Mostly Harmless Science Blog

Thursday, April 14, 2016

Where I'm At, Four Years On

I thought I ought to cross-post this from my anonymous blog, since an anonymous declaration of faith is no declaration of faith at all.

You will recall my strong and often repeated affirmation of the quote attributed to Max Planck: ‘Experiments are the only means of knowledge at our disposal. Everything else is poetry, imagination.’

For some time I have been having a discussion with Marco and scute1133 about what qualifies as science in the historical sciences-  in disciplines like biology, geology, astronomy, where you cannot do an experiment, how exactly do we obtain knowledge? Knowledge, that is, of the how, as opposed to the what; for it is very easy to catalogue stars or beetles. [‘All science is either physics or stamp collecting’ (Ernest Rutherford)]  You may also recall that I previously flagged the problem of knowledge in the historical sciences as the main problem of philosophy of science.

We are agreed that basically what we do in the historical sciences is rely on experiments that have been done for us by nature. We postulate a model for how something occurs that suggests that we should never observe a particular phenomenon in nature, and if we do observe that particular phenomena, that model is falsified, in the same way as a model that suggests we will not obtain a particular result in an experiment will be falsified if we do the experiment and obtain that result. We are agreed on the additional proviso that the model should not contradict any of the physical laws we have determined with the experiments we can do in the here and now – the principle of uniformitarianism, endorsed by faith alone, since we are in virulent disagreement about the validity of parsimony as a guiding principle which would lead us to uniformitarianism. Where I also differ from Marco is on an insistence that this lack of contradiction be made explicit in terms of a mechanism: a story that is not entirely implausible that explains exactly how this observation distant in space or time can be explained using the physics and chemistry we have nutted out here on Earth.

A distinction that we have come up with in the course of this discussion is between the primary and secondary utility of a model.

If our model predicts that we should observe something that we have not yet observed, and we look for it, and find it, then it has primary utility. It is scientifically useful in the proper sense.

Everything else our model might be good for comprises its secondary utility. If our model fits comfortably with our worldview in other matters, or provides us with a good job, or helps maintain the stability of the Overlord’s rule, or is a great plot element in action adventure films, it has secondary utility. The realisation that Marco has had for a long time, which  has dawned on me much more slowly, is that a great deal of what we teach as science in the historical sciences is taught for its secondary utility rather than its primary utility.

Thus the models of anthropogenic global warming have made terrible predictions over the past quarter century; but there is a lot of money in anthropogenic global warming, and it dovetails beautifully with the statist agendas of all kinds of powerful lobbies, so it trundles along unstoppably. The models of abiogenesis we have are laughable and have predicted nothing, but the alternative of special creation is anathema, so we defend to the death our ‘science of the gaps’ against the ‘God of the gaps’. In the tiny and specialised hothouse of cometary science where Marco and Andrew live and breathe and have their being, the ‘contact binary’ model for the formation of bilobed comets, incredibly implausible to begin with, becomes less plausible with every example that is observed; but (IMHO) it allows the valuable fiction that comets are unchanged relics of the cloud from which the Solar System formed to continue, so its flaws are excused or ignored.

This realisation of the narrow limits of primary utility threw me back on my resolution a few years ago to only believe what I could not disbelieve.

Quoting myself:

“What do I mean by ‘believe’ or ‘disbelieve’? I favour the definition provided by the 19th century American philosopher Charles Sanders Peirce: ‘A belief is a habit, i.e., a readiness or disposition to respond in certain kind of ways on certain kinds of occasions.

With this definition, it should become evident that there are some things that cannot be disbelieved. We cannot disbelieve F = GMm/r2, in that we cannot habitually behave as if it were not true: each time we behave as if it were not true, we are likely to injure ourselves, and if we attempt to make it a habit we are sure to break before the universe does.

In the same time as we cannot disbelieve F = GMm/r2, we cannot disbelieve that life is better than death. Believing this, which means acting upon it, we cease to exist.

I think the idea that death is better than life is one of a small number of beliefs that, believed in a Peircean way, will destroy any functioning society, and so collectively cannot be believed. The antithesis of these beliefs is what C. S. Lewis called the ‘Tao’: the nugget of ethics common to every ethical system we know about.”

Now, it is obvious to me that outside the narrow limits of primary utility where we can carry out experiments there is a vast sea of habits that are necessary for individuals and societies to uphold the ‘Tao’. These habits cannot be justified by experiment; they have predictive value only over a scale of millennia, in terms of the fitness of the societies that practice them.

I have argued before that Max Planck’s quote is not pejorative: that imagination and poetry are beautiful and necessary things. And I have argued before that Max Planck’s quote leaves us free to choose our own poetry: the facts of science in no way force us to pick the pessimism of Housman over the joy of Manley Hopkins.  And for some time I have been feeling useless, adrift in idea space, paralysed by anger and intermittently making efforts to ignore all news beyond the narrow limits of home and work.
Then I looked up from the realisation of the narrow limits of primary utility brought about by this discussion to realise that my intellectual quarrels with the Catholic Faith had somehow evaporated while I was not trying to be Catholic anymore. I recalled the quote ‘truth cannot contradict truth’ and remembered again that the Church teaches nowhere anything that is in contradiction to the certain knowledge of the experimental sciences. 
And I realised that I did not really have a free choice of poetry: I had a clear duty to chose the poetry that could best serve the overwhelming secondary utility of protecting and advancing the ‘Tao’.
Against the abyss of relativism where the punishment of anyone who dare to claim 2 + 2 = 4 is swift and vicious, against the apocalyptic tide of rage convulsing Dar-al-Islam, I can see only one thing standing firm in the world.

