Brian Martin's "Healthy dissent: resisting attacks on alternative medicine"

I was going to retweet a link to this article critical of skeptic attacks on anti-vaccine loons, saying that we should be careful not to step beyond reiterating “these ideas are dangerous, stupid, and wrong” into outright harassment or censorship. Then I realised, first, that was too long to fit into a tweet; and second, that I was still kind of conflicted and needed to make a more nuanced statement.

As someone who has plenty of idiosyncratic ideas myself, I don’t want to be harassed or censored. But I am also pretty far along the free speech continuum. I don’t have any problem with ‘behead those who insult Islam’, for instance.  Because I am pretty far along this free speech continuum, I also don’t have any problem with the techniques labelled ‘Disruption of Discussions’ and ‘Verbal Abuse’ in Brian Martin’s article. I have been on both ends of these techniques on numerous issues in the past, and think the Internet would be a dull and listless place without them. 

Boycotting advertisers, and applying moral pressure to venues and media outlets that provide platforms for your opponents. are also time-honoured methods of grass-roots protest.  These techniques are disingenuously shoehorned in Brian Martin’s article into the categories ‘Threats’ (together with some actions that are truly vile and beyond the pale) and ‘Censorship’ (I don’t think that word means what you think it does). I think it is well and good that you just have to be prepared to suck these up if you are in the public arena.

Where I am conflicted is the technique ‘Complaints’. On the one hand, trying to use the power of the state to silence your opponents is something I find repugnant.  On the other hand, lives are at stake. Someone you know is far more likely to die due to the activities of an anti-vaccine activist than a terrorist. If we are justified in using the power of the state to nip potential terrorists in the bud while they are still probably just wannabes and haven’t actually blown anything up, why shouldn’t we use the state to stop anti-vaccine loons from gaining traction before their actions lead to mass casualties?  On balance, I don’t think we should, and would disavow the techniques described under ‘Complaints’; but I think this is mostly for the selfish reason that I wouldn’t like to have them used against me, and because I have an ideological aversion to government meddling, rather than on any proper moral calculus about the public good.

Common Misconceptions About Electric Circuits

• What do I believe? 


•  Is what I believe sensible and logical or simply a set of ideas which I acquired without a lot of thinking about it?


• Does what I believe explain the world which I observe?


• Are there any inconsistencies in my thought processes? Does belief A logically contradict belief B?


• Are there sensible and logical alternative beliefs that better explain the world which I observe?




From “Common misconceptions about electric circuits”, http://www.physicsclassroom.com/Class/circuits/u9l2e.cfm


But applicable to EVERY BLOODY THING.

Things I won’t include in my First Year Chemistry Textbook (except as cautionary historical episodes)

1. Negative electron affinities

How can you force something that doesn’t want an electron to accept an electron? How would you measure the energy in doing that? Okay, in an ionic lattice you can get the energy back somehow and do some algebra to get a number. Maybe this exercise gives you a number that is negative. Is that a number we should be confusing first year students with? I think, no.  Meaningfully, things that don’t like forming anions should be listed with a first electron affinity of ~0. Why? This would be consistent with what we tell students later about intermolecular forces, where electrons move to give transient dipoles giving attractive forces between anything and anything.

2. Hybridisation

Atoms have atomic orbitals. When you combine atoms in molecules, the resulting molecules have molecular orbitals. These things have physical significance and their properties can be calculated using quantum mechanics and group theory.  ‘Hybrid orbitals’ are a non-physical halfway house with no real explanatory power.  The labels sp, sp², and sp³ are useful shorthand for motifs that recur in molecular orbitals. Nothing more.

3. Crystal Field Theory

We teach this theory and then immediately segue to the spectrochemical series, which is the opposite way around to what the theory predicts. This is okay if you are the kind of student who just memorises things for the exam without thinking about them, but if you are the kind of student who wants to make logical connections between the things you learn, you will just go: ‘WTF? Coordination chemistry is stupid.’ I suggest the handwaving explanation ‘d-orbital electrons go in MOs with antibonding character’ as a substitute introductory-level model.

