Darwin’s Theorem


Science, religion, evolution, romance, action, siphonophors!

Darwin’s Theorem is a story about stories(the working title for a long time was “Metastory”) that’s also a mystery, a romance, an adventure, and various other things besides. Not quite science fiction, excessively didactic… think of it as “Dan Brown meets ‘Origin of Species’.”

If you like to see plot, action and strong characters deployed in the pursuit of big, speculative ideas, you should check it out!

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‘Tis the Season…

…to look back at the year just past. Things I’ve done so far this year, an incomplete list in no particular order:

  • Sold my boat :-)/:-(
  • Taken a short-story writing course from an award-winning author and learned a bunch about story structure and mechanics.
  • Moved into a bigger, better place where I want to be at very reasonable cost.
  • Published my novel and done a small amount of marketing for it.
  • Written multiple short screenplays that have been produced, and acted in a couple of them.
  • Written and directed a short film that has been produced.
  • Seen my elder son graduate from Queen’s geological engineering.
  • Spent some time with both offspring over the summer.
  • Built a canoe-ak, bought another one, and joined Kits Yacht Club. Got some time on the water that way.
  • Taken a screenwriting course and written a screenplay.
  • Written some good poetry (Hilary finished a couple of paintings a few weeks ago that were nicely inspiring.)
  • Wrote a bunch of short stories and a few poems that I’ve submitted for publication, all without success, although I got some pretty nice rejection letters.
  • Traveled the Sunshine Coast and a bit of the Interior with Carrie.
  • Did some skiing at Whistler.
  • Went paragliding with Carrie.
  • Saw an opera on stage for the first time, with Carrie, and enjoyed it. Saw another that was less good, but still worthwhile.
  • Saw some good theatre, including the Holy Grail with Alex and Tim, and had a good Fringe.
  • Read some good books, including an excellent ethnography of Canada’s Indians and a good biographies of both Marlborough and Marlowe (the century that separates them is an enormous gap, comparable to 1800 vs 1900… far bigger than 1900 vs 2000). I’ll write a separate post about books, I think.
  • Designed and built some bookshelves that I’m very happy with.
  • Bought a 3D printer and started experimenting with it.
  • Kept things afloat at my day job.

I’ve done a lot of thinking about stories, and have something close to a working definition. It’s been a year of learning about stories.

There are other things I won’t talk about here, which have also been good.

I’ve still not figured out what I’m going to do with my life. I’m getting closer, though. There are a few wheels left to turn.

In my experience direction is more important than rate, but after a few decades of almost zero progress in some directions, rate becomes kind of important. I have a finite number of years left, and I’d like them to go into some “work of noble note” that uses my unique abilities, insofar as I have any. It’s hard to tell sometimes.

I’m engaged in a rather complex learning experience right now that I don’t have a lot of guidance on. It’s a learning-by-doing thing that I’m finding deeply challenging, and I’m not sure I’m doing all that well at it. But it’s something I’m set on doing, and “As I see, I will, and as I will, I do.”

Come to think of it, there are a couple of things that could meet the description, all of which I’m doing fairly badly at. That’s why I write these things, as an excuse to meditate on what I’m doing with my life and why.

The next year is going to be a branching point, I think. If things come together, I go in one direction, otherwise, I go in a different one. Or maybe I just press insistently on. That’s kind of what I do.

One difficulty I have is I never have any idea where I am until I get there. I can’t envision the future very well, I can only create it. This makes forward planning and a whole lot of other things remarkably difficult. I make it up as I go along, but in parallel with formal plans that I know are the right ones, theoretically, but which have no tangible meaning to me even as I execute them. I don’t know how to describe my inner experience more clearly than that, but it’s a weird, detached, disengaged way to live. And yet it works pretty well. I’ve done OK in my life on a lot of axes, and plan to do more. I just have no idea how.

One thing I’m doing in the new year is taking a drawing course at Emily Carr. What’s the point in living just down the street from a world-class art school if I don’t learn me some art? I have an idea that it’s important that I’m doing that, but again: I have no idea why.

One last thing about this year: there are still a few weeks to run, but unless something unexpected happens, which it admittedly it could, the same number of people I care about are above ground at the end of it as at the beginning. This by my reckoning makes it a good year. It’s a good year by other standards as well, but an awful lot could go wrong and so long as that one fact is true it’ll still won’t be too bad a year.

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Socio-moral vs Techno-economic Problems and Solutions

When all you’ve got is a hammer, everything looks like a nail. This is especially true when you really like bashing things with hammers.

Recently, there has been an upsurge in talk about the role of nuclear power in the dealing with climate change, with some serious advocates arguing for the use of nuclear fission.

