, such as the logical positivists. Marxism for example is a teleological view of the evolution of society that implies that the rise of the proletariat against the Bourgeoisie is a final inevitable state of human society. So anti-Marxist philosophers have used anti-teleological arguments against logical positivism (see Karl Popper's The Poverty of Historicism).

The End Of Science

This was the cover title for a series of articles in Wired in July 2008. They were welcoming us to the petabyte age - where we will routinely deal with datasets containing petabytes of data. Inside the titles are less provocative the first is - The End of Theory.

In this article Chris Anderson looks at how tools like Google and the Cloud are chaging the way we look at data. He raises the question of how we have to dea
l with such massive amounts of data.

It forces us to view data mathematically first and establish a context for it later

Peter Norvig has gone so far as to change George Box maxim "All models are wrong but some are useful" to "All models are wrong, and increasingly you can succeed without them."

... faced with massive data, this approach to science - hypoyhesize, model, test - is becoming obsolete.

There are a couple of problems with this idea:

1. It becomes very difficult to distinguish science and pseudo-science. The Bible Code and other such books suddenly become more convincing.
2. There is still a model, or rather an assumption and that is that homology between already seen examples will apply to new unseen examples.

What is actually happening is you no longer look for the universal laws but what they actually produce. This is actually how science has worked before. That is the process by which Newton produced his Laws of Gravitation, but the explanation in a more fundamental sense of what gravity means had to wait for Einstein.

Anderson goes too far when he talks about the limits of biology:

Now biology is heading in the same direction. The models we were taught in school about "dominant" and "recessive" genes steering a strictly Mendelian process have turned out to be an even greater simplification of reality than Newton's laws. The discovery of gene-protein interactions and other aspects of epigenetics has challenged the view of DNA as destiny and even introduced evidence that environment can influence inheritable traits, something once considered a genetic impossibility.

This is over-stating reality. Biology according to pure Darwinian evolution is likely to be wrong and there are some epigenetic factors that follow a Lamarckian process but not all and Darwin and Mendelian inheritance is still true for most genes. We only know that it is not completely true because we know the mechanism of epigenetics, which is precisely what Anderson had said we do not need to know.

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.

Sorry but he should read any statistics textbook about data-mining that show you can find any possible correlation depending on the way you partition the data. The higher the dimensionality of the data (more variables) the more likely this is to happen. So this paragraph is nonsense.

Finally:

Correlation supercedes causation, and science can advance even without coherent models, unified theories, or really any mechanistic, explanation at all.
There's no reason to cling to our old ways. It's time to ask: What can science learn from Google?

To understand the importance of mechanism you need to read studies like those of Richard Peto looking at heart attacks and the use of aspirin as a primary medical treatment when patients are hospitalised. Why did they think to use aspirin? Because its mechanism of action is to prevent clotting.

Conspiracy Theories

From the assasination of Lincoln to 9-11 nothing seems to attract the public imagination more than a conspiracy theory. Now there is an entire conspiracy theory literature and books are written about the dangers of conspiracy theorists. We live in the "brave new world of big brother" (people should read the books before slinging the names around indiscriminantly including me). Governments do want to hide some of the things they do and how can we tell when we are being lied to.

This blog entry was in fact inspired by the book "You are being lied to". Some of the articles are by respected authors such as Noam Chomsky and Howard Bloom but many of the authors are unknown to me, so why should I believe anything they say?

How can we tell if there is any truth to the claims? Well we need to use logic, science and reason and we need to find hard evidence.

Take for example the article by Jim Marrs - What is Missing from this Picture. I read the article about how much evidence is missing from high profile cases and you have to wonder. How can the police and the government lose so much evidence? What do they have to hide? The problem is that this is building a whole story on one or two pieces of information. To use a phrase from Terry Pratchett you are living on narativium. You have a story and you make the facts fit the story you want to believe in. So when you read articles like this you have to be careful not to be caught up by the story.

One example is the campaign to find illegal behaviour in the Clinton-Gore adminsitration and to connect this with the death of Vince Foster and Ron Brown (and even TWA 800). Now we know that certain right-wing groups were trying their hardest to smear Clinton after they had got the Republicans to employ a special prosecutor in an operation called the Arkansas Project. In the end it was the people behind the smears and the prosecutor who ended up as the losers. It is very easy to find coincidence and circumstantial evidence but if this is all you have then you have to be very careful at what conclusions you make.

For a Holywood take on conspiracy theories you can enjoy:

• The Net - A hacker's identity and life is destroyed as she uncovers a conspiracy.
• Conspiracy Theory - Mel Gibson hams it up
• Enemy of the State - The NSA bad guy's birthday is 9/11
• JFK - but read the websites about Oliver Stone's playing with history.

