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Tuesday, 15 July 2014

Review : God's Philosophers

Science in the medieval period was virtually non-existent. The Catholic Church did not take at all kindly to anything that contradicted its rigid, inflexible teachings, and the few people brave enough to speak out were summarily dismissed as heretics and burned at the stake. At least, that's what we're all taught. And that's what many people today would like to believe. But it simply isn't true, says Dr James Hannam, graduate of both Oxford and Cambridge, in his fascinating 2009 book God's Philosophers. You can read the first two chapters of the book for free on his website.

Rather than a detailed review of the style of the book, instead I'll give a short summary of some of the aspects I found more interesting. I'm going to concentrate on the philosophical and moral aspects of the relationship between science and religion; if you want more direct examples of how highly devout medieval Christians contributed to modern science, you should read the book itself.

As far as style goes, suffice to say it's very accessible, with a good balance between science, philosophy and theology. You don't need to be a scientist, philosopher or theologian to understand it. However, to get anything out of the book you'll have to be prepared to surrender many of the impressions of the medieval Church you've probably grown up with. If you're one of those people convinced that only science has led us out of the darkness of religion and into the light of reason, well now's a perfect time to put your money where your mouth is. You're not allowed to extol the virtues of science unless you're prepared to question your own viewpoints - otherwise you ain't no scientist at all, boyo.

Hannam is under no illusions that science (or natural philosophy as it was then) and religion did not sometimes come into direct conflict, and that when push came to shove, the Church had the upper hand. But the extent to which that meant the Church actively suppressed freedom of thought has been vastly exaggerated, and the achievements of medieval theologians (yes, theologians) that were crucial for the breakthroughs of Copernicus, Kepler and Galileo - who were all devout Christians - have been unfairly airbrushed from history. It's not an attempt to convert anyone, only to point out the debt modern science owes to medieval Christian thinkers. They not only rediscovered the works of ancient philosophers, but surpassed them.

Theology, Doubt, and Natural Philosophy

As a fervent and unswerving agnostic, the concept I found most interesting from the book was the idea that theology and science were closely linked. Although I was aware that medieval universities existed, I've normally dismissed them as being irrelevant theological schools, producing nothing of any real consequence. This was a huge mistake. Theological training, says Hannam, not only included the study of mathematics and natural philosophy, but was virtually obsessed with logic. The underlying idea, it seems, was that by studying the natural world one could understand God. Natural philosophy was seen as, "the handmaiden of theology" - not perhaps a very flattering label, but completely at odds with the (mis)conception that science and the Church were mutually exclusive.

The obsession with logic produced some genuinely very interesting consequences. Could God create a weight so heavy he couldn't lift it ? No, said the theologians - that would be a logical contradiction, and even God isn't that omnipotent. Moreover, not even the most devout scholar (and remember that these people were members of the Church) believed in the literal truth of the entire Bible. They couldn't, because that is simply impossible. If you took the Biblical phrase, "four corners of the Earth" literally, you'd believe it was flat*. The idea of interpreting the scriptures figuratively goes at least as far back as St (emphasis : Saint) Augustine, 354 - 430 AD.

* Which they didn't, even by 1000 AD - this is a more recent myth about medieval scholarship. Other examples included various passages which state that the Earth does not move, the interpretation being here that it meant "from the perspective of someone standing on the Earth".

In a somewhat roundabout and almost perverse way, the Church actually encouraged freedom of thought. While initially the teachings of Aristotle were almost treated as Gospel, the omnipotence of God would allow him to create anything he liked (so long as it wasn't a logical contradiction). So it was perfectly fine to contemplate vacuums (which Aristotle didn't believe in) since, even though they might not exist naturally, God could potentially create one if he wanted. By today's ideologies this is a truly bizarre way of overcoming difficulties with mainstream theories, but it was certainly better than assuming the ancients had already got natural philosophy licked - most of Aristotle's ideas were complete gibberish. His prestige kept his ramblings at the forefront of scientific theory long after they should have been rejected, but medieval inquiry was (albeit very, very slowly) able to come up with better ideas.

Interestingly, God's ability to do as he pleased in no way hindered investigations into the workings of the natural world. God was seen as the primary cause of all things, but he usually operated by invoking secondary, natural causes that proceeded to operate with strict rules. Moreover, if God didn't like what you were up to, he was free to cause a miracle to stop it. If you were sick, you could try using magical remedies to get better, but if God wanted you to be sick, then sick you would damn well stay*.

* At least one popular image of the medieval world appears to be entirely correct : doctors were something to be avoided like the... err, plague. Prayer actually did have a much better chance of success - supernatural deities aside, at least priests weren't going to bleed you half to death as a "cure".

The Burden of Proof

When something was found that disproved a statement in the Bible, or a decree by the Church, this was accepted. The flat Earth is one example, the fact that the antipodes are inhabited (a notion condemned by the Pope sometime in the 8th century) is another*. When the level of proof was 100% certain - as in finding people living in the antipodes - then even matters of faith had to give way to rational science.

* The Church was, however, quite right that the hot, sweaty tropics are uninhabitable. The fact that people stubbornly continue to live there anyway is beside the point.

A running theme of the book is that (for instance) the image of the Earth being at the center of the Universe was the most rational, logical viewpoint given the evidence available at the time*. Proving the Earth is round is easy; proving it goes round the Sun with only the evidence of your eyes and nothing else is very, very hard. It's extremely difficult to see the world as medieval thinkers would have, though Hannam makes a valiant effort. Of course, we know today that the acceleration of a rotating Earth isn't sufficient that we can all feel ourselves whirling round at tremendous speed, but at the time, that was a logical, sensible reason to reject the notion of a rotating Earth.

* Interestingly, Earth wasn't placed at the center to reflect its importance - quite the opposite. Heaven was the most important place (the medieval Universe believed to be about 90 million miles across), so anything further away from the surface of the Earth was closer to God. Conversely, anything deep in the ground was closer to Hell and therefore worse. We were literally living on the surface of a "Middle Earth", if you like.

Hannam makes the important point that science cannot function where every idea requires absolute, irrefutable proof. For instance, I wasn't around when the Earth started forming, so I cannot proove God didn't do it. But to make any further progress, I must assume (based on other lines of inquiry and well-tested theories) that this is the case, and proceed from there. That is the essence of a scientific principle, something which unfortunately seems to have largely escaped the medieval mind. Having speculative models was fine, as we'll see, but being allowed to assume they were true was quite another. When it came to theorising, religion definitely had the upper hand over natural philosophy. And that caused some very acute unpleasantness when Copernicus's model of the Solar System was found to be much more accurate than the then-mainstream Earth-centered view.

The Limits of Freedom

There were most certainly limits on what ideas the Church would put up with - cross them, and you would indeed meet with a very nasty fate indeed. But those limits were very much larger than I realised.

