Show me the metabolism! Part Three.

Kauffman is chiefly concerned with reproduction as the defining feature of life. He makes only a superficial discussion of metabolism that does not consider its central thermodynamic requirements. But ultimately, metabolism is what is most important. Without petrol, the most splendidly engineered automobile will just sit there. Without a plausible metabolism, the most elegant net of autocatalytic reactions is an empty exercise in symbol manipulation.

Kauffman’s network and Eigen's hypercycles are susceptible to the well-known ‘747 Argument’ of Fred Hoyle et al. and can only plausibly have arisen in two ways:

(1) Through a long and complicated process of prebiotic development containing all the most interesting parts of the story of the origin of life.

(2) As a system created by someone or something.

I don’t intend this as an argument in favour of intelligent design [see definition 1], still less of Intelligent Design [see definition 2]. Ockham’s razor suggests we should stick with explanation (1) unless we should find some very compelling evidence for (2). At any rate, the essential requirements of the pre-biotic processes leading to life based on the chemistry we know are going to be the same as the requirements of pre-biotic processes leading to life based on different chemistry.

What I am arguing is that both the ‘RNA world’ and the ‘Protein world’ are historically late phenomena, and that the critical events for the origin of life lie much deeper. There is no reason to expect that living systems today preserve the same chemistry of the first living systems. It makes much more sense that we have pulled ourselves up by our own bootstraps, as one phase of pre-biotic evolution succeeded another, perhaps as one phase of pre-DNA-life succeeded another. At each stage, we have doubtless destroyed our history more effectively than any Red Guards- for all less successful implementations of life qualify as food. Looking at RNA and Protein is the equivalent of looking under the streetlight for the keys we dropped out in the darkness.

It is as though we are trying to reconstruct the invention of the telegraph, knowing only the mobile phone. Arguing about whether RNA or Protein came first is something like arguing: Which came first, the handset, or the system of towers dotting the landscape?

As far as the ultimate origin of life is concerned, it is useless to try and work backwards. We need to work forwards, by considering the necessary requirements for a CSCP to arise and where and how such a system might realistically arise. If we want to understand where chemicals came from, chemistry is useless to us. We need to use physics. If we are researching the origins of culture, anthropology itself is little help. We need to use evolutionary biology. If we are researching the origins of life, then biochemistry- with its specific, fragile, optimised reactions, the product of ever-so-many years of pre-biotic and biotic evolution- is not the place to start. We need to plant ourselves on a solid base of physical chemistry, stop worrying about designing elaborate systems for allowing pre-biotic reproduction, and concentrate on nutting out a possible proto-proto-metabolism simple enough to arise spontaneously.

Definition 1: ‘intelligent design’ = ‘life as we know it was created by entities based on some different sort of chemistry’

Definition 2: ‘Intelligent Design’ = ‘life as we know it was created by God in some ‘supernatural’ fashion’

Show me the metabolism! Part Two.

What are the requirements a catalytic system of complex polymers (CSCP) must have in order to be relevant to the origin of life?

The CSCP must be secured from the overwhelming tendency of matter and energy to become more randomly distributed in the universe.

Condition 1: An Edge.

The easy part of securing the CSCP from the tendency of matter and energy to become more randomly distributed is the barrier to separate the system from the surroundings: something to draw a surface around the CSCP and keep it together. Kauffman mentions vesicles and protein coacervates as possible CSCP microcontainers for the early terrestrial environment, and plenty of other possibilities have been canvassed. It is not very hard to think of a plausible container that could possibly arise to keep polymers in.

Condition 2: A Proto-metabolism.

The hard part is allowing the CSCP to increase the disorder of its surroundings in order to persist in time. The energy to maintain the CSCP must be coming from somewhere. The CSCP must be part of an overall system of spontaneous reactions that is converting a relatively unstable chemical reactant (or reactants) into a relatively stable chemical product (or products). The CSCP polymers must be intermediates in this net of spontaneous chemical reactions, somewhere on the path between energy-rich ‘food’ and energy-poor ‘waste’.

Condition 3: A Selectively Permeable Edge.

The energetic requirements of this net of reactions also make the easy part- the physical barrier around the CSCP- less easy. The low molecular weight intermediates have to stay in, not just the polymers. The ‘food’ has to get in. The ‘waste’ has to get out. Some selectivity is therefore required in the barrier separating the system from the surroundings. Biological membranes have evolved extraordinarily complex ways of getting the right things in and keeping the wrong things out. I am having a devil of a time trying to make a non-biological membrane to do just one thing: let ethanol through more readily than water. The tendency of matter and energy to become more randomly distributed makes generation of selective membranes a tricky business.

