Monday, March 31, 2014

Shakespeare’s other tragedies

In popular culture one particular tragic play by William Shakespeare is vastly over-represented.  This is, of course, Romeo and Juliet.  Every generation, artists from all over the English speaking world channel the Bard through these characters, a process that gives short shrift to all of his other tragic figures, such as King Lear.

It doesn't have to be this way, though.  After all, each of the singer-songwriters who most closely associate with the love story is herself in part a product of her surroundings and upbringing; in another time and place, they could have other interests, and different narratives to tell.  For example, if Taylor Swift had been born the youngest of three British princesses 2800 years earlier, she might have reflected on her life experiences like this:

I was still young when I first lost you
I knot my tongue- And the nightmare starts
I’m standing there
In the throne room with other heirs.

You begot
Me, bred me, loved me;
Honor, obey, yes I most loved you
But that’s all, little did I know

That truth would be my dower, my land digested
And my daddy said Burgundy or France it is
I refused the glib and oily art,
Begging you please don’t go. No, I said

Goneril, take my castle and we’re all done
Don’t scheme with Regan, put me on the run
Lear is the king and I’ll be the heiress
My love is earnest, daddy will say yes.

So my sisters can’t stand to see you
Disquantity your crown retinue.
Sumpter and slave,
Walk the moors for a little while.

But I still have France, spies and speculation
And daddy said stay away from British Isles
But they were everything to me
I was begging him please to war. And I said

Goneril, take my castle and we’re all done
Don’t scheme with Regan, put me on the run
Lear is the king and I’ll be the heiress
My love is earnest, daddy will say yes.

Goneril has my castle but we’re not done
Regan’s a coward, my French will never run
France is the king and I am his princess
My love is earnest, baby just fight best.

Oh Oh

Daddy, do you know me?
I’m no spirit, I’m still far and wide.
I do not mock thee
If France wins I will take you inside. Except…

Goneril took my castle and I’m all done
She schemed with Regan, put France on the run
Lear is in prison and I’m going in next
My love is earnest, daddy can’t fix this.

Butterflies gilded
Singing like birds in a cage
Wipe thine eyes; the good-years will devour your
Sisters’ young beauty, ere they make us weep; We’ll
See ‘em all starve we’re… together at last.

Oh oh
Oh oh
I may die young but I will die true.

Friday, March 14, 2014

Editors ask the wrong questions

Attached is a screen pic from the summary sheet of a review I did for an academic journal a while back.  Note the phrasing of the middle question, and how the poor wording on the summary sheet required an out-of-the-box answer.

Table and figures are a good thing.  The tables, in particular, contain all the data that everything else in the paper is based on (I don't review pure theory papers.  Theorists should be thankful). Frankly, I don't understand the trend towards depositing data and methods, rather than publishing them.  Depositing a machine readable version of datasets IN ADDITION to publishing them (or a representative sample of data, for really large sets) is a sensible thing to do, but in general we would all be better off if papers contained data and results, and the speculative waffling, overly broad impacts, and long bows stretched to make the paper seem to appeal to fields it doesn't really effect were all banished to the online supplementary material.

Mount Tsukuba

Tsukuba is a science and technology town, built by the Japanese Government in the 1960’s.  It features a number of research campuses, a university, and a satellite assembly facility.  Like many places built in the 60’s, it is not particularly culturally striking in the architecture department, and in fact it is ignored entirely by many tourists guidebooks that focus on Japanese culture. 

Tsukuba is also the home of Japan’s newest SHRIMP, so I was there for three weeks as part of a team that upgraded that instrument from single collector to multicollector. And as the research park and the downtown area were a bit utilitarian, a few of us decided to look for something a bit more distinctively Japanese on our day off. 

Luckily for us, 20 km north of Tsukuba is Mount Tsukuba.  This 800 meter peak dominates the eastern plains NE of Tokyo, and is significant in Japanese culture.

At the base of the mountain is a Shinto shrine.  I’m not up on my Shinto, bet the gardens were fantastic.  Even if there was still ice on the pond, the Japanese Cedar were stately, the arrangement and general attention to detail were striking and pleasing.  
I didn’t spend much time around the shrine itself- there were a fair few people praying there and I didn’t want to make an ass of myself, so I headed up the mountain to meet my colleagues for lunch.