The Inquisition wasn't a good thing, but don't confuse the Papal and Spanish Inquisitions. The latter (see Toby Green's Inquisition) was a brutal, oppressive system that was largely politically motivated, and did indeed place very tight restrictions on what you could and could not say. The former, however (as Green also says) was quite different. If you admitted your "crime" (and by today's standards of course they would not be crimes at all) to a Papal inquisitor, you'd be set free (though woe betide repeat offenders). Not so with the Spanish Inquisition, where torture was common and confession still meant death more often than not. The Inquisition of the Papacy was not a nice thing, but the Spanish Inquisition was far, far worse.

So what would it take to be declared a heretic ? Well, quite a lot, actually. You could speculate about almost anything, so long as you were clear to state, "this is just an idea, I don't know if it's really true." Take Cardinal Nicholas of Cusa (1401 - 1464), who had the notion that maybe the Universe was limitless and the Earth was just another star moving through space, and not in the center at all. He even postulated the existence of aliens. He was a Cardinal, for crying out loud, and no-one thought anything amiss with this. It's worth noting that this idea was based on the idea that the Universe would have to be limitless to "reflect God's majesty", not for any scientific reasoning. There was absolutely no scientific observation (or even discussion - Olber's Paradox being centuries in the future) at the time that gave any evidence of an infinite Universe.

What about Giodarno Bruno (1548 - 1600), that noted visionary burned at the stake for believing that the Earth wasn't at the center of the Universe ? Nope. Bruno was, quite simply, a nutter.  He seems to have tried to come up with an entirely new religion based on magic, plagiarised more competent thinkers (though Galileo also did this) whose mathematics he simply couldn't understand, and had the annoying habit of loudly telling everyone he was a genius. Basically, he would be this guy :

Now, being a bit of a jerk and believing in magic are pretty stupid reasons to convict someone, but, although he did believe the Earth went around the Sun, that's not what he was investigated for - it wasn't declared a heresy until 16 years after his death. Unfortunately, the list of charges has not survived, so we can't be sure what the real charges were. Certainly, Bruno was an example of the Church behaving at its worst and this is clearly an example of suppression of freedom of thought, but Bruno wasn't a martyr for science by any stretch of the imagination. He was a magician and a mystic, with no more claims to scientific genius than Cardinal Nicholas.

Not that even heresy was always a guaranteed immolation, mind you. Virgil of Salzburg (700 - 784) not only got away scot-free for teaching the antipodes were inhabited by people not descended from Adam, but was later even canonized. William of Ockham (he of the razor) also escaped, although in this case quite literally by hiding under the protection of the Holy Roman Emperor. And Galileo (more on him in a minute) was, for a while, allowed considerable leniency by a somewhat corrupt and capricious pope.

Before returning to Galileo, it's worth noting one very clear example of religious doctrine impeding scientific inquiry. Nicholas of Autrecourt (1300-1369 AD) attempted to claim that everything was made of atoms. Unfortunately, this appeared to make the transubstantiation in the Eucharist (bread into flesh and wine into blood) not merely miraculous, but a logical contradiction - something cannot appear to be made of bread but really made of atoms of flesh. Nicholas was forced to recant and the offending document burned, but he himself gained a cushy job as a dean and lived more or less happily ever after. Hannam contends that this is a rare example, and if he'd only not made the link to the Eucharist so explicit and just been a little more careful to emphasise that it was "only an idea" (which would have been sensible given the lack of definitive evidence at the time), everything would have been tickety-boo. He doesn't use the words "tickety-boo" though, which is a shame.

And Yet It Moves ?

Galileo is the archetypal heretical scientist. Unlike Bruno, he was certainly no mystic, and his ideas were based on solid observational evidence. Ultimately, this one does boil down to science versus religious ideology... well, sort of. Maybe. It's far from as open-and-shut as you might think.

Many discoveries essential for Galileo's work had already been made. Copernicus had published his Sun-centered Solar System model (dedicated to the Pope) in 1543, with a careful foreword by his friend Osiander stating that it was only a hypothesis. Interestingly, this seems to have been more to ward off scholarly skepticism than Church wrath. At the time, the model seemed at odds with the observation that the constellations do not change throughout the year. Since the medieval Universe was only 90 million miles across, if the Earth moved through a significant fraction of that, the constellations would appear distorted as it approached the sphere of the fixed stars.

Copernicus's solution was the correct one, but so dramatic it was very hard for everyone else to accept. To reconcile the theory and observations, he increased the distance to the stars by a factor of a billion. Changing theory has never been a popular move - the idea you need to create multiple Universes to kill a cat still causes problems for quantum theorists today, as does the idea of changing Newtonian gravity to fit observations of galaxies. We seem to have an innate tendency to prefer to think that we're basically on the right lines, unless the evidence becomes overwhelming. And in 1543, Copernicus' case was not overwhelming.

But it worked. There seems to have been little or no ecclesiastical backlash (perhaps because the book was so mathematical, suggests Hannam) and by the 1570's a Papal commission was using the Copernican model to develop our modern calendar. There was no getting around the fact that it produced much better results than the alternatives, though it seems that people were happy to accept it as "only a theory". The trouble only began when people began to believe it might also be a true description of reality.

By 1588, Tycho Brahe had demonstrated that the planets were not moving in giant crystal spheres. His model of the Solar System still had the Earth at the center, but the planets orbited the Sun rather than the Earth. In 1596, his protégé Johannes Kepler published a model with the Sun at the center, and no-one seemed to mind. Very few people believed the idea, but some priests stated that it while it was religious unobjectionable, it was scientifically unsound.

So three great scientists had already postulated alternative models of the Solar System that directly contradicted scripture and no-one had even got so much as lightly singed. For a long time, Galileo also got along just fine, conducting scientific observations and publishing them in what amount to 17th-century popular science books. He was also on good terms with the Pope. As we've seen, no-one at the time was particularly bothered by Copernicus or Kepler's theories.

That all changed though with a particularly strict Inquisitor, Cardinal Bellarmine. Galileo held the opinion (as did many others, theologians included) that the Bible should be taken figuratively except in matters of morals - leading to the famous quote, "The intention of the Holy Spirit is to teach us how one goes to heaven, not how the heavens go.". The official Council of Trent had said much the same thing.

Bellarmine was having none of it. His view was, unusually, that the Bible was the literal word of God and should be taken as such unless absolutely irrefutable proof was given. The Italian friar Foscarini had recently forced the issue by writing a letter tackling the problems with scripture and the movement of the Earth head-on. It failed utterly. His letter was banned and Copernicus' work suspended pending corrections. Galileo got off with a warning not to teach Copernicus' theory. Hannam's implication (he does not say this explicitly) is that Bellarmine was the main proponent responsible for turning the previously unobjectionable Copernican model into a heresy, but I would have liked a lot more detail on this point.

