A little note about chain transfer to butyl methacrylate

For good or evil, this paper, which I began writing in 1999 at the request of Professor Bob Gilbert, is finally published. It is a tremendous pleasure to finally be a co-author with David Sangster, the eminence d'or of Australian polymer science. He is the source of the quote which informs my every waking action:

'Just because the model fits the data, it doesn't mean the model is true.'

I have today (10/11/09) found a splendid biography of David Sangster on the website of the University of Sydney.

Royal Society Discussion Paper, Ocean acidification due to increasing atmospheric carbon dioxide. Part Two.

The RSC discussion paper explains the division of ocean waters between an upper zone, where calcium carbonate formation is possible, and a colder lower zone, where it is not possible. The fact that mass transport between these zones is very slow is stressed. The paper does not actually give a pH profile of the ocean, but here is one:

(The little dark dots are the data from today; the big circles are attempts to figure out the situation at various times in the past, which is what the paper I sourced this from is about.)

Note that the vast majority of the volume of the ocean is cold, and relatively acidic. This deep ocean is where an enormous amount of carbon is stored. Transport of carbon dioxide out of or into this layer will not be controlled by thermodynamics (i. e., where carbon dioxide it would most dearly love to be), but by kinetics (i. e., how fast it can get there). Thus, it does not matter to this zone whether or not we are adding carbon dioxide to the atmosphere at a rate unparalleled in Earth’s history or not, because that will not control how fast it gets there. It has to run the gauntlet of the warm water- where it may or may not be converted into calcium carbonate- first.

Remember the figures in the last post on how the carbonic acid equilibria change with temperature. I am now going to make the assertion- which I should now go out and try to verify- that the deep ocean is more acidic *because* it is cold.

To qualify this as-yet-unverified assertion of mine, I should say that I have not yet found any data on the pressure dependence of the pKa values in solutions of reasonable ionic strength, which is also likely to be important.

I suggest that the temperature gradient of the ocean is probably what generates the pH profile, and because transport of carbon dioxide into or out of the ocean is slow compared to how much is already there, it is the temperature dependence of the carbonic acid equilibria which control the speciation observed. Note also that the boundary between the carbonate-forming zone and the non-carbonate forming zone, from our figures below showing what the equilibria do, is going to be dependent both on the pH of the upper layers and their temperature.

Now… if climate change means anything, it means the oceans warming up. Heating the ocean and reducing the pH will pull the carbonate/bicarbonate equilibrium in different directions. I don’t know which is likely to be more significant.

Because the historical record does not show carbon dioxide spouting out of the ocean immediately as temperature increases, but lagging about 1000 years, I am not at all worried about degassing of carbon dioxide starting some feedback loop of badness : until that cold lower ocean where most all of the carbonic acid species are sitting warms up, there is no reason for significant amounts of carbon dioxide to leave the ocean. That is, if degassing of the ocean *is* the reason for the increase in carbon dioxide lagging historical temperature changes. It might not be.

Royal Society Discussion Paper, Ocean acidification due to increasing atmospheric carbon dioxide. Part One.

My thoughts keep returning to the ‘de-alkalinisation of the oceans’. I started thinking about this the other day, first because I came across that article on coccolithophores in Science, and second because one of my students is writing a review article on the use of polymer additives to stop scale formation in desalination plants. The main scales formed in these plants are calcium sulfate at high temperatures, but at somewhat lower temperatures calcium carbonate or magnesium hydroxide.

The first thing you want to know about, if you want to stop scale forming, is what are the characteristics of the solution it is forming from. So early on in the draft appears this table:

(TDS is ‘total dissolved solids’.)

I went back and had another look at the Royal Society discussion paper that I referenced before. This is the paper referenced everywhere in the web where people are fretting about ocean de-alkalinisation. The range of pH values quoted in this table is greater than the range shown in the pretty map in the Royal Society report. In fact, the range of pH values in this table is greater than the size of the maximum change in surface water pH they predict for Figure 5.

So my first thought was, if changes in surface seawater alkalinity are likely to cause bad effects, we ought to be able to see these effects already in ‘canary in the coalmine’ water bodies- shallow, warm places like the Persian Gulf. The reefs there don’t seem to be in particularly good shape but there doesn’t seem to be any evidence that seawater alkalinisation is contributing to their woes. Anyway, this table got me thinking about the problem again.

In discussing the formation of calcium carbonate scale, my student had to talk about the dependence of the equilibrium constants K₁ and K₂ on temperature and the total ionic strength of the solution, and had referenced this paper by Millero et al., where the following figure appears:

The Millero et al. paper also summarises data from a lot of previous work and gets it all to fall on the same line- see this, for instance:

In case you don’t remember,

pK_a = –log₁₀(K_a),

and in this case, K₁ is the equilibrium constant for the reaction:

H₂CO₃ → HCO₃^– + H⁺

and K₂ is the equilibrium constant for this reaction:

HCO₃^– → CO₃^2– + H⁺

These figures are telling us that in seawater (where I^0.5 ~ 0.83), the equilibrium position of both these reactions is further over to the right hand side than if they were happening in common or garden distilled water. And they also tell us that the warmer the water, the further the equilibrium will be over to the right hand side as well.

I plotted up a graph showing how the speciation of pH should change in seawater using the values in this paper and got this figure:

The Royal Society Figure 2 is pretty much the same as mine. It shows carbonate kicking in at a slightly lower pH, but there are different K₂ values floating around in the literature and I'm not sure what value they used.

