Follow the reluctant adventures in the life of a Welsh astrophysicist sent around the world for some reason, wherein I photograph potatoes and destroy galaxies in the name of science. And don't forget about my website, www.rhysy.net



Monday, 2 May 2016

Nemesis : Everyone's Favourite Death Star

The Ask An Astronomer Anything At All About Astronomy posts have become the most popular regular feature here. Usually this involves digging around in my own head for the answer, occasionally doing some quick calculations, almost always some Googling to make sure I'm not spouting nonsense, sometimes watching (usually bad) documentaries, and very occasionally reading papers. But never before have I gone to the lengths of reading an entire book because of what some moron I've never even met has written on social media.


But this post was different. Nemesis, some claimed, was "junk science" or worse, "drivel", and the post should be removed. I could not let that pass. Richard Muller's Nemesis : The Death Star was one of my favourite popular science books from my early teenage years. I had quite clear memories of it being exceptionally well-written, ruthlessly honest, and giving a detailed and interesting account of what it's really like to actually do science on a day-to-day basis. Most outreach books tell you only about the theories, whereas Nemesis also told you about the other aspects : the workload involved of getting a result, how other scientists and the media reacted, how people changed their minds or became dogmatic - in short, what the scientific method is really like, not what it's supposed to be.

So I ordered my copy for some ridiculously small amount of currency, and three weeks later it finally arrived. Three days later, I'd finished reading it, having found it quite hard to do anything else.


Nemesis is a real gem. The fact that it's about a star that disturbs comets and is likely wrong is absolutely irrelevant - it's a tour de force in intellectual honesty and a brilliantly clear description of what front-line research is really like. Still, for the sake of it, I suppose I should explain the basic premise.

The book is actually about two ideas. The first is the now well-established idea that the impact of a comet or an asteroid killed the dinosaurs 65 million years (Myr) ago. The key evidence for this is a layer of iridium across the globe at the end of the Cretaceous period. Other claims that this could have been due to a supernova or from volcanoes were very carefully examined and found to be wrong. Not merely unlikely, but quite wrong.

Image credit : me.
The second idea is more controversial. Both mass extinctions and cratering of the Earth appear to occur on regular intervals of about 26 Myr. Not everyone agrees with this, but following that assumption, the idea is that there's some event which causes a regular bombardment by comets or asteroids. The Nemesis hypothesis is that this is due to a low-mass star which orbits the Sun, perturbing the comets in the Oort cloud every 26 Myr, plus or minus a little bit. These "comet storms" last around 2 Myr and around 0-5 comets might impact the Earth during this time, hence the periodicity might not be exact and the magnitude (and duration) of the extinctions can vary.

From this summary article. The arrows are separated by 26 Myrs.
A minor point of fact : on the original post it was stated that there's a more recent alternative idea that the extinctions follow the Sun's motion through the galactic disc, which also follows a ~26 Myr cycle. Actually, this was an earlier idea considered at around the same time as the Nemesis model, and dismissed because the Sun is currently in completely the wrong place for this to work.

I've decided that this review should concentrate on the philosophy of science aspects of the book. Hence while the book itself forms a clear, straightforward narrative, I'm going to organise this review thematically. This deceptively simple theory provides an excellent lens through which to examine the complex nature of the scientific method. As I've described before and no doubt will again, the forefront of research has little resemblance to the fact-checking approach taught in schools.


Is It Really A Theory ?



"But I thought 'theory' had a special meaning for scientists", you might say. Yes and no. I suspect I've probably put about confusing mixed messages on this myself, so it's worth trying to clear this up. Throughout the book, Muller uses "theory" just like anyone else does : a synonym for "model" or "possible explanation that fits the currently-known facts". He never uses it with the special sense of also being extremely well-tested, which is a common retort to anyone who says, "just a theory" today. Indeed, he even uses, "just a theory" himself. So do real scientists, all the time. Happens every day.

While it would certainly be extremely useful to have a distinct word for very well-tested model, as opposed to hypothesis, the reality is we just don't. The word isn't used like that. To hell with whatever the "official" definition is - it's usage that matters. And as I've described very recently, even very sophisticated models which explain the facts with very impressive precision can still be utterly wrong. So is it fair to say, "only a theory" after all ?

Without some rigorous, objective definition of "very well-tested", I think it has to be done on a case-by-case basis. Certainly you cannot say that evolution is only a theory, because speciation has been observed to be happening. And it's certainly not fair to say that relativity is "only" a theory either, because its predictions have been verified time and time again with insane precision. It could still be wrong, but it makes no sense to call it "only" a theory - that cheapens the immense workload involved in both creating the idea and testing its predictions. But you definitely can say "only a model" for lesser ideas that have not withstood decades of careful testing.


Extraordinary Evidence Requires Extraordinary Claims



Or as Muller puts it on page 4, "ludicrous results require ludicrous theories". This is the flip side of the famous quote, "Extraordinary claims require extraordinary evidence". Not everyone likes this, though I tend to agree with it. If your claim (or theory) is in stark contrast to very well-established results, the burden of proof is firmly on you. To disprove a widely-accepted idea (except during those rare cases* when the establishment has reached a stupid conclusion), you ought to have pretty good evidence against most (not necessarily all) of the major points. Collectively, the strength of this evidence would have to be extraordinary - though, importantly, each individual piece of evidence need not be especially strong.

* There was a very nice recent article I wanted to link here, on describing what actually happened to scientists who claimed that animals could think, but I can't find it. Do let me know if you think you've found it.

But somehow the reverse of this had never really occurred to me - at least, not in such an eloquent way. In fairness I have mentioned on occasion that sometimes evidence forces you to a conclusion you may not like. That is, after all, how science works. The difference is that this is a nice succinct, quotable reminder that sometimes you cannot avoid seemingly crazy ideas.


Don't Be Hasty



Or more importantly, don't be overly-critical. In Muller's words, skepticism needs to be "finely honed". This is one of my favourite aspects of the book, a running theme for which many examples are given. It's a simple enough idea which I've pointed out elsewhere many times : if you really attack an idea too strongly (especially when it's in its infancy), you can shoot anything down - even really good ideas. It's the difference between true skepticism and denial.

Knowing where to draw the line isn't easy. Muller gives many examples of when he and others seemed to be straying into denial (and even outright abuse) rather than skepticism. Indeed the book opens with his former PhD supervisor arguing that an idea is just stupid based on authority. Obviously real scientists aren't supposed to do that, but they do anyway. Although Muller wins the argument, near the end of the book we find his supervisor apparently hasn't learned anything, dismissing a related idea as "just nonsense" without examining it. Yet these are exceptions - far from being a critique, much of the book actually feels like a bromance with his supervisor. Scientists aren't saints.

