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.  

What's not to like?

It is the greatest happiness of the greatest number that is the measure of right and wrong.  

(Jeremy Bentham)

It was an impulse buy. Sandy had given up on those sort of gimmicks a long time ago. Once or twice a year self-loathing would goad her into a calorie-controlled diet, but lack of visible results and the impossibility of coping with work while feeling hungry all the time meant she could never stick at it for long. As for miracle weight loss products, fad diets, and programmes, she had long since stopped paying attention.

It was the woman on the box that did it. She looked so genuinely happy. Sandy couldn't remember the last time she had seen anyone - in real life, on TV, or one of the perfect people plastered over every available advertising surface - who looked so utterly content and authentic in their consumer ecstasy. And it was on special. Half price.  'Choose happiness!'  it said in friendly letters underneath the woman's picture. 'If only' muttered Sandy sadly to herself, and without really thinking put the package of meal-replacement drinks in her trolley. It was a brand she had never seen before.

I don't blame Sandy. If it wasn't Sandy, it would have been somebody else. Or if no one had ever bought it, They would have found some other way.

The next day was Monday.  Sandy came home from work with her gut tied in knots  from what Tamika had said and slumped on the couch watching impossibly fit young people play tennis. She hated tennis but couldn't get up the energy to change the channel. She couldn't face making a proper dinner either, so she got one of the meal-replacement drinks. It was the sort of fine powder that gets everywhere no matter how carefully you try to open the packet, and that takes forever to stir to get rid of the lumps. She hardly tasted it at all. And it didn't make her feel like the woman in the picture.

At least, not until the next morning.

When the alarm went off, Sandy realised her bedroom was beautiful. In the pre-dawn, the contours of the junk on the bedside table looked like the towers of an alien city at sunrise, gleaming with mysterious potential. The fragment of poetry 'rose-red city half as old as time', which she had once seen on a poster in a travel agent's window, flamed into her thoughts. Then a vision of one of the cities in Ray Bradbury's 'Martian Chronicles', which she had read as a teenager, and a brief unbearable tang of bittersweet affection for the doomed Martians.  She swung herself out of bed. The knot of despair in her gut was gone. She felt no dread of the put-downs and petty nastinesses she was sure to face at work.  She felt good. The heavy pall of self-loathing that had hung over her constantly since she was fourteen years old was gone.

It was another rubbish day at work. Tamika and Marcella were even more vicious than usual. But today Sandy didn't seem to mind. Life was beautiful. She was happy. Instead of ending up weeping in the loo at lunchtime, she sat in the tearoom and looked out at the sunlight playing on the windswept leaves of the trees by the carpark. She had never noticed before how beautiful it all was. It wasn't until then that she thought just how strange it was that she felt so happy.

'If this is because of that stuff I had last night, there's no way it can be legal. This is crazy.' A mental image of a box labelled 'Uncle Arthur Conan Doyle's Heroin-Infused Bran Flakes' came to her, and she giggled. A voice - it sounded like Darren - said something that could only have been 'crazy fat bitch' from the other side of the room, and Sandy only felt a pang of bittersweet affection for him, like he was one of the doomed Martians.

That night she had The Dream.

She was walking with the woman from the package. Or flying, in that way dreams sometimes blur two things together that could never really be blurred together. In the same way the woman from the box was covered with tiny little kingfisher-blue feathers - or not - in the same ambiguous dream fashion.

'This is how you are meant to feel' the woman said. 'This is how people should be. How you felt before was a wrongness. A disease.'

'I get that' said Sandy. She had the sense that she and the woman were not alone, that there were more of the kingfisher-blue people walking or flying nearby, hundreds or thousands or millions of them.

'Would you like to feel like this forever?' asked the woman.

'Oh yeah' said Sandy. 'Oh yeah.'

Sandy stayed happy. Life stayed beautiful. At work, she found she could just smile sweetly at people who would have left her a sullen mass of self-hatred the week before.

By Friday morning, everything she tried on was too loose. She started weighing herself again and found she was rapidly losing weight. Not rapidly enough to be frightening -  to be, for instance, another symptom of a brain cancer that was also causing her strange euphoria - just nice. It was like the celebrities in the magazines whose 'baby bodies' miraculously melt away without leaving any dangling wattles of skin.

'If I feel sick - at all - I'll go to the doctor' she promised herself. 'There can't be anything wrong with me if I feel fine.'

Day by day she effortlessly shrank towards the socially most acceptable body shape for a woman of her age.

Two weeks after The Dream Sandy swam up out of sleep an hour before dawn. Her skin was tingling, trembling for joy, like the skin of women in soap commercials. Through her sleep-blurred eyes she saw that her arm was shiny. Opalescent. A little like kingfisher feathers. Startled, she moved her arm, and the shininess on it took flight, a cloud of little dancing motes. They scattered in the air and faded, leaving only the faintest sheen remaining on her arm. She got out of bed, her heart pounding hard. They were streaming off her everywhere like solar flares, more slowly than the initial flight from her arm, in long coiling patterns of wilful smoke that seemed to make their own way toward the door. It was terrifying, but beautiful. The tingling in her skin stopped, the last motes faded, and she wasn't shiny any more.

'I should see the doctor' Sandy said to herself. 'I must be going crazy.'

But when she had finished breakfast she had changed her mind to: 'If I have any more weird hallucinations like that, then I'm going to see the doctor.'