So I have resolved, by the grace of God, to henceforth display consistently a readiness or disposition to respond in Catholic ways on as many occasions as possible.

Monday, February 1, 2016

Vale Professor Bob Carter

I was very sorry to learn on the weekend from my Mum that Prof Bob Carter had died. I had not known before that he had actually been hired by James Cook University to fill my grandfather's position, when he retired. I cannot remember ever meeting Prof Carter, but I did try to contact him once in 2007 - despite doing my best to grab his attention, see below, he must have been too overwhelmed with unsolicited email to notice me. 73 once seemed an impossibly distant age; but from here at 45 I am alarmed to realise that it is just as close as 17, which doesn't seem long ago at all. I haven't been back to Nong Khai or Pearl Harbour or Bellagio or Fargo or Bochum in the past 28 years. I probably never will.  And actually talking with Prof Carter is now something that I certainly never will do. So swiftly life passes.

Carpe diem, gentle reader, carpe diem.


I am Bill Lacy’s grandson, PhD graduate of JCU, and a lecturer in physical chemistry at UNE.  You must be deluged with mail all the time, so I thought I would put all those biographical bits in the first sentence to try and grab your attention!

I think the reason there is a ‘scientific consensus’ about anthropogenic global warming is because the mechanism is so good, even though the y = mx+c plot of temperature vs. [CO2] looks so spotty.  ( )  This makes it the opposite of continental drift, where the evidence was so good for hundreds of years but nobody could think of a mechanism so they quite rightly dismissed the idea.  Of course, the mechanism that is so good also implies that AGW cannot possibly be the existential threat it is made out to be.

What I mainly want to say is that ‘AGW does not exist’ is a position that has uncertain supply lines and is too exposed to enemy fire.  Veterans like yourself are needed to fall back and defend the stout battlements of ‘attempting to stop AGW is doomed to failure and a witless failure to prioritise’, with Bjorn et al. (Including me, in a tiny way- see Chemistry in Australia, Jan/Feb 2007).

Best regards,


Edit 11th February: I should say that I have reconsidered the position that I proposed to Prof Carter in the email above. While I still think that 'AGW does not exist' is not a proposition that has any chance of victory in the foreseeable future, I think that is important that people are prepared to voice it articulately and intelligently. This is because the 'Overton Window' - the volume of acceptable ideas in idea space - is defined not only by what it contains, but by what is outside it. Its limits are not fixed, and if all the ideas being expressed articulately and intelligently are within it, it will tend to contract. Keeping it open as wide as possible is good for our species.

Tuesday, January 19, 2016

The Science Delusion

I have some sympathy for people who believe dumb things just because everyone else does, but I find it very tedious arguing with them on the internet. I am equally sympathetic toward people who believe sensible things just because everyone else does, but I am always a little nervous because I have seen in my own life just how quickly and completely they can turn into the first kind of people.  It is awkward when they join in to help me argue on the internet and I would rather they didn’t. Ideally I would like people to believe sensible things for good reasons; but a close second would be people who are willing to stand up, unsupported by a community of like-minded believers, and believe dumb things for bizarre idiosyncratic reasons.

Which brings me to Rupert Sheldrake and ‘The Science Delusion’. I haven’t read  the book, I just watched the TED Talk (Banned! ZOMG!).  Sheldrake starts by defining ‘The Science Delusion’ as ‘the belief that science already understands the nature of reality in principle, leaving only the details to be filled in.’ This is indeed a delusion; and a dangerous one. Making overblown claims for science, like making overblown claims for dialectical materialism or the healing power of turtle gall bladder extract, is going to make science look stupid when it turns out that reality is different from what we said it was. This will lead people to distrust science and more readily embrace the alternative, which is usually to believe all sorts of dumb things just because everyone else does. I was heartened by this first statement of Sheldrake’s and would have been very happy if he had gone on to explain what science is and how it works; and how science does not, and cannot, understand the nature of reality in principle. This would be a very valuable thing to do in a TED talk and might just be possible in 18 minutes.
But instead, ah, Sheldrake first accuses science of being a wholly owned subsidiary of the materialist worldview, which has never been true, but was much more true in the late 19th century than now; then lists ten ‘dogmas’ of science which he thinks would be better phrased as questions; and then explores - sort of - a few of these in detail by expounding his own bizarre idiosyncratic theory of ‘morphic resonance’ and talking about evidence for variations in fundamental physical constants.

The ten dogmas Sheldrake quotes are:

1.       Everything is like a machine.

2.       Matter is unconscious.

3.       The laws of Nature are fixed.

4.       The total amount of energy and matter in the universe is constant.

5.       Nature is purposeless.

6.       All heredity is material.

7.       Memories have a material existence in the brain.

8.       The mind is inside the head.

9.       Psychic woo is impossible.

10.   Mechanistic medicine is the only kind that really works.

I’ll take each of these in turn, rephrase it as a question, and see if I can find anything valuable in doing so.