Four years later, in 1620, the Church released the corrected version of Copernicus' work. It was hardly a ruthless censorship (as the Spanish Inquisition would have done) - ten corrections, released as a special insert, in a book hundreds of pages long. Hannam gives the example that "admitting the Earth moves" became "assuming the Earth moves", emphasising that it was just an idea, not a proven fact. Which, after all, it wasn't - this is scarcely worse than having a paper or thesis go through peer review today (albeit with potentially more extreme consequences in the case of failure to comply).

Bellarmine died a year later, and soon after Galileo began work on a a popularisation of the Sun-centered Solar System, confident that as long as he was careful, his friend the Pope would support him. And perhaps he would have done, had he not (according to Hannam) made a single catastrophic error of judgement, by what amounted to mocking the Pope. It's worth noting, however, that initially it did pass muster from the Papal censors and it was allowed to be published. Only when the Pope read it did things get ugly.

The problem, it seems, was that Galileo did not have a good enough explanation of tides. His idea that they were caused by the rotation of the Earth, with the water being left behind and so sloshing around. He not only tried to use this to prove the Earth rotates (even though he'd been warned not to) but for the counter-argument in the dialogue of the book he used an argument by the Pope that God can create any circumstances he wanted (basically saying that, "no, the tides are caused by the will of God"). Worse, he put this toward the end of the book, which the Pope took as adding insult to injury.

The resulting trial didn't exactly see Galileo stand up for his ideas, and I can't say I blame him. Initially claiming he didn't support Copernicus at all, when pushed he admitted that, "well I suppose some moron might read my book that way" (not a direct quote, unfortunately). No-one but believed him, but, threatened with torture, he stood his ground and called their bluff. Satisfied by his apparent conviction, the threat was withdrawn. Though he avoided the rack or a burning, he was condemned to life imprisonment under house arrest.


Hannam does  an admirable job of demonstrating the debt modern science owes to medieval theologians. Within this very limited scope, the book is excellent. It would have been nice to have added a least a few related points though - in particular, it's clear that Universities offered protected intellectual havens, but almost no mention is made of how academic ideas were regarded in society. Similarly, there's no discussion on what the academics thought about more broad issues : morality, the Crusades, etc. Although this lack is understandable, given the obvious subtext of the book it would have been nice to include something.

There are certainly examples from history of the Church suppressing freedom of thought, sometimes brutally. But these are rare, and in the case of scientific inquiry, practically non-existent. The ultimate weapon, the auto de fe, potentially could have been used against troublesome scientists, but it doesn't seem to ever actually have been. The fact that the Church was ever allowed to have any say over what people could publish and could punish (or even execute them, if only in principle) for stepping over the mark was not, of course, a good thing. In practise, this was extremely rare. Medieval theologians contributed far more to modern science than the Church ever held it back. At least, Hannam does a good job convincing me of this.

Maybe it's possible to argue science would have been better off without the Church, I don't know. But at the very least, the popular idea that the Church only worked to hinder progress is now simply untenable as far as I'm concerned. It's also worth remembering that even in the modern age, espousing viewpoints too far from the mainstream may not get you burned alive, but it will certainly get you laughed at and ejected from academia. Given the intensely rational nature of medieval theology, the line between heresy against scripture and unconventional ideas is, perhaps, thinner than we might like to think.

Perhaps the most glaring omission from the book, however, is any discussion relating to what happens next. Hannam concludes with the trial of Galileo. What a future version of the book is badly in need of is an epilogue to summarise the next few centuries. What I would especially like - and this would probably need a whole other book - is some discussion on how we went from being able to say, "well, obviously the Bible isn't meant to be taken literally about everything" in mainstream medieval theology, to the current view of a disturbing number of people that the Earth is only a few thousand years old.

Far from condemning modern scientists as heretics, a medieval theologian - if properly briefed on the current evidence - would almost certainly have little good to say about modern creationists. These ideas do not take us back to a medieval world view - they're much worse than that. Even Cardinal Bellarmine would be forced to concede to modern evidence. Small wonder that Frank Herbet once quipped that in religion there is "always the unspoken commandment, thou shalt not question !". Ironically, such a view is a far better description of modern extremists than it is about the logical, questioning mind of the medieval theologian.

Wednesday, 2 July 2014

Referees Who Move Goalposts Make Lousy Peers

My latest paper, The Arecibo Galaxy Environment Survey VII : A Dense Filament With Extremely Long HI Streams, has finally been accepted for publication. This has consumed, in one way or another, about the last year or so of my research time. So I'm going to indulge myself with not one, not two, but three entire blog posts. In this first one I'll look at the peer review process, which for this particular paper was slightly less fun than being given an enema by a bear. In the next post I'll describe how we went about searching for galaxies using Blender, and in the third, thrilling conclusion, I'll say something about what it is we actually learned.

Peer review does not mean writing articles in the Guardian about what you think of Jeffrey Archer, unless you're a journalist. In science, the idea behind peer review is simple : someone writes a paper, and someone else (usually anonymous and selected by a respected academic journal) checks to make sure it makes sense. In this way, scientific literature is pretty well-defended against giant space bananas and moon landing conspiracy theorists. No-one think's it's perfect - a perfectly objective system is probably impossible - but it's the only system we've got for checking that everyone else is basically sane.

In this case it took over seventh months from first pushing the big scary, "WARNING : THIS WILL SUBMIT THE ARTICLE ! ARE YOU ABSOLUTELY, POSITIVELY, DAMN WELL BLEEDIN' SURE YOU REALLY REALLY WANT TO DO THIS ?!?!?!" button to having someone say, "This looks decent, let's publish it." Almost as long as creating a baby, though less icky, and as you can imagine I'm none too happy about that.

Although now I come to think about it, if it's a choice between one or the other, I'll take the publication, thanks.

I've never had to referee a paper, mercifully. I don't imagine it would be much fun. Several weeks trying to make sense of other people's wranglings with no time for your own research can't be much of a hoot. But I have received several referee's reports on my own work. Typically, this results in my mental processes going something like this :

First reading
"Add error bars in figure 6 ? What a JERK ! No-one else puts error bars on this plot. This guy is clearly a complete amateur."
Two hours later
"Huh, errors aren't so hard to calculate after all, maybe I should add them in instead of insulting the referee's mother at the next submission..."
The next day
"Hey ! With error bars this figure looks waaay better !"

Which is precisely why this post has been in draft form for several months, but I'm not going to even try claiming an unbiased viewpoint.

Referee's comments come in all varieties, from the extremely helpful (which are probably the majority, if I'm honest) to the extremely unhelpful (more on them later). A few are just downright strange. One I've seen every single time is, "shorten the text." This is like saying, "There are too many notes, that's all. Just cut a few and it'll be perfect.". It doesn't make any sense. Tell me which bits you think are too long, or I'm just not going to do anything*.

* Actually what I'm going to do is cut out one paragraph just so I can say I've done something. What I'd like to do is remove the final word from every sentence.