How you feel about this depends in part on what kind of problem you think climate change is: is it a social/moral problem with a social/moral solution? Or is a technological/economic problem with a technological/economic solution?

And in particular, is it one of those things in absolute exclusion to the other?

The environmental movement has historically been a social movement that is aimed at dealing with climate change and other environmental issues as social problems, which is a known-failed approach when applied to the exclusion of all else. By continuing to insist that climate change is a social problem that can be dealt with only by direct legal regulation and interference with individual behaviour, and fighting hard against alternative economic and technological solutions, the social environmental movement ensures that things that are known to work won’t get done.

We can see similar arguments between social/moral and techno-economic approaches across a range of non-environmental issues. Drug warriors treat drug use as a social problem that they try to prevent by legal prohibition on supply and the use of punishment to modify individual behaviours, which has proven to work very badly. Legalization and medicalization treat drug use as benign and addiction as a medical problem, not a moral failing, and work pretty well.

Anti-contraception advocates insist that the only solution to teenage pregnancy is abstinence, despite that being a clear and well-documented failure. Their argument appears to be that premarital sex is bad, so anything that makes it safer is also bad. If you think that premarital sex is bad only because it has bad consequences, technology to reduce the risk of those consequences is good.

Anti-prostitution advocates focus on criminalization and legal intervention aimed at individual behaviour to prevent people from exchanging money for sex, while others suggest that legalization, regulation and ordinary worker-rights protections will be more effective in dealing with the problems exchanging money for sex can create while avoiding the problems that prohibition creates.

In each of these cases the techno-economic approach is to forgo any attempt at controlling individual behaviour or directly imposing a moral vision, but to instead change the distribution of incentives, consequences and capabilities and let individuals make their own choices within that framework, even if they happen to be choices we might not approve of ourselves.

Social environmentalists routinely attempt to enact legal prohibitions on and control of specific actions–from fossil fuel extraction to fuel efficiency standards to pipelines–and attempt to modify individual behaviour by various legalistic means. They also are apt to say we have to “change everything” because tweaks to global capitalism are inherently incapable of yielding the kind of moral and social order they find attractive.

And as technological solutions like wind farms and solar farms have become a bigger deal social environmental groups (including the Sierra Club) have turned from supporting to opposing them. They aren’t opposed to all wind and solar, mind you, just specific projects: ones that are too close to human habitation, and ones that are in pristine wilderness. So long as a project is built on uninhabited land far from any humans and not on uninhabited land far from any humans, it will have everyone’s full support.

In the meantime, here is an incomplete list what social environmentalists oppose:

Think of any power source whatsoever. Search “environmentalists against <<that power source>>” and you will get hits. Lots and lots of hits.

Being against building new energy projects of any kind is what social environmentalists do.

Techno-economic environmentalists are on a very different course. Economically, carbon taxes are proven-effective at reducing fossil fuel use, and they also allow income taxes and corporate taxes to be lowered, which only a wealth-hating socialist could object to. Technologically, nuclear power is a proven-effective replacement for base-load coal. People who care about the environment–as opposed to people who merely want to impose their personal social and moral agenda on others–should be in favour of these things.

To be clear, I’m not opposed to shifting social and moral norms in the direction of more environmentally friendly behaviours. If people like Naomi Klein would embrace high-density urban living and abandon their environmentally calamitous village life the world would be a better place. There is no doubt about that. But there is a great deal of doubt that people like Klein will ever forgo their environmentally destructive lifestyles for the kind of environmentally friendly, sustainable lifestyle I enjoy in a densely populated urban area. While my carbon footprint is a tiny fraction of that found in a suburban, rural or coastal community, I can’t expect the average person to adopt this lifestyle, and it is not reasonable for me to expect everyone else to “change everything” simply because I know my lifestyle is vastly more sustainable than some hypocritical author’s.

Fortunately, we don’t have to. Technological and economic solutions to climate change exist. Carbon taxes work to reduce CO2 emissions. And nuclear power can replace base-load coal. If only social environmentalists would start putting the environment ahead of their moral agenda.

Posted in economics, ethics, politics, technology | Leave a comment

Ockham’s Razor is a Special Case of Bayes’ Rule

William of Ockham was an English cleric who eponymous principle of logic looms large in far too much of what passes for “debate” on the Internet.

People who deploy Ockham’s razor never seem to stop and and wonder why they have never once convinced anyone by using it, but there are quite fundamental reasons why the use of Ockham’s razor should be be abandoned and the underlying Bayesian argument used instead. The problem is that Ockham’s razor as frequently stated is easier to misuse than not, so arguments using it are red flags for most people because we have seen it misused so often. On the other hand, if in the cases where Ockham’s razor or something like it is valid, it is nothing but a particularly simple special case of Bayes’ rule.