Condition 4: A Complexifiable Proto-Metabolism.

Not just any thermodynamically favourable driving reaction will do. This central driving reaction must proceed relatively slowly, so there are plenty of intermediate molecules around. This reaction must also have many steps, with many intermediates capable of being transformed in various ways. A great deal of complexification of the net of reactions must take place before we arrive at a CSCP. Before a CSCP can form, all of its constituent parts must be present as intermediates in this net of thermodynamically favourable reactions. I have only shown a few intermediates in the picture, but very many are required...and the relative sizes of the energy barriers and depths of the energy wells must be such that reasonable quantities of all the substrates present for making catalytic polymers are present.

I believe these requirements allowing a CSCP to persist in space and time are very difficult to meet. Nothing approaching them has ever been observed, except in two instances:

(1) Living systems

(2) Systems we have designed ourselves with a great deal of effort.

The question of how systems meeting these requirements can spontaneously arise is the key question for the origin of life.

Show me the metabolism! Part One.

Being some comments on ‘The Origins of Order: Self-Organization and Selection in Evolution’, by Stuart A. Kauffman.

I thought I would expand my central criticism of Kauffman’s model a bit in the hope of clarifying what I was saying and starting a fruitful discussion.

My thesis is that the network of catalytic polymers and substrates that Kauffman postulates as an initial self-organising complex system which can give rise to more lifelike systems is so inordinately complex and unlikely that it in no way addresses the crucial problem of the origin of life.

Specifically, what is first needed is not a mechanism for self-replication and complexification, but a plausible metabolism enabling some tiny corner of the universe to dump entropy outside itself and accumulate order within.

My initial statement of the thesis:

Marco sometimes has to contend with people who find the evolutionary transition monkey → man as implausible as the transition unlife → life. If I were arguing with one of those people, then a clear exposition of how a ‘primordial protoplasmic globule’ (PPG) might have unfolded into the bewildering variety of life we know on Earth today might be of value. In the 19th century, or in the darker corners of the 21st century, a layman might suppose a PPG simple enough to have arisen spontaneously. For such a layman, an exposition of the pageant of evolution from the PPG to the diverse biosphere we see around us might seem to be a complete materialist description of the history of life.

To the biologist, this pageant is far from a complete description. The biologist knows the complexity of the prokaryote, the PPG, and finds the unfolding of its descendants almost trivial. The PPG is not the simple explanation: it is the complicated thing that needs to be explained.

In a similar way, to the chemist, the unfolding of Kauffman’s ‘complex system of catalytic polymers’ (CSCP) to give rise to something recognisable as life seems almost trivial. The CSCP is the complicated thing that needs to be explained.

Kauffman’s statement: ‘the origin of life, rather than being vastly improbable, is instead an expected collective property of a complex system of catalytic polymers and the molecules on which they act’ should become: ‘the origin of life, rather than being vastly improbable, is instead an expected collective property of a vastly improbable complex system of catalytic polymers and the molecules on which they act’.

I do not think I am alone here. I think if you were to show Kauffman’s system to any chemist anywhere in the world, there is a 99% probability they would find it unsatisfactory. Not because such a system could not exist, but because ‘it just happened’ is an entirely implausible explanation for its existence. Saying 'it just happened' is hardly more satisfactory than pointing at a functioning cell and saying 'it just happened'. (The remaining 1% would be those who have a quasi-religious faith in the self-organising properties of matter.)

Any chemist would ask: 'What is driving this cycle of reactions? Where is the energy coming from? What is preventing this system from dissipating?'

There is no such thing as 'Order for Free'. That is the Law. If you want order at point A, you need to dump your disorder at points not-A. Should anyone claim there is such a thing as 'Order for Free', let them be unto you even as the homeopaths and the creationists.

The Curious Incident of the Dog in the Night-Time

Some graduation ceremonies are very dull. Others are dead interesting, and provide enough material for numerous anecdotes. If you are Jenny, you already know two anecdotes about the graduation ceremony I went to a few weekends back. This is a third one.

The main speaker at the graduation was John Ellice-Flint, distinguished alumnus, ex-CEO of Santos, and 2020 summiteer. He talked about climate change. He did it ably enough that he never had me offside. I shall give a very rough paraphrase of his speech, as it is not the done thing to take notes, and my memory is not what it once was.

He didn’t waste any time emoting about environmental catastrophe, and stated at the outset that he was going to set to one side the whole debate about the nature and extent of global warming.

