Mostly Harmless Science Blog

Bad habit

2011-10-09T17:44:00.000-07:00

One of my bad habits is checking almost every day to see how many papers have cited my work.

Today, a milestone!

The 2011 Nobel Prize and the Anthropic Principle

2011-10-05T03:11:00.000-07:00

Congratulations to the physics Nobel laureates for being recognised for their discovery that the rate of expansion of the universe is increasing!

I was thinking, is there any way that we could have predicted that we would observe the rate the universe was expanding was accelerating, given only the fact that we are here to observe it? Or, given only the fact that we are here, plus a few common-sense assumptions?

So in principle, we could have found the universe was growing, shrinking, or staying the same size.

If it was staying the same size, it seems a bit much to think of it being created ex nihilo at some finite size, so either it would have to be infinite in space and time, or it would have to have started out long enough ago that it had time to grow to a particular size and lose all trace of ever having been growing. And by the principle of uniformitarianism – which is to say that our position is nowhere special – if we saw that it wasn't growing, we would have to assume that it stopped growing a looooong time ago. I think, given all that time, it makes sense that life would have started long ago, and spread throughout the universe, and changed things to suit itself, so that primitive life 'red in tooth and claw' like we have here would never have gotten started, and chances are we would not be here to observe the universe being the same size.

If the universe was shrinking, it would make sense that it was shrinking toward a 'Big Crunch' of some size. Now, we know all sorts of quantities that are conserved in the universe, and also that singularities are not really singularities, but emit radiation. So it would make sense from those observations that the Big Crunch would not be the end of the universe, but would be followed by a Big Bang, and that we were living in an oscillating universe that had most likely- uniformitarianism again- been through very many Big Crunches, and was really really old. And, it makes sense that in one of its previous cycles life would have gotten clever enough to pass information on to a future universe, information that would have given life a leg up early, so it spread throughout the universe, and changed things to suit itself, so that primitive life like us, etc. etc., and we wouldn't be here to observe the universe shrinking in this cycle.

So, chances are the universe has to be expanding for us to observe it.

If it is expanding and deccelerating, we don't have any good reason to expect it to stop deccelerating – which means eventually we would expect it to be shrinking instead of expanding – which gets us back to that oscillating universe we aren't around to see.

So I would suggest, given the uniformitarian idea that we aren't at any uniquely special time in the life of our universe, the optimistic idea that the conservation laws we see have broad validity, and the other optimistic idea that sentient beings are damnably clever and can figure out how to do all kinds of neat stuff, a universe that we are here to observe is most likely to be a universe that is expanding at an accelerating rate. IMHO.

Book Report, Part Two

2011-09-26T05:07:00.000-07:00

There is a tide in the affairs of men,

Which, taken any way you please, is bad,

And strands them in forsaken guts and creeks

No decent soul would think of visiting.

You cannot stop the tide; but now and then,

You may arrest some rash adventurer

Who--h'm--will hardly thank you for your pains.

Vibart's Moralities, Rudyard Kipling

Further observations on the third strand: The author as curmudgeon

I had a few nit-picky observations on the third strand in the book, the generalised grumping about how everything has gone to pieces, but have decided to leave them behind and talk instead about the appearances of science in Bloom's book.

First they came for the philosophers...

Near the end of the book Bloom takes a tour of various disciplines, examining how they have fared in the twenty-odd years of the collapse of the idea of the university and to what extent they brought the calamity upon themselves. The hard sciences are the only ones that come out looking reasonable. They have not participated in the philosophical and political hijinks that have precipitated the crisis; their standards are maintained; their enrolments are solid; they are thought to be necessary: “Modern regimes were conceived by reason and depend on the reasonableness of their members. And those regimes required the reason of natural science in every aspect of their activity, and the requirements of scientific advance largely determine their policy.” Furthermore, the hard scientists are still essentially in touch with the 'philosophic use of reason' in a way that the rest of academia has largely abandoned. “The demonstrations of science come from within man, and they are the same for all men. When I think the Pythagorean theorem, I know what is in me at that moment is precisely the same as what is within anyone else who is thinking that theorem. Every other supposedly common experience is at best ambiguous.” From the vantage point of now, it looks like a perfectly splendid time to be a scientist. I can see why Bloom is at times a bit irritable with them.

Bloom sees the main flaw of the hard scientists within the university as rejection of community: collectively they are happy to hover Laputa-like over the chaos below; individually they are happy to pursue interests so narrow as to be 'immoral nonsense' to practical men, and do not lift their eyes to see the necessity of a philosophy to unify what they do. Both these criticisms are more or less true. On page 351 he says: 'inwardly they believe that the only real knowledge is scientific knowledge'. So we do. So the desire to ignore all the tomfoolery going on around us is strong. And most of us are very narrowly focussed. We are aristocratic in Bloom's sense in that we believe details are important, and that progress is not often made through generalisations. When we venture into the wider world even the greatest of us are apt to write things that are shallow and silly.

Yet in defence: science is the radical democratic form of knowledge. There is room for all on the floating island. Join us. And, while most of us do might not lift our eyes to make sense of what we do within a coherent philosophical view of the world, Bloom does not offer any philosophy worthy of our attention. Neither does he pay any attention to the great philosophy that was in fact created by a working scientist: pragmatism is not mentioned until p.378, only a few pages before the conclusion, and Peirce not at all.

And the last 29 years have not been kind to us. The natural sciences are no longer a 'Gibraltar' standing aloof from the relativism of the wider institution. The graduates of '82 are the movers and shakers now, the people at the top of their careers, and we live in the world they have made. The graduates of '82 were brought up under the shadow of nuclear war, with Rachel Carson's “Silent Spring”, and Three Mile Island, and they do not much like us. Seen only as a commodity for maintenance of a technological society, we are in oversupply in the developed world. It is easier to outsource our function to other lands. On this utilitarian basis science has been hollowed out across Australia: a scary number of Australian 'universities' have ceased to offer an internationally recognisable physics or chemistry major. In the country Bloom was writing about, science no longer commands the respect it once did. It is not exciting. There is no money in it. There are the best science departments in the world, and the native-born, still filled with Tocqeville's democratic spirit after all these years, stay away from them.

Book Report, Part One

2011-09-17T00:49:00.000-07:00

Through the trick of taking a lazy holiday I have made it to the end of Allan Bloom's “The Closing of the American Mind”, which my father sent me. I found it difficult going. It is a book that reads as if it was translated from the French – it has the opacity, the peculiar internal structure, and the sort of elliptical, rhetorical, arguments that abound in the few books translated from the French on philosophical matters that I have read and forgotten the titles of.

I am sure Bloom structured the book the way he did for some purpose. But to me the structure did not help. To my reading there are approximately three separate strands in the book, which I will go through in order of importance.

The first strand is the description, not of how higher education has failed democracy, but rather how democracy has failed higher education: how the democratic habits of mind described by de Tocqueville as corrosive to the idea of a university have proved, in fact, to be corrosive of the classical idea of a university. The hyperindividualism, the utilitarian view of knowledge as a means to profit, the disregard for the past: these are just American traits, not unique to American university students of the late 20^th century. They are all traits observed and explained by de Tocqueville in the 1830s as consequences of democracy and of the peculiarities of the American circumstance.

Bloom asserts that a university ought to act as a counterbalance to the particular tendencies of thought encouraged by a democratic society. This is a perfectly reasonable assertion, and the problem then becomes the internal motivation for the members of universities to keep swimming against the current, so to speak. “To sum up, there is one simple rule for the university's activity: it need not concern itself with providing its students with experiences that are available in democratic society. They will have them in any event. … The universities never performed this function very well. Now they have practically ceased trying.” (p.256)

Why did universities perform this function badly? Why have they ceased trying? The explanation suggested by Bloom for them ceasing to try is the adoption of bad German philosophy, and an extensive discussion of the intellectual genealogy of this philosophy forms the second strand of the book. I found this part difficult to follow as an argument, though it is clear as a history of thought. Bloom traces the modern university to the Enlightenment, as an effort to bring philosophy to bear in the shaping of society, instead of remaining a separate thing. Of this enterprise he says: “It was not by forgetting about the evil in man that they hoped to better his lot but by giving way to it rather than opposing it, by lowering standards” (p.296).

Bloom is never clear about which thinkers he agrees with and which he disagrees with, so the extended history lesson serves mainly to show – to me, at least - that the ideal of the modern university is poisoned at the root. To my mind Bloom vindicates the American tendency to ignore the past and makes a very good case for ignoring Rousseau, Hobbes, Locke, Kant, Nietzsche, etc., as wreckers and blind guides. The fundamental assumption of political philosophy held by these thinkers – that man is by nature a solitary being - is rubbish. I think Bloom sees this, but he does not state it until much later in the book, and then obliquely: “Reading Aristotle helps to lay bare the hidden premise underlying modern social science, that man is by nature a solitary being, and could provide the basis for making a debate of it again.” (p. 366)

The culmination of the strand of philosophy which Bloom traces is Weber, in the early twentieth century, who says that old-style Enlightenment rationalism is dead. “All future discussion or study must proceed with the certainty that the perspective was a 'naïve' failure. Reason cannot establish values, and its belief that it can is the stupidest and most pernicious illusion.”[1] Thus the university, seen as an Enlightenment project, cut off its own legs. There are very conflicted and contradictory signals about the value of the Enlightenment and post-Enlightenment philosophers in Bloom's book. Like Simone Weil, but by demonstration rather than explicit argument, he seems to be saying that its all there in Plato and that all the philosophising done between us and Ancient Greece is bosh. I am not sure if that is what he means to say, but that is what he seems to be saying.

The third strand in the book is essentially cranky reactionary old man. He complains about the sexual revolution and the intellectually deadening effects of the kind of music young people listen to nowadays. To a large extent I find this congenial, but it isn't convincingly tied to the rest of what he says to make a coherent argument for how and why society has gone wrong and what the university can do about it. It is just grumbling garnished with learned quotations.

All in all 'The Closing of the American Mind' is not a very good advertisement for an open American mind. It lacks clarity, it lacks structure, it lacks a sense of proportion, and it lacks a positive program. The book is a good illustration of my (thoroughly unoriginal) analogy that religion and science are the two eyes of humanity: if you only have one, you will have a two-dimensional picture of the universe. If you don't have either, you will stumble around blindly running into things. To my mind the great enemy, the cause of the evils that have cast down the university, is relativism. To fight relativism you need to assert an absolute. And you need to do this with authority, not like the scribes and Pharisees.

Further observations on the first strand: How Democracy Has Failed Higher Education

It is all there in de Tocqueville's “Democracy in America” As Tocqueville says: “I think that in no country in the civilized world is less attention paid to philosophy than in the United States.”

The way organisation of society on democratic principles leads its members to distrust elitism in all its forms works against higher education, traditionally understood, making a significant impact. De Tocqueville again: “The nearer the citizens are drawn to the common level of an equal and similar condition, the less prone does each man become to place implicit faith in a certain man or a certain class of men. But his readiness to believe the multitude increases, and opinion is more than ever mistress of the world.”

And for a third time, here is one more long quotation from de Tocqueville: “Permanent inequality of conditions leads men to confine themselves to the arrogant and sterile research of abstract truths; whilst the social condition and the institutions of democracy prepare them to seek the immediate and useful practical results of the sciences. … Men living in democratic ages cannot fail to improve the industrial part of science; and that henceforward all the efforts of the constituted authorities ought to be directed to support the highest branches of learning, and to foster the nobler passion for science itself. In the present age the human mind must be coerced into theoretical studies; it runs of its own accord to practical applications; and, instead of perpetually referring it to the minute examination of secondary effects, it is well to divert it from them sometimes, in order to raise it up to the contemplation of primary causes.”

How can people who are themselves part of a society distance from themselves sufficiently in order to coerce it in an unnatural direction? Only if they are consumed with a fiery ideal. Since they are now divided, confused, and themselves steeped in the practical, egalitarian principles of democratic culture, it is quite beyond their capacity.

Bloom points out that in 1930 the American universities could have disappeared from the face of the Earth without any great impact on human intellectual activity, and that the dominance of American universities in the post-War period is due to the influx of refugee intellectuals from Europe. Thus, it seems to me that the failures he notes are due largely to the retirement of this generation, the reassertion of historical inevitability, and the failure of the exotic transplant to flourish on the infertile soil of the New World.

I think de Tocqueville's observations about the effect of democracy on higher learning are correct, and the decay of the university on American soil to a large degree historically inevitable. I do not see a remedy.[2]

To see how perniciously the anti-elitism encouraged by democracy, and the 'practical applications' (i.e., profitability as the sole criterion of value) encouraged by democracy, dominate Australian higher education today, I recommend perusal of the blog 'The Common Room' at the Australian newspaper. See here, for instance.

There is no discussion about the role of a university any more. We exist to perpetuate our own existence by doing things that are profitable. That is about it. Bloom's graduates of '82 are now the movers and shakers of the system, the people in the prime of their careers, and his conclusion is even more true today: “It is difficult to imagine that there is either the wherewithal or the energy within the university to constitute or reconstitute the idea of an educated human being and establish a liberal education again.”

Further observations on the second strand: Philosophical trends in higher education since the Enlightenment

I have been reading a lot of Chesterton so I will be essentially parrotting him here, but an analysis of the Western university that begins with the Enlightenment begins halfway through the story. There is no acknowledgment that the modern university grew out of an older institution that had a defined role in Western civilisation and went along fulfilling it without existential crisis for more than half a millennium. There are few and slighting references to Aquinas in this book, but at the end Bloom admits that Catholic universities will be one of the few places study of philosophy will cling to existence, thanks to the Scholastic connection with Aristotle. Higher education is not after all poisoned at the roots, but poisoned halfway up the trunk, by the Enlightenment. When Bloom says “because there is no tradition and men need guidance, general theories that are produced in a day and not properly grounded in experience, but seem to explain things and are useful crutches for finding one's way in a complicated world, have currency” (p. 254), whether he intends to or not, he is referring to all the theories of the Enlightenment.

The classical university of the Middle Ages recognised Man as a social animal: as a creature that is born into a society and cannot exist alone. The most 'primitive' tribe is a complicated net of social obligations, and this net of obligations is the main adaptation for survival of our species. Any theory based on the idea that 'man is by nature a solitary being' will fail. This agreed-upon net of social obligations also entangled the members of the university in its original conception. Without it, the cohesiveness of the university disappears and it becomes unable to resist the society in which it is embedded. A small group of zealots can perhaps maintain a cohesiveness based on shared principles other than those that animate it society: but as the university expands, this will inevitably be lost.

Bloom explains the failure of universities to hold their nerve to the corrupting influences of a philosophy that ended up by devaluing reason, the philosophy of Nietzsche and Weber. But I think this can only be of minor importance. As Bloom has outlined in the first strand of the book, the nature of democratic society is inherently hostile to the traditional university project.

In the later 20^th century, as the university expanded towards mass participation, whatever capacity it had to resist the pressures of the society was diluted. The two things are strongly coupled: so long as participation inexorably increases, so will the fact of the university diverge from the idea of the university.