Ockham himself put his principle not in terms of “simplicity”, as moderns generally do, but in terms of “entities”. He said, more-or-less, that it is “futile to do with more things what can be done with fewer.”

He himself seems to have believed only one Thing was required: God. Everything else was just God imagining stuff into apparent existence, for reasons inscrutable and perhaps ineffable.

Since we know that Bayes’s Rule is the only consistent way to update our beliefs in the face of new evidence, we should care if there is any Bayesian reason to accept this form of the principle, and in fact there is. Any explanation of a phenomenon that involves more things is going to be a priori less likely than an explanation that involves fewer things… except in those cases where the additional factor is really important.

Consider some evidence E, and two possible hypotheses, H1 and H2, where:

H2 = H1 & K

where K is something really implausible, like “intelligent aliens are visiting the Earth”.

Bayes’ rule tells us:

p(H1|E) = p(H1)*P(E|H1)/P(E)


p(H2|E) = p(H2)*P(E|H2)/P(E)

But p(H2 = p(H1)*p(K), and by hypothesis p(K) is very small, so p(H2) is much less than p(H1). But P(E) is the same in both cases, and P(E|p(H2) can’t be that much more than P(E|H1) simply because we wouldn’t even be considering H1. So given that, p(H2|E) must always be less than p(H1|E).

So “adding entities” is an anti-Bayesian move unless they are pretty plausible to begin with–at least as plausible as “the evidence is somehow in error”, which is a good deal more plausible than most people think.

Likewise, “When you hear hoofbeats think horses, not zebras” is pure Bayes: the probability of the evidence (hoofbeats) is the same regardless of whether it’s a horse or a zebra, but the prior plausibility of horses is much higher than that of zebras. The nominally Ockhamian claim is therefore nothing but Bayes’ rule in action: if the evidence is just as likely from two causes, the one with the higher prior is more plausible.

There are many variations of “Ockham’s razor” that involve “simplicity”, but simplicity is quite frequently in the eye of the beholder. As noted above, the explanation with the fewest entities will generally have higher plausibility than one with additional ones that are a priori much less plausible.

When we move beyond simply counting entities the measure of simplicity becomes complex. There are two well-studied measures of complexity: Shannon entropy and Kolmogorov complexity. Either of these might do as a measure of simplicity, but it isn’t clear in most contexts how to apply them.

But perhaps we don’t have too: simple explanations like “The Nineteen Nitwits were responsible for the events of 9/11 with some help from al Qaeda” involves considerably fewer entities than “The Nineteen Nitwits were helped along by the Jews, the US government, the Illuminati… etc” and is subject to the argument above.

“Explanations” that deny the existence of the Nineteen Nitwits necessarily involve many other entities as well.

So it may be that this argument is general. I dunno. This is first-draft thinking, and I’ll have to think more about it.

Posted in bayes, Blog, epistemology, probability | Leave a comment

Some Notes on Screenwriting

I’m taking a course on screenwriting, and have just completed the zeroth draft of my first screenplay. It is not a masterpiece, but was an exercise in understanding screenplay structure. Here are some of the things I’ve learned.

The course (at UBC, Introduction to Screenwriting) is focused mostly on structure. Increasingly I have come to see connections between poetry and screenplays. Poems are highly structured. Screenplays are highly structured. Neither is formulaic (when done well) but both can be rote exercises without artistic merit, things that fulfill the structural requirements but do not breathe with the life of art.

The structural breakdown being taught is the conventional one of beats and plot points and the hero’s journey, with a smattering of dramatic question and answer tying the third act to the first. The instructor (Steven Hahn) is terrific, and brings genuine insight and experience to the classroom. I’ve been blessed this year with two really excellent courses on writing, the other taught by Caroline Adderson at SFU.

I’m mostly a poet, and a very formal one. I’m also an engineer, and believe deeply in the engineer’s proverb: “Form is liberating”. So understanding the screenplay as a form is a powerful tool for me.

Breaking down a screenplay into four parts is basic to the form: Act I, two parts of Act II, and Act III. The two parts of Act II are focused first on “investigation” and second on “confrontation”.

Each of the four parts can be broken down further into roughly fourteen scenes, and each ends with a dramatic moment: the point of no return for Act I, a moment of revelation and reversal for the first part of Act II, the canonical “all is lost” (or possibly “false victory” if you’re that-way minded) moment at the end of Act II, and the denouement at the end of Act III. Furthermore, each part has its own internal three-act structure.

This is significant to me as a poet who has spent an inordinate amount of time writing and studying sonnets, because they they happen to have exactly fourteen lines, a three-quatrain structure, and a dramatic couplet at the end.

A screenplay is four sonnets in three acts.

