Bacteria don’t think.

8 06 2013

It seems a statement of the obvious, but bacteria don’t think.

Yet bacteria get around, and indeed are remarkably successful. Same with viruses. So thriving as a species does not require planning, studying, concentration and imagination, all the things we humans are so arrogant about.

And I’m not just talking about surviving, I’m talking about achieving the incredible. Think of the fungi that take control of ants, get them to climb up to a good spot and hunker down so that when the fungus bursts out from the corpse like a slow motion firework (see the picture) it’s got a fair chance of spreading its spores.

Did the fungus plan it? Of course not, the trick ‘evolved’ as the most successful of many different permutations, via, of course the process of natural selection.

So what?

Well, what about humans? We like to think we are the pinnacle of evolution with our big brains and our consciousness and our self-awareness. Our abilities to plan, co-operate and imagine have led us to dominate the planet. Or have they?

Could it be, that just as no ant envisions the design of the anthill, none of us can claim to have masterminded very much? Yes perhaps a building, a harbour or a town’s zoning, but who can claim to have masterminded New York or world trade or democracy?

Surely these ‘real’ achievements are not ours to claim, but should also be laid at the door of the power of evolution, of the unstoppable force of trial and error, of the natural emergence of order from the chaos?

See more about the Cordyceps fungus:

The compensation factor – or why shoes might just be bad for your feet

10 06 2011

There are many modern innovations around which we take for granted as good, that are, indeed, not.

Some interventions, such as seat belts, are shown by statistics to save lives, and as the cost of strapping in is not too high, so the case in favour is strong.

But what about modern running shoes? It may be turning out that nice cushiony running shoes actually cause more injuries than they prevent – and for a similar reason that taking out all the safety features from a traffic intersection may actually make it safer.

Why is this so?

It seems in these latter cases that making people safer only leads them to take more risks, sometimes cancelling out the benefit completely – this is has been termed “risk compensation” – but how does that apply to running shoes?

It turns out the cushioning makes us feel safe – safe to slam down our heels without feeling the shock. It also turns out that while it may feel ok, it allows us to use our foot in a way it was never intended, and results in far greater forces going up our legs.

Think for a moment about the foot of a cheetah, or a deer, or a dog. Ask yourself, where is the heel?

Of course, it is clear once you think about it, it’s way up the leg, far from the floor! And do you think a cheetah has thuds of force going up its spine? I don’t!

Ok, so someone could point out we did not evolve from gazelles and they could also point out that no other primates show a raised heel; true enough – but primates started off as rubbish runners, and it was only the humans that  started down the road to better feet for running during all those years hunting on the African savanna. Whenever there is selective pressure to run, that great engineer (evolution) eventually finds that a raised heel is the optimal solution – remembering of course that the engineer has only the stump of a redundant old fin to work with. Of course, the invention of shoes (and ultimately cars) has completely removed the shaping forces, so I guess our heels will fall once more.

Don’t agree? Ok, pop on those big comfy shoes, and just like a beemer driver cruising at 100mph, tell yourself its safe to slam down those heels 😉

Some interesting sources:

  1. Walking robot – gee look, to make it work, they abandoned heels:
  2. Walking robot “with heels” seems to need bizarre extra hip mobility:
  3. Even Nike, they who started the whole thing now seem to admit openly that bare is best, and sell you the shoe that does it for $90:
  4. Take a sneak-peek into the barefoot community:
  5. Oh, and I got put on the scent of this by Christopher McDougall’s excellent book, Born to Run:
  6. In the wiki for Risk Compensation it interesting to learn that in Sweden, traffic collision rates dropped for 18 months after they changed which side of the road they drove on. Wow!
  7. The classic tale about how making roads seem more dangerous made them safer:

Stuff I Wish I Had Read When I Was Younger

6 11 2010

Over the years I have supervised and mentored several PhD students, and recently our firm started to award scholarships to undergrads, and I was asked to support one such scholar. These scholars are from the best and brightest and so I got to thinking…

Graduates today have it tough, competition is tough, people work longer and harder than ever and stress is hitting us earlier and earlier in life – or so it seems. I would argue that, to some real extent, things have always been getting worse, and therefore by induction, we can prove that they have haven’t really changed at all.

No, the graduates of today have unparalleled opportunity to learn, to travel and to experience. The brightest graduates have the world at their feet and will be its commanders when we are are all retired and done for.

So what could I do to support this scholar? In the end it was easy – I asked myself – what do I know now that I wish I had known sooner? Most of this is in attitudes and is deep in my psychology, and is the result of direct experience – but it turns out that a healthy chunk of my scientific learning experience can be re-lived – by reading some of the books I think steered my course.