He pointed out that the large developing nations were not going to abandon fossil fuels, whatever we did: we would have to accept that fossil fuels were going to be a major part of the world energy mix for some time to come.

He gave an internet factoid about the number of wind turbines China would have to build every day in order to equal the number of coal-fired power plants it was building.

He said the only way we could hope to make an impact on carbon dioxide emissions in the short-term was to throw barrow-loads of money at scientists and engineers- the one outcome of Global Warming hysteria that I have always felt to be an unqualified good.

He said he felt confident that the new government would rise to the challenge of providing these barrow-loads of money, and that in achieving world-class expertise in these areas Australia would soon earn it back many times over.

He talked a bit more about renewables, and a bit more about carbon-capture. I forget exactly what he said. I was waiting for him to mention the ‘N’ word.

But he didn’t!

Not once.

The word ‘nuclear’ did not pass his lips.

He is obviously on top of the whole big picture of greenhouse-gas abatement. He is obviously a clever bloke. He is obviously well-connected.

And it is pretty obvious that the nuclear option is one that is going to be adopted by a lot of our neighbours in our Near North, whether or not an ice age starts tomorrow, because we are going to run out of coal eventually, no matter how clean it is. It seemed obvious to me that the arguments he made with respect to developing expertise in renewables and carbon-capture applied equally well to expertise in nuclear power. And it seems obvious to me that since we are already involved in the nuclear industry as a supplier of uranium, we have not only an economic opportunity but a moral duty to take responsibility for the whole fuel cycle: to provide processed fuel to our customers (to reduce proliferation concerns) and to take back their waste (because it was ours to begin with, because we have ideal political and geological conditions to store it, and again, to reduce proliferation concerns).

But Mr Ellice-Flint didn’t mention nuclear power at all.

I am sure it didn’t just slip his mind.

I am sure he had some perfectly good reasons not to mention it.

But unfortunately, by not mentioning it, he couldn’t help but come across as someone pushing a narrow carbon-capture agenda, rather than an honest broker surveying the challenges of our energy future.

The Myth of Terra Stasis

I never seem to actually take pictures of the things I end up wanting to talk about later. Last week I was just outside of Broken Hill, walking around some splendid desert landscapes at a place called the Living Desert. I took lots of pictures of plants for a post I will possibly get around to writing on convergent evolution, but I didn’t take a picture of a set of brush shelters, nor of the sign describing them.



You will have to imagine that if you turned around from where you were standing and seeing this, there they would be, looking quite shady and inviting at that hour of the afternoon.

The sign describing the shelters did something that is relatively common in things written about Aboriginal culture for popular consumption but which always irritates me as a pedant.

It said something like: ‘The Wiradjuri people have used shelters like these for 20,000 years.’

This cannot possibly be true.

It is sloppy shorthand for two things that are almost certainly true:

(1) The Wiradjuri people used shelters like these.

(2) Traces of shelters like these have been found dating back to 20,000 years in this area.

It should say: ‘The people of Wiradjuri country have used shelters like these for 20,000 years’.

If you were in Spain and you saw a sign on a replica shepherd’s hut that said ‘The Spanish people have used shelters like these for 5000 years’, you would automatically read ‘Spanish people’ as ‘people who lived in what is now Spain’, and think it was a bit of an odd way of putting it.

Here is a worse example, as near as I can remember it, from a newsletter put out by my old university many years ago:

‘The original meaning of these images [in 4000 year old rock art in the Chillagoe region of North Queensland] is unknown because the Aboriginal people of the area were removed to Palm Island and their stories were lost.’

It is a very real tragedy that the stories of these people were lost. But there is no way they had any idea of the ‘original meaning’ of 4000-year-old images. You wouldn’t dream of writing:

‘The original meaning of the Uffington white horse is unknown because the villagers of the area were removed to make way for a motorway and their stories were lost.’

We know that the oral history of England is not trustworthy over thousands of years. We know that peoples have come and gone, and that there is no real memetic link between the people that made the Uffington white horse and the people who happened to live near it in the 20th century.

Why should we believe the oral history of North Queensland could be trustworthy over thousands of years? Why should we believe that peoples have not come and gone, and that the people who happened to live near Chillagoe in the 20th century had any memetic link to the people who lived there 4000 years ago?

These are only two examples of the denial of Aboriginal history.

Here is a third, which is not just of interest to pedants, because it means potentially interesting and important science is being ignored.

I was recently at Lake Mungo National Park. The visitor’s centre made no mention at all of the controversial mitochondrial DNA studies that appear to show that the 40,000 year-old ‘Mungo Man’ remains are genetically distinct from all modern humans- something that I had heard about and was keen to know more about.