The track up started off through plantation Japanese cedar, but got scenic and atmospheric as I got above about 450 meters and the snow deepened. The last half of the walk was a bit treacherous, but the forest gets more mature and spectacular on the steep upper reaches of the mountain.  

The Japanese Cedar, which grows in fantastic stands on the south side of the mountain, gives way to deciduous trees on the ridgeline and north face. Jules and James will note that the camellia was not blooming.  I don’t know what the signs said.  The first character is “mountain”, the second “fire”. I haven’t learned the next three yet; Bushfire blah blah blah.  Hopefully the message is less urgent with snow everywhere.

Mount Tsukuba has two peaks: Nantai-San (male) and Nayotai-san (female).  The top of Mount Nantai-san is topped by two shrines to the gods Izanagi-no-mikoto and Softbank. Mount Nayotai had fantastic views to the south and East, which disappeared in a snow flurry just as I reached the top.

Due to the icy conditions, we headed down on the cable car.  I then took another walk, this one going around the mountains base. This forest included Japanese cedar and cypress, but also had a fir species and some very large plum or cherry trees, which I could not distinguish without flowers or leaves. As this was my first weekend in the winter hemisphere, the snow was a welcome novelty after a very hot Australian summer.
Oh the rocks.  Well, it was my day off, and most of them were covered with snow, but here and there a coarse grained dolerite reared its pyroxinitic head.

Wednesday, March 12, 2014

The crap app

As civilizations haul themselves out of traditional pre-industrial lifestyles, and into the modern world, they, collectively or individually, need to choose what to modernize and what to keep traditional.  That's fine, and I respect that.  And as an old manual typewriter, chemical film, rotary dial phone fossil, I realize that these things strike many young people of today as being as old fashioned as vacuum tubes, or crank-start engines.  And of course of the the great drivers of mechanization and automation is convenience.  But still, despite knowing these things intellectually, I still have my get-off-my-lawn moments.  So I gotta say.  Asia, you're amazing, and I love my phone and computer chips and clothes and everything else that you make.  And even though I don't like remote controls, I appreciate that others find them handy.  But seriously guys, You don't need them for everything.  And this one strikes me as just a little bit asinine.

Wednesday, March 05, 2014

Sign, sign, everywhere a sign

I grew up and went to college in America, and most of my friends are still there.  My friend Julie, however, headed off across the Atlantic not long after graduating, about the time I first went to Australia.  We have both been mostly overseas since. Having crossed opposite oceans, we've only caught up in person three times since then, in three different countries, but we try to keep up electronically, in part through our blogs.  Hers is much better than mine- so go read that if you're bored here- and for a while she had a theme if bizarre "Do not X" signs pulled off the various mass transit systems of Europe.

The last place I saw Julie and her husband Scott was Tokyo, a year ago.  Sadly, they're stuck in the rainy part of Europe this year.  But I'm back in the land of blossoms, bows, and raw horse, and dedicating this post to my friends.

Try not to get bashed in the head by a boom gate, guys, and hopefully the next year will bring more adventure than the last.

Monday, March 03, 2014

The first rule of microanalysis

 There are lots of rules in microanalysis. In the sort that I practice, elemental and isotopic in-situ mass spectrometry, most of these are more what you’d call guidelines than actual “rules.” But there is one rule that is not so malleable; the first rule. And that is this:

Don’t run out of atoms.

Figure 1. The protagonist in this figure has insufficient iron atoms for his proposed procedure.

In ordinary life, we think of atoms a something so gobsmackingly small that they are essentially innumerable in any visible object (like a rock).  And for things you can pick up and throw at crows, that is generally correct.  In fact, even for things that need a handlens or a low power optical microscope to see, there are still a lot of atoms there.  But the combination of small scales (particularly nanoscales), low concentration of trace elements, and high required analytical precisions can all multiply rather quickly to leave one atomically short handed.  Fortunately, atom counting is fairly straight forward.

How many atoms do you have?

A good ballpark number of atoms in crystalline solids is 100 atoms per cubic nanometer.  For the mineral zircon (the Mick Jagger of mineralogical microanalysis), the actual number is about 92.  It is higher in densely packed phases like corundum (119), and lower in loosely packed ones like sanidine (72). Of course, the great thing about cubic nanometers is that you get one BILLION of them per cubic micron.  So a smallish SHRIMP spot (e.g. 15x10x1µm, or 111 µm3) would have about 1013 atoms in it, while a large (160x160x50µm, or 1 million µm3) laser ICPMS spot would have 1017 atoms.