[1] Bloom says that 'We hold these truths to be self-evident' is an example of reason establishing values. Maybe that is how the framers understood it. But a truth that is 'self-evident' is by definition not established by reason! The muddy argument in this book is a far cry from the clarity of Chesterton: “The fault of the great mass of logicians is not that they bring out a false result, or, in other words, are not logicians at all. Their fault is that by an inevitable psychological habit they tend to forget that there are two parts of a logical process – the first the choosing of an assumption, and the second the arguing upon it; and humanity, if it devotes itself too persistently to the study of sound reasoning, has a certain tendency to lose the faculty of sound assumption. It is astonishing how constantly one may hear from rational and even rationalistic persons a phrase such as 'He did not prove the very thing with which he started' or 'The whole of his case rested upon a pure assumption,' two peculiarities which may be found by the curious in the works of Euclid.” (From the essay on Carlyle in 'Twelve Types')

[2] Democracy is not the only social structure that discourages the university. The centralised authoritarian state also discourages it as any more than a training place for practical pursuits: it does not matter whether we are all equal under God or under the party. I am afraid that Bloom's assertion “There is no intellectual ground remaining for any regime other than democracy” (p. 330) has turned out to be overly triumphalist. In the past twenty years I have seen the universities of the PRC go from a joke to the arbiters of quality to the rest of us, through the Jiao Tong ratings!

Us and Them

2011-08-05T17:47:00.000-07:00

Any model for global warming has to explain the following figures, which show significantly more warming in the northern hemisphere than the southern hemisphere:

(Bottom figure from http://nsidc.org/sotc/sea_ice.html)

One obvious difference between the northern hemisphere and the southern hemisphere is that there is a much larger fraction of ocean in the southern hemisphere than the northern hemisphere, and the ocean surely acts to moderate the air temperature. Whatever mechanism is heating the atmosphere, this heat may be being transferred to the ocean at an appreciable rate, despite the very slow mixing between surface water and deep water.

Let’s do a rough estimation of this thermal buffering capacity using Google and our mad arithmetic skillz. If we suddenly spiked the temperature of the atmosphere by 10 degrees, how much would this increase the temperature of the deep ocean, assuming all that heat was transferred across?

8.50 km = height of atmosphere if it were all at 1 atm pressure

3.80 km = average depth of ocean

So volume of atmosphere : volume of ocean (assuming ocean covers 70% of Earth)

8.50 : 2.66

90% of the volume of the ocean is below the thermocline and will have at temperature between 0 and 3, saith the interwebz. Let’s assume at equilibrium we have just heated up this cold water, and the air and surface water have returned to the same temperatures they are at now.

So volume of hot atmosphere : volume of cold ocean

8.50 : 2.40

Volumetric heat capacity of dry air: 1.3 J.K^-1.dm^-3

Volumetric heat capacity of water: 4180 J.K^-1.dm^-3

So if the heat change in the air is

10 K x 8.50 V x 1.3 J.K^-1.dm^-3 = 110.5 J.V.dm^-3

Then the ocean will increase by a temperature T, where

T K x 2.40 V x 4180 J.K^-1.dm^-3 = 110.5 J.V.dm^-3

T = 110.5/(10042) K

My mad mental arithmetic skillz have deserted me, but instead of opening another window and doing it in Excel I will round it off to 100/10,000 K – near enough to 0.01 degrees. So the net effect of whatever cockamamie stuff we have done to increase the temperature of the atmosphere ten degrees has been to increase the temperature of the deep ocean from 1.5±1.5 C to 1.51±1.5 C.

Just something to think about.

But, maybe the difference between hemispheres is not due to the effectiveness of heat transfer to this ubersink. Since there is another obvious difference between the hemispheres. About 90% of the human population – and all that other stuff associated with humans – is in the northern hemisphere.

Most of the things we do to the atmosphere change what is going on near the surface, where there are big fluxes for all sorts of other reasons. But we have made big changes to parts of the atmosphere where not much usually happens. Pumping carbon dioxide and water vapour into the upper atmosphere with our big jet planes, f’rinstance.

I’ve stolen this picture of a place in the northern hemisphere where there is a lot of air traffic. It often looks like this, though not quite as bad, where I live, which is a relatively air-traffic-crowded part of the southern hemisphere. The picture is at sunset because, while I don’t know much about clouds at all, it is obvious from standing around under them that they have a cooling effect during the day and a warming effect at night. And the Cloudspotter’s Guide by Gavin Pretor-Pinney, which I can recommend without reservation, assures me that the warming effect wins.

Just another thing to think about.

****

September 13th:

Of course, if you pick a different zero point, the two curves don't look all that different:

So probably there is nothing in it after all.

It's a small world after all

2011-05-29T20:04:00.000-07:00

My uncle Chuck has already hand-tooled instruments that have ended up in orbit around Titan. Now, he is at the forefront of mankind's asteroid-molesting efforts!

ZOMG CHEM 400

2010-10-13T18:40:00.000-07:00

A little while ago I put together a presentation which gathers/scatters some of my thoughts on teaching chemistry in the 21st century for a learning and teaching symposium, which my colleague Dr Erica Smith very kindly presented for me while I was on long-service leave.

If you are at all interested, you can go here for a link to the first draft.

Erica tells me it went very well, though there was an interruption from the audience when I referred to non-scientists as 'muggles'; one gentleman apparently took exception to being called a muggle. Though I still think this is a perfectly valid characterisation - scientists are (1) the people who understand what is really going on, and (2) those who have the power to influence their environment in a meaningful way - I have removed it in the second draft. Muggles cannot help being muggles, after all, whereas it is open to everyone to learn to think in a scientific way.

***

September 16th 2011:

I thought I would just add the slide for the Conclusion in the powerpoint presentation of this and the accompanying text I sent to Erica...

"Chris put this line of untranslated Greek in on purpose and not (just) to show off.
Until recently, this was part of the common body of knowledge expected of an educated person in our civilisation: educated people would know a little bit of Greek and recognise this as a saying of the philosopher Heraclitus.

Now, anyone who sees it, whether they are educated or not, can look it up on Wikipedia. Chris doesn’t have to tell you what it means. It is pathetically easy for you to look it up so if you have the will to know you can go and do it.

(NB: If anyone asks about the years 1900-2000, you can make derisory comments about the ‘Age of Stupid’ … that was what I was going to do.)"

Image Results for Chris Fellows

2010-06-27T16:51:00.000-07:00

Of the Chris Fellowses in the world, the one with the largest web footprint is possibly the South African wildlife photographer known for his action shots of great white sharks. So if you google me you are likely to get results like this:

("So, Mrs Jones, number four is the man you say pulled your husband from his surfboard and bit his leg off above the knee?"
"*sniff* Yes, Officer... I'd know that face anywhere... *sniff*")

Best. Exam. Ever.

2010-06-27T16:41:00.000-07:00

This is a reproduction in its entirety of my favourite exam of all time. It was for one of three coursework units we had to do in the Honours year and Dr Ken Adam had given me three books to read at the beginning of the year- one on Ab Initio Self-Consistent-Field Theory, one on Semi-Empirical SCF methods, and one on the application of computers to chemistry in general, with instructions to read them, except for one chapter in the last one. (Of course that chapter was about spectroscopy of molecules in interstellar space which was wildly exciting so I read it anyway).

In praise of Control+C

2010-05-27T22:16:00.000-07:00

Paper 1: Important for the transfer of energy and matter across the ocean/sea air interface are some parameters called the roughness length, z₀, and the friction velocity, U_*, of the interface that can be determined by measuring the velocity of the sea air at various heights above the water and fitting an equation, like so:

In 1969 a group of scientists from the Massachusetts Institute of Technology went out and did a bunch of measurements like this. They looked at the variation in z₀ and U_* as functions of U₁₀, the air speed 10 m above the ocean surface. They took 299 separate wind speed profiles, binned by U₁₀like so:

From which they got the following graph for U_* vs U₁₀ :

And the following graph for z₀vs U₁₀:

Now, the values in Fig. 3 and Fig. 2 come from the slope and intercept, respectively, of equation (1) fitted to the same data. So I don't know why they didn't put error bars on this second graph or why they drew such a wacky line through the data points, since they didn't have Excel with 'draw a stupid non-physical line through the points' as a default option.

Paper 2: When they were sailing near Block Island this same group of scientists also did some more experiments where they poured oil on troubled water and took the same measurements, which they reported in another paper. This paper only has a graph for z₀vs U₁₀:

And here they have only shown the trend line for the non-oil data because this paper was concentrating on explaining the oil data. They explained the difference between the oil data and the non-oil data using one model and not long afterward another scientist put out a paper (in Science, so no slouch of a paper) giving a different explanation for the difference.

Paper 3 (Science): The data presented in this paper (and cited as coming from Paper 2) looked like this:

Note that the data points that are from Paper 2 are exactly the same, but the data points that are not actually shown in Paper 2 (and are presumably from Paper 1) have wobbled around quite a bit. Paper 3 doesn't say so, but it is possible that all the points in these two plots that aren't the published points from Paper 2 come from the data used in Paper 2 but not shown (and hence for the no-oil curve, the same as Paper 1) Note that the positions of the open circles in the open circles in the z₀ graph are actually quite different between Paper 1 and Paper 3, which suggests to me that the author of Paper 3 got hold of the raw U(z) plots for Paper 1 and re-fit them to the first equation we thought of.

Paper 4: Now for the fun part. This is from a much more recent review paper.

Exhibit 1:
This is cited as being 'after Paper 1 and Paper 2'. Sure enough, it is the data from Paper 2. But it isn't the data from Paper 1. It's the silly fitted line shown in Paper 2 with spurious data points added in crayon! How lame is that?

Exhibit 2:

This is reported as being 'data collected by [author of Paper 3] (after Paper 3)', as if it is a totally independent experiment!

...

This sort of thing could have been avoided if people in earlier decades had the ability to scan papers they were interested in and cut and paste bits of screenshots of them, like I've been doing.

FWIW this is what I reckon the curves should look like, drawn on the figures sourced from Paper 3 as they appear in Paper 4 - suspect points flagged from having big error bars and lying way off the U* trend-line as reported in Paper 1:

"Any unauthorised use is strictly prohibited"

2010-05-16T19:26:00.000-07:00

Here is a totally unauthorised reproduction of a seminar notice from the University of Sydney. It seems to describe a philosophical goal devoutly to be wished, with which I am in complete agreement:

SCHOOL OF PHYSICS COLLOQUIUM

http://www.physics.usyd.edu.au/local/coll

Monday 17th May, 2010 at 3:15 pm

refreshments from 3pm

Venue: Slade Lecture Theatre, School of Physics

Title: Quantum foundations research @ Sydney

Presenter: A/Prof. Stephen Bartlett

University of Sydney

Abstract:

Despite a century of development since Einstein's explanation of the photoelectric effect, the foundations of quantum physics remain mysterious and surprising. Rather than accept the strangeness of quantum physics as a necessary evil, the research group in Quantum Foundations here at the University of Sydney is attempting to uncover the meaning and interpretation of the mathematical structure of quantum physics in terms of understandable concepts based on an external reality.

In this talk, I'll provide an introduction and overview of the Quantum Foundations research group here at Sydney, which includes researchers in Physics, Philosophy and HPS as well as a large-scale collaboration - the Perimeter Institute-Australia Foundations (PIAF) project.

The email concluded: "This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited."

So come and get me, seminar programme Nazis. :(

Red Mars, p.211

2009-11-13T12:28:00.000-08:00

On re-reading Red Mars after more than a decade, I have been struck with how strongly 'red' my sympathies are. I don't remember feeling strongly one way or another when I first read the book. Now the prevailing mood among the first hundred Martians to begin terraforming immediately seems appallingly reckless to me, and I find myself in complete agreement with Ann Claiborne:

'Here you sit in your little holes running your little experiments, making things like kids with a chemistry set in the basement, while the whole time an entire world sits outside your door. A world where the landforms are a hundred times larger than their equivalents on Earth, and a thousand times older, with evidence concerning the beginning of the solar system scattered all over, as well as the whole history of the planet, scarcely changed in the last billion years. And you're going to wreck it all. And without ever honestly admitting what you're doing, either. Because we could live here and study the planet without changing it - we could do that with very little harm or even inconvenience to ourselves. All this talk of radiation is bullshit and you know it. There's simply not a high enough level to justify this mass alteration of the environment. You want to do that because you think you can. You want to try it out and see- as if this were some big sandbox for you to build castles in. A big Mars jar! You find your justifications where you can, but it's bad faith, and its not science.'

On page 173, the explorers find it 'startling in the extreme' to run across the tongue of a glacier, looking like a big white Uluru, even though they knew it would be there. I'm afraid they won't find anything startling, because they will have Google Mars.

Dunes in the Vastitas Borealis - let's not drown them just yet!

Of course, there isn't nearly enough water to do so- only 820,000 km³ or so.

Some changes we've made to the surface of Mars already- rover tracks on the edge of Victoria Crater:

Happy Happy Joy Joy

2009-11-12T04:21:00.000-08:00

Just thought I should say something about Peter Garrett blocking the Traveston Dam. This is a good, good, good, good thing. The Australian Lungfish is a species of global importance that we have a duty to look after. We make do at my place with the water that falls on our house and shed, and all those people in Southeast Queensland ought to do the same. Plants that won't thrive on rainwater have no place in Australian gardens.

Anyway, if Queenslanders want to be profligate, we have plenty of perfectly fine rivers in Northern New South Wales that we could dam to collect water to sell them...

Glass half full...

2009-11-09T20:19:00.000-08:00

The system for electronic submission and return of assignments that came in this year is beset with all the usual follies and aggravations of new technology, but I have just made a jpeg to use in marking assignments that I am looking forward to using:

On trying to read Schopenhauer

2009-11-06T19:04:00.001-08:00

Earlier this year Klaus Rohde made a number of posts about the ideas of Schopenhauer, the famous philosopher. I read one of the essays Klaus recommended on Schopenhauer’s thought and wrote a response to it.

I also read a book of extracts from Schopenhauer's ‘Parerga and Paralipomena’ in English and wrote two documents outlining some of the places where I agreed with what Schopenhauer said in the extracts, and some of the places where I disagreed with him.

But Schopenhauer wrote a magnum opus- practically the archetype of the magnum opus- outlining his mature thought, ‘The World as Will and Appearance’, which takes up three volumes in our library, and to argue about what he thought without reading it is really very lazy. So I thought I would have a go. I got out volume one, skipped the preface, and started wading in.

Unfortunately I did not get very far. And oddly enough I got hung up at the same point that a friend of mine got hung up on at the onset of ‘Mere Christianity’, by C. S. Lewis, when I lent it to him as an undergraduate. I rejected Schopenhauer’s initial argument, the foundation of the whole three volumes. The ‘oddly enough’ is because it was the identical initial argument of ‘Mere Christianity’- the assertion that consciousness is inexplicable by materialism. Lewis argues that consciousness is an irruption of the supernatural other into the natural universe, and from that goes on the derive Christianity; Schopenhauer argues that consciousness is the fundamental fact of the universe, the ultimate reality that generates the world of appearances around us, and that data from that world of appearances cannot explain consciousness.

I reject solipsism- the argument that the only data point I have is my own consciousness, therefore only I exist- because it is fruitless; you can’t do anything with it. It is an idea that leads nowhere and achieves nothing.

The idea that consciousness in general, as opposed to ‘my consciousness’ is the fundamental fact of the universe requires the existence of other minds.

How do we know these other minds exist? By observations we make of the world of appearances. So we must base our understanding of mind in general not only on the one data point we truly have access to, inside our own heads, but on how we observe mind to be manifested in space and time within this world of appearances. I think we cannot do this and fail to observe that mind is an emergent property. There is no sudden transition from things that are conscious to things that are not. We see insects displaying apparently conscious behaviour that we can model with a simple circuit. As we traverse the angora shawl of being*, more and more complex organisms display more and more complex behaviours, which we can explain more and more tentatively in terms of mechanistic inputs producing certain outputs. Eventually we get to us. Made out of the same kind of stuff, with a nervous system obviously just a more complicated version of the same nervous system the bugs have.