4. Intermediate Stability as an Explanation for Selectivity

All first year organic chemistry textbooks will tell you that you get substitution of hydrogen in addition of HX to a double bond at the place where there are more hydrogens already because the intermediate is more stable. They will trot out this same kind of explanation for all sorts of other things. This is a bogus argument because it reverses causality. The reaction can’t go a particular way because it will form something that is more stable; how can it possibly know what it is going to form until it forms it? This ‘explanation’ is lazy shorthand for something that everyone ought to be taught in first year but isn’t.

Formation of an intermediate is endothermic by definition. The transition states of endothermic reactions usually resemble the products (Hammond’s Postulate). So the structure of the intermediate is important as a pointer towards the structure of the transition state. A stable intermediate implies a low energy transition state; that is, a lower activation energy.

Note that Hammond’s postulate is not called Hammond’s Law. And note that this is only going to be worth invoking for kinetically-controlled reactions; for thermodynamically-controlled reactions, we just have to tally up the bond enthalpies of the possible products... and that is a full and complete explanation for observed selectivity.

For the Love of God, Montresor

Of course, evolution is not the only thing I argue about on the Internet. My other old pal winstoninabox is dissecting Lennox’s “God’s Undertaker” on a website made especially for the purpose.

To clarify where I am coming from in this argument, I thought I should do one of those Pyramid of Logic things, like I did for Anthropogenic Global Warming.


1. The Universe is not a Self-Existent Thing. The “known universe”; this thing of things that seems to have started 15 billion years ago and obeys certain very complicated rules, is not all there is. It is dependent on some greater reality. Something must exist without having developed from something else: but the “universe” of the cosmologists is not it.

2. The Self Existent Thing is something beyond our comprehension. Look how mind-bogglingly incomprehensible we find things like quantum electrodynamics and black holes, only a few orders of magnitude away from the reality we evolved to comprehend.

3. We can't get there from here. The chain of causation between the mind-bogglingly incomprehensible Self Existent Thing and ourselves is likewise too complicated for us ever to figure out.

(These three points seem more or less self-evident to me, and were very ably outlined by the 14th century Arab historian Ibn-Khaldun)


Which brings us to points 4:

4. With respect to our universe, this Self-Existent thing may be:

a. Omniscient, in the sense of knowing everything about it.

b. Omnibenevolent, in the sense of being favourably disposed towards everything in it.

c. Omnipotent, in the sense of being able to do whatever it wants to it. Which obviously includes:

i. Personal, in the sense of being able to interact with transient epiphenomena within it as if it were one of them, and

ii. Interventionist, in the sense of actually doing what is in its power to do.

(Postulating any of these points 4 is not irrational, and is not a priori stupid, any more than postulating that the Self-Existent Thing does not have these qualities is irrational or a priori stupid. You are perfectly free, as far as I can see from the facts accessible to us, to believe either way on any of these. Since I agree with Peirce that to “believe” in a thing can only mean “behave as if such a thing were true”, I would say that I believe in point 4.)


5. We can't preemptively dismiss revelation as bogus. Now, if 3 is true, the only way we can have any information about this Self-Existent Thing is what it communicates to us using 4.c.i/ii. So we have no grounds for a priori rejecting the statements about God from any revealed religion as mere “fairy tales”. We can only compare them to the facts we have gleaned about the universe on our own and judge whether they make sense or not on a case by case basis.

(I think, though I often wish I didn’t, that they all fall down rather badly on the details. But that’s just me.)

Yes, natural selection on random mutations is sufficient

My old pal Marco has begun a quixotic crusade against Ockham’s Razor, claiming that it has been used unfairly to browbeat dissenters and prop up flimflammery. Exhibit #1 in his crusade is the hypothesis that natural selection on random mutations is sufficient to explain the staggering diversity of the natural world. 
 

Okay, so there are such things as horizontal gene transfer and the intriguing symbiotic relationship at the beginning of eukaryotes. And trivially, some stretches of DNA will be less stable than others, and some cellular environments will be more exposed to mutagens than others, so mutations are trivially “non-random”. He insists this is not what he means. There must be some “non-random” mechanism to generate “good” mutations. I said, no, this is bogus. I said this at great length through a long rambling argument in the comments on his blog before I got tired of saying it, but having a pretty good stamina for argument I recovered after a few weeks and thought I would come back and say it again here.  