And Muller gives plenty of examples of when he spots his own over-skepticism too. Toward the end, he gets word of a similar rival theory in which he finds a flaw. He called the authors :
"A few days later he called back and said my criticism was indeed valid, and their old theory was in fact wrong. But now they had a revised variation on the theory that didn't have the same weakness... I asked myself why I hadn't attempted to salvage their old theory, rather than just knock it down ? I realised once again that I had been getting lazy. I had a theory of my own, and I was trying to disprove other theories. I wasn't trying to find alternatives that worked."
The Platonic ideal of science is that it's about finding out what's happening. In practise, it's at least as often about disproving your rivals - which is part of the reason why peer review is important. It's usually a lot easier to find out what doesn't work than what does, and all too often we fall into the trap of trying to shoot people down rather than uncovering the truth. Which is not to say that some ideas don't deserve to be shot down. It's complicated. A couple of passages deserve to be quoted at length :
"Skepticism, the ability not to be fooled, was clearly important, but it is also cheap. It is easy to disbelieve everything, and some scientists seemed to take this approach. Sometimes Luis was skeptical, but more often he seemed to embrace crazy ideas, at least at first. He rarely dismissed anything out of hand, no matter how absurd, until he examined it closely. But then one tiny flaw, solidly established, was enough to kill it. His openness to wild ideas was balanced by his firmness in dismissing those that were flawed. He had a finely honed skepticism... A scientist differs from other people in that he knows how easily he is fooled, and goes through procedures to compensate."
And later :
"Scientists are trained to be skeptical, to doubt, to test everything... but they never mention that too much skepticism can be just as bad as too little. When presented with a new, startling, and strange result, it is easy to find flaws and come up with reasons to dismiss the finding. Even if the skeptic can't find an outright mistake, he can say, "I'm not convinced". In fact, most scientists (myself included) have found that if you dismiss out of hand all claims of great new discoveries, you will be right 95% of the time. But every once in a while, there will be that rare occasion when you are wrong. Likewise you cannot afford to lose your skepticism or you will waste your time in hopelessly blind alleys.
How do you develop the right sense of skepticism - when to dismiss and when to take seriously ? How do you argue with someone who has a different level of skepticism ? How do you respond to the statement, "I'm not convinced" ? The best way, the only possible way, is to go on with the work. Be grateful that the competition has not even entered the race, and has left all the fun to you. Someone had once said, "Research is the process of going up alleys to see if they are blind.""
One technique I've recently been finding useful is to numerically estimate the odds you think that a new idea could be correct. It really doesn't matter how you arrive at the number, that's not the point. The point is to remind yourself that you might be wrong. You can give extremely high odds if you want, but there is almost always some wiggle room which demands you consider the unknown unknowns. Trying to put a number on it forces you to consider possible alternatives, which you might otherwise not do.


You're Usually Wrong


Another extremely important running theme is that humans are quite a lot like dogs, though it's not phrased like that in the book. Dogs rely heavily on trial and error, especially when a human tries to teach them a new trick. So it is with science more than we might like to admit. Muller's advice is to try to have one good idea per week, and to keep trying out the crazy ideas. The book is replete with examples of outlandish ideas being tested. Most of these don't survive more than about twenty minutes of discussions with colleagues -  a few last days, and a very few go to to be published.

And these ideas really are outlandish and ridiculous. There was the idea that the dinosaurs were all killed by a HUMONGOUS tsunami that somehow swept entire continents clean. There was the one about hydrogen from the Sun combining with water in the atmosphere to form excessive clouds that darkened the sky. How about the one that comets impacting sunspots get vaporised and blown back to Earth where they cause a magnetic field flip ? Or the one about the Sun going nova, which any undergraduate astronomer could tell them is fundamentally impossible ?


This ties in closely with the idea that you shouldn't be overly-skeptical. What you should do, in my view, is be aware of the alternatives but not necessarily investigate them yourself. That's really a personal choice and you're not obliged to investigate someone else's crazy idea. But if you raise an objection, you're obliged to hear their counter-argument.

For example, right at the start of the book there was the statement that Nemesis' apogee would be about 2.8 light years from the Sun. They considered this to be close enough that it wouldn't get pulled away by other stars. That had me extremely worried that the book was, after all, junk science. 2.8 light years is more than half the distance to the nearest star, so the Sun won't affect it as much as the other stars*. So if I'd been in the room, I'd have shot the idea down instantly.

* They also had more sophisticated models where the orbit wasn't so large but the star still managed to enter the Oort cloud every 26 Myr, but found that these didn't work.

This is still my strongest objection, but they did (eventually) come up with a clever counter-argument. Passing stars, they say, will only influence Nemesis when they are within about a light year or so (not sure where they get this number from) and at the speed they're typically moving this will rarely last for more than 30,000 years. The time between perturbing stars is more like a million years, so passing stars don't act for long enough to do much. And the direction they perturb Nemesis will be random, whereas the gravitational attraction towards the Sun is always in the same direction. They also came up with numerical models to investigate this, though no details were given.

Having experienced first hand how difficult orbital dynamics can be, I ended up less skeptical than at the start. But without more details, I'm still not fully convinced. My perhaps naive concern is that once you end up deeper in the gravity well of another star than the Sun, you're in big trouble. I don't know.


Observations Can Be Wrong


While we're dealing with the things I don't like about the book (few as those are), the thing I found strangest was a consistent attitude that if the observational numbers were in conflict with the theory, then the observations must be wrong. Now, I've just publically rubbished the EmDrive, which claims to be producing minute amounts of thrust even though theory says it shouldn't - so you might well accuse me of hypocrisy. But the theory against the EmDrive - the conservation of momentum - has literally been tested for centuries, whereas Nemesis had been investigated by a handful of people for a few months. So I found it a mite strange that when they found a number that didn't agree, they didn't immediately regard it as falsifying their theory.

And yet, reluctantly, I'm forced to agree that their approach was correct. They cite several examples where, on checking, the observational numbers were indeed found to be in error. Sometimes those changes were in favour of their theory, but sometimes they were against it. And when they were against it, they did the only reasonable thing possible : they changed their minds. Importantly, they attacked their own findings with the same zeal they applied to others.

By far the best example concerns an early idea that the dinosaurs were killed by a supernova. The experiment they ran to test this looked for minute amounts of plutonium by irradiating a sample of Cretaceous rock. It was not a straightforward procedure. It took two weeks just to prepare, then required a literally all-night session (since the radioactive material produced quickly decays) to make the measurement. Initially, the results were astonishing. It seemed like a clear, decisive victory, and for a few glorious moments it seemed as though a select few people knew what really killed the dinosaurs before anyone else did. And yet... the amount of plutonium detected was too low. So they re-did the entire thing, and discovered they'd picked up contamination from elsewhere in the lab. Their initial result was simply wrong.

Observations have the last word, of course. But observational measurements involve just as much care as the theoretical predictions, and if the two are in conflict, it's maybe not quite so easy to decide which is correct.


Don't Be Fooled



As mentioned earlier, a scientist should be aware of how easily they can fool themselves - even, as we've just seen, with observational results. That's why we demand statistical significance. Sometimes raw numbers aren't enough, which is demonstrated in this case by the extinction and cratering periodicity. Luis Alvarez, Muller's former supervisor, wasn't convinced by their statistical analysis, finding it too weak to be worth considering. So Muller devised a way to let Luis convince himself. He generated artificial plots of the cratering, some of which were random and some with periodicity. He gave these to Alvarez unlabelled, along with the true data and told him to select the three he thought were the most periodic. Alvarez's selection included the real plot and two of the plots with artificial periodicity - without knowing it, he'd rejected the ones which were purely random.

This is all very convincing stuff when you read it. On reflection, I'm nearly there, but I can't quite make the leap to conviction. It shouldn't be necessary to emphasise statistically weak effects like this. Muller himself admits on his website that not everyone agrees it's significant, and without this, the theory is dead. And yet there seems to also be a matching rate in large craters and, possibly, in magnetic field flips, so if I have to choose I'd say it's probably real.