To a poet, that’s pretty much all you need to say. The rest follows.

I wrote my outline as sonnets. They are without question the worst poems qua poems I have ever written. Vogon-level bad. But that’s OK, because this is all about structure. All about form.

Then over five evenings of the following week, working from about six to midnight, I cranked out the screenplay itself, which runs to just over 90 pages (which by that curious alchemy of the screen implies it’s a 90-minute film). I’m pretty sure it’s not hideous, although working at that speed even I have to lean pretty hard on cliche and moderately hard on co-incidence.

That said, this is what I learned.

One of the things Steven Hahn has emphasized is the degree to which the screenplay is a technical document that allows a couple of dozen people to co-ordinate and do their jobs. It turns out this is literally true.

I’ve spent a moderate part of my time doing technical writing of one kind or another, and during the writing process I was struck again and again by how, well, technical this all was. I’ve been on the wrong end of a camera before (the director’s end, in case there’s any doubt about the question) and so am aware of the degree of co-ordination required to produce even a modestly ambitious film. The screenplay is the central instrument in that co-ordination. It is where everyone starts and is the medium where-through the director’s ego expresses itself by pissing all over the writer’s vision. But it is still central.

A screenplay is not a story. It is a technical specification for a story. This makes it a very different animal than anything else a creative writer might touch.

This has led me into a contemplation of what a story is, which it turns out is the question I have been in pursuit of the answer to this year.

My years generally have themes, and this is the year of the story.

When I moved out of academia and into commercial software development, I said to a colleague, “I don’t really know what an application is, and that’s the first thing I need to learn. I know what a program is, but an application has way more moving parts than that: multiple programs, documentation, installers… I need to understand that.”

An application is a complete, self-contained tool for fulfilling a user’s needs. A program is a component of that tool.

I’m big on definitions of human artifacts in terms of “tools”, based on Lois McMaster Bujold’s definition, “A weapon is a tool for changing your enemy’s mind.” That is a truly beautiful statement, both inclusive and disruptive.

My definition of “money” follows the same pattern: “Money is a tool for shifting demand through time.”

All of this has got me asking, at the end of my exploration of what a story is, “What kind of tool is a story?”

I have a couple of ideas, and they mostly involve “meaning”, which I’m not sure I can handle in a non-circular way.

“A story is a tool for giving facts meaning and significance in the minds of readers.”

(I say “readers” but of course any medium will do as the carrier wave for a story.)

I’m still deciding if that’s a definition that’s good enough for going on with, and may have more to say about it in future, but either way I’m within a hair’s breadth of having a working definition of “story”, and that, for a writer and poet, is kind of a big deal.

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Islamism is Stupid

In the past few days Islamist nutjobs have killed two Canadians. Why they are doing so is pretty clear: they are stupid.

It is stupid to attempt to intimidate Canadians by killing a few of us.

It is stupid to think that attacking innocent soldiers going about their lawful duty will result in anything other than what it always results in: solidarity amongst the vast majority of people who are on the side of law, democracy, diversity and dialog as a means of solving our problems–that is, things that actually work–against those who think mouthing arrogant, stupid, slogans about the infinite power of their god does anything other than show what a bunch of ignorant pricks they are.

“Our religion is true because it is true! We know it is true so it is true! We will be victorious! God is great!” is not a convincing argument. It is not an argument at all. In fact, it translates as, “I am stupid! I am very stupid! You would not believe how stupid I am! Soooo stupid!”

Religion–if taken seriously–is a mildly harmful delusion in the private sphere, which leads to a litany of petty miseries as the payment it demands in return for the comfort it offers its adherents. But the costs of private, personal religion are borne almost exclusively by the poor souls who are engaged in it.

Public, political religion, on the other hand, is a stupid obsession that endangers everyone.

We know this, because we have been here before.

Canada, via Great Britain and France, is a product of religious wars. Islamists don’t seem to be able to grasp–because they are stupid–that we did not get to our current state of secular paradise by being weak, we got here by being smart. It only took us a few hundred years, but we finally noticed that religion and politics, while both somewhat unsavory enterprises on their own, when mixed together generate a toxic miasma that makes chemical weapons, which only destroy human bodies, look fairly benign.

Politicized religion destroys whole societies.

Between 1547 and 1745, politicized religion did its best to destroy England, and was none too kind to France, nor Germany, neither. We fought wars over it. We burned heretics and hung, drew and quartered traitors, where their “treason” was little more than their mode of Christian worship. We rarely engaged in anything so civilized as mere beheading, which was considered a kind death. We killed and we tortured and we killed some more. We engaged in terrorism and spying and proxy wars and civil wars and real wars.

And we came to realize, slowly and by degrees over the centuries: this is stupid.