I think consciousness is just what a system of registering and reacting to sense impressions looks like from inside. A simple system, where we can see and understand that it is completely deterministic, might still feel like something from the inside. It might feel, to the moth, as if it chooses to dive toward the light.

It feels to me that I am composed of sense impressions and memories of sense impressions, and that there is nothing else. This no longer bothers me. (Of course you can come back and say: ‘Who is this ‘me’ who is feeling, Chris? Who is this ‘me’ who is no longer bothered?’ But this I will reject as mere semantic gymnastics, arguing about words rather than things.)

So I reject Schopenhauer’s fundamental division of the world into Mind and Matter. Solipsism is not rendered less vacuous and fruitless if Will, some fundamental thing underlying all consciousness, replaces my individual consciousness.

I went back some months later and had another go at ‘The World as Will and Appearance’. This time, I tried to do things properly and started with the preface. It reminded my strongly of the pretentious author’s note quoted in ‘Ghastly Beyond Belief’”:

Author's note: It is suggested that the reader not attempt to read this book at one sitting. The intellectual content of these stories, taken without break, may cause brain damage. This note is intended most sincerely, and not as hyperbole.

ARTHUR BYRON COVER, The Platypus of Doom and Other Nihilists

Really. Schopenhauer says that the entire book of ‘The World as Will and Appearance’ was the shortest way he could find to write what he wanted to say, that it was impossible to summarise, and that I would have to read the whole thing to grasp his idea. Now, I am not of the opinion that every idea can be squeezed into a thirty-second soundbite, but this seems to me just a teensy bit ridiculous. All the really big ideas that really are ideas can be squeezed down into something small enough for us to get our heads around. This does not mean that there are not lifetimes of work in unpacking everything that is involved with and implied by

‘It is impossible to convert heat completely into work in a cyclic process.’

Or

‘Do unto others as you would have them do unto you’

Or

‘The square on the hypotenuse is equal to the sum of the squares on the other two sides’

…but all these really big ideas can be expressed in a few little words. Claiming that your idea is bigger than all these ideas is up there on the angora shawl of pretentiousness with Mr Cover and his Platypus of Doom.

The other thing Schopenhauer told me in the preface was that ‘The World as Will and Appearance’ was intended as an extended gloss on his earlier essay, ‘On the Fourfold Root of the Principle of Sufficient Reason’, and should be read in conjunction with it, and that it was useless- Useless, I tell you! – to read his magnum opus without having first read ‘On the Fourfold Root of the Principle of Sufficient Reason’. I dutifully went back to the library to find it. But it was not there.

Right next to the works of Schopenhauer that were on the shelf was a slim book by Schrödinger, ‘My View of the World’. I took it home as a consolation prize.

Curiously, I found that it was not only next to Schopenhauer in alphabetical space, but in idea space. It contained what appeared to me to be practically the same Vedic philosophy of the primacy of mind.

He says, in a fine and honest way in his opening remarks, that there is very little about physics in his book, and that is because he came to his ideas about the nature of reality before he ever got into quantum mechanics: he was already marinated in the same ancient Hindu ideas that Schopenhauer had discovered and embraced so enthusiastically. I have taken the book back to the library already, so I can’t quote you the quote I wanted to quote you,*** but Wikipedia tells me: ‘At an early age, Schrödinger was strongly influenced by Schopenhauer. As a result of his extensive reading of Schopenhauer's works, he became deeply interested throughout his life in color theory, philosophy, perception, and eastern religion, especially Vedanta.’

Schrödinger did not ‘discover’ all the New Agey hippy-dippiness in Quantum Mechanics; he brought it with him. It was part of his worldview while he was figuring things out about the world of appearances, and he fit them in where they fit in his personal philosophy - and there we have one root of the muddle we are in now.

So I still have not read Schopenhauer’s Magnum Opus. Which is sad, since as Schrödinger says in a possibly apocryphal quote I found on the web just now: ‘If you cannot - in the long run - tell everyone what you have been doing, your doing has been worthless.’ I have not given up. But I have gathered enough, I think, to sum up my disagreement with Schopenhauer in a table contrasting him with the most useful and clear-headed philosopher since Aristotle and my personal favourite, 'the one American philosopher that could sing outdoors', Charles Sanders Peirce**:

*: This is my ad hoc replacement for the ‘chain’ or ‘ladder’ of being, which is what I really want to say, but which I am too conditioned by my reading of Stephen Jay Gould to dream of saying.

**: I have doctored this Hilaire Belloc poem to show you how to pronounce his name, in case you don't know:

***: Actually, I didn't take it back to the library, I lost it on my own bookshelves! Here is the quote: Not a word here is said of acausality, wave mechanics, indeterminacy relations, complementarity, an expanding universe, continuous creation, etc. ... On this I can cheerfully justify myself: because I do not think that these things have as much connection as is currently supposed with a philosophical view of the world. ... In 1918, when I was thirty-one, I had good reason to expect a chair of theoretical physics at Czernowitz ... I was prepared to do a good job lecturing on theoretical physics ... but for the rest, to devote myself to philosophy, being deeply imbued at the time with the writings of Spinoza, Schopenhauer, Mach, Richard Semon and Richard Avenarius.

Once more with the splendour of the historical sciences!

2009-11-05T19:02:00.000-08:00

Last week or the week before I went to the niftiest seminar I have been to for a long time. It was by Prof Ian Metcalfe, who is a master of conodont lore- conodonts being the premier biostratigraphic animal. If you know enough about conodonts, and you are lucky enough to find enough conodonts, you can tell when a stratum of rock was laid down and what biogeographic province it belonged to, over a vast range of space and time. And the degree of detail that is possible with these little guys was enough for Prof Metcalfe to deconvolute the whole extraordinarily complex geological history of Southeast Asia, which is basically a matter of bits breaking of of Gondwanaland and different times and sailing away north and mashing into the ancient subcontinents of Siberia and Kazakhstan.

I remember one thing that struck me forcefully, long ago, in the writings of Stephen Jay Gould, was all the ancient oceans that we would never know anything about, because they were subducted away completely- all those primordial analogues of the Hawaiian islands, with their unique fauna and flora, irrevocably lost.

But not always! That was the most impressive bit of Prof Metcalfe's talk for me. I have pinched one of his figures so I can show you, as like me you are probably too lazy to follow the link.

In between the dark orange Sibumasu block that used to be part of the Cimmerian Continent and the pink bit that is the mashed remains of the ancient archipelago of Cathaysialand, there runs an ancient biogeographic divide: at the same time in prehistory, the fauna on one side was quite different from the fauna on the other side. And mashed up in between those two blocks are sediments that are the remains of the Palaeo-Tethys ocean. Not all subducted away! Some of it is still there, enough of the ocean for us to tell a lot about its history and the sort of things that lived there, in a kind of Reader's Digest condensed version squashed into a discontinuous squiggle across central Thailand. I think that is so cool...

Could be a coincidence...

2009-11-01T13:36:00.000-08:00

There are, after all, only about 200 gazillion Facebook users, and the name might be as common in Chennai as 'Kylie Smith'. But I have deactivated my Facebook account (not in my real name, 'Wayne' and 'Nick'! :p ) anyway. Since otherwise to make that 'friend suggestion' Facebook would have had to have found out who I really am from my email address, then collected earlier email addresses belonging to me, and looked up users whose names appeared in lists with those earlier email addresses. Probably a long bow to draw. Such omnipotent data-trawling AI's probably have less frivolous things to do. More likely a coincidence. Freaky anyway.

My brother is participating in Movember, I am sure he would be pleased if you clicked the link and made a donation. I am too far gone, as you probably know, and am now only eligible for 'Look-like-the-unabomber-ovember'...

Think. Quantitatively.

2009-10-06T01:50:00.000-07:00

Every year I tell my students something like: ‘When you finish any calculation in physical chemistry, have a look at the number you have ended up with and see if it is a reasonable number. Is it about the size you would expect? If it isn’t, go back and find the mistake. If you are in an exam and pressed for time, write: ‘I know this number is the wrong size, but I can’t find where I went wrong.’ Or, just change the order of magnitude to the order of magnitude it ought to be, and hope I don’t read your working carefully.’

Every year, I get more cautionary tales to tell my students when I tell them this- assignments I have received with chemical bonds blithely reported as longer than the distance from here to Alpha Centauri, molecules heavier than the Sun, energies for chemical reactions greater than the annual output of all the power plants in Europe.

The chapter ‘The Spur of the Moment’ of Kim Stanley Robinson's book 'Green Mars' is about a project to build a sea in Hellas Planitia in the southern hemisphere of Mars, a sea that is quoted as being ‘1000 by 300 km’. It order to give the project verisimilitude, numbers for amounts of water are quoted throughout the chapter.

p.400:

It was a running river, in an obviously riverine valley, placid in some places, agitated in others, with gravel fords, sandbars, braided sections, crumbling lemniscate islands, there a big deep lazy oxbow, frequent rapids, and far upstream, a couple of small falls. Under the tallest waterfall they could see the pink foam turn almost white, and patches of white were then carried downstream, to catch on boulders and snags sticking out from the bank.

‘Dao River,’ Diana said. ‘Also called the Ruby River by the people who live there.’

‘How many are there?’

‘A few thousand. … Upstream there are family homesteads and the like. And of course then the aquifer station at the head of the canyon, where a few hundred of them work.’

‘It’s one of the biggest aquifers?’

‘Yes. About three million cubic metres of water. So we’re pumping it out at a flow rate- well, you see it there. About a hundred thousand cubic metres a year.’

10⁵ m³ per year = 274 m³ per day = 3 litres per second

To put this number in perspective:
“Older firehoses with 2.5 inch diameter equipped with a 1.5 inch nozzle can typically deliver 20-40 litres of water per second” (Physics of Continuous Matter: Exotic and Everyday Phenomena in the Macroscopic World, Benny Lautrup)

I suppose the description of the river *could* apply to something that one could easily step over, but I do not think this was the author’s intention.

p.416

One day at the office, news came in from the Hellespontus. They had discovered a new aquifer, very deep compared to the others, very far away from the basin, and very big. Diana speculated that earlier glacial ages had run west off the Hellespontus range, and come to rest out there, underground- some twelve million cubic meters, more than any other aquifer, raising the amount of located water from 80 % to 120% of the amount needed to fill the basin to the -1-kilometer contour.

Let’s see, the Hellas Planitia basin is quoted as being 1000 by 300 km. That’s an area of 10⁶ m × 3 × 10⁵ m, or 300 billion square metres.

Twelve million cubic metres would cover 300 billion square metres to a depth of

1.2 × 10⁷ m³ / 3 × 10¹¹ m²

= 4 × 10^-5 m.

40 microns.

So if this raises the amount of located water from 80 % to 120 %, at a first approximation the Hellas Sea will be 0.12 mm deep.

I confess myself unimpressed by this feat of areological engineering.

I expect KSR made the common undergraduate mistake of assuming
1000 cubic metres = 1 cubic kilometre. I wonder if the numbers have been corrected in later printings?

Green Mars, p.346

2009-09-30T03:59:00.000-07:00

My favourite bit so far has been the chapter 'The Scientist as Hero'. Unfortunately, from time to time poor Sax is set up as a bit of reductionist straw man. Take this exchange, from the beginning of the chapter 'Social Engineering', where Saxifrage Russell is talking to a hippy-dippy psychologist type:

There is a drive towards complexification that is directly opposed to the physical law of entropy. Why should that be?

I don’t know.

Why do you dislike it so when you can’t say why?

I don’t know.

This mystery of life is a holy thing. It is our freedom. We have shot out of physical reality, we exist in a kind of godlike freedom, and the mystery is integral to it.

No. We are still physical reality. Atoms in their rounds. Determined on most scales, random on some others.

Ah well. We disagree. But either way, the scientist’s job is to explore everything. No matter the difficulties! To stay open, to accept ambiguity…

I've written some new lines for Sax. I reckon it should go like this:

There is a drive towards complexification that is directly opposed to the physical law of entropy. Why should that be?

There isn’t a drive towards complexification. There’s a drive towards differentiation, a drive which is basically the same as the physical law of entropy. You have just selected your data to focus on the end of the bell curve where complex things are happening, ignoring the fact that the curve is getting bigger and broader all the time.

Well, you’re entitled to your opinion. But I think your view saps all the mystery out of the universe. This mystery of life is a holy thing. It is our freedom. We have shot out of physical reality, we exist in a kind of godlike freedom, and the mystery is integral to it.

Why are you so eager to call everything you don’t understand ‘a mystery’?

Its not that I’m eager, it’s just that I feel there’s more to life than can be explained by physical science.

Why don’t you stop feeling, and try thinking, instead? What if the mystery is just an artifact of your imperfect understanding? What if the mystery, and the ‘godlike freedom’ just exist in your head? And what exactly do you mean by ‘shot out of physical reality’? You should define your terms.

Ah, my friend, don’t be mean! We disagree. But either way, the scientist’s job is to explore everything…

Green Mars, pp.135, 177, 251-253

2009-09-29T19:47:00.000-07:00

One problem with schemes for the terraforming of Mars is the need for a source of an inert gas to give an atmosphere of similar composition to Earth. A higher partial pressure of oxygen than we have here would ‘vigorously accelerate combustion’, tend to intoxicate us, and make technological civilisation impossible, while a much lower total atmospheric pressure would not be able to support Earth-like weather. The partial pressure of oxygen required to support combustion declines with declining total pressure, so even this lower total atmospheric pressure option might be dangerously combustible if it had enough oxygen present to support life. So, where is this inert gas to come from?

Getting nitrogen from Titan won’t stand up to any sort of cost-benefit analysis.

There are unlikely to be enough noble gases trapped deep underground from radioactive decay to amount to a hill of beans.

Thus, it has been suggested that molecular nitrogen could be obtained by ‘burning nitrates’, which seem to be present (or may be present) in considerable amounts in the Martian crust.

However, simply heating nitrates will not be very effective as a way to ‘dilute’ oxygen. For instance:

2Na(NO₃)₂ + heat → 2NaNO₂ + O₂

2NaNO₂+ moreheat → Na₂O + NO + NO₂

2Ca(NO₃)₂ + heat → 2CaO + O₂+ 4NO₂

Thus ‘burning’ nitrates generates lots of toxic gas, and some extra oxygen.

Of course, with more energy input:

2NO₂ + much more heat → N₂ + 2O₂

So we have got some nitrogen eventually, but at a cost of 2.5 oxygen molecules per nitrogen molecule.

If we don’t want to add lots of extra oxygen to the atmosphere, we will have to add a reducing agent instead, and do something more like ‘burning’ . On Earth, if we had lots of extra nitrogen dioxide we wanted to get rid of, we would do something like:

NO₂ + 2H₂ → N₂ + 2H₂O

NO₂ + C → N₂ + CO₂

Or more realistically, something like

4NO₂ + C₃H₈ → 3CO₂ + 4H₂O + 2N₂

The problem is that there is not a lot of carbon or hydrogen on Mars that is not already incorporated in carbon dioxide or water. I haven’t googled to find out how much hydrogen has been located/postulated on Mars, but a crude atom balance suggests that if we want to burn nitrates with enough hydrogen to generate one nitrogen atmosphere, we need to burn at least two whole hydrogen atmospheres. I don’t think this is available, it would surely have outgassed long ago. I have found references to methane clathrates on Mars, which may be there in similar amounts to the nitrates (perhaps) and would allow the reaction

2NO₂ + CH₄ → CO₂ + 2H₂O + N₂

The problem here is that it would be a very significant bit of geo-engineering to mine the methane and get it to the nitrates, or vice versa, and we are adding to the carbon dioxide load that we need to get rid of later.

