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.
Tuesday, April 24, 2007
Monday, April 16, 2007
An especially egregious example...
...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? :)
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.
Saturday, April 14, 2007
Thursday, April 12, 2007
The Electrochromic Effect
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:
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!
"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!
Friday, April 6, 2007
Twitch, twitch, twitch, twitch...
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...
Thursday, April 5, 2007
In the beginning was the Metabolism
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.
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.
Tuesday, March 27, 2007
Such things are sent to try us
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:
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?'
Sunday, March 25, 2007
Bearing fruit in keeping with repentance
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.
The Funneled Web currently has an article about other universities that have not yet seen the error of their ways.
Friday, March 23, 2007
Delta T
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 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.
Monday, March 19, 2007
The Prolific Anonymous Writes:
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!
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!
Sunday, March 18, 2007
Intelligent Design
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
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
Thursday, March 15, 2007
I want a shoehorn, the kind with teeth
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...]
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...]
Monday, March 12, 2007
XTC vs Adam Ant
Richard Feynman, ‘The Feynman Lectures on Physics’:
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.
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.
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