God doesn’t care how, or if, we worship. God certainly doesn’t care how we run our political systems. God doesn’t care about law, or politics. God doesn’t need us to worry about other people’s behaviour. Only, perhaps, about our own, which at least has the virtue of being something we can actually do something about. You know, without killing anyone.

God is infinite. God is incomprehensible.

Now tell me again how you know exactly what God wants.

And if you answer, “Because it is written in our holy book!” what I and anyone else with two brain cells to rub together will hear is, “I am stupid!”

And if you answer, “I will kill you if you disagree with me!” what I and everyone else with a shred of human decency will hear is, “I am stupid and evil!”

Politicized religion is stupid.

Islamism is politicized religion.

You finish the syllogism, Socrates.

Canada is amongst the most peaceful, prosperous, happy nations on Earth. We treat women as equal to men, and allow and encourage them to partake in every opportunity our society offers to anyone. We fornicate with wild abandon while our gay friends sodomize each other happily within and without the boundaries of legally recognized marriage. We worship our gods in a diversity of ways, and some of us worship none at all and think it’s a bit sad that anyone else does, while non-religious people are looked upon as lost sheep by our religious fellow-citizens. We lionize the freedom that everyone has to join any religion and then leave it, peacefully and unmolested. We treat our Jewish citizens as the nice and law abiding people they generally are.

We violate God’s laws every day of the week and twice on Sundays.

And you know what? We prosper.

God does not strike us down, which an infinite, all-powerful God could surely do.

Anyone claiming otherwise, or claiming that God needs help or that they must do personally what God has chosen not to do is: stupid.

Your infinite, all-powerful God does not need help.

You do.

Because you’re stupid.

Anyone who genuinely believes in an infinite, all-powerful God does not believe in political Islam, or political Christianity, or any other variety of politicized religion. Only unbelievers could possibly have such a belief, because only unbelievers could possibly hold that God is so limited as to need human assistance.

It follows from this that Islamists are not only stupid: they aren’t even Islamic. Because Islam is very clear that God is infinite and all-powerful.

And since Islamists are not Muslims, yet once were, they must be apostates.

And it follows from this that it is the religious duty of Islamists to kill themselves, as this is clearly the penalty that Sharia law–which Islamists claim to hew to–dictates for the crime of apostasy.

It is not my way to wish harm on any human being, but in this case I have to say I’d like to make an exception, and encourage all Islamists in Canada and elsewhere to save us the trouble of tracking you down, watching you until you do something overtly evil, and then capturing or killing you. It would be way more efficient for you to do the job yourselves. But you’re probably too stupid to follow the logic above, so I guess there’s no real point in asking.

Finally: I am deeply grateful to moderate Muslims in Canada who have helped the RCMP and others keep track of the nutjobs in our midst. I obviously don’t share your religion–and expect many of you disapprove of my particular brand of qtheism[*]–but I recognize that you derive comfort and cultural cohesion from yours and hope that Canada continues to provide a safe and welcoming environment for all peaceful, law-abiding citizens, regardless of how wacky their personal beliefs may be.

[*] Not a typo, although I just invented the term and will expand on it at a later date.

Posted in history, politics, religion | Leave a comment

Power Too Cheap to Meter

There has been some not-entirely-unjustified skepticism about Lockheed-Martin’s recent announcement of a novel fusion reactor configuration. This post is intended to explain why I’m hopeful about this, rather than simply dismissive.

I’m a technological optimist.

But you knew that.

Timelines, etc

I don’t believe that the LM timeline is likely to pan out, but that’s simply because I know from practical experience how hard it is to get a new technology to market. Even the iterating process will take longer and cost more than expected.

However, the ability to iterate on a design rapidly is a huge, huge benefit to technology development. The kind of massive, multi-decade project that is ITER, for example, has many fewer chances to try out new things or course-correct if an assumption or calculation doesn’t prove out in reality. Despite it’s name, ITER doesn’t actually allow for iteration.

Some people are suspicious that LM is approaching this as a closed, commercial, engineering project rather than an open, scientific one. This is a bit odd, as LM is a closed, commercial, engineering company. They appear to be seeking partners to a) lay off financial risk; b) bring in additional expertise; and c) keep fundamental secrets, secret. They may be wrong in taking this approach, but there is nothing particularly untoward about it.

Details Matter

Which leaves us with the plasma physics, but then again, what doesn’t?

There are features of the high-beta design that are promising, and they say they have stolen ideas from Bussard’s variant of the Farnsworth machine and elsewhere. None of these things on their own are capable of coming close to commercial break-even, but in combination?

Details matter.