By that time, although no-one had realised it, there was already a Scanning Electron Micrograph of one of the motes, taken two days before by a palynologist at Victoria University. It was a faceted ellipsoid, with three axes of length approximately 21.3, 13.2, and 8.1 microns. The same objects had also been seen in semen samples from the stud ram 'Wairarapa Roger', which meant they had to be thrown away, and - in vast numbers - in the blood of a Miss Allanah Sanderson, whose childhood leukaemia had suddenly gone into remission.  Some of the objects from Miss Sanderson's blood sample were sent for further analysis, but by the time the results came back, events had moved on.

Forty-five minutes after Sandy got to work that day, the first social media exchange between two people who had dreamed slightly different versions of The Dream took place. I didn't notice it until I woke up - 6:18 pm New Zealand time - by which time it was all over the internet. And I didn't decide that the only hope for humanity was to nuke New Zealand for another two hours. But even if I had been Emperor of Earth, it probably wouldn't have worked. Those things were drifting in the ocean by then. Carried on planes to places all over the world. Burrowing deep in the subsoil.

That afternoon The Dream had come up in the tearoom at Sandy's work. Afternoon tea ended with a group hug.

That was a week ago. The only other people I know who rejected The Dream are my friend James, who is aspergers, and the Pakistani couple that run the Asian music store on Hollins Road. Even after They issued Their statement, making it perfectly clear what Their plans were,  and letting people know they were free to change their minds whatever they chose, 998 out of a thousand people have chosen happiness. The last time I checked Their manifesto had 870 million 'Likes'.

You get to live forever. You get to fulfill your potential to be happy all the time. The only downside is that your real flesh and blood body gets replaced by a community of free-willed nanites - all immortal, all happy like you, all happy to be your friends and help you out. They mimic the body you had before, except you never get sick. Or, you can change it. If you ask nicely, They'll give you wings. Or gills. Or any kind of frigging superpower compatible with the laws of physics. They've converted most of the soil into Themselves. They're working Their way down into the crust, rearranging it into a different kind of sentient happy nanite. Animals and plants - anything without free will - They're replacing those too. Abolishing suffering. No more tortured mice. No more caterpillars writhing with ichneumon wasp larvae in their guts. What's not to like? But I don't like it.

They've promised to keep enough of the old ecosystem going to provide all the necessities of life for Luddites like me and James as long as we live. But They already outnumber us quintillions to one. God knows what Their plans for the planet are after we're gone.

I just watched the video of Sandy telling her story for the ninth time. I can't help myself. She looks so happy. She looks so beautiful. Damn. Damn. Damn.

Notes: 

 

1. There are doubtless more prosaic ways to successfully mount a Grey Goo invasion, of course. This one has not just been invented for novelty value, but as a solution to some potential problems that might arise for the invaders in a world subject to real world physics.

In the real world, space is full of violent cosmic rays and any journeys between stars will take a very long time, so any object carrying the nanites from somewhere else will need to be well shielded, and hence relatively large - I am thinking at least the size of a beach ball - but not so large as to make a big obvious fuss coming down. It makes sense to me for this thing to get down to Earth's surface in one go, instead of dispatching tiny probes from its limited resources to brave the atmosphere individually.

Now, this beach ball contains some billions of sentient beings. They won't follow a prearranged plan, but work out things as they go along based on all the information they collect from us as they approach our planet. They will want to be careful to kickstart their propagation as quickly as possible, to avoid the chance of being noticed by these curious ape-descended creatures and possibly being nipped in the bud. And I think something they would be quite likely to do, given their initially limited resources and desire for speed, is to hijack an efficient terrestrial system for gathering energy and matter and replicating complex structures - i.e., something alive - rather than rolling out their own systems. There is no reason this would be particularly easy, no matter how advanced their science. They need to get a lot of information into a living organism; certainly quite a few of their people - maybe some highly specialised sorts of nanites that a lot of work has gone into; and it is quite likely that they might need significant amounts of some trace elements not common in Earth - in the initial stage of rapid propagation, when they control few living systems, these would be a limiting factor on their growth and it would make sense to supply a bolus of them to the initial host for distribution through the first several generations. The nanites have few resources at this narrow window in time: they are psychologically conditioned to scarcity from thousands of years of living in a beach ball. So they won't scatter a lot of baits around willy-nilly where most of them will be wasted and they might be picked up by curious ape-descended scientists. No, I think it makes good sense for them to minimise waste by putting a lot of effort into one really good bait, designed for the biochemistry of a particular species. And if their study of our electronic traffic suggests a way that they can ensure self-selection of an individual member of that species who can easily afford the excess metabolic load, and who will be pleasantly surprised rather than freaked out if they suddenly lose a lot of mass... ? What's not to like?

2. The story is actually set in New Zealand because I thought of the idea when I happened to be there some years ago. Of course, a beach-ball-sized meteorite is large enough to be interesting, so landing in a remote bit of deep ocean before heading to the nearest supermarket is a sensible strategy, which would make New Zealand a more likely starting place than most.

3. As I was writing, I was thinking of the 'I' in the story as a male Anglo in his early 20s, geeky not nerdy, named 'Luke' and living in Oldham in the UK. But you can feel free to imagine him/her as being whoever you like, living in any English-speaking country in that approximate time zone.