You might be wondering how an impact could change the magnetic poles. Well, they came up with a remarkably ingenuous mechanism to explain this. The magnetic field is generated at least in part through the molten outer core of the Earth. If the spin of the solid crust and mantle were to change, this would cause a twist in the magnetic field as the core lagged behind. The impact itself couldn't alter the spin enough to do this directly. But the after effects just might. The dust thrown up from the impact, along with the soot from forest fires, could cause a significant temperature drop and increased snowfall near the poles. That shifts a not insignificant fraction of the Earth's water, altering its spin.

But is this just, err, spinning an elaborate idea to explain something of marginal significance ? Possibly. The discoverer of the magnetic field flip periodicity withdrew his claim, saying it wasn't significant enough (though he maintained that extinctions are periodic). Which ties in quite well with the old adage about beautiful theories being slain by ugly facts. Not though, as Muller repeatedly points out, that all wrong theories are devoid of merit.


It's Not Always Fun To Be Wrong


The whole point of science is to find out things you didn't know before. Sometimes the most wonderful and rewarding part of the process is to have your entire world view overturned by a new discovery - it's a thrill, an intellectual adrenaline rush. But not always. Nemesis deals with this in a blunt and incredibly honest way.

Muller notes that when the supernova theory (which his group supported) was proven wrong, this was still progress. It also wasn't their idea originally. It's easy to be pleased when you've disproved someone else, even if you agreed with them, which is another reason for peer review. If, however, your goal is to find out what's really happening and not merely disprove ideas, even this can be disappointing rather than elating. Muller makes it clear that he went through a lot of long periods of frustration as he struggled to work out what was really going on. Wrong idea followed wrong idea with no light at the end of the tunnel.

Sometimes these days there seems to be a lot of emphasis on the idea that you can't ever prove anything in science. I profoundly disagree. The Earth was proved to be round by observations. Evolution was proved to happen by observations. The Universe has been proved - near as damn it - to be expanding by observations. The existence of Neptune was predicted by theory then proved with observations. As long as you accept the existence of an objective, measurable reality, then of course you can prove a theory. Which is why the ideas of the Universe being a simulation or an illusion are just unscientific gibberish (Note : I haven't read those links). Proof may be rare, but it does happen.

Muller also notes a difference between theorist and experimenters : if an experimenter publishes a result which is found to be wrong, it will damage their reputation, whereas if a theorist comes up with a wrong idea then it does them little harm so long as it's clever. The issue is, of course, one of competence. Experimenters are supposed to understand how to use the equipment correctly to get the right numbers - if they get something wrong, they've exposed their own incompetence*. Theorists are much more free to speculate.

* Which is not to say that they can't ever make mistakes. Muller recounts how Alvarez was delighted with him when he dropped and broke a $15,000 piece of equipment, because these things just happen even to the best of us.

Even for theorists, though, Muller notes how he felt free to discuss outrageously stupid ideas with some colleagues but not others. No-one likes exposing their own stupidity in front of strangers, but being able to discuss ridiculous ideas with trusted colleagues is vital. The thing is, when you've established a strong and prestigious reputation like Muller, you can get away with exposing the stupid ideas you came up with along the way. The rest of us can't afford to do that. Transparency isn't always such a virtue.


Media Mania


At first, Muller says he enjoyed the attention, despite already being a prominent scientist. But then he's honest enough to confess that he likes prestige and was jealous of Alvarez when he demonstrated that a meteor likely killed the dinosaurs. Maybe science shouldn't be motivated by such mundane trivia as money or fame, or have political concerns about whether publishing a paper will damage one's reputation - but in the real world all these things happen, like it or not.

Soon though, he began to realise the damage the attention was doing. He was, he says, secretly pleased that the New York Times ran an article insulting the Nemesis theory, even comparing it with astrology, as this meant he couldn't be accused of doing science by press release. This quickly soured. Local news agencies always go to local scientists for comment, but often they haven't read the original paper so they're only commenting on the press releases. Like Chinese whispers, errors quickly multiply, and the theory's reputation suffered.

Worse, and much more surprising, was that scientists were not just giving quick responses to requests for media interviews - in which case the errors would be understandable - but also writing rebuttal papers without having read the original. Or as Muller says :
"When colleagues asked me whether we had any response to the 'latest criticism', I often responded by saying, 'Yes, and you can read it in our original paper.'"
Even the scientifc journals were not above dubious behaviour. The original draft of their paper contained a wonderful footnote :
"If and when the companion is found, we suggest it be named NEMESIS, after the Greek goddess who relentlessly persecutes the excessively rich, proud, and powerful. Alternative names are : KALI, the "black", after the Hindu goddess of death and destruction, who nonetheless is infinitely kind and generous to those she loves; INDRA, after the vedic god of storms and war, who uses a thunderbolt (comet ?) to slay a serpent (dinosaur ?), thereby releasing life-giving waters from the mountains, and finally GEORGE, after the saint who slew the dragon. We worry if the companion is not found, this paper will be our nemesis."
I love it. It injects both self-doubt and self-deprecation. The journal, however, promoted the footnote to a paragraph and deleted all the names except Nemesis without the author's permission. I think that's pretty awful. Clearly, the people have been working hard at making papers unreadable for some time. Depressingly, problems in the media extend from the lowest tabloid to the most prestigious journal.


Nobody Reads The Literature Any More


This is a phrase oft-repeated throughout the book. And it's perfectly understandable, because most papers are unreadable. Now, obviously scientific papers don't need to feature lolcats. They have to contain the nitty-gritty details other researchers need to understand exactly what was done, and for heavily mathematical works there's only so much that can be done to make them readable. But there's absolutely no reason at all the comment about George had to be taken out, any more than the name of Boaty McBoatface needs changing. The occasional mild chuckle will do absolutely no-one any harm and an awful lot of good, because people will be far more willing to read papers thoroughly.

Whether the implication of, "any more" that people read more literature in the past is true, I don't know. I suspect not. At least, I haven't noticed any obvious trend for older papers to be any more readable. On the other hand publication rates are higher so the sheer volume of material now makes reading the literature a daunting prospect.

This is a large topic. All I'll say is that the state of academic writing could be easily improved with a very few changes : the authors should feel free to speculate provided they are clear they are speculating and don't contradict the facts, colloquial expressions should be permitted in moderation, clarity should be emphasised over brevity, obfuscation should be seen as a black mark, a narrative flow should be encouraged where appropriate, and above all meaning and implication should be as explicit as possible - to the extent of assuming the reader hasn't been studying that particular topic for fifteen years.


Epilogue : Death of the Death Star ?



To summarise : it's a fantastic book. You should buy it. But the obvious question must be asked - is the theory correct ? Well... no, probably not. Any fool could have told them that their predictions of detecting the star in three months were wildly optimistic. You don't need hindsight to see that, just practical experience of doing astronomy. And yet, more than twenty years and many large-area surveys later, the silence from the sky is deafening.

Absence of evidence is not evidence of absence. Actually that's not entirely true : you most certainly can have evidence of absence; you can, with difficulty, prove a negative. You can't necessarily prove that Bigfoot doesn't exist somewhere, but you can prove he doesn't exist in this particular patch of forest. In this case it seems there have been enough surveys that an object with the properties of Nemesis would have been detected by now if it existed - or at least, that's the claim. Having read the book, anyone with any sense ought to get the message that science is hard, and jumping to conclusions without having read the literature (even if that it is really tedious) is foolhardy. It's not always obvious to spot where the mistake is.