Instead, there was stuff along the lines of what is quoted in this article:

“Non-indigenous Australians too often have a desperately limited frame of historical reference. The Lake Mungo region provides a record of land and people that we latter day arrivals have failed to incorporate into our own Australian psyche. We have yet to penetrate the depths of time and cultural treasures revealed by those ancestors of indigenous Australians,” [Prof Jim Bowler] says.

“The messages from the ancient Mungo people challenge us to come to terms with the history and dynamics of this strange land, especially with the rights and richness of their descendants.

“Indeed it is those descendants, in the person of the three traditional tribal groups of the Willandra region (the Barkandji, the Mutthi Mutthi and the Nyampaa) who facilitated and cooperated closely with this project. This represents an important new phase in the collaboration between science and traditional owners. Science and the Australian community owe them a special debt of gratitude.”

If you were excavating 40,000 year-old remains in Spain, you wouldn’t expect them to shed any light on the ‘rights and richness’ of present-day Spaniards. Pretending that the present inhabitants of an area that has experienced dramatic and extensive climatic changes necessarily have memetic or genetic links with the people who lived there 40,000 years ago is not endearing and culturally sensitive.

It is unscientific. It is deeply irritating to pedants. And what is more, it is insultingly patronising.

The Aboriginal population were not part of the scenery, waiting around in the same place doing the same things for thousands of years so that white folks could turn up and history could begin. They had a history that was surely every bit as rich and interesting as the pre-Colombian history of North America. People moved around. Cultures changed. Peoples replaced other peoples. Interesting history happened. We don’t know what it was, and to a large extent we can never know. We have yet to ‘penetrate the depths of time’. But it is an important and interesting part of human history that I would love to know more about.

Update: I went back two years later, and here they are:

Things I learned in Canberra

First, there is mitochondrial DNA.

All eukaryotes have mitochondrial DNA.
This DNA codes for things that are useful in mitochondria.
This set of things, however, is different across different species.

Over all species, however, there is not one thing useful in mitochondria that is not coded for in nuclear DNA.

Second, I learned that there is extremely good evidence for transposons acting to transfer a beneficial characteristic from one species to another- specifically, to transform an inert species of fungus into a wheat pathogen. I always thought this sort of thing was a theoretical possibility, but I had never heard any good evidence of it happening in eukaryotes before. Voila, it happens!

Third, I learned that I need to learn a lot more about plants.

Green plants are more complicated then us. They have larger genomes, on average, and have chloroplasts with their own DNA as well as mitochondria with their own DNA. They make an awful lot of things that we have to get by eating other things, so they have more complicated metabolic pathways. Our sense of how natural selection works is also skewed by us usually thinking of animals rather than plants, despite all that rigmarole with peas back in Mendel’s time: one animal individual crosses with one other individual to make some offspring. But consider your typical tree, covered with gazillions of flowers: it is more like one individual crossing with the whole population within ever so many kilometres to make some offspring. Actually, don’t a lot of animals in the ocean do the same sort of thing?

I learned specifically that I need to learn more about the immune system of plants. It seems plants have no acquired immune system. Each plant cell is autonomous, and just has the genetic potential for immunity that it started out with. A plant can’t acquire antibodies to something new and strange the way we can. (Memo to self: how do we actually do this, again? I need also to revise what I sort of kind of once knew about the immune system of us.) You would think, without any acquired resistance, plants would need a rapid turnover of generations to have any chance of adapting to pathogens. Sure, a lot of plants do seem to have a rapid turnover of generations. Yet, we have these things called trees that live for hundreds or thousands of years. How do they do it? They are likely to be facing a completely different pathogenic environment at the end of their lives than at the beginning. They are supposed to have no more resistance than what they were genetically programmed with.


Action: Learn about the molecular biology and evolutionary biology of plants. It is interesting.


I ought to point out that Marco's thoughts about evolution were rattling about in my head while I was learning these things.

A Talk to some National Youth Science Forum Students, 8/2/08

Where am I?

What’s going on?

These are not just questions I ask myself when I find myself up in front of a roomful of people, but questions I ask myself every day of my life. If I ceased to ask myself these questions, I would cease to be a scientist. I would become a non-scientist: or ‘muggle’ as we call them in the trade.

But, it is not enough to ask these questions. I could ask these questions and still not be a scientist. I might be a mystic, or an astrologer, or an internet conspiracy theorist.

What makes me a scientist is the way I try to answer these questions.

I haven’t been able to find this quote in the original German, but in English I think it is a perfectly dandy little quote. It is very measured and pedantically accurate, as a scientific quote ought to be.