1.       Is everything – the universe, animals, plants, us – like a machine?  Well yes, and no. This depends on what we mean by ‘machine’ and what we mean by ‘like’. The human mind operates on metaphor and analogy and imperfect simplified models for complicated things, so it is quite right to say that all of these things are ‘like a machine’ in the same way as it is right to say that the planet Earth is ‘like a grapefruit’ or an electron is ‘like the planet Earth orbiting the sun’; they are imperfect analogies that fit some properties of the object or phenomena, and it is important to remember that this is to some extent true of every model we use, no matter how complicated and beautiful . Every model will be shot through with metaphors and analogies that carry emotional baggage for good or evil, and every model will fail to correspond adequately to reality under some conditions. They may be near and common, and we might stick with our model simply because it is the best rule of thumb we have; or they may be far and few, and we may be misled into thinking that our model is the true picture of reality. So yes, all these things are like machines, in that like machines, there are conditions where simple inputs give simple outputs where we can follow all the intermediate steps of cause and effect. We press the green button, it engages lever C, which turns cog B, and some flap opens and we get a can of Coke. Using the analogy of a machine for all sorts of things can be incredibly useful. Of course, we know that living systems often use rely on complex systems with lots of inputs and surf the interface between chaos and order (to hand wave around a lot of things that have a solid mathematical basis) where we would be mad to design machines that work that way. And we know that as far as we can tell, when we drill down towards more fundamental building blocks of all the things we see, we get to the quantum world, where particles behave less like machines than anything we can imagine. 
       All in all, thinking of things in the universe as being like machines is usually going to be a fruitful way to think about them; but we must remember that this is an analogy, while at the same time not falling into the hippy-dippy trap of imparting quantum weirdness to the macroscale.

2.       Is matter unconscious?  I would answer not ‘yes’ or ‘no’ or ‘yes and no’ but ‘meh’.  My take on the (un)importance of consciousness is here. I think it is quite clear that we are part of a continuum of entities, and that a dog, for instance, has an inner life the same as we do; and that a moth probably does, and that in some sense so does any system that is taking in impressions from the outside and reacting to them.  It does not seem to me that the fact that we are conscious is of any great importance for our understanding of the universe. I feel quite strongly that setting up consciousness as something distinct from the material world would be a retrograde step that would impede, rather than improve, our understanding of reality; I am one of those materialists who believe it is exhilarating and wonderful that everything is made of matter, this fantastic and mysterious stuff.

As far as sentient galaxies and conscious electrons – well, matter is strange. I have no evidence one way or another. Why not? If these hypotheses can explain things otherwise unexplained, I see no reason not to entertain them.

3.       Are the laws of nature fixed? This is a question that is amenable to observation. Looking at rocks laid down billions of years ago, and out into space at places billions of light years away, show things that are consistent with the laws of nature being the same, or very, very, very similar, everywhere and everywhen that is observable, until we get to these messy ‘singularities’. So in practical terms, the laws of nature are fixed, with the exception of things that physicists are well aware of and worry about a lot. This of course has nothing to do with the nature of reality in principle. The laws of nature may not be fixed of necessity over the extent of time and space over which we see them fixed, any more than the endless streams of traffic we might watch from an overpass are necessarily going to stay in their right lanes. Maybe it is just electrons obediently following Schrödinger’s equation the way commuters are obediently following the road rules. We don’t know. But for any practical purpose, sure. The laws of nature are fixed.

4.       Is the total amount of energy and matter in the universe constant? This is a really a subset of 3. This is undoubtedly one of those key laws of nature that are fixed for all practical purposes. So far, every time we have thought this law wasn’t true, we have found another source of energy to balance it out. But ‘continuous creation’ was a viable cosmological hypothesis within living memory. And we know particles can ‘wink into existence’ in the vacuum.  But again, like 3, *for any practical purpose* the answer is ‘yes’. I would be very, very, very wary of postulating ‘maybe matter and energy aren’t conserved here’ as a hypothesis to explain any macroscopic phenomenon.  Experience has taught us that such a hypothesis is very, very, very likely to be wrong.

5.       Is Nature purposeless?  The only answer to this is ‘we don’t know’. We cannot know without information about whatever larger reality our universe is embedded in, information which we cannot obtain by any conceivable observation made within our universe. It may be as futile and purposeless as a Quentin Tarantino movie on the inside, and have been crafted  for some purpose that makes sense on the outside with the same meticulous care, like a Quentin Tarantino movie has the purpose of making oodles of money.

6.       Is all heredity material? Trivially, the answer is ‘no’, because culture is non-material heredity, and lots of social ‘higher’ vertebrates have culture. New cultural behaviours have been observed being developed and inherited in baboons, whales, probably magpies, and of course, us. Less trivially, all the inherited features of organisms can be explained perfectly well by material causes – recombination of genes, horizontal gene transfer, maternal effect genes, environmental effects on gametes and developing young, etc. There is *no need* to postulate an alternative explanation based on some kind of mysterious woo that has no plausible mechanism, to explain phenomena that are already well-explained in terms of well-understood mechanisms.  This mysterious woo in Sheldrake’s case is what he calls ‘morphic resonance’ and his explanation of the evidence for it is as unconvincing as twenty-seven unconvincing things found in a viral list of ‘The Twenty-Seven Least Convincing Arguments of 2015’.

7.       Are memories stored as material traces within the brain? Well, you can erase memories by destroying  bits of brain. Not feet, or eyeballs, or sections of colon, or paperclips in a desk drawer, or trees in Africa, or mountains on the dark side of the moon. This is good prima facie evidence that memories are indeed localised in the brain, and again there is *no need* to postulate an alternative mechanism based on mysterious woo.

