If Human Made of Sun

The start of the last Earth-shaking week in science now feels like a long time ago…! In the background, though, I’ve had a steadily-growing file on my computer since then called “If Human Made of Sun“, inspired by the birthday of Dmitri Mendeleev. He’s the person who noticed patterns of common behaviour among certain substances that led him to create the Periodic Table of the elements. And his chart has been a fixture on the wall of every school science room for most of the rest of history, with good reason.

As part of the twitterness inspired by that anniversary, @JohnRMoffitt tweeted a chart showing “What Dave is Made of”:

Probable credit: Jim Marsh at RationalDiscoveryBlog.com

“How nice that someone’s broken me down by element”, I thought. “If I ever get atomised in a futuristic sci-fi battle, here’s the recipe for the ensuing mess.”  The chart shows how much of each element there is in ‘a Dave’ weighing 70 kg *coughs at underestimate*, listed in decreasing order of mass, and it’s pretty cool! You get to see what ingredients it takes to build a functioning human body! The data were data tabulated by Ed Uthman, who got them in turn from John Emsley’s The Elements, though I think the graphic might be due to @Arg362.

Anyway, it turns out the graphic wasn’t personalised: it’s for the average human mass. I suspect they’re using “Dave” as a generic, everyman kind of name (although: this may change soon – expect TV channels called “Ethan”,’”Josh”’ or “Mason” in a few years’ time).

Looking at the leaderboard, I was a little surprised that oxygen was the winner. Since we’re mostly made of water (H20), you might think there’d be twice as many hydrogen atoms for every one of oxygen. But then, oxygen weighs 16 times as much as hydrogen – so it wins out in the end.

Mendeleev’s periodic table arises because of patterns in how electrons arrange themselves in different elements. Some of those electron patterns repeat (or “are periodic”) as you increases the number of protons in the nucleus. While I’m not a chemist or material scientist, that fact is of enormous use to people like me who use atomic spectroscopy to understand what’s going on in the universe, and what various objects are made up of. Similarities between certain elements help us to decode distinct colours in the visible and invisible spectrum of light, and that lets us work out what element gives off that colour. For example, yellow street lights contain sodium: it’s what lets them be a very specific yellow.

One of the things I liked about the chart above was that it showed how much of each element there was, not just in mass but in size… So I started wondering what would happen if you did the same thing with the Sun? If I could survive getting to the surface of the Sun, scooping up 70kg of it into a bag, and then bringing it back to Earth…

In space exploration, this is known as “sample return”: you bring a chunk of something back to the lab on Earth, where we can use all the world’s most advanced tools (or sometimes just a fancy hammer) to investigate what it’s made of. The Apollo astronauts brought back  382 kg(!) of Moon rocks to analyse in this way, and Hayabusa/Hayabusa-2 did/will return samples from an asteroid.

Since 70 kg of “solar stuff” is about the weight of an adult human, I’m going to call it a solar human. If it helps your imagination, you could reshape that plasma in your mind into a lovely, glowing mannequin shape. You can even give them a name, if you like. (I’ll silently judge you if you don’t.)

What would our solar human be made up of? And if you could separate those elements out, how much space would each one take up in your hand?  Well, fortunately, the Sun shines a lot of light our way, which we can use to make a spectrum that tells us a) what it’s ingredients are, and b) how much there is of each one.

SolarHumanMetals 3
The contributions of different elements in a 70-kg person, if they were made up of the same composition as the Sun: identical ingredients in the same proportions. (I’ve marked the centre of the bigger bubbles with a blue dot to help you find it.) I simultaneously a) call this person a “Solar Human”, and 2) doubt my sanity. 70 kg equates to 3 hundredths of a billionth of a billionth of a billionth of how much the Sun weighs. And if you’d like to play with the data, I’ve published them on figshare.

The centre of each bubble shows you how much material is in 70 kg of Sun, and right away you can see that oxygen is again a heavy hitter. This mightn’t be too much of a surprise when you consider that we’re made up of stuff that’s found on Earth, and the Earth and the Sun came from the same original cloud of gas and dust, 4.5 billion years ago.