Best of all and a must watch for anyone interested in conspiracies, is Arlington Road. This is absolutely brilliant, especially as it showed how the US was vulnerable to home grown terrorism before 9/11.

Chariots of the Gods and Pseudoscience

I have always been a science-fiction geek and so from this I was always interested in stories of alien encounters and secret government cover-ups such as project bluebook and Majestic-12.

One of the early books I read probably when I was about 12 or 13 was "The Gold of the Gods" by Erich von Daniken. In this book von Daniken describes being shown into a huge system of tunnels that extended out under the Pacific Ocean and that were filled with gold artefacts and a library that was written on a huge collection of metal discs. The books has photos of the entrance to the cave system and of some of the artefacts.

This is one of a series of books that develops his theme from "Chariots of the Gods" that the meso-american civilisations were exposed to Alien technology and that we have been visited by Aliens who we think of as Gods and that UFOs are their chariots.

So here is more evidence of these visitations because there is a level of technology that does not fit with what we know of meso-American history. The problem is that it does not exist. The poor archaeologist who showed him the site then had to explain to the authorities where all these artefacts had gone as they did not actually exist. He had made up the extent of the tunnel system and the library. This is an example of pseudo-science, the hijacking of scientific language and presentation to make something appear to be scientific while not actually following scientific method. You cannot always trust what you read or believe the photos that you see.

For a clear debunking of von Daniken's claims you should read Ronald Story's book The Space Gods Revealed. Sadly it looks like Story's book is out of print but von Daniken's frauds continue to sell well. As wikipedia would say knowledge is not democratic. Just because lots of people believe it, does not mean it is true.

The Curious Case of "The Total Synthesis of Taxol - K.C. Nicolaou"

This is an interesting case of scientific competition which is discussed in hushed tones amongst synthetic organic chemists. K.C. Nicolaou is one of the leading exponents of total synthesis of natural products. One of the early natural products to be produced synthetically was taxol which is the naturally occuring toxin in Yew trees. Taxol stops cell division and so it is a potential anti-cancer drug.

Nicolaou had been competing to be the first to produce a total synthesis against Robert Holton's group from the State University of Florida. Holton submitted his two papers on the synthesis to the Journal of the American Chemical Society on Dec 21st 1993. Nicolaou has submitted a paper on synthesis of related Taxoids three weeks earlier to the same journal on the 30th of November (this would appear in the February 1994 issue of JACs as the Holton papers).

Meanwhile Nicolaou submits a paper on the Total Synthesis of Taxol to Nature on the 24th of January which was accepted on the 31st of January and published in the 17th February edition of Nature. The paper before Nicolaou's in the journal was submitted 27th September 1993 and accepted 21st December 1993. So more usually it took 3 months to review a paper and not one week and even after acceptance Nature could take another six to seven weeks to publish not the two and a half weeks seen for Nicolaou's paper. Nicolaou would then go on to elaborate the synthesis in four papers published in JACS in 1995. Nicolaou included the synthesis of Taxol in his book Classics in Total Synthesis.

Now we cannot know whether Nicolaou was a reviewer for the Holton JACS paper but he would have been a logical choice unless Holton expressed that he should not be allowed to review because of a conflict of interest. Even if he did not review the paper, he was probably aware that it had been submitted but doesn't the rapid submission of the paper to Nature and its fast-track review and publication deserve some further investigation?

All in all this case raises questions about the publishing ethics of the journal Nature, the confidentiality of submissions to JACS and the integrity of scientists. Nicolaou has since gone on to be a highly acclaimed scientist with many significant international awards. Meanwhile Robert Holton's biography is rather more modest.

When Peer Review Fails - Fabricated Results

The idea behind peer review is that your peers are also experts in the field and so they should be able to spot weaknesses in the science and prevent the publication of fabricated results.

Here are a few cases where this has not worked.

• Mayo Clinic Immunology Papers
• Jan Hendrik Schön
• Hwang Woo-Suk
  

This is likely to be the tip of the iceberg, these are serial offenders who had fabricated most of the data for their entire careers. It is much harder to find the one off fabrication or just the science that turns out to be wrong by error and irreproducible. Peers should be able to reproduce the experiment, that is what makes it science but this is not always the case as was seen with Cold Fusion.

Here is an article about retraction rates which shows Science and then Nature are at the top of the list. It also suggests a correlation between impact factor and retraction rates. Nature is affectionately referred to amongst the scientific community as the Journal of Irreproducible Results (cold fusion paper, memory of water paper ...)