It doesn’t say that everything else is rubbish: it says that everything else is poetry, imagination, two fine and splendid things. And it doesn’t rule out other means of knowledge: it doesn’t say there is no such thing as divine revelation; it doesn’t say that knowledge *won’t* be beamed directly into our brain by the Cephalopod Overminds of Omicron Ceti. But there is no possible way those possible means of knowledge can be considered to be ‘at our disposal’.

The only thing this quote lacks, as a description of the scientific way of trying to answer the question ‘what’s going on?’ is a definition of ‘experiment’. And here is the best definition of ‘experiment’ that I have come across:

An ‘experiment’ is just a small, controlled bit of ‘experience’. That’s all.

Because I endorse these last two quotes, I was moved to amend a third quote, which I found on a whiteboard in a student office:

The successful scientist and the raving crank are not separated by the quality of their inspirations. There is no mystical attribute of ‘quality’ that raises the scientist above the muggle. I would argue that most successful scientists spend a great deal of their time thinking up stupid ideas. Linus Pauling- another Nobel laureate- has said that the way to have good ideas is to have lots of ideas, and throw the bad ones away.

We decide which ideas are bad not by appealing to the Church, or the Central Committee of the Party, but by the procedure outlined in Feynman’s quote. That is what makes us scientists. What makes us ‘successful scientists’ depends on how you want to define ‘successful’.

You will note that these quotes seem biased in favour of what are called the ‘experimental’ sciences. The experimental sciences where you can take a small piece of the universe that you pretty much control- a test tube, or a nuclear reactor, or a bit of perfused llama liver- and do pretty much the same thing over and over again, with you controlling the conditions, until you discover a new physical law.

The historical sciences are things like astronomy, geology and biology where you are trying to make sense of somewhat larger pieces of the universe that are beyond your control. You can’t go out and blow up a star, or drop a few finches on an island and come back in a million years, or squash two continents together to see what will happen. But this doesn’t mean the historical sciences are not sciences.

In the historical sciences, you are observing experiments that nature has done for you.

You don’t have acccess to the experimental logbooks showing exactly what happened with the ancestor of the moa arrived in New Zealand, or when India started running into Asia, and you know that a lot of unique historical events, impossible to predict, went into the speciation of the moas and the exact shape of the Himalayas. So you can’t make the kind of exact predictions that you can in the experimental sciences. But on the other hand, nature has done a lot of these experiments and left them lying around.

The first principle that makes the historical sciences sciences, rather than history, is uniformitarianism. This means that we assume the same physical laws apply everywhere in space and time.

Our explanation of the stars have to use the same physics that we have figured out using light bulbs and nuclear reactors.

Our explanation of the moa has to use the same biochemistry and physiology that we have figured out using chickens and polyacrylamide gel electrophoresis.

Our explanation of the Himalayas has to use the same chemistry and rheology that we have figured out using test tubes and corn starch.

Now, this is just a guess, as in Richard Feynman’s quote. It is the simplest guess we could make, which is why we made it.

Einstein never said this.

[Note 1]

And William of Ockham never said this. (This is a late Mediaeval Latin way of saying the same thing; ‘entities must not be multiplied beyond necessity’).

We made this because it was the simplest guess we could make. But it is a good guess.

We have never found anything yet- out there among the stars, or back there buried under kilometres of limestone in the distant past- which cannot be explained using the physical laws we have figured out here and now. We have found things that can’t be explained by anything we actually see happening now, but we can postulate processes that make sense, that follow the same rules, that explain those things.

[Note 2]

This is just a picture to remind me of the dangers of hubris. [Note 3]

[Note 4]

Now, when I was growing up I was captivated by the historical sciences. I still am.

When I was growing up, a man named Carl Sagan was on the television talking about this incredible sweep of cosmic history, these countless galaxies like grains of sand,everything spewing out from an ancient singularity, and the accidents of history making Earth like Earth and Venus like Venus.

A man named Stephen Jay Gould was writing these articles in ‘Natural History’ about this incredible sweep of biological history, everything radiating out from a primeval protoplasmic globule, and the accidents of history giving us penguins and Staphylococcus aureus and whatnot.

And as for geology- well, my grandfather is a geologist. My father is a geologist. My brother is – now - a geologist. So I can never remember not knowing that I lived on a thin crust of rock trundling inexorably toward Asia, can never remember not having this vision of the continents scuttling about, mashing into one another and splitting up again, the accidents of history making the world we know.