What's almost worse and just as common is that the referee will simultaneously state that the paper is too long and require major additions. Referees, please don't do this. It makes you sound like a crazy person. You have to at least suggest where the cuts should be made, or it makes no sense. I can't possibly make it any shorter if you're telling me to add stuff.

In like vein, the weirdest, most incomprehensible suggestion I've received so far was that I should add "supporting figures to the paper" (there wasn't any context to this). What, you mean like a picture of a giraffe or something ? A self-portrait in crayon ? Maybe a drawing of Atlas, he's a supporting figure, after all. Love to help, but I'm not psychic ! Of course, the assume-everyone-is-psychic factor affects us all, but not usually to that degree.

Fortunately, this particular mystery was solved in consultation with a friend, who brilliantly realised :
"It means there aren't enough characters. You need to flesh out your story with supporting figures that the referees can relate with. Maybe add a downtrodden scientific paper reviewer, who started out with the bright-eyed idea of changing the world through peer reviewed science, but instead met paper after paper of nonsense and flim-flam, and now has no joy left when a paper of some real worth comes through."

Much more annoying are criticisms of the second draft that could have been made at the first submission. Now obviously there's nothing wrong with saying, :
"Oh and I forgot, you need to correct the spelling of GALAXIE on page 2 and make the caption bigger."
No-one can spot every typo at the first reading. But if you're going to suggest :
"You should replot all your figures so that they actually show something completely different, because although I didn't bother to mention it last time, I think they're all wrong. And also I don't think you wrote your code in C, so please do that."
... then that's fine too - it's the referee's job to do this - but don't suggest this at the second draft when you could do so at the first. This is unfair and unprofessional - it's moving the goalposts, which is traditionally frowned upon. Especially if it's done by a referee. Also, it really wastes a huge amount of time - I could have made the changes months ago and have the paper ready for publication already.

Perhaps the most annoying of all is to repeat verbatim criticisms of the first draft that the author quite clearly, unmistakably and - above all - directly addressed in the second draft. As in :
Referee : "You need to say how many galaxies are in your sample."
Author : "There are 5 galaxies in this sample."
Referee  : "You need to say how many galaxies are in your sample."
That's not a real example, but some comments really are every bit as inane as that. They're even worse when they're longer comments that took correspondingly longer to address. I can only assume in these cases that the referee didn't actually read the author's response - which makes it a no-win situation. If you're not going to even read my response, why should I bother making corrections at all ?

The worst example of this was a referee who insisted that there were better data processing techniques we could use. Great ! It was obvious to anyone that the method we were using, while an accepted and well-tested approach, might not be ideal. So in my response I asked the referee to provide a reference so that I could try this new approach for myself. Unfortunately in the second report the reviewer didn't answer my question at all, but instead did a copy+paste job of their previous comment.


But we all have bad days. In my response to the second report, I again asked (twice this time, just to make sure) for a reference to these shiny new methods. In the third report, the referee flat-out ignored this altogether, merely stating simply that our measurements must be wrong - and worse, that not only were the numbers wrong, but all of the major results were also wrong. Even though they hadn't raised any previous objections, and simultaneously stated that the paper was now "much improved".

In this case this rather brusque dismissal, at the third iteration of the paper, was particularly galling since I'd spent a very, very long time making sure those measurements were as good as I could damn well make them. The end result was quite nice, agreed with previous measurements (where available) and wasn't particularly controversial. All lines of inquiry pointed to the same result. To have the referee then suddenly dismiss them - after not raising any previous objections - without giving a clear reason why was simply too much, so we asked for a second referee.

Now, as an aside on the much-vaunted objectivity of science, it may interest readers that referee 2.0 had no qualms whatever with the data analysis, which was vindicating. Whereas referee 1.0 was perfectly happy with the introduction, referee 2.0 thought parts of it were incomplete and misleading, and provided a list of some genuinely interesting papers in support of this. Which is great, and I happily made the requested changes (although I'm not sure I agree with the referee's sentiments, a happy compromise was easily reached)... but, it does, of course, expose a basic flawed truth of peer review : not all scientists agree with each other. But referee 2.0 provided justification for their assertions, whereas referee 1.0 didn't.

Make no mistake : I support the peer-review process. And philosophically, I don't like the notion that if you disagree with the reviewer, you should find another reviewer - but let's not go nuts. Sometimes, just like everyone else, reviewers are just jerks. Peer review may not be the perfect, objective solution we'd all like it to be - but it's a damn sight more objective than not doing it at all.

In short, reviewers :
  • Specify what it is you want the authors to do. Authors aren't psychic. They'd like to be, but they're not. This means vague instructions really aren't helpful. Asking the author to "do this bit again, but better" (that's a real example, albeit paraphrased) won't work !
  • Don't make non-constructive criticisms. Ask questions rather than stating that the authors have missed something obvious - it at least gives the impression of benefit of the doubt. There's no point whinging that the paper has lots of typos - send them a list instead*. As above, vague, hand-waving instructions help no-one.
  • Don't move the goalposts. Spend longer on the first draft so that the authors will be able to address as much as possible at stage one. Telling them that they need minor revisions at the first draft, then saying major revisions at the second draft (after the previous comments have been addressed) is misleading, unprofessional and delays publication. And if you do find a major error at the second draft, have the common courtesy to apologise for not spotting it sooner !
  • Demand rigour, but don't be anal about it. Life's too short to worry about half-spaces, or, more importantly, the precise meaning of a word. Insisting that the author uses a long-winded phrase (e.g. "galaxies in the overdensity between redshift 0.02 and 0.03") just in case a commonly-used word (e.g. "population" - seriously, referee 1.0, WTF have you got against the word "population" ?) is misunderstood helps no-one.
  • Check that the author hasn't already addressed your point in the paper or their response. There's really no reason for the author to bother if you're not going to read what they write - it makes the whole process meaningless and unworkable.
  • Remember that not everyone is a native English speaker. Many of my non-Anglo/American colleagues report that referees can be very unhelpful when it should be obvious enough that the author might not speak English as their first language !** If you suspect this is the case, then criticising their writing flaws is simply rude. Don't do it. Instead, give them a list of corrections.
  • If you can't justify your assertions, don't make them. The same applies to the authors, of course. Unless you can point out why something is wrong - and, if at all possible, how to correct it - don't say what you think is wrong. If the authors have justified what they've done, you may disagree with them - but unless you can prove that they're wrong, that should be the end of it. You've got to allow people to publish things you disagree with.
* And no, they can't be "easily avoided." If you've read your own work a dozen times it becomes literally impossible to spot any more typos. Fresh eyes are needed, and it makes a lot of sense to me that those eyes should be provided by the referee/editor. To say, "please check more carefully in future" is condescending.
**Helpful hint : if the author's name is Pierre von Hindenberg, chances are they're not a native English speaker - and with a name like that, they're probably way more awesome than you will ever be.