Zooming in on the pH range important for discussing what is going on in the oceans:

Getting rid of the log scale, and looking at the carbonate/bicarbonate equilibrium only:

More to follow.

C'est la vie

A while ago the prolific Anonymous asked me:

What do you think about the de-alkalinisation of the oceans. Anything ruinously doom and gloom possible there? Is adaptation of water species quick enough by your reckoning?

I have recently been thinking about this a lot, due to work I am doing on calcium carbonate formation in desalination plants, and will offer a substantial critique of this particular bugbear soon.

But in the meantime, I came across this nifty figure in Science the other day and thought I would share it with you. If someone had asked me, 'how will marine organisms respond to changes in total carbonic acid species concentration?', I like to think I would have been prescient enough to draw a figure like this one. Find a niche and fill it: such is the way of living things!

Dialogo

Simplicio: Have you heard? The Powers wish to reduce the amount we teach, so that we will have more time for research, and thus will produce more and better research.

Sagredo: I think the second part of your syllogism does not follow from the first.

Simplicio: Why, how is that?

Sagredo: One of us cannot have more than twenty-four hours in a day. But if one has a single intelligent and dedicated postgraduate student, then one has forty-eight. If one has two, one has seventy-two, and so forth. It is the many hours that come from having many students that enable us to produce more and better research.

Simplicio: True, but I cannot see how having a few more hours for research can hurt us.

Sagredo: Where do you suppose postgraduate students come from?

Simplicio: Most of them are from places like Tartary and Hind, are they not?

Sagredo: Yes, many of them are. They are attracted from diverse foreign lands by the splendour of the learning in our land. But many other places of learning seek also to attract them, and day by day the scholars of their own lands grow wealthier and more astute, so that one day no more will come to us.

Simplicio: That would be a calamity! So where else do they come from?

Sagredo: We raise them here, by teaching undergraduates.

Simplicio: Aha! There is no problem, then. Under the new system we will surely continue to teach undergraduates.

Sagredo: Simplicio, do you suppose all undergraduates are suitable to become postgraduates?

Simplicio: I guess not. Some are damnably simple.

Sagredo: Yes, it is only the few who hunger and thirst for knowledge that are suitable to become postgraduates. If we give our undergraduates half as much as we did before, and other places of learning continue to offer a full cup of learning, where will undergraduates like that go?

Simplicio: You think they will not come here?

Sagredo: Many of them will not.

Simplicio: But surely there are many who would not leave our lovely place of learning for the City of Dreadful Night or other distant places?

Sagredo: Yes, we must pin our hopes on such as those. But consider: if we teach them half as much, what will we need to do when they commence as postgraduate students?

Simplicio: I am not sure. I recall there are forms to fill out?

Sagredo: Besides that. We must perforce teach them the other half, if they are to work as well as postgraduates in the City of Dreadful Night work. And when we have done that, what must we do?

Simplicio: I suppose we must fill in some more forms.

Sagredo: Yes, for by then the first year of their candidature will be over.

Simplicio: It would seem, then, that you think this change will diminish our chances of doing more and better research, rather than increase them?

Sagredo: Most certainly. Why would a student who would make a good postgraduate in Physics or Chemistry do an undergraduate degree at a place of learning that does not take that discipline seriously?

Simplicio: Then I suppose the Powers wish to reduce our teaching hours for some other reason?

Sagredo; That is what I had thought.

Simplicio: Perhaps it is that they must be reduced because of this thing that has come from Bologna?

Sagredo; Ah, but the places of learning that have already gone down that path teach many more hours than we do.

Simplicio: Hmm. Perhaps it is, Sagredo, that those studies they wish to cut are only those where the numbers of undergraduates have been falling, so that we may conserve our resources, as our wealth wanes?

Sagredo: That would be a sensible course of action- but you see, Simplicio, it is the studies where numbers of undergraduates are holding steady that the Powers wish to cut back.

Simplicio: Ah.I see. Perhaps- no, that makes no sense. (sighs)
I wish Salviati was here to explain what was going on.

Sagredo: So do I, Simplicio.

Simplicio: It is a pity the Powers never replaced him, when he took his renowned research group to Brescia...

Two Cultures are Better than One

I have been asked to read this document in preparation for a meeting of the School Research Committee. It would be cruel to ask you to do so as well, but if you want to, please go ahead. It is basically a proposal for muddling the 'Two Cultures' back together in a porridge by structuring humanities studies around 'evolutionary theory' and stressing that 'evolutionary theory' is a 'form of narrative that functions within its social and historical context'.

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.

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 mystical Copenhagen interpretation waffle about an ‘observer’, or worse yet, the deeply dippy ‘Many Worlds’ interpretation.

But why the de Broglie-Bohm model doesn’t get into trouble with the wavefunction collapsing- that’s something I don’t yet understand.

Down to four out of six

This letter, to The Australian's Higher Education Supplement, didn't get published either. So here it is:

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

TANSTAAFL

I heard this on the radio this morning.

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...

We are our most valuable resource

The monthly publication of the Royal Australian Chemical Institute, Chemistry in Australia, has just printed my reply to an article they reprinted from Chemical and Engineering News a few months ago. It is not on the Web, and I don't have the scanner attached at the moment, but this is what I said:

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

Our Chancellor has said:

'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.

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.