The size of each bubble shows you something different: it shows how much space each element would take up in a lab back on Earth, if we could distill it out of our 70 kg. (For this I assumed room temperature and atmospheric pressure – data for standard atomic weights are taken from NIST, and pure-element densities at atmospheric pressure are from periodictable.com.)

Oxygen again takes up the most space on this chart, filling a balloon about 80 cm across. Carbon is the next most heavy, but it’s a solid at room temperature, and the size of a snooker ball. Then comes a balloon of solar neon (about half a metre wide), followed by about enough solid magnesium to fill a ping-pong ball, roughly a beachball of nitrogen gas, and so on in ever smaller weights…

Comparing these ingredients in a “solar human” with the composition of a real human, you can see the proportions are very different. This is even though we, the planets, and the Sun – the whole frickin’ Solar System, in fact – came out of the same collection of material. And the ratios of these ingredients are different not just for humans and the nearest star: they’re different for the Sun and comets, or between comets and asteroids, or rocky planets (like Earth) versus gas giants like Jupiter… in fact, the balance of the different elements (and the chemicals they form) is one of the most powerful tools we have to work out how things formed in the universe, and where they came from.

Some people might be looking at the graph above and thinking, “wait a second… why are the two most important ingredients in the Sun missing??”

Well, I deliberately left out hydrogen and helium in the first plot because…

The same chart/plot/diagram as above, but now i) it includes H and He, and β) the mass axis is shown logarithmically, which means that for every tick you go up, the mass in a 70 kg bag of Sun-stuff gets 10 times bigger. Using a logarithmic a great way to show the really, REALLY tiny amounts of things like germanium, krypton and tin that we can detect in the Sun. Even I’m not tripping out enough to use logarithmic balloon sizes on this though. Balloons are perfect. Don’t try to change balloons.

… they completely dwarf everything else! They’re the most abundant elements in the universe, and they’d be by far the biggest in terms of weight and volume. I’m particularly proud that I finally managed to find a scientific reason to draw a helium balloon!

In fact, yesterday (Thursday) was the UN’s International Day of Women and Girls in Science, and @theastroholic marked it with a really nice vlog about Cecilia Payne-Gaposchkin, author of ‘the most brilliant thesis in all of astronomy’, proving that most of the visible universe is hydrogen! The same is true in the Sun: add up helium and all the other bubbles in our second chart, and they still don’t come close to the amount of hydrogen.

Early on in the universe, hydrogen’s dominance was even more true: almost everything (that wasn’t dark matter) was made of it. Hydrogen is like the 1×1 Lego brick atom of the cosmos, but when large stars started appearing, nuclear fusion turned most of the hydrogen inside them into helium (2×2), then some of that into carbon, and later some of that into magnesium and neon. This is why you can see these ingredients featuring higher up in the list: lots of the earliest stars made lots of them. (As carbon-based life-forms should be VERY glad.)

Using the second chart’s logarithmic scale, you can also see that amount of vanadium, cobalt, zinc or gallium in the Sun isn’t actually zero – although the regular first plot might lead you to think that. In both plots, I’ve only included elements which actually have detectable traces in the Sun (data from Table 1 of Asplund et al. (2009)), so those numbers aren’t zero, they’re just very small; there would be just 4 microgrammes of solar lithium, the lightest contributor to our 70 kg sample.)

Although we haven’t yet been able to achieve sample return from the Sun itself, we’ve had a go at it from a great distance. Starting in 2001, NASA’s inspirational Genesis mission spent 28 months holding its aerogel hand out and collecting tiny particles from the solar wind, which is constantly thrown off by the Sun. The idea always reminds me of that gorgeous scene where Wall-E flies through the rings of a planet, touching the grains of dust as they fly past.