Peer Review

The aim of Peer Review is to make sure that publications and grant submissions meet an acceptable standard as defined by a community of peers (The idea of trial by your peers goes back to Magna carta). The question is does it work?

Only 8% members of the Scientific Research Society agreed that 'peer
review works well as it is.' (Chubin and Hackett, 1990; p.192)

"A recent U.S. Supreme Court decision and an analysis of the peer review system
substantiate complaints about this fundamental aspect of scientific research."
(Horrobin, 2001)

"is a non-validated
charade whose processes generate results little better than does chance."
(Horrobin, 2001)

"Peer Review is one of the sacred pillars of the scientific edifice" (Goodstein,
2000)

"Peer Review is central to the organization of modern science…why not apply
scientific [and engineering] methods to the peer review process" (Horrobin,
2001).

Currently most peer review is carried out anonymously. That is the reviewers are anonymous but the authors of a paper or grant proposal are known to the reviewer. Often when you submit a paper you are asked for a list of potential reviewers, some of whom will be used to review your paper. These two features of the review process often combine to make success or failure of a paper submission dependent on how good the submitting author is at "networking". Well known names with a large circle of connections select members of this group as their reviewers and so they are more frequently published and become more famous as an expert in that area and have more connections. This is a "rich get richer" scenario, which makes it very difficult for new researchers to break into a field. Especially a field which is fiercely competitive and in which the leading members have large egos.

Some of the open source journals are proposing alternatives:

1. Publish the reviews alongside the paper.
2. Name the reviewers so they are no longer anonymous to the authors.
3. Anonymise the papers so that the reviewers do not know who the authors are.
4. Publish the papers online before peer review and let the community review them before they take a fixed form.

The consequences of (1) are to moderate the language of reviews. Reviewers are likely to be more careful about what they say if they know these reviews are going to be made public. Combining (1) and (2) is even better as it forces reviewers to act objectively as their reputation amongst the community matters. Idea (3) is hard to achieve as reviewers will be able to work out who the authors are from a knowledge of their field and the literature cited (all scientists cite themselves more than others). The problem with (4) is how active will the community be? If there is a very active community in a small field this might work, but there is still the question of the status of the papers in the depository before they reach their final form when they are effectively not peer reviewed.

The quotes above were taken from an e-mail advertisement for a conference on improving peer review.

References

Chubin, D. R. and Hackett E. J., 1990, Peerless Science, Peer Review and U.S. Science Policy; New York, State University of New York Press.

Horrobin, D., 2001, "Something Rotten at the Core of Science?" Trends in Pharmacological Sciences, Vol. 22, No. 2, February 2001. Also at http://www.whale.to/vaccine/sci.html and http://post.queensu.ca/~forsdyke/peerrev4.htm (both Web pages
were accessed on February 1, 2010)

Goodstein, D., 2000, "How Science Works", U.S. Federal Judiciary Reference Manual on Evidence, pp. 66-72 (referenced in Horrobin, 2000)

Extrapolation to Absurdity

Here is a typical newspaper article using statistics wrongly, this particular article is from The Independent about the number of people who can recognise Winston Churchill. The article describes a study carried out on behalf of the Royal Mint to celebrate 70 years since Churchill became Prime Minister for the first time. People were asked to identify famous 20th Century Prime Ministers and only 19% could not name Churchill but this increased to 32% of 25-34 year olds and 44% of those aged 16-24.

So assuming a linear model and extrapolating beyond the range of the dataset the report predicts that in about 80 years time Churchill will no longer be recognised. This is wrong for two reasons:

1. The model is unlikely to be linear - the recognition factor is likely to tail off more slowly in the future as there will always be a core of Churchill recognisers that will be above zero (historians and politicians for example).
2. You cannot extrapolate outside of the experimental range with confidence. So what they could say that in 8 years time the number of 24-34 year olds who cannot recognise Churchill will rise to 44% (those sampled who are now 16-24 and did not recognise him, still cannot do so in the future sample).
   

Making Mountains of Surmise from Molehills of Evidence

The title of this post is taken from an article by the great exponent of popular mathematics and early skeptic, Martin Gardner who died last Saturday. I knew of Gardner because of his books like the Mathematical Carnival, which made maths fun and accessible. These were books that I would read along with my best friend when we were 12-13 and wonder at the beauty of mathematics. Gardner wrote a puzzle column for Scientific American which combined puzzles with magic and shows the strong link between Maths, Logic and Magic.