Is it junk science ? Like hell. Is it drivel ? Screw you ! Regular readers will be aware of just how much time I spend fighting the pernicious myth of the dogmatic scientist - but when people behave like this, they are indeed being dogmatic. You're not helping me out here guys. And yet... Nemesis is a true story of science, warts and all. It's full of people at their best, when the evidence changes their mind, and at their worst, when they dig in their heels and refuse to listen to reason.

It's also a story of drive, determination, doubt, human fallibility, and sheer complexity. I am left in no doubt that they team did the absolute best that any reasonable human being could expect of them. But ultimately it's a reminder of the importance of the long game : trust no new results, because there almost certainly hasn't been time to check them properly, but don't dismiss them out of hand either. Treat media claims of "mystery solved" as though they'd reported the discovery of the Loch Ness monster. Real science is a process of continuous self-doubt and external criticism. Even if there is a key paper that solves a mystery, it usually takes years before you can be sure of that. Don't be hasty indeed.

I've really only scratched the surface with this pseudo-review. I haven't told you half as much about Muller's forthright attitude as I should, how he admits to thinking his supervisor was being overly-skeptical or did the whole project as an excuse to work with his estranged son. Or how Muller himself felt jealously and envy - even to the point of being relieved when a Nemesis candidate turned out to be false because his team hadn't found it. Nor have I said much about the continuous process of investigating new ideas, with the many knife-edge moments when it looked like the whole thing would come crashing down. I think it's wonderful. If I have to rate it, I can't give it anything other than 10/10.

Saturday, 30 April 2016

Who's Afraid Of The Big Bad Reviewer ?


Peer review is something I've talked about before from time to time, but apparently I'm not making myself clear. I don't know why, I use plain simple language, and it's not very hard to understand. But for the sake of having a go-to post, let me try and put things as briefly and as clearly as possible.

Peer review is not some forced, artificial method of enforcing dogma. It is an inherent and unavoidable part of the scientific method. It occurs at many different levels, from freewheeling discussions with colleagues, to the classical "some random experts read your paper" technique that is now synonymous with the term "peer review", right up to how other experts react when the findings are made public and/or the paper is published. While it's important to be aware that the journal-based peer review (JBPR) technique we all know and loathe today is a modern invention, it's also important to remember that science has never avoided some form of peer review entirely.

Skeptical inquiry demands that all ideas be subject to relentless attack, with a deliberate attempt to falsify them. The reasons we do this are really quite simple : we want to establish the truth, be that for old (apparently secure) ideas and new, novel ones. If an idea stands up to at least one expert trying to disprove it, it's probably worth exploring further en masse. If it can't, it almost certainly isn't. JBPR is a way of restricting access to potentially blind alleys before we get lost in them. In that sense, it is a fundamental part of the scientific process, not some forced product of ivory-tower academia.

Mind you I'd quite like to live in an ivory tower as long as it didn't hurt any elephants.
JBRP varies from journal to journal, but essentially it works like this. An author writes a paper and submits it for publication in a journal. The journal chooses at least one or two other scientists (usually recognized experts in the particular subject area) who decide if the paper be accepted, rejected, or re-reviewed after modifications. If the paper is rejected or modifications are requested, the author can argue their case both with the reviewers and/or the journal editor, who provides oversight to the process. Normally the editor is known to both the author and the reviewers, but the author won't normally know who the reviewers are. Ultimately the author can request another referee if the editor agrees, or even submit it to another journal.

Different journals have different policies, but the role of JBPR is* not necessarily to establish whether a result is either novel or interesting - a result which agrees with an existing finding is still valuable, albeit usually less interesting if it fits established models. Nor does a journal entry absolutely have to contain elaborate interpretation : it's entirely accepted, normal practise to publish papers which are nothing but catalogues of measurements. Sometimes that's literally all there is to it. Really. Honestly. I mean it, dammit.

* Or at least should.

Contrary to unpopular belief, it's fine to simply report results even if they fly in the face of accepted theory. Provided, that is, that you clearly explain how the experiment was done, how the measurements were taken, and don't go overboard with trying to explain the results. And of course the methods you use have to be rigorous : normally, saying, "we picked the data we liked best" (or reporting results which aren't statistically significant) will ensure a rejection letter.

If you're not a fan of JBPR, I implore you to think for a moment. What, exactly, is so unreasonable about asking someone to convince another expert that they have a publishable result if that doesn't even require any interpretation ?

JBRP is not supposed to be a method of proof or disproof. Absolute proof is very rare anyway, but widespread acceptance, which is much more common, almost never happens with the first publication of a result. For that to happen takes time - usually lots of time - for others to verify the findings. Alas this very simple guideline of waiting to see whether the wider community can confirm or deny the initial result is something which is almost entirely lost on the media, who think results are ludicrously black and white... but I digress.

They're also often very stupid.
Likewise, when a paper or proposal is rejected, that does not mean the result is disproven. It simply means it isn't good enough for a paper yet. In no way does that stop you from using other means of communication to the scientific world : conferences, proceedings, arXiv, social media, press releases, whatever. But the chances are that if you couldn't persuade one anonymous expert that you had something worth investigating, you should either abandon your research (sometimes things are just wrong, deal with it) or get better data before you try again.

You might legitimately wonder, why, if peer review doesn't actually disprove anything, scientists cry out for it like a flock of hungry seagulls who have just spotted a bunch of tourists eating bags of chips. The reasons are really very simple. Science is often an incredibly specialised process, and everyone makes mistakes - the reviewer is there both to criticize and to help. At least they are if they're doing their job properly.

Would that Beiber would be eaten by seagulls instead of this nice lady.
If you can convince someone who intimately understands the particular work you did, you're on much surer footing. You've reached a minimum level 0 standard worthy of further investigations : one of the few other people in the world who fully understands what you're doing is convinced you're not a crackpot, allowing others (who may not be so specialised) to have some (but by no means complete) confidence in what you've done. If you can't manage this, you're on very thin ice indeed, along with UFO believers and fans of Justin Beiber, probably. Remember, all you need to do is state your results and make it clear when you're speculating. You don't have to solve the entire mystery.

To be useful, JBPR has to be skeptical, as opposed to denial. Where a paper does present interpretation, attacking weak points is not supposed to mean ripping it to shreds : i.e. the authors should probably say, "we think this is more likely" rather than, "we now know what the answer is". The reviewer should huff and puff and maybe try a chisel, but they aren't supposed to dowse the thing in petrol and throw it to the piranhas - you can find faults with pretty much anything if you really want to.  The reviewer's job is only to decide if the article is worth drawing the attention of the wider community or not. It's not exactly verification or communication, just, "they haven't done anything obviously wrong, here, you take a look at it."

Of course, only a brain-dead gibbon would pretend that this process is perfect. A perfectly objective system run by inherently subjective creatures is fundamentally impossible. One guard against the inevitable bias of the reviewers is their anonymity (which they can discard if they so wish). Thus the reviewer's reputation is in no danger if they accept a publication that contravenes existing ideologies. Obviously that doesn't mean their own biases don't get in the way of being objective, but it greatly reduces the danger of a false consensus. Hence this is one area where transparency is undesirable.

