Tuesday, June 24, 2008
Two Cultures are Better than One
I assert that:
Inappropriately mixing poorly-thought-out ideas from biology with the humanities gave us the First World War, the Second World War, and the Holocaust.
Inappropriately mixing poorly-thought-out ideas from the humanities with biology gave us the only comparable man-made catastrophe of the second half of the 20th century, the famine associated with Mao's 'Great Leap Forward'.
Let's not go there.
Sunday, June 22, 2008
Things I don’t understand: The ‘Collapse’ of the Wavefunction
(NB: Let it not be supposed that the long delay since I last wrote something headed ‘Things I don’t understand’ means that there are not many, many, many, many other things that I don’t understand.)
In chemistry, the results of quantum mechanics that we are interested in are spectra. Whether these are lines in the ultraviolet/visible region corresponding to transitions between electronic states, or lines in the infrared region corresponding to transitions between vibrational states, or lines in the microwave region corresponding to transitions between rotational states, they are all transitions between energy states which are quite nicely defined.
We cannot ‘observe’ a chemical system in a particular state. We do not make a ‘measurement’ to see what state it is in. What we observe, what we measure, is its transition from one state to another. It seems entirely useless, as well as nonsensical, to say that a particular molecule was not in its first excited vibrational state until we hit it with a photon to give an anti-Stokes Raman peak.
In fact I am really quite vague about what sort of experiment you would do, in the traditional orthodox quantum mechanical sense, to measure the state of a system in such a way that its wavefunction ‘collapses’.
I don’t like the ugly discontinuity that the ‘collapse’ of a wavefunction introduces to quantum theory.
I don’t like the appearance of a privileged status for an ‘observer’ it introduces.
I especially don’t like the whole elaborate mass of New Age piffle that has been erected on this privileged status, a mass which has infected and compromised the otherwise splendid ouevre of Greg Egan, for instance.
A while ago I first came across de Broglie’s pilot-wave theory, and was impressed in my naive chemist’s way by the straightforward way it cut through the paradoxicality of the two-slit experiment. I wanted to know how this model had been developed since de Broglie cast it aside, and how the ‘collapse of the wavefunction’ looked in the pilot wave model. I couldn’t find anything then, because I didn’t know enough to look for the ‘de Broglie-Bohm’ model.
Apparently the collapse of the wavefunction is not a problem in the de Broglie-Bohm model. So it is non-local. Big deal. Every 1s hydrogen orbital wavefunction we tell our first year students about has a non-zero value at every point in the universe (though Excel, bless its heart, says with 15 digit precision that it is zero more than about a nanometre away from the nucleus). Better non-locality than mysticalBut why the de Broglie-Bohm model doesn’t get into trouble with the wavefunction collapsing- that’s something I don’t yet understand.
Wednesday, June 18, 2008
Down to four out of six
I was saddened to read Barry Brook's endorsement of the cry 'Don't feed the troll!' If you are in the business of science education, you should treat every comment on your blog as a legitimate inquiry from a seeker-after-truth and respond politely. If your science is good, it will be obvious to your other readers if their response is to "sidestep valid critiques and ignore counter-evidence". If your science is good, it also doesn't matter how many times you repeat yourself. You will be improving the delivery of your message all the time.
It doesn't do any good to call people who disagree with you names ("sceptics, denialists, contrarians, delayers or delusionists" ... "cut of the same anti-intellectual cloth") or accuse them of being on the take ("Groups with vested interests in business as usual..."). If you are trying to communicate with those who are not already in your camp, such ad hominem attacks are worse than useless.
I thought it was unfortunate that an article entitled 'Science must prevail' contained no actual science. A calm 622 words outlining the physical mechanism of the Greenhouse Effect and the observational evidence for anthropogenic global warming would have been a much better use of space.
Best regards,
Chris Fellows
Monday, June 9, 2008
TANSTAAFL
I direct your attention to this fragment in particular:
...you can creep along just using the electric motor which is great, you have zero emissions...
Well, no, if you creep along just using the electric motor, eventually you will run out and stop moving. From my vague understanding of how these things work, you need to run the gasoline engine to charge up the batteries.
I worry how much these sort of fuel-efficient vehicles are affected by what we might call the 'low-calorie pretzel' effect. The diet snack food has fewer calories, so you eat more of it. You are already 'doing the right thing' by driving your gee-whiz environment-friendly car, so you take it on trips where a person with a vehicle which is more expensive to run might walk, bike, or use public transport to save money...
Thursday, June 5, 2008
We are our most valuable resource
Just felt compelled to write in response to the reprinted article by Rudy Baum, ‘Too many people?’, in ‘Your say’.
I grew up in the desert of Arizona, and I too have been saddened to see that landscape submerged under urban sprawl. I have no doubt that rising global temperatures will shift Earth’s arid bands further from the equator, making Victorian rangelands and many other environments more marginal for agriculture. I mourn every species lost as we humans have spread across the arid landscapes of America and Australia with our livestock and feral animals.