The results from Genesis, on the composition of the solar wind, were hugely valuable (and challenging!). In 2½ years’ time, though, we’ll be doing something far more challenging: flying really close to the Sun with the Solar Orbiter mission! This is a radically different way of observing the Sun – it’s far more similar to a planetary-encounter mission than anything we’ve used to observe our star before: think Cassini/Huyghens visiting Saturn, or the Voyager missions (which inspired my interests as a kid). This style of mission means we’ll get closer to the Sun than Mercury, and be able to inspect it up close using telescopes armed with cameras and spectrometers (great news for me). But also – really exciting – we’ll be able to hold Orbiter‘s hands out and catch the particles that make up the solar wind and the Sun’s dramatic eruptions!

In fact, we know that within the material thrown off by the Sun, the balance of the elements it throws off can change, depending on where on the star it comes from. For example, bright active regions, where sunspots live, give off a slower solar wind with a different mixture of elements than the darker coronal holes, where the fastest solar wind roars into space.

But even up close, there’s still quite a distance between where the mission will go and the Sun itself – 40 million kilometres – and not everything leaves the Sun in a straight line. So the only way we can be sure we understand the connection between what Solar Orbiter sees being thrown off the Sun and what it catches with its hands is to see that the balance of the elements is the same in both: and that’s exactly what its 4 hands and 6 telescopes are set up to do!

We’ve already begun to work on the techniques to do this, and once we’ve conquered all the technical challenges to getting up close and personal with the Sun, the data are going to give us an incredible view into how a star interacts with its solar system – including solar systems that harbour life.

Things I learned while doing this

  • Oxygen is still the biggest contributor to the mass of the Sun once you knock out hydrogen and helium (helium isn’t kept in the body because it’s a loner and refuses to make any meaningful bonds with anything else. We’ve all met people like helium.) But in a 70kg bag of Sun-stuff, the oxygen only amounts to about 400 grammes, less than 1% what it is in a person.
  • I have never known, nor do I now know, all the element names, never mind their names AND symbols… This did not make me feel big or clever as a scientist 😭
  • Everyone only cares about the elements that they use in their science. NONE of my usual or Google-able sources listed all the elements in order of nuclear mass, even when they could just put a zero beside the ones that don’t appear 😅
  • Related: people seem to list things for people to read, not for computers to read in. I spent most of my time looking into this tabulating or reformatting data, and writing new functions to read them in. I can’t wait until computer-readable tables are mandatory, in science publishing at least.
  • Most solar and stellar databases I could find stop caring pretty much at Fe (Z = 26).
  • “Hafnium” is a very satisfying word to say 🙂
  • I never knew there were so many spoof periodic tables out there, like figures of speech, operators in IDL, swearing, beer styles,  typefaces, and even social issues.
  • Working out the abundances of the different chemicals in the Sun is REALLY HARD, and is basically a craft in itself. Read the review by Asplund et al. (2009) if you’d like to get a feeling for how much technical skill is involved.
  • Selenium has not been detected in the Sun (I find this poetically very pleasing 🙂)
  • Someone is going to have to teach me how to say “praseodymium” (I’m looking at you, @jamiebgall & @funsizesuze).
  • Every time I see the word “strontium”, I immediately think “Dog” afterwards
  • I can’t wait to learn Python properly. Python cares about physical units. IDL just pretends it does and then breaks your effing heart 💔
  • I look forward to one day including Lemmium on this chart, even though the value will be 0 µg of human and/or Sun  😊

Solar Orbiter is a European Space Agency (ESA) mission, in collaboration with NASA, scheduled for launch in October 2018.

If Human Made of Sun

IDAHO, Light and the Human Spectrum

Today’s the UN’s International Day Against Homophobia, Transphobia and Biphobia (you might be seeing a fair bit of #IDAHO flashing across Twitter for that reason), and this year it falls in the UN’s International Year of Light. As a gay astronomer, both these things are very close to my heart.