Saturday, 21 June 2014

Learning To Love The Bomb

One of the first spaceships I ever modelled was the Discovery from 2001 : A Space Odyssey. This was back in 2002 when I first started learning Blender, for one of those absurdly ambitious, doomed-to-failure projects that all 3D hobbyists go through. I wanted to render all of the space scenes in the novel which weren't included in the film. I failed miserably, of course, but I did learn how to model spaceships. Not very well, you understand, but it was a beginning.

More ancient historical images can be seen here.
OK, it's a crappy render, but it's still recognizable as the classic design featured in the film - a long boom connects the obvious habitation module and compact drive section, with some standard-looking rocket motors at the back. The boom turns out to be to keep the crew well-separated from the nuclear drive unit. The whole design is very practical - everything serves a purpose, but it's also elegant (well, the real movie version is, at any rate). The only major concession to form over function is the lack of waste heat radiators (we'll get to them a bit later).

But there was another, quite different design that was originally considered. This one wouldn't have used rockets. It would have used bombs. This would have been the first mass-popularisation of the Orion* drive, where nuclear bombs are used to blast a ship forwards. The whole thing is made survivable for the crew by a pusher plate connected to the main ship by huge pistons, reducing the acceleration to survivable (actually quite modest) levels of a few g.

* Absolutely nothing to do with the modern NASA vehicle, this was a conceptual study from the 1950's.

Image credit : me.
I've written about and animated Orion before quite extensively, of course (have a look at the first link if you're not familiar with it). Briefly, it was a 1950's plan to sidestep useless chemical rockets altogether and use the massively greater power of nuclear explosions (which were quite in vogue at the time) to launch truly stupendous payloads (thousands of tonnes) into space. It would also be pretty good for nipping around the Solar System - journeys could be shortened from months to weeks. So, naturally, an Orion drive was considered as an early concept for the Jupiter-bound Discovery in the 1968 masterpiece 2001 : A Space Odyssey.

Image courtesy Winchell Chung.
Looking at the design, though, it's clear why it was rejected for the film. It looks more like something constructed in Kerbal Space Program than anything that Kubrick, with his notorious use of visual clues to manipulate the audience, would ever have allowed. You can't have this sort of ship convey any kind of subtle message, or any message at all except perhaps, "YEEEEEE-HAAAAAAAH !".

No ! That's another Kubrick film entirely !
Only the spherical habitation module is recognizable from the final movie version, and it's rather crudely bolted on to the main ship by what is essentially a big stick (it was only concept art, after all). There also appear to be two, grossly asymmetrical cooling fins, which don't help matters. The rear of the ship looks far more similar to something you'd find in a James Cameron movie - a plausible, practical design that would look just fine on its own, but which is completely inconsistent with the front end.

We can deduce a few things from this drawing. Its overall ungainly appearance suggests an orbital construction instead of a ground launch. Given the size of the habitat module it appears to be about the same size as the movie version, 10-20m diameter. That's pretty small for an Orion though it would be on the long side - about the same as the movie version at 140m. The big cylindrical tanks are presumably for storing fuel (i.e. bombs), with their bulk suggesting this is a ship built for speed.

That would seriously impact the movies's depiction of a remote, isolated crew, and there'd be absolutely no need for most of them to hibernate. I also imagine that convincingly animating the movement of the pusher plate and pistons would have been extremely difficult with 1968 special effects. For all these reasons, I reluctantly conclude that it was rejected for the best. But Orion and 2001 are two of my favourite things, so I can't not model this. I would lose the same amount of self-respect as if I suddenly decided to become a naturist, join the BNP and work for a bank*.

* Though I'm not quite sure all of those are morally equivalent.

I like to think this is an improvement on my 2002 version.
I deliberately set out with the aim not to re-create the reference picture in exact detail, but to make something with all its major features in a way that Kubrick wouldn't have spat on in disgust. 2001 paid exceptional attention to detail in terms of... well, everything really, but perhaps most unusually in terms of making the spaceships realistic. Not merely believable, but almost to the point of being NASA-worthy design studies.

Nonetheless, Kubrick was not adverse to breaking realism's house and burning its legs down (or possibly the other way around) if it helped make a better movie. I've already mentioned the lack of cooling fins in the movie-version Discovery; another noticeable example is the massive size discrepancy of Space Station V in different shots (which frankly is almost as bad as in certain Godzilla movies). And rightly so : there's absolutely no point in making a realistic spaceship for a feature film if it leaves the audience cold.

So, the main change was to make the propellant magazines quite a lot smaller, no wider than the habitat module. That in turn also makes the pusher plate smaller, giving the ship a much sleeker profile and looking less like it's butt-heavy. It's still an ungainly thing, but hopefully looks more like a respectable spaceship and less like a a bunch of flying grain silos on pogo sticks.

Other changes are subtler. I don't like the crude join of the habitat and drive sections in the sketch, so I used something based on the movie version of the ship. Potentially this could also be another piston, reducing the shock that the crew experience still further.

I considered ditching the giant cooling fins and replacing them with some much smaller, recessed panels. These might actually be more accurate. Most nuclear engines produce huge amounts (gigawatts) of waste heat from their reactors, which they have to get rid of to stop the ship from melting. But not Orion - its waste heat goes straight out into space*. The ship will probably still need a nuclear reactor for powering other systems, but only a few megawatts, and even that might be a stretch. The only major power requirements would be for a powerful radar transmitter (via the AE-35 unit) or possibly a high-tech magnetic shield to deflect the solar wind. 

* Some people criticize Orion for being inefficient, since not all of the material from the bomb impacts the pusher. This is like saying solar power is inefficient since the Earth only receives a minute fraction of the Sun's energy - true, but totally irrelevant.

In the end I liked the big cooling fins too much. So they stayed, but now they're symmetrical and rather heavily braced to deal with high accelerations. They're still pretty substantial, probably overkill for a ship like this, but meh. Perhaps it uses its radar to vaporise passing asteroids instead of studying them. Maybe its RCS thrusters use nuclear power so that it can... umm... turn around... really, really quickly. Yeah.

The main thrusters are big, obvious rocket nozzles, but there are also other smaller exhausts scattered about the whole ship. So it can orient itself however is needed, albeit in a slow and stately manner. The exhaust from the main nozzles doesn't quite intersect the cooling fins, so they're safe, but it will scour the hull of the magazines. That could be unsightly, so I added some protective teardrop-shaped panels, based on Apollo design drawings.

I made a small modification to the mounts of the pistons to the pusher plate. Here I used hexagonal prisms in imitation of the rockets on the movie Discovery. I wanted to pay as much homage to the movie as possible, while still largely following the concept art.

Orion aficionados will have spotted that this version does not have a protective plasma deflection sheath around the pistons, as the original design did. The purpose of the sheath was to divert any plasma that made it through the hole in the pusher plate around the shock-absorbing pistons. A trapdoor was supposed to open and close to let each bomb through - it's never been clear to me whether this trapdoor was supposed to be on the pusher plate itself, or on the end of the ejection tube. Anyway this version doesn't have a sheath, so presumably it relies on a trapdoor on the pusher plate.