So, why have I ended up in an experimental science, instead of a historical science? There are some trivial, historical reasons for why I ended up where I am – which may be the real ones - and a more profound one which I may have made up many years later.

[Note 5]

In Queensland twenty or twenty five years ago, the way to get a good score to get into university was to do all the maths and science subjects in years 11 and 12. But I wanted to keep doing German, which I’d done up to the end of year 10. And I figured from what we did in year 10 that biology was a subject that was easy enough that I could learn it all out of books by myself. So I did German instead of biology. Not that I can remember very much German now. Doof bleibt doof, da hilfe keine Pillen.

I’ve found that there have been times in my life when I have worked really hard at things, and at these times I have usually done well. First semester of year eleven was one of those times, and in first semester year eleven I topped the class in Physics - which I never did in any other semester, mind you - so I got this idea in my head that I would go on and do Physics.

[Note 6]

I didn’t have any concrete plans for where I wanted to go in the future and wanted to keep my options open, and when I got to uni I did physics, maths, chemistry, and- this was a mistake- computer science. I don’t know why I did computer science. I can’t remember. Maybe it was peer pressure. I was useless at computer science. I should have done something biological or geological...and then maybe I would have ended up in the historical sciences. But there I was in first year, not doing any historical sciences.

I found- this is just me- that while high school physics had been easy, uni physics was really really hard. This was mostly because I did not work hard enough at my maths. On the other hand, the physics pracs were great. I had a lot of fun in the pracs and did really well- but the exams were about as much fun as eating broken glass. Chemistry was the other way around. I found- this is just me- that the exams were easy, but the pracs were terrible. There was real, not metaphorical, broken glass everwhere.

So I ended my first year still uncertain, a little bit disspirited about how badly I had done in physics. And with no strong motivations, liable to be batted one way or another by small influences.

In between 1^st year and 2^nd year I read this book about Quantum Mechanics – an example of what I would now call the nitwit’s interpretation of Quantum Mechanics - and this inspired me to keep going with physics.

Second year was more of the same. Good pracs and bad exams in Physics, Bad pracs and good exams in Chemistry. I finished the year still uncertain, still at the whim of the winds of fate.

And in between 2^nd year and 3^rd year, I happened to read something about the discovery of the structure of DNA- I think it was this famous book- and I thought, aha! I will do biochemistry. Biochemistry really is the science of the 21^st century. It is where the big discoveries are being made that will cure cancer and give us potatoes that grow plastic instead of starch and let us genetically modify ourselves so we look like Klingons.

So in the next year I did 2^nd year biochemistry and molecular biology and some 3^rd year chemistry and maths units.

And the next year I did 3^rd year biochemistry and molecular biology and the rest of the 3^rd year chemistry units.

And over this time, I discovered that biochemistry pracs were even worse than chemistry pracs. With chemistry pracs, if they didn’t work, you usually could figure out why. Biochemistry pracs didn’t work for no reason. 50% of the time. Again, this is just me. I had thought molecular biology was all shiny machines that buzzed and clicked and spat out beautiful numbers, but it turned out to be all artsy-craftsy, full of messy polyacrylamide gels that never worked out properly. Of course, it is better now, I expect.

[Note 7]

And sometime around then, I happened to do a subject called ‘Advanced Physical Chemistry’ which was basically a reading list and a two-week project in a research lab. I did a project with A/Prof Ernie Senogles which involved playing with liquid nitrogen and fire, and it was a lot of fun. Exactly what I was doing there I’ll tell you after you’ve had another couple of years of science, because it will take too long if I start explaining now, and people will suspect me of trying a hard-sell to get you all to do chemistry.

But physical chemistry is more or less the exams of chemistry combined with the pracs of physics. And I decided this would probably suit me pretty well. When I looked at all I had done at uni, physical chemistry was pretty much in the middle, with wings stretching out to biochemistry in one direction and 1^st year computer science in the other.

Those are the trivial, historical reasons I ended up where I am, I guess.

Now for the deeper reason that I may have made up years later.

I don’t think I really picked physical chemistry because it was in the middle of the things I had done up until then, or because I was good at it. I think I picked it because it was a field where I could actually *do* those experiments and edge closer to truth. I realised I would rather work in a field where I got to do my own experiments, rather than look at the results of experiments nature had done for me. And the first of those experiments I met happened to be in this subject area in the middle of my degree, and involved playing with liquid nitrogen and fire. Because everything I had done in the lab up until that project, with the liquid nitrogen and the fire, had not really been an experiment, had been, in a way, something inherently pointless, because we already knew what should happen in the experiment, and it had been done so many times that the only possible explanation for an unexpected result was that I had stuffed it up. Real science is not like that; real science is doing experiments where you don’t know the answer.