This isn’t the first time I’ve written about being gay, but it is one of the first times. I’ve tended to hold back from it because I didn’t want to be seen as anything other than my primary identity: a human. That human also happens to be a scientist, and that scientist also also happens to be gay. I’m really at peace with all these identities – probably now more than at any time in my life so far. But I’m paid in the public domain, research and teach at UCL, and it’s a job requirement for me to publish my scientific results, plus there’s Twitter; you can quickly tell I’m a scientist. As for being human: seriously, only the weirdest of A.I. projects would produce something that yaps like me, so you can probably safely assume I’m homo** sapiens. And third of all: I’m gay. But it’s not on my business card, and that’s always presented an interesting sort of problem when it comes to the overlap with my first two identities: is it in my interest, or anyone else’s, to talk about it at all?

(**if you giggled, we might just become friends)

I actually think it doesn’t matter that I’m gay. I think it matters that I’m a bit different. That’s why IDAHO[TB] and awareness efforts like it are so important: there is no such thing as a Standard Human, and the sooner we get past this, the sooner we’ll be able to let everyone in our communities flourish. This is also kinda important for the survival of our species: we have some really, really scary problems banging on our door, fellow humans, and we’re going to need every brain we can have, operating at full capacity, to solve them. If they’re worrying about being scape-goated, demonised, beaten up, or barred from being a real member of society (yep, that’s a lot of what people worry about), they won’t be doing what we need them to do.

A few things have happened in my life recently to make me think it was worth speaking up. Most recently, they’ve included the incredible support in Ireland for removing the second-class status of same-sex couples, in the run-up to the Equal Marriage referendum. Now, I’m from ‘The North’ (i.e., Northern Ireland), but most of my extended family and many of my friends are in or from the Republic. As a result, my sample of the internet has been filling with some pretty wonderful articles, videos, tweets and Facebook posts. Colm Tóibín’s public lecture at Trinity College Dublin, this week, contained a gently powerful argument for visibility (the 5th paragraph in the Irish Times coverage, but the whole thing is really worth reading). And I warmly recommend David McRaney’s excellent podcast on how disclosing your circumstances as a victim of prejudice is a vital tool in getting people to see you as human (rather than ghetto-ising, or existing in an overlapping but never-touching world).

Now, I’m in a safe situation where I can say I’m gay, and that safety’s important. Telling people you’re ANYTHING other than straight carries a risk if you’re somewhere where it is illegal, not accepted, culturally taboo, rejected by your family, or any number of things that could land you in trouble. So I’m NOT advocating that everyone reveal their sexuality so we can instantly live in Fluffy Bunny Magical Luck Dream Joy Wonderland (if that’s an actual place, I’m sorry – I couldn’t find you on Google, and I needed a metaphor). The fact is that I feel like I can, and I’m lucky that’s true. (Oh, and I’m otherwise in the hyper-priveleged majority. Like, HYPER. So there’s that…)

There’s a final aspect to all this for me, though. One of the greatest joys of the multi-dimensional continuum of LGBTIQ+++ (helpful explanation of those termsand more) is that it reveals that for so much of our history, our thinking was too simple – just as much as when we thought the Earth was flat, or that all humanity had the same skin colour as us and our neighbours, or that everything revolved around the Earth. All the observational evidence tells us that there is so much more to life, and we learn, every single time we find evidence that breaks the old models, that we adapt our understanding, and that we reach a new and more revealing view of our existence as one species of ape on this pale blue dot.

IDAHO, Light and the Human Spectrum

Egypt and the farce of the righteous majority

As I crack open this story, Desmond Dekker’s “Pretty Africa” shuffles onto iTunes. It’s a sentimental sausage of a tune, but it slowly reminds me I’ve visited one place in the entirety of Africa, once, and that wasn’t Egypt. So I don’t have any first-hand experience of the place I’m about to discuss. But I read, and when you see a cry for help, most humans read a little closer…

Recently, Egypt’s government has taken to monitoring its citizens online, including what they post on Facebook. This can’t come as a surprise to anyone in the US or UK, because internet monitoring is exactly what our governments have been doing to us, too! So if our lot are doing it, why shouldn’t everyone else’s, right?

(Aside: there’s a good write-up here of some of the pro-privacy arguments – spolier: it’s not a FAQ with questions like:

“I’m a benefit cheat/seeking to bring down your decadent western way of life. How can I best hide my private e-mails about crime plans from the government/security services?”