However, I think there is no evidence whatsoever that we need a ‘new economic paradigm’. In my lifetime, I have seen our current economic paradigm deliver incredible benefits to the peoples of Asia, and more and more countries reach a standard of living where responsible environmental management can become a duty, rather than an unaffordable luxury. As standards of living rise, population growth rates fall. In Europe today I understand only Albania and Iceland have birth rates above replacement level. Even countries like Iran are rapidly nearing zero population growth. At some point in the next fifty years, on current trends, world population growth is going to stop. This will be long before we reach the limits of the carrying capacity of the Earth. Long before we even come close.
The suburbs of Phoenix may be ugly, but the density of population in the Arizona deserts is less than historical population densities in many Asian deserts. Furthermore, population density need not correlate directly with environmental degradation. Those suburbanites are not grazing goats in the desert. They are not collecting firewood there. I confidently venture that they are using much less water per capita than Australian suburbanites are. You would need thousands of them to make the same impact as one irrigated cotton farm- cotton farms like the ones that used to line the highway between Tucson and Phoenix, and which were all gone the last time I was there.
Not long ago I visited another desert landscape rapidly being covered by urban sprawl, in Dubai. I didn’t find it depressing. I found it exhilarating, and was filled with wonder at the capacity of human beings to create, to build, to adapt. As we humans change the world, we adapt to the changes we make. The richer we are, and the better-educated we are, the better we adapt.
There is no need to run around calling for a new economic paradigm. Why should anyone listen to us, anyway? We have no special expertise in social engineering. If we want to change the world, let us do it in the time-honoured way that scientists have been changing the world for centuries: by figuring out interesting things about the universe that can be used to solve technical problems. There are cost-neutral or cost-saving actions that we can take to reduce the waste associated with our economic system by orders of magnitude. All that is required is that we continue to think imaginatively, and in an evidence-based way.
I guess what I am trying to say can be summed up in the words: ‘half full, not half empty’. Even the shift in the arid bands further from the equator is very far from being an unmitigated catastrophe - when was the last time you heard about drought in the Sahel?
(Why was there a reprinted editorial from Chemical & Engineering News in ‘Your say’, anyway? Don’t we have any opinions of our own, making it necessary for us to import American ones? I at least have been a naturalised Australian since 1996.)
Best regards,
Chris Fellows MRACI
Unsafe at any speed
'UNE is lagging behind all other Australian Universities in one area – it is the most dependent on Federal Government grants. I perceive this as a high risk – and one that must be quickly addressed by opening up and attracting other sources of funding, particularly in the areas of research and development, from sources other than the Federal government.'
It has always been true that 'he who pays the piper calls the tune'.
But given that the piper must be paid by someone, what entity should do so?
I think it is obvious that it should be the entity that most shares the values of and is most accountable to those listening to the tune. An ancient and venerable private university ought perhaps to be funded by rich alumni. A Catholic university ought to be funded by the Catholic Church. And a public university ought to be funded by the voters.
For a regional university, the obvious source of funding which will be accountable to stakeholders will be the State Government. For a university with pretensions to national importance, the Federal Government is just as good. It is not 'high risk' for a public university to be funded by the Government. The public sector is, rightly or wrongly, cushioned against the slings and arrows of the market. This is why the economy of a city like Canberra is so placid and stable compared to the economy of a city like Cairns. And public funding cannot be withheld or redirected on ideological or economic grounds with the same ease as other sources of funding- because ultimately, the State and Federal Governments are accountable to the electorate.
It is high risk for a public University to receive a large proportion of its funding from:
* Corporations which are accountable ultimately to institutional shareholders overseas, rather than the Australian electorate.
* Overseas fee-paying students whose numbers will wax and wane with the vagaries of the market and the whims of foreign governments.
Parenthetically, I am one of those staff members who have no confidence in the Chancellor. He is not properly carrying out the task he was appointed to do (for instance, he has attended only 13 of the last 24 graduation ceremonies) and instead he is trying to do a job he was not appointed to do, subverting the authority of the Vice-Chancellor. He should go. Now.
Sunday, April 27, 2008
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.
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.
Wednesday, April 23, 2008
Show me the metabolism! Part One.
Being some comments on ‘The Origins of Order: Self-Organization and Selection in Evolution’, by Stuart A. Kauffman.
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
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.
Sunday, March 9, 2008
The Myth of Terra Stasis
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’.
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.
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.
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.

Things I learned in Canberra
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.
Sunday, February 10, 2008
A Talk to some National Youth Science Forum Students, 8/2/08


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







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 25thcentury that Jean Marie Lehn is dreaming about.