So I went on and worked with Ernie Senogles for five more years, and came out with a PhD in physical chemistry and could call myself ‘Dr Chris’. During this time I went to a talk by Jean Marie-Lehn, who won the Nobel Prize for Chemistry in 1987. He said this:

What he meant was, once we understand what is going on with the physics, the basic ground rules of the universe, and once we have nutted out precisely what is happening with the sort of life we have on our planet that is all based on a very, very, very, small subset of the possible chemical reactions, we can go off and create things that are as complicated as life, but that use different chemistry. The buzzword ‘nanotechnology’ is a first little prefiguring of that 25^thcentury that Jean Marie Lehn is dreaming about.

After I finished my PhD, I went to the University of Sydney, and I worked there for five years, with some very interesting people, and some very smart people and some people who were scary beyond reason. And that was a very exciting place to work and we did a lot of good science.

But since I grew up in a provincial city, under balmy tropical skies, living in Sydney for me was too much like living in a box full of starving weasels, and I couldn’t possibly see myself living the rest of my life in *that* sort of place. [Note 8]

And then I came here, to the University of New England, and I’ll have been here four years in April, working with some very interesting people, and some very smart people and no scary people as yet. This is an exciting place to work and we’re doing good science here, and I intend to keep going until they pry my test tubes from my cold, dead hands.

So that is how I got where I am. And a bit about what’s going on.

But, if the truth be told, I find monologue really boring.

I think dialogue is much more interesting.

So, if we have time, I would love to answer some questions.

Notes

1: The font is Baskerville, an allusion to William of Baskerville in Umberto Eco’s ‘Name of the Rose’

2: The picture is ‘The Death of Smaug’. If you don’t get the reference, you need to re-read ‘The Hobbit’.

3: I was thinking that there was one problem that seemed obvious, after I had written that no mattter how far back in time we go we haven’t found exceptions to the laws of nature we’ve figured out, because we have these highly peculiar initial conditions for what we call ‘the universe’. I prepared a slide in case anyone asked me a question about this and tacked it on the end, but nobody asked me about it.

4: I was hoping someone would ask me about this picture in the question time. Nobody did. Looks a lot like Shoalwater Bay, doesn’t it? It’s not.

5: This is a picture of Pimlico State High School. I found it on a website in Brazil.

6: This is a picture of the Molecular Sciences building at James Cook University. Thanks to Maree Hines for sending the photo!

7: This is actually an experimental set-up where one of my current PhD students is doing something similar to what I used to do with liquid nitrogen and fire.

8: Technically, my fixed-term appointment was not renewed, and I was casting desperately about for a job somewhere, anywhere- South Dakota, Izmir, Bermuda... But I think my manifest lack of enthusiasm for the big city was one of the things that did me in.

Four Things I Never Heard

...in any of the many reports on the radio about the New South Wales Government's recent decision to kinda sorta lift the moratorium on planting of genetically modified canola:

* 70% of NSW canola is herbicide-resistant strains generated by conventional breeding.
These are mostly resistant to triazine herbicides, which build up in the environment. The genetically-modified versions available are resistant to glufosinate ammonium or glyphosate, herbicides which degrade rapidly and do not build up in the environment. So GM canola is unlikely to lead to increased herbicide use and there is a clear environmental benefit in introducing them in terms of the herbicides used.

* Our non-GM bulk canola gets the same price in world markets as Canadian GM canola.
So there is no question of us throwing away a 'premium' for a non-GM product. Our yields are just a lot lower because the triazine-resistant varieties are not as high-yielding.

* No 'organic' canola is grown in New South Wales.
So there is no chance of us jeopardising a small boutique industry which is getting a premium price for its product.

* EU and Japanese regulations on the labelling of non-GM foods allow up to 0.9% GM material (EU) and 5%(!) GM material (Japan).
This is far more than documented cases of accidental contamination of non-GM fields from the GM field across the fence, so if a premium non-GM market *did* develop, the fact that GM canola was being grown in the same part of the country would do nothing to stop farmers from participating in it.

This goes to show that there are great benefits to be gained in travelling to other institutions and attending seminars one wouldn't normally go to. I have known for years that the health and environmental arguments against GM foods were bogus, and is interesting to find that the economic ones are (at least in this case) bogus as well.

