Mostly Harmless Science Blog

Monday, October 10, 2016

The Golden Rule

It can be said that the PhD thesis is an artificial and pointless form of literature. Nobody ever reads a thesis for pleasure. Seldom is one read for profit. Nobody who writes one will ever have to write one again.  Better, it is increasingly said nowadays, to publish a bunch of papers and stitch them together into a ‘thesis by publication’. There may be disciplines in which it is appropriate to do this: in my discipline, in which publications are almost invariably multi-author, it is a terrible idea.

So when this question arose on Twitter:
I gave this answer:
So, why?

Benefits for the Candidate
·         You can, for at least one time in your life, tell the story of your scientific endeavours unconstrained by the petty limitations of a paper. No page limit; no limit on the number of figures; no savage truncation of the introduction and relegation of everything really useful to ‘supplementary information’; no limitations of ‘journal scope’ requiring you to break off and deform pieces of your multidisciplinary project to appeal to  different journals. You can go as broad and as deep as you like and you don’t have to pander to the prejudices of the Editors.

·         There is an expectation with a thesis that you will do all the writing yourself. When you publish a paper, this is not the case, and shouldn’t be. You do not want to miss out on all the accumulated writing talent of your co-authors, most of whom have done this many times before. The readers of the Kirghiz Journal of Analytical Chemistry deserve the best-written paper they can get. And that paper is not going to be a demonstration of your talents, unless you are rare and awesome.  You should not do all the writing on a paper yourself.  But, if you are like most people, you will need practice writing a lot. And you will get a job where writing is an important skill - that may well not be in academia, where nobody cares if you have papers or not. So it is much more important for your future that you sit down and successfully tackle a big task of writing - and organising your writing - than that you contribute to a bunch of papers where the bulk of the writing, and certainly the bulk of the organisation of the writing, ought to be done by somebody else. Of course, you may be an awesome writer, and capable of writing great papers from year one of your PhD. Which brings me to the next point.

·         The purpose of a thesis is to demonstrate that you are awesome: that you have mastered a field and made a valuable contribution to it. A thesis cobbled together from multi-author papers does not convincingly do this. Maybe you did design the project; maybe you did do all the work; maybe the stellar interpretation is yours. But if you did, what exactly did those three other authors contribute?  Yes, you may write that Prof X contributed only 10% to paper Y; and maybe it is true; but your colleagues know Prof X, and know how she has carried weak students in the past, how she rules her group with an iron hand, how not a sparrow falls in her laboratory that she does not notice.  I know of groups that will not consider applicants who have done a PhD by publication for a PostDoc, because of just this uncertainty hanging over how much of the work is really theirs.  Maybe none of your PostDoc applications will end up in the inbox of a Professor who thinks like this. But maybe they will.

·         If you are in a typical group, you will end up doing things that contribute to papers where the lead author is someone else. Where you are the person who – truly – has contributed 10% to a paper, you are going to look ridiculous binding that paper in your cobbled-together thesis. But that 10% may well perfectly legitimately be fit somewhere into the coherent narrative of your journey that you present as a traditional thesis.

Benefits for the User
·        The theoretical purpose of a scientific paper is to communicate information, but the real purpose is to score points in the publishing game. So the false starts and dead ends are hidden, figures and procedures that should fit naturally into a flow of argument are hacked out and dumped in supplementary information, and the context and background of the work is stripped down to the bare minimum to save space. None of these things should be true of a thesis. A thesis should give the whole story, as a clear and coherent narrative with all the warts left in. And with today’s electronic repositories, it has never been easier to get hold of theses and consult them.

Benefits for the Examiner
·        You can judge the candidate fairly. You don’t have to guess what is the student’s work and what isn’t. You are never in the position, as I once was, of giving a glowing report about the quality of a student’s work and then sitting through a talk at your next conference in which another student presents part of the same work as theirs.  You don’t have to worry if the thing you think is important that has been left out has been left out to fit the requirements of the journal, or because the candidate is slack.

·       You aren’t redundant. If you present a thesis made up of peer-reviewed papers that have been cobbled together, then for every correction or suggestion that you make, the candidate can simply point to their peer-reviewed papers and say; ‘the august reviewers at the Kirghiz Journal of Analytical Chemistry were happy with what I did, so nyah nyah.’ Presenting a thesis made up of published papers is a way to bullying you, as an examiner, into nodding and smiling.