1. Heritable random mutations happen all the time. The environment of cellular replication is rife with things that can cause mutations, the mechanisms intended to pick these up don’t always work, and if you irradiate living things it is easy to generate non-viable mutant offspring, because most change is bad.  This is the basis for every post-nuclear-holocaust movie ever and my political philosophy. And yet:

2. Changes that are good happen all the time. There are lots of examples of this unfolding in real-time as we speak. Of course, these good changes might not have anything to do with random mutations. But there is no *clear and pressing need* to postulate any mechanism beside random mutation. If there is no clear and pressing need to introduce a new parameter, we don’t do it, because then we are off chasing will-o’-the-wisps all the time. This is why Ockham’s Razor is good. On the off chance a random mutation makes an organism that isn’t non-viable, the random change will propagate through the population.

3. The 747 argument is bollocks. Marco is (I think) convinced for a need for non-random mutations by the dodgy statistical arguments of various creationists and steady-state-universists that random changes are insufficient to explain dramatic changes in speciation, because there isn’t enough time in the universe for little changes to add up to the big complicated changes we see. This is assuming an oversimplified linear y = mx + b of what living systems are like and how changing them works. Living systems are complex systems where arbitrarily small changes on the molecular level can have arbitrarily large effects on the macroscopic level. Think of all those genetic diseases that can be traced back to one little residue on one protein being skew-iff. The butterfly effect is the explanation for butterflies. And any arbitrarily large change that is not too large to make an organism unable to reproduce is allowed. 

4. You can only find out what the programme does by running the programme. There is no way for a system to know in advance that a change is going to be good. You don’t know for sure when you add a new ingredient to your omelet, no matter how many other foods you’ve added dried cranberries to and it worked out fine. The Vice-Chancellor doesn’t know for sure when he brings in a midnight to dawn teaching period, no matter how many highly-paid consultants recommend it. To find out what changing a line of code does, you need to run the programme. To find out what changing the genotype does, you need to generate the phenotype. There are no shortcuts.

So, there is no need (points 1-3) for “non-random” mutations and there is no conceivable mechanism (point 4) for “non-random” mutations.

This may seem like a series of disconnected ex cathedra pronouncements. Very well, it is a series of disconnected ex cathedra pronouncements. That is just for brevity. I am prepared to defend them all to the death with copious citations and ninja logic.

Mmm... pancakes...

A scientist's aim in a discussion with his colleagues is not to persuade, but to clarify. (Leo Szilard)

 

I've just finished reading "Order out of Chaos: Man's New Dialogue with Nature" by Nobel Laurate Ilya Prigogine and Isabelle Stengers. Wary as I am of criticising a Nobel Laureate, I have to say I was disappointed with it.  

The first few chapters, on the history of science, were most enjoyable, and I appreciated the clarity Prigogine and Stengers brought to the distinction between traditional physics as the science of reversible processes and chemistry as the science of irreversible processes. (I should declare my bias here at the outset. By training and inclination I regard reversible processes as no more than useful mathematical fictions. All real processes are irreversible. Hier steh ich.)

I began to have serious misgivings in Chapter IV, where free energy is introduced.  Gibbs’ conception of free energy is a powerful tool for understanding the universe because it combines that which is seen and that which is not seen: the entropy change in the system and the entropy change in the surroundings, the rest of the universe.  In “Order out of Chaos”, free energy is introduced merely as a function used to define equilibrium in closed systems, without describing its fundamental link to entropy, and its usefulness in understanding the formation of dissipative structures is explicitly (and incorrectly) denied in subsequent chapters.