So I made a point to summarize some of the best science related books I have read (and some of the most useful internet resources I have found), and dumped the list complete with hyper-links in an email to the scholar. I hope she goes on to be president!

Now having gone to the effort, it would be a crime to keep this email secret, so here it is, (almost) verbatim!


As promised, here is a list of useful resources I wish I had known about when I was an undergrad. I am glad I got round to this, it should be useful for several other students I work with, and has also led to me revisiting a few things! I think I may brush it up and pop in on my blog if you don’t mind…obviously I won’t mention you!
Anyway, back to the business. To me, science is not all about chemistry, molecules, atoms, valence electrons and so on. To me, is is the process of trying to understand the world, and this set of materials I have hand picked, should you get through even a part of it, will not only educate but inspire.

This may not be the very best list, and I am sure there are many great books I have not read, but I have stuck with ones that I have, so you will have to rely on other people for further recommendations.

Jarrod’s reading list: science/psychology/economics & so on

  • I’ll start with something really easy, relevant and engaging – an excellent (if quirky) summary of material science: The New Science of Strong Materials – Prof Gordon  has written another on Structures that is also worth reading.
  • Ok, this next one is not a book, but a paper; I like it because it shows that many stuffy professors are wrong when they prescribe boring scientific prose for papers. This paper uses the criminal “us” and “we” and discusses subjects as if with a friend. Shocking form, especially for a junior scientist. This paper by an unknown, changed the world.
  • Guns, Germs and Steel” – this is large-scale scientific thinking at its best- the book looks at how we can explain why the world is the way it is (especially the inequality) by looking at how technology spreads through societies.
  • Mistakes were made…but not by me” – this is required reading if you want to work with other people, so its basically for everyone then…
  • Then to take it to the next level – “How the mind works…” – Stephen Pinker‘s other books are also good if you like this one.
  • “Flatland”, (full text here) was written in 1884, and is essential reading because it defines the cliche “thinking outside of the box”.
  • To make your upcoming economics courses more interesting, first read this easy-to-read popular book: “The Undercover Economist“.
  • Also, Freakonomics– it’s shameless self promotion by egotistical authors, but hell they are smart, so put up with it.
  • The Tipping Point –  Malcolm Gladwell is a current thinker I really like; he’s not satisfied to focus on one thing for very long – his other books are on totally different stuff, but are equally thought provoking.
  • The selfish gene” – Obviously I would firstly recommend “On the Origin of Species”, (full text here) but if you are short of time (which you should be as an undergrad), you can learn most of the basics, and also get updated (well up to the 1970’s at any rate) by reading Dawkins’ classic.
  • I couldn’t ignore statistics, so I will include two – one classic, “How to Lie with Statistics”  and a more modern one “Reckoning with Risk“, they are quite different, but either will get the important points across.

Alas, books are perhaps becoming obsolete, so I better include some other media:-

  • The first one is so good I can’t believe its free – try watch at least one a week, but the odd binge is essential too.
  • Next, an excellent physics recap (or primer) – but  you need lots of time (or a long commute!) to get through this lot – look on the left menu for Podacts/Webcasts on this webpage: – I cannot begin to praise the worthwhileness of this enough. It used to be called “Physics for future presidents” because it teaches you enough to understand the risks of nuclear energy, and the likelihood that we will all run our cars on water – and let you know when you are being duped or dazzled by big words.
  • When I was somewhat younger there was a TV show called Cosmos, hosted by Carl Sagan, you may know of it. You could watch in now here, though obviously it is dated, so perhaps you shouldn’t; the reason I mention it, is because it was key in creating a generation of scientists, people who were inspired by Carl to be inspired by the universe. The previous generation had the space race and the moon landings to inspire them, but since then science has been on a downhill, with 3-mile island, global warming, etc, etc, and we have had no more Carl Sagans to cheer for us; Cosmos was a rare bit of resistance in the decline of the importance of science in society. You may also know that there have been battles in society (well in the circles on intelligentsia at any rate) about science – on the one had the ‘two cultures debate‘ and more recently, the ‘anti-science’ movement (suggested in books like “The Republican War on Science“. I do not wish to indoctrinate you, but rather make you aware that being a scientist used to be cooler and used to be more respected and something is indeed rotten in the state of Denmark.
  • Getting back on track, here is an excellent guide to critical thinking (something else sadly lacking in the world) – don’t read it, listen to the podcast versions (also on itunes):
    “A Magical Journey through the Land of Logical Fallacies” – Part 1 and Part 2
    I think this should be taught in school. Brian Dunning’s other Skeptoid podcasts put these lessons into practice showing how a scientific approach can debunk an awful lot of the nonsense that is out there (alternative medicine, water dowsers, fortune tellers, ghost hunters, etc etc).
  • If you do happen to have any time left, which I doubt, there are several other podcasts on critical thinking – that use a scientific approach to look at the world and current affairs: –