So what other reducing agents are available? I suggest that much more cost-effective than bringing nitrogen from Titan would be to bring down some Iron-Nickel asteroids and rust them in nitrogen dioxide. The mass that would be transported would be much larger, but the distance would be much shorter, and there would be no need to do any complicated collection and packaging and transport, just provide the right nudge of energy to send the asteroid on a collision course with Mars.

The following reaction is certainly thermodynamically favourable, though I don’t have an idea of what its activation energy might be:

6NO₂ + 8Fe → 3N₂ + 4Fe₂O₃

While this uses considerably more mass of reductant to produce the same amount of nitrogen than methane would, instead of having to be painstakingly mined and collected like the methane, the asteroids could be crashed down into the nitrate deposits in one foul swoop. The reaction does not produce any extra carbon dioxide that will need to be scrubbed out later.

Some Knols

2009-09-09T18:11:00.000-07:00

I thought I should put a link to Marco Parigi's knol on reading Richard Dawkins 'The God Delusion', and my knol on reading Stuart Kauffman's 'The Origins of Order: Self-Organisation and Selection in Evolution', as a prod to get myself to finish the latter!

Dark Matter?

2009-03-02T22:09:00.000-08:00

Every time I read back over my list of publications, I am struck by how most of the good ones seem to have sunk without a trace. Most of the ones where I thought I had discovered something interesting and novel about the universe, or had hit upon an interesting and novel way of looking at something we already knew about, have very few citations, or none at all. Perhaps I should do a series of posts on my top five papers with no non-author citations? Hmm, I have been neglecting this blog lately, and a theme like that might help.

Anyway, a few years ago a colleague gave me a weighty chapter he had written, entitled A Quantum Approach to Dark Matter, which I was slack (It is 63 pages long) and never got around to reading (It *is* 63 pages long). Remembering it today, I thought I would first check to see what other people thought of it- I am a mere chemist, and can only identify very dubious theoretical physics as dubious at a glance. I found my colleague had four published articles in the area over the past half-decade, and none of them had been cited at all. This is a tragedy. It is dreadful to spend years wrestling with an idea, to hone and shape it into a form you think is fit to present to the world, expound it with all the energy and clarity at your command, shepherd it into print, and then see it be ignored completely. Hence, I thought I would put a link to the chapter here. And I really will read it myself, I promise. And put an ignorant chemist's critique here on the web, at the very least, so Google can find it.

2009-01-20T21:34:00.000-08:00

Some time ago I was asking the question: ‘How good are these climate models? What sort of predictive value have they shown in modelling future climate? After all, we’ve been doing them for a few decades now.’

A nice person on realclimate.org (there are some, not all of them treat people who disagree with them as the demonised other) directed me to a classic paper by Hansen et al.

"If you want an indication of how well these models do you can go get (J. Geo Res. 93 (1988) 9341) the Hansen GCM paper that people talk about, and compare their results with observed patterns of warming and other things."

Here is the plot from that paper showing the response of overall global temperature (which the authors argue convincingly is a much better parameter than any subset of the data, e.g., whether it snowed at my house or not in a given year) for three different scenarios- A being continued exponential growth, B being a more subdued form of business as usual, and C if drastic cuts are implemented starting a few years ago.

I went and got the Hadcrut3 data set and plotted it on top of this one, as near as I was able, and got this.

There are other data sets out there. I shall plot some of the others and put them up for you.

The Hansen et al. model predicts the greatest degree of warming at high latitudes, fitting observations, but the model also reproduces another feature of observed weather, that those latitudes have the highest natural variability from one year to another.

In which I place myself beyond the pale of civilised discourse

2008-11-03T21:15:00.000-08:00

Firstly, an observation on scientific models, coagulated in the enthralling world of emulsion polymerisation:

Whenever you are trying to model some complex phenomenon, the fit of the model to the data can be improved by adding more adjustable parameters. A complex phenomenon will usually be dependent on a large number of factors, but the fact that the model fits the data better when you incorporate an additional factor may or may not mean that new factor is important: it might just mean that the additional parameter(s) you have incorporated are improving your fit. This is another thing the David Sangster told me: ‘With enough adjustable parameters, you can fit a camel.’

So there is a tension between the complete model, which contains all the factors that ought to be physically important – but might be meaningless because of all the guesstimated parameters you have put in to quantify these factors- and the simple model, which ignores things that might be physically important, but also avoids adjustable parameters. If you go too far in one direction, you get a model that can fit any possible data; too far the other, you get the well-known ‘assume a spherical horse’ punchline.

This also means that when you are modelling a complex phenomenon, you will tend to base your model on the processes that are best known, where you don’t have to pick numbers out of the air for your adjustable parameters, and you will ignore if you possibly can the role played by processes that are less understood, which would force you to bring in rubbery parameters.

Now to place myself beyond the pale. Some time ago I made the assertion:

‘Anthropogenic global warming is a fact, but we shouldn’t do anything about it.’

The second part of this statement is a considered opinion, based on facts and reasoned deductions from them. The first part of this statement, I have realised over the last few months, is based on an irrational mood.

That is: in the laboratory, and considering the atmospheres of the planets in toto, there is a perfectly splendid mechanism by which increasing the concentration of atmospheric carbon dioxide should increase temperatures. It is a really good mechanism, based on rock-solid physics. But is there any evidence that this mechanism is responsible for observed temperature change globally? Evidence, in the scientific sense, is where a model has predictive value: it does not just fit the data we have, but tells us what future data is going to look like. I did not examine this question before I made the statement above. Instead, I relied on the irrational mood that it seemed like wishful thinking that there was some sort of feedback mechanism providentially cancelling out this Greenhouse warming effect.

Let us consider these two famous graphs:

What do they tell us? They show us a correlation between carbon dioxide concentration and average global temperature. They also tells us, very clearly, that there are factors other than carbon dioxide which contribute to the world’s temperature.

We could also draw graphs that show some sort of a correlation between sunspot activity and global temperature, and earthshine and global temperature, and the number of pirates and global temperature. The last of these three graphs would be a joke circulated by the Church of the Flying Spaghetti Monster. The other two are graphs where it is easy to construct a testable mechanism for how the correlation might work. These mechanisms are not as solid or as well understood as the Greenhouse mechanism. They rely on more rubbery adjustable parameters. If we ignore them, do we have a spherical horse? If we include them, do we have a camel?

What is signal, and what is noise, in the Hadcrut3 temperature curve?

An idea that was in fashion when I was an undergraduate was the Gaia hypothesis of James Lovelock. You don’t hear much about it nowadays. You might remember that it was all about negative feedbacks keeping the global ecosystem in balance, life keeping things tickety-boo for life. I bring it up here as a hand-waving justification for a recent shift in my irrational mood: given that there is a grain of truth in Lovelock’s ideas, it now seems to me reasonably likely that there would be a negative feedback mechanism tending to minimise the effects of any carbon dioxide we add to the air.

I must now revise my assertion:

‘Anthropogenic global warming is a conjecture with limited predictive value, and we shouldn’t do anything about it.’

And I have to apologise for some of the slighting references to global warming denialists I have made previously.

And unfortunately I have nerfed one of the major motivations for establishing this blog, which was to use any perceived authority associated with my real name to push the line that we shouldn’t take any action to stop anthropogenic global warming. By denying AGW to be a fact, I have placed myself outside the pale of civilised discourse and disqualified myself from making any statements on the issue that will be taken seriously.

Son cosas de la vida…

14% more First Year students agree balancing redox equations is fun!

2008-09-30T20:33:00.000-07:00

In a striking improvement over last year's already high student enthusiasm for balancing redox equations, the proportion of students agreeing that balancing redox equations is fun has risen to 83%!

Googling Professor Ronald Laura? Part Five.

2008-09-04T03:11:00.000-07:00

“It is foolish, generally speaking, for a philosopher to set fire to another philosopher in Smithfield Market because they do not agree in their theory of the universe. That was done very frequently in the last decadence of the Middle Ages, and it failed altogether in its object. But there is one thing that is infinitely more absurd and unpractical than burning a man for his philosophy. This is the habit of saying that his philosophy does not matter, and this is done universally in the twentieth century, in the decadence of the great revolutionary period.”
- G. K. Chesterton

Here is part of an email I received last Friday which contains the gist of my correspondent's remarks:

I am requesting that you remove the abstract on nurturing gifted students from your blog, also remove any reference to Professor Laura (including his name) and I'd like that done as soon as possible please, today if feasible. I do not want to take further action but I will if the comments are still there next week. I feel I have to do this before any more damage is done to others that don't deserve it.

Here is another bit:

Considering you did not stay for the whole of Prof Laura's presentation, and that those who have posted on your blog have not even attended
any of or only one of his talks how can you justify comments like 'I have met the enemy!' That's disgusting! considering all the amazing
work that Professor Laura has done for others. How can you defame someone like that?

I think it is rather more disgusting that I could have googled Ronald Laura and not immediately found any criticism of his ideas or the way he presents them. If you have ideas that you believe are worthwhile, and you are at all interested in truth- as I am- then you hunger and thirst for criticism, for it is in responding to criticism that your ideas are tested and improved. If you are interested in convincing other people of the truth of your ideas- as I am- then you also welcome criticism of the way you present them, because this enables you to present them better. Even if you are not interested in truth, but only want to be transgressive in an adolescent way- as I hope I am not- then you have a positive need for reactionaries to jump up and down criticizing you. Otherwise, what would be the point?

I do not need to send my criticism explicitly to Ronald Laura, because I know he will find it. The beauty of the web is that all this criticism can take place in a completely public forum, and anyone can join in. Anyone who can find value in our competing visions of truth can derive value from it. Anything stupid I say is open to the world, as anything stupid he says is open to the world.

Users of the Web are perfectly capable of taking on board conflicting opinions and making up their own mind. If I told people to look up something Noam Chomsky wrote, they would find plenty of material on the Web written by other people who bitterly disagree with Noam Chomsky. If I told them something by Cardinal Pell could be useful to them, they would find plenty of harsh words directed against Cardinal Pell and his ideas. If I directed them to the work of Richard Dawkins, they would find no end of web-pages saying he was talking rubbish. If I asked them to google ‘string theory’ they would immediately find people claiming it is fraudulent drivel. If I asked them to google ‘global warming’ they would find pages claiming it is a vast left-wing conspiracy to abolish property rights, and pages claiming anyone opposing extreme measures to combat it must be a knuckle-dragging shill of Big Oil.

What is so uniquely fragile about Ron Laura that he should be shielded from all this? If he does not want to be part of this world, he should not post stupid things on the Web. My friend Klaus Rohde asserts on his blog that it is ‘common sense’ that John Howard should be put on trial for war crimes. This is vastly more insulting than anything I have written about Ron Laura, yet Klaus is yet to tell me of any good friends of Mr Howard writing him to demand he not 'defame' our former Prime Minister.

I do not intend to take down any of these posts. That said, should any readers with a legal background have the opinion that anything said could be likely to be construed as defamation, please let me know, as I have no wish to be sued by a rich and powerful Professor!

Update: I found a version of Ronald Laura's analogy about the Garden of Eden on the ABC website. It is not entirely clear whether he really thinks clothes are a bad idea, but that would explain his concern with developing washboard abs:

If there is a single defining characteristic of the modern age, then as I see it, it's probably the mindless commitment we have to technology as the panacea for virtually all our ills. In fact we have committed ourselves and been so bedazzled by technology if you like, that we have essentially theologised technology. We've turned it into a way of, I suppose, taking on the pretence of playing God ourselves. In the Garden of Eden story the serpent tempts Eve to eat of the Tree of Knowledge. She then in turn tempts Adam to eat of the Tree of Knowledge. When he does, they suddenly become shamed and conscious of what seems surprising in itself, their nakedness.

Now within that context, occurs the first act of technology if you like, namely the sewing of the figleaf. They sew the figleaf and turn to technology to do that, as a way of covering their external nakedness. I want to suggest that the problem at the outset was never their external nakedness, it was their internal nakedness. Their shame in respect of alienation from God, their disobedience, their failure to live by way of honouring the beauty of the garden, the gift of the garden, the gift of their life in relation to God.

So in essence what I'm saying is that by virtue of sewing the figleaf, and covering their external nakedness, what they actually really do is turn away from the deeper problem, and what it does is to apply or appeal to technology as a way of avoiding having to confront the wages of their actual sin. The sin of disobedience, the sin of alienation, the sin of not living as God would have them live in the garden.

So for me the story is very powerful as I've recast it as a way of saying that first of all the Garden of Eden story, in this sense, needn't be construed as a past and defined event which occurred long ago in time. I see it as a dynamic event, unfolding constantly in history in the way it reproduces itself through our interactions with nature and each other. We're constantly as a race, a group, humankind, presented in beautiful garden scenarios which unfortunately we continuously despoil.

In fairness I also read the hardcopy text of this article, from 1986, which is actually quite reasonable. His theology of transcendence is not particularly new- I'm sure I've read C. S. Lewis saying essentially the same thing, and before him, St. Augustine (So possibly it goes back to Plato- what did they teach me in those schools?)- but it appears that once upon a time Prof Laura was doing intellectual work of some value, before he went off the rails into a technology-is-evil obsession.

A little note about chain transfer to butyl methacrylate

2008-07-31T21:28:00.000-07:00

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.

2008-07-28T23:05:00.000-07:00

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.

2008-07-17T20:39:00.000-07:00

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 K₂values 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

2008-07-15T21:41:00.000-07:00

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

2008-07-08T23:01:00.000-07:00

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...

Googling Professor Ronald Laura? Part Four

2008-06-26T16:06:00.000-07:00

Another extended comment has arrived on my first post on Professor Laura:

Quoth Anonymous:

Do the words "baffle with bulls#*t" ring much truer when talking about Ron Laura.

I have a Masters degree in Exercise Science and have worked all over the globe in professional sport and also competed at a very high level in a strength and power sport and feel that regarding Professor Laura's words on Health and Fitness are just that, words. Professor Laura is somewhat of a running joke in academic circles regarding his philosophies on health and fitness.

Many peer reviewed experts in this field shake their heads in disbelief when hearing of the advice professor Laura gives. I will give him one bit of credit, that is, he is a marketing genius.

No one i have come into contact with in the powerlifting, bodybuilding or the strength community has even heard of Professor Laura, areas in which he claims to have excelled in. Also if Professor Laura is such an expert in this field then why hasn't he published proven research to his claims in peer reviewed journals or spoken at conference's whereby experts in their respective fields gather to exchange ideas and debate current issues? No not Professor Laura he only preaches to the general population whereby he can get away with extravagant words and stories.

Last of all I graduated from the education faculty at the University of Newcastle and can assure you that in the four years I attended Professor Laura did not lecture in the PDHPE or secondary education department the only area I know of that he was involved in was the final year teacher research project whereby he was quite popular amongst the students as he was known to never fail anyone and always give high grades.

People like Professor Laura really upset me because I worked very hard in sport and study to get where I am today and it saddens me that there are some people out there that use technical jargon and marketing brilliance to fool the general population into forfeiting lots of money on schemes and gimmicks.

So Chris don't worry there are many, many people some in very prestigious positions in education and health that feel exactly the same as you.

Two Cultures are Better than One

2008-06-24T16:35:00.000-07:00

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.