In the aerospace museum in Ottawa there is a copy of an early Bleirot monoplane built by an Ontario farmer after seeing one in France. He didn’t get a very good look, though, and didn’t understand the importance of dynamical stability (which was one of the Wright Brothers’ bigger discoveries) so while it looks like an airplane, it doesn’t actually fly because it doesn’t have ailerons (Bleirot) or warpable wings (Wrights).

If that plane had been built first, the person who built it would be an expert in the field. Although it’s a question as to what that field would actually be. There were plenty of experts in “aviation-before-anyone-had-actually-flown” (pre-aviation? failed-aviation?) but despite Edison’s famous dictum that “we have not failed, we have merely discovered a thousand ways that do not work”, having expertise in how not to do something–while valuable–is an imperfect guide to judging how do to something, especially in the absence of details.

Clarke’s First Law is a reflection of this reality: “When a distinguished but elderly scientist states that something is possible, he is almost certainly right. When he states that something is impossible, he is very probably wrong.”

Let me temper this by saying, as an expert in a few things myself, I certainly appreciate that laypeople often fail to see what is wrong with certain approaches. It is easy for non-experts to go down false trails that have already been thoroughly explored by experts. But in this case, the lead researcher, Thomas McGuire is not a neophyte. It is reasonable to assume he is aware of the landscape of failure in this field, and has avoided the known false trails.


Neither I nor anyone else who knows what they are talking about has said this is anything like a sure thing. But it’s hopeful. We used to say, “practical fusion power is thirty years in the future and always will be”. Now, I’d say the time-scale in that joke has come down to a decade, and it will likely be sometime this century that it comes down to a year. Shortly after that, “tomorrow” will finally be here.

Posted in physics, science, technology | Leave a comment

Fear in a Time of Ebola

I’ve seen a number of people in the past few days attempting to spread fear about the possibility of Ebola “becoming airborne” and thought it worth saying a few words about that. Although I’m a physicist by education, I’ve spent a good part of the past decade working in various health disciplines, including a lot of time related to bacterial detection, and I was an adjunct in the Department of Pathology and Molecular Medicine at Queen’s for some years (mostly working on cancer genetics.) I’ve even written a speculative novel about the outer limits of evolutionary theory that turns on a new kind of pathogenic evolutionary relationship. So I’ve spent a lot of time thinking about pathogens and evolution.

The Ebola virus is an RNA virus, like the rhinoviruses that give us colds. They are about 19 kilobases long, which is small. There are plenty of human genes over 100 kilobases, and they just have to code for one lousy protein, not manage a whole life-cycle of infection and propagation.

Rhinoviruses are tuned up for “airborne” propagation, which is more properly “aerosol” propagation. Aerosols in this context are tiny droplets of (mostly) water with a diameter of less than five microns. Droplets much bigger than this have a hard time getting into the upper respiratory tract, and so don’t propagate the virus. Aerosols also are small enough to remain suspended in the air for many minutes, creating more opportunities for inhalation and therefore infection, if they contain a virus capable of aerosol propagation, which Ebola is not.

One of the (many) tricks that rhinoviruses use to get into our bodies is to bind to a specific molecule (variously known as ICAM-1 and CD54 in the charming tangle of nomenclature that is modern biochemistry). It finds this molecule on the surface of epithelial cells in the upper respiratory tract. Rhinoviruses also have a preferred temperature that is 32 C, not the 37 C of the human body’s core. This makes them well-adapted to upper respiratory infection, and nothing else. Ever caught a cold through a cut on your hand? Me neither. Being adapted to one path of infection makes rhinoviruses maladapted for others.

There is a reason for this that goes beyond the specifics of any particular virus, which is the evolutionary realities of pathogen/host relationships. Pathogens are incredibly specialized. This is true across all kinds: viruses, bacteria and parasites are all aimed and extremely narrow niches in their host’s defenses. These niches are narrow almost by definition: if they were wide, the host species would have died out.

Most parasites and pathogens are adapted to a single host species. A few rarities like rabies and influenza have more general tricks, but that is because they’ve found a biochemical flaw that is shared across species, not because they’re especially versatile. Pathogens don’t do versatile. They can’t afford to: any genetic material taken up by one function is lost to all others, and to slip through the host’s immunological armor they need all the bases they can get.

So bugs like rhinovirsuses have a whole range of specialized adaptations that allow them to get into our bodies via aerosol propagation and upper respiratory infection. Ebola does not. Nor is there anything like an easy pathway for it to adapt to aerosol infection. It would have to alter its structure to bind to an appropriate molecule on the surface of epithelial cells. It would have to adapt to operate at a much lower temperature than normal. It would have to pull off a dozen other biochemical tricks that could only be performed at the cost of giving up some other function, and therefore would most likely become much less deadly in the process.