Postscipt – Dear readers, please feel free to append your own recommendations to my letter in the comments section below. If there is one thing I know well, and that’s how little I know. I feel I only started to read ‘the good stuff’ far too late in life, and so those with more years than me (or better mentors), please do share. But bear in mind, this is principally a science oriented list, and is meant to be accessible to undergraduates – I left out books like Principia Mathematica (Newton) because it is really rather unreadable – and the Princeton Science Library (though awesome) is probably a bit too intense. Also, in the 30 minutes since I sent the email, I have already thought of several others I sort of, well, forgot:

That’s it for now…

Confessions of Scientific Atheist

31 05 2010

The Evolutionary theory of Natural Selection makes extraordinary claims. It explains the ability of creatures to convert sunlight to useful energy, to spin silk, to metabolise sulfurous rock – and much more besides.

Such amazing feats in nature require an amazing explanation. The existence of a God is very helpful in this regard; after all, humans have designed diesel cars and digital computers, so why couldn’t an entity with God’s power and talent create all the nature we see?

The trouble many people have with Natural Selection, is that while it can clearly explain some biology, using it to explain away practically all biology (and psychology, language, culture, etc.)  is an extrapolation – and a big one at that.

Why do scientists allow such an extrapolation? Surely this is arrogance?


Thinking about this, I have an proposition…

If you come from the premise that there is nothing outside of nature (see my recent post), then it comes easily. If the God option is written off a priori, we have no other logical option than to expect that the gaps in our knowledge of evolution will be filled in eventually. This allows us to sleep at night with the extraordinary.

If you start from the premise that there is a God, then this will strike you are arrogant.


The constant supply of greater details, filling in the gaps, gives encouragement to those who feel the theory is right (see God of the Gaps). It’s a bit like looking for Nessy – we can’t do a Star-Trek style ‘scan for lifeforms’ to be sure she does not exist, but the more we search the less likely she is to exist.

Of course, while evolution explaining away the wondrous variety in life does not prove there is no God, it sure makes God less necessary, and less necessarily capable.

Overlapping Magisteria

30 05 2010

Those who say science and religion are mutually exclusive are working from the philosophical premise that there can be something outside of nature.

Those who claim that religion can be scientifically investigated, come from the philosophical premise that there is nothing outside of nature.

As neither position is superior one cannot use logic to assign greater truth.

However, the claim that there is anything beyond nature (i.e. supernatural) is the more extraordinary claim, and thus carries with it the onus to justify and explain how to reach this conclusion.

The futility of being outside of nature:

If religion is truly outside of nature it can have no measurable effect on it. If it has no measurable effect then, even if existant, it would be fair to say it couldn’t be detected by science – but then neither could it be detected by the clergy.

Thus in a non-overlapping model, the benefits of a benevolent God, such as good crops, good weather, good luck, healing or charity are impossible, as they are generally detectable.

I guess you could argue that God goes to the trouble to disguise the causes for His blessings, but why is he so afraid to show it was the result of your good faith? This argument gets a little stretched once the solutions to that are proposed. It is similar to the argument that God planted the fossils in the order of their evolutionary development to fool us into thinking that life evolved…

What exactly is ‘science’?

14 05 2010

I used to think science was the practice of the scientific method; i.e. you propose a hypothesis, you develop a test of the hypothesis, execute it and prove the hypothesis.

That worked for me until the end of high school.

At university, I was a true nerd. I read all my textbooks cover to cover (mainly because as I was too shy for girls and too poor for booze). During this time, the definition above started to fail. So much of the science was maths, statistics, observation, pattern recognition, logic and quite a bit of rote learning. Not all of it fitted into my definition of science. I became a fan of a new definition: science is the study of the nature of reality .

But then I did post-grad, and I realised that not much in science is ‘proven’ (I guess this is the point of post grad study). Evolution, for example, is not proven. That the sun revolves around the earth is not ‘proven’. I discovered that the only things that could be proven were ‘ideas’ about ‘other ideas’. Bear with me on this one.

Let us say we define the number system – this is an ‘idea’ or conceptual construction. Within this construction we can ‘prove’ that one and one is two. Because we ‘made’ the system, with rules, then we can make factual and true statements about it. We can’t do this about the real world – we cannot say anything with absolute certainly because we rely on flaky inputs like our own highly fallible perception.