Well worth a read.)

Anyway, the governments now in power in many of the countries that experienced the ‘Arab Spring’ are not quite so worried about losing votes in the next general election if they’re found out to be snooping. Like, maybe they just decide to ignore or rig the general election results? I’m not going to get into who Egypt’s government should be, ‘cos I have no clue, but I DO have a clue that what the current government is doing to many humans right now, in this until-recently more liberal African nation, is extremely inhuman.

The history of what happens when a lot of people experience significant, simultaneous discomfort is now a disgusting cliché. Either the absent rights of a minority are campaigned for (note that they don’t even have to be won, just campaigned-for) and a privileged group perceives that it is now threatened or has already lost its relative position in society; or there is social upheaval, the economy goes down the tubes for a bit, life starts to bite – hard – and people want a solution. The solution, it is decided by the political cliques, isn’t to hold to account the political cliques (you saw that coming), but to bully someone else – someone vulnerable, like a minority that can’t fight realistically back. That bullying tricks you into feeling you’re doing something about your problems, and makes you feel like you’re not at the bottom of the heap yourself. That bullying, though, takes forms from stigmatisation, through vilification, persecution, accusation, segregation, incarceration, vigilante/militia beatings on the streets, maybe dragging people them from their homes first, to physical humiliation, rape, torture, mutilation, eventually to murder. It’s a broad spectrum, I admit, but put your hand up if you want to be anywhere on it? Nope – I didn’t think so…

What’s worse is that people frequently get to be in several places on that spectrum at once. In Egypt right now, Egyptian citizens are being arrested by their own police for things like “debauchery”. When they get to prison, they can experience threats of rape and undergo unethical “anal examinations” by the Forensic Medical Authority, presumably to see how “debauched” they have been.

That these people are perceived to be gay, or transgender is beside the point. Beside the point morally, because they’ve DONE nothing wrong: it’s really their EXISTENCE that’s de facto being made illegal, they simply ARE wrong – a Kafkaesque charge that you cannot defend against. And it’s beside the point legally, because there’s no legal basis for their detention: no legislation has been passed. Debauchery isn’t even a well-defined thing in Egyptian law. Sections of the media share some serious shame in all this, too, brutishly violating citizens’ (viewers’!) rights in the name of joining the moral superiority band-wagon, stirring up vilification and publishing names and photos of people they want to accuse. Of… something…

In almost every respect, I’m in the hyper-privileged demographic:

  • male,
  • Caucasian (although I do enjoy the comedy decision between White (British) and White (Irish) in questionnaires),
  • middle-class,
  • Christian up-bringing,
  • higher degree with the entirety of my education paid for (sorry, but it’s true),
  • native English-speaking,
  • from a wealthy European country
  • and my passports let me travel at will to loads of countries without even needing a real visa.

The only persecution that I had to get angry about recently was that I couldn’t get married in my own country if I wanted to, but that’s now taken care of. So what have I got to complain about? Even if homophobia were erased in Britain tomorrow, I would still have to complain about the ill treatment that OTHERS face. And consider that it doesn’t take much to find yourself in the gun-sights. People are inclined to make divisive mountains out of molehills of difference, especially if they feel like they would be on the wronged and/or righteous majority side of the division that’s created. It makes them feel better, in more ways than one, and that’s particularly powerful when everything else that’s happening to them is (frankly) pretty shitty. So would you be so sure you’d be in the moral majority on every single measure conceivable? Look at my profile: I would still have been blamed for causing floods (not the super-power I would’ve chosen) or of wanting to redefine other people’s marriages (seriously, I really, really don’t.)

These moral-superiority divisions are always a fallacy, because difference is everywhere, and it’s heartening to see so many people now celebrate and value diversity, because to exclude people from society is to hold us all back.