So while it’s true that given enough time “Ebola could become airborne” it is also true that given enough time “hydrogen could become people” (supernovae are required as an intermediate step in the latter case). While not quite on the same timescale as “evolution of life as we know it” such profound changes in an infection pathway would require vast amounts of time, and over such enormous periods almost everything else poses a far greater danger to us: coronal mass ejections, giant asteroid strikes, cows, coconuts, you-name-it. An influenza pandemic is far, far more likely to kill us all than Ebola: we know this because we know that in 1918 it damned near did. The flu really is a few mutations away from a 10% mortality rate.

Physically, Ebola can be carried into the air in aerosol droplets, but it simply isn’t very good at getting into the body via the upper respiratory tract, which is what is required for a virus to pose a significant airborne transmission risk. Still, if someone with the disease were to cough on an open cut on your skin you’d be at risk, so you probably want to avoid that, which… shouldn’t be too hard?

The odds that someone reading this will die from being trampled by a cow in the next year are many orders of magnitude greater than the odds that anyone reading this will die from an airborne Ebola infection. The odds that *everyone* reading this will die from a pandemic flu in the next year are orders of magnitude higher than anyone reading this will die from an airborne Ebola infection.

So if you see someone spreading panic along the lines of “Ebola could become airborne”, feel free to ask them why they are concerned about Ebola, but not about cows, coronal mass ejections, or the flu?

Posted in evolution, probability, psychology, science | Leave a comment

What a Difference a Data-Point Makes

I just recently found out about a nice bit of work from a few years ago, involving the tracking down, digitizing and processing of Nimbus satellite images from 1964 that include the poles, so sea-ice estimates could be made.

I was a bit disappointed in the graph showing the new Arctic data in context, as it doesn’t give a sense of how far back in the past this extends our record of Arctic sea ice, so I made my own:

Effect of Nimbus 1964 Data Point on Arctic Sea Ice Minima Fits

Effect of Nimbus 1964 Data Point on Arctic Sea Ice Minima Fits

This single data point resolves a significant ambiguity in the modern record: how long as the sea-ice extent during the summer minimum been falling? You can get an OK fit to the modern data (1979-2000) with a straight line, as shown, and if you add a second-order term so the line can be curved the overall quality of the fit gets slightly worse. So are we seeing a long linear decline, or something that “turned on” sometime in the the past twenty years?

The fits to the graph shown here indicate clearly it is the latter: September sea ice in 1964 was about 6.9 million square kilometres, and if you fit with that point included up to anywhere between 1990 and 2000, you get a line that is flat. Fit the later data and you get a line that is sloped downward as shown.

There is a cautionary tale here for people who want to point to a decade or two of data and make claims about the world. Unless we have comparably good data from a lot further in the past, there is little basis for wild extrapolations. The climate is non-linear and noisy, and that means climate data must be approached with enormous caution. If they are not, there is a significant risk of making wild predictions that turn out to be completely false, which does not do your reputation any good.

Posted in physics, politics, prediction, science | Leave a comment

How News Stories Ought to be Written

The government of Iraq is requesting American troops to defend Baghdad from ISIS attacks.

Here is information the story omits.

President George W. Bush signed a “Status-of-Forces Agreement” with the Iraqi government in 2008 that specified a December 31st 2011 final withdrawal date for all American troops from the country.

President Barack Obama slowed the withdrawal of combat troops–extending the duration of their stay by ten months–but maintained the final withdrawal date of December 31st 2011 that President Bush set.

In a major diplomatic failure, the Obama Administration failed to reach agreement with the government of Iraq on maintaining bases in the country. This failure occurred in October 2011, two months before the final withdrawal of about 39,000 American troops who remained in the country to assist and train Iraqi security forces.

All of this information is relevant to the current context, and it leaves very little room over for partisan sniping.

1) The December 2011 withdrawal date was set by President Bush and implemented on a delayed schedule by President Obama.

2) The failure of negotiations to maintain American bases in Iraq was a serious failure on the part of the Obama Administration, but you’d have to be insane to suggest that the seeds of that failure hadn’t been sown by the Bush Administration’s mismanagement of the Occupation, particularly with regard to mercenaries but also failures like Abu Ghraib. “Hi! We invaded your country, freed you from a brutal dictator, then reduced the place to armed chaos, killed and tortured your friends and neighbours, and we’d like to keep somewhere between one and four huge military bases in your country but we aren’t ‘extending the occupation’ or anything! Really!”

Unfortunately, the story in the National Post contains none of this information, which took me about five minutes to track down.

Posted in politics, psychology, war | Leave a comment

Sampling Fossils

Sometime in the late 80’s or early 90’s I read an article in Nature that argued we should expect “first discovery” dates in the sciences that involve digging up fossils to take periodic leaps backward.