The particular case he was referring to was the book Atlantis written by Ignatius Donnelly in 1885, which pointed out the possible links between the South American civilisations and Ancient Egypt. They both built pyramids, they both had a calendar of 365 days and they both had flood legends. What he could not have known is that the South American civilisations such as the Incas and Aztec flourished from the 12th century AD over 3500 years after the building of the Great Pyramid. Even the Maya pre-classic period does not begin until 2000 BC, 500 years later.

This is an example of correlation that does not imply causation. They both happen to have discovered the same things. The same calendar is sensible as this is the right one that corresponds to the Earth's orbit. Flood legends are ubiquitous in human civilisations, because floods happen everywhere and pyramids are a strong and simple structure to build if you want a large monument with limited materials.

This is also a perfect example of another phenomenon from biology, that of Convergent Evolution. We end up with the same products from very different histories because of the environmental constraints. This lesson about constraints and convergence is a very important one as it is easy to fall into Donnelly's error and think that events are less probable than they actually are.

MMR and ex-Doctor Wakefield

This is perhaps one of the clearest cases of unethical behaviour in medical research. It also had devastating consequences for the vaccination program in the UK -Times article on the consequences (note the comments in support of Wakefield). There is also an article in the Telegraph on MMR and autism

Andrew Wakefield carried out a study which was published in the Lancet (and later retracted by the journal) that showed a link between giving children the MMR vaccine and autism. Finally after finding Wakefield guilty of conducting unethical medical treatment, fabricating results and not-declaring conflicting interests today was sentencing day by the General Medical Council and Wakefield was struck-off the medical register.
BBC report

A nice cartoon summary of the case sums up the most important points by the Tall Guy.

One of the lead campaigners in the UK against the vaccination deniers is Ben Goldacre who has reported on the case extensively in his Blog as well as in his book Bad Science.
The media's MMR hoax
Goldacre's comments on a Today Programme interview with Wakefield

David Aaronovich's Tweet comments on the Today Programme interview.

• Peculiar opening question to Wakefield. If you had known how much fuss it would cause would you have spoken out?
• Wakefield says 'let us have an open debate' unchallenged with the fact of the overwhelming evidence. Now on 'choice' theme.
• Wakefield's dishonest red herring on single vaccine unchallenged. Simply challenged on drop in MMR uptake.
• Getting better as he's forced to admit he didn't have proof, then told he didn't actually have evidence. Now he's evading and eliding.
• Now the point about his egregious conflict of interest. And the amount Wakefield was paid as expert in litigation.
• He 'has no idea' how much money he received for involvement with litigation. Is allowed self-serving last word. Too short.
• Remarkable that, on the day that he is struck off, the Today programme tweets that Wakefield "defends his investigation". Still not got!

BMJ article by Dr Evan Harris - about who else is responsible.
Guardian Article - Importance of Ethics in Science

Science and Politics - The Creation of Synthetic Life

Yesterday the media had the splash headlines that a group lead by Craig Venter (of Human Genome fame) has successfully created the first synthetic living organism. This new life is also known as Synthia. There has already been a media response about the potential dangers and the need to think about the possible implications. The BBC coverage of the story is linked below:
Artificial Life Breakthrough
Susan Watt's Blog post

Ben Goldacre was less impressed
"This new Synthia lifeform business is slightly overstated, nice proof of concept and doubtless fidlly as f**k, but nothing amazingly new."

The US Government has made a response with President Obama sending a letter to request a Bioethical review of the matter.
Obama Letter to Presidential Commission for the Study of Bioethical Issues

This provoked some interesting Tweet responses:

"*Of course* Obama has to consult *faith communtities" about Synthia. What a ridiculous country the US has become. :<"

"Obama was doing so well until he mentioned faith communities. No point, we know they'll be up in arms about Synthia, the halfwit Luddites."

PS I just read the front pages of today's papers which have headlines like God2.0. The problem with Venter is he has a very large ego and he likes to create a big spectacle. I suspect that he will regret the God2.0 epithet as when Obama consults the faith communities it is not going to go down well and I would predict harsh legislation.

There is also this Guardian article on the atheistic background to the research:
Andrew Brown - Guardian CiF

Pharyngula has summarised the ill-informed responses in the media
Pharyngula's Blog

Google is objective isn't it?

How many people think about the results they get back from Google?

You just type in a search and off it goes and find you the information impartially - Right?

Well not necessarily. There are ways for people to make sure they get higher on the Google's output than competitive ideas. This has been used during political campaigning to smear opponents by associating their webpages with searches for insulting descriptions. It was also used by a certain German car firm that was blocked by Google from searches because they had been manipulating the system.

Behind all of this Google also has to make money and some of that money is through advertising and adwords and people who pay the cash want the impact. So they want to come higher up on the search outputs.