Finally, the AE-35 communications antenna. Lots of people have pointed out that the pulse unit magazines would block its field of view if it points backward. And they would, but this is a non-issue. I'm assuming that the antenna is fully steerable (as is the ship), so it can still point up or sideways. Given the movement of the planets along their orbits, there's no guarantee that Earth would always be directly behind the magazines... but more importantly, spaceships don't have to point in the direction they're travelling. And wherever the unit is placed, the ship will block part of the antenna's field of view.  

Finally finally, as you'll already have noticed, I also added the ships' name, American flag and NASA logo, none of which are visible in either the drawing or the final movie version. There's no doubt they would be if the ship were ever built though. Since another concept ship recently drew some astonishingly hostile criticism by large parts of the internet, I'd better state it in no uncertain terms : NASA isn't planning to build a ten thousand tonne spaceship propelled by enough nukes to devastate a small country. Just in case you were wondering.

On then, to the artwork. A nice thing - well, one nice thing - about 2001 is that there are different accepted versions of the story. In the movie, the ship goes to Jupiter, discovering an alien monolith in orbit.

In the novel, the monolith is on Japetus (or Iapetus, whatever), which turns out to be a frickin' awesome moon of Saturn. Saturn was rejected for the film because it was difficult to render in the 1960's, but that, of course, is no longer an issue.

The moon here is Enceladus, a proposed target for the original Orion project. Fewer images exist of Iapetus that were suitable for making a nice composition.
The story never describes Discovery in Earth orbit, but of course it was bound to have been there at some point.

Animation ? Duh. Winchell Chung says it best :

"Wild horses couldn't prevent Rhys from animating an Orion drive Discovery from 2001. It is just too much fun for an ordinary person, but infinitely too much fun for an Orion fanatic like Rhys."

Quite right. The main task was to get the firing sequence right. In my first video I deliberately rendered the explosions in an unrealistic way because I wanted to clearly illustrate a basic principle of the ships' operation : the shaped nuclear charges. Most of the mass of the bomb can be directed towards the ship, which is a good deal more efficient than if the debris expands in a sphere. Shaped charges can be extremely good at collimating the plasma into a respectably narrow cone of 20 degrees or less (the exact figure is still classified).

The main problem with this early rendition is that the speed of the plasma is much too low - absurdly low. So in subsequent videos I've tried to make things much more realistic. According to George Dyson's "Project Orion" book, the whole nuclear event - from detonation to impacting the pusher plate and re-expansion - takes about 1 millisecond : less than 1 frame in standard 25 fps video. Rendering only a single frame is not really a viable option (I want the audience to see the explosion, not get a subliminal impression of it), but I restricted myself to 5 frames for the whole event. That's still fast enough that it appears instantaneous to the eye (at least at 25fps, probably not in the GIF though).

Unlike my previous efforts, this version features both the spherical detonation and the plasma jet from the shaped charge.
But is this really what it would look like ? Perhaps not. Project scientist Freeman Dyson says (in his son's book) : 
"The debris goes out from the bomb essentially invisible. You don't see anything until the stuff is stopped... that won't produce anything very spectacular in the way of a flash until it hits the ship. Then all its energy is converted into heat and so you get about a millisecond or so of intense white flash. And very little else."

My naive understanding says that anything which is hot will radiate. And the atomic fire is very hot indeed (10,000 K in the jet, over 100,000 K when it hits the plate) so presumably something would be seen in visible light, however faintly. But I am not a plasma physcisit, so if you have more information, let me know. As for the exact shape, colour and density of the plasma, that is of course a complete guess. I chose to make it look like a gun-muzzle flash because I thought it would look cool.

The firing rate here is about 1 bomb per second, which is about the typical design spec for a ground-launched Orion. It doesn't need to be so fast for obrital manoeuvres because it's not trying to avoid crashing, but it's an aesthetically nice rate to depict. Interestingly, early on in the real-life Orion project a much higher firing rate was considered : 4 (smaller) bombs per second. Since the detonation point is something like 50-100m behind the ship, you need a powerful gas gun to shoot the 1-tonne bombs out the back. But you can't reload a gun like that four times per second. There are two solutions, both of which ought to worry even the most steely-eyed of astronauts.

Option 1 was not to shoot the bombs through the pusher plate at all. Instead, the bombs would be ejected through the side of the hull, guided along rails, and then either shot by a catapult system or propelled by rockets to their detonation point. Presumably the rockets would also adjust the orientation of the bombs to ensure they were pointed toward the pusher plate - in some designs this meant the bomb would do a full 180-degree flip. Well, what could possibly go wrong ?

Option 1 being rejected on grounds of sanity, option 2 was scarcely less dramatic. From Dyson's book again :

"... a gun a metre in diameter... 10 metres long, weighing 2.5 tonnes to project a 1.5 tonne projectile at 200g's. Obviously this can't be reloaded every quarter of a second so you need maybe 10 of them... this will probably wind up as a battery of Gatling gun-type gadgets."

That's right - they wanted a Gatling cannon that fired nukes, because science. Whether you'd need such a gobsmackingly terrifying contraption for the more leisurely rate of one bomb per second, I don't know.

Before I shut the hell up and let you watch the video, Orion always begs the question : "would it have worked ?" The answer, I think, is probably yes - with a catch. Experiments like Operation Plumbob do seem to indicate that a pusher plate (and therefore the ship) could survive the explosions, but there are plenty of unanswered questions. 

For instance, could a system be engineered to reliably eject one-tonne nukes at 200 mph, with an absolute guarantee that they wouldn't detonate too close to the ship ? What would happen if the ship veered off course and had to be destroyed ? What about if a bomb did detonate early - would it risk the others detonating too ? Even if everything worked perfectly, would the fallout from the bombs be anything to worry about ? Well, the answer to that last one is no, but - and this is the catch of course - it doesn't matter.

Orion is a scheme so monumentally audacious that barring the threat of an asteroid stike, it isn't ever going to fly, assuming it would work at all. The total explosive yield for a 10,000 tonne ship for a Mars-bound mission is something like half a megaton of TNT - enough to destroy Hiroshima thirty times over. Does anyone really believe, deep down, that it would be perfectly safe to launch that kind of devastating firepower, or that doing so wouldn't cause massive public outrage, however misguided that outrage might be ?

Of course not. Perhaps Orion could open the road to the stars, but it is, and will only ever be, a dream. Let it go, people, let it go. 

But it still makes for good science fiction. On that note, I suggest you set the volume to "deafen", watch the video and forget about crappy old reality for a couple of minutes.

... if you're one of those people who are chronically unable to forget about reality, you might be worried about the EMP. Well, don't. Unless specifically designed to cause it, a nuke at these orbital altitudes wouldn't cause enough of an EMP on the ground to do any damage unless it had a yield of about a megaton or more. These blasts are much smaller (few kilotons) and would cause problems only for nearby satellites. Or so I'm told.