It’s like that old chestnut: how can you be sure you are not living in a giant simulation? Of course you can argue that it is pretty unlikely and I would agree, and right there we have a clue to a better definition of science.

It turns out that much of modern science deals in ‘likelihood’ and ‘probability’ rather than proof and certainty. For example, we can say that the theory of evolution is very likely to be more-or-less right, as there is a lot of corroborating evidence. Science cannot be run like a law court – where the prosecution only need to reach a threshold of reasonable doubt to ‘prove’ someone guilty.

Aside for nerds: Science says you can use logic to prove things absolutely, but logic only works with ideas, and there is a breakdown between ideas and reality, so one can never prove things in reality. So it is thoroughly wrong for a court to say that someone has been proven guilty. The courts use this language as a convenience, to “draw a line under” a case as they have not found a moral way to dole out punishments based on probabilities. Imagine a world in which a murder suspect gets a 5 year sentence because the was a 20% chance he was guilty! Sports referees often operate in this decisive way, perhaps because it saves a lot of arguing!

Anyway, good science cannot just give up and say once there is consensus something passes from theory to fact. This is sloppy. We have to keep our options open – forever.

Think for example of Newton’s Laws of Motion. They are called ‘Laws’ because the scientific community had so much faith in them they passed from theory (or a proposed model) to accepted fact. But they were then found wrong. Strange that we persist in calling them laws!

It took Einstein’s courage (and open mindedness) to try out theories that dispensed with a key plank of the laws – that time was utterly inflexible and completely constant and reliable.

So it is that the canon of scientific knowledge has become a complex web of evidence and theories that attempt to ‘best fit’ the evidence.

Alas, there are still many propositions that many so-called scientists would claim are fact or at least ‘above reproach’. Evolution is attacked (rather pathetically), but the defenders would do well to take care before they call it ‘fact’. It is not fact, it is a superbly good explanation for the evidence, which has yet to fail a test of its predictions. So it is very very likely to be right, but it cannot be said to be fact.

This is not just a point of pedantry (though I am a bit of a pedant) – it is critical to keep this in mind as it is the key to improving our model.

Two great examples of models people forget are still in flux…

1) The big bang theory

2) Quantum theory

I will not go into global warming here though it is tempting. That is one where it doesn’t even matter if it is fact, because game theory tells you that either way, we better stop making CO2 urgently.

Back to the big bang.

I heard on the Skeptic’s Guide podcast today about an NSF questionnaire that quizzed people about whether they believed the universe was started with a massive explosion, and they tried to paint the picture that if you didn’t believe that, then you were ignorant of science. This annoyed me, because the big bang theory is now too often spoken of as if it were fact. Yes, the theory contributes viable explanations for red-shifted pulsars, background radiation, etc, etc, but people are quick to forget that it is an extrapolation relying on a fairly tall pile of suppositions.

I am not saying it is wrong, all I am saying is that it would be crazy to stop exploring other possibilities at this point.

You get a feeling for the sort of doubts you should have from the following thought experiment:

Imagine you are a photon born in the big bang. You have no mass, so you cannot help but travel at ‘light speed’. But being an obedient photon, you obey the contractions in the Lorentz equations to the letter, and time thus cannot pass for you. However, you are minding your own business one day when suddenly you zoom down toward planet earth and head straight into a big radiotelescope. Scientists analyse you and declare that you are background radiation dating from the big bang and that you have been travelling for over 13 billion years (they know this because they can backtrack the expansion of the universe). Only trouble is, that for you, no time has passed, so for you, the universe is still new. Who is right? What about a particle that was travelling at 0.999 x the speed of light since the big bang? For it, the universe is some other intermediate age. So how old is the universe, really?

This reminds us of the fundamental proposition of relatively – time is like a gooey compressible stretchable mess, and so is space, so the distance across the universe may be 13.5 billion light years, or it might be a micron (how it felt to the photon). It all depends on your perspective. It is much like the statement that the sun does not revolve around the earth and that it is the other way around. No! The sun does revolve a round the earth. You can see it clearly does. From our perspective at least.

Now, quantum theory.

Where do I start? String theory? Entanglement? Please.

The study of forces, particles, EM radiation and the like is the most exciting part of science. But being so complex, so mysterious, so weird and counter intuitive, it is super vulnerable to abuse.

Most people have no idea how to judge the merits of quantum theories. Physicists are so deep in there, they have little time (or desire or capability) to explain themselves. They also love the mystique.