Googling Professor Ronald Laura? Part Three

2008-06-23T23:19:00.000-07:00

I just thought I would take a comment that appeared recently on my first post on Professor Laura and put it up here in a post of its own, with my response.

Quoth Anonymous:

Hi Chris,

I have seen Ron Laura speak too (in January this year) and I completely understand your perspective given your experience.

However, I stayed through until the end and was left with a different response. I thought it was the most inspiring piece of speech making I have ever heard.

I was not alone.

Another woman like me sat silently afterwards in awe of his level of insight. Her comment; 'it is rare to have the good fortune of being in the presence of someone with such a deep level of understanding'.

I can understood your feelings about the lack of dialogue (and no doubt he would too). However, I felt he connected with us in a different and much deeper way with his speech.

And when I spoke to him afterwards I found him very open to dialogue and totally lacking in arrogance. I don't think he could have transferred his insights with the same degree of effectiveness with dialogue.

What I found most impressive about Ron was that he supported spritual insight with intellectual rigour. It is all too common for spiritual insights to be destroyed by intellectual rigour ...or for them to be conveyed without intellectual rigour.

As for the suit...I understand that you may have related that to the rich and expoitative. I interpreted it as a sign of respect for us as his audience (and for himself).I felt honoured by it and prefer it to the "i don't think you are worth getting out of my jeans' attitude'.Not dressing formally can be a sign of arrogance too. I'll meet you half way on that point...perhaps smart neat casual would have sufficed.I would prefer to see him look more comfortable himself.

All in all Chris I understand your viewpoint given your limited experience of Ron and your frustrated desire to receive support for your child. I really do.

However, I think your blog could do a good man alot of harm. And by the sound of it you don't seem to be the kind of person who would be consciously malicious. Those of us who are creative or gifted ...or who have gifted or creative children or children who need their creative expression supported ...truly need people like Ron in positions of power and influence. With further listening I think you might find that he is actually batting for the same team as you.

I would recommend giving Ron and his work a second chance (or at least let him be).

Good luck with getting the support that you need for your child.

Mary

To which I replied:

Thanks for your message, Mary! I’m glad you put in the effort to write to me. I don’t know if you will ever come back here to read this, but here goes.

Did you read my other post where I unpack a bit more just what I thought was wrong with what Ron Laura said and how he said it?

Given that the content of the talks we attended may well have been different, I also felt how inspiring he was. This is what scared me. A lacklustre speaker with dangerous ideas is nothing to be afraid of. Someone who can get people nodding happily in response to ideas that have been proven to be extremely harmful (e.g., the ‘culturally appropriate’ Aboriginal education I referred to) is a real danger.

I’m not saying that he should stop saying what he believes, still less that anyone should try and stop him from saying it. I did a search and couldn’t find any mention of his name in the context of ‘the Emperor has no clothes’. If I had, I probably wouldn’t have written anything. But I didn’t find anything, so I felt it was up to me to provide a smidge of balance.

I don’t think my little blog can do him any harm whatsoever. When our ideas are challenged, we are either driven to improve how we explain them, or we abandon them in favour of better ones.
Again, the talks may have been very different, but I did not detect a great deal of intellectual rigour in the talk I attended. He only tore down what other people had built, he did not give any coherent picture of what he would replace it with. I couldn’t find a logical exposition of his worldview on his website, either, nor in his book ‘The Perils of Progress’. This is another thing that worried me.

If someone want to throw away the one means of knowledge at our disposal, I want to know what they intend to use instead. If they say: ‘I believe in the infallible Qur’an’, fine. If they say: ‘Here, I am following Marx,’ fine. If they say: ‘My philosophy is based on these seven core axioms revealed to me by the Squid God,’ sure, why not. But leaving your own position cloaked in fog puts the other person at an unfair disadvantage.

Things I don’t understand: The ‘Collapse’ of the Wavefunction

2008-06-22T20:14:00.000-07:00

(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

2008-06-18T21:14:00.001-07:00

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

2008-06-09T22:36:00.000-07:00

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

2008-06-05T23:16:00.000-07:00

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

2008-06-05T20:06:00.000-07:00

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.

Googling Professor Ronald Laura? Part Two

2008-05-05T22:40:00.000-07:00

You may ask yourself, why am I so upset.

1. What Ronald Laura says is wrong and dangerous.

From the website of RPL I extract this core of his philosophy of science- wrong, and stupid, and dangerous. (http://www.dr-ronlaura.com/philos.html)

“My view is thus diametrically opposed to the orthodox philosophical view of knowledge and technology which holds that neither knowledge nor technology is 'good' nor 'bad' in itself; it is only how they are used, so the argument goes, that makes them good or bad.

Against this, I am urging that because the conventional and covert rationale which drives technology is to manifest power over nature, its deployment will inevitably lead on the on hand to the degradation and exploitation of nature, while on the other to our alienation and increasing detachment from the world of nature and the earth which sustains all life.

One of the major reasons why our form of technological instruction in schools is so obsessed with reducing the things of the natural world into reconstructed forms or manufactured things is that the more chemicalised, decomposed and inert we can make the world, the easier it is for us to predict its behaviour and thus secure a modicum of power over it. Indeed, at first blush it does seem that we have succeeded in making the world predictable and thus more amenable to subjudgation by reducing and then redescribing the natural world in terms of the statistical and mathematical representations intended as a substitute for it.

Once the reduction is complete, we make this abstraction of the natural world more concretely predictable by reconfiguring our statistics in graphs, grids, and tables replete with abbreviations, acronyms, and even pseudonyms designed to give the illusion of life to our reconstructions of nature, whose technologised forms are actually increasingly synthetic, artificial, inert and unreal.”

Of course we all want to be able to predict and control our environment. If we cannot do this, we are unable to act at all. We become passive victims. All ‘knowledge’ is useless if it does not enable us to somehow predict and control what is going on around us.

Science is distinguished in being the radical democratic form of knowledge. It is the form of knowledge open to everyone. There is no gnosis, no hidden way to truth only known to the alpha males or alpha females of the tribe. Anyone can do it.

Like Feynman said:

How to Discover a New Physical Law

First you guess.

Don't laugh, this is the most important step.

Then you compute the consequences.

Compare the consequences to experience.

If it disagrees with experience, the guess is wrong.

In that simple statement is the key to science.

It doesn't matter how beautiful your guess is or how smart you are or what your name is.

If it disagrees with experience, it's wrong.

That's all there is to it.

What does Ronald Laura posit in opposition to this egalitarian method of seeking truth? He does not offer the valid mystical insight that the ultimate nature of reality is unknown and unknowable. He is not content to bow humbly before the vastness and wonder of-all-that-is, conscious of how inadequate his mind is to grasp it all.

No, he offers the only alternative that has ever been offered to science. And he offers it with all the dogmatism and all the irrationalism with which it has usually been offered. The alternative to science is submission to authority. Believing what someone else tells you. In this case, what he tells you. That's why he has all those testimonials to the effectiveness of his body-building system on his website.

2. Where Ronald Laura said what he said on Saturday May 3rd 2008 was an abuse of his position.

We came to hear him give a talk cogent to the abstract I have quoted below. I have been informed that he did get around to talking about it eventually. But first, he spent a long time outlining his stupid wrong and dangerous philosophy, with all the rhetorical eloquence and all the alpha-male authority-figure symbols at his command. That is not what was advertised.

On Friday May 2nd 2008 I gave a talk about the Greenhouse Effect and Anthropogenic Global Warming to a group of foreign students finishing their English studies before beginning their degree programs (volunteers are called for to lecture every year so the students can practice their note-taking in practice lecture situations).

As you know if you have ever been to this site before, I have very strong and idiosyncratic views about what should be done about Anthropogenic Global Warming. The students I spoke to still have no idea whatsoever what those views are. I told the coordinator I was going to talk about the science, and that's what I did. I talked about the same settled science and gave the same talk outlining the very solid theoretical basis and the reasonably solid experimental basis for Anthropogenic Global Warming that someone with diametrically opposite views to mine would have given.

I would consider it an abuse of my position as a perceived authority figure to get up and foist my individual philosophical or political views on an audience who are listening to me because of my expertise in another field. That would be unprofessional behaviour.

Googling Professor Ronald Laura?

2008-05-03T19:01:00.000-07:00

I have met the enemy.

And he is this man.

I attended 2/3 of a talk he gave yesterday. While garnished with the usual eduspeak, the abstract of his talk had sounded pretty good:

As the parent of gifted children out in the boondocks, feeling these effects of personal and emotional isolation, I was hoping to gain some useful insights from the Professor’s talk. And I agree completely that there are limitations to what technology can do in education, that a lot of the ‘gee-whiz’ education material on the internet is a waste of time, and that technological resources need to be balanced with more ‘personal and interrelational’ ways to – er – ‘support the development of children’s socioaffective natural potential into performance.’ I also think that over-reliance on Powerpoint is doing bad things for teaching and communication in my discipline, so he immediately had me onside by not using it, striding back and forth talking to us conversationally instead. He spoke very well. And he had a beautiful voice. A deep, authoritative, voice, with a mellifluous Bostonian accent.

By 2/3 of the scheduled time through his lecture, he hadn’t yet said anything that was cogent to the abstract.

He had started with some funny anecdotes about when he first arrived in Oxford to do his doctorate.

He had talked about a Mercedes-Benz advertisement announcing that they were putting air-bags in the rear, as well as the front, after an accident involving someone trying to negotiate a motorway exit at 240 km/h in one of their cars, in which the occupants of the air-bag equipped front of the vehicle had lived and the passengers in the back had died. ‘We think we can solve all of our problems with technology,’ he said. ‘There wasn’t any suggestion in the ad that maybe people ought to slow down a bit. Or that we should make cars that don’t go so fast. We immediately resort to technology to shield ourselves from the natural consequences of our actions.’ Well, okay. That was an okay sort of analogy. Maybe making cars a bit slower would be good. If you could sell them.

He talked about the Garden of Eden, and how the first act of Adam and Eve after eating the fruit of the knowledge of Good and Evil had been to invent technology: sewing themselves clothes out of fig leaves.

He told us a pointless story about the nine-times table.

He talked about how in our Western societies knowledge was seen as power which was the same as dominance which was the same as something else which I couldn’t see because that bit of the whiteboard was hidden behind some useless bit of audio-visual equipment.

He said that the technology that came out of this knowledge shared the same original sin, if you will, as the knowledge itself.

On he went- sonorous, sweeping, sincere, non-sequitur after non-sequitur, abusing western science and technology as authoritarian and dehumanising. He didn’t call for dialogue with us, the audience. He wore a suit. Nobody else wore suits. He had degrees from Harvard, Cambridge, and Oxford. We didn't. The authority in his voice repelled dialogue, compelling me to sit meekly in my seat trying to project ‘I know more than you’ through body language.

‘He is sweeping everyone along,’ I told the person next to me. ‘But what he is saying is wrong. And dangerous.’

He said something about how we should not be educating aboriginal children with the same kind of knowledge that we educated our own children with: it was tainted, unnatural knowledge, and it was more appropriate to teach their culturally-appropriate, natural knowledge. There was , unbelievably, what I took to be a gentle murmur of assent from the audience. Earlier that day another speaker had quoted figures saying that 20% of Year 7 aboriginal students in remote parts of New South Wales met the numeracy benchmarks. (These are pitifully easy benchmarks, met by more than 90% of students in metropolitan areas).

I left.

So I don’t know if he got to talking about nurturing the socio-emotional needs of gifted children or not. He might have, and he might even have said something that would be useful to me as a parent. But I didn’t stick around. I couldn’t take it anymore.

And- would you believe, would you believe- googling him this morning, I find that he has written a book with John Ashton!!

This man was Dean of the Faculty of Education at the University of Newcastle. Heaven help us!

Show me the metabolism! Part Three.

2008-04-27T22:41:00.000-07:00

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.

2008-04-27T21:54:00.000-07:00

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.

2008-04-23T21:49:00.000-07:00

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

2008-04-23T05:00:00.000-07:00

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

2008-03-09T15:51:00.001-07:00

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

2008-03-09T14:04:00.000-07:00

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

2008-02-10T18:47:00.000-08:00

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

2008-01-31T21:58:00.000-08:00

...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

2007-12-05T14:11:00.000-08:00

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!

2007-11-05T18:41:00.000-08:00

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

My run of luck ends

2007-11-04T16:39:00.000-08:00

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!

2007-10-30T21:08:00.000-07:00

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!

2007-08-03T02:14:00.000-07:00

Listening to the Sky

2007-07-22T21:17:00.000-07:00

I went to a public lecture by Geraint Lewis last night on cosmic background radiation and the inflationary model of the universe.

Curiously, I have come away with rather more scepticism about the Big Bang model than I had hitherto. I still think that the weight of the evidence is vastly in its favour. Declaring my biases, I still find it vastly more congenial to my worldview. However, I would no longer put it in the ‘that’s settled, then’ basket with continental drift and the evolution of all terrestrial life from a common ancestor.

(1) Briefly, the basic big bang model predicts background radiation in the universe that fits the blackbody radiation curve and is homogeneous with the same intensity in all directions. The steady-state model doesn’t. We have found background radiation which beautifully, definitely, fits the blackbody radiation curve. However, it is not homogeneous. Is it easier to tweak the big bang theory so that the radiation isn’t homogeneous, or the steady-state theory so that the background is thermal? Probably the former. And there are a lot of other problems with the steady state theory. Still, I can’t help wondering- if for purely historical reasons most theorists had stayed in the steady-state paradigm and devoted their lives to tweaking it, and only a few crackpots had kept beavering away at the big-bang model, would we have an elegant steady-state model today that fit all the data perfectly? Maybe we wouldn’t, but maybe we would. I just am not as sure as I was before that the universe is busily beating us over the head with the right answer.

(2) This is not an objection to the theory at all, but it is something I hadn’t known before, and it would certainly be something that would be shouted to the rooftops if a similar situation were to arise today- e.g., if a researcher affiliated with an oil company came up with a theory for climate change that confirmed the expected biases of their employer, even if it fit the data better than the anthropogenic global warming one. The Catholic church is not just perfectly happy with the Big Bang because it is consistent with Catholic ideas: it was a Catholic priest who came up with the theory.

The Clone Wars

2007-07-13T15:04:00.000-07:00

I don’t see anything intrinsically wrong with reproductive cloning.

I think it would be handy for all sorts of people who because of disease, accident, sexual orientation, or vocation, are unable to pass on their genetic material in the regular way. It has two problems, but these are problems shared by other assissted reproductive technologies:
(1) Wastage of ‘surplus’ embryos. I know nature does this, but I still think we should strive to keep it to a minimum.
(2) Health problems in the offspring. These are well documented but relatively minor for children put together by in vitro fertilisation. With cloning on the other hand, in the mammals we have looked at so far there are all sorts of peculiar and unexplained health problems. It would be criminal to experiment on human reproductive cloning at the moment because of these problems.

But there is no reason we should not keep on experimenting on our near relatives. Primates seem to be tricky things to clone. By all means let us try to clone chimpanzees. Once we can reliably clone perfectly healthy chimpanzees with a minimum of embryo wastage, why not apply the same technology to ourselves? I see no rational reason not to.

I do see therapeutic cloning as intrinsically wrong.

I think deliberately creating human embryos in order to destroy them is going too far. I don’t lose a great deal of sleep over it, because I was lucky enough to hear a talk in February 2006 by Graham Parker who is on the board of the journal ‘Stem Cell Research’ and works at a research hospital in Michigan. I learned the following things:

(1) The more differentiated a stem cell is when you start messing around with it, the more effective it is. This is why we still need to donate blood, and don’t just culture haemotopoetic stem cells. Inner-cell-mass-derived (aka embryonic) stem cells are less differentiated than somatic (aka adult) stem cells and appear much more likely to turn into invasive cancers when you inject them into mice.