EDIT : It's also worth noting that the journals generally don't pay the reviewers anything, it's just an expected part of any researcher's job. As well as ensuring the referee's are free to speak their minds - a junior postdoc can refute a distinguished professor - anonymity means there's no glory to be won as a reviewer. Refereeing is also an extremely tedious chore for most people that takes weeks of their time they could be spending on their own projects, so the direct tangible rewards of the process are essential nil. Really, what more can you ask of the system ?

Not all reviewers are created equal. Some are pedantically anal idiotic twerps. Others are paragons of virtue and wisdom. Just like any other group of people, really.
That said, there's one aspect of the process I think would benefit from transparency immensely : the exchanges between the authors and the reviewers. This might have been technically difficult not so long ago, because paper costs money, but nowadays no-one reads the paper journals anyway. It would be easy enough to publish everything online. That way the review process itself could be reviewed, which would help everyone understand what the process is really about, not what some people like to think it's about (who've usually never experienced it for themselves).

So no, JBPR isn't perfect, and it can't be. Is it better than not doing it at all ? Yes. The system includes many safeguards against idiotic referees - if you fail to convince two different reviewers and the journal editor that you even just measured something correctly, then the unfortunate truth is that you're probably just wrong. And there's absolutely nothing, err, wrong with that, getting things wrong is fundamental to the scientific method. But it's just not worth publishing fundamentally incorrect data if you can avoid it.

A very strange comment was raised that replication matters more than review. I suppose this might seem sensible if you've never heard of systemic bias, but... no. A thousand times, no, literally ! If you fail to convince an even larger number of reviewers of the validity of your result, the evidence against you has got stronger, not weaker. The only way that would work is if there's a mass bias or widespread incompetence among experts, which is frankly just silly. Remember, there are far more idiots than experts, so it is entirely possible and plausible to get large numbers of people producing stupid results. And I repeat : all you have to do is report your result. You don't have to explain it. You just have to say, "we measured this" with some rigour (i.e. repetition, statistical significance, etc.). That's all. This is not an unreasonable request for a level 0 requirement for publication.

If you insist on finding faults with journal-based science, here's one that's both real and serious : writing style. That's another topic, but in brief, it's god awful. Certain authors seem to take a perverse delight in making their result as obfuscated as possible. It's the old axiom, "if you can't convince, then confuse" writ large. It's bad for science and bad for public communication. Refusing to allow contractions (e.g. isn't, don't, can't, etc.) or insisting on using "per cent" instead of % is just bloody stupid. But that's a rant for another day, or possibly not because the Atlantic article linked is pretty comprehensive.


So, that's it. Journal-based peer review is not a big scary monster hell-bent on enforcing dogma, nor is it any kind of authority with a monopoly on truth. It's just a recognized minimum standard of quality. Where it goes beyond that - and inevitably sometimes it does - it's straying into dangerous territory. You may well argue for particular flaws in particular journals or with particular reviewers. But there's nothing remotely wrong with the method itself. You simply cannot do science without skeptical inquiry - and absolutely no-one is competent or trustworthy enough to be allowed a free hand. Get someone else to have a stab at it, and if it doesn't bleed to death on the first attempt, let everyone else have a go. That's all there is to it.

The Most Boring Thing In The Universe

I once read a popular article on mathematics that stated that if it was possible to calculate how boring each number was, there must be a Smallest Boring Number. Which would thereby make it interesting, so the next smallest boring number would claim the title and become interesting, and so on. Therefore, all numbers must be interesting.


Sorry mathematicians, but - no dice. Being superlatively uninteresting doesn't make something fun, not even if you set them on fire. If that were true, football, cricket, golf, sewing, ironing and Formula 1 racing would be considered spectator sports fit only for adrenaline junkies. They're not.

Excepting the rare crashes, how is watching a car go round a track fifty seven times in any way shape or form considered to be exciting ?
The Universe isn't without its duller moments too. Some people spend their entire lives studying cosmic dust, despite the fact that it is objectively extremely dull*. Or baryon acoustic oscillations, whatever those are. Or the dynamics of star clusters, which have all the excitement of kitten wrestling except that the kittens are replaced with small and particularly inactive pieces of toast.

* Well what did you expect ? It's dust.

But there's one thing which is much less interesting than any of those : aliens.


To be more accurate, it's not really that aliens are boring. It's just that I am bored of aliens - both kinds. Both ? Yes, both. There are only two. First, there are the purely fictitious kind that are supposed to have visited earth and done unspeakable things to American farmers that would have had them arrested in most Arabic countries. Second, there are the entirely speculative distant kind who live way off in space, possibly watching our old TV shows or maybe just quietly living under a stone, no-one is quite sure.


I find that both of these types of aliens fill me with the same excitement as does a small tub of lard.


That's What They Want You To Think

Doctor Who isn't boring at all, obviously.
First, the kind who are supposed to visit or have visited us. Please no more of this, it's just stupid. It's my own fault, I suppose. I grew up on a diet of all things paranormal, from the Loch Ness monster to Nostradamus and Mothman (yes really, Mothman for crying out loud*). I've even got a signed copy of The Orion Mystery probably still hanging about somewhere.

* With hindsight it was probably Mothman that started me thinking that the whole thing was just too bloody far-fetched.

This was all tremendously interesting to the younger me, but what exactly have we learned since then ? What new compelling evidence of aliens from the Pleiades cluster has turned up ? What's the point of the cattle mutilations, the anal probing, and of course all those lovely crop circles ? What Mayan prophecies have been vindicated ? What, given the massive rise of smartphones, new high-quality photographs have emerged of all those spaceships from species apparently intent on both absolute secrecy and massive incompetence ? What benefit has all the ongoing research been to humanity ?


None. It exists only for the benefit of the researchers' egos : the competition is so fierce because the stakes are so low. Oh, they won't agree, obviously. Many of them are really sincere in their beliefs that because a rock on Mars looks a bit like Bigfoot from a certain angle, the entire planet is awash with beautiful princesses. Whereas the other lot are equally sincere in their belief that the entire operation is yet another NASA hoax and that the Mars rovers don't even exist.

Stop it. Just stop it. Not all of parameter space is worth exploring every time some blurry photograph appears on the internet. The Illuminati aren't coming to mutilate your cows or spray you with chemtrails because there's a fuzzy blob in a photo some dude posted on the interweb. You aren't going to be herded into death camps because a politician fiddled their expenses claims. The fact that a Renaissance painting looks absolutely nothing whatsoever like the Orion nebula, which in turn looks absolutely nothing whatsoever like a brain, proves precisely 100% finely distilled nothing. With perfect accuracy.

One of the arguments that used to convince me about the whole UFO thing was that while 95% of cases are obviously mistaken identity, the remaining 5% aren't so easily explained. And if just one of them turned out to be something interesting, then that would be the greatest discovery in history. The problem is that it's a complete fallacy to imply that if you have a lot of things at least some of them must be interesting by sheer numbers. It's entirely possible to have a huge number of boring things, such as every game of cricket that's ever been played or every single episode of The Wire.

You're not fooling anyone mate.
Such people will often invoke the idea that "lots of people can be wrong" to suggest that the establishment view that flying saucers don't exist could itself be wrong. Yes, that's possible. So could all those stupid fuzzy blobs on Mars. Having a lot of dodgy photos does not mean you must have at least some interesting ones - statistics just doesn't work like that. 1% of nothing is still nothing.