Once a persecution machine gathers pace, it’s hard to stop it before it wreaks horrible damage. But if the larger majority from around the world scrutinises this immoral, illegal persecution, we can find ways to pressure the persecutors, and even if we can’t stop it from outside, we can lend our support to the people who are fighting it. We let them know that they’re part of a larger community of humans out there who believe what they believe, and reassure them that they shouldn’t doubt themselves – it IS their government that’s wrong and not their existence, or the existence of their friend or sister or nephew. The people with power have invented a “problem” to which they have a quick & nasty “solution” – and, too often, it happens because they won’t face up to the real problems that people have.

If you read this far, I appreciate it. And if this issue moves you to tweet about it, you can use the hashtag:
to show your awarenss and support, and add any of these if you have room:


Egypt and the farce of the righteous majority

Happy 7th EIS-a-versary, everyone!

On Sat 28th October, 2006, somewhere in low Earth orbit, a small bit of wax on a satellite heated up and melted, right on cue, releasing a sprung aluminium door and illuminating the inside of a telescope with solar ultraviolet light. Astronomers call this moment “first light” – the first time that the telescope fulfils its purpose and takes an image of what it was always meant to. EIS’s first light image came through in real time, as we huddled around a laughably ancient (but very important) computer screen in the bowels of the mission control centre; but we couldn’t have asked for a better first glimpse.

EIS first light image
Left-hand X-ray image from HInode XRT shows the position of EIS’ slit and slot fields of view on the Sun when the EIS telescope door was opened. The trio of images on the right shows XRT, EIS transition region and EIS corona images seen with the slot. A small active region is seen near the bottom of the slit. Lower panel shows the spectrum taken from a single pixel along the dashed slit seen on the full-Sun XRT image.

The EIS spectrometer was pointed at a really lucky combination of the two most common sets of conditions on the Sun: a solar active region, where intense magnetic field pokes through the Sun’s surface; and the background ‘quiet Sun’, the Sun’s normal state in the absence of these strong fields. It gave our team the perfect demonstration that EIS was working well and revealing the ingredients, flows, heating and cooling of the million-degree solar atmosphere.

EIS was the last part of Hinode‘s three-instrument payload to go live. The months leading up to this were stressful for a lot of people concerned. Most recently, we’d been taking, reporting and checking measurements of all the instrument’s vital signs at every overhead satellite contact we could muster. Then, our instrument engineers from across the world would make sure it was all behaving normally, as they pain-stakingly brought EIS up from its boot state to the state in which we could start using it for scientific observations. Being involved in that work gave me a lot of respect for the guys who were there with us to commission the instrument, and I’d like in particular to thank Jason Tandy (EIS’s chief instrument engineer), Louisa Bradley, Charlie Brown, Clarence Korendyke, Hiro Hara, David Brooks and Matt Whillock for keeping a cool head and sense of humour throughout those often intense days.

The seven years since first light have brought observations, discoveries and questions that we didn’t imagine on that first day: EIS was designed to observe a largely uncharted part of the spectrum, to probe the vibrant corona and transition region of the Sun. In those seven years, there have also been huge advances in atomic data calculations, plasma theory and numerical simulations of the solar atmosphere from beneath the surface to the corona. The feedback between these different disciplines in solar science enriches the whole subject area; solar physics feels like it has moved on a lot between 2006 and 2013, with EIS playing a lead role in that evolution.

A lot of us who are involved with the Hinode project are now thinking about the seventh mission conference that’ll take place in the mountains of Japan’s Gifu prefecture in just two weeks.  I’m looking forward to a reunion with some of the people who were in that room when we got the first spectrum, of course, but also to find out what our unique instrument is continuing to bring to science at large. And I’m proud that EIS has made a powerful contribution to our understanding of our parent star and how that star affects its planets, of which our pale, blue dot is one.

Happy 7th EIS-a-versary, everyone!

Solar wind visualization at NOAA SWPC

The IDL Data Point

George Millward and his colleagues at the NOAA Space Weather Prediction Center (SWPC) use IDL, among other tools, to study, monitor and forecast solar events that impact GPS, power grids and communications networks on Earth. On the WSA-Enlil Solar Wind Prediction page, Dr. Millward uses IDL Object Graphics to visualize output from a model of solar activity and Javascript to animate the result as a time series. Here’s a sample frame from the animation:

WSA-Enlil solar wind prediction at 2013-03-15, 00:00 UTC

(Click to embiggen.)