(2) Nobody has a clue how stem cells really work clinically. It does not look like they just move in and turn into the sort of cells that are around them. They do other weird things that nobody understands yet.

(3) The chaps who first discovered inner-cell-mass-derived stem cells never claimed they had clinical uses. They still don’t. They are of fundamental importance in understanding developmental biology, which is important fundamental research and will eventually lead to all sorts of innovations- but they won’t involve injecting people with stem cells. 97+% of this fundamental research could (and should) be done with stem cells of the other mammals that we share so much of our DNA with.

This suggests to me that we are not likely ever to have a situation where therapeutic cloning would be done on an industrial scale and would be a big moral quandary for anyone with a serious illness. And if someone says, ‘I want to experiment on human embryonic stem cells’, the correct response is, ‘go do your experiments on chimpanzee embryonic stem cells’. There is no justification for playing with human embryonic stem cells. Maybe, once you have demonstrated that you can reliably and safely repair damaged chimpanzee brains, or whatever, then we can sit down and have a debate on extending the technology to humans.

Granddad's Biography

2007-06-14T18:55:00.001-07:00

Me Mum just sent me the link to this biography of my grandfather, Foundation Professor of Geology at James Cook University.

I was pleased to discover his philosophy of examinations:

I always felt that an exam should be a learning experience and, at a graduate level, all exams were take-home exams where a student could consult with any book or person. The catch, however, was that the questions had no answers, and the grade was based upon the approach to unanswerable questions. Students have come back later to tell me that this was the greatest experience they had in preparing them for the real world.

2007-06-05T19:03:00.000-07:00

Had we but world enough and time

2007-06-04T20:22:00.000-07:00

There seems to be a reasonable amount of interest in Precambrian organic matter because of its relevance to oil and gas exploration, but not so much work on what the distribution of organic molecules implies for the nature of life at the time. Nobody seems to have done anything specifically on the Ediacaran organisms to see whether they were chemically related to the later Metazoans or not, but the molecular evidence for a single unified biochemistry on Earth for the last 3.8 billion years seems very strong. I have found a couple of articles by Brock et al. about investigations of a 2.7 billion year old formation in the Pilbara (Science 1999, 285, 5430; Geochimica and Cosmochimica Acta 2003, 67(22), 4289) that report sterols, made today only by Eukaryotes, straight-chain alkanes with a ¹²C:¹³C isotopic ratio characteristic of modern cyanobacteria, and isoprenoid compounds, typically made today by Archaea, with a ¹²C:¹³C isotopic ratio characteristic of modern methanogen Archaea.

This means that the chemical phenotypes of these classes of organism were well-established at least 2.7 billion years ago. Thus the genetic differences between these classes, which are vast, either:

* Have to be compressed into the time between 2.7 billion years ago and the origin of life on Earth, which has to be after the crust solidified. This is vaguely possible, as there is no plausible reason that the ‘molecular clock’ has run at the same speed all the time.

* Arose, if one extrapolates the molecular clock sphexishally backwards, well before the Earth’s crust solidified.

Isotopic distributions of ¹²C:¹³C in organic deposits show no sharp discontinuity as we move further back in time, but are consistent with a biological origin (Schidlowski, Precambrian Research, 2001, 106(1-2), 117-134). Thus the essential biochemistry of today’s methanogens, or something very similar, were already established in the very oldest sedimentary rocks we know about, about 3.8 billion years old.

The Splendour that is the Historical Sciences

2007-05-30T00:24:00.000-07:00

I had the good fortune to attend a lecture on Friday by Dr John Paterson about the Cambrian Explosion, and how good inferences about the behaviour of organisms from that distant springtime of life can be made by considering such things as fossilized organisms that have healed after an injury, fossilized gut contents, and the size distribution of ensembles of organisms fossilised in different environments. The earliest dates for things like predation and herd/school behaviour seem to be being pushed further and further back.
Once again I was inspired by the magnificent beauty and complexity of the vision that is deep time, and how the contingent, irreproducible events of history have shaped the world that we know.

Best of all, I now realise there is an excellent way to push our search for the origins of life back beyond the fossil record. Molecular fossils! While most of the actual molecules that comprise ancient organisms are long gone, in some strata some of these molecules are tenacious and remain, and others have been transformed in systematic ways into compounds that still preserve some information about their origin. Perhaps succeeding generations of proto-life have not truly eradicated all traces of their predecessors as effectively as I thought.

These molecular fossils also seem to be a fantastic way to answer a question of great relevance to the 'Dr Jumba' theory of intelligent design. How closely related to the Cambrian Explosion beasties were the Ediacaran beasties? The Ediacaran world was very different, Dr Paterson told us- flat microbial mats with flat beasties: nothing that dug beneath the mats, nothing that ate anything else. Were those beasties based on the same chemistry as us? Or not? Surely the chemicals associated with them would give us a clue. I will explore the literature and return with a report.

Here tis

2007-05-16T22:25:00.000-07:00

John Ashton rang me up the other day, after I wrote to that creationist website to complain about the same thing I have complained about here (i.e., the implication that Francis Collins supports young earth creationism). One of the things they make a lot of on that same creationist website is that we haven't bothered to refute John Ashton's arguments, we've just shouted 'rubbish!' and I told him I would put up a refutation here.

This is it.

John Ashton’s essay conflates two very different things.

(1) Does the variability of living organisms in space, and the inferred variability of living organisms in time, arise partly or completely from supernatural factors?

This is what I have called ‘Intelligent Design’ with capital letters, in previous posts. This is not a testable hypothesis, and is not a scientific hypothesis, but it is not necessarily stupid. Science is concerned with the reproducible features of the universe, and when we claim that the universe can be explained entirely through study of those reproducible features we are making a statement of faith. We cannot exclude, through science, the existence of supernatural factors or the possibility that they act or acted upon the Earth now or at some other time. We can only demonstrate that there are entirely plausible explanations that do not invoke supernatural phenomena to explain features of the observable world that other people invoke supernatural phenomena to explain. That is as far as we can go.

Some scientists have argued that it is useless to debate people whose worldviews are orthogonal to that of science. This is probably true for completely orthogonal views, but I think it is possible that a person could answer ‘yes’ to this question while holding a worldview that overlaps to an extent with a scientific worldview.

(2) Are the creation accounts given in the Book of Genesis literally true? That is, the world is 6000 or so years old, and the apparent age of the world is a cruel trick played on us by a God who created the world so it looked that way?

This is not a supernatural explanation of experimentally verifiable facts, but a denial of those facts. This was a position abandoned by all reputable thinkers long before Darwin was born. Every roadside cutting, every hill, every meadow, every map, every cell in our own bodies testifies that this is false. Si contradictio requiris, circumspice. This position can only be maintained by postulating a God who intentionally set out to mislead us and make a mockery of our faculty of reason. I think anyone who has been appraised of the experimentally verifiable facts who answers ‘yes’ to this question has lost the good of the intellect and can be considered to hold a worldview completely orthogonal to that of science. I have no common ground to argue with such people.

To draw an analogy with another debate of much more relevance to public policy, the person who would answer ‘yes’ to question 1 is more-or-less equivalent to the sort of ‘Greenhouse skeptic’ who says: ‘global warming has nothing to do with humans and is caused by an as-yet-unidentified natural factor’. They are disputing the explanation for the facts. The person who would answer ‘yes’ to question 2 is more-or-less equivalent to the sort of ‘Greenhouse skeptic’ who would say ‘The earth is not warming, but rapidly cooling. What’s more, there is no such thing as carbon dioxide.’ They are disputing the existence of a large number of well-attested facts.

Accordingly I will take the liberty of slicing John Ashton’s essay into two pieces.

For that part of his essay addressing (1) which is not entirely orthogonal to a scientific worldview, I will offer a plausible non-supernatural explanation for the observed variations of living organisms in space and time and explain why it is more consistent with the hypothesis of a benevolent God than his hypothesis.

For that part of his essay addressing (2), I can only rend my raiment and emote about how a God who would create such a stupid universe would be utterly unworthy of human worship.

My glosses are in brackets, [like so].

Essay One. Quoth John Ashton:

One rarely reads creationist perspectives on science first hand in journals such as Chemistry in Australia. Secular and atheistic views have dominated western education for many years and it is now very difficult to get a theistic based theory taught or discussed as illustrated by the uproar in 2005 about a proposal to teach evidence for intelligent design.

However, I believe there is a sufficient case for the alternative view that in the beginning God’s creative power brought everything into existence to warrant teaching the evidence for this view in science classes.
My first observation is that a number of unproven scientific hypotheses have become widely accepted (or talked about) as fact. This makes it very difficult for the non-expert or layperson to distinguish what is a proven fact from what is merely a theory about origins.

Evolution is a case in point.
There is no denying that biological change occurs. However, Darwinian evolution, as the origin of Life on earth, is now known to be impossible.

[This is a category mistake: Darwinian evolution has nothing to say about the origin of Life on earth. It is a model for how biological change occurs. Given some simple organism to start with- Gilbert and Sullivan’s ‘primordial protoplasmic globule’- it provides an entirely plausible picture for how changes arising by whatever means are spread by natural selection, and the aggregate of beneficial changes can lead to the variety of living organisms we see today.]

Let me illustrate the difference. Over the past 30 to 40 years a number of new strains of food poisoning bacteria have evolved. That is before the 1970s or thereabouts they did not exist (or were at least unknown). Now they are a threat to food safety. The evolution of these bacteria has been traced to the transfer of genetic information (toxin genes or acid resistance genes etc.) from one type of organism to another.

[Exactly! These changes have arisen, and then they have been spread by a Darwinian process of natural selection. Darwin’s theory does not depend on any particular mechanism for introducing changes. I agree that horizontal transfer of genetic information is an extremely important mechanism for introducing these changes. But this does not preclude other mechanisms. A copying error in which the daughter gene is not quite the same as the mother gene may be a felix culpa: indeed, given the vast numbers of genes being copied all the time, it is certain that beneficial errors are happening all the time. When these mutations affect genes that are involved in regulating embryonic development, for example, quite marked changes in an organism can be induced from minor genetic changes.]

And it is a similar situation for all the observed cases of evolution involving mutations. They all involve either the transfer of existing (i.e., created) genetic information from one organism to another or the loss of some pre-existing (created) genetic information.

On the other hand, there are no known instances of meaningful or purposeful genetic information arising spontaneously by chance- not a single known example- yet this is a fundamental requirement of Darwinian evolution, which teaches that microbes evolved into higher organisms, etc.

[While I am also unaware of any cases where a beneficial change has been unambiguously demonstrated under laboratory conditions, the mechanism is entirely plausible. There have certainly been many instances of heritable genetic damage, and this is not a ‘loss’ of genetic information, just a change. Out of a large ensemble of changes, some will doubtless be beneficial under certain conditions. Mutations do not have any meaning or purpose, and their utility will be dependent on the environment. Mutations that are harmful under one set of conditions may be beneficial under another.]

Darwinian evolution also requires abiogenesis, that is living cells spontaneously arising from non-living molecules (chemicals). Again, as George Javor, Professor of Biochemistry at the Loma Linda Medical School in California, points out, this has never been observed despite experimental attempts, and on the basis of current biochemical knowledge is absolutely impossible.

[Please see my post here on why seeking an understanding of abiogenesis based on ‘current biochemical knowledge’ is futile. This in no way make abiogenesis ‘absolutely impossible’.]

Not surprisingly, Francis Collins, director of the National Human Genome Research Institute, believes that it was God’s creative power that brought everything into being in the first place.
Oxford educated philosopher Ronald Laura and myself have also shown that an intelligent design or ‘blueprint’ based model is more effective in predicted adverse health outcomes resulting from new technologies than are conventional reductionist science models.

And this is my brief response to essay 1.

We do not need a supernatural explanation for biological change.

The mechanisms by which beneficial genetic variation might arise (genetic damage leading to copying mistakes, or horizontal transfer of genetic material) are either well attested by experimental evidence, or entirely plausible in light of experimental evidence for heritable genetic damage.

Once a beneficial genetic variation arises, there is a vast amount of real-time experimental evidence that this can be rapidly communicated throughout a species.

There are many, many places where anyone who is interested in truth can go to find a clearer explanation for the process and the experimental evidence for it than I can provide.

Why would anyone possibly want a supernatural explanation for biological change, anyway? For millenia, a challenge to theodicists has been how to reconcile the suffering of the biological world with the workings of a just and merciful God. Evolutionary biology lets God off the hook. One no longer has to believe in a God who just decided the animal world would be full of misery and suffering. Who just happened to make countless species eminently adapted to a life of parasitism or carnivory. Instead, the biological world can be seen as a collaborative work between God and Life. Living things were offered choices, with whatever smidgen of free will you want to postulate they have, and the sum of All Decisions Antecedent to Mankind resulted in the fallen world we see around us.

Essay Two.Quoth John Ashton:

Scientists and educators have been taught for decades that the earth and the universe are billions of years old, and this message permeates our culture to the extent that it has many people doubting the Bible’s record of the history of the world. Yet the historical accuracy of the Bible has been consistently validated by archaeology and secular historical records to within two generations after Noah’s flood (e.g., ancient Egypt was founded by and named after Noah’s grandson).

Although it is true that, on the basis of radioactive dating methods, scientists have calculated certain rocks to be millions and even billions of years old, we need to remember that these methods cannot be validated for pre-historical dates. Furthermore the calculations can give inconsistent and even wild results for some historical objects, for example recent lava flows. This kind of knowledge is why some highly educated geologists, geophysicsts, and physicists reject the ‘billions of years’ hypothesis and believe the earth is only thousands of years old. Some of their testimonies are freely available on the internet.

[You don’t need atomic dating to know that the earth is really very old. You just need to look at any geological formation. The idea that the earth was ‘thousands’ of years old was discredited centuries before atomic dating was invented. And Noah's grandson was named after Egypt by the authors of Genesis, or I'm a spotted hyena.]

Most of us have heard of the Big Bang model for the origin of the universe. This model uses black hole cosmology and assumes the ‘cosmological principle’ which requires a hypothetical fourth dimension. Even though this model has now essentially been disproved because it fails to predict observed data (such as proton decay) it continues to be the dominant model. However, if we hypothesise ‘white hole’ cosmology, i. e., matter stretched out in three-dimensional space (no hypothetical fourth dimension) we would have an ‘event horizon’ mwhere the gravitational field would be enormous and the speed of light would be very much faster and atomic clocks would run almost infinitely fast. Using this model the earth and universe could be very young- only 6000 years old.

[Two things are conflated here: the observations that matter is flying away from other matter, which can be extrapolated back to the origin of all matter at a single ‘point’, and the precise mechanism for the ‘Big Bang’, which is a matter for debate. But an ‘old universe’ is not dependent on one or any of these models being true. Cosmologists hypothesise all sorts of things all the time: but they can’t be totally inconsistent with the facts we are living with on Earth. We are justified in immediately rejecting ‘white hole’ cosmology purely because of the weight of terrestrial evidence for an old earth.]

The US mathematician Robert Herrmann, former professor of mathematic at the United States Naval Academy, gives powerful arguments for scientific observations upholding a plain interpretation of Genesis chapter one, while allowing for starlight to travel for billions of light years.