8.       Is the mind inside the head? Well, yes, see #7.

9.       Is telepathy, etc., illusory? Probably. There is no evidence for it that is screaming out to be explained. Like this paper about gender bias in physics teachers in the German-speaking world, it is just humans seeing patterns in noise. IMHO. If evidence for telepathy or whatever emerges that screams out to be explained, my patient conservative biases would lead me not to discount it out of hand, but to seek explanation for it in terms of the physical science we already know, rather than embracing the mother of all paradigm shifts into a brave new world of woo. And I am confident that 'in terms of the physical science we already know' is where the explanation would be found.

10.   Is mechanistic medicine the only kind that really works? Here again it depends on our definitions. There is absolutely no compelling evidence that any treatment for anything is effective unless it affects the physicochemical status of the human body. Do we understand the mechanism of every treatment that is effective? We don’t. Modern medicine is still (scarily, to me) very much a matter of ‘take this cocktail of drugs that have been statistically shown to be effective’.  Does this mean treatments whose mechanisms are unknown will turn out to depend on crazy new principles unrelated to existing science? Experience suggests the answer to this is ‘no.’ Mechanistic medicine is the only kind that works, even if we don’t understand the mechanisms yet.

So expressed with a bit of humility and nuance, there is something in most of Sheldrake’s questions. He probably is a crazy ideologue pushing a daft agenda (like Richard Dawkins); but a lot of what he is actually saying is worth thinking about (again, like Richard Dawkins).

Wednesday, December 16, 2015

Okay, here's another modest proposal

You know if you’ve had more than a cursory look at this blog that I am some way along the ‘sceptical’ continuum as far as Anthropogenic Global Warming goes. But one thing I have learned is that it is not enough to complain about things, one ought to make constructive suggestions. So here goes.

If we were serious about (a) proving cause and effect as far as Anthropogenic Global Warming is concerned; and (b) trying to stop it, there is one bold action I would happily get behind.

This would be grounding all the world’s aircraft for a few years. Take all the money currently being spent on various carbon trading schemes and bureaucracies and uneconomic renewable energy schemes and give it to the airlines to pay them to mothball their machines and pay their staff to sit around doing nothing. 

The rationale for this is two-fold:

1. We have a pretty good idea anthropogenic cirrus clouds from aircraft have a significant warming effect. And the warming observed over the past half-century is localised most strongly where these anthropogenic clouds are: in the northern hemisphere, not the south; and over continents, not oceans. 

2. All greenhouse gases are not equal. When I drive my car down the Princes Highway past the towering eucalypts of Royal National Park, I know that the water and carbon dioxide bands in the atmosphere at ground level are pretty nearly saturated, so the emissions of my car will not make a great deal of difference to how much additional infrared energy is absorbed. And I know also that my car’s emissions are not going to stay in the atmosphere for long, because those aforesaid towering eucalypts and other green plants are going to enthusiastically suck them up. When I fly down to Sydney, though, it worries me. The plane I’m riding is spewing carbon dioxide and water vapour out into a part of the atmosphere that doesn’t have a lot in it already, a long long way away from any plants that can use them.

I’ve made these arguments before on this blog, but not recently. So I figured it was time for some repetition.

Stopping aircraft for a few years should give a very good idea what proportion of the observed warming is due to anthropogenic cloud and emissions of greenhouse gases at altitude, and hence whether carbon dioxide emissions per se are worth stressing over.

I think the economics of this are solid. The maximum annual profit airlines have made recently seems to be of order $30 billion, and there probably aren’t more than 4 million people who would need to be paid to do nothing, as opposed to being swapped immediately to productive jobs elsewhere in the newly frisky sea and rail freight sectors. So maybe another $100 billion paid to them. That’s less than we’ve been spending in silly ways in recent years, I’m pretty sure.

Tuesday, December 15, 2015


Historically, scientific journals got started as a way to share information. They were the most effective ways to tell other researchers what you were doing and find out what they were doing. Nowadays, they aren’t really. They are complicated intermediaries – which add some value, true – between you and the people you want to share information with. They have rules which are largely arbitrary and which impact negatively on how useful  they are as media for sharing information with people – rules about how long a paper should be, about how it should be structured, about what should be put in and what should be left out. More importantly, their primary function nowadays is not to share information, but to score points in The Academia GameTM, one of the first and most dramatic successes of the ‘gamification’ craze.
Anyhow, I think the search engines we have nowadays are good enough to cope with a bit of disintermediation; so I thought I would have a go at sharing my information here instead. Some of it, anyways. I’ve got a piece of work, you see, that I can’t see scoring any points, and I want to tell you about it.

Back in my PhD I came across a paper on work done by two researchers at the University of Texas El Paso in the 1970s, Wang and Cabaness. In this paper they had investigated the copolymerisation of acrylic acid (AA) and acrylamide (AAm)  in the presence of a number of Lewis Acids of general formula XCl4, and reported that tin tetrachloride could induce the formation of a copolymer with the regular repeating formula ((AA)4(AAm)) – four acrylic acid residues in a row, followed by an acrylamide unit, rinse repeat – which they attributed to a 1:1 alternating copolymerisation of a SnCl4(AA)4 complex and acrylamide.
Structure postulated by Cabaness and Wang 1975
I was intrigued by this article, because I was also studying polymerisation with Lewis Acids (only alkyl aluminium chlorides rather than the XCl4 species), in systems where we got 1:1 alternating copolymers of donor monomers (like styrene, butadiene, vinyl acetate, or acenaphthalene) with acceptor monomers (like acrylates, methacrylates, and oh yes, acrylamides and methacrylamides). The whole basis of our understanding of these systems was that complexes of acceptor monomers with Lewis Acids made them fantastically better at being acceptor monomers, and I couldn’t see how four monomers that were all complexed to a single Lewis Acid ought to polymerise together: if they were better acceptors, they would be less likely to polymerise with each other, and once one added onto a growing polymer chain it seemed to me that it would be more likely to add a (relatively donor-ish) free acrylamide rather than one of its fellow complexed acrylic acids that was probably held in a sterically unfavourable position, as well as an electronically unfavourable condition. And 4:1 regular polymers had never been reported with acrylic acid and any more conventional donor monomers that would be more likely to behave themselves. It was all very mysterious. Nobody had ever confirmed or followed up on this work of Wang and Cabaness; which was disappointing, but not very surprising, because the whole field of playing with various Lewis Acids and donor and acceptor monomers had been a big thing over approximately the years 1968-1975 and had then petered out for no good reason.