I do not want to ingratiate myself with physicists, so I will add that the vast majority have complete integrity. They do want to understand and then share. However, I have been working in the field for long enough to know that there are weaknesses, holes and downright contradictions in the modern theory that are often underplayed. In fact these weaknesses are what make the field so attractive to people like me, but is also a dirty little secret.

The fact is that the three forces (weak nuclear, strong nuclear and magnetic) have not been explained anything like as well as gravity has (by relativity). And don’t get me started on quantum gravity.


Anyway, thinking about all these issues, I concluded that science was (definition #3) the grand (platonic) model we are building of reality, ever evolving to best fit our observations.

My man, Plato

That works well for me. However, I recently came across a totally different definition for science:

# 4) “Science is a tool to help make the subjective objective.”

OK I paraphrased it to make it more snappy. It was really a discussion about how science was developed to overcome the fallibility of the human mind. Examples of weaknesses it needs to overcome are:

  1. The way our perception is filtered by preconceptions
  2. How we see pattern where there is none
  3. How we select evidence to match our opinion (confirmation bias)
  4. How we  read too much into anecdotal evidence
  5. etc etc.

I could go on. So ‘science’ is the collection of tricks we use to overcome our weaknesses.

I like this definition. We are all going about, and in our heads we are building our model of the world… and its time for an audit!

Evolution in the toilet bowl

2 04 2010

No, this blog is not about how evolution theory is going down the toilet, crushed in the cold grip of reason by The Discovery Institute.

This blog is about how toilet bowls can be used to show speciation forces at work [speciation – the birth of new species].

You see, I have just recently moved to the US, and have noticed the toilets here exhibit characteristics different to their UK and European cousins. Most specifically, US toilets are filled far higher with water and the water surface is greatly increased in diameter. Furthermore, the flush-handles in the US are more often on the left, rather than on the right as they are in the UK.

How can it be in such a small and networked world, such a speciation could occur and indeed survive?


A short stroll on the ‘net does not reveal much about how Americans came to prefer deep water, so I will have a guess. Presumably some big brand (like American Standard) was strongly dominant and the flagship model offered deeper water –  perhaps to prevent skid-marks, or maybe to ensure ‘complete submersion’. As this brand was so strong it was copied, and became the standard. Time passed, and now the average american might turn their nose up at the European low-level option (or indeed the interesting Asian options).

Question: When a European sees an American toilet, are they amazed at its superiority?

No. People don’t like change – and the deep American version is probably not actually any better. For example, the chance of urine splashing on the seat (or on one’s rear for those sitting) is increased, and so therefore, if anything, I would say the ‘deep dish’ is inferior.

So what does this say about evolution? It shows how a contraption, in different environments, will evolve to become different. But more interesting (to me at least) is that Americans and Europeans are not really significantly different and thus the pressures at play were really rather random. It is not as it American toilets have evolved to be stronger because Americans are larger (that would be no surprise) –  this ‘depth’ evolution is different – and very real, but the result of an almost random mutation (of the water depth) that is perhaps not any fitter, just different, and it has survived, despite its weaknesses, due to its isolation across the pond.

What I am saying is that in replicating systems, things will drift apart (there is a natural divergence) on a fast time scale, and the survival of a trait is on a longer time scale. Perhaps in 200 years time we will see no more deep toilets, but right now we have a new species.

Thus I propose you may actually get speciation from drift alone without fitness actually being tested.


So will a device that gently catches one’s emissions and silently whisks them away, instantly, with no splashing, odour, mess or need to flush will supplant the lot? No, because it will probably be expensive, and this cost pressure will always ensure room in the ‘ecosystem’ for multiple solutions – the “two planks over a ditch’ option will always be around because it is so cheap and simple.


Anyway,  next time you go, think about what the toilet might teach us about the subtler aspects of evolution by selection. It’s valuable thinking time after all!  🙂


Epilogue: an aside on valves…

There are obviously several competing technologies for the flush valve, and none has proven clearly superior; so the fact that the US does not (in my short experience) have a very high penetration of the siphon valve (‘claimed’ by Thomas Crapper), does not surprise me. It is indeed much more leak-proof than the popular ‘flapper’ valve, but more complex and thus prone to breakdown. However, the newly popular half-flush siphon valve, which can be easily retrofitted looks to be a clear leap in its evolution. Competition is hot though, and heading to the US, we will wait with bated breath to see which technology wins out 😉

Some references: – some history – the famous inventor of certain improvements

Environmental pressures are a new force in the future evolution of the toilet. First we had the dual flush, now we have the “No Mix” toilet that keeps 1’s and 2’s apart for tailored treatment!