[If the arguments are powerful arguments, why are they not given? The argument from authority ('Dr X says so') is the weakest form of argument. And argument from authority is all the next paragraph amounts to:]

My second observation is that while we regularly read about scientists who believe in the Big Bang and life on earth being billions of years old, such as Stephen Hawking, Paul Davies and Richard Dawkins, we rarely read articles in the media about scientists like Professor Herrmann who believe that the heavens and the earth were created in just six days about 6000 years ago. Yet scientists who believe the creation account and a young earth include dmany eminent scientists such as Professor David Gower DSc (London), Emeritus Professor of Steroid Biochemistry at the University of London; Dr Ker Thomson DSc (Colorado School of Mines), former director of the US Air-force Terrestrial Sciences Laboratory; and Professor Werner Gitt D. Eng (Aachen) a former director of the German Federal Institute of Physics and Technology (the same institute where Einstein studied). These scientists emphasise the observation that much about origins that is often presented as facts is actually based on unproven hypotheses and that the weight of factual evidence favours creation.

[Why not give the titles and potted CVs of Hawking, Davies, and Dawkins? Once you start arguing from authority, you have lost this game. These eminent scientists are not household names, like the first three are, because they are not really all that eminent. We don’t hear about scientists who hold creationist views because there aren’t any working in fields of relevance to the questions of the origins of life and the universe who hold such views.]

On re-reading this I can’t help but feeling a sneaking suspicion that maybe John Ashton is having us all on and is going to shout ‘gotcha!’ any minute now. Essay (2) is just so very, very, very silly.

There is an overwhelming mass of evidence that the earth and the universe are very, very old. I will requote Francis Collins because I am still upset about the shabby way he was quoted to make it look as if he was in favour of the content of essay (2).

'If the tenets of young-earth creationism were true, basically all the sciences of geology, cosmology, and biology would utterly collapse. It would be the same as saying 2 plus 2 is actually 5. The tragedy of young-earth creationism is that it takes a relatively recent and extreme view of Genesis, applies to it an unjustified scientific gloss, and then asks sincere and well-meaning seekers to swallow this whole, despite the massive discordance with decades of scientific evidence from multiple disciplines. Is it any wonder that many sadly turn away from faith concluding that they cannot believe in a God who calls for an abandonment of logic and reason?'

If, in the face of all this evidence, anyone persists in believing that the earth and the universe are 6000 years old, than this requires belief in a God who set out to make all the evidence point to a wrong conclusion. This requires a God who wants to frustrate rationality. This God is more like the jumped-up fraud of Robert Heinlein’s Job than anyone worthy of human respect. Could our ideals of justice and mercy possibly derive from such an entity? I think not.

I know you're out there!

2007-05-14T16:47:00.000-07:00

Just was informed that there is a link, established on the 24th of April, from a creationist website to the letters catigating the Royal Australian Chemical Institute for publishing a creationist article that I posted so I could link to them here. There is *no link* to those letters on the Polymer Division website. Either Google found them, even though they were parked nigh-linkless, or someone has been through here and found them.

The creationist article says that our criticism is ill-founded because we have not specifically refuted the claims made in John Ashton's article. I will specifically refute them all here, real soon.

Chris Barner-Kowollik tells me that since the creationist website linked to his letter, he has been receiving hate mail from certain Christians, saying things like: "Your days are numbered and the wrath of god will hit you hard." He says I should leave the letter up on the web anyways, because he is a man of principle and integrity.

If Google is not nigh-omnicompetent, and you, dear reader, found those letters through here, please feel free to publicise my name and contact details to receive abusive messages as well. For the God of young-earth creationism is a despicable God, a God who holds his creatures in contempt by filling the natural world with suffering for no good reason and mocks sentience by constructing a universe made to look in every way like it is billions of years old and governed by rational laws. I want no truck with him. Humanity deserves a better God than that.

Things I Don't Understand: The Gibbs Paradox

2007-05-09T19:54:00.000-07:00

I was told a while back that there is no such thing as entropy of mixing for ideal gases, and it makes sense to me.

In an ideal gas, the components of the gas don’t take up any volume, and they don’t have any specific interactions with each other.

If you start out with two ideal gases, A and B, in a container separated by a partition, and remove the partition, then gas A will expand into the whole of the volume previously occupied by A and B. Each molecule of A will have more options available to it than it had previously, and entropy will increase. Similarly, gas B will expand into the whole of the volume, etc. See, there is no entropy of mixing. There is only the entropy of expansion. If the volume of A equals the volume of B, this entropy of expansion turns out to be R.ln2, where R is the ideal gas constant.

But, let’s say we had equal pressure of gas A on both sides of the partition. We remove the partition, and gases A and A mix. Both of them expand, so we ought to get an entropy increase. But the pressure and volume and temperature of the final A + A system is exactly the same as the initial one: there has been no change, and the entropy of expansion turns out to be 0.

This is the Gibbs Paradox.

It bugs me because, let’s say we didn’t stop at one partition, but kept putting in more and more partitions until every particle was in its own little box, surely that would mean we had a system with less entropy?

Or not?

I keep looking for experiment data on entropy of mixing of gases, and all I find is people writing theoretical papers explaining the paradox away in different ways.

This one is particularly good, and says more or less- I think- that the thermodynamic entropy that we can use to do work with is not really a well defined function in the same way that energy is. It will depend on the things we have selected to characterise the system, and if we were to find out new ways of distinguishing particles that were indistinguishable before, we could exploit these to do work, and see an entropy change on mixing. This seems perfectly valid, but troubles me because I have been teaching first year in such a way that energy is an abstraction from entropy as a more fundamental concept. Which I will have to rethink without confusing myself totally.

Another paper that I have to read over again to try and start thinking clearly is this one, which is about the confusion between thermodynamic entropy and informational’entropy’.

So it seemed to me that when we remove the partition between A and A′, we had to be increasing the informational ‘entropy’ of the system, but maybe because there is no way to exploit this to do work, we haven’t done anything to the thermodynamic entropy.

I was talking about putting particles in boxes before, so I thought I should go all quantum and actually put our particles in boxes.

Let’s say we have some energy kT available for partitioning all our particles into translational states. These translational states will be separated by energies proportional to 1/a², where a is the size of the box. So the number of translational states available if the temperature stays the same but we double the size of the box doesn’t go up by a factor of 2, but by a factor of 4.

So I was thinking that there seemed to be a lot more ways of putting 2n objects in 4m boxes than of n objects in 2m boxes, and so there ought to be an increase in informational ‘entropy’ when we double the size of the box. Sure enough, when I looked up how to calculate the number of permuations there are a whole lot more permutations. But informational entropy is related to the log of the number of permutations. The log of the number of permutations at the end seems to be converging to twice the log of the number of the permutations I had in a box half the size... but it is converging towards one too slowly for the factorials I can do in Excel to cope. Is it going to go to one or not? Does ‘entropy’ of A + ‘entropy’ of A = entropy of (A+A)?

So I have to say this is something I don’t understand.

Next up: Quantum Teleporation.

Aha!

2007-05-02T20:31:00.000-07:00

It would seem that there is more positive selection in a large population than a small population, because statistically more beneficial mutations will arise and spread throughout the population. This seems logical.

Here is a link to Zhang's article on the human and chimpanzee genomes, which I admit is well beyond me as a mere chemist. :P

What is Chemistry? A Preface to an as-yet unwritten Book.

2007-04-24T22:00:00.000-07:00

Chemistry is the science of things that we can see and that we can control.

When I was young, I never gave chemistry a second thought. I loved the grand sweep of biological evolution, with its single unifying idea and its endless ramifications, every twig on life’s branch subjected to a neat exegesis by my idol, Stephen Jay Gould. I loved the vastness of space, the unimaginably gigantic and inhuman universe subjected to the breathless exposition of Carl Sagan. I was brought up in an atmosphere suffused with geology, and I cannot remember ever not knowing that I lived on a thin chunk of crust moving inexorably towards Asia. These, the descriptive sciences, the historical sciences, were where I lived. I wanted to know where I was; I wanted to know where I was going.

But...

It is not enough to know. If you actually want to do something, all of these sciences have serious flaws. You cannot crash galaxies together to see what will happen. You cannot evolve your own species of toothed whale. You cannot smear an archipelago onto the Pacific coast of North America. You can only watch, and collect data, and hope for a ‘natural laboratory’ which will test whatever hypothesis you have developed. The essential bits of the historical sciences, the most interesting bits, are inaccessible to our tinkering.

As I grew older, I grew to lust after the secret and paradoxical wisdom of the physicists, the world of Schrödinger’s cat and Lorenz’s butterfly and the modest goal of the Theory of Everything. Here again, I was driven by the desire to know what was going on. Once upon a time physics was a science where you could do things.

But now, alas, they have mostly been done. Now you need obscene amounts of money to do experiments and whatever result you get can be explained by the theoreticians. Is that falsifiability?

Actually, I must be honest. I cannot discount physics. I am a failed physicist. Somewhere among the ordinary differential equations I got lost, and fell off the mathematical billycart. When I say that the great achievements of what we call ‘Modern Physics’ ended in the 1930s, and that since then it is chemistry and its biological metastases that have transformed the world, you must discount it as sour grapes. Likewise, when I proclaim: ‘physics has given we chemists our tools, and now its job is done.’ Sour grapes.

Essentially, chemistry drew me in because it let me play with liquid nitrogen and fire.

If you actually want to do something, chemistry is the only science worth considering. With physics, we can control things, but we can rarely see them or even imagine them. We can see the subjects of the historical sciences everywhere, but cannot control them. Chemistry is the science of things we can both see and control.

Chemistry is called by some of its practitioners the ‘Central Science’, a term that I have always found naff. It is the ‘Human-Sized Science’.

A few more facts about chemistry:

Chemists are allowed to:

(a) Appropriate any part of physics they like and call it ‘physical chemistry’

(b) Invade and subvert any ‘softer’ science they like and turn it into chemistry.

It is no coincidence that so many Deans, Pro-Vice Chancellors, Vice Chancellors and Prime Ministers (e.g., Margaret Thatcher) have been chemists. Those whose job it is to manipulate matter naturally want to manipulate it wherever they find it.

An especially egregious example...

2007-04-16T23:39:00.000-07:00

...of something that greatly irritates Marco is the language used in this popular science article.

The thing that greatly irritates Marco- and me too, for that matter- is the pervasive image of evolution as a 'ladder' leading step by step to 'more highly evolved' beings. Nothing can be 'more highly evolved' in general. A species can be 'better adapted' for circumstances X, Y, or Z; but circumstances are subject to review (by climate change, giant asteroids, motorways, etc.).

One thing that confuses me is the relationship between population size and genetic change mentioned in the extract below. It seems counterintuitive. Perhaps a real biologist could help? :)

Zhang's team found that 233 chimp genes, compared with only 154 human ones, have been changed by selection since chimps and humans split from their common ancestor about 6 million years ago.
The result makes sense, he says, because until relatively recently the human population has been smaller than that of chimps, leaving us more vulnerable to random fluctuations in gene frequencies. This prevents natural selection from having as strong an effect overall.

The Great Gametopathy Info-Dump

2007-04-14T04:06:00.000-07:00

Is here!

Sadly, I am too lazy to deconstruct the pdf file into proper blog entry format .

The Electrochromic Effect

2007-04-12T00:58:00.000-07:00

We are very coy and subtle folks, sometimes, we scientists. The other day I was skimming through 'Molecules and Radiation' by Jeffrey Steinfeld while preparing some lectures and came across this sentence:

"The Hamiltonian for the interaction of an atom with a static electric field [called the Stark effect after its discoverer, Johannes Stark (1874-1957); also called the electrochromic effect by other spectroscopists who did not like Stark] is just the electric-dipole interaction:"

Other spectroscopists who did not like Stark?

Why should other spectroscopists not like Stark?

My curiosity was piqued, and it did not take long for me to discover why.

The electrochromic effect it is!

Twitch, twitch, twitch, twitch...

2007-04-06T19:13:00.000-07:00

When will the world listen to reason?
I get the feeling it'll be a long time.
When will the truth come into season?
I get the feeling it'll be a long time.

- The Offspring

I can't take much more of this kind of thing, I really can't. I will burst a blood vessel somewhere. This unwarranted hyperbole about climate change is going to harm the reputation of science for generations. I used to think that the collective insanity of the early 20th century was caused by mass heavy metal poisoning of urban populations and we would see saner arguments and saner policies as we moved into the 21st century. But it appears I was sadly mistaken.

If we are worried about people in the poorest regions of the Earth suffering 'malnutrition, disease, and increased untimely death rates because of heat waves, floods, storms, fires and droughts', then the logical thing to do is to bring them to a standard of living so that they will suffer as little as we in the developed world do from heat waves, floods, storms, etc.

If we are worried about the alkalinisation of the oceans, we should take a deep breath and acquaint ourselves with how flimsy the evidence for this particular doomsday scenario is.

If we are worried about coastlines disappearing, we should get rid of those dams upstream and regenerate those coastal swamps we have cleared. And we should move people away from that dangerous big blue thing which is always going to twitch and kill people, no matter what the climate does.

If parts of the planet become too hot or too cold for traditional crops, then we should switch to different crops, shouldn't we? We do this kind of thing all the time.

I can't imagine any possible scenario where Bangladesh would run out of drinking water. Very dry poor countries with high population densities survive by economising on all the other things we do with water besides drink it. Very dry rich countries don't care, because if they want more water, they just build more desalination plants.

If we are worried about extinctions, we should address the primary cause of biodiversity loss- the dangerous fragmentation of habitats. We can move people out of marginal regions to amalgamate little reserves into big reserves. The little reserve is always vulnerable. If global climate change means your preferred habitat shifts a hundred metres uphill, in a large enough reserve you move a hundred metres uphill. Conversely, if a minor local event means your preferred habitat shifts a hundred metres uphill, in a reserve that is too small you're not going to be able to move.

Coincidentally, I just came back from holidaying on the seaside at a house with very little in the way of reading matter. There were three copies of the Readers' Digest there, the oldest from August 1974. This magazine had an article about the alarming drop in global temperatures of 0.5 C since 1940 and forecasts of the dire effects to come...

In the beginning was the Metabolism

2007-04-05T22:34:00.000-07:00

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

If I was arguing with one of the people Marco sometimes has to contend with- those who find the transition monkey --> man as implausible as the transition unlife --> life- then an 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 might seem to be a complete materialist description of the history of life, and might well shake their worldview to its foundations.

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 will now try to justify this assertion by considering the requirements a CSCP needs to have in order to be relevant to the origin of life.

Firstly, the CSCP must be secured from the overwhelming tendency for matter and energy to become more randomly distributed in the universe. This has one easy part and one hard part.

The easy part 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.

The hard part is whatever reaction allows the CSCP to increase the disorder of its surroundings in order to persist in time. The molecules making up the CSCP cannot be just any old polymers we happen to be fond of. They must be- if the system is to persist in time- intermediates in a spontaneous chemical reaction. This is whatever reaction converts energy-rich ‘food’ into energy-poor ‘waste’. The requirements of this net of reactions also make the easy part 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.

Secondly, not just any thermodynamically favourable driving reaction will do. It would be preferable for this central driving reaction to proceed relatively slowly, so there plenty of intermediate molecules around. This reaction must also have many steps, with many intermediates capable of being transformed in various ways- because 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 a net of thermodynamically favourable reactions.

I believe this set of 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 common instances: living systems, and systems we have designed. The question of how systems meeting these requirements can spontaneously arise is the key question for the origin of life.

Kauffman, understandably invigorated by the Central Dogma¹ of molecular biology like so many in the last half century, 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.