Google Shock

I just typed 'Polymer' into Google, since I wanted to get to the website of the journal 'Polymer' and this is usually a good way to get to journals even if their names are very common words. Sure enough, the journal was #3. #1 was the Wikipedia article, unsurprisingly. But #2 was something I wrote. And I am webmaster on #5. Maybe Google cranks the gain waaaay up on Australian sites? Or maybe it has become so intelligent that it now panders to my ego? Whatever is happening, it's pretty scary...

Good on him!

Dr Karl has issued a correction. Let's hope it gets as much media coverage as the original statement!

My run of luck ends

I was 4/4 for letters to major newspapers over the last couple of years. (Finding these is left as a Googling exercise for the reader). This time I have had a go at Dr Karl, and my letter has passed into limbo.

In this article in the Sydney Morning Herald on Friday, Dr Karl is quoted as claiming that Sydney produces a cubic kilometer of carbon dioxide every day, and that this makes carbon capture technologies ‘impossible’. Ignoring the dictum that the first person to mention the Nazis in an argument loses, he cites ‘clean coal’ as an example of Goebbels’ ‘big lie’.

Back in May we were told that Australians produce ‘more than five’ tonnes of carbon per capita per annum. That is, more than 18 tonnes of carbon dioxide per capita per annum.

This other site indicates that total Australian greenhouse gas emissions are of the order of 600 million tonnes of carbon dioxide per annum.

Thus, we can guess at 20-30 tonnes of carbon dioxide per capita per annum in Australia.

This gives 80-120 million tonnes of carbon dioxide per annum in Sydney.

This is 1.8-2.7 trillion moles of carbon dioxide.

Which is 40-60 trillion (10¹²) litres of carbon dioxide at atmospheric pressure.

Which is admittedly a lot.

There are a trillion litres in a cubic kilometre.

So, we have 40-60 cubic kilometres of uncompressed carbon dioxide per annum. That is more like one a week, not one a day.

Week, day, whatever. Near enough is good enough, as my uncle who builds space probes for NASA says.

The article claims that Sydney would produce a cubic kilometre of ‘compressed’ carbon dioxide per day. I don’t think Dr Karl would have said this, because it sounds too silly.

One mole of carbon dioxide at atmospheric pressure will occupy 22.4 litres. By pV= nRT, if we put it under a pressure of 100 atmospheres, it will occupy near enough to 1% of that. I don’t know what sort of pressure is appropriate for the zeroth-order ‘pumping it into empty oil and gas reservoirs’ sort of carbon capture technology. But I do know that the grail of this sort of thing is converting carbon dioxide into a solid.

One mole of carbon dioxide converted into, say, calcium carbonate, will occupy 37 cubic centimetres.

So, rather than ‘one cubic kilometre per day’ we have 0.10-0.15 cubic kilometres per day, which could be theoretically converted into 0.0002-0.0003 cubic kilometres of calcium carbonate per day. That would be about 20 times as much as the solid waste currently produced by Sydney per day. So it is still a lot. But, for the love of God, calling it a ‘big lie’ is a bit rich.

Here is how I ended my letter:

‘The fact that many different people are working on many different strategies to solve a problem should be a source of optimism and joy. That a group called the Climate Change Coalition would malign the motives of researchers pursuing carbon sequestration technologies is depressing, to say the least.’

O tempora! O mores!

And what extreme slackness on my part. Yet another zombie blog cluttering up cyberspace, alas!

Here are two more things I don't understand, which I will have a proper stab at real soon now:

(1) What is it with quantum teleportation? My gut feeling is that ‘teleportation’ is an illusion arising from us looking at things the wrong way.

(2) Ditto for the ‘collapse’ of a wavefunction.

What happens to these concepts in the De Broglie pilot-wave model? This is a model which can explain the mysterious double-slit experiments- where electrons (and neutrons, and helium nuclei) seem to interfere with each other as if they were waves *even if only one is sent through at a time* - in terms of each particle really being a particle but being guided by a 'pilot wave'. I find this much more satisfactory than wave/particle duality- which of course has no bearing on whether it is true or not.
De Broglie's abandoned this theory, but other people have been mucking about with it and optimising it from time to time. But, as a mere chemist, I don't really understand what they are saying.


“One singular deception of this sort ... is to mistake the sensation produced
by our own unclearness of thought for a character of the object we are
thinking. Instead of perceiving that the obscurity is purely subjective, we
fancy that we contemplate a quality of the object which is essentially
mysterious; and if our conception be afterward presented to us in a clear
form we do not recognise it as the same, owing to the absence of the feeling
of unintelligibility.”

- Charles Sanders Peirce, ‘How to Make Our Ideas Clear’

Survey proves: 69% of 1st Year Students think balancing Redox Equations is Fun!