·         You can actually read the thing. Without flipping back and forth to the most important figure, which is lurking in the supplementary information. Without having to read through basically the same introduction again and again and again.

Which brings me to what is probably the real reason why I strongly discourage my students from submitting theses by publication. I sincerely believe the reasons I’ve given above about the benefits to a student of writing a traditional thesis. But ultimately, it comes down to this. A guy I greatly admire once said these words: Do unto others as you would have them do unto you. And I never, ever, ever, ever want to mark a thesis made up of papers cobbled together again.  Ever.  For the reasons given above. It is horrible. So I don’t want to inflict one on any other examiner.

Monday, September 5, 2016

Why I Like Our Logo

Most universities with two or three letter abbreviations on their official logos use capital letters. We used to, too, until about five years ago, when we swapped to a logo that uses small letters. I like the new logo better than the old logo. The main reason is historical. Those Roman capitals look very bold and impressive and lots of universities use them. They are used in pretty much all the languages of western Europe. Why? Well, the Romans had a lot of good qualities, but basically, it comes down to violence. The Romans went around conquering people, so that if they wanted to get ahead in life they had to learn their language and write it their way. Behind fonts like ‘Times New Roman’ and ‘Trajan Pro’ there are treacheries and massacres and cities plowed and salted and the ghosts of a hundred lost languages that never got to be written down. The memoirs of victorious generals and the triumphal inscriptions on monuments and the death warrants of uncounted multitudes were written in letters very like those.

Now, the letters our new logo is written in remind me very much of the first lowercase scripts. Letters that were invented in the ‘Dark Ages’ by people concerned with preserving knowledge. Behind them I feel the presence of millions who lived and died in a tradition of scholarship, of self-sacrifice, of hospitality, and keeping out of the way of the barbarian hordes. They are entirely appropriate for the logo of a university, as the sort of letters used by the people who established the first universities.

Then there is a modern reason to prefer small letters: in common discourse today, capital letters are RUDE. They are IN YOUR FACE and commonly indicate that THE USER IS AN IDIOT. So in general, small letters are more fitting for humble scholars.

And our new logo makes us much less likely to be confused with other places.

And I like the colour. It reinforces, whether it was meant to do so or not, the vision of the university as a place preserving learning against an age of darkness, with that fine monkish gaelic green surrounded by black.

Thursday, September 1, 2016

Divestment Speech

I wanted to speak against the fossil fuel divestment motion at the meeting of the NTEU (National Tertiary Education Union) in September 2015, but was unable to attend the meeting due to sickness in the family. To assuage my conscience, I wrote up a little speech saying what I wanted to say and sent it to the local branch organiser. But I thought I would go one step further and post it here. So here goes:
Around the world there are over a billion people without access to electricity. These people disproportionately die of avoidable respiratory conditions caused by smoky cooking fires. They disproportionately die of water-borne diseases because they cannot boil water as readily as we can. Of food-borne diseases because they cannot store their food as safely as we can. Of every sort of communicable disease, because vaccines cannot be stored as easily without electricity.  They do not have the access to communication and education that we do - the access that we know is the single greatest factor for the empowerment of women and improved opportunities to be anything other than subsistence farmers.
These people are our equals. We have a moral duty to work towards a world where they have what we have. Their governments have this same moral duty. All over the world, governments are seeking to improve their citizens’ access to electricity. They are seeking to do this as economically as possible. In the real world, this still overwhelmingly means by generating electricity using fossil fuels.  Coal is still the most economical way to provide electricity. Providing electricity in a more expensive way means less of it is provided. If less electricity is provided, more people die, and more people live without access to educational and economic opportunities.