So many years later I found a bottle of SnCl4 lying around (it’s a liquid; it comes in bottles – the Sn(IV)-Cl bond has a lot of covalent character) and remembered this paper and thought I would have a go. Wang and Cabaness had only looked at their polymers using elemental analysis, which realistically tells you about 2/10 of not very much about polymer structure, whereas I had spent quite a lot of time looking for regularity in polymer sequences using Nuclear Magnetic Resonance Spectroscopy, which tells you an awful lot, and I thought I would make the polymers they made and have a look at them with NMR. The proton NMR spectra of polymers are always broad, and the backbone protons of acrylic acid and acrylamide residues (as you can guess from their structures) end up on top of each other in a messy way.  So the way to tell what is what is to do carbon-13 NMR spectra, which gives you nicely resolved peaks in the carbonyl region, and reasonably well resolved peaks for the methine carbons.  If you look at the carbonyl region of a copolymer of AA and AAm, you can pick out the six different nearest-neighbour environments quite nicely. In the figures below, for example, you can see clearly how base hydrolysis of PAAm generates isolated AA units on the chain, which have a protective effect on neighbouring AAm and make it much less likely that they will be hydrolysed.
Carbonyl (left) and methine (right) regions of  13C-NMR spectra of polyacrylamide at different levels of base hydrolysis. From: Yasuda K, Okajima K, Kamide K. Study on alkaline hydrolysis of polyacrylamide by carbon-13 NMR. Polym J (Tokyo) 1988:20(12):1101-1107.
Carbonyl region of 13C-NMR spectra of AA-AAm copolymers. From: Candau F, Zekhnini Z, Heatley F. I3C NMR Study of the Sequence Distribution of Poly(acrylamide-co-sodium acrylates) Prepared in Inverse Microemulsions. Macromolecules 1986:19:1895-1902.
 Now, when I got back and had a look at the paper again, I was troubled by the times given by Wang and Cabaness for these reactions. These sort of radical reactions usually have an inhibition period when nothing much happens at the beginning, even if you take pains to get rid of dissolved oxygen from the system first. The reported reactions were done under nitrogen. So, if you bubble nitrogen through a reaction mixture enough to get rid of oxygen, to do a halfway decent job you need to do it a lot longer than the 100 s or less quoted for these reactions. So you would have to bubble nitrogen through at room temperature, then shift to a higher temperature, at which it would take a lot longer than 100 s to warm up to the quoted temperature values. Maybe the times quoted were the time it took after the inhibition period finished, but before the reactions were quenched? Which would mean Wang and Cabaness would have had to have been watching their reactions like hawks, and even so quoting reaction times to a precision of one second was a bit ridiculous. So, anyhow, I resolved to cut the temperature down to 60 °C to give me a bit more time to work with and quote reaction times in minutes rather than seconds.
Table 3 - the tin tetrachloride data - from Wang and Cabaness 

I first tried doing what I would usually do, which is freeze/thaw degassing I still had a significant inhibition period after I put the samples in a 60 °C oil bath. When anything happened, it happened too fast for me to stop it, and what it was, was my polymer ‘popcorning’ into a solid mass. This is something that happens with monomers that polymerise very quickly. Polymer solutions are viscous, and transfer heat worse the more viscous they get.  Polymerisation reactions are exothermic. So, a polymerisation that goes quickly generates a lot of heat and a viscous solutions which makes it difficult for the heat to dissipate, and as the temperature increases the reaction goes faster, making it even hotter and more viscous, and you get very quickly to a temperature where your solvent vaporises, and your polymer chars, and if you are doing a reaction in a 20 tonne reactor instead of a tiny little tube you ring the insurance company. That is what happened to my first attempts: they polymerised into intractable masses that I couldn’t get out of my reaction vessels without smashing them and then wouldn’t dissolve once I’d smashed them out.
I decided to drop the freeze/thaw degassing and use the dodgier ‘sparge with nitrogen’ method in round bottomed flasks that would be (should be) easier to get the polymer out of.

Yes, I could get the polymer out without smashing anything. But the reactions that formed it were the same: the vessel sat there for a while without doing anything, then suddenly there was the popcorny noise of solvent vaporising and insoluble masses with yields of approximately 100%.
I cut the temperature a bit further, and cut the concentration of everything a bit, and still couldn’t get any useful polymer. 