These are heaps of atoms.  

How many atoms could we possibly need?

 This depends on three things.  The concentration of the analyte, the precision of the measurement which is desired, and the detection efficiency of the instrument. Since the presence or absence of individual ions of interest in an analytical volume is a poisson process, the minimum number of atoms needed in the least abundant species measured is the square of the inverse of the desired precision.  So 1% precision  requires 10,000 of the least abundant atom.  A permil requires a million, and 0.1 permil requires 108.

For isotopic ratios, the abundance of the least abundant isotope must be multiplied by the chemical abundance of the element of interest in the sample. And finally, the detection efficiency of the analytical equipment must be considered.

So, the atoms you have are:
~100 x # of cubic nanometers
The atoms you need are: 1/ (required precision^2 * lowest isotopic abundance x volumetric concentration * detection efficiency)

Detection efficiency cam be further broken down into useful yield * dwell time.

Some examples:
A small (100µm3) SHRIMP spot for 3 permil 207Pb/206Pb ratios in a 1.5 billion year old zircon with 50ppm (atomic) 206Pb.
You need:
1/ (0.003^2 (precision) * 0.1 (207Pb/206Pb ratio)  * 0.00005 (206Pb concentration) * 0.02 (Pb useful yield) * 0.15 (dwell time on 207Pb) = 7.4E12
You have:
100 (atom/nm3) * 109 (nm3 per µm3) * 100 (analytical volume- see above) = 1E13

So there are enough atoms, but only barely. All of a sudden, ten trillion atoms seems rather stingy instead of extravagant.

If you want a 0.1 permil 46Ca/40Ca ratio in a  multi-collector SHRIMP spot of the same size on calcite,

You need:
1/ (0.0001^2 (precision) * 0.00004 (46Ca abundance)  * 0.2 (Ca concentration) * 0.1 (estimated useful yield) *0.9 (estimated multicollector dwell time).

1.4E14 atoms required.  

You have:
100 (atom/nm3) * 109 (nm3 per µm3) * 100 (analytical volume in µm3- see above) = 1E13

So you need 14 times more atoms than the measly ten trillion atoms the small spot contains.

Insufficient atoms available.

Even though the target is a major element with great ion yield, the high precision required, combined with the low isotopic abundance of 46Ca, means that a larger volume is needed.

Alternatively, a lower analytical precision could be desired, or a more abundant isotope could be targeted. Or, you could choose the option which every instrumentalist wants the inquiring scientist to propose:

“Just use a bigger spot”

A 2000 µm3 Spot is about the largest analytical volume that most sane ion probers would generally use. So although a patient man could do that with SIMS (It’s hard to work with SIMS craters of more than a couple thousand cubic microns), there’s always a shark willing to sell laser beams to the impatient scientist.  Would LA-MC-ICPMS would work?  While the volume of the big laser spot above is sufficient, the order-of-magnitude lower useful yield needs to be considered.  So you need 1.4E15 atoms.  Luckily, a the 1 million µm3 blast hole yields 1017 atoms.  So this problem can be solved with a bigger laser. And really, who doesn't want a solution like that?

Saturday, March 01, 2014

The year that was

So February is almost over, and here I am, only just now trying to wrap up last year.  2013 was a busy travel year.  As you can see by the map below, I went a lot of places (red: destinations; blue: stopover countries), almost all of which were work related.  But building high end mass spectrometers is a funny business.  We travel halfway around the world, only to sit in climate-controlled windowless rooms and work on machines that we built.  So there is this strange friction, between trying to work as quickly as possible in an environment where we can’t understand any writing or speech which we might need to get suppliers, and trying to actually pick up a thing or two about the bizarre and wondrous cultures which we find ourselves dropped into. 

As the map above shows, I went to countries with a total of 6 different languages written in five different character sets (“alphabets” doesn't do Asian languages justice), not counting Arabic, since I was barely on the ground there long enough to grab a coffee. So that, in addition to trying to master the technical aspects of my job, means I haven’t had a lot of spare brainpower left over for blogging.

Hopefully that will change, though. Most of the places I’ve gone since starting this job are places I haven’t been to at all before (e.g. Asia).  So I’ll try to at latest make an occasional observation or insight into the myriad was that humans can organize themselves. And if I actually manage to get far enough outside to look at the rocks or the trees, well so much the better.