Of course, there are varying levels of belief in flying saucers : from the casual, "maybe there have been a few alien visitations" down to, "snake women from Jupiter are using chemtrails to make us all believe the Earth is round !". If you put a gun to my head I suppose I could be persuaded to admit the possibility of a few alien visitations that have been captured on camera*. But a large-scale cover up which only a few (generally speaking) uneducated and incoherent people on the internet can expose** ? No. That shouldn't even need a rebuttal, because it's buggeringly obvious why it's just stupid.

* Bearing in mind that, "admit the possibility" and, "think that's a load of tripe" aren't mutually exclusive.
** Of course They let them have their YouTube videos exposing the truth as part of a multiple-bluff. Layers within layers within layers. Such people wouldn't understand Bill's Razor if it gently trimmed their nose hair while they were sleeping.

It's not really that I find the idea of alien visitors boring. It's just that the same overblown arguments are made again and again and again on the basis of the same dodgy "evidence". It's just tiresome. If you want to keep researching this stuff, then fine - but I won't accept anything less than a flying saucer landing on the White House lawn or in the gardens of Buckingham Palace*. Those are my terms. I don't think that really solid in-your-face proof is too much to ask, especially considering that there's not a lot I could do about a global conspiracy anyway.

* And no, you twerp, President Obama isn't a reptile. 

In other words, unless your UFO video contains something like this I'm just not going to bother evaluating it any more.

Aliens, Schmaliens

On then, to the second kind of aliens : those who haven't visited Earth at all but are just "out there" somewhere. An equally originally interesting idea which has become less exciting than watching a tortoise hibernate in slow motion. At least with UFOs there is some evidence to debate, even if the photographic quality is such that it makes a celebrity sex tape look like a Stanley Kubrick masterpiece of cinematography. With the non-visiting aliens, however, we've got absolutely zilch. At least zilch in terms of solid proof - which puts us back on exactly the same terms as for the alien visitors.

I suppose Eyes Wide Shut is the closest we'll ever come to seeing what would happen if Stanley Kubrick directed a celebrity sex tape. Unsurprisingly, it was dire. It consists solely of Tom Cruise not having sex for two and a half hours.
I have absolutely no idea if aliens exist or not. "But they must, there are so many stars, it would be an awful waste of space !" Blah blah blah blah blah. Or, "If they existed they would be here." Or you can harp on about how unlikely it is that intelligent life will evolve, or come up with some dribble (it's like drivel but worse) about the difficulties of interstellar travel, or deliver a magnificent sermon on how life might be unrecognisable to us or be so infinitely more advanced that it wouldn't care about us.


The point is we have no actual data. We can keep discussing the same stuff over and over again if you want, but new arguments for and against appear to have long ago stagnated. Sure, the mathematical probability of life arising may or may not be very high, but then again it also seems pretty reasonable to assume that life will try and spread itself. Which of these wins ? We have no idea. No idea at all. It doesn't matter how sophisticated the models are we use to make predictions, they're all just speculation until we have hard numbers.

Which is not to say that we shouldn't try and produce any of those sophisticated models, or that the ones we have weren't worth producing. Not at all. Speculation is an extremely valuable exercise... it's just that the speculations have all become variations on a theme. Every so often a headline emerges with a claim that there's a "new" solution to the Fermi paradox, or a new model about why earthlike planets should either be rare or so common it's a wonder the Earth itself isn't bashing into them every five minutes. All of them are just new ways of expressing the old ideas.


OK, I'm bored of aliens - but that doesn't mean you should be. If you haven't heard the various arguments a dozen times, many of them are extremely interesting. It's just that we're apparently stuck with this God-awful mystery and the theoretical side of things appears to be moving as slowly as a paralytic slug being chased by a sloth that took an arrow to the knee. There are two ways to make this interesting again :

1) A genuinely new theoretical argument, rather than yet another nuanced solution to the Fermi paradox. None of the proposed solutions are particularly convincing and all debates degenerate into "well, maybe the aliens blah blah blah." Yeah, maybe. Without knowing anything about the aliens you can speculate any solution you like.
2) Observational constraints. We don't have to detect aliens, but if we had some limits on how common they are then at least our speculations would be informed. E.g. if we detected no earthlike planets or artificial signals (of comparable strength to our own) within 50 light years, we could begin to say how common aliens are. And don't blather on about only looking for life as we know it - how the hell do you expect us to look for life as we do not know it ?

And aliens are also used as a sort of ultimate-level justification for space research. "You may not understand why I'm putting this shrimp on a treadmill today, but you'll thank me when I work out how to contact aliens tomorrow". Talking to aliens is seen as an end in itself with no further justification needed. Why is China building a giant radio telescope ? To talk to the aliens. Why do astronomers look for extrasolar planets ? To work out where the aliens live. Why do we study star formation ? To see how common planets (and thereby aliens) might be. Gamma ray bursters ? Might be nasty for the aliens. Dust ? Important in planet (and thereby alien) formation. Hydrogen line ? Best way to listen for aliens.


Aliens are depicted as a singularity event - something of such awesome mind-expanding potential that whatever happens after contact is completely unpredictable. Knowing that we're not alone in the Universe will either cause us to unite and form a global utopia or becoming angsty emos who are too depressed to get out of bed. But would it ? Would it really be such a revelation given that we're already intensely familiar with the concept, indeed have been for many centuries ? I rather doubt it. Despite the total lack of any evidence, most people overwhelmingly favour the notions that aliens do exist rather than that they don't*. It would be a bit like finding out about government spying programs : lots of hoo-hah,very little that actually happened as a result, and consequently one of the least surprising discoveries of all time.

* Furthermore, a huge swathe of the population just don't care.


Sci-fi is supersaturated with aliens. We've considered them as overlords and conquerors and invaders and refugees and parasites and gods and ordinary people. They've been super-intelligent, very stupid, factionalised, united, had pointy ears or been formless energy clouds. There's really not much more of parameter space left to explore. If and when we finally do make contact, it will almost certainly be a massive anti-climax. Instead of aliens landing on the White House lawn to mutilate our women and steal our cows (or possibly the other way around), it's likely to be some kind of transmission. And unlike in Contact, it will take years or decades to decode and won't contain any instructions for building a wormhole machine. It will, in short, be really really boring.


Yet aliens are being sold as this incredibly profound event, presumably by lazy public outreach types who can't be bothered to try and understand or explain scientific projects for their own sake. Now, my being bored doesn't necessarily mean that the whole thing is ridiculous, but we do have a few examples of how boring the discovery of aliens would be, of which the most famous is That Rock from Mars. You remember, the one with the fossils, right ? You probably do, since if you're reading this blog you're likely at least vaguely interested in science.

But it's very possible that you don't : I distinctly remember my sister's near-total lack of reaction. Massive controversy in the popular press which was sustained for considerable time, but twenty years later and its Wikipedia entry is shorter than that of Cardiff Bus. Doctor Who's blasé attitude, "it's them aliens again, I'll bet my pension", may well be far closer to the reality of contact that the singularities of other popular fiction.


The opposite question is much more rarely asked : what if it's just us ? Forget whether you think that's more or less likely or not, that's irrelevant. Rather, just consider the possibility. What does that mean for us ? Does it make us more or less special ? Would we still want to reach the stars if there was no-one there to meet ? Have you ever really stopped to even think about this before ?