Then my colleague Daniel Keddie suggested something that made a lot of sense which I should have thought of a long time before: why not put in a chain transfer agent? This is something that cuts the length of the polymer chains but shouldn’t (knock wood) have any more dramatic effects on the chemistry of the reaction: it just introduces a ‘jump to a new chain’ step that replaces some of the propagation steps. So I put in enough butanethiol to reduce the degree of polymerisation to about 25 and had another go. And I got polymers I could remove from round bottom flask, which actually dissolved up okay! These proceeded to a conversion of about 40-60% when heated at 60 °C for 30 minutes – again, almost all of this time was inhibition period, so I couldn’t actually stop any of the reactions at a low enough conversion to get an unambiguous relation between the composition of the polymer and the feed composition of the monomers.
Following the next step of the procedure – dissolving in water and reprecipitating in methanol – was a little tricky, because the polymers were reluctant to dissolve in plain water. So I added a bit of base to convert the acrylic acid residues to sodium acrylate – and crossed my finger and kept the temperature low to avoid hydrolysing any of the acrylamide residues to sodium acrylate. And I managed to get some halfway decent carbon-13 NMR by running these overnight, like so:

Carbonyl region of 13C NMR spectra of AA:AAm:SnCl4 polymers made by lil' ole me
Now the area of these peaks should be pretty much proportional to the amount of carbon contributing, so what you can tell straight away from these results is that the products  don’t have a constant  4:1 AA:AAm composition, so the mysterious result of Wang and Cabaness is artefactual.
The spectra aren’t similar enough to be of 1:1 alternating copolymers, either – there is always excess AA, and the main AA peak always starts out as  the one with one AA and one AAm neighbour. If I was getting a 1:1 alternating copolymer and then hydrolysis, I would expect to see significant amounts of AA with two AA neighbours coming in as soon as the AA with two AAm neighbours started to disappear.

Besides these negative results, though, there isn’t a lot that I can say. The tin tetrachloride is doing something: it is making the reaction go a lot faster than it would.  It *might* be encouraging a tendency towards alternation. Because of composition drift, though, and because of the uncertainty in the literature reactivity ratios, I can’t tell for sure whether there is any shift in the polymer composition compared to what I would see without the tin tetrachloride.  It looks to me like I am getting a significant amounts of base hydrolysis of any acrylamide residues which aren’t alternating – which is what you would expect from the literature.
In order to publish this, I would need to make sure my 13C NMR was quantitative, which wouldn’t be too hard. I would also need to work out a way to kill my reactions quickly, and I would need to figure out a way to reprecipitate the polymers without hydrolysing the acrylamide residues. Obviously these are soluble problems, but this system isn’t doing the really exciting thing it was reported as possibly doing, and doesn’t appear to be doing anything moderately exciting, so I don’t know if it is worth carrying on with.


1)      I have no idea how Wang and Cabaness got something out their system that they could dissolve and reprecipitate and find viscosities of.

2)      There is no evidence that the 4:1 acrylic acid: acrylamide composition they report can be reproduced.

3)      People probably tried to repeat their work before, and came to the same conclusion, but didn’t put it on the internet.

Wednesday, July 1, 2015

One may be regarded as a misfortune; two begins to look like carelessness.

This is a post not so much about planetary science, as about the sociology of science. If you have been following recent developments in the astronomy of the solar system at all, you will know that the comet 67P-Churyumov-Gerasimenko has a funny shape. The standard working explanation for this is that it has a funny shape because it has been formed from two comets that have collided and stuck together, a ‘contact binary’, and explanations that ascribe its shape to deformation or ablation of an initially more spherical object are marginalised.

I have not understood why, but now I think I do.

First of all, I should explain that my biases are all the other way around. I would be inclined to go through the most elaborate mental gymnastics to avoid having to suppose a body was formed  from two things running into each other. This is based on two things: firstly, common to all people who do not get their picture of space primarily from space opera, my perception of space is of someplace that is very big and very empty where things move very fast. I do not expect to be hit by a comet any time soon. If I am, I expect the relative difference in our velocities to be such that we will not end up as a ‘contact binary’, but as a mass of superheated comet and minor scientist-derived dust. Secondly, in my particular case, I am used to thinking about chemical reactions, and I know that almost all collisions of molecular bodies in the gas phase do not end up with them sticking together; without a third body to take excess kinetic energy away, they are too energetic to stick together, and fly apart again. I know very well that comets are not very much like molecules, and there is no reason to behave in exactly the same way, but that is the intuitive bias I have about things running into each other in a big empty space: chances are that if they not smashed to flinders they will bounce off one another, and never come within coo-ee of each other ever again.

I have been drawn inexorably into thinking about comets by Andrew Cooper and Marco Parigi, and I interpret the shape of 67P-Churyumov-Gerasimenko as they do, in terms of the ‘Malteser’ model I have outlined below: a brittle, dense crust has developed on the comet surrounding a deformable core, and at some time in the past this crust has ruptured and the gooey interior has stretched. If this were true, unless it happened a very long time ago indeed, the neck of the comet should be less depleted in volatiles, and that is where most of the water sublimation should be coming from. This seems to be the case.
67P-Churyumov-Gerasimenko, being awesome.

Yesterday I found out, being a slow newcomer in the comet world, that 67P-Churyumov-Gerasimenko is not the only comet with a funny shape. There is 103P-Hartley 2. It has a relatively smooth neck, and this neck is also associated with direct sublimation of water, as would be expected if it had a fresher surface that had been exposed for a shorter time.

103P-Hartley2. The bright light from the rough end is coming predominantly from chunks breaking off a frangible surface and subliming, if I have understood correctly.
And – ahem – it was also suggested that 103P-Hartley 2 is a contact binary. To quote Lori Feaga and Mike A’hearn of the University of Maryland*, 8th October 2011: "The heterogeneity between lobes is most likely due to compositional differences in the originally accreted material. We are speculating that this means that the two lobes of the comet formed in different places in the Solar System.  They came together in a gradual collision and the central part of the dog-bone was in-filled with dust and ice from the debris."