Another way that Google influences the way people search is in the automatic completion of the search phrases which can lead people is directions that do not reflect the actual community. One such case has been reported for nano-technology:
http://www.nanowerk.com/news/newsid=16330.php

Fruitbatgate - The case for academic freedom

WARNING THIS ARTICLE CONTAINS DESCRIPTIONS OF A SEXUAL NATURE.

Why did I have to put that header? Well I open myself to the possibility that I might be repremanded the same way as Dr Dylan Evans because in discussing his case I have to mention  the cause of it all. Dr Evans has been found guilty of sexual harassment by his employers University College Cork because he showed colleagues an article from PLOS One (A journal in which I have published as well and for which I review) which was titled "Fellatio by fruit bats prolongs copulation time."

One of his female colleagues objected saying that she felt harassed and "disgusted". This was the final act in Dr Evans "inappropriate" behaviour as he had kissed her on both cheeks and had complimented her on her appearance.

Here is a blog discussing the case:
http://scienceblogs.com/pharyngula/2010/05/bat_sex_is_not_protected_by_ac.php

Here is the evidence presented at the case and the UCC statement regarding the release of confidential information.
http://felidware.com/DylanEvans/

Here is the Telegraph article about the case
http://www.telegraph.co.uk/science/science-news/7734926/Academic-disciplined-over-fruit-bat-sex-paper.html

Who do you trust? Trusting in Reputation

We live in a world of "Information Overload". So how do we know which information we can trust and what we cannot?

One way we often sort opinions from each other is based upon reputation. Everyone has their own favorite intellectuals/scientist whose views you are more likely to agree with than their opponents. In this way knowledge is very much like politics and it cannot claim to be completely objective. This is a warning to always beware hype, especially when someone is telling you they know the absolute definite truth.

Now one of my favorite TV scientists is Professor Robert Winston. He is a very well respected fertility expert and a pioneer of IVF treatment, for which he received a peerage. He is currently Professor of the Public Understanding of Science at Imperial College London. So his recent work has focused more on the media aspects of science than on the scientific research itself, but he still is an expert and he still should be carrying out decent science and he should be someone whose opinions I can trust. Here is one of his articles:
Are women more likely to conceive if they enjoy sex?

Ok so is this a good article? Can I trust what it says? Here is a bit of the text:

"Publication of an inconclusive study like this might encourage infertile
patients to feel even worse about themselves when there was no clear evidence
that orgasm improves fertility in the majority of women. "

So another question. Is it responsible to publish this anecdotal study in a newspaper, especially in the women's section? He is saying that it might be true but we have not got enough evidence.

Here are some links to pages critical of this sort of article and also some of Prof Winston's other endorsements:
Petra Boynton on a similar sexual health article in the Times
Ben Goldacre criticising his promotion of Omega-3

So there is not always one view and even the most respected scientists can get things wrong (Linus Pauling and vitamin C). So what is the best judge of what to trust? There is a growing movement towards waht is called "evidence based" approaches in fields such as medicine and even politics. So we do not make decisions based on hunches or ideologies but instead based on evidence.

How do I know if anything is right?

Q: Why do you think that the world is round?

A1: It has to be round as we can travel from one point in any direction and return to the same point without leaving the surface.

A2: It is round because we have seen it from space.

Which of these two answers is most convincing?

We like to see things for ourselves and that is perhaps some of the strongest evidence (there are plent of optical illusions and magicians to show that we can sometimes not believe our eyes). Everyday experience says that the world is flat. So we depend on the ideas of a shared experience, after all we cannot all experience everything and there are many things we do not want to experience at all. For example we do not want to have to experience poisons or toxic chemicals.

The other answer is perhaps more interesting as it is more abstract but more revealing. It shows how we can create an artificial model in our minds that can take into account all possible worlds - all possible realities and we can show that it is true for all of these cases. This is part of the reason there is such a strong connection between mathematics and knowledge.

Reliable Knowledge

This is the title of an inspirational book by John Ziman that I read as an undergraduate. So I must give thanks for inspiring me to write this Blog but I must also point out that there is no other connection between Ziman's book and what I write here.

The actual reason for writing this Blog is to provide a set of course materials for an MSc course on Scientific Method that I will be running in September. This Blog is to provide the pre-course reading and also some of the resources for discussion groups during the week long course. The idea is to create a large-scale narrative frame-work that can by followed in a non-linear way depending on the views and questions of the students.

Another way to think of it is like a set of post-it notes each with a single bite-sized piece for revision. It is the way you link them together that makes the course.