Friday, 13 June 2014

Prague Peacocks Pumas Pubs And Parks

Left to my own devices I naturally revert to modelling nuclear pulse rockets, or playing Skyrim. Even when it's very sunny outside. However, occasionally even I can't stand sitting quietly in my room not talking to anyone, so I go outside and not talk to a whole bunch of people instead. Most of the time this just involves walking for miles and miles, but with a mighty effort of will I can sometimes force myself to actually go somewhere. Deliberately.

When my parents visited we discovered the fabulous white peacock of the Wallenstein gardens. On that first visit, the wretched creature chose to display its natural Elizabethan ruff the moment we saw it, for all of five seconds. That's just spiteful, really. However, on my return visit the bird had obviously overcome its fit of pique, and cooperated marvellously for the camera.

I don't know why I find the peacock so fascinating - a regular peacock, some chloroform and a can of spray paint would do just as good a job with much less effort - but I rate it as the Greatest Peacock In The World. Even the weird-looking wall and owlery in the gardens just don't compete.

There being an unfortunate lack of any coastline in Prague, the closest I can get to any kind of maritime adventure is to ride a boat down the Vlatava river. Which I did, and it whiled away an hour happily enough, but it wasn't massively different from seeing the city from the riverside.

However, I soon discovered that a far more interesting approach would be to hire a barbecue boat. Yes, those are a thing. Picture a round picnic table with an umbrella and a grill in the middle. Actually don't bother, because I took a photograph.

A far more satisfying excursion was when I decided to visit the New* Town Hall for no particular reason (and no, not because it's right next to Hooters - stay classy, Prague). This turned out to be a very wise move indeed. While its claim to offer the "best view in Prague" is simply wrong, it is a very nice view. The ascent is 221 steps, but it feels a lot less because there are several floors and it's not a narrow spiral staircase like St Vitus. It's also cheaper than the Astronomical Clock tower.

* Constructed 1348.

No explanation was given as to the presence of "ye olde toilet" in the bell room.
But its main advantage is that absolutely no-one else visits it. There was not a single other person in the tower the whole time I was there - and I was at the top for a good 20 minutes. I spent most of that time pointing and laughing at the people down below, shouting* things like, "HAH ! Ya daft buggers. For 50 CZK you could have seen this fabulous view, you petty FOOLS !"

* Alright, thinking.

Putting a sexploitative diner next to medieval architecture or a bunch of hot coals on a very small boat are all well and good, but don't really compare to putting pumas in a pub. Apparently, some forward-thinking (or possibly just mad) landlord decided that a pub would also be a good place to double as a puma breeding centre. Well, why not ? I mean apart from the several dozen very good reasons, like the customers getting mauled or the pumas escaping (it's the only pub I've seen which has barbed wire above the "beer garden") or basic animal welfare.

On the first visit, the female puma had become a mother that very day, so we didn't see them (presumably successful breeding bodes well for the animal welfare issue). A month or two later and we were able to see all three. This place really needs a "beware of the cat" sign -  the pictures haven't come out too well, but trust me when I say an adult puma is a serious piece of cat.

FUN FACT : Baby pumas do not meow. In fact, they sort of quack. The closet noise I can think of is police chief Wiggum's distinctive, "waaaaahhh".

That's all for this time. Tune in next week, when I discover a café full of armadillos and see the world's only albino sheep walking around Wenceslaus Square. Or something.

Tuesday, 27 May 2014

The Importance Of Being Idle

I don't usually reblog science stories, but this week there's an article so interesting, and so close to my own research, that I'd feel silly if I didn't. And also I think the various websites which have re-printed the official press release have kind of missed the point of why this particular story is so interesting, so I'm going to try and redress that here. This is all about "dark galaxies", which are the very thing that led me into radio astronomy in the first place.

This is going to be a pretty long post. If you're already familiar with dark matter, skip section 1. If you already know about dark galaxies and why they might be important, skip section 2 and go straight to section 3, where I describe the latest results.

1) Dark... what now ?

Although not everyone likes the term, a "dark galaxy" is generally reckoned to be a cloud of gas sitting quietly inside a dark matter halo minding its own business. The point being that the gas isn't forming - or has ever formed - any stars, making it dark. Technically this means it's only dark to visible light - it can still emit at other wavelengths, like radio waves, so some people prefer to call them "optically dark galaxies" or "gas only galaxies".

People who worry about such things probably don't get invited to parties very much, so I'm going to stick with plain-old dark galaxies for the rest of this post.

Firstly, the dark matter. Over the years, "being mostly made of dark matter" has become the de facto definition of a galaxy. Dark matter is pretty simple really - galaxies are rotating too fast to be stable, so without something else beside the visible matter to hold them together, they should just fly apart. The links have more details if you like that sort of thing.

This is what happens if you take the dark matter away.
There are alternatives to dark matter (like different theories of gravity) and I'll admit to holding a small degree of skepticism about it even now. However, the evidence is leaning pretty far in favour of dark matter's existence (Ethan Siegel has this excellent summary), so I can't justify my skepticism rationally. For the rest of the post, let's go with the consensus and assume it does indeed exist.

Sometimes, it can be tricky to tell the difference between a cluster of stars and a genuine galaxy (I stole this idea from Robert Minchin while he wasn't looking). What gives the game away is the dark matter - if the object needs dark matter to hold it together it's a galaxy, if it doesn't, it's a star cluster. Keep a copy of this identification chart handy if you have any doubts.

Mind you, not everything without dark matter is a star cluster.

With dark galaxies we're looking for clouds of hydrogen that need dark matter to hold them together, but haven't bothered to form any stars. If "dark galaxies" is a controversial term, then perhaps we could go with "lethargic galaxies" ?

In some ways, they wouldn't be all that remarkable. In almost all cases, the hydrogen gas extends further from the center of galaxies than their stars do (usually by a factor ~2, but sometimes much further) - so in that sense, all galaxies have a dark component. But the idea of objects which don't have any stars at all is intensely controversial.

2) Are you sure you're talking about "dark matter" and not "doesn't matter" ?

Pretty much everyone, I think, accepts the idea that some dark galaxies might exist. The sticking point is : are there just a few exotic, weird objects, or are there bajillions of the little blighters ? And that brings us to the "missing satellites" problem. This is nothing to do with China blasting satellites out of the sky - it's about how many smaller "satellite" galaxies should be buzzing around large galaxies like our own Milky Way.

Theories suggest that there should be about ten times as many dwarf galaxies orbiting the Milky Way as we actually see. Huge projects like the Millennium Simulation (below) attempt to re-create the Universe inside computers. And they do very well on large scales, like filaments and voids, but fail miserably on the much smaller scales of individual galaxies.

Dark matter (used as a proxy for galaxies) distribution in an artificial Universe.