From the WSA-Enlil Solar Wind Prediction page, a description of this plot:

The top row plots show predictions of the solar wind density. The bottom row plots show solar wind velocity. The circular plots on the left are a view from above the North Pole of the Sun and Earth, as if looking down from above. The Sun is the yellow dot in the center and the Earth is the green dot on…

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Solar wind visualization at NOAA SWPC

Calculating the period of the sunspot cycle

Nice to see solar data being used to illustrate a fundamental tool of the astronomer: the FFT :o)

The IDL Data Point

Two weeks ago, I used the sunspot number data provided by the Solar Physics Group at NASA’s Marshall Space Flight Center to demonstrate positioning plots in window. This week, I’d like to show how to calculate the period of the sunspot cycle.

If you haven’t already done so, download the sunspot numbers file and place it in your IDL path. Read it with the astrolib READCOL procedure:

file = file_which('spot_num.txt', /include)
readcol, file, year, month, sunspots

Next, transform the sunspot series to the frequency domain and compute magnitude and power spectra:

mspec = abs(fft(sunspots))
pspec = mspec^2

(Aside: FFT: it’s all you need.)

I’d like to display the power spectrum as a function of frequency. This requires a few statements to set up a frequency vector based on the time data from the sunspot numbers file:

sampling_interval = 1/

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Calculating the period of the sunspot cycle

Emotion Pictures

I’ve recently converted two “perfectly good” QuickTime movies into MPEG-1 format to accompany a journal article in a widely-read astrophysics journal. This made me sad.

Scientists make animations all the time, and being (unapologetically) quite a visual person, I see a strong case for animations when we’re trying to illustrate dynamic phenomena. We’re animals that perceive time, after all, and in the case of the paper we resubmitted, it definitely helped get the context of the paper across. But converting these animations to an old standard like MPEG-1, from the beautiful H.264 .MOV files I started with, was a little heart-breaking. And then I caught myself…

As a Mac-less scientist (until a few years ago) I remember swearing under my breath at the growing use of .MOV files as a format for solar and simulation movies. Although the quality was fantastic, these files were big, and in a proprietary format – so they took ages to download and were very difficult to play on Linux machines (think back to the mid-2000s). Since then, I’ve converted to being a Mac user, and got into the habit of making movies in QuickTime format, even paying for the licence to do so. MOVs are pretty reliable, and presentation-quality, but really… can everyone play them? Or do I just subconsciously generalise from my own case now? Is there convergence or divergence of formats these days? Are video-dedicated resources like Vimeo and YouTube now the only ones that can cope with the variety of different types?

What format should we default to for animations at this point in the 21st century? Is M4V already replacing the old MOV format? Will Windows and Linux machines play nicely with them, or are they wedded to other formats of their own?

And, last of all, should we be trying to publish (and pay for) movies in journals when there are services out there like Figshare that will not only host them, but give them a DOI – right away – for free?

I’d be intrigued to know the landscape of opinions on this*, so I set up my first poll. I even had a hot whiskey to celebrate**.

(*if there are any readers out there. I’m braced for some enforced humility…)

(**actually, it was to medicate a suspected case of man-fluenza.)

Emotion Pictures

The Hinode anniversary: both of it.

This weekend marks the sixth anniversary of the launch of the Japanese/US/UK* satellite, Hinode. It was launched on the 22nd of September at 21:39 UT. But in Japan, where we saw it blast off, it was already daybreak on the 23rd, so that’s the anniversary I keep in my head…

Launch site, post-launch A younger me, at the launch rail in Uchinoura, a couple of hours after Hinode took to the skies.