I don’t intend this as an argument in favour of intelligent design², still less of Intelligent Design³. My main aim is to defend a strongly held view 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. We are trying to reconstruct the invention of the telegraph, knowing only the mobile phone: Which came first, we argue, the handset, or the system of towers dotting the landscape? It is an unquestion. We have pulled ourselves up by our own bootstraps, as one phase of pre-biotic evolution succeeded another, as one phase of pre-DNA-life succeeded another. At each stage, we have destroyed our history more effectively than any Red Guards, as we cannibalised previous stages for chemical substrates. Perhaps there have been shifts in pre-DNA evolution radical enough that unassimilated chemical traces of previous stages remain, somewhere. Perhaps we will be lucky, and find somewhere out there traces of pre-DNA intelligent designers. But 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.

1: I hate this term, 'Central Dogma'. Similarly, when Kauffman describes his theory as 'heretical'. This quasi-religious language makes scientific discussions sound very silly to outsiders, I am sure.

2: Defined as manipulation by, for instance, Jumba Jootika, vide infra...

3: Defined as manipulation directly by God.

Such things are sent to try us

2007-03-27T19:54:00.000-07:00

The magazine of our professional association, Chemistry in Australia, has just published an article by a creationist chemist, John Ashton. Perhaps this is an experiment to see how many people are actually reading the magazine. Well before the magazine appeared in my pigeonhole I was being cc'ed messages from fellow chemists who rightly saw this as a very dumb thing for Chemistry in Australia to do. The perilous aspect of this is not that we should be publishing unscientific articles that aren't at all about chemistry (though that bugs me) or that some chemists are silly (though hardly any, of course), but that getting non-refereed articles into publications with scientific-sounding names is apparently a favourite creationist tactic.

I am peeved by John Ashton's attempt to drag Francis Collins into the fray as a supporter. In an entirely sensible address on science and faith, the Christian director of the National Genome Project has this to say about creationist views:

'If the tenets of young-earth creationism were true, basically all the sciences of geology, cosmology, and biology would utterly collapse. It would be the same as saying 2 plus 2 is actually 5. The tragedy of young-earth creationism is that it takes a relatively recent and extreme view of Genesis, applies to it an unjustified scientific gloss, and then asks sincere and well-meaning seekers to swallow this whole, despite the massive discordance with decades of scientific evidence from multiple disciplines. Is it any wonder that many sadly turn away from faith concluding that they cannot believe in a God who calls for an abandonment of logic and reason?'

Bearing fruit in keeping with repentance

2007-03-25T22:22:00.000-07:00

I have confirmed that our Bachelor of Health Sciences (Homeoapthic Medicine) was discontinued last year, as I thought, and this link will soon be inactive. Hurrah!

The Funneled Web currently has an article about other universities that have not yet seen the error of their ways.

Delta T

2007-03-23T19:45:00.000-07:00

I thought I should see if I could justify my Panglossian comment on Klaus Rohde’s blog that the Ganges Delta should be able to keep pace with sea level rise.

The historical vertical deposition rates quoted in this interesting paper of 5-8 mm/year seem adequate to keep pace to all but the most extreme rates of global warming-related sea level rise. This deposition rate should also increase with any increasing incursion of saline waters into the delta, since the stability of colloidal clay particles to aggregation is reduced markedly with increasing ionic strength of the solution.

However, I had not realised that the amount of sediment reaching the Ganges Delta has already been severely reduced by the construction of dams in India, and the effects of this on the western Ganges delta were already obvious by the time the paper was written at the end of the 1980s. Hopefully India will be moved to correct this problem out of self interest, as it puts many millions of its own citizens at risk.

It also appears that intensive human use of the most marginal coastal lands- where more than a million people died the day I was born, and where nobody ought to be living- contributes significant horizontal erosion, even if overall vertical deposition rates can keep up the level of the delta.

The Prolific Anonymous Writes:

2007-03-19T00:28:00.000-07:00

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

It seems to me that the figure in this Wikipedia article on ocean acidification, the only evidence presented there for ocean acidification as a fact, cannot possibly be based on data. In fact, the citation is a computer simulation based on carbon dioxide transport across the air/water interface.

The vast majority of these simulations are based on incorrect physics. When I was in Sydney last year I went to a talk by a physical chemist from New Zealand who talked about how mass and heat transport are coupled: you can’t calculate the flux of carbon dioxide from water to atmosphere and vice versa just by looking at the concentrations, you need to know the relative temperatures too. I worked out his equations in Excel, and a gas will move against a pressure gradient if it is moving with a temperature gradient: i.e., if the air is hotter than the water, the concentration of carbon dioxide in the water will be higher than in the air.

This physical chemist wrote two papers on this in 1991-1992 in the climate scientists’ journal of record, Geophysical Research Letters (Phillips, Leon F.. Carbon dioxide transport at the air-sea interface: Effect of coupling of heat and matter fluxes. Geophysical Research Letters (1991), 18(7), 1221-4.; Phillips, L. F.. Carbon dioxide transport at the air-sea interface: numerical calculations for a surface renewal model with coupled fluxes. Geophysical Research Letters (1992), 19(16), 1667-70.) The papers have each been cited exactly four (4!) times. I found a paper from 2003 by a collection of climate scientist chaps from Princeton and other places, who estimated carbon uptake in various places and come to the conclusion: ‘there is more carbon dioxide uptake at low latitudes, and less at high latitudes, than the models predict.’ Well, this is because the physics in those models is wrong.

This coupling of heat and matter transport also means that there will be strong diurnal and seasonal variations in carbon dioxide transport across the air/sea interface, and local concentration of carbon dioxide very much higher than those in equilibrium with the atmospheric concentration as a whole (see some of the data in here): thus organisms in the surface water layer are regularly exposed to a pH range as great as that postulated for the 'gloom and doom' prognostications.

The Royal Society summary paper on ocean acidification does not produce any convincing evidence for an overall increase in ocean pH over the period of industrial civilisation. The 0.1 increase they cite is based on a combination of proxy data (deposits of other species correlated to pH)and simulations. I am inclined to take this value with a grain of salt (NaHCO₃) and recommend that it not be used to influence policy!

Intelligent Design

2007-03-18T20:55:00.000-07:00

Here's a letter I sent to Alex Reisner of The Funnelled Web in October 2005:

Greetings Alex,

Everything we have discovered over the last 500 years has taken us further and further from the idea that the Earth is the centre of the Universe. We are nowhere special; why should life have happened to start here? There might be all sorts of chemistries that are not at all like the life we know that started out in environments not at all like the ones we know: you just need to get life started somewhere, sometime, and sooner or later it will come up with iPods and weird new organisms based on different chemistry than itself. Maybe it will even come to planets where life is already humming along nicely and play around with horizontal gene transfer. Given enough time, the probability of an alien mad scientist as in “Lilo and Stitch” might become significant...

Let's say that we keep probing the origins of life, and every possible mechanism for kicking the process off requires some fantastically entropically unfavourable combination of highly complicated molecules that we can easily produce in a test tube, but can't envision surviving long enough to reach the required concentrations in any plausible environment on the primitive earth.

Do we:

(a) Keep on asserting that this highly thermodynamically-disfavoured process must have happened, nevertheless, in some highly implausible and forever unobservable environment?

(b) Apply Ockham's Razor and say that if we can make life in a test tube, then, maybe, life as we know it was made in a test tube?

We know this is not what the Intelligent Design people *really* mean by Intelligent Design, but it is perfectly consistent with what they *say* they mean, so we shouldn't just jump up and down and say that Intelligent Design is pseudo-scientific rubbish. If you discard the supernatural component it is many orders of magnitude more scientific than homeopathy, which several blinkered, insane-with-greed Australian universities prostitute their good name to support.

This version of Intelligent Design is a perfectly valid scientific theory. We can think of things we could do to test it. For instance, we could search for the aliens' fossilised iPods...

Cheers,

Chris

Possible Intelligent Designer, Dr Jumba Jootika

I want a shoehorn, the kind with teeth

2007-03-15T13:21:00.000-07:00

The blogosphere is full of posts by reasonably intelligent people pooh-poohing anthropogenic global warming (AGW). They cite anecdotal evidence for local cooling and sea level stasis, every bit as relevant as the anecdotal evidence for local warming and sea level rise trotted out by the other side. They look askance at the admittedly scattered plot of temperature rise vs. time (Figure 1). The messianic fervour with which the AGW propagandists push totalitarian 'solutions' to the problem pushes them to deny that AGW exists, in the same way as William Jennings Bryan was pushed into denying evolution by the way it was abused to justify Prussian militarism and robber-baron capitalism.

Figure 1: HadCRUT3 Global Temperature Data Set

Why are scientists convinced, in the main, that the AGW hypothesis is correct? It is not because of some spotty y = mx + b fit to a curve of surface temperature vs. atmospheric [CO₂](Figure 2). It is because there is a very clear mechanism by which increasing atmospheric carbon dioxide concentration should increase surface temperatures, as sure as eggs are eggs. This mechanism is dependent on fundamental physical laws that are as incontrovertible as anything can be in this crazy mixed up world of ours.

Figure 2: y = mx + b ono

In many ways AGW is the converse of continental drift. For hundreds of years, anyone with eyes could see, and say: 'Hey! This bulge in Brazil fits perfectly into the Bight of Benin!' But for hundreds of years, scientists quite properly pooh-poohed the idea of continents moving around. There was no plausible mechanism for this to happen. As soon as evidence for a mechanism arrived, so did continental drift as a reputable theory. With AGW, the lump in South America might not look very much like the dint in Africa, but the mechanism is so good that any claim that it isn't happening is bound to look like clutching as straws.

Here is the mechanism:

Energy cannot be created or destroyed. Therefore, the energy in the sunlight incident on the Earth has to be balanced by the energy in the light re-radiated by the Earth, or the temperature of the Earth will increase.

The sun sends all kinds of electromagnetic radiation out in all directions, some of which impacts the Earth, as shown in Figure 3.

Figure 3: Radiation Incident on the Earth

The difference between the upper dotted line (sunlight at the top of the atmosphere) and the lower solid line (sunlight at the bottom of the atmosphere) is the first lot of energy we need to worry about. Part of it looks like it is scattered back into space (the general fact that the solid line is lower than the dotted line) and part of it goes into increasing the kinetic energy of various molecules floating around in the air (those are all the little dimples in the solid line). These molecules (mostly water) can then knock into other molecules and increase the general kinetic energy- that is, the temperature- of the air. The more scatterers there are in the air- dust, soot, water droplets, etc.- the more energy will be scattered away, and the more water vapour (mostly) there is, the more the atmosphere will be heated directly. But on average, the solid line should not change much over time.

Now, what happens to the solid line when it reaches the earth’s surface? Either it will be reflected, and zip back off into space, or it will be adsorbed. This will be very variable indeed, and will depend on where the clouds are (they count as surface), and where the snow is, etc. Nobody is at all sure how this balance between reflection and adsorption will respond to an increase in global temperature, but a reasonable guess might be that it is likely to stay about the same.

The adsorbed energy heats the Earth’s surface. But because the whole thing has to balance to keep the Earth’s temperature the same, it has to go somewhere: and where it goes is the energy radiated by a black body heated to a not-terribly-high temperature, as shown in Figure 4.

Figure 4: Heat radiated by Earth cf. Black Body curve

The heavy green line is the theoretical curve for a black body at 255 K, and the narrower green line is observational data from an area of the Pacific ocean at about 290 K. Now you can see the bending signal of carbon dioxide! This is the big dip in the middle of the Pacific ocean curve. This dip is the rational basis for being fretty about carbon dioxide. If the dip caused by carbon dioxide gets bigger, the total area of the curve has to increase to balance the average energy coming in with the energy being radiated out. Let’s say the dip increases to where it takes up an extra 10% of the total area under the curve: the surface temperature then has to increase by a factor of approximately the fourth root of 1.1, an increase of about 6 K. 10% is of course a ruinously gloom and doom eyeballing estimate by me that probably requires a quintupling of carbon dioxide concentration, so people are worried about an increase rather less than that.

Those who are concerned about the big government, anti-Third-World-economic-development prescriptions for slowing global warming should abandon the indefensible trenches and fall back to the more defensible ones. Nobody has demonstrated conclusively that a warmer Earth will be a bad thing. A warmer Earth ought to be better for biodiversity. If some regions become unviable for human settlement, they will be regions that were marginal and dangerous for human settlement anyway. Nobody ought to live on a table-flat coast where five metre storm surges are possible, or in a fragile semi-arid region where every decade brings a drought that kills all your stock. Evidence to date is that global warming is much stronger in high latitudes, where it will improve human health, reduce energy consumption, and be an enabler of economic development. Adapting to global warming is a challenge and an opportunity. Stopping global warming is an impossible dream.

[Memo to self: remember to add citations for the images...]

XTC vs Adam Ant

2007-03-12T18:37:00.000-07:00

Richard Feynman, ‘The Feynman Lectures on Physics’:

If, in some cataclysm, all of scientific knowledge were to be destroyed, and
only one sentence passed on to the next generations of creatures, what statement
would contain the most information in the fewest words? I believe it is the
atomic hypothesis (or the atomic fact, or whatever you wish to call it) that all
things are made of atoms- little particles that move around in perpetual motion,
attracting each other when they are a little distance apart, but repelling upon
being squeezed into one another. In that one sentence, you will see, there is an
enormous amount of information about the world, if just a little imagination and
thinking are applied.

It is this fundamental principle of science that is assaulted by homeopathy. Homeopathy claims that you can dilute a substance to such an extent that there are no molecules of that substance left in the solution, and the dilution will be a pharmacologically-active product. (The homeopaths have attempted to avoid assaulting the atomic hypothesis head on by postulating ‘molecular memory’. It is true that when something is dissolved in water, for instance, it imposes structure on the water, but there is no reason for this imposed structure to remain. Remember, water molecules are in perpetual motion. Weak bonds between water molecules are continuously being formed and unformed, and only interactions that require much more energy than the thermal background energy to break will remain for any length of time. The order imposed by the presence of a solute involves energies of much lower energy than background thermal energy.) Essentially, however, homeopathy is incompatible with the atomic hypothesis.

Intelligent design postulates one or more momentary suspensions of the scientific laws we know at some indeterminate time in the past. It does not claim that those laws are false. Homeopathy requires the fundamental principle of chemistry to be false.

Intelligent design makes postulates about essentially unobservable events with little relevance to daily life. This makes it relatively harmless and excusable. We would still have a functioning technological civilisation if everyone believed in intelligent design. Homeopathy make postulates about events that are easily amenable to experiment and are observed countless times every day, events that are essential to countless processes impacting on everyone’s daily lives. This makes it dangerous and inexcusable. We would not have a functioning technological civilisation if everyone believed in homeopathy.

Intelligent design has never killed anyone. Homeopathic medicine kills people all the time.

Who am I?

2007-03-11T04:18:00.000-07:00

I am a mostly harmless chemist at a University that, as Stitch of Lilo and Stitch says of his family, is 'small, but good.' I have foolishly stuck my neck out and made the first comment on the blog of Klaus Rohde, one of my colleagues, so now I thought I may as well go ahead and create the science blog I have been meaning to create for some time.

I am most interested in free radical polymerisation, though my research covers a much broader area and my teaching covers a much, much broader area. I expect the first things I will do here will be to:

(1) Explain why homeopathy is even less scientific than 'intelligent design',

(2) Explain in physical chemist's language exactly how this global warming thing works, and

(3) Work in some more extended Lilo and Stitch references.