There are lots of possible explanations for this - finding galaxies can be quite hard, we may not understand the physics of galaxy formation all that well, or possibly there are just too many problems with our whole cosmological model and we should just give up and start again. That last one probably isn't as outlandish as some of us might like, but let's assume that we don't need to resort to such drastic measures. Even so, the missing satellite problem is a big problem in cosmology, and solving it would be a seriously major breakthrough*.

* It's unclear whether the newer, spectacular Illustris simulation has any answers to this - we'll have to wait and see.

Dark galaxies could offer a way out of this if most of those missing galaxies just haven't formed any stars. And, just like black holes, that would make them fiendishly difficult to spot. I'll let Red Dwarf's Holly explain why.

Quite. But it's possible that some of those dark galaxies could have hydrogen in them - just enough to detect, but not so much that they'd start forming stars (more gas => more star formation... usually). Now, if there are only a very few such objects, then perhaps they don't really matter much in the grand scheme of things. But if we can prove that even one exists, then that allows the possibility that there could be many more, potentially solving the missing satellite problem.

Proving the existence of even one dark galaxy turns out to be darn tricky. Which leads us on to the object that got me into radio astronomy in the first place : VIRGOHI21. It's not too much of a stretch to say that if this gif hadn't been shown at my PhD interview, I probably would have ended up doing something completely different*. I stole this one off Robert Minchin again. Poor Robert... allow me to compensate by saying, "go and read Robert's awesome blog !"

This is just one particularly famous example. During my PhD I discovered 8 other objects that might be sort-of similar to this one, but we don't have such good data for these yet. Various other candidates have been proposed over the years, but none have ever quite satisfied everyone.

VIRGOHI21 is in the center, linked by a stream to the nearby galaxy NGC 4254 (the biggest, brightest blob). This is the hydrogen "data cube" for the region - for more on these, have a look here, here and here - well, throughout the whole blog, really.
Robert has a detailed post about this object, so I'll just give a short summary. Basically, it's a cloud of hydrogen in the Virgo Cluster that's rotating too fast and seems to have interacted with a the spiral galaxy NGC 4254, with a long stream linking the two. It looks as though the hydrogen cloud be a dark galaxy that's pulled some of the gas out of NGC 4254... but the interaction is the problem. It's possible that the apparent rotating "dark galaxy" was formed when some other object pulled the gas out of NGC 4254, creating the illusion of a stable, rotating cloud of gas.

And that's the crux of the matter. It's easy (ish) to prove that a gas cloud is rotating too fast and would require dark matter to be stable. It's far more difficult to prove that it actually is stable, and not just tearing itself apart.

3) Jeez Louise, get on with it and tell me about the new results already !

Which bring us on, at last, to the latest awesome press release, concerning an object called the Smith Cloud. This is an object which is interacting with our own Milky Way galaxy called a high velocity cloud - simply because it's gas that's moving more quickly than gas in the disc at a similar position on the sky.

Lots of other HVCs are known, and there are almost as many theories as to what they are - maybe just gas thrown outside the galaxy by supernovae, though for the Smith Cloud this doesn't seem very likely... it's too massive. As the authors of the study say, it would take the power of 1,000 supernovae to eject it (you know you've got something cool when you cut out the bit about one thousand exploding stars from your press release). Or perhaps they're torn off by other interacting galaxies, or maybe they're primordial gas that's condensing from the intergalactic medium. Some of course, might be dark galaxies. In all likelihood, different clouds are probably formed in different ways.

From the official press release : "If it were visible with the naked eye, 
the Smith Cloud would cover almost as much sky as the constellation Orion."
The idea that (some) HVCs could be dark galaxies is by no means new. The difficulty is proving it. In the current paper, the authors describe the result of simulations of the Smith Cloud as it orbits our galaxy. From observations, they've been able to constrain its orbit (how well, I'm not sure) and find that it passed through the disc of our galaxy about 70 million years ago. They've gone to some lengths to test lots of different models, with and without dark matter, using different gas densities, to see what should happen to a cloud this massive as it punches through the Milky Way's own gas disc.

What they find is that without dark matter, the gas density needs to be very high for anything to survive that even remotely resembles the cloud we actually see - and then it would end up having more gas than we observe. With dark matter, however, they're able to reproduce something that not only looks quite remarkably similar to the observations, but more quantitatively, also has the correct mass and density of gas. Here's their figure :

Contours indicate the dark matter.
Impressive stuff, especially since they have the comparison simulations without dark matter that just don't work. As far as I'm aware, the paper hasn't been accepted for publication yet, but it looks extremely interesting to me. What would be really exciting about this is that it implies that at least some other HVCs could also be dark galaxies. That would really overturn a lot of current ideas and could, potentially, totally knock the missing satellite problem on the head.

But let's be cautious, and remember VIRGOHI21. When this object was announced to the world, the controversy was intense, and the debate more than a little heated - in the end, few people still think it's a likely dark galaxy candidate. To me, it looked like a very plausible candidate initially, but as more observations were completed and more simulations run, it looked less and less plausible.

I shall certainly be awaiting the final version of the Smith Cloud paper with baited breath (or in reality, with a nice cup of tea). The devil's in the details, of course... and it's always possible that this object is special, and not really representative of HVCs in general (it is, after all, a lot more massive than most of them). The authors themselves make no claims in their paper for anything as grandiose as solving the missing satellites problem - even if it is a dark galaxy, it doesn't mean there are more out there. Ultimately, though, if this object fits the bill, then it certainly makes dark galaxies look like a perfectly valid way to solve the problem.

My biggest concern is a philosophical one : the authors have found a model that works, but that doesn't mean there isn't another model they haven't considered. Such things have been known to happen in the past. Also, I'm not an expert on simulations, so I can't tell if you what they've done is sensible or bonkers. Actually they don't give very many details about the simulation setup, or much description of exactly what happens during the simulation. Some of those details could be very important.

For example, how high does the gas density get when the cloud and disc collide - high enough for star formation ? Would the simulation have allowed star formation to happen, or was it turned off to save CPU hours ? Or does the complex hydrodynamics actually make the gas density decrease in some way ? The simulation reproduces the observed cloud, yes, but that's all we're shown. It would certainly be nice to watch how the cloud evolves.

Make no mistake, I'm excited about this paper. But I also don't want to leave readers with a feeling that any minute now someone will reach an exciting or uninteresting but definitive conclusion - science isn't like that. It's a process - people have been observing the Smith Cloud for years, and it's very unlikely we'll get a decisive result anytime soon, if we ever get one at all.

So, what would it take to prove a dark galaxy, definitively ? It would be difficult, but not impossible. The gas would have to show all the features of ordered, stable rotation we see in normal galaxies. It would have show no any signs of interacting with another object - otherwise there could always be some doubt that it was formed by the interaction, somehow. It would have to be extremely isolated, to avoid any suggestion that it formed by an interaction in the past. The Smith Cloud research is very exciting, but the platonic ideal of dark galaxies has yet to be found. Until then, the hunt goes on.