I have a strong personal connection to this mission. I was a scientist-in-residence at ISAS and still am a so-called “chief observer” for the UK on its EIS spectrometer (don’t get excited: there are a lot of “chiefs” in Hinode nomenclature). I was in Japan from before launch, got to see it successfully “born” by a Mu-V rocket from Uchinoura, and then returned to ISAS to help out in the process of commissioning the satellite’s EIS spectrometer, getting the data to start flowing from the instrument, and learning how this mission actually worked.

It might sound odd to say that, because isn’t the working all written down in documents? Aren’t all the processes understood? Well, I heard an interesting line from Salman Rushdie’s memoirs this week:

“…when a book leaves its author’s deskit changes

The same is true, I think, of any substantial work. A mission is a living thing: just like a book, Hinode left its many authors’ collective desk and took on a life of its own. In the months and years that followed launch, we learned how this complex system interacted within itself, with us, and with the wider scientific world. Almost simultaneously, NASA’s STEREO satellites were launched and our perspective on the solar system changed again, and its scientists, engineers, and other staff will have their own stories to tell.

The experience of Hinode was profoundly life-changing, professionally but also personally, and I look on my time at ISAS and in Japan with great fondness. By chance, I recently found a video message I made, for (now fellow-blogger) amacrojot, on the night after I moved to Japan. It makes me chuckle to see the “pre-experience” me, hear his less-diluted accent, and think of of what was going to happen over the next three years there. The reason I bring this up is that science isn’t all just about contributing to the economic success of the countries involved, although it can’t help doing that. Science also gives you a much, much broader experience. You travel, you’re exposed to different ways of thinking, and for every frustrating problem or situation you encounter, you also come across one of the most surprising people who can solve or see the way around it. And space science has this collaborative international nature that produces these great moments so often.

Enough evangelising. I really just wanted to pay respect to all the people I’ve been lucky enough to work with on Hinode, and those who put up with me being away. The list is long, but you know who you are :o)

(*note the countries involved, Huffington Post )

The Hinode anniversary: both of it.

The transit of Venus, EIS-Style!

On 2012 June 5 and 6, the Hinode observatory joined thousands of telescopes around (sometimes literally around) the world in watching Venus cross the face of the Sun.

Hinode’s Extreme ultra-violet Imaging Spectrometer (EIS) had a few scientific and technical goals in mind in observing the transit: from looking for the interaction of the solar wind with Venus’ atmosphere; to using the precisely known path of the transit to work out the minute roll of the telescope’s field of view – what you might think of as “which way is up?”.

In this movie, you see Venus first quite far off the Sun’s disc to the left (solar “east”), but it’s still silhouetted. This is because the Sun’s corona extends far beyond its surface. Then, we see it going (conveniently!) past a bright active region – 2nd and 3rd panels from the left – and a dark coronal hole – 4th panel – before exiting on the solar west. The wavelength of light that we use here is 195 ångströms, which is the wavelength emitted by iron so hot that it’s lost 11 of its tightly-held electrons. It’s possibly of interest that these are what we call slot data, whereas we also have “slit” spectra that will reveal much more about the precise balance of ions and electrons in the solar atmosphere and (hopefully) Venus’ atmosphere, too.

It takes a lot of people to achieve data as seemingly simple as these, so thanks in particular to David Brooks (NRL/GMU), Shinsuke Imada (NAOJ), Toshifumi Shimizu (ISAS/JAXA), Alphonse Sterling (NASA) and Kunichika Aoki (NAOJ), as well as many other members of the Hinode team, for arranging these observations so expertly.


1) The gaps in the coverage are due to what we call “orbital events”: these are when the satellite passes through radiation zones — when the detectors are bombarded with particles to create a TV static effect — or when the sunlight is blocked for a short while by the Earth’s atmosphere, a transit of a different nature!

2) The apparent up-and-down wiggle of the planet as it crosses the sun is actually a parallax effect, caused by the orbit of Hinode, which circles the Earth along the line between day and night, crossing the north and south poles. This is the same effect that was used, in the 1769 transit, to work out the distance from Earth to the Sun. Fun fact: knowing this distance and how much Venus appears to wiggle up and down in this movie, you can work out the mass of the Earth ;o)