Here's how I would handle the whole situation. Continue the research exactly as is being done right now (or heck, increase it - just because it's boring right now doesn't mean it wouldn't be interesting if we had some actual numbers), but with one teensy-weensy change : stop making major press releases whenever a tiny incremental adjustment is made. That could make the whole thing exciting again. Alternatively, I should take a holiday. One which doesn't involve radio astronomy in any way shape or form. That sounds nice.


Saturday, 16 April 2016

Nope


Sometime late last summer I saw a job advert I was morally obligated to apply for. Astronomy Visualisation Specialist ? I am one already ! Experience with visualisation software and generic programming languages, e.g. Python ? The 11,000 lines of Python code for Blender that I wrote ought to tick that box and then some. New ways of visualising data ? Assisting astronomers cre... look, just visit my website. It's all there. All of it. Never have I seen a job description that felt so precisely tailored to me.


The application deadline was 1st October, though I submitted mine well before that. It's normal in astronomy for responses to take at least one month, sometimes two or even three. A few places - which are downright rude - never bother to respond. Still, by early December I was beginning to suspect that despite being objectively very, very qualified for the job, they must have given it to someone else. Well, it did say, "as soon as possible" on the job description.

They hadn't. I'm not sure if you'd call it an early Christmas present or not but I had a Skype interview on 18th December. Which was the day after I moved out of my flat in Prague (roomate left, couldn't possibly afford the place on my own) which had involved a week of hauling heavy suitcases back and forth to move my stuff to the institute. And it was the day after I got back to Cardiff, just to make things as frantic as possible.

Anyway it went well, but unfortunately it went well for everyone else as well. After a rather nervous Christmas, in early January I got en email saying that they'd go to a second stage round where they'd send us all a data set to visualise. Which they duly did a couple of weeks later.

It was actually quite a fun little project to work on, because the data set wasn't in a format I was familiar with. 3D data sets generally describe the density or temperature or whatever at different locations in space. The location is specified by 3 positions : x, y, z. Nothing very complicated about that.


And that's fine if, as is usually the case, your data set describes something that's roughly box-shaped. And by roughly I mean very roughly indeed, like this :

Simulation of a star-forming filamentary cloud, or something.
But this data set didn't use ordinary "Cartesian" coordinates, it used spherical polar coordinates. These aren't difficult either, but they may be unfamiliar. Instead of specifying 3 linear distances from the origin, they specify one distance and two angles :


Why in the world would you want to use such things ? Surely, it's more intuitive to think in terms of distances, not angles ! No, not always. There's a very simple everyday example that should help you understand : maps. With a street map, you could easily specify a position in Cartesian coordinates. You could say, for example, that Cardiff Castle is about 150m north and 25m west of the Revolution bar, if you thought that breaking into the castle on a Saturday night was somehow a good idea.

You could also specify how high the castle keep is, if it was vitally important to reach a precise level for some reason.
On a scale this small, the fact that the Earth is curved doesn't matter. You could hold out your arm and say, "go 50 metres in that direction" and no-one would have any difficulty. But if you said, "go 5,000 miles in that direction", anyone taking you literally would have ended up in space. Of course, they intuitively understand that you mean "along the surface of the Earth", not really, "in the path followed by a perfectly straight laser beam going in that direction". Unless they're a cat, of course.

This is why you don't give cats directions using laser pointers, because if it involves going into space then damn it that's what they'll do.
North, south, east and west are really just angles. Nothing very complicated about that : if you want to go to Australia you can say it's around 140 degrees east of Great Britain and 20 degrees south of the equator. Or you can give this in miles, it's the same thing.

We don't normally specify the distance from the centre r unless you're a mountaineer, pilot, miner, or deep sea diver. OK, you'd normally give distance from sea level rather than the centre of the Earth, but it's the same thing.
Or is it ? Well, not quite. 50 miles north or south is the same everywhere, unless you're so close to a pole you can't actually go that far. E.g. if you head in a northerly direction when you're 25 miles south of the north pole, after 25 miles you'll find yourself heading south. Much worse is the case of walking east or west if you're near the pole. You can't actually go east or west if you're standing on the pole itself, and if you're just a few steps away from the pole, then walking 25 miles east or west is going to involve walking around in a lot of circles until you get dizzy.

And at the north pole it will also involve discovering Santa's secret hideout or being eaten by a polar bear.
Using angles makes things a lot easier for cartographers. Line of longitude (east or west position) have constant angular separation, even though the physical distance between them varies (i.e. 1 degree involves walking a much larger distance at the equator than near the poles). And the mathematics to convert between the two is easy and precise, so if we have two lat-long positions we can easily compute how far we have to travel to get from one to the other - even if we're at weird positions like the poles.

In numerical simulations, polar coordinates have some other advantages, which are a bit more complicated. Imagine if you will a cat on a record player*. If you wanted to specify any point on the cat, you could give its x,y position. Or you could state its r,φ (pronounced "phi") coordinates instead. There's not really any advantage to either... unless the record player is turned on and it stars spinning.

*Conjecture : there is no scientific concept which cannot be explained with the right cat gif.

If that happens it's very much easier to specify how fast each point is moving in the φ direction. If you wanted to specify its velocity using x,y coordinates, you'd have to give two velocities - which is much less intuitive than saying, "it's spinning at such-and-such a speed". And anyway the velocities in the x,y directions are constantly changing and depend on distance from the centre of the record player, whereas the angular speed in the φ direction remains constant everywhere.


"The cat is spinning at 20 rpm (or 120 degrees per second)", vs, "the cat's x velocity is 1 m/s and its y velocity is 0.5 m/s, no wait now it's 0.6 m/s and 0.2 m/s, no wait it's changing again, aaaaaargh !"
Or to illustrate this slightly more scientifically :



When the green point is at the top or bottom of the circle, it has no velocity in the y-direction at all. Similarly, when it's at the extreme left or right, it has no velocity in the x-direction. But it always has a constant angular velocity.

So polar coordinates are much more useful for describing rotating discs. The problem is that of course for rendering images, pixels generally aren't in polar coordinates : we have to convert back to Cartesian. That's a problem when visualising simulations : just like trying to map the spherical Earth with a flat surface, you can get horrible distortions or lose detail if you're not careful.

Converting between polar and Cartesian coordinates is literally like trying to square the circle.
My first approach was to convert the data into the regular Cartesian system : knowing the r,θ,φ coordinates directly from the data, it was easy to convert to x,y,z. Which gave me this :

video
It's simulation of a protoplanetary disc.

... at which I make a brief interjection because at about that moment I received the following email, which I will keep anonymous because I'm not a total douchebag :
...and I do my first steps in scientific visualization. I am very interested in astronomy, though my main job till now was connected only with graphic design in university sector. I have some 3D modelling experience (several years ago me and my colleague made a fulldome video). Now I learn Blender and try to write my first scripts in Python. Slowly I become the idea, how everything works. Although the more I read, the more question I get...But it is normal I guess :)
Hopefully soon the quantity of my knowledges will transfer to their quality. About a month ago I got a chance to apply for a position as a specialist for astronomical visualization. My interview was quite successful and now we got a test task, which will probably define the proper candidate. I have already an idea, how to solve it. But it would be nice to find someone, who understand the materia, could evaluate my job and give me some practical advices. So I would like to ask you, if you had time and wish to answer some of my questions.
OK... one of the other candidates is asking me for help without even realising that I'm applying for the same job.


I decided the only safe course of action was to make absolutely no response whatsoever, so that's what I did.