The argument is compelling: because fossilization and preservation of fossils are rare processes, they sparsely sample the living population. Under these circumstances the odds of us discovering the earliest of any instance of a thing are very low.

As near as I can tell, people who work in these fields don’t read Nature, because the argument still doesn’t seem to have much currency. So I thought it would be fun to put together a simple computational example that roughly models the human population. I made most of the numbers up, but the results are nicely illustrative of the phenomenon.

Consider a simple model where the human population grows exponentially from two people–call them “Madam” and “Steve”–a million years ago to three million people 12,000 years ago (which is the best estimate for the pre-agricultural human population)

Fitting this to an exponential, this gives us an e-folding time of about 70,000 years, so the population looks like 2*exp(years/70178) with time zero being a million years ago and 12000 years ago being time 998000.

Now assume that fossil preservation is a linear ramp that starts with zero probability a million years ago and ramps up to a one-in-ten-billion chance 12000 years ago: 1E-10*years/12000

If we instantiate this as a few lines of Python and randomly sample the mean number of preserved fossils each year, we get the following code:

import math
import random

fA = 0.998E6/math.log(1.5E6)
print fA

def g(fT): # population growth
	return 2*math.exp(fT/fA)
def f(fT): # fossil preservation
	return fT*1E-10/998000
# sample from a million years ago to 12000 years ago
for nI in range(0, 998000):
	fAvg = f(nI)*g(nI) # average number of fossilized remains
	if random.random() < fAvg: # actual number
		print 1e6-nI, fAvg # date of first discovery (years past)

Running this code produces dates for the oldest discovered fossils that vary nicely around the age of the oldest know fossil for anatomically modern humans, which is about 195,000 years.

But here is the distribution of results, which is unsurprisingly broad.


The red line that peaks around 200,000 years ago is for a fossil preservation probability of one in ten billion, the green line that peaks around 300,000 years ago is for a fossil preservation probability of one in a billion. Or rather, those are fossil preservation and discovery probabilities, as a fossil that has not been discovered may as well not exist in this calculation.

It should be clear on this basis that to assert, as the Wikipedia page linked above does, that "Anatomically modern humans evolved from archaic Homo sapiens in the Middle Paleolithic, about 200,000 years ago" when the oldest known anatomically modern human fossils date from 195,000 years ago is to reject some pretty basic mathematics. However many anatomically modern humans there were to begin with, the number was bound to be small, so the odds of the earliest discovered fossil being dated to a few thousand years after the evolution of a species is very small.

That "about 200,000 years ago" should really read, "sometime before 200,000 years ago, quite likely earlier than 500,000 years ago" unless the number of modern human fossils is really very high starting 200,000 years ago. And it is not: we find the earliest anatomically modern human fossils only in a few sites dating from 75,000-130,000 years before present (Klasies River Mouth), 92,000 ybp (Qafzeh) and 90,000 ybp (Skhul). So we are genuinely dealing with a sparsely sampled population.

On this basis we can and should expect that as we search more diligently for anatomically modern human remains, we will find "surprising" leaps back into the distant past. It wouldn't shock me, based on this simplistic model, if our earliest anatomically modern ancestors were a million years old. It would, however, shock the people who work in this field, just as they were apparently shocked by the Omo remains, which took things back a mere hundred thousand years earlier than previously known.

This is a all a bit sad. As I said, I read an article about this phenomenon in Nature over twenty years ago. We should have robust models of fossil survival probabilities and discovery probabilities now, which would allow us to use the actual data to make valid Bayesian inferences about how old our earliest ancestors are likely to have been, rather than innumerate statements that claim fossils that are 195,000 years old support origin dates of less than 300,000 years old, when in fact they almost certain make far older dates much more plausible, and dates of less than 300,000 years before present very, very unlikely.

To claim otherwise is to claim either that the early human population wasn't growing much over hundreds of thousands of years, but became almost immediately high and stayed high for the rest of pre-history--which doesn't seem very plausible--or it is to claim that fossil preservation and discovery is a common process, which also doesn't seem very plausible.

Although the model presented here is exceedingly simple-minded, it significantly increases the plausibility of the proposition that early anatomically modern humans existed for much longer than would be naively inferred.

As sampling becomes less sparse--as we move more closely toward the present day--this phenomenon will become smaller, but it wouldn't shock me if our evidence for the peopling of North America turns out to underestimate the antiquity of that process, for example.

To refute the argument I'm making here requires that one create a plausible model of population growth, and fossil preservation and discovery that allows in the typical case for the date of the earliest discovered fossil to be very close to the date of earliest appearance of the fossilized species. I can't think of such a thing, but perhaps someone else can, which would be fascinating indeed.

Posted in bayes, evolution, history, probability, software | 2 Comments