The discussion of oscillating reactions in Chapter V is obfuscatory in referring to ‘products’ what should strictly be called ‘intermediates’, and in neglecting to state not only that the overall driving force of the reaction A --> E is the free energy change in the system, but that the direction of each of the intermediate steps at each point in time is determined by the free energy change.  By focussing on the chimeric idea of achieving maxima in thermodynamic functions – something only valid at equilibrium – and ignoring the paramount importance of changes in these functions (all we ever talk about in chemistry!) the authors draw a veil of muddle over exciting and interesting phenomena. They claim that ‘the concept of probability that underlies Boltzmann’s order principle is no longer valid in that the structures we observe do not correspond to a maximum of complexions’, but this is only true if a myopic focus is made on the system, rather than the surroundings.  The complex oscillations – and dissipative structures in general – come about because they are the most efficient means, given the history of the system, to increase the entropy (the number of complexions) of the surroundings.  Structure does not arise spontaneously within the system: it is propagated from the interface between the system and the surroundings.  This is more clearly seen in the physical system of the Bénard cell which is also discussed in Chapter V, but it is equally true for chemical systems.  The confusion that arises from blurring the distinction between system and surroundings continues throughout the book.

Chapter VI suffers from an overabundance of metaphors drawn from diverse fields of study that serve to obscure whatever fundamental point the authors are trying to make.  In between a discussion of how termite mounds are formed and a brief discussion of homogeneous nucleation of phase changes, they state: “although Boltzmann’s order principle enables us to describe chemical or biological processes in which differences are levelled out and initial conditions forgotten, it cannot explain situations such as these, where a few ‘decisions’ in an unstable situation may channel a system formed by a large number of interactive entities toward a global structure”.  It is not true that Boltzmann’s order principle only enables us to describe chemical or biological processes in which differences are levelled out: a global structure will spontaneously form in any number of situations, such as micellisation of a surface active agent, driven by an increase in the entropy in the unstructured component of the system fully explicable by Boltzmann’s order principle.  In the real world, homogeneous nucleation of structure is relatively rare. Physical and chemical transformations to give structure are nucleated heterogeneously – from the surroundings, and as order propagates inward from interfaces very different effects can be seen: it is true that Boltzmann’s principle cannot tell us a priori which structure will form, whether homogeneously or heterogeneously nucleated, but this does not mean structure formation per se is in any way incompatible with it. 

Not being terribly familiar with Prigogine previously, I had expected that Stuart Kauffman’s wild concept of ‘order for free’ was based on a misreading of Prigogine’s work, but all the ingredients for it are here, alas...:(

They're just not that into us

Well, for a while I was pretty upset.  This was my first reaction:

 

Then I was *sure* it was a typo, because of what was written in the 03 section report; and then I figured out it wasn’t, and got really upset.  Luckily instead of dabbling further in ‘career-destroying tweet’ waters, I went off and gunned down a bunch of Egyptian cultists. 

You see, I consider the 2012 ERA rankings a *personal* smack-down and humiliation because I was the one who was crankiest about us not submitting anything last time around and falling off the radar, who pushed hardest for going in this year, was most confident that the assessors would see through any spin and hype to the bone and sinews beneath, and most confident that we could and would make a 3.  

But I have reached a kind of equilibrium.  There are lots of people who have suffered worse. St. Sebastian, for instance:  

And I am a contrarian who always regarded the whole process with caustic cynicism, so it is not like I have any starry-eyed illusions about the results being objective or having any intrinsic meaning.

More importantly, I have realised that what is being measured as ‘research quality’ has nothing to do with what we in a university fulfilling the traditional functions of a university consider to be ‘research quality’.

In a publicly-funded university that has a legally mandated mission to deliver the ‘whole of knowledge’ to its community, we believe that the interests of our academic staff in chemistry should cover the ‘whole of chemistry’.  We think that every potential PhD candidate interested in any branch of chemistry should be able to do their PhD with a respected chemist and publish work of internationally-recognised quality. We think this is in the best interest of our students and the best interests of the nation.

The ERA exercise would clearly be happier if all our students and all our resources were funnelled to one high-flier publishing in one field so we could meet a totally arbitrary cut-off of number of papers for a four digit 03** code. But that is the opposite of what we’re about.  I suppose that means by the ARC’s lights that we see research as subordinate to teaching. If so, so be it. Teaching is the rationale for our existence.