Anyway the first result was not bad, but not great. The problem is that when you convert between coordinate systems there's no guarantee the Cartesian data set will be completely filled - especially at large radii. The polar coordinates tell you the centres of each data cell (pixel) and the density (or temperature or whatever) in that entire cell. But the centre of that cell only corresponds to the position of one particular pixel in Cartesian coordinates - it's not the same as checking every pixel in Cartesian coordinates and finding which polar cell they're in. The upshot is that you end up losing detail in the centre (where the polar cells are closer together than the Cartesian cells) and large blank areas at the edges (where the polar cells are further apart than the Cartesian cells).

To illustrate that, let's take another look at the comparison between polar and Cartesian grids. First in the very centre :

Every large square of the Cartesian grid contains multiple points from the polar grid. So multiple polar cells get reduced to a few Cartesian cells - detail is lost.
And now in the outskirts, shading every Cartesian cell that's intersected by at least one polar cell corner point :

Oh noes ! Not every Cartesian cell is filled ! And this only gets worse at larger radii.
That's not a hopeless problem. One nice feature when converting is that you're free to choose how many Cartesian pixels you want very easily, so you can optimise for a balance of detail in the centre vs. empty regions on the outskirts. In principle, you could then fill in the blanks based on the nearest pixel, or accurately determine the value for each Cartesian cell by working out which polar cell it corresponds to. Doable, but not easy - and certainly not doable in the space of an afternoon, which was the stated scope of the exercise.

There's a more fundamental problem : to you show all the detail in the central regions, you'll need a lot more cells in Cartesian coordinates than if you used polar. Large data sets can easily run into hundreds of millions of cells, which means hundreds of millions of pixels : ouch ! Wouldn't it be better if we could somehow have non-square pixels ? Then we could show the data in its original polar form, with no loss of detail and no need to have a single pixel more than we really needed.

It turns out that we can do just that in Blender. Consider a slice right through the centre of the protoplanetary discs. If we pretend that r and φ are really y and x, we get this :


Of course they're not really x and y at all, which means we're looking at something that's weirdly distorted. But we can correct for this. The method I came up with was to assign each pixel to a face in Blender (UV mapping). Then we can move each vertex (i.e. distort each face) to put it back where it would have been in polar coordinates.


Bingo - we can have our cake (original spherical polar coordinates) and eat it too (no need to convert to square pixels). Of course, the real data isn't just one slice - it's lots of slices, each of a constant angle θ. So what we have is a series of cones :



And if we show all the cones, we get this - which is a pretty convincing way to fake a volumetric render, with the gaps between the cones only becoming apparent at certain angles :


video

In the above, density controls bother temperature and opacity (transparency). But it doesn't have to be density. It could be, for example, this mysterious Q parameter which is apparently heat transport that I know nothing about except that it looks nice :



video

In principle, we could fill those gaps by switching to spheres when the viewing angle is through the cones. Actually, I started with spheres because I'd already tried this* - I only had the idea to use cones during a long and boring meeting. They look nice enough on their own, though to really get things perfect we'd need to combine the two.

* Spheres are much easier to do because there's no need for UV mapping - Blender can calculate the distortion to a sphere itself just fine, but not cones.


video

So having figured out this somewhat complicated process, some considerable time passed before I heard anything back. It felt like forever.


Eventually at the beginning of March - a full five months after the application deadline, I got the news that... I was invited to an on-site interview ! Which led me to an odd mix of glee and frustration.


Many wisecracks did ensue, of course. Maybe, said colleagues, they just wanted more data visualised as a sort of way of getting cheap labour. Maybe they hadn't rejected anyone from the first two rounds. Maybe the number of candidates was actually increasing at each stage.

Nonetheless, I want along to said interview about three weeks later and went at it hell for leather. I brought along both glass cubes, 3D glasses, a copy of the Discover magazine in which I nuked a potato, and I even organized most of my Blender files and scripts from the last 14 years. It would be a five year position with the possibility of a permanent contract at the end, with a salary far more... European than those of the Czech Republic. Worth fighting for, even if the "as soon as possible" phrase had long since rung hollow.

Getting to Heidelberg involved a 7 hour bus trip. It was a very nice bus and I had the whole lower compartment to myself, which was nice. With wi-fi. Heck, it was better than most British trains by a considerable margin. There wasn't much to look at on the trip, but I've always thought that it's far easier to make my own entertainment than it is to make my own legroom.


The only real event that happened was that there was a perilously short connection between the bus to Mannheim and the train to Heidelberg, so I ended up jumping on a plausible-looking train (German trains do not indicate the destination and route very clearly) more out of hope than expectation. Which resulted in a fairly tense 20 minutes until the train stopped at the correct destination. After hauling my really quite surprisingly heavy bags to my hotel, I had little enough time in the evening to do anything except a short walk. I didn't get to see any of the pretty parts of Heidelberg.

Of course I did see the Haus der Astronomie the next morning. My interview went as well as it could have gone. With hindsight I wouldn't have changed a damn thing. There wasn't time to show everything, but I left fully satisfied that I'd done as much as I could possibly have done. I answered all their questions. I showed them the extremely heavy data cubes and 3D movies. I was a little peeved that - bizarrely - they really did want someone to start extremely soon, but I'd have been more than prepared to take the job anyway (even though I'd really, really, really like an extended period back in the UK). So off I went back to Prague while they interviewed the other candidate.

Alas the return trip was not without incident. About one hour in to the seven hour trip, the bus ground to a halt due to an accident up ahead. It didn't move an inch for the next four hours. The bus driver let everyone off to walk around (and even some people on to use the toilet). I talked to some otherwise politically like-minded Germans who were, it must be said, none too fond of the Czechs, but even the nicest bus becomes wearying after 11 hours. I eventually crawled back into my room - still dragging my laptop and heavy glass cubes, of course, at about 2:30am.



Then I proceeded to play the waiting game. Again. For another three weeks. Until finally :
Dear Rhys,
thank you for your patience. It was a difficult decision, but in the end we offered the job to the other remaining candidate. This is in no way a reflection on the skills you demonstrated - we were very much impressed by your visualizations, found that you communicated well with the astronomers who would have been your colleagues here, and you would have been a great addition to our team. In the end, it came down to experience - the candidate to whom we offered, and who has now accepted, the job, is older than you and had put those additional years to good use in the visualization field.
We wish you all the best for your future career - you have an unusual and interesting mix of skills, and I hope you will find a good place to put them to the best possible use, either in astronomy or beyond!
It's a very nice rejection letter, but a rejection all the same. All of that effort had been for absolutely nothing except a free but incredibly exhausting 24 hours in Heidelberg. Was it worth it ? I'll let John Cleese answer that. Skip to 46:28 if it doesn't automatically.


On the one hand, the successful applicant is about 10 years older than me, done four-dimensional relativistic raytracing calculations, and has written a freakin' book. Fair enough, I'd have hired him instead of me. On the other hand, it doesn't take six months to decide who's more experienced. You can do that from the start. Especially if you use the words, "as soon as possible" in the advertisement.

Oh well. As Captain Picard once eloquently put it, "shit happens". In another reality, alternate me is taking a short break in Cardiff before preparing to move to yet another country despite never wanting to leave home in the first place. Actual me is now in the more mundane process of searching for a flat before he gets kicked out of the institute's accommodation. Aaaargh.