I might be prepared to grant one contact binary, since the universe is a strange place, and all manner of things can happen. But two from such a small sample size? I don’t think so.

But as I said at the beginning, this isn’t supposed to be a post about planetary science. It finally struck me yesterday why so many people would cling to the idea that funny comets are formed by bodies sticking together.

Paper after paper refers to comets as ‘primitive’; relics of the primordial Ur-cloud out of which the solar system accreted, from which we can learn about the nature of the Ur-cloud. If comets are not primitive – if they have suffered all sorts of physical and chemical transformations as a result of repeated annealing by swinging by the sun – then they don’t tell us anything about the Ur-cloud.

I think a lot of people who study comets are very interested in the Ur-cloud. They got into comets in the first place as the best way they could approach this beast, whose nature is so important for understanding the overall history of the solar system and all those other solar systems out there. They are not necessarily interested in comets as ends in themselves. The contact binary model is the one way that observed heterogeneous, oddly-shaped and oddly-behaved comets can be reconciled with observable comets as primordial bodies. So, if you are interested in the antiquity of the solar system, what are you going to do? Accept that ‘you can’t get there from here’, or grab at this improbable lifeline that leaves the road unblocked?
*: In the interests of full disclosure, I was once a resident of Maryland, when my father was in the army. We moved back to Arizona when I was 2.

Tuesday, June 30, 2015

Questions Nobody is Asking, #2137 in a series

My Google skills are failing me.

I've tried a couple of times recently to find an answer to the question, 'How does Google Scholar decide what order to list your co-authors in?'

Clearly, it's not alphabetical.

It doesn't seem to be based on any of the six indices that are quoted for each academic: not total publications, or publications since year x, or h-index, or h-index since year x, or i10-index, or i10-index since year x.

It doesn't seem to depend on *when* we published together.

Or when my co-authors took ownership of their Google Scholar profile.

Or how often we have published together, or how well the publications we have *together* have been cited.

It doesn't fit with any indices divided by years since first publication, or when a co-author first published, or any simple combination of any of the above that I can think of.

The one thing I can be sure of is that it is linked to individual papers somehow,
And I was about to say, aha, it is something to do with the impact factor of where we first published together, since my last two co-authors I am only on conference papers or book chapters with; but that isn't going to work either.
I dunno. I expect it is some complex proprietary multi-factorial algorithm. Names never seem to move once they are in the list, so maybe it would make sense if I looked at the values of some parameter or other at the time a co-author was added to the list. Or else my basic observation skills and Google skills are equally weak lately and I need a holiday to be fit for mental work. Or - maybe it is totally random, so no one has to feel bad about being everybody's last listed co-author. 

Monday, March 16, 2015

Another Brief Statement of the Obvious

There are four chief obstacles to grasping truth, which hinder every man, however learned, and scarcely allow anyone to win a clear title to knowledge: namely, submission to faulty and unworthy authority, influence of custom, popular prejudice, and concealment of our own ignorance accompanied by ostentatious display of our knowledge.

                        - Roger Bacon (1266)

Wednesday, March 11, 2015

A naive look at comets

Okay, the relentless drip-drip-drip of Marco's comet obsession has finally gotten to me. I said I was going to post something about how you could get a mass distribution in comets that was consistent with the 'brittle crust, gooey low-tensile strength centre' required for the observed morphology of 67P-Churyumov-Gerasimenko.

So here it is.

I’m going to assume we start with a homogeneous mass containing all the things that will be solid grains out at a temperature of very few K and that have been shown to be in comets. So sodium and magnesium silicates, and ammonia, and methanol, and carbon dioxide, and carbon monoxide, and water, and methane – and importantly some higher hydrocarbons, which haven’t showed up in the gas from 67P-Churyumov-Gerasimenko but seem to be attested in other systems. I guess the primordial assumption behind this is that comets formed from the outer edges of the big solar system Ur-cloud, so weren’t subjected to much in the way of fractionation processes beforehand. If this is some terrible error in cometology, please let me know.
We roll all these things into a ball using gravityTM and hurl it towards the sun.
As it gets warmer on the surface stuff that is most volatile, like methane, will sublime first, and leave behind a very fluffy residue of stuff that doesn’t want to sublime as easily.

Some of this fluffy stuff will flake off and float away; probably a lot; but it will also invariably compact as bits flake off and lodge with other bits, and at temperatures where higher organics are not volatile but the small molar mass stuff is, these latter will end up concentrated on the surface where they can soak up all those lovely cosmic rays and start forming larger crosslinked molecules by radical-radical recombination.
Okay, if the mass of the comet  is small this evaporation process will just continue until you are left with a relatively dense mass of non-volatiles. But if the mass is bigger, this surface layer – which is gradually getting more compact and more enriched in high molar mass organics as we approach the sun – will start acting as a barrier to the progress of gas molecules from the warming interior.
And eventually, I can imagine this means there won’t be vacuum at the interior surfaces where sublimation is occurring, but appreciable pressure. There seem to be abundant studies in the literature for gas building up in comets.

Now, once the pressure and temperature increase above the triple point of any of the constituents of the comet interior, there will be the possibility for liquid to exist there.
I’ve plotted the triple points of some constituents of comets below.