Globally, the majority of fossil fuel is produced by the private sector, rather than the public sector. This is because they are doing it efficiently. Producing fossil fuel efficiently means electricity can be provided more cheaply and fewer people die. Yes, there is significant environmental degradation associated with extraction of fossil fuels. Yes, there is exploitation of workers and their exposure to unsafe conditions. Governments have a role in ensuring companies behave themselves. The Media has a role in ensuring companies behave themselves. And, historically, shareholders have a significant and disproportionate role in ensuring companies behave themselves.
These people without electricity are reliant on burning locally-sourced biomass for cooking and heating and as such contribute disproportionately to deforestation and land-degradation. Two-hundred years ago New England in North America was almost entirely deforested. Fifty years ago South Korea was almost entirely deforested. Both these places now have very extensive forest cover, despite large increases in population, because their populations are no longer reliant on locally sourced biomass. Yes, if we continue to burn fossil fuels, it is likely that many habitats will be degraded in a hundred years. But if we, through some evil miracle, stop the private sector from producing fossil fuels, it is certain that those habitats will not be there at all, because they will have been destroyed by people desperate for food and fuel.
I do not have any fear of this apocalyptic vision coming to pass, because it is vanishingly improbable that our divestment from fossil fuels will bring the private sector to its knees. Divestment is not a strategy for effecting global change. What it is, instead, is a futile sentimental gesture that can only diminish the environmental and social responsibility of fossil fuel producers, by reducing the influence of environmentally and socially investors on their boards.

Tuesday, June 14, 2016


I have not been able to find out any details beyond what has been reported in the Oz (behind paywall), but having had a few peripheral interactions with Prof Peter Ridd over the time I was at James Cook University many years ago, I was upset to hear that he appears to have been rapped over the knuckles by his employer for making perfectly reasonable statements about the need for quality assurance in studies of the health of the Great Barrier Reef.

My letter to Vice-Chancellor Prof Sandra Harding is reproduced below:

Dear Prof Harding,
I am writing to express my dismay at the recent treatment of Prof Peter Ridd, as reported in the media, for expressing his considered professional opinion about issues relevant to his expertise.

As a proud graduate of James Cook University (BSc 1991, PhD 1998), I am unhappy to see such weak commitment by my alma mater to a free and robust expression of thought.

As a practicing physical scientist (70 peer-reviewed publications, h-index = 19), I expect anything I publish to be frankly and fearlessly criticised if my methodology or assumptions are deficient, and would be horrified if potential critics were to refrain from such criticism on the grounds that it would be ‘disrespectful to my reputation’.  If such a criterion – as reported in the media as grounds for the censure of Prof Ridd – were to be generally adopted, it would mean the death of science.

 And parenthetically, as a former resident of Townsville (1983-1998), I can remember many episodes of panic that one event or another would lead to the death of the Reef. I vividly recall my grandfather, E/Prof Bill Lacy (Foundation Professor of Economic Geology at James Cook University), saying that such episodes had been a feature of life in North Queensland since he first visited the region.

Yours Sincerely,

Dr Chris Fellows FRACI
Associate Professor in Chemistry
School of Science and Technology
The University of New England
NSW 2351

Update 17th June 2016: A reply! And a brief additional correspondence...

Dear Associate Professor Fellows

Thank you for your email to Professor Harding in relation to this matter. Professor Harding has asked me to advise you that media reports that a James Cook University scientist was censured for questioning the veracity of another academic’s research are incorrect. 
Any action that may be taken by the University under the JCU Code of Conduct would be in relation to matters of personal behaviour and not for questioning the veracity of another researcher’s science.

Media reports that the member of staff was threatened with dismissal are also incorrect. Under the JCU Code of Conduct there is a broad range of responses to any inappropriate behaviour, and dismissal would only be applied for the most serious or repeat offences.

James Cook University values intellectual freedom and its marine science is subject to the same quality assurance processes that govern the conduct and delivery of scientific research internationally.

Kind Regards

Russ Parker
Executive Officer to the Vice Chancellor and President
James Cook University
Dear Mr Parker,
Thank you for very much your response. In light of what must then be widespread misrepresentation in the media, is a statement of clarification explaining exactly what matters of personal behaviour were found to be inappropriate and why publicly available anywhere?
Best regards,
Chris Fellows
Dear Chris
As you will understand, the specifics of any staff matter are protected under the Information Privacy Act and we are not at liberty to discuss them directly or make them public.
Regards, Russ


Update 8th July 2016: Prof Ridd has kindly shared with me the censure letter and the document that prompted it and has told me he has no objection to them being disseminated more widely.

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 dares 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.

Edit 15th June: I found out quite by accident the other day that my parents sat next to Ian Plimer at Bob Carter's funeral, which pleases me in a six-degrees-of-separation way.

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. These conditions 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 rely on complex systems with lots of inputs that 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.