(Note, if you are unfamiliar with triple points, that these are the bottom points of triangular areas where the liquid state can exist. The exact phase diagrams of things are much more difficult to find than the triple points and may not have been mapped out in detail for all of these.)
The species that are going to be liquid at relatively low temperatures and pressures are relatively minor constituents of comets, of the order of a few percent in total (probably), so we won’t get a gooey liquid core, but a ‘moist’ core with liquid on the surfaces of solid grains, like a fairly dry soil. This will happen at temperatures and pressures far below what we would need to liquefy water, and these liquids will persist in the core as more volatile components turn into gas and bubble out, while the shape of the comet is maintained by the outer layer of non-volatiles gummed together by organic polymer.

Now, when the comet flies out into the cold again, the interior part of this liquid core is likely to freeze before it evaporates, leaving the core of the comet no longer a loose aggregation of stuff, but particles of relatively non-volatile components sintered together with a layer of frozen hydrocarbons. This will still have a low tensile strength, but I would think this sintering would significantly improve its compressive strength. And the different levels of degassing possible from a fairly rigid external shell would fit the great variability in comet densities observed.  There may also be interesting fractionation of one component freezing before another, depending on how good the outer layer is at retarding heat and mass transfer from the interior. How hot can it get inside? How high can the pressure get? I guess I should look up people's best guesses for those questions. I can imagine the shell getting stronger and stronger on repeated passes of the sun if it doesn't break, sustaining higher pressures inside, and eventually allowing the same sintered morphology to be reproduced with water ice holding inorganic particles together.

So, in summary, comets should end up kind of like MaltesersTM.

Saturday, February 14, 2015

Define. Clarify. Repeat.

Being A New Post for Marco to Hook Comments On

Like most people with an interest in the historical sciences, Alfred Wegener is one of my heroes. He marshalled an overwhelmingly convincing mass of evidence of the need for continental drift, argued his case coherently and courageously against monolithic opposition, and was eventually vindicated long after he disappeared on a macho scientific expedition across the Greenland ice cap.

Like most people who have thought about it seriously, the pillars of the scientific establishment who mocked Alfred Wegener are also my heroes. Because no matter how much evidence there is of the need for a new theory, you can’t throw out the old theory until you have a new theory. And for a new theory to be science, it needs to have a plausible mechanism. And in the case of continental drift, there was no proposal for how it could possibly have happened that was not obviously wrong until the mid-ocean ridges were discovered, long after Wegener’s death.

To generalise: if you are an iconoclast who wants to convince me to change my mind about something scientific, you need to do two things. (1) Present an overwhelming mass of evidence that the existing models are inadequate: there has to be something that needs to be explained. (2) Present some vaguely plausible model, consistent with the other things we know, that explains this stuff that needs to be explained.

 The rest of this post is just going to be me arguing with Marco, so I’ll see the rest of you later. :)

From the most recent comment of Marco down on the ‘Yes,  Natural Selection on Random Mutations is Sufficient’ post:

I'm just going to summarise what I believe to be the source of our differences.

It does not make sense to talk about the source of our differences. You have not yet clarified your model sufficiently for it to be meaningful to talk about the differences between us. As the iconoclast, you need to present overwhelming evidence that the existing model needs to be changed, and some plausible mechanism for an alternative model. These are both necessary. Reiterating that you see the need for a change, and advancing very vague mechanisms that are not linked to the known facts of molecular biology, are never going to convince me. Of course there is no need for you to convince me; but if you want to convince anyone in the scientific community, these are the two things that you need to do. 

1) Experimental basis - your mentioning that a synthesis cannot be experimentally derived by definition, is to me an admission that it is not strictly science. You do believe it to be science by a reasoning I do not accept.

The only way I can construe this statement is that the historical sciences in toto are not science. To me, this is an unreasonable limitation of the meaning of ‘science’. It impacts all possible mechanisms of evolution.

2) expanding informatics principles to genetics - genes as a store of information and instructions analogous to a computer algorithm. To me it is obvious and valid - to you (and biologists in general) it is a big no-no.

This is because biologists know more than you do. The relationship of genes to computer algorithms is only an analogy, and it is a very weak analogy.

3) definition of randomness - Ditching a statistically valid definition of random in favour of a statutory functional one makes the synthesis *not falsifiable* in the statistical sense. One should be able to verify that a simulation based on statistical randomness would come to the same probability distribution.
4) Dismissal of trivial non-randomness. You appear to do this equally for biochemical reasons that mutations would happen in certain areas more than others that are not proportional in any way to the function, but also it appears for things like horizontal gene transfer and epigenetics effects. To me it is an admission that random is incorrect even in your functional description. For instance, I think it is as reasonable a synthesis that horizontal gene transfer explains the spread of all beneficial mutations. I do not think that it is the whole story, but the standard evolutionary synthesis crowds out other ideas as if it had been experimentally verified.

I am absolutely sure that a simulation based on statistical randomness  could show natural selection on random variations was sufficient to account for biological change. I am absolutely sure that a simulation based on trival non-randomness could show natural selection on what I call trivially non-random variations was sufficient to account for biological change. Alternatively, I am sure that a simulation based on statistical randomness could show natural selection on random variations was not sufficient to account for biological change. None of these simulations would necessarily tell us anything about reality. The real system that we are trying to simulate is too complicated. Modelling is not experiment. All models are only as good as their assumptions. This quibbling about definitions of randomness is, to me, irrelevant and uninteresting. It does not get us one step closer towards identifying a deficiency in the standard model, nor clarifying a